tag:blogger.com,1999:blog-64180003947505388162024-03-17T22:03:25.183-05:00From the Editor’s Desk of The American NaturalistThoughts and comments about <i>The American Naturalist,</i> the journal of the American Society of NaturalistsASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.comBlogger84125tag:blogger.com,1999:blog-6418000394750538816.post-10992186737244423382022-09-29T08:13:00.007-05:002023-01-06T18:56:32.716-06:00 EIC Update: American Naturalist policy on data and code archiving<h2 style="text-align: left;"> <span face="Calibri, sans-serif" style="text-align: center;">American Naturalist policy on data and code archiving</span></h2><style class="WebKit-mso-list-quirks-style">
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</style><p align="center" class="MsoNormal" style="font-size: medium; text-align: center;"><o:p></o:p></p><p align="center" class="MsoNormal" style="font-size: medium; text-align: center;"><o:p> </o:p></p><p align="center" class="MsoNormal" style="font-size: medium; text-align: center;">Daniel Bolnick, Editor-In-Chief<o:p></o:p></p><p align="center" class="MsoNormal" style="font-size: medium; text-align: center;">September 5, 2022<o:p></o:p></p><div style="border-bottom-color: windowtext; border-bottom-width: 1.5pt; border-style: none none solid; padding: 0in 0in 1pt;"><p class="MsoNormal" style="border: none; padding: 0in;"><o:p> </o:p></p></div><p class="MsoNormal" style="font-size: medium;"><o:p> </o:p></p><p class="MsoNormal" style="font-size: medium;">In the past year, the Editorial Board of The American Naturalist has implemented several new policies aimed at improving the reproducibility and openness of the science that we publish. Starting in 2011, the journal required authors to publicly archive data on DataDryad or equivalent, version-controlled, public repositories. Options include Figshare, Dataverse, Zenodo, and Dryad. This requirement is been crucial in enabling re-analyses of data for meta-analyses and other follow-up research, and at detecting some cases of error or misconduct. However, compliance with that data archiving policy has been less than optimal. A review of Dryad repositories from past years revealed that many archives are incomplete (missing key data), or uninterpretable because they lack sufficient metadata documentation. These findings are summarized in a recent AmNat Editor’s blog (guest post by lead Data Editor Bob Montgomerie), and in Roche et al 2014 PLoS Biology (<a href="https://doi.org/10.1371/journal.pbio.1001779"><span style="color: #606060; font-family: inherit, serif; font-size: 10pt; text-decoration: none;">https://doi.org/10.1371/journal.pbio.1001779</span></a><span style="color: #606060; font-family: inherit, serif; font-size: 10pt;">)</span> In response to these problems, the Editorial Board has initiated several new policies. <span style="color: #606060; font-family: inherit, serif; font-size: 10pt;"><o:p></o:p></span></p><p class="MsoListParagraphCxSpFirst" style="mso-list: l0 level1 lfo2; text-indent: -0.25in;"><!--[if !supportLists]-->1)<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]-->We now require that authors archive both data and any code used to generate the results reported in the paper. Data may include empirical measurements, outputs of simulations, and collections of previously published data assembled into new dataframes for analysis. Code may include statistical analyses (e.g., in R or Python), scripts summarizing statistical commands in proprietary software (e.g., JMP), simulations, or Mathematica notebooks. <i>You can find The American Naturalist’s guidelines for data and code archiving here: </i><a href="https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcomments.amnat.org%2F2021%2F12%2Fguidelines-for-archiving-code-with-data.html&data=04%7C01%7Cmont%40queensu.ca%7C3152a303f64246c7b54b08d9d6a7256e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637776835669272376%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=zGQ301jCL%2Bu9gDa%2BBjplUvGfg2rqsTx48NFywz2U4r4%3D&reserved=0"><i>https://comments.amnat.org/2021/12/guidelines-for-archiving-code-with-data.html</i></a><i>. </i>Dryad also publishes a list of best practices (<a href="https://datadryad.org/stash/best_practices">https://datadryad.org/stash/best_practices</a>) you may wish to consult, though we do not specifically require that authors use Dryad, per se. <o:p></o:p></p><p class="MsoListParagraphCxSpMiddle" style="mso-list: l0 level1 lfo2; text-indent: -0.25in;"><!--[if !supportLists]-->2)<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]-->The data and code archive must be created prior to manuscript submission, and a private URL key provided to the journal upon submission. For instance, DataDryad allows the creation of a private archive that you can share exclusively with the Editors and reviewers, which later becomes public upon publication. Do note, however, that Dryad charges authors a fee once the article is published (AmNat used to cover this fee, but the expense became untenable recently). This allows reviewers and editors to check the contents of the data for completeness, to evaluate the technical accuracy of the code used in analyses, and, potentially, to rerun analyses, while keeping the repository private. We encourage, but do not require, reviewers to examine the data and code. We ask reviewers and data editors not to comment on the elegance of the code, as we simply care that it works to generate the results reported in the manuscript. <o:p></o:p></p><p class="MsoListParagraphCxSpMiddle" style="mso-list: l0 level1 lfo2; text-indent: -0.25in;"><!--[if !supportLists]-->3)<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]-->Data and code archives must be accompanied by a README file that clearly indicates the contents of the archive. Variable names should be explained (units, etc) so that readers can determine what variables were used in the analyses reported in the paper. If there are multiple data files, the relationship between them should be clearly stated (e.g., what column allows information in different files to be merged appropriately). If there are multiple code files, in what order should they be run, and what does each do. <o:p></o:p></p><p class="MsoListParagraphCxSpLast" style="mso-list: l0 level1 lfo2; text-indent: -0.25in;"><!--[if !supportLists]-->4)<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]-->The data archive will be checked during the review process, by a new cadre of Data Editors. This is a team of colleagues who evaluate whether the provided data files are complete and in csv format, and whether the code runs and is clearly annotated. A Data Editor report to is provided to the authors of all provisionally accepted manuscripts. Any data archiving weaknesses identified by a Data Editor must be addressed prior to final acceptance.<o:p></o:p></p><p class="MsoNormal" style="font-size: medium;"><o:p> </o:p></p><p class="MsoNormal" style="font-size: medium;">We will not penalize authors who, voluntarily and in good faith, find and correct data or code errors after publication. We believe that corrections should be encouraged when warranted. This is not a new policy, but is important to reiterate.<o:p></o:p></p><p class="MsoNormal" style="font-size: medium;"><o:p> </o:p></p><p class="MsoNormal" style="font-size: medium;">While we are on the topic of reproducible science, here are some pointers for authors who use code in their data analyses and simulations. Even professional programmers make errors that affect the performance of the code that they write. The question is, what can authors do to minimize the resulting risk of incorrect inferences? And what can journals do to help minimize such mistakes?<o:p></o:p></p><p class="MsoNormal" style="font-size: medium;"><o:p> </o:p></p><p class="MsoListParagraphCxSpFirst" style="mso-list: l1 level1 lfo1; text-indent: -0.25in;"><!--[if !supportLists]-->1.<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]--><b><u>Programming habits for authors.</u></b> There are many good sources of recommendations for how authors can be better coders. For example, Wilson et al. (2014, PLoS Biology, <a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745">https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745</a>; 2017 PLoS Computational Biology, <a href="https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005510&type=printable">https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005510&type=printable</a> ) outline recommendations. To highlight a few:<o:p></o:p></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 1in; mso-add-space: auto; mso-list: l1 level2 lfo1; text-indent: -0.25in;"><!--[if !supportLists]-->a.<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]-->Annotate thoroughly, especially focusing on documenting the purpose of each step, not just the mechanics.<o:p></o:p></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 1in; mso-add-space: auto; mso-list: l1 level2 lfo1; text-indent: -0.25in;"><!--[if !supportLists]-->b.<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]-->Use pair programming. Work in teams on code, preferably as you write.<o:p></o:p></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 1in; mso-add-space: auto; mso-list: l1 level2 lfo1; text-indent: -0.25in;"><!--[if !supportLists]-->c.<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]--> If this is not a collaboration, find a colleague to check your code with you, and return the favor for their project.<o:p></o:p></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 1in; mso-add-space: auto; mso-list: l1 level2 lfo1; text-indent: -0.25in;"><!--[if !supportLists]-->d.<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]-->After doing an analysis, close and reopen the software and re-run the code to make sure you get the same result.<o:p></o:p></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 1in; mso-add-space: auto; mso-list: l1 level2 lfo1; text-indent: -0.25in;"><!--[if !supportLists]-->e.<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]-->Generate some simulated data, where you know the true pattern. Run this through the code and make sure it generates correct results. This gives you more confidence that the inferences derived from your real data may be correct.<o:p></o:p></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 1in; mso-add-space: auto; mso-list: l1 level2 lfo1; text-indent: -0.25in;"><!--[if !supportLists]-->f.<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]-->Don’t overwrite original data, create new versions as you modify data tables to track the process. There are many ways to version your data files and this is highly recommended, rather than giving each file a new neame and number.<o:p></o:p></p><p class="MsoListParagraphCxSpLast" style="margin-left: 1in; mso-add-space: auto; mso-list: l1 level2 lfo1; text-indent: -0.25in;"><!--[if !supportLists]-->g.<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]-->Make bite-sized sections of code, each for its own task, preferably ordered in the sequence presented in the publication. It is also a good practice to have a unique data file and code script file for each figure, so readers can readily recreate each figure on their own.<o:p></o:p></p><p class="MsoNormal" style="font-size: medium; margin-left: 0.75in;">These, and other author best practices, are explained in our optional checklist: <a href="https://www.amnat.org/announcements/MS-Checklist.html">https://www.amnat.org/announcements/MS-Checklist.html</a><o:p></o:p></p><p class="MsoNormal" style="font-size: medium; margin-left: 0.75in;"><o:p> </o:p></p><p class="MsoListParagraphCxSpFirst" style="font-size: medium; margin-left: 1in;"><o:p> </o:p></p><p class="MsoListParagraphCxSpLast" style="mso-list: l1 level1 lfo1; text-indent: -0.25in;"><!--[if !supportLists]-->2.<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><!--[endif]--><b><u>The role of a journal.</u></b> Given the risk of data analysis code not reproducing the reported results, or violatiung statistical principles and assumptions, it is very tempting for journals to initiate a code review procedure. However, this would be a daunting task. and reviewers will be far less likely to accept review requests. Moreover, there is a high likelihood that a particular reviewer simply will not have the expertise to evaluate a particular bit of code, as not everyone ‘speaks’ every programming language. As well, some author-generated software is highly resource-intensive, requiring computer cluster time, or very long runs, that cannot readily be duplicated in a time- and cost-effective way. <br /><br />Periodically at The American Naturalist we do get reviewers (or, Associate Editors) asking to see code so they can check that a given step was done correctly. Often this is in the authors’ best interest: reviewers frequently raise questions about analytical methods that are not described in sufficient detail. Did the authors transform their data? Did they do type I or II or III sums of squares? Often authors have done analyses appropriately, but not described their work in sufficient detail in the text. Reviewers then get concerned, raise questions, and become more critical of the paper. With code available, a reviewer has the opportunity (though, not the obligation) to check the code directly and answer their own question, potentially avoiding a misunderstanding that could derail a paper’s prospects.<br /><br />Providing code for reviewers to examine should have two benefits. First, it allows reviewers the <i>option</i>of examining code for errors, or to clarify steps that were not clearly described in the manuscript text. Second, and perhaps more importantly, it should motivate authors to check and annotate their code more carefully before submission. We deem it likely that the added concern about having a stranger check one’s code will encourage authors to be careful. This self-policing should help identify errors pre-emptively. <o:p></o:p></p><p class="MsoNormal" style="font-size: medium;"><o:p> </o:p></p>Dan Bolnickhttp://www.blogger.com/profile/05181664810897127126noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-69483710171214412282022-03-02T11:46:00.041-06:002022-03-02T12:00:54.732-06:00Ensuring data and code archive quality: why and how?<p style="text-align: left;"><span style="font-size: medium;"><span style="background-color: transparent; color: black; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: inherit;">This post was co-written by Dan Bolnick (The American Naturalist, Editor), Tim Vines (DataSeer.ai), Bob Montgomerie (AmNat Data Editor). This blog post addresses the value and flaws in current open and reproducible science practices, and hopefully is of interest to authors, other editors, and students considering publishing in biological sciences.</span></span></span></p><p style="text-align: left;"><span style="font-family: inherit; font-size: medium;"><span style="background-color: transparent; color: black; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span><br /></span></span><span style="font-weight: 400; white-space: pre-wrap;">Part 1 articulates the value of data and code archiving, and can be skipped if you are already a convert. Part 2 explains what we see as weaknesses with the current system. Part 3 explains the new Data Editor role adopted by The American Naturalist and the associated workflow including DataSeer.ai's role. Part 4 addresses some remaining issues for consideration, and Part 5 provides some parting thoughts. </span></span></p><h2 style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt; text-align: left;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 19pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></h2><h2 dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 19pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Part I: The Value of Data and Code Archiving</span></h2><p dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">In 2010, a group of journal editors announced that some of the leading journals in evolutionary biology would adopt a new policy requiring authors to archive all of the raw data needed to obtain published results (</span><a href="https://www.journals.uchicago.edu/doi/full/10.1086/650340" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Whitlock et al, 2010 American Naturalist</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">). Previously, some kinds of genetic data (e.g., DNA sequences) were often required to be archived on databases such as GenBank. However, researchers in ecology and evolution often work with system-specific types of data, so that attempts to build standardized databases had typically failed. Sometimes data were provided in tables within a paper or provided as online supplements once journals moved much of their material online in the early 2000s. But, the most common approach was to simply state in the article that data were “available upon request”. </span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Relying on authors to provide data on request, however, was largely ineffective because authors too often would either ignore requests for data, or respond that they no longer had access to the relevant data (“it was on a computer whose hard drive crashed years ago”). As time passes, it’s more and more likely that those datasets are </span><a href="https://www.vanityfair.com/news/2013/12/whoops-improper-storage-methods-means-80-percent-of-scientific-data-is-awol" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">lost forever</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (see </span><a href="https://www.cell.com/current-biology/comments/S0960-9822(13)01400-0" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Vines et al 2014</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">). As an example, in 2012 one of us emailed 120 authors asking for raw data underlying effect size estimates used in a previous meta-analysis, and received only five replies. This kind of poor response has been studied more rigorously (see for instance </span><a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007078" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Savage and Vickers 2009 PLoS One</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> and Vines et al 2014), and is a widespread problem. The result has been calls to adopt more rigorous systems (e.g., </span><a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0394-z" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Langille 2018 Microbiome</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">).</span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The Editors of some evolution journals sought to change this by requiring data sharing. The American Naturalist adopted this requirement in January 2011 for all new manuscripts, and reached out to authors of previous papers to encourage them to archive their data retroactively. Notably, this is a move that is only now being followed by biomedical sciences, which is being dubbed a “seismic mandate” (</span><a href="https://www.nature.com/articles/d41586-022-00402-1" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Nature News, 2021</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">).</span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Although the initial response from some members of the research community was hostile, the benefits of archiving data are by now widely recognized:</span></p><ol style="margin-bottom: 0px; margin-top: 0px; padding-inline-start: 48px;"><li aria-level="1" dir="ltr" style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; list-style-type: lower-alpha; text-decoration: none; vertical-align: baseline; white-space: pre;"><p dir="ltr" role="presentation" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Archives are useful as a back-up for your own data, in a secure location. Once archived, you will have access to your own data in perpetuity, safe from the vagaries of damaged hard drives or stolen laptops. Most data repositories also use version control to track changes to files so you can go back and retrieve earlier versions if necessary.</span></p></li></ol><p><b id="docs-internal-guid-fbe5915c-7fff-045a-6126-0353804c7ad7" style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><ol start="2" style="margin-bottom: 0px; margin-top: 0px; padding-inline-start: 48px;"><li aria-level="1" dir="ltr" style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; list-style-type: lower-alpha; text-decoration: none; vertical-align: baseline; white-space: pre;"><p dir="ltr" role="presentation" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Archived data can be re-used for new studies, providing a cost-effective framework for building upon or consolidating past results. Meta-analyses are an increasingly popular tool for combining discipline-wide findings from a large number of studies. Traditionally meta-analyses have been based on an aggregated analysis of summary statistics from many published studies. But, far more effective approaches are possible when the raw data can be analyzed directly. Re-analyses by third parties do run the risk of (i) scooping an author who plans further publications from a data-set, or (ii) committing errors based on a poor understanding of the biology of the system or experimental details. In practice, we are aware of few, if any, examples of (i) in evolution or ecology, but some clear </span><a href="https://royalsocietypublishing.org/doi/10.1098/rsbl.2010.0160" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">examples</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> of (ii). There was some debate in recent years whether such re-use represents “</span><a href="https://researchparasite.com/" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">research parasitism</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">”, but as long as the findings of re-analyses are correct and provide added value then everyone wins.</span></p></li></ol><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><ol start="3" style="margin-bottom: 0px; margin-top: 0px; padding-inline-start: 48px;"><li aria-level="1" dir="ltr" style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; list-style-type: lower-alpha; text-decoration: none; vertical-align: baseline; white-space: pre;"><p dir="ltr" role="presentation" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><a href="https://researchdata.library.ubc.ca/deposit/cite-and-get-credit-for-your-data/" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Data archives are citable products</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> one should put on one’s CV. In practice, few people have done this in the past, and data archives have rarely been cited (see a small-scale personal analysis of this </span><a href="https://ecoevoevoeco.blogspot.com/2022/01/what-happens-to-those-dryad-repositories.html" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">here</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, by one of us, or </span><a href="https://eos.org/opinions/data-sets-are-foundational-to-research-why-dont-we-cite-them" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">this analysis by Vannan et al</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">). Nonetheless, there is increasing recognition that data archives are an important work product that might influence decisions about hiring, grant success, and promotion (</span><a href="https://www.nature.com/articles/sdata2018259" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Cousijn et al 2018</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">).</span></p></li></ol><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><ol start="4" style="margin-bottom: 0px; margin-top: 0px; padding-inline-start: 48px;"><li aria-level="1" dir="ltr" style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; list-style-type: lower-alpha; text-decoration: none; vertical-align: baseline; white-space: pre;"><p dir="ltr" role="presentation" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Archives provide a valuable tool for teaching. Students learning statistics and the graphical presentation of data can benefit from downloading data and code underlying published results, then trying to replicate or improve upon published figures or statistical analyses. By simultaneously examining the data and code, students can learn how to conduct certain kinds of analyses or generate different kinds of graphs, which they can then apply to their own scientific work. Such learner-driven downloads may represent a large fraction of downloads from data repositories, and are surprisingly common (for data on download rates in a small case study, see </span><a href="https://ecoevoevoeco.blogspot.com/2022/01/what-happens-to-those-dryad-repositories.html" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">this ecoevoevoeco blog</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">). This may be especially valuable for graduate students starting work in a new lab, where they can access data and code from their professors or lab alumni to learn more about the biology of the research system they are beginning to work on. From the </span><a href="https://ecoevoevoeco.blogspot.com/2022/01/what-happens-to-those-dryad-repositories.html" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">surprisingly large number of downloads that archives seem to get</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, we’d suggest that download numbers are better than citations as a reflection of an archive’s value (with the caveat that archives containing suspect data may also be downloaded extensively).</span></p></li></ol><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><ol start="5" style="margin-bottom: 0px; margin-top: 0px; padding-inline-start: 48px;"><li aria-level="1" dir="ltr" style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; list-style-type: lower-alpha; text-decoration: none; vertical-align: baseline; white-space: pre;"><p dir="ltr" role="presentation" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Reported results can be re-evaluated by other scientists who can re-run analyses. This helps to improve confidence in the veracity of published claims. Readers should therefore have more trust in, and thus be more inclined to cite, journals and papers with data archives that allow reproducible analyses. At times this can lead to discoveries of errors. For instance, The American Naturalist recently published a </span><a href="https://www.journals.uchicago.edu/doi/10.1086/715870" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">retraction</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (Gilbert and Weiss 2021) of a </span><a href="https://www.journals.uchicago.edu/doi/10.1086/701785" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">paper</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (Start et al 2019) whose core finding was based on an incorrectly conducted statistical analysis. The retraction was made possible by a re-analysis by one of the co-authors, who gained access to the original data posted on Dryad by the lead author. We believe that voluntary self-retractions of honest mistakes should be lauded as a healthy correction process.</span></p></li></ol><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><ol start="6" style="margin-bottom: 0px; margin-top: 0px; padding-inline-start: 48px;"><li aria-level="1" dir="ltr" style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; list-style-type: lower-alpha; text-decoration: none; vertical-align: baseline; white-space: pre;"><p dir="ltr" role="presentation" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Data archives provide key information for forensic evaluations in cases of alleged scientific fraud, misconduct, or sloppy practices. For instance, a prominent animal behavior researcher has had numerous articles retracted in 2020-2021 after </span><a href="https://ecoevoevoeco.blogspot.com/2021/05/17-months.html" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">biologically implausible patterns were found in his data archives</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. Forensic evaluations of archived data identified blocks of numbers that were </span><a href="https://laskowskilab.faculty.ucdavis.edu/2020/01/29/retractions/" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">copy-and-pasted within files</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. In a separate case, data were found to be similar between two supposedly unrelated publications, resulting in retractions (</span><a href="https://www.pnas.org/doi/10.1073/pnas.2117483118" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">McCauly and Gilbert 2021</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">). Such discoveries would not have been possible without archived data. This point is highlighted by the experiences of other journals that lacked data archiving policies, but became concerned by strings of retractions at other journals. The journal Ecology, for example, lacked an archive policy until relatively recently and has therefore been unable to evaluate their papers authored by an author with multiple retractions elsewhere. We mention this not to criticize that journal, but rather to illustrate the value of archiving. </span></p></li></ol><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><ol start="7" style="margin-bottom: 0px; margin-top: 0px; padding-inline-start: 48px;"><li aria-level="1" dir="ltr" style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; list-style-type: lower-alpha; text-decoration: none; vertical-align: baseline; white-space: pre;"><p dir="ltr" role="presentation" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The datasets obtained during any research are, in a sense, the property of the public whose taxes paid for the research. Thus, there’s an ethical and political argument to be made for the necessity of making all raw data available. The failure to make data available has, in fact, been weaponized by politicians seeking to undermine environmental rules. In recent years, moves by a certain US President’s administration aimed to block any policies based on scientific results that didn’t follow open data practices. This means that most research in toxicology or conservation biology from previous decades would be tossed out, undermining environmental protections. Data archiving protects your science against such political maneuvers. </span></p></li></ol><p dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Following the adoption of data archiving rules, the number of data repositories at major host sites has skyrocketed (</span><a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002432" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Figure from Evans et al 2016 PLoS Biology reproduced below</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">) </span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-left: 36pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="border: none; display: inline-block; height: 370px; overflow: hidden; width: 389px;"><img height="370" src="https://lh4.googleusercontent.com/6aVsbMfij8dlVDhYWDKEsuV1G2If9XRkKpVzIN1Bh0Qf_1_bjElUaaRAboP8w3A2TD4a692C4E9kQCjw5DguqpiIdhmzXmmksw5NC_id4LoQoRF2vmfFHbst_ecw53ydupW_9J5H" style="margin-left: 0px; margin-top: 0px;" width="389" /></span></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The adoption of data archiving policies was not without resistance. Authors quite reasonably have a sense of ownership of their data (but see (g) above) and worry about being scooped on any further analyses of their own data. To allay that fear, journal editors can accommodate reasonable requests in this regard: long-term datasets that might yield multiple papers can be embargoed for a reasonable period of time, but must nevertheless be archived at the time of publication to ensure that when the embargo ends the data become visible to the public. These concerns seem to have largely evaporated as the community has habituated to the rules. For instance, in nearly five years as Editor of AmNat, Dan Bolnick received only a couple of requests for waivers or embargos. A few requests were clearly from authors not wanting to bother archiving their data, but who readily provided data when their excuses were questioned. Some had valid reasons such as being bound by confidentiality rules about the precise geographic locations of threatened species. At other journals that publish data on human subjects, individual confidentiality rules or cultural group requirements may legitimately bar the sharing of some forms of data.</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"></b></p><h2 dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="color: black; font-family: Arial; font-size: 19pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; vertical-align: baseline; white-space: pre-wrap;">Part 2: Problems with the Current State of Data Sharing</span></h2><p dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="color: black; font-family: Arial; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;">To realize the benefits outlined above, data archives must be complete, readable, and clear. Unfortunately, many are not. This problem first really came to the attention of The American Naturalist’s editor (Dan Bolnick) with the </span><a href="http://ecoevoevoeco.blogspot.com/2021/05/17-months.html" style="text-decoration: none;"><span style="color: #1155cc; font-family: Arial; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">retractions and corrections of Jonathan Pruitt’s papers</span></a><span style="color: black; font-family: Arial; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;">. Most of the problems with those papers involved implausible patterns in the available data. However, the investigating committee also found that some key data were simply missing. Shortly after this case was made public, a reader reached out to the AmNat Editor to request that a different author provide missing information for an incomplete archive. The Editor contacted the author who (after several contacts) found the file, but then claimed to be unable to figure out how to update their Dryad repository. This was eventually resolved, but entailed a year of back-and-forth emails. Shortly on the heels of this case, an anonymous whistle-blower contacted the Editor to point out missing data files for several papers by author Denon Start. When contacted, Start explained that the data were no longer available, having been lost when a laptop was stolen, evcen though those data should have been archived before publication in the journal as requested by journal policy. The author provided a court case number which the Editor confirmed was legitimate and involved stolen material, and that Start was one of the victims, though could not confirm the specific involvement of a laptop, nor whether the laptop contained the only copy of the data (e.g., there were no backups;see </span><a href="https://retractionwatch.com/2021/05/03/ecologist-who-lost-thesis-awards-earns-expressions-of-concern-after-laptop-stolen/" style="text-decoration: none;"><span style="color: #1155cc; font-family: Arial; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">RetractionWatch article</span></a><span style="color: black; font-family: Arial; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;">). After consulting with Dryad and the Committee on Publication Ethics (CoPE), it was clear that data sharing rules are recent enough that CoPE does not have formal recommendations for handling incomplete archives (such guidelines are in preparation now). Following recommendations from Dryad and CoPE, the journal published a set of Editorial Expressions of Concern for Start’s missing data files (eg </span><a href="https://www.journals.uchicago.edu/doi/10.1086/714375" style="text-decoration: none;"><span style="color: #1155cc; font-family: Arial; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Bolnick, 2021</span></a><span style="color: black; font-family: Arial; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;">) </span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Missing data are not the only issue. In a recent survey of repositories for papers published in The American Naturalist in 2020, Bob Montgomerie found many cases where authors posted only summary statistics (means, standard errors) rather than the original data used to generate those results. Only a small fraction of repositories was complete, well-documented, and useful for re-creating all of the published results (</span><a href="https://comments.amnat.org/2021/01/note-since-fall-2020-robert-montgomerie.html" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">see AmNat blog post by Montgomerie</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">). Typical problems with data repositories included missing datasets, summary rather than raw data, no information about variable names in those files (many of which were indecipherable), and, in a few cases, no data repository at all (eventually fixed by contacting the authors and Dryad; </span><a href="https://comments.amnat.org/2021/01/note-since-fall-2020-robert-montgomerie.html" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">see AmNat blog post by Montgomerie</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">)</span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">These observations led to a growing realization that requiring data archiving is not enough. We cannot simply trust that authors are creating complete and clear archives, because often this is too often not what happens. It has become clear that we also need to proactively check the archives to confirm that they meet our minimum standards. There are data archive checks that occur within the Dryad office. However, these checks occur after a paper is accepted, whereas we believe it is crucial that acceptance be conditioned on confirmation that archives are complete and useable. Checking before acceptance ensures that the journal retains leverage to encourage authors to adopt acceptable practices. This then avoids the difficulty of having authors who simply do not respond, claim data are missing, or take years to act because they have no incentive to make corrections once their paper is published. Moreover, Dryad does not currently check data archive contents against the text of the corresponding manuscript to confirm that all data files and variables represented in the published article are present in the archive. </span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><h2 dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 19pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Part 3: New Procedures to Check Data Archive Quality</span></h2><p><br /></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">In the summer of 2021, The American Naturalist began having a small team of data editors, led by Bob Montgomerie, look at the data repositories for all papers accepted for publication. Once a paper has been accepted by the handling editor, Montgomerie uses our Editorial Manager to download the manuscript and its data repository and immediately sends the manuscript to </span><a href="https://dataseer.ai/" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">DataSeer</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> for evaluation. DataSeer uses a machine-learning process to read the manuscript and identify all mentions of data and code, providing a summary within 48 hours that matches the mentions of data and code to the data and code in the repository. One of the data editors then writes a summary of the findings from DataSeer and makes recommendations to the author(s) to make their repository complete and useful. The manuscript then goes to the editor in chief (Bolnick) for final decision. In cases where the repository is seriously deficient, the data editor might ask to see the repository again before the manuscript is finally accepted for publication.</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">One thing that authors should be aware of: the Data Editors are not there to judge the elegance of your code. They do check that the code actually runs, and they may encourage you to make clearer annotations. If they incidentally identify errors in the code (not their assigned task), they’ll let you know to avoid you having to correct a mistake after publication. But authors should not feel bashful about the ‘style’ of their code. Code is a tool, and if the tool gets the job done correctly, it is a useful tool. And if you don’t trust your code enough for someone to see it, well then perhaps it is time to ask a collaborator to double-check your code. Having a coding mistake identified after publication is far more embarrassing (one of us had to go through such a </span><a href="http://ecoevoevoeco.blogspot.com/2016/12/wrong-lot.html" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">retraction due to a coding error</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">).</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">By the end of 2021, the data editors had evaluated the data repositories of 63 accepted manuscripts, all of which were submitted to the journal before a data editor had been appointed. Thus, the analysis of those repositories provides a glimpse at what repositories looked like before authors knew that anyone was going to look at them very closely, at least not before their paper was published (as a reminder, </span><a href="https://ecoevoevoeco.blogspot.com/2022/01/what-happens-to-those-dryad-repositories.html" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">repositories do get more views & downloads than you might think</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">).</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">For each of the 63 repositories evaluated in 2021, Montgomerie subjectively gave them a rating on a scale of 1-5 where 5 is complete and informative, 3 is moderately useful but missing some data files or some raw data, and 1 indicates a virtually incomprehensible and thus almost useless set of files. Expectations for a high-quality repository are not especially stringent, and are </span><a href="http://comments.amnat.org/2021/12/guidelines-for-archiving-code-with-data.html" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">outlined in a recent blog post for authors</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. Here is a summary of his ratings of the data repositories for those manuscripts:</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="border: none; display: inline-block; height: 441px; overflow: hidden; width: 624px;"><img height="441" src="https://lh4.googleusercontent.com/yyw_oNEO20A09wQEn2AciMwNicqYcTsEdKHhPjG3oTMetq2Q7jq7OfRxjD-5hSohHVMfqMymrKRQdfYmdO_cQDMX84241KvLsAmg7lNV8I7sY2oQJl6NYWVzA43OTyFhFugj8oZn" style="margin-left: 0px; margin-top: 0px;" width="624" /></span></span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Clearly, the data repositories evaluated in 2021 were generally incomplete and few were very good. The most frequent problems were (i) absent or uninformative README file, (ii) missing raw data files, (iii) code absent, not annotated or could not run on a clean computer, and (iv) broken links to repositories. Note that authors were not required to provide code at the time those manuscripts were submitted, so the provision of code was not a factor in the ratings shown above. Moreover, we did not set our standards to be particularly high and thus wrote reports that provided a few usually relatively simple suggestions to authors to improve their repositories. We felt that this soft approach was desirable at the outset until authors get used to the new (and old) data requirements, and the newly adopted (January 2022) requirement that authors archive code (if code is used) as well as data.</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /><br /><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The perennial problem with promoting open data and open code is knowing exactly what needs to be done for each article: it’s relatively easy to write a broad policy (like the </span><a href="https://datadryad.org/docs/JointDataArchivingPolicy.pdf" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">JDAP</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">), but it’s much, much harder to work out how that policy applies to each manuscript.</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Authors are obviously best placed to understand which datasets they’ve collected and what code they wrote to analyze their data, but by the time the manuscript is accepted for publication the work itself is months or years in the past and their focus is on writing up their next manuscript. As noted above, the incentives for sharing data and code are diffuse and take time to accrue, while the benefits of publishing just one more paper are more immediate. It’s therefore difficult to persuade authors to spontaneously compile a list of their datasets and code objects and then put these all onto public repositories. Our experience has been that the setting up of data and code repositories, and a useful README file, is best begun at the outset of a project rather than waiting until a final manuscript is ready to submit.</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Back when Tim Vines was the Managing Editor for Molecular Ecology, he read each manuscript and compiled a list of all the data for each article that was accepted for publication. One day in 2014, it occurred to him that this 20-30 minute job could be completed in seconds by a machine: Natural Language Processing (NLP) excels at picking out data collection sentences (e.g. “We measured snout-vent length with Vernier calipers”) and determining what kind of data was collected. With that information in hand, authors can then be led through the data and code sharing process for their articles without intensive attention from an Editor.</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">That NLP solution is now the basis for DataSeer, which has been integrated into the editorial workflow at The American Naturalist to help their Editors promote open data and open code. We processed our first article in July 2021 and have looked at over 100 articles in the intervening months. It’s been fascinating. The American Naturalist publishes a wide range of articles: some are entirely theoretical and make no use of empirically collected data, while others combine pre-existing datasets and novel analyses. Other articles collect and analyze entirely new datasets. </span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">We find that a few issues are common. First, many empirical datasets are vague about where and when samples were collected – a problem also noted by </span><a href="https://onlinelibrary.wiley.com/doi/10.1111/mec.13254" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Pope et al</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> for</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: italic; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Molecular Ecology. Ideally, a reader should be able to find out where and when a sample was taken. One immediate reaction might be ‘what possible use is that level of detail?’, to which the reasonable answer is ‘we have no idea’ – yet. However, by not recording detailed collection metadata, we deny our future selves (or our future colleagues) the opportunity to test as-yet unimagined hypotheses. At the simplest level, providing detailed metadata is the only way to allow anyone to re-sample at exactly the same spot, which is important for myriad reasons.</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Second, authors working with existing datasets should make it clear which individuals and variables were included in their analyses. Two efficient ways to do this include (i) providing the code that accesses and then parses the existing data, or (ii) providing the subset of the dataset that was re-analyzed as a read-in file for the analysis code. This is particularly important when re-using data from sources that are continually updated (e.g. </span><a href="https://www.worldclim.org/" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">WorldClim</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">), as without these details readers have no hope of reproducing the results in the article. A corollary is that when authors collect data that they do not use in a particular paper, at least some version of their data archive should be pared down to only the subset of data actually used to generate reported results, to avoid burdening end-users with extraneous information not pertinent to the study’s results.</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Finally, some manuscripts that focus on theory give the impression that the authors only worked with pencil and paper before transcribing their work into Word or LaTex – the existence of a Mathematica or MatLab notebook where they actually did the work is never mentioned. For readers to fully understand the research, they also need to see and interact with those notebooks. </span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">DataSeer is privileged to be part of this experiment in open science at The American Naturalist, and we will be keeping a close eye on how the new approach affects the reproducibility and stature of their published articles. </span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /><br /></b></p><h2 dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="color: black; font-family: Arial; font-size: 19pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; vertical-align: baseline; white-space: pre-wrap;">Part 4: Future Needs</span></h2><p><span style="font-family: Arial; font-size: 12pt; white-space: pre-wrap;">Our experiences so far suggest some ways forward for both authors and journals.</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">For authors, the first and essential step is to make a plan. Many agencies now require such plans in grant applications and these should include when (now) and where to set up your repository for the study. There are many free online sites for data repositories that you can use during project development and manuscript writing. Your plan should also include details on who will manage the repository, file structure, versioning, and what to include (everything possible at the outset at least). The second, and we hope obvious, step is to stick to that plan. This is a hard one as we all want to get on with data analysis, writing and publishing but all of those—and especially the provision of a useful repository on manuscript submission are made easier by sticking to your plan and keeping your repository up-to-date and well documented. There can be no doubt that a complete, well-organized and well-documented data repository can be a lot of work and this should be recognized by granting agencies by covering the additional costs.</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">For journals, we think (of course) that having a data editor is a good idea, essential even. Editors and reviewers simply do not all have the time (or the inclination and expertise) to vet data repositories. Our experience so far, and especially with the use of DataSeer, is that a repository for an accepted manuscript can be fully evaluated in about 45 minutes. That’s not much time compared to the job that most reviewers and editors perform. As authors become more in tune with this process, repositories (we hope) will become much more complete and useful, moving most repositories into category 5 on the graph above, and taking much less time to evaluate. </span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">At The American Naturalist, data editors do not see repositories until a manuscript has been accepted by a handling editor, or is resubmitted following a request for minor revisions where one might reasonably expect final acceptance. This policy helps limit the burden on Data Editors down to approximately 20% to 25% of manuscript submissions at The American Naturalist. In practice it might be more efficient and useful to authors if repositories were evaluated on first submission, and papers desk rejected before review if repositories are not up to scratch. Such a change in workflow is not practical for us, yet, as it would require a large increase in the number of repositories to evaluate, and might alienate some authors from submitting to the journal. We expect, though, that within a few years, papers submitted to The American Naturalist will all have high quality repositories, especially as more journals take seriously the need for useful data and code. </span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Conversations are ongoing with other journals to encourage wider adoption of data editing practices, but at present The American Naturalist is (we are proud to say) the only journal we know of to be actually checking the content of data archives against manuscript descriptions to ensure completeness. Ecology Letters has implemented a slightly different set of procedures but also typically checks on archives. We also have been in conversations with Dryad, which also conducts some quality control checks on their repositories. As a result, some of what the journal’s Data Editors do is duplicating Dryad efforts (one might say, helping authors meet Dryad expectations in advance). The reasons for these duplications, however, is that Dryad’s quality control steps do not consider what </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: italic; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">should</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> be in the archive based on manuscript text, nor do the evsaluators at Dryad necessarily have the expertise to evaluate data from all fieeld of research and all forms of coding. Also, as noted above we believe it is important that authors be asked to bring their repositories up to our standards before acceptance, rather than after as Dryad does. </span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /><br /></b></p><h2 dir="ltr" style="line-height: 1.38; margin-bottom: 12pt; margin-top: 12pt;"><span style="color: black; font-family: Arial; font-size: 19pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; vertical-align: baseline; white-space: pre-wrap;">Part 5: Conclusions</span></h2><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">A decade after data sharing began in evolution and ecology, it is now widely accepted practice. Even those laggards—the biomedical sciences—are catching on despite muttering about “data parasites”. A few years ago, The American Naturalist began “strongly encouraging” code archiving as well, and we quickly found that the vast majority of authors were voluntarily doing so. When The American Naturalist began requiring code (if any is used) in January 2022, we have yet to hear a complaint or a request for an exception. The biological research community seems to have accepted the many benefits of data and code archiving. The final frontier in this move towards better reproducibility and open science is quality control to ensure adherence to the standards we say that we require. The first decade of data archiving rules were effectively an honor system. That honor system has resulted in a shocking number of incomplete or unclear archives, so a bit more supervision is, we believe, warranted. Thanks to the streamlining by DataSeer, our Data Editors can efficiently check a given paper’s archive in less than an hour, including writing the report to the Editor and authors identifying steps needed. Where data archives are seriously deficient, we do delay acceptance. The end result, we hope, is that authors will have more confidence in the results reported in our journal, and thus be more likely to read, trust, and cite the papers.</span></p><p><b style="-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; caret-color: rgb(0, 0, 0); color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><br /></b></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 12pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">We recognize that adherence to these rules takes time, effort, and training. The time and effort are part of the publication process. In our experience if authors prepare their README files, organize data well, and annotate their code as they obtain data and analyze their data, then the additional time required is minimal. Graduate training programs should (we think) make sure to take time to train students in data archiving and code annotation practices, as a key part of ethical science education. Meanwhile, experienced Data Editors may be willing to provide advice to authors struggling with how to comply with the ever-changing (and hopefully improving) open science landscape.</span></p><p><br /><br /><br /></p>Dan Bolnickhttp://www.blogger.com/profile/05181664810897127126noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-84521959857612193782021-12-01T14:42:00.005-06:002023-01-06T18:58:38.805-06:00Guidelines for archiving Code with Data<span id="docs-internal-guid-c61d2f13-7fff-1c63-6421-c18456d557e1"><p><b style="font-family: Calibri, sans-serif; text-align: center;"><span style="color: black; font-family: Times;">The following is a cross-post from the Editor's blog of The American Naturalist, developed with input from various volunteers (credited below).</span></b></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">A CHECKLIST FOR REPRODUCIBLE ARCHIVING DATA AND CODE IN ECOLOGY, EVOLUTION, AND BEHAVIOR</span></b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">December 1, 2021</span></b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Daniel I. Bolnick (</span><u><span lang="EN-CA" style="color: #1155cc; font-family: "Times New Roman", serif; font-size: 13pt;">daniel.bolnick@uconn.edu</span></u><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">), Roger Schürch (</span><u><span lang="EN-CA" style="color: #1155cc; font-family: "Times New Roman", serif; font-size: 13pt;">rschurch@vt.edu</span></u><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">), Daniel Vedder (</span><u><span lang="EN-CA" style="color: #1155cc; font-family: "Times New Roman", serif; font-size: 13pt;">daniel.vedder@idiv.de</span></u><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">), Max Reuter (</span><u><span lang="EN-CA" style="color: #1155cc; font-family: "Times New Roman", serif; font-size: 13pt;">m.reuter@ucl.ac.uk</span></u><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">), Leron Perez (</span><u><span lang="EN-CA" style="color: #1155cc; font-family: "Times New Roman", serif; font-size: 13pt;">leron@stanford.edu</span></u><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">), Robert Montgomerie (<a href="mailto:mont@queensu.ca" style="color: #954f72;">mont@queensu.ca</a>)<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br /><br /><br /><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Starting January 1, 2022, The American Naturalist will require that any analysis and simulation code (R scripts, Matlab scripts, Mathematica notebooks) used to generate reported results be archived in a public repository (e.g., Dryad, FigShare, DataVerse, Github archived on Zenodo). This has been our recommendation for a couple of years, and author compliance has been very common. As part of our commitment to Open and Reproducible Science, we are transitioning to make this a requirement. The following document, developed with input from a variety of volunteers, is intended to be a relatively basic guide to help authors comply with this new requirement.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></b></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">RATIONALE</span></b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">The fundamental question you should ask yourself is, “If a reader downloads my data and code, will my scripts be comprehensible, and will they run to completion and yield the same results on their computer?” Any computer code used to generate scientific results should be readily usable by reviewers or readers. Sharing this information is vital for several reasons as it promotes: (i) the appropriate interpretation of results, (ii) checking the validity of analyses and conclusions, (iii) future data synthesis, (iv) replication, and (v) their use as a teaching tool for anyone learning to do analyses themselves. Shared code provides greater confidence in results. <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br /><br /><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">The recommendations below are designed to help authors conduct a final check when finishing a research project, before submitting a manuscript for publication. In our experience, you will find it easier to build reusable code and data if you adhere to these recommendations from the start of your research project. We separately list requirements, and recommendations in each category below.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 13.5pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">1. <b>CLEAR DOCUMENTATION</b><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> <b>Great template available here:</b> </span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><a href="https://github.com/gchure/reproducible_research" style="color: #954f72;">https://github.com/gchure/reproducible_research</a></span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">REQUIRED:<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Prepare a single README file with important information about your data repository as a whole (code and data files). Text (.txt or .rtf) and Markdown (.md) README files are readable by a wider variety of free and open source software tools, so have greater longevity. The README file should simply be called README.txt (or .rtf or .md). That file should contain, in the following order:<o:p></o:p></span></p><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Citation to the publication associated with the datasets and code </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Author names, contact details</span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">A brief summary of what the study is about </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Identify who is responsible for collecting data and writing code.</span></p></blockquote><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">List of all folders and files by name, and a brief description of their contents. For each data file, list all variables (e.g., columns) with a clear description of each variable (e.g., units)<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Information about versions of packages and software used (including operating system) and dependencies (if these are not installed by the script itself). An easy way to get this information is to use sessionInfo() in R, or 'pip list --format freeze' in Python.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt 94.5pt; text-indent: -22.5pt; vertical-align: baseline;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">RECOMMENDED (for inclusion in the README file):<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Provide workflow instructions for users to run the software (e.g., explain the project workflow, and any configuration parameters of your software)<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Use informative names for folders and files (e.g., “code”, “data”, “outputs”)<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Provide license information, such as Creative Commons open source license language granting readers the right to reuse code. For more information on how to choose and write a license, see </span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><a href="https://choosealicense.com/" style="color: #954f72;"><span style="color: #1155cc;">choosealicense.com</span></a></span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">. This is not necessary for DRYAD repositories, as you choose licensing standards when submitting your files.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> If applicable, list funding sources used to generate the archived data, and include information about permits (collection, animal care, human research). This is not necessary for DRYAD repositories, as it is also recoded when submitting your files.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Link to Protocols.io or equivalent methods repositories where applicable<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><b><u><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br /><br /><br /></span></u></b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><b><u><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">2. CLEAN CODE</span></u></b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br />REQUIRED:</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> </span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Scripts should start by loading required packages, then importing raw data from files archived in your data repository.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> </span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Use relative paths to files and folders (e.g. avoid setwd() with an absolute path in R), so other users can replicate your data input steps on their own computers. <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Annotate your code with comments indicating what the purpose of each set of commands is (i.e., “why?”). If the functioning of the code (i.e., “how”) is unclear, strongly consider re-writing it to be clearer/simpler. In-line comments can provide specific details about a particular command<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Annotate code to indicate how commands correspond to figure numbers, table numbers, or subheadings of results within the manuscript.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> </span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">If you are adapting other researcher’s published code for your own purposes, acknowledge and cite the sources you are using. Likewise, cite the authors of packages that you use in your published article.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">RECOMMENDED:</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Test code before uploading to your repository, ideally on a pristine machine without any packages installed, but at least using a new session.</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Use informative names for input files, variables, and functions (and describe them in the README file).</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Any data manipulations (merging, sorting, transforming, filtering) should be done in your script, for fully transparent documentation of any changes to the data.</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> </span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Organise your code by splitting it into logical sections, such as importing and cleaning data, transformations, analysis and graphics and tables. Sections can be separate script files run in order (as explained in your README) or blocks of code within one script that are separated by clear breaks (e.g., comment lines, #--------------), or a series of function calls (which can facilitate reuse of code).<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Label code sections with headers that match the figure number, table number, or text subheading of the paper.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Omit extraneous code not used for generating the results of your publication, or place any such code in a Coda at the end of your script.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Where useful, save and deposit intermediate steps as their own files. Particularly, if your scripts include computationally intensive steps, it can be helpful to provide their output as an extra file as an alternative entry point to re-running your code. <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> If your code contains any stochastic process (e.g., random number generation, bootstrap re-sampling), set a random number seed at least once at the start of the script or, better, for each random sampling task. This will allow other users to reproduce your exact results.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Include clear error messages as annotations in your code that explain what might go wrong (e.g., if the user gave a text input where a numeric input was expected) and what the effect of the error or warning is.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">3. CLEAN DATA</span></b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Checklist for preparing data to upload to DRYAD (or other repository)</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Repository contents </span></b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">REQUIRED: </span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> </span><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> All data used to generate a published result should be included in the repository. For papers with multiple experiments or sets of observations, this may mean more than one data file.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Save each file with a short, meaningful file name and extension (see DRYAD recommendations here).<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Prepare a README text file to accompany the data. Our recommendation is to put this in the single README file described above. For complex repositories where this readme becomes unmanageably long, you may opt to create a set of separate README files for the overall repository, with one master README and more specific README files for code and for data. But, our preference is one README. The README file(s) should provide a brief overall description of each data file’s contents, and a list of all variable names with explanation (e.g. units). This should allow a new reader to understand what the entries in each column mean and relate this information to the Methods and Results of your paper. Alternatively, this may be a “Codebook” file in a table format with each variable as a row and column providing variable names (in the file), descriptions (e.g. for axis labels), units, etc. <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Save the README files as a text (.txt) or Markdown (.md) files and all of the data files as comma-separated variable (.csv) files. <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Save all of the data files as comma-separated variable (.csv) files. If your data are in EXCEL spreadsheets you are welcome to submit those as well (to be able to use colour coding and provide additional information, such as formulae) but each worksheet of data should also be saved as a separate .csv file.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">RECOMMENDED:<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> We recommend also archiving any digital material used to generate data (e.g., photos, sound recordings, videos, etc), but this may require too much storage space for some repository sites. At a minimum, upload a few example files illustrating the nature of the material and a range of outcomes. We recognize that some projects entail too much raw data to archive all the photos / videos / etc in their original state.</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br /><b>Data file contents and formatting </b> </span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">REQUIREMENTS: <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Archived files should include the raw data that you used when you first began analyses, not group means or other summary statistics; for convenience, summary statistics can be provided in a separate file, or generated by code archived with the data.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Identify each variable (column names) with a short name. Variable names should preferably be <10 characters long and not contain any spaces or special characters that could interfere with reading the data and running analysis code. Use an underline (e.g., wing_length) or camel case (e.g., WingLength) to distinguish words if you think that is needed.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">RECOMMENDATIONS: <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Omit variables not analyzed in your code.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> A common data structure is to ensure that every observation is a row and every variable is a column.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Each column should contain only one data type (e.g., do not mix numerical values and comments or categorical scores in a single column).<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Use “NA” or equivalent to indicate missing data (and specify what you use in the README file)<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><b><u><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br /><br /></span></u></b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">4. <b>COMPLETING YOUR ARCHIVE FOR UPLOAD TO DRYAD (or equivalent)</b><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">REQUIREMENTS:</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Upload your data and code to a curated, version-controlled repository (e.g., DRYAD, zenodo). Your own GitHub account (or other privately or agency controlled website) does not qualify as a public archive because you control access and might take down the data at a later date.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Provide all the metadata and information requested by the repository, even if this is optional and redundant with information contained in the README files. Metadata makes your archived material easier to find and understand.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> From the repository, get a private URL and provide this on submission of your manuscript so that editors and reviewers can access your archive before your data are made public.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">RECOMMENDED:<br /></span><span face=""Segoe UI Symbol", sans-serif" lang="EN-CA" style="font-size: 13pt;">➤</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> Prepare your data, code, and README files, before or during manuscript preparation (analysis and writing).<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><span style="font-family: Calibri, sans-serif;">➤ </span></span><span style="font-family: "Times New Roman", serif; font-size: 17.33333396911621px;">If you use a Github repository and generate an archive on Zenodo, we recommend removing ALL extraneous files except the core dataset and code and README file, so as to not clutter the archive in wahs that make it harder for readers to understand what files to use.</span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><b><u><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br /><br /></span></u></b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">5. <b><u>FOR MORE INFORMATION</u></b><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br /><b style="font-family: Calibri, sans-serif;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">More detailed guides to reproducible code principles can be found here:</span></b></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><span lang="EN-CA" style="font-size: 13pt;">Documenting Python Code: A Complete Guide - </span><span lang="EN-CA" style="font-size: 13pt;"><a href="https://realpython.com/documenting-python-code/" style="color: #954f72;"><span style="color: #1155cc;">https://realpython.com/documenting-python-code/</span></a></span></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br /><span lang="EN-CA" style="font-size: 13pt;">A guide to reproducible code in Ecology and Evolution, British Ecological Society: </span><span lang="EN-CA" style="font-size: 13pt;"><a href="https://www.britishecologicalsociety.org/wp-content/uploads/2019/06/BES-Guide-Reproducible-Code-2019.pdf?utm_source=web&utm_medium=web&utm_campaign=better_science" style="color: #954f72;"><span style="color: #1155cc;">https://www.britishecologicalsociety.org/wp-content/uploads/2019/06/BES-Guide-Reproducible-Code-2019.pdf?utm_source=web&utm_medium=web&utm_campaign=better_science</span></a></span><span lang="EN-CA" style="font-size: 13pt;"> </span></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br /><span lang="EN-CA" style="font-size: 13pt;">Dokta tools for building code repositories: </span><span lang="EN-CA" style="font-size: 13pt;"><a href="https://github.com/stencila/dockta#readme" style="color: #954f72;"><span style="color: #1155cc;">https://github.com/stencila/dockta#readme</span></a></span></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br /><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Version management for python projects: </span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><a href="https://python-poetry.org/" style="color: #954f72;"><span style="color: #1155cc;">https://python-poetry.org/</span></a></span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br /><span lang="EN-CA" style="font-size: 13pt;">Principles of Software Development - an Introduction for Computational Scientists (</span><span lang="EN-CA" style="font-size: 13pt;"><a href="https://doi.org/10.5281/zenodo.5721380" style="color: #954f72;"><span style="color: #1155cc;">https://doi.org/10.5281/zenodo.5721380</span></a></span><span lang="EN-CA" style="font-size: 13pt;">), with an associated code inspection checklist (</span><span lang="EN-CA" style="font-size: 13pt;"><a href="https://doi.org/10.5281/zenodo.5284377" style="color: #954f72;"><span style="color: #1155cc;">https://doi.org/10.5281/zenodo.5284377</span></a></span><span lang="EN-CA" style="font-size: 13pt;">).</span></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><br /><br /><br /><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Style Guide for Data Files</span></b><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> See the Google R style guide<span style="color: #1a73e8;"> (</span></span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><a href="https://google.github.io/styleguide/Rguide.html" style="color: #954f72;"><span style="color: #1a73e8;">https://google.github.io/styleguide/Rguide.html</span></a></span><span lang="EN-CA" style="color: #1a73e8; font-family: "Times New Roman", serif; font-size: 13pt;">) </span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">and the Tidyverse style guide<span style="color: #1a73e8;">(</span></span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><a href="https://style.tidyverse.org/syntax.html#object-names" style="color: #954f72;"><span style="color: #1a73e8;">https://style.tidyverse.org/syntax.html#object-names</span></a></span><span lang="EN-CA" style="color: #1a73e8; font-family: "Times New Roman", serif; font-size: 13pt;">) for more information</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="color: #3c4043; font-family: "Times New Roman", serif; font-size: 13pt;">Google style guide for Python: </span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><a href="https://google.github.io/styleguide/pyguide.html" style="color: #954f72;"><span style="color: #1155cc;">https://google.github.io/styleguide/pyguide.html</span></a></span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 6pt;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">6. <b><u>WHY DRYAD OR ZENODO?</u></b><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"><o:p> </o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"><span lang="EN-CA" style="color: #3c4043; font-family: "Times New Roman", serif; font-size: 13pt;">The American Naturalist requests that authors use DRYAD or zenodo for their archives when</span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;"> possible. <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 12pt; margin: 0in 0in 3pt 0.5in; text-indent: 0in;"><span lang="EN-CA" style="font-family: Symbol; font-size: 10pt;">·<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span></span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">DRYAD/zenodo are curated and this means that there is some initial checking by DRYAD for completeness and consistency in both the data files and the metadata. DRYAD requires some compliance before they will allow a submission.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 12pt; margin: 0in 0in 3pt 0.5in; text-indent: 0in;"><span lang="EN-CA" style="font-family: Symbol; font-size: 10pt;">·<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span></span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">We are finding it much easier and more convenient to download repositories from DRYAD/zenodo rather than searching the ms etc for the files or repository<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 12pt; margin: 0in 0in 3pt 0.5in; text-indent: 0in;"><span lang="EN-CA" style="font-family: Symbol; font-size: 10pt;">·<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span></span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">Files on DRYAD/zenodo cannot be arbitrarily deleted or changed by authors or others after publication. DRYAD will allow changes if a good case can be made—all changes are documented and all versions are retained.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 12pt; margin: 0in 0in 3pt 0.5in; text-indent: 0in;"><span lang="EN-CA" style="font-family: Symbol; font-size: 10pt;">·<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span></span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">DRYAD is free for Am Nat authors and we have a good working relationship with them and they take seriously our suggestions for improvement etc.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 12pt; margin: 0in 0in 3pt 0.5in; text-indent: 0in;"><span lang="EN-CA" style="font-family: Symbol; font-size: 10pt;">·<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span></span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">editors, reviewers, and authors will all become familiar with the workings of DRYAD<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in;"></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 12pt; margin: 0in 0in 3pt 0.5in; text-indent: 0in;"><span lang="EN-CA" style="font-family: Symbol; font-size: 10pt;">·<span style="font-family: "Times New Roman"; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span></span><span lang="EN-CA" style="font-family: "Times New Roman", serif; font-size: 13pt;">DRYAD and zenodo are now linked. DRYAD is for data files and zenodo for everything else (code, PDFs, etc). You need only upload all files to DRYAD and they will separate your archive into the appropriate parts. As you will see your DRYAD repository provides a link to the files on zenodo and vice versa</span></p></span>Dan Bolnickhttp://www.blogger.com/profile/05181664810897127126noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-17183465201903436512021-12-01T14:26:00.000-06:002021-12-01T14:26:04.184-06:00New American Naturalist editorial staff<p>Since Trish Morse retired in October 2020, Owen Cook has heroically managed all of the parts of The American Naturalist's editorial office solo. This includes checking incoming manuscripts for compliance, contacting Associate Editors picked by the Editors to handle a paper, and contacting reviewers for the AEs, sending reminders about overdue reviews and recommendation letters, responding to author queries, checking manuscript files and giving feedback on figure formatting, and much much more. He has truly been doing two jobs for the past year. Thanks Owen!</p><p>Luckily we now have been able to recruit two part-time helpers to assist Owen. Please extend a warm welcome to:</p><p><b>Alex Yu:</b></p><p><span style="font-family: "Times New Roman", Times, serif; font-size: 16px;">Alex (she/her/hers) is a Master of Humanities(MAPH) student at UChicago, currently working on her creative writing & translation thesis; in her spare time she is a travel writer, poet as well as vlogger. </span></p><p></p><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiPYAySqU3zN7707S536W9hCPK5fnPqfYZ7Hx_MNvoNfb0i4qk31HqpceRUgomxAGT42UGVVytclEBdvfGgsOsmRUA_SKq1sWWf4fk1FF-YpVNbEBUkJNAlwVVfWKIcmXAyF7qMFgLCeSw/" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="2048" data-original-width="1536" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiPYAySqU3zN7707S536W9hCPK5fnPqfYZ7Hx_MNvoNfb0i4qk31HqpceRUgomxAGT42UGVVytclEBdvfGgsOsmRUA_SKq1sWWf4fk1FF-YpVNbEBUkJNAlwVVfWKIcmXAyF7qMFgLCeSw/" width="180" /></a></div><span style="font-family: "Times New Roman", Times, serif; font-size: 16px;"><br /></span><p></p><p><span style="font-family: "Times New Roman", Times, serif; font-size: 16px;"><br /></span></p><p></p><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;"><b>Evan Williams</b></div><div class="separator" style="clear: both; text-align: left;"><span style="font-family: Helvetica; font-size: 12px;">Evan Williams (he/him/his) is a poet and essayist studying at the University of Chicago where he writes on topics ranging from surrealism to masculinity to the Svalbard Global Seed Vault. </span></div><div class="separator" style="clear: both; text-align: left;"><b><br /></b></div><div class="separator" style="clear: both; text-align: left;"><b><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgC_pcEmu_Q_P86pO0Fx27whXrvL6ehVE5yt94dTe9maiDoLwbdGtx_Oy-GPtXlmQi5uS0G-s1EsV3BMxzUlSEVo8MjLO98jlMwH1XdpsjLni6wZbMXqq2srQI63OW71oLRm0yM0rqDP-4/" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="1365" data-original-width="2048" height="213" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgC_pcEmu_Q_P86pO0Fx27whXrvL6ehVE5yt94dTe9maiDoLwbdGtx_Oy-GPtXlmQi5uS0G-s1EsV3BMxzUlSEVo8MjLO98jlMwH1XdpsjLni6wZbMXqq2srQI63OW71oLRm0yM0rqDP-4/" width="320" /></a></div><br /><br /></b></div><br /><br /><p></p>Dan Bolnickhttp://www.blogger.com/profile/05181664810897127126noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-73708300913875944132021-01-21T10:05:00.004-06:002021-01-21T10:08:14.342-06:00<p> Editor's Note:</p><p>Since fall 2020, Robert Montgomerie has been leading a group of nascent Data Editors in a task of designing a framework for monitoring compliance with Data Sharing requirements at The American Naturalist. This entails both setting up policies for a future board of Data Editors whose job will be to evaluate compliance of manuscripts' data and metadata before acceptance, and evaluating where problems lie in the past. What follows is a brief summary from Bob Montgomerie of his findings looking back at 2020 publications' compliance. -Dan Bolnick</p><p><br /></p><p><b style="font-family: "Optima Regular"; font-size: 13pt;"><span lang="EN-GB">Data Transparency 2020</span></b></p><p>Bob Montgomerie, mont@queensu.ca</p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB">For the past decade, authors of papers published in The American Naturalist have been required to make their raw data publicly available (Whitlock et al. 2010), either as an online supplement or in a recognized public data repository. The American Naturalist was one of the first journals to make this commitment to reproducibility and transparency but in the intervening 11 years, many biology journals have followed suit. Despite this requirement, however, compliance has too often been spotty (Roche et al. 2015) with data too often being incomplete, unintelligible, inconsistent or non-existent, though by 2020 all papers in Am Nat have made some data available to readers.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB">The myriad forms of, and problems with, data associated with papers is hardly surprising as journals rarely, if ever, provide guidelines for authors. For that reason, The American Naturalist now has a specific set of guidelines for providing data (<a href="https://www.journals.uchicago.edu/journals/an/instruct">https://www.journals.uchicago.edu/journals/an/instruct</a>)—much like the usual guidelines to authors for manuscript style—and a small team of data editors to help authors comply. Our policies and procedures for data will undoubtedly evolve in the coming months as our goal is to help authors make their data as transparent as possible, while also saving time for both authors and downstream users of those datasets.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB">To provide a summary of the current state of data available for Am Nat papers I looked at 100 papers published in 2020 (issues 1-5). By my count, 78 of those papers analyzed data that I expected to be made available (e.g., not analytical theory, or a synthetic review). The good news is that all but six of those papers made their raw data available—3 of those had embargoed their data for a reasonable period, and three others had not yet made their data available, which we immediately rectified. The not so good news—and this applies to all journals that I use regularly—is that those data are too often incomplete, or inscrutably difficult to understand (see graph).<o:p></o:p></span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB"><br /></span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-vc7pZE-NUnOyxVyNKo4kZMxgMRwKjeyM1oy7Y2wHmLFHltuVy2pWbXBxrpM75NCUdGWWu5qUaKZXqIHz45FBZg7XsFxrPTnf_qC8491Xpfz7QmL4DBZJHqRvzPbiCU5tjnCKwD84uzE/" style="font-size: 13pt; margin-left: 1em; margin-right: 1em; text-align: center;"><img data-original-height="684" data-original-width="1548" height="276" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-vc7pZE-NUnOyxVyNKo4kZMxgMRwKjeyM1oy7Y2wHmLFHltuVy2pWbXBxrpM75NCUdGWWu5qUaKZXqIHz45FBZg7XsFxrPTnf_qC8491Xpfz7QmL4DBZJHqRvzPbiCU5tjnCKwD84uzE/w626-h276/Screen+Shot+2021-01-21+at+11.03.34+AM.png" width="626" /></a></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; margin: 0cm 0cm 0.0001pt;"><br /><br /></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB">The biggest issue, and easy to resolve, is that only about 25% of those papers with data are what we would now call ‘complete’ in that they provide useful information about the datasets and variables provided. On trying to use data from a variety of journals in my statistics courses over the past decade, I often found that it would take me hours or even days to replicate analyses, too often involving correspondence with the authors to figure out cryptic variable names and complex data structures.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB">Those 75 data repositories that I looked at are remarkably diverse, involving 5 different repositories, 1-100s of files, some 34 different files types, and total repository size ranging from 20 Kb to >13 Gb. Anyone who has tried to open VisiCalc files from 1981, as I have, will appreciate the usefulness of simple file structures that will be accessible for years to come as the landscape of data-handling software evolves.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB">The survey of papers published in 2020 provides a baseline to gauge our progress in making data associated with Am Nat papers useful and transparent, and our research optimally reproducible. We will revisit this sort of analysis in a year’s time and we welcome your comments and suggestions.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><b><span lang="EN-GB">References<o:p></o:p></span></b></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB">Roche DG, Kruuk LEB, Lanfear R, Binning SA. Public Data Archiving in Ecology and Evolution: How Well Are We Doing?. PLOS Biol. 2015; 13 (11): e1002295. https://doi.org/10.1371/journal.pbio. 1002295 PMID: 26556502<o:p></o:p></span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="font-family: "Optima Regular"; font-size: 13pt; line-height: 19.066667556762695px; margin: 0cm 0cm 0.0001pt;"><span lang="EN-GB">Whitlock MC, MacPeek MA, Rausher MD, Rieseberg L, Moore AJ. 2010 Data archiving. American Naturalist 175: 145-146),<o:p></o:p></span></p>Dan Bolnickhttp://www.blogger.com/profile/05181664810897127126noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-29706751147459745212021-01-17T20:30:00.003-06:002021-01-18T21:26:36.371-06:00Call for Special Topics paper submissions<p> <span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-weight: 700; white-space: pre-wrap;">Nature,</span><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;"> Data, and Power: How hegemonies shape </span><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">biological </span><span style="font-family: "Times New Roman"; font-size: 12pt; font-weight: 700; white-space: pre-wrap;">knowledge</span></p><div dir="ltr" style="font-family: Helvetica; font-size: 13px;"><div dir="ltr"><span id="gmail-docs-internal-guid-889fed1e-7fff-f959-280f-fa8bae6a0efc"><br /><br /><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">The American Naturalist calls for proposals of manuscripts that address how systems of power and oppression have shaped theory and practice in </span><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">organismal biology (including but not
limited to </span><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">behavior, ecology, evolution, and genetics</span><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-weight: 700; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">)</span><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">. </span><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">Social relations of power, such as white supremacy, colonialism, misogyny, cissexism, ableism, and heteronormativity, have long shaped scientific understandings of the world. Investments in the maintenance of social hierarchies have manifested at the structural, institutional, and personal level--whether overtly or implicitly, intentionally or not--at all stages of the scientific process. They influence the kinds of questions scientists ask, the formation of scientific expertise and networks of knowledge production, and research outcomes themselves. In this Special Section, we will assemble papers that investigate the cultural, social, and political foundations of the theories and practices of contemporary </span><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">organismal biology</span><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">.</span></p><br /><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">Papers should be written for an audience of biology researchers, and should both identify problems within current theories and practices, and make suggestions on how we can transform our thinking and produce more just science. Such contributions are aligned with Am Nat’s mission to “pose new and significant problems, introduce novel subjects, develop conceptual unification, and change the way people think.” We seek submissions from authors of varied disciplinary and interdisciplinary backgrounds in the social sciences, humanities, and natural sciences. We particularly encourage cross-disciplinary collaborations.
</span><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;"><br />
<br />
</span></p><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">Proposal and manuscript review will be managed by a cross-disciplinary editorial team. Following proposal review, we will invite authors to submit full manuscripts. A</span><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">n invitation to submit a full manuscript does not guarantee publishing in the American Naturalist</span><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">. Publication charges will be waived for full manuscripts included in this special section. </span></p><br /><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">Submission process/timeline: </span></p><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">Please submit a 500 word (maximum) proposal describing your paper idea and why you think it would be a good fit for this Special Section to </span><a href="mailto:amnat@press.uchicago.edu">amnat@press.uchicago.edu</a> <span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">with subject line “Nature, Data, and Power Special Section” by </span><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">February 15 2021</span><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">. Invitations for full papers will be issued by March 15 2021. The deadline for full manuscripts will be June 15 2021. Anticipated publication of the section is before July 2022.</span></p><div dir="ltr"><span><br /></span></div><br /><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">Papers will be handled by a special Editorial team, in consultation with the Editor-In-Chief (Daniel Bolnick): </span><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;"><br />
</span></p><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">Nancy Chen, Department of Biology, University of Rochester</span></p><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">Vince Formica, Department of Biology, Swarthmore College</span></p><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">Ambika Kamath, Department of Environmental Science, Policy, and Management, University of California Berkeley</span></p><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">María Rebolleda-Gómez, Department of Ecology and Evolutionary Biology, University of California Irvine</span></p><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: #222222; font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">Banu Subramaniam, Department of Women, Gender, Sexuality Studies, University of Massachusetts Amherst</span></p><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">Beans Velocci, Department of History, Yale University</span></p><p dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;"><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">Ashton Wesner, Department of History, University of California Berkeley</span></p><br /><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">If you have any questions, please contact </span><a href="mailto:amnat@press.uchicago.edu">amnat@press.uchicago.edu</a></span><span style="font-family: "Times New Roman"; font-size: 12pt; font-variant-east-asian: normal; font-variant-ligatures: normal; vertical-align: baseline; white-space: pre-wrap;">. </span><br /></div></div><br class="Apple-interchange-newline" />Dan Bolnickhttp://www.blogger.com/profile/05181664810897127126noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-36311860211174816492021-01-04T12:56:00.003-06:002021-01-06T10:33:49.231-06:00Registering complaints or concerns about published papers<p><i style="font-family: "Palatino Linotype", "Book Antiqua", Palatino, serif; font-size: 16px;">The American Naturalist</i><span style="font-family: "Palatino Linotype", "Book Antiqua", Palatino, serif; font-size: 16px;"> would like to clarify its procedures for handling comments on previously published work, and offer new protections for researchers who have valid reasons for maintaining their anonymity while commenting on previously published work.</span></p><p>For decades, scientific journals such as The American Naturalist have had an established protocol for handling criticisms of already-published papers. Readers are able to submit Comments that clearly document and justify their concerns about a published paper. These may identify factual errors (including mistakes in analyses, code, etc), flaws in experimental designs, or disagreements about interpretation of results or context. Such Comments are reviewed, and the authors of the original paper are given a chance to review the Comment. If the complaint is found to have merit (even if the original authors disagree), then the complaint is accepted for publication. The authors have an option to publish a rebuttal if they disagree with the points raised in the Comment. If the authors acknowledge the merits of the critique, then they may leave the Comment unanswered, or they may submit a Correction that updates the paper with more correct information such as new statistical results or mathematical analyses (which also gets reviewed). In extreme cases, if the Comment identifies demonstrable errors that significantly undermine the conclusions of the original paper, the original authors and/or Editorial Board may opt for a retraction instead. </p><p>Note that papers can receive Comments for a whole range of reasons, from minor errors that don't change the main message, to fundamental mistakes of factual presentation (e.g., incorrect statistical results), suspect patterns in data, or critiques of interpretation or context. There's a gradation from papers having minor flaws, to major ones, and flaws ranging from demonstrable evidence to matters of interpretation. Not all warrant Comments, and certainly not all need Correction or Retraction even when the critiques are true, depending on the magnitude of the problems and how compelling the evidence is for the problem. </p><p>We should emphasize that a reader's first action, on finding something that is unclear or appears wrong, should ideally be to contact the author for clarification. This might ultimately resolve the problem without involving the journal. Or, it may induce the authors to publish a Correction (or, in principle, even a retraction). Writing a Comment to the journal should be a plan-B option when direct communication with the authors has failed to resolve the issue, or if the critics have a valid reason to avoid direct contact (e.g., fear of retaliation). I am aware of at least one case where not only did an author (Bob Holt) agree with a Comment's critique, he joined in the effort and ultimately became a co-author on the Comment moving the field forward in the process. I know of cases where authors self-retracted after critics contacted them before the journal. Indeed, we recently published a Correction to a paper from the 1980's that the original authors submitted after a colleague found an error.</p><p>In recent years, the Editors of this journal have been receiving criticisms of papers through unofficial channels. These include direct emails to the Editors, tweets, or PubPeer posts. Until now, our policy has been to take these complaints seriously and conduct a full evaluation to identify whether the concerns have merit. This has resulted in multiple committees being formed, and has been a significant drain on the energies of the Editorial Board as a whole, but has indeed identified both some genuine problems, and some cases where there is a simple difference of opinion. </p><p>The problem with this approach, of responding fully to informal critiques, is growing clearer to us on the Editorial Board. First and most troubling, it becomes plain that an individual with a personal vendetta against an author could use such informal critiques to recruit the journal as an unwitting tool for bullying the author, whether or not the critiques hold water or are severe enough to ultimately require action. Second, it simply is not possible for the Editorial Board, with their other responsibilities to the journal, to fully monitor all possible social media venues where people post criticisms of papers (PubPeer, Twitter, etc). Rather than assuming that the journal has seen a criticism posted elsewhere, we prefer that critics submit Comments to the journal where the criticism can be fully vetted through a standard review process. This takes time, but is the traditionally accepted means of evaluating scientific arguments. Third, tweets and PubPeer posts are also often used for the milder goal of carrying on an honest and open scientific debate on a topic of honest disagreement, or about minor errors that may not warrant the effort of Correction. If we initiated a multi-person investigatory committee for every such disagreement, the journal would collapse under the weight of re-evaluating past work and become a partisan in adjudicating honest debates. Let's face it: when was the last time you were in a journal club reading a new paper and nobody had a question that couldn't be clearly resolved, nobody had a quibble with interpretation, nobody had a suggestion for a better experimental design. Therefore, we need a mechanism for distinguishing between which debates are best left alone, versus those that require investigation and possible corrective action. That mechanism is the same as it has long been: when we receive a submission of a Comment manuscript. Fourth, submitting informal critiques to the journal (e.g., by alerting us to a PubPeer post, or emailing an informally written diatribe) shunts the work of checking the paper off onto the journal's editorial board, when the critic is often better placed (by virtue of their expertise) to write a careful and complete criticism. It is akin to telling someone else to write a comment. As a case in point, some recent committee reports have turned out to be many times longer than the original email or PubPeer complaints, and that is work that has fallen on already-overburdened volunteer Associate Editors, which is not a sustainable approach. We rely in part on our community of readers to identify problems that were missed in review (and let's face it, peer review isn't perfect), and the mechanism for doing this is through Comments.</p><p><b><u>Therefore, it is the policy of the Editors of The American Naturalist, that henceforth we will expect that criticisms of published papers be written as Comments and submitted to us through Editorial Manager, to be subject to review through our editorial software that appropriately archives all steps in the process. </u></b>These Comments need not be long, but they must effectively document errors in the published paper's data, analysis, or interpretation. I will emphasize that the Comments' author(s) will be known to the Editor-In-Chief handling the complaint, but that the review process can henceforth be double-blind to ensure the critics' anonymity. In extreme cases where a Comment author is afraid to have their name listed on the final publication, the Editorial Board will consider requests for anonymity on the publication itself, on a case by case basis. It is not our desire to make all Comments anonymous by default (we encourage openness once things are published), but neither will we refuse a request for anonymity when accompanied by a clear justification to the Editor-In-Chief. It is possible there are situations that arise where a Comment is not the best course of action, and readers may of course contact the Editor to inquire.</p><p>The primary exception is that readers may notify the Editor-In-Chief (Daniel Bolnick) by email (daniel.bolnick@uconn.edu) if they find that an article published since 2010 does not provide complete and publicly available data (e.g., a Dryad repository) sufficient to recreate the analyses. Compliance with data sharing has been imperfect (based on a <a href="https://comments.amnat.org/2020/10/data-archiving.html" target="_blank">survey of data archives posted for AmNat papers in 2020</a>, many of which are incomplete or have unclear metadata). Readers are encouraged to directly contact authors first to request correction of flawed data archives. But when authors are unresponsive, the journal may help step in to encourage correction. When we become aware of missing or incomplete data archives (or, unusably unclear metadata), we will contact the author to request its completion on Dryad (or other repository). If the authors have not fixed the data archive in a reasonable window of time, or if they are unable to do so having lost the original data files, then the journal would as a rule publish an Editorial Expression of Concern noting that the data for a paper are missing. This applies only to papers published after data archiving became a condition for publication (e.g., 2010 and after). Authors who are habitual offenders may see their current submissions delayed while we check their data archives more thoroughly. And, as noted in a <a href="https://comments.amnat.org/2020/10/data-archiving.html" target="_blank">previous Editors blog post on data archiving</a>, we encourage authors to create data archives prior to submission, for the journal to evaluate during the review process. On Dryad, where the pre-review archiving process is free and you can generate a private key to provide to the journal.</p><p>To close this blog post, I wish to briefly consider some of the motives for why people have been using informal venues for registering criticisms, at least as far as I can discern. </p><p>First, many posts on PubPeer, twitter, and other venues, are not meant for journals. Rather they are aimed at establishing a constructive but critical conversation between authors and readers. This is a healthy and valuable element of scientific dialogue, though when done in a less constructive tone it becomes stressful for authors and can devolve into a one-sided process. Such posts are not meant for our consideration. Comments, Corrections (or Retractions) are not meant for carrying on simple conversations, but for identifying and resolving errors of fact. This, again is one reason why journals should not be expected to react to all PubPeer posts.</p><p>Second, the next best rationale I have come across is that the critic of a paper is afraid of professional or personal retribution, and so wishes to remain anonymous. Our process of anonymous review of Comments, and openness (in principle) to well-justified requests for anonymity upon publication, should serve to alleviate this concern and thus encourage people to use the established route of Comments.</p><p>Third, in at least one case, the critic openly acknowledged that they simply did not wish to take the time to write a formal Comment to be reviewed and published. As noted above, this simply offloads the work onto others (our busy Associate Editors) who may not be as expert in the details of the subject. This is unfair to our editorial board, as it amounts to saying that the problem isn't important enough for the critic's time, but is important enough to consume the editorial board's time. It is true that the editorial board (especially the editors) have a greater obligation to ensure the quality of the work published in their journal, but ultimately we rely on the community to help with this (as we do with submissions, and reviews).</p><p>Fourth, some critics seek rapid dissemination of their criticisms, and prefer not to wait for a lengthy review process. This rapid science view point has merit, but risks damaging authors' reputation and imposing severe stresses before the validity of the criticisms has been considered. By placing attacks in public before the attacks are verified, this approach is indeed fast but can do great damage when the attacks ultimately prove to be misplaced. I have seen specific cases where statistical criticisms posted on PubPeer are later found to be incorrect, and a review process helps protect authors' reputation from flawed criticism.</p><p>Finally, there are cases where critics mistrust the institutional process. I have heard directly of cases where critics contacted journals and were rebuffed or ignored.Readers sometimes believe (rightly or wrongly) that journals are more interested in protecting their own reputation and their authors', and so have motives to sweep criticisms under the carpet. I am shocked by many of these stories. It saddens me to think that we Editors are mistrusted, when we go through such efforts to ensure quality of our published work. I will admit that Editors may hesitate to pursue aggressive steps towards retraction out of fear for legal attack by affected authors. But more often, in my experience, a critic feels ignored when they submit a complaint but the journal finds the complaint to be insufficiently severe for corrective action (either misplaced, or insufficiently documented, or just not substantive enough a change to the paper's core message). But having been involved in both retractions and corrections and decisions to not do either, I can say that my view from behind the curtain has taught me that journals' decisions (at least AmNat's, and a few others I've watched from the sidelines) are done carefully and thoughtfully, with great effort and with good intentions, even when the critics (or I) don't fully agree with the outcome.</p><p>I will also acknowledge that evaluating criticisms is a large drain on our already-stretched time running regular journal functions. Personally, in 2020 I have spent far more time writing R code to analyze other people's potentially flawed datasets, than in analyzing data of my own. I have written more words regarding investigations into past publications this year, than I have written words on my own papers or grants. But, it is an Editor's job to ensure the quality of published work in their journal. The journal's reputation is bolstered not by sweeping problems out of sight, but by being proactive about correcting known problems. But, we Editors need the community's participation in this process, by following procedures set down by the journal for evaluating problems. Ultimately, it is a journal that publishes a paper, and so it is a journal that has leverage to pursue Corrections or Retractions or Expressions of Concern. This means that if critics really want their concerns to lead to corrective actions they ultimately do need to work through journals, which means using journals' established means of handling complaints.</p><p>All of this is not meant to deter Comments or criticism of published work. Science advances by self-criticism and self-correction. We should never shy away from fixing what is wrong (when it is clearly wrong, and important enough for the effort - nobody would publish a Correction for a grammatical mistake for instance). But, procedures for doing so exist, and I'd like to see those procedures used more, favored over backchannel approaches.</p><p><br /></p>Dan Bolnickhttp://www.blogger.com/profile/05181664810897127126noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-76346794567156206462020-10-23T13:51:00.000-05:002020-10-23T13:51:01.128-05:00Data archiving<p><span style="font-family: Verdana; font-size: 13px;">The following is a guest post by Bob Montgomerie, Queens University</span><br style="font-family: Verdana; font-size: 13px;" /><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">The text was posted, lightly edited, and approved by the Editor In Chief, Dan Bolnick</span><br style="font-family: Verdana; font-size: 13px;" /><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">As you may know, this is Open Access Week (19-26 October) celebrating the progress made so far with making science open and accessible to all, but reminding us that there are still some challenges. One key feature of open science is providing free access to the data underlying published reports. To that end, The American Naturalist requires that all authors make their data available either on DRYAD (free to authors), on another public repository, or as a supplement published along with their paper. My own experience seeking data from work published in a wide variety of journals has been, shall we say, mixed in recent years. So, it seemed like a good time to assess the availability and quality of recent data made available with American Naturalist papers. </span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;"> </span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">To evaluate the quality of data archiving with The American Naturalist, I looked at 100 papers published in 2020 (the first 50 and most recent 50). Of those 100 papers, at least 78 were based on data that should have been made available—the others were reviews, commentaries, or model-based (though some of those models seem to use data). The good news is that all but four of those papers had made data available either on DRYAD (56 papers), on other public repositories (3) or as appendices/supplements available with the paper as supplementary material (12). Three papers have data embargoed for a while, and only 4 papers made none of the data available. This is, in my experience, a remarkably high level of compliance.</span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;"> </span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">The downside is that only 7 of those 56 of those papers with datasets on DRYAD have provided data in such a way that I, and I assume most users, would find convenient or even comprehensible. Here are the main issues:</span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">• no README (or any other) file explaining the variable names in data files</span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">• data files in EXCEL and other formats that are not easily read by statistical software. Yes, I know that R can read Excel files but only if they are set up properly, and many of those were not</span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">• odd file extensions that are not explained. I counted more than 30 file extensions in those 58 repositories, a few of which I had never heard of, and many of which are unlikely to be accessible without expensive or eventually obsolete software</span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">• not all data made available—I did not check every paper, as that would have taken too long, but I did check a few and could not find the data supporting a couple of figures and tables. Sometimes authors provided summary data (means, SDs) and not the raw data from which those summaries were calculated.</span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">• no R, Python or other scripts or notebooks to replicate the analyses</span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">• analysis code not well-enough annotated to be comprehensible</span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">• code that does not run, presumably created in earlier versions of the software with unknown packages and package versions</span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;"> </span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">None of this is unexpected as (i) this whole idea about making data available is relatively new and not often part of our formal training in graduate school, (ii) journals rarely (ever?) provide guidelines for authors that detail what they consider to be best practices, and (iii) most journals have nobody checking to see if authors have actually complied with their requirements. There are many excellent reasons for all of us to want data to be freely available for every published study and I feel that we should take pride in doing as good a job with that as we do with our published papers. Good data will always be useful, whereas most papers have a short half-life if citation metrics are any indication.</span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;"> </span><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">The American Naturalist is now publishing guidelines for best practices in data archiving (link here) and will have a small team of data editors checking each paper’s data repository to make sure that it is complete, comprehensive, and adequately documented. We are probably the first biology journal to fully embrace the value of open data in this fashion and we welcome your comments as we put this policy in place. We also now encourage authors to submit private Dryad data links upon submission, so reviewers and editors have the option of checking compliance before manuscript acceptance (see Author Instructions for Submission for details). We will be asking authors resubmitting revisions to provide data links for checking prior to final acceptance.</span><br style="font-family: Verdana; font-size: 13px;" /><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">If you find a published paper's Dryad or related archive that is unusable (incomplete, or unclear), please contact the author and ask that they fix the deficiencies, with a cc the editor (e.g.,</span><a class="moz-txt-link-abbreviated" href="mailto:daniel.bolnick@uconn.edu" style="font-family: Verdana; font-size: 13px;">daniel.bolnick@uconn.edu</a><span style="font-family: Verdana; font-size: 13px;">). Since 2011, The American Naturalist has made complete data archiving (sufficient to reproduce the analyses and results) a condition of publication. Authors that have not done so are failing to live up to their side of the bargain that led to their publication. </span><br style="font-family: Verdana; font-size: 13px;" /><br style="font-family: Verdana; font-size: 13px;" /><span style="font-family: Verdana; font-size: 13px;">It is now our Editorial policy that the American Naturalist reserves the right to publish Editorial Expressions of Concern when we are made aware of grossly deficient data archives that are not amended in a reasonable amount of time. In extreme cases, we reserve the right to retract papers that are not supported by appropriately archived data, or to hold up an author's future submissions until past deficiencies are amended. However, we also recognize that new policies entail growing pains and that compliance is understandably imperfect as we adjust to a new culture of more rigorous and complete data sharing.</span></p><style class="WebKit-mso-list-quirks-style">
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</style>Dan Bolnickhttp://www.blogger.com/profile/05181664810897127126noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-89418004960486477742020-10-16T12:50:00.000-05:002020-10-16T12:50:02.898-05:00Behavioral Ecology<h2>
<span style="font-weight: normal;">Recent Papers</span></h2><div><span><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710568" target="_blank">State-Dependent Decision-Making by Predators and Its Consequences for Mimicry</a></b></div><div>Thomas G. Aubier and Thomas N. Sherratt</div><div><br /></div></span></div><div><span><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710764" target="_blank">Spite and the Geometry of Negative Relatedness</a></b></div><div>Philip G. Madgwick</div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Nov-Madgwick.html">https://www.amnat.org/an/newpapers/Nov-Madgwick.html</a></div><div><br /></div></span></div><div><span><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710211" target="_blank">Host Plant Choice Determined by Reproductive Interference between Closely Related Butterflies</a></b></div><div>Naota Ohsaki, Masaaki Ohata, Yoshibumi Sato, and Mark D. Rausher</div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Oct-Ohsaki.html">https://www.amnat.org/an/newpapers/Oct-Ohsaki.html</a></div><div><br /></div></span></div><div><span><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709465" target="_blank">Relative Brain Size Is Predicted by the Intensity of Intrasexual Competition in Frogs</a></b></div><div>Chun Lan Mai (麦春兰), Wen Bo Liao (廖文波), Stefan Lüpold, and Alexander Kotrschal</div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Aug-Mai.html">https://www.amnat.org/an/newpapers/Aug-Mai.html</a></div><div><br /></div></span></div><div><span><div>FREE</div><div><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709479" target="_blank">Metabolic Rate Interacts with Resource Availability to Determine Individual Variation in Microhabitat Use in the Wild</a></div><div>Sonya K. Auer, Ronald D. Bassar, Daniel Turek, Graeme J. Anderson, Simon McKelvey, John D. Armstrong, Keith H. Nislow, Helen K. Downie, Thomas A. J. Morgan, Darryl McLennan, and Neil B. Metcalfe</div><div><br /></div></span></div><div><span><div>FREE, AMERICAN SOCIETY OF NATURALISTS ADDRESS</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709699" target="_blank">What Do Ecology, Evolution, and Behavior Have in Common? The Organism in the Middle</a></b></div><div>Ellen D. Ketterson</div><div><br /></div></span></div><div><span><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708721" target="_blank">The Ecology of Individual Differences Empirically Applied to Space-Use and Movement Tactics</a></b></div><div>Quinn M. R. Webber, Michel P. Laforge, Maegwin Bonar, Alec L. Robitaille, Christopher Hart, Sana Zabihi-Seissan, and Eric Vander Wal</div><div>Blog: <a href="https://www.amnat.org/an/newpapers/July-Webber.html">https://www.amnat.org/an/newpapers/July-Webber.html</a></div><div><br /></div></span></div><div><span><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708531" target="_blank">Maternal Investment, Ecological Lifestyle, and Brain Evolution in Sharks and Rays</a></b></div><div>Christopher G. Mull, Kara E. Yopak, and Nicholas K. Dulvy</div><div>Blog: <a href="https://www.amnat.org/an/newpapers/June-Mull.html">https://www.amnat.org/an/newpapers/June-Mull.html</a></div><div><br /></div></span></div><div><span><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708155" target="_blank">Age-Related Brood Parasitism and Egg Rejection in Magpie Hosts</a></b></div><div>Juan Gabriel Martínez, Mercedes Molina-Morales, Marta Precioso, and Jesús Miguel Avilés</div><div>Blog: <a href="https://www.amnat.org/an/newpapers/May-Martinez.html">https://www.amnat.org/an/newpapers/May-Martinez.html</a></div><div><br /></div></span></div><div><span><div>FREE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707519" target="_blank">Reinforcement Learning Theory Reveals the Cognitive Requirements for Solving the Cleaner Fish Market Task</a></b></div><div>Andrés E. Quiñones, Olof Leimar, Arnon Lotem, and Redouan Bshary</div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Apr-Quinones.html">https://www.amnat.org/an/newpapers/Apr-Quinones.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707544" target="_blank">Safety Cues Can Give Prey More Valuable Information Than Danger Cues</a></b></div><div>Barney Luttbeg, Maud C. O. Ferrari, Daniel T. Blumstein, and Douglas P. Chivers</div><div>Blurb: <a href="https://www.amnat.org/an/newpapers/Apr-Luttbeg.html">https://www.amnat.org/an/newpapers/Apr-Luttbeg.html</a></div></div><div><br /></div></span></div>
<div>
<div>
<b><i>Note</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704773" target="_blank">Early Sibling Conflict May Ultimately Benefit the Family</a></b></div>
<div>
Alyssa Laney Smith, Daniel Z. Atwater, and Ragan M. Callaway</div>
<div>
Blurb: <a href="https://www.amnat.org/an/newpapers/Oct-Smith.html">https://www.amnat.org/an/newpapers/Oct-Smith.html</a></div>
<div>
<br /></div>
</div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704593" target="_blank">Within-Individual Canalization Contributes to Age-Related Increases in Trait Repeatability: A Longitudinal Experiment in Red Knots</a></b></div>
<div>
Eva M. A. Kok, Joseph B. Burant, Anne Dekinga, Petra Manche, Darren Saintonge, Theunis Piersma, and Kimberley J. Mathot</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/Sep-Kok.html">https://www.amnat.org/an/newpapers/Sep-Kok.html</a></div>
</div>
<div>
<span style="font-weight: normal;"><br /></span></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704089" target="_blank">Individual Variation in the Social Plasticity of Water Dragons</a></b></div>
<div>
Kasha Strickland and Céline H. Frère</div>
<div>
<br /></div>
</div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703158" target="_blank">Assessing Behavioral Associations in a Hybrid Zone through Social Network Analysis: Complex Assortative Behaviors Structure Associations in a Hybrid Quail Population</a></b></div>
<div>
David M. Zonana, Jennifer M. Gee, Eli S. Bridge, Michael D. Breed, and Daniel F. Doak</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/JuneZonana.html">https://www.amnat.org/an/newpapers/JuneZonana.html</a></div>
<div>
<br /></div>
</div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700566" target="_blank">Space Use and Leadership Modify Dilution Effects on Optimal Vigilance under Food-Safety Trade-Offs</a></b></div>
<div>
Rémi Patin, Daniel Fortin, Cédric Sueur, and Simon Chamaillé-Jammes</div>
</div>
<div>
<i>Lay summary:</i> <a href="https://www.amnat.org/an/newpapers/JanPatin.html">https://www.amnat.org/an/newpapers/JanPatin.html</a></div>
<div><br /></div>
<div>
</div>
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</div>
ASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-43594082639573994632020-10-15T17:03:00.000-05:002020-10-15T17:03:37.686-05:00Adaptation<h2>
Recent Papers </h2><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710338" target="_blank">A Comparative Test for Divergent Adaptation: Inferring Speciation Drivers from Functional Trait Divergence</a></b></div><div>Sean A. S. Anderson and Jason T. Weir</div></div><div>Blurb: <a href="https://www.amnat.org/an/newpapers/Oct-Anderson.html">https://www.amnat.org/an/newpapers/Oct-Anderson.html</a></div><div><br /></div><div><div>FREE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708274" target="_blank">Evolution of Reproduction Periods in Seasonal Environments</a></b></div><div>Zepeng Sun, Kalle Parvinen, Mikko Heino, Johan A. J. Metz, André M. de Roos, and Ulf Dieckmann</div></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710039" target="_blank">Male-Male Competition Causes Parasite-Mediated Sexual Selection for Local Adaptation</a></b></div><div>Miguel Gómez-Llano, Aaditya Narasimhan, and Erik I. Svensson</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Sep-Gomez-Llano.html">https://www.amnat.org/an/newpapers/Sep-Gomez-Llano.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710022" target="_blank">The Origin and Spread of Locally Adaptive Seasonal Camouflage in Snowshoe Hares</a></b></div><div>Matthew R. Jones, L. Scott Mills, Jeffrey D. Jensen, and Jeffrey M. Good</div></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709426" target="_blank">Transformational Mimicry in a Myrmecomorphic Spider</a></b></div><div>Stano Pekár, Yun-Yun Tsai, and Radek Michalko</div></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709610" target="_blank">Selection and Constraints in the Ecomorphological Adaptive Evolution of the Skull of Living Canidae (Carnivora, Mammalia)</a></b></div><div>Fabio Andrade Machado</div></div><div><br /></div><div><div>FREE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709479" target="_blank">Metabolic Rate Interacts with Resource Availability to Determine Individual Variation in Microhabitat Use in the Wild</a></b></div><div>Sonya K. Auer, Ronald D. Bassar, Daniel Turek, Graeme J. Anderson, Simon McKelvey, John D. Armstrong, Keith H. Nislow, Helen K. Downie, Thomas A. J. Morgan, Darryl McLennan, and Neil B. Metcalfe</div></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708496" target="_blank">Survival Benefits of Group Living in a Fluctuating Environment</a></b></div><div>Sarah Guindre-Parker and Dustin R. Rubenstein</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/June-Guindre-Parker.html">https://www.amnat.org/an/newpapers/June-Guindre-Parker.html</a></div><div><br /></div><div><div>HISTORICAL PERSPECTIVE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708498" target="_blank">The Adaptive Geometry of Trees Revisited</a></b></div><div>Thomas J. Givnish</div></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707518" target="_blank">Adaptive Maternal Investment in the Wild? Links between Maternal Growth Trajectory and Offspring Size, Growth, and Survival in Contrasting Environments</a></b></div><div>Tim Burton, Njal Rollinson, Simon McKelvey, David C. Stewart, John D. Armstrong, and Neil B. Metcalfe</div></div><div>Blurb: <a href="https://www.amnat.org/an/newpapers/Apr-Burton.html">https://www.amnat.org/an/newpapers/Apr-Burton.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707597" target="_blank">Belowground Competition Can Influence the Evolution of Root Traits</a></b></div><div>Sara M. Colom and Regina S. Baucom</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Apr-Colom.html">https://www.amnat.org/an/newpapers/Apr-Colom.html</a></div><div><br /></div><div><div>SYNTHESIS</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707322" target="_blank">Context Dependence of Local Adaptation to Abiotic and Biotic Environments: A Quantitative and Qualitative Synthesis</a></b></div><div>Ryan D. Briscoe Runquist, Amanda J. Gorton, Jeremy B. Yoder, Nicholas J. Deacon, Jake J. Grossman, Shan Kothari, Marta P. Lyons, Seema N. Sheth, Peter Tiffin, and David A. Moeller</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Mar-Briscoe-Runquist.html">https://www.amnat.org/an/newpapers/Mar-Briscoe-Runquist.html</a></div><div><br /></div><div><div>SYNTHESIS</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707323" target="_blank">Local Adaptation to Biotic Interactions: A Meta-analysis across Latitudes</a></b></div><div>Anna L. Hargreaves, Rachel M. Germain, Megan Bontrager, Joshua Persi, and Amy L. Angert</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Mar-Hargreaves.html">https://www.amnat.org/an/newpapers/Mar-Hargreaves.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707324" target="_blank">Evolution Transforms Pushed Waves into Pulled Waves</a></b></div><div>Philip Erm and Ben L. Phillips</div></div><div>Blurb: <a href="https://www.amnat.org/an/newpapers/Mar-Erm.html">https://www.amnat.org/an/newpapers/Mar-Erm.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707209" target="_blank">Gene Flow Limits Adaptation along Steep Environmental Gradients</a></b></div><div>Judith C. Bachmann, Alexandra Jansen van Rensburg, Maria Cortazar-Chinarro, Anssi Laurila, and Josh Van Buskirk</div></div><div><br /></div><div><div>NATURAL HISTORY NOTE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706905" target="_blank">Transitions between the Terrestrial and Epiphytic Habit Drove the Evolution of Seed-Aerodynamic Traits in Orchids</a></b></div><div>Xu-Li Fan, Guillaume Chomicki, Kai Hao, Qiang Liu, Ying-Ze Xiong, Susanne S. Renner, Jiang-Yun Gao, and Shuang-Quan Huang</div><div>ORCIDs: Fan, https://orci</div></div><div><br /></div><div><div>NOTE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706181" target="_blank">Evolutionary Rescue from a Wave of Biological Invasion</a></b></div><div>J. David Van Dyken</div></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706258" target="_blank">The Evolution of Immigration Strategies Facilitates Niche Expansion by Divergent Adaptation in a Structured Metapopulation Model</a></b></div><div>Éva Kisdi, Helene C. Weigang, and Mats Gyllenberg</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Jan-Kisdi.html">https://www.amnat.org/an/newpapers/Jan-Kisdi.html</a></div><div><br /></div><div><div>FREE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706196" target="_blank">Niche Construction Affects the Variability and Strength of Natural Selection</a></b></div><div>Andrew D. Clark, Dominik Deffner, Kevin Laland, John Odling-Smee, and John Endler</div></div><div><br /></div><div><div>FREE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706251" target="_blank">Why Do Phytoplankton Evolve Large Size in Response to Grazing?</a></b></div><div>Pedro Branco, Martijn Egas, Spencer R. Hall, and Jef Huisman</div></div><div>Blurb: <a href="https://www.amnat.org/an/newpapers/Jan-Branco.html">https://www.amnat.org/an/newpapers/Jan-Branco.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705680" target="_blank">Meta-analysis Shows That Rapid Phenotypic Change in Angiosperms in Response to Environmental Change Is Followed by Stasis</a></b></div><div>Lucas D. Gorné and Sandra Díaz</div></div><div><br /></div>
<div>
<b><i>Introduction to Special Feature on Maladaptation</i></b></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705020" target="_blank">Understanding Maladaptation by Uniting Ecological and Evolutionary Perspectives</a></b></div>
<div>
Steven P. Brady, Daniel I. Bolnick, Rowan D. H. Barrett, Lauren Chapman, Erika Crispo, Alison M. Derry, Christopher G. Eckert, Dylan J. Fraser, Gregor F. Fussmann, Andrew Gonzalez, Frederic Guichard, Thomas Lamy, Jeffrey Lane, Andrew G. McAdam, Amy E. M. Newman, Antoine Paccard, Bruce Robertson, Gregor Rolshausen, Patricia M. Schulte, Andrew M. Simons, Mark Vellend, and Andrew Hendry</div>
</div>
<div>
<br /></div>
<div>
<div>
<b><i>Free Access, Special Feature on Maladaptation</i></b></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702716" target="_blank">Maladaptive Shifts in Life History in a Changing Environment</a></b></div>
<div>
Olivier Cotto, Linnea Sandell, Luis-Miguel Chevin, and Ophélie Ronce</div>
</div>
<div>
Blurb: <a href="https://www.amnat.org/an/newpapers/AugCotto.html">https://www.amnat.org/an/newpapers/AugCotto.html</a></div>
</div>
<div>
<br /></div>
<div>
<div>
<b><i>Free Access, Special Feature on Maladaptation</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704780" target="_blank">Maladapted Prey Subsidize Predators and Facilitate Range Expansion</a></b></div>
<div>
Mark C. Urban, Alice Scarpa, Justin M. J. Travis, and Greta Bocedi</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/Oct-Urban.html">https://www.amnat.org/an/newpapers/Oct-Urban.html</a></div>
<div>
<br /></div>
<div>
<b><i>Special Feature on Maladaptation</i></b></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703743" target="_blank">Seed Masting Causes Fluctuations in Optimum Litter Size and Lag Load in a Seed Predator</a></b></div>
<div>
Andrew G. McAdam, Stan Boutin, Ben Dantzer, and Jeffrey E. Lane</div>
</div>
<div>
<br /></div>
<div>
<div>
<b><i>Special Feature on Maladaptation</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702313" target="_blank">Phenotypic Plasticity and Local Adaptation in a Wild Hibernator Evaluated through Reciprocal Translocation</a></b></div>
<div>
Jeffrey E. Lane, Zenon J. Czenze, Rachel Findlay-Robinson, and Erin Bayne</div>
</div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704772" target="_blank">(In)exhaustible Suppliers for Evolution? Epistatic Selection Tunes the Adaptive Potential of Nongenetic Inheritance</a></b></div>
<div>
Etienne Rajon and Sylvain Charlat</div>
</div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704608" target="_blank">Pulsed Immigration Events Can Facilitate Adaptation to Harsh Sink Environments</a></b></div>
<div>
James H. Peniston, Michael Barfield, and Robert D. Holt</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/Sep-Peniston.html">https://www.amnat.org/an/newpapers/Sep-Peniston.html</a></div>
<div>
<br /></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703483" target="_blank">Phenotype-Environment Matching Predicts Both Positive and Negative Effects of Intraspecific Variation</a></b></div>
<div>
<div>
Christopher J. Dibble and Volker H. W. Rudolf</div>
</div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703187" target="_blank">Biotic Interactions Contribute to the Geographic Range Limit of an Annual Plant: Herbivory and Phenology Mediate Fitness beyond a Range Margin</a></b></div>
<div>
John W. Benning, Vincent M. Eckhart, Monica A. Geber, and David A. Moeller</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/JuneBenning.html">https://www.amnat.org/an/newpapers/JuneBenning.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703159" target="_blank">Adaptive Differences in Circadian Clock Gene Expression Patterns and Photoperiodic Diapause Induction in <i>Nasonia vitripennis</i></a></b></div>
<div>
Elena Dalla Benetta, Leo W. Beukeboom, and Louis van de Zande</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/JuneDallaBenetta.html">https://www.amnat.org/an/newpapers/JuneDallaBenetta.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><i>Free Access, Synthesis</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703172" target="_blank">A Practical Guide to the Study of Distribution Limits</a></b></div>
<div>
Yvonne Willi and Josh Van Buskirk</div>
</div>
<div>
Blurb: <a href="https://www.amnat.org/an/newpapers/JuneWilli.html">https://www.amnat.org/an/newpapers/JuneWilli.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><i>Historical Comment</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703055" target="_blank">Revisiting a Key Innovation in Evolutionary Biology: Felsenstein’s “Phylogenies and the Comparative Method”</a></b></div>
<div>
Raymond B. Huey, Theodore Garland Jr., and Michael Turelli</div>
</div>
<div>
<br /></div>
<div>
<div>
<b><i>Free Access</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701779" target="_blank">The Evolutionary Ecology of Metamorphosis</a></b></div>
<div>
Hanna ten Brink, André M. de Roos, and Ulf Dieckmann</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/MayTenBrink.html">https://www.amnat.org/an/newpapers/MayTenBrink.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><i>American Society of Naturalists Address</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700960" target="_blank">The Snail’s Charm</a></b></div>
<div>
Kathleen Donohue</div>
</div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700720" target="_blank">Evolutionary Consequences of Sex-Specific Selection in Variable Environments: Four Simple Models Reveal Diverse Evolutionary Outcomes</a></b></div>
<div>
Tim Connallon, Shefali Sharma, and Colin Olito</div>
</div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700719" target="_blank">Ecological Genetic Conflict: Genetic Architecture Can Shift the Balance between Local Adaptation and Plasticity</a></b></div>
<div>
Olof Leimar, Sasha R. X. Dall, John M. McNamara, Bram Kuijper, and Peter Hammerstein</div>
</div>
<div>
<i>Lay summary</i>: <a href="https://www.amnat.org/an/newpapers/JanLeimar.html">https://www.amnat.org/an/newpapers/JanLeimar.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><i>Open Access</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700833" target="_blank">Biophysical Modeling of Water Economy Can Explain Geographic Gradient of Body Size in Anurans</a></b></div>
<div>
Sidney F. Gouveia, Rafael P. Bovo, Juan G. Rubalcaba, Fernando Rodrigues Da Silva, Natan M. Maciel, Denis V. Andrade, and Pablo Ariel Martinez</div>
</div>
<div>
<i>Lay summary</i>: <a href="https://www.amnat.org/an/newpapers/JanGouveia.html">https://www.amnat.org/an/newpapers/JanGouveia.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700838" target="_blank">Population Variation, Environmental Gradients, and the Evolutionary Ecology of Plant Defense against Herbivory</a></b></div>
<div>
Philip G. Hahn, Anurag A. Agrawal, Kira I. Sussman, and John L. Maron</div>
</div>
<div>
<i>Lay summary:</i> <a href="https://www.amnat.org/an/newpapers/JanHahn.html">https://www.amnat.org/an/newpapers/JanHahn.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><i>American Society of Naturalists Address</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700565" target="_blank">From the Past to the Future: Considering the Value and Limits of Evolutionary Prediction</a></b></div>
<div>
Ruth G. Shaw</div></div>
<div>
</div>
ASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-69571687268546281932020-10-15T16:28:00.000-05:002020-10-15T16:28:33.342-05:00Life History<h2>
Recent Papers</h2><div><div>NATURAL HISTORY NOTE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710151" target="_blank">Experimental Amelioration of Harsh Weather Speeds Growth and Development in a Tropical Montane Songbird</a></b></div><div>Adam E. Mitchell, Jordan Boersma, Anthonio Anthony, Kanehiro Kitayama, and Thomas E. Martin</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Oct-Mitchell.html">https://www.amnat.org/an/newpapers/Oct-Mitchell.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709503" target="_blank">A Stochastic Model for Predicting Age and Mass at Maturity of Insects</a></b></div><div>Geoffrey Legault and Joel G. Kingsolver</div></div><div>Blurb: <a href="https://www.amnat.org/an/newpapers/Aug-Legault.html">https://www.amnat.org/an/newpapers/Aug-Legault.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708719" target="_blank">Species Differences in Phenology Shape Coexistence</a></b></div><div>Christopher Blackford, Rachel M. Germain, and Benjamin Gilbert</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/July-Blackford.html">https://www.amnat.org/an/newpapers/July-Blackford.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708271" target="_blank">Parental Age Effects and the Evolution of Senescence</a></b></div><div>Patrick M. Barks and Robert A. Laird</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/May-Barks.html">https://www.amnat.org/an/newpapers/May-Barks.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/10.1086/708155" target="_blank">Age-Related Brood Parasitism and Egg Rejection in Magpie Hosts</a></b></div><div>Juan Gabriel Martínez, Mercedes Molina-Morales, Marta Precioso, and Jesús Miguel Avilés</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/May-Martinez.html">https://www.amnat.org/an/newpapers/May-Martinez.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707371" target="_blank">Life-History Plasticity and Water-Use Trade-Offs Associated with Drought Resistance in a Clade of California Jewelflowers</a></b></div><div>Ian S. Pearse, Jessica M. Aguilar, and Sharon Y. Strauss</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Apr-Pearse.html">https://www.amnat.org/an/newpapers/Apr-Pearse.html</a></div><div><br /></div><div><div>SYNTHESIS</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707322" target="_blank">Context Dependence of Local Adaptation to Abiotic and Biotic Environments: A Quantitative and Qualitative Synthesis</a></b></div><div>Ryan D. Briscoe Runquist, Amanda J. Gorton, Jeremy B. Yoder, Nicholas J. Deacon, Jake J. Grossman, Shan Kothari, Marta P. Lyons, Seema N. Sheth, Peter Tiffin, and David A. Moeller</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Mar-Briscoe-Runquist.html">https://www.amnat.org/an/newpapers/Mar-Briscoe-Runquist.html</a></div><div><br /></div><div><div>NOTE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706235" target="_blank">The Effects of Body Mass on Immune Cell Concentrations of Mammals</a></b></div><div>Cynthia J. Downs, Ned A. Dochtermann, Ray Ball, Kirk C. Klasing, and Lynn B. Martin</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Jan-Downs.html">https://www.amnat.org/an/newpapers/Jan-Downs.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706182" target="_blank">Fecundity-Longevity Trade-Off, Vertical Transmission, and Evolution of Virulence in Sterilizing Pathogens</a></b></div><div>Eva Janoušková and Luděk Berec</div></div><div><br /></div><div><div>FREE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706195" target="_blank">Comparing Life Histories across Taxonomic Groups in Multiple Dimensions: How Mammal-Like Are Insects?</a></b></div><div>Adam T. Bakewell, Katie E. Davis, Robert P. Freckleton, Nick J. B. Isaac, and Peter J. Mayhew</div></div><div><br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705380" target="_blank">Eco-Evolutionary Feedbacks Predict the Time Course of Rapid Life-History Evolution</a></b></div>
<div>
David N. Reznick, Ronald D. Bassar, Corey A. Handelsman, Cameron K. Ghalambor, Jeff Arendt, Tim Coulson, Tomos Potter, Emily W. Ruell, Julián Torres-Dowdall, Paul Bentzen, and Joseph Travis</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/Nov-Reznick.html">https://www.amnat.org/an/newpapers/Nov-Reznick.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705241" target="_blank">A Spatial Perspective on the Phenological Distribution of the Spring Woodland Caterpillar Peak</a></b></div>
<div>
Jack D. Shutt, Malcolm D. Burgess, and Albert B. Phillimore</div>
</div>
<div>
Blurb: <a href="https://www.amnat.org/an/newpapers/Nov-Shutt.html">https://www.amnat.org/an/newpapers/Nov-Shutt.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><i>Special Feature on Maladaptation</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703743" target="_blank">Seed Masting Causes Fluctuations in Optimum Litter Size and Lag Load in a Seed Predator</a></b></div>
<div>
Andrew G. McAdam, Stan Boutin, Ben Dantzer, and Jeffrey E. Lane</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/AugMcAdam.html">https://www.amnat.org/an/newpapers/AugMcAdam.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704220" target="_blank">Plastic Senescence in the Honey Bee and the Disposable Soma Theory</a></b></div>
<div>
Jack da Silva</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/Sep-da-Silva.html">https://www.amnat.org/an/newpapers/Sep-da-Silva.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><i>Note, Open Access</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704155" target="_blank">Generation Time Measures the Trade-Off between Survival and Reproduction in a Life Cycle</a></b></div>
<div>
Stefano Giaimo and Arne Traulsen</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/AugGiaimo.html">https://www.amnat.org/an/newpapers/AugGiaimo.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><i>Note</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704110" target="_blank">The Equivocal Mean Age of Parents in a Cohort</a></b></div>
<div>
François Bienvenu</div>
</div>
<div>
Blurb: <a href="https://www.amnat.org/an/newpapers/AugBienvenu.html">https://www.amnat.org/an/newpapers/AugBienvenu.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704111" target="_blank">Environmental Veto Synchronizes Mast Seeding in Four Contrasting Tree Species</a></b></div>
<div>
Michał Bogdziewicz, Magdalena Żywiec, Josep M. Espelta, Marcos Fernández-Martinez, Rafael Calama, Mateusz Ledwoń, Eliot McIntire, and Elizabeth E. Crone</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/AugBogdziewicz.html">https://www.amnat.org/an/newpapers/AugBogdziewicz.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704156" target="_blank">Lifetime Fitness, Sex-Specific Life History, and the Maintenance of a Polyphenism</a></b></div>
<div>
Alycia C. R. Lackey, Michael P. Moore, Jacqueline Doyle, Nicole Gerlanc, Ashley Hagan, Morgan Geile, Chris Eden, and Howard H. Whiteman</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/AugLackey.html">https://www.amnat.org/an/newpapers/AugLackey.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><i>Open Access, Special Feature on Maladaptation</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702716" target="_blank">Maladaptive Shifts in Life History in a Changing Environment</a></b></div>
<div>
Olivier Cotto, Linnea Sandell, Luis-Miguel Chevin, and Ophélie Ronce</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/AugCotto.html">https://www.amnat.org/an/newpapers/AugCotto.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><i>Synthesis</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704168" target="_blank">Dormancy in Metacommunities</a></b></div>
<div>
Nathan I. Wisnoski, Mathew A. Leibold, and Jay T. Lennon</div>
</div>
<div>
Blurb: <a href="https://www.amnat.org/an/newpapers/AugWisnoski.html">https://www.amnat.org/an/newpapers/AugWisnoski.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702856" target="_blank">Higher Nest Predation Favors Rapid Fledging at the Cost of Plumage Quality in Nestling Birds</a></b></div>
<div>
Lea M. Callan, Frank A. La Sorte, Thomas E. Martin, and Vanya G. Rohwer</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/MayCallan.html">https://www.amnat.org/an/newpapers/MayCallan.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702848" target="_blank">Condition-Dependent Begging Elicits Increased Parental Investment in a Wild Bird Population</a></b></div>
<div>
E. Keith Bowers, Jonathan B. Jenkins, Alexander J. Mueller, Kelly D. Miller, Charles F. Thompson, and Scott K. Sakaluk</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/MayBowers.html">https://www.amnat.org/an/newpapers/MayBowers.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701826" target="_blank">Two-Year Bee, or Not Two-Year Bee? How Voltinism Is Affected by Temperature and Season Length in a High-Elevation Solitary Bee</a></b></div>
<div>
Jessica R. K. Forrest, Regan Cross, and Paul J. CaraDonna</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/AprForrest.html">https://www.amnat.org/an/newpapers/AprForrest.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702304" target="_blank">Age-Specific Offspring Mortality Economically Tracks Food Abundance in a Piscivorous Seabird</a></b></div>
<div>
Oscar Vedder, He Zhang, Andreas Dänhardt, and Sandra Bouwhuis</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/AprVedder.html">https://www.amnat.org/an/newpapers/AprVedder.html</a></div>
<div>
<br /></div>
<div>
<div>
<i><b>Note</b> (an F1000 recommendation as Exceptional)</i></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701043" target="_blank">Shifting Vital Rate Correlations Alter Predicted Population Responses to Increasingly Variable Environments</a></b></div>
<div>
David T. Iles, Robert F. Rockwell, and David N. Koons</div>
</div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701299" target="_blank">Queen Longevity and Fecundity Affect Conflict with Workers over Resource Inheritance in a Social Insect</a></b></div>
<div>
Edward J. Almond, Timothy J. Huggins, Liam P. Crowther, Joel D. Parker, and Andrew F. G. Bourke</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/FebAlmond.html">https://www.amnat.org/an/newpapers/FebAlmond.html</a></div>
<div><br /></div>
ASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-2330707508069508812020-10-15T16:09:00.000-05:002020-10-15T16:09:03.593-05:00Evolutionary Dynamics<h3 class="post-title entry-title" itemprop="name">
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<div class="post-header">
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<h2>
Recent Papers</h2><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/711019" target="_blank">Miniaturization, Genome Size, and Biological Size in a Diverse Clade of Salamanders</a></b></div><div>Louis Paul Decena-Segarra, Lilijana Bizjak-Mali, Aleš Kladnik, Stanley K. Sessions, and Sean M. Rovito</div></div><div>Blog and Spanish abstract: <a href="https://www.amnat.org/an/newpapers/Nov-Decena-Segarra.html">https://www.amnat.org/an/newpapers/Nov-Decena-Segarra.html</a></div><div><br /></div><div><div>FREE</div><div><b><a href="https://www.journals.uchicago.edu/doi/10.1086/708274" target="_blank">Evolution of Reproduction Periods in Seasonal Environments</a></b></div><div>Zepeng Sun, Kalle Parvinen, Mikko Heino, Johan A. J. Metz, André M. de Roos, and Ulf Dieckmann</div></div><div><br /></div><div><div>FREE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710353" target="_blank">Predicting Multivariate Responses of Sexual Dimorphism to Direct and Indirect Selection</a></b></div><div>Changde Cheng (成常德) and David Houle</div></div><div><br /></div><div><div>FREE; AMERICAN SOCIETY OF NATURALISTS ADDRESS</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709699" target="_blank">What Do Ecology, Evolution, and Behavior Have in Common? The Organism in the Middle</a></b></div><div>Ellen D. Ketterson</div></div><div>Blurb: <a href="https://www.amnat.org/an/newpapers/Aug-Ketterson.html">https://www.amnat.org/an/newpapers/Aug-Ketterson.html</a></div><div><br /></div><div><div>NATURAL HISTORY NOTE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709018" target="_blank">Floral Trait Evolution of Angiosperms on Pacific Islands</a></b></div><div>Molly C. Hetherington-Rauth and Marc T. J. Johnson</div><div>Blog: <a href="https://www.amnat.org/an/newpapers/July-Hetherington-Rauth.html">https://www.amnat.org/an/newpapers/July-Hetherington-Rauth.html</a></div><div><br /></div></div><div><div>NOTE</div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707139" target="_blank">The Population Genetics of Evolutionary Rescue in Diploids: X Chromosomal versus Autosomal Rescue</a></b></div><div>Robert L. Unckless and H. Allen Orr</div></div><div>Blurb: h<a href="ttps://www.amnat.org/an/newpapers/Mar-Unckless.html">ttps://www.amnat.org/an/newpapers/Mar-Unckless.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707195" target="_blank">Tolerance of Novel Toxins through Generalized Mechanisms: Simulating Gradual Host Shifts of Butterflies</a></b></div><div>Kristin L. Sikkink, Reilly Hostager, Megan E. Kobiela, Nathan Fremling, Katherine Johnston, Amod Zambre, and Emilie C. Snell-Rood</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Mar-Sikkink.html">https://www.amnat.org/an/newpapers/Mar-Sikkink.html</a></div><div><br /></div><div><div><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706475" target="_blank">Integrating Fitness Components Reveals That Survival Costs Outweigh Other Benefits and Costs of Group Living in Two Closely Related Species</a></div><div>Lyanne Brouwer, Andrew Cockburn, and Martijn van de Pol</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Feb-Brouwer.html">https://www.amnat.org/an/newpapers/Feb-Brouwer.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706182" target="_blank">Fecundity-Longevity Trade-Off, Vertical Transmission, and Evolution of Virulence in Sterilizing Pathogens</a></b></div><div>Eva Janoušková and Luděk Berec</div></div><div><br /></div><div><div><b><i>Open Access</i></b></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701857" target="_blank">Stage-Structured Evolutionary Demography: Linking Life Histories, Population Genetics, and Ecological Dynamics</a></b></div><div>Charlotte de Vries and Hal Caswell</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/AprDeVries.html">https://www.amnat.org/an/newpapers/AprDeVries.html</a></div><div><br /></div>
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<b><i>Open Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/abs/10.1086/706476" target="_blank">Shared patterns of genome-wide differentiation are more strongly predicted by geography than by ecology</a></b></div>
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Diana Jessie Rennison, Kira E. Delmore, Kieran Samuk, Gregory L. Owens, and Sara E. Miller</div>
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<br /></div>
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<div>
<b><i>Note</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704773" target="_blank">Early Sibling Conflict May Ultimately Benefit the Family</a></b></div>
<div>
Alyssa Laney Smith, Daniel Z. Atwater, and Ragan M. Callaway</div>
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<div>
Blurb: <a href="https://www.amnat.org/an/newpapers/Oct-Smith.html">https://www.amnat.org/an/newpapers/Oct-Smith.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704594" target="_blank">Evolution at the Edge of Expanding Populations</a></b></div>
<div>
Maxime Deforet, Carlos Carmona-Fontaine, Kirill S. Korolev, and Joao B. Xavier</div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704156" target="_blank">Lifetime Fitness, Sex-Specific Life History, and the Maintenance of a Polyphenism</a></b></div>
<div>
Alycia C. R. Lackey, Michael P. Moore, Jacqueline Doyle, Nicole Gerlanc, Ashley Hagan, Morgan Geile, Chris Eden, and Howard H. Whiteman</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/AugLackey.html">https://www.amnat.org/an/newpapers/AugLackey.html</a></div>
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<br /></div>
<div>
<div>
<b><i>Note</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703484" target="_blank">Eco-Evolutionary Dynamics in the Wild: Clonal Turnover and Stability in Daphnia Populations</a></b></div>
<div>
Christopher F. Steiner and Carly J. Nowicki</div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703563" target="_blank">Evolutionary Hysteresis and Ratchets in the Evolution of Periodical Cicadas</a></b></div>
<div>
Jaakko Toivonen and Lutz Fromhage</div>
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<div>
Blog: <a href="https://www.amnat.org/an/newpapers/JulyToivonen.html">https://www.amnat.org/an/newpapers/JulyToivonen.html</a></div>
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<br /></div>
<div>
<b><i>Open Access</i></b></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703457" target="_blank">Evolution of Stress-Induced Mutagenesis in the Presence of Horizontal Gene Transfer</a></b></div>
<div>
Yoav Ram and Lilach Hadany</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/JulyRam.html">https://www.amnat.org/an/newpapers/JulyRam.html</a></div>
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<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702588" target="_blank">Evolution of the Two Sexes under Internal Fertilization and Alternative Evolutionary Pathways</a></b></div>
<div>
Jussi Lehtonen and Geoff A. Parker</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/MayLehtonen.html">https://www.amnat.org/an/newpapers/MayLehtonen.html</a></div>
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<br /></div>
<div>
<b><i>Open Access</i></b></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702847" target="_blank">Sexually Antagonistic Variation and the Evolution of Dimorphic Sexual Systems</a></b></div>
<div>
Colin Olito and Tim Connallon</div>
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<div>
Blog: <a href="https://www.amnat.org/an/newpapers/MayOlito.html">https://www.amnat.org/an/newpapers/MayOlito.html</a></div>
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<br /></div>
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<div>
<b><i>Open Access</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701779" target="_blank">The Evolutionary Ecology of Metamorphosis</a></b></div>
<div>
Hanna ten Brink, André M. de Roos, and Ulf Dieckmann</div>
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<div>
Blog: <a href="https://www.amnat.org/an/newpapers/MayTenBrink.html">https://www.amnat.org/an/newpapers/MayTenBrink.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701827" target="_blank">Grow Where You Thrive, or Where Only You Can Survive? An Analysis of Performance Curve Evolution in a Clade with Diverse Habitat Affinities</a></b></div>
<div>
Silas B. Tittes, Joseph F. Walker, Lorena Torres-Martínez, and Nancy C. Emery</div>
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<div>
Blog: <a href="https://www.amnat.org/an/newpapers/AprTittes.html">https://www.amnat.org/an/newpapers/AprTittes.html</a></div>
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<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701667" target="_blank">The Evolution of Marine Larval Dispersal Kernels in Spatially Structured Habitats: Analytical Models, Individual-Based Simulations, and Comparisons with Empirical Estimates</a></b></div>
<div>
Allison K. Shaw, Cassidy C. D’Aloia, and Peter M. Buston</div>
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<div>
Blog: <a href="https://www.amnat.org/an/newpapers/MarShaw.html">https://www.amnat.org/an/newpapers/MarShaw.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701782" target="_blank">The Effect of Pollen Limitation on the Evolution of Mating System and Seed Size in Hermaphroditic Plants</a></b></div>
<div>
Qiaoqiao Huang and Martin Burd</div>
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<div>
Blurb: <a href="https://www.amnat.org/an/newpapers/MarHuang.html">https://www.amnat.org/an/newpapers/MarHuang.html</a></div>
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<br /></div>
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<div>
<b><i>American Society of Naturalists Address</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700960" target="_blank">The Snail’s Charm</a></b></div>
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Kathleen Donohue</div>
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Blurb: <a href="https://amnat.org/an/newpapers/FebDonohue.html">https://amnat.org/an/newpapers/FebDonohue.html</a></div>
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<b><i>American Society of Naturalists Address</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700565" target="_blank">From the Past to the Future: Considering the Value and Limits of Evolutionary Prediction</a></b></div>
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Ruth G. Shaw</div>
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<div><br /></div></div>Trish http://www.blogger.com/profile/16821726769230478329noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-45289631340106160642020-10-15T15:17:00.000-05:002020-10-15T15:17:33.415-05:00Natural Selection<h2>
Recent Papers</h2><div><div><b><a href="https://www.journals.uchicago.edu/doi/10.1086/710708" target="_blank">Fledging Mass Is Color Morph Specific and Affects Local Recruitment in a Wild Bird</a></b></div><div>Chiara Morosinotto, Jon E. Brommer, Atte Lindqvist, Kari Ahola, Esa Aaltonen, Teuvo Karstinen, and Patrik Karell</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Nov-Morosinotto.html">https://www.amnat.org/an/newpapers/Nov-Morosinotto.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710353" target="_blank">Predicting Multivariate Responses of Sexual Dimorphism to Direct and Indirect Selection</a></b></div><div>Changde Cheng (成常德) and David Houle</div></div><div>Blurb and Chinese abstract: <a href="https://www.amnat.org/an/newpapers/Oct-Cheng.html">https://www.amnat.org/an/newpapers/Oct-Cheng.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709610" target="_blank">Selection and Constraints in the Ecomorphological Adaptive Evolution of the Skull of Living Canidae (Carnivora, Mammalia)</a></b></div><div>Fabio Andrade Machado</div></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/10.1086/707597" target="_blank">Belowground Competition Can Influence the Evolution of Root Traits</a></b></div><div>Sara M. Colom and Regina S. Baucom</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Apr-Colom.html">https://www.amnat.org/an/newpapers/Apr-Colom.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/10.1086/707017" target="_blank">Stochastic Dynamics of Three Competing Clones: Conditions and Times for Invasion, Coexistence, and Fixation</a></b></div><div>Sylvain Billiard and Charline Smadi</div></div><div>Blurb: <a href="https://www.amnat.org/an/newpapers/Mar-Billiard.html">https://www.amnat.org/an/newpapers/Mar-Billiard.html</a></div><div><br /></div><div><div><b><i>Synthesis</i></b></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707322" target="_blank">Context Dependence of Local Adaptation to Abiotic and Biotic Environments: A Quantitative and Qualitative Synthesis</a></b></div><div>Ryan D. Briscoe Runquist, Amanda J. Gorton, Jeremy B. Yoder, Nicholas J. Deacon, Jake J. Grossman, Shan Kothari, Marta P. Lyons, Seema N. Sheth, Peter Tiffin, and David A. Moeller</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Mar-Briscoe-Runquist.html">https://www.amnat.org/an/newpapers/Mar-Briscoe-Runquist.html</a></div><div><br /></div><div><b><i>Synthesis</i></b></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707323" target="_blank">Local Adaptation to Biotic Interactions: A Meta-analysis across Latitudes</a></b></div><div>Anna L. Hargreaves, Rachel M. Germain, Megan Bontrager, Joshua Persi, and Amy L. Angert</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Mar-Hargreaves.html">https://www.amnat.org/an/newpapers/Mar-Hargreaves.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706475" target="_blank">Integrating Fitness Components Reveals That Survival Costs Outweigh Other Benefits and Costs of Group Living in Two Closely Related Species</a></b></div><div>Lyanne Brouwer, Andrew Cockburn, and Martijn van de Pol</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Feb-Brouwer.html">https://www.amnat.org/an/newpapers/Feb-Brouwer.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706196" target="_blank">Niche Construction Affects the Variability and Strength of Natural Selection</a></b></div><div>Andrew D. Clark, Dominik Deffner, Kevin Laland, John Odling-Smee, and John Endler</div></div><div>Blurb: <a href="https://www.amnat.org/an/newpapers/Jan-Clark.html">https://www.amnat.org/an/newpapers/Jan-Clark.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701629" target="_blank">Limiting Similarity? The Ecological Dynamics of Natural Selection among Resources and Consumers Caused by Both Apparent and Resource Competition</a></b></div><div>Mark A. McPeek</div></div><div><br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705810" target="_blank">Lifetime Fitness in Wild Female Baboons: Trade-Offs and Individual Heterogeneity in Quality</a></b></div>
<div>
Emily M. McLean, Elizabeth A. Archie, and Susan C. Alberts</div>
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<br /></div>
<div>
<div>
<b><i>Special Feature on Maladaptation</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703743" target="_blank">Seed Masting Causes Fluctuations in Optimum Litter Size and Lag Load in a Seed Predator</a></b></div>
<div>
Andrew G. McAdam, Stan Boutin, Ben Dantzer, and Jeffrey E. Lane</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/AugMcAdam.html">https://www.amnat.org/an/newpapers/AugMcAdam.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704772" target="_blank">(In)exhaustible Suppliers for Evolution? Epistatic Selection Tunes the Adaptive Potential of Nongenetic Inheritance</a></b></div>
<div>
Etienne Rajon and Sylvain Charlat</div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704060" target="_blank">Individual and Population Differences Shape Species Interactions and Natural Selection</a></b></div>
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Denon Start</div>
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<br /></div>
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<div>
<b><i>Special Feature on Maladaptation</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702314" target="_blank">Unpacking Conditional Neutrality: Genomic Signatures of Selection on Conditionally Beneficial and Conditionally Deleterious Mutations</a></b></div>
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Jonathan A. Mee and Sam Yeaman</div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703436" target="_blank">Why So Variable: Can Genetic Variance in Flowering Thresholds Be Maintained by Fluctuating Selection?</a></b></div>
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Mark Rees and Stephen P. Ellner</div>
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<div>
Blog: <a href="https://www.amnat.org/an/newpapers/JulyRees.html">https://www.amnat.org/an/newpapers/JulyRees.html</a></div>
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<div><b><i>Open Access</i></b></div></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700567" target="_blank">Fitness Consequences of Female Alternative Reproductive Tactics in House Mice (<i>Mus musculus domesticus</i>)</a></b></div>
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Manuela Ferrari, Anna K. Lindholm, and Barbara König</div>
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Summary & photo: <a href="https://www.amnat.org/an/newpapers/JanFerrari.html">https://www.amnat.org/an/newpapers/JanFerrari.html</a></div>
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<br /></div>
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<div>
<b><i>Historical Comment</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700718" target="_blank">Divergent Uses of “Parallel Evolution” during the History of <i>The American Naturalist</i></a></b></div>
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Yoel E. Stuart</div>
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<br /></div>
<div>
<b><i>American Society of Naturalists Address</i></b></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700565" target="_blank">From the Past to the Future: Considering the Value and Limits of Evolutionary Prediction</a></b></div>
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Ruth G. Shaw</div>
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<div><br /></div>
ASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-72090082149126427142020-10-15T14:04:00.000-05:002020-10-15T14:04:07.646-05:00Host-Parasite Interactions<h2>
Recent Papers</h2><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/711033" target="_blank">The Size, Symmetry, and Color Saturation of a Male Guppy’s Ornaments Forecast His Resistance to Parasites</a></b></div><div>Jessica F. Stephenson, Martin Stevens, Jolyon Troscianko, and Jukka Jokela</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Nov-Stephenson.html">https://www.amnat.org/an/newpapers/Nov-Stephenson.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710486" target="_blank">Resistance Genes Affect How Pathogens Maintain Plant Abundance and Diversity</a></b></div><div>Simon Maccracken Stump, James H. Marden, Noelle G. Beckman, Scott A. Mangan, and Liza S. Comita</div></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710039" target="_blank">Male-Male Competition Causes Parasite-Mediated Sexual Selection for Local Adaptation</a></b></div><div>Miguel Gómez-Llano, Aaditya Narasimhan, and Erik I. Svensson</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Sep-Gomez-Llano.html">https://www.amnat.org/an/newpapers/Sep-Gomez-Llano.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709962" target="_blank">Defensive Symbiosis and the Evolution of Virulence</a></b></div><div>Paul Nelson and Georgiana May</div></div><div><br /></div><div><div><b><i>Open Access</i></b></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710005" target="_blank">Deconstructing the Impact of Malaria Vector Diversity on Disease Risk</a></b></div><div>Amber Gigi Hoi, Benjamin Gilbert, and Nicole Mideo</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Sep-Hoi.html">https://www.amnat.org/an/newpapers/Sep-Hoi.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709163" target="_blank">Parasitism Risk and Infection Alter Host Dispersal</a></b></div><div>Celina B. Baines, Salma Diab, and Shannon J. McCauley</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Aug-Baines.html">https://www.amnat.org/an/newpapers/Aug-Baines.html</a></div><div><br /></div><div><div><b><i>Open Access</i></b></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708530" target="_blank">Host Transcriptional Responses to High- and Low-Virulent Avian Malaria Parasites</a></b></div><div>Elin Videvall, Vaidas Palinauskas, Gediminas Valkiūnas, and Olof Hellgren</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/June-Videvall.html">https://www.amnat.org/an/newpapers/June-Videvall.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708188" target="_blank">Vertical Transmission of a Nematode from Female Lizards to the Brains of Their Offspring</a></b></div><div>Nathalie Feiner, Sueli de Souza-Lima, Fátima Jorge, Soraya Naem, Fabien Aubret, Tobias Uller, and Steven A. Nadler</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/May-Feiner.html">https://www.amnat.org/an/newpapers/May-Feiner.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708272" target="_blank">Individual Specialization and Multihost Epidemics: Disease Spread in Plant-Pollinator Networks</a></b></div><div>Stephen P. Ellner, Wee Hao Ng, and Christopher R. Myers</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/May-Ellner.html">https://www.amnat.org/an/newpapers/May-Ellner.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707457" target="_blank">An Empirical Test of the Role of Small-Scale Transmission in Large-Scale Disease Dynamics</a></b></div><div>Joseph R. Mihaljevic, Carlos M. Polivka, Constance J. Mehmel, Chentong Li, Vanja Dukic, and Greg Dwyer</div></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707545" target="_blank">Thermal Variability and Plasticity Drive the Outcome of a Host-Pathogen Interaction</a></b></div><div>Laura V. Ferguson and Brent J. Sinclair</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Apr-Ferguson.html">https://www.amnat.org/an/newpapers/Apr-Ferguson.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707355" target="_blank">Pathogens and Mutualists as Joint Drivers of Host Species Coexistence and Turnover: Implications for Plant Competition and Succession</a></b></div><div>Jiang Jiang, Karen C. Abbott, Mara Baudena, Maarten B. Eppinga, James A. Umbanhowar, and James D. Bever</div></div><div>Blurb: <a href="https://www.amnat.org/an/newpapers/Apr-Jiang.html">https://www.amnat.org/an/newpapers/Apr-Jiang.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707138" target="_blank">Stochasticity and Infectious Disease Dynamics: Density and Weather Effects on a Fungal Insect Pathogen</a></b></div><div>Colin H. Kyle, Jiawei Liu, Molly E. Gallagher, Vanja Dukic, and Greg Dwyer</div></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706182" target="_blank">Fecundity-Longevity Trade-Off, Vertical Transmission, and Evolution of Virulence in Sterilizing Pathogens</a></b></div><div>Eva Janoušková and Luděk Berec</div></div><div><br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704182" target="_blank">Can Community Structure Causally Determine Dynamics of Constituent Species? A Test Using a Host-Parasite Community</a></b></div>
<div>
Ryan E. Langendorf and Daniel F. Doak</div>
</div>
<div>
Blurb: <a href="https://www.amnat.org/an/newpapers/Sep-Langendorf.html">https://www.amnat.org/an/newpapers/Sep-Langendorf.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703534" target="_blank">Host Responses to Foreign Eggs across the Avian Visual Color Space</a></b></div>
<div>
Daniel Hanley, Karel Gern, Mark E. Hauber, and Tomáš Grim</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/JulyHanley.html">https://www.amnat.org/an/newpapers/JulyHanley.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703437" target="_blank">The Critical Role of Infectious Disease in Compensatory Population Growth in Response to Culling</a></b></div>
<div>
Eleanor Tanner, Andy White, Peter W. W. Lurz, Christian Gortázar, Iratxe Díez-Delgado, and Mike Boots</div>
</div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702959" target="_blank">Trait-Based Modeling of Multihost Pathogen Transmission: Plant-Pollinator Networks</a></b></div>
<div>
Lauren L. Truitt, Scott H. McArt, Andrew H. Vaughn, and Stephen P. Ellner</div>
</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/JuneTruitt.html">https://www.amnat.org/an/newpapers/JuneTruitt.html</a></div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702846" target="_blank">Predicting the Thermal and Allometric Dependencies of Disease Transmission via the Metabolic Theory of Ecology</a></b></div>
<div>
Devin Kirk, Pepijn Luijckx, Andrijana Stanic, and Martin Krkošek</div>
</div>
<div>
Blurb: <a href="https://www.amnat.org/an/newpapers/MayKirk.html">https://www.amnat.org/an/newpapers/MayKirk.html</a></div>
<div>
<br /></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701126" target="_blank">Within-Host Priority Effects Systematically Alter Pathogen Coexistence</a></b><br />
Patrick A. Clay, Kailash Dhir, Volker H. W. Rudolf, and Meghan A. Duffy<br />
Lay summary: <a href="https://www.amnat.org/an/newpapers/FebClay.html">https://www.amnat.org/an/newpapers/FebClay.html</a><br />
<br />
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700564" target="_blank">Sexual Conflict and Sexually Transmitted Infections (STIs): Coevolution of Sexually Antagonistic Host Traits with an STI</a></b><br />
Alison M. Wardlaw and Aneil F. Agrawal<br />
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</div>
ASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-74851336165562321692020-09-29T15:36:00.000-05:002020-09-30T12:41:31.207-05:00Paleobiology<h2>
Recent Papers </h2><div><div><div><div style="font-weight: bold;"><a href="https://www.journals.uchicago.edu/doi/10.1086/710176" target="_blank">High Preservation Potential of Paleogeographic Range Size Distributions in Deep Time</a></div><div>Simon A. F. Darroch, Michelle M. Casey, Gwen S. Antell, Amy Sweeney, and Erin E. Saupe</div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Oct-Darroch.html">https://www.amnat.org/an/newpapers/Oct-Darroch.html</a></div></div><div style="font-weight: bold;"><br /></div><div style="font-weight: bold;"><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709819" target="_blank">Mammal Community Structure through the Paleocene-Eocene Thermal Maximum</a></div><div>Danielle Fraser and S. Kathleen Lyons</div></div><div><b><i><br /></i></b></div><div><b><i>Open Access</i></b></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706340" target="_blank">Community Assembly and Climate Mismatch in Late Quaternary Eastern North American Pollen Assemblages</a></b></div><div>Clarke A. Knight, Jessica L. Blois, Benjamin Blonder, Marc Macias-Fauria, Alejandro Ordonez, and Jens-Christian Svenning</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Feb-Knight.html">https://www.amnat.org/an/newpapers/Feb-Knight.html</a></div><div><br /></div>
<div>
<div>
<b><i>Open Access</i></b><br />
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/697642" target="_blank">Evidence for Trait-Based Dominance in Occupancy among Fossil Taxa and the Decoupling of Macroecological and Macroevolutionary Success</a></b><br />
Peter Wagner, Roy E. Plotnick, and S. Kathleen Lyons<br />
<br />
<b><i>Open Access</i></b><br />
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/696265" target="_blank">Model Adequacy and Microevolutionary Explanations for Stasis in the Fossil Record</a></b><br />
Kjetil Lysne Voje, Jostein Starrfelt, and Lee Hsiang Liow<br />
<br />
<b><i>Synthesis</i></b></div>
<div>
<b><a href="http://www.journals.uchicago.edu/doi/full/10.1086/689739" target="_blank">Shaping the Latitudinal Diversity Gradient: New Perspectives from a Synthesis of Paleobiology and Biogeography</a></b></div>
<div>
David Jablonski, Shan Huang, Kaustuv Roy, and James W. Valentine</div>
<div><br /></div></div>
<div>
<div>
<b><a href="http://www.journals.uchicago.edu/doi/full/10.1086/693346" target="_blank">Historical Biogeography and Extinction in the Hawaiian Honeycreepers</a></b></div>
<div>
Robert E. Ricklefs</div>
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ASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-10430414962133550422020-09-29T13:12:00.001-05:002020-09-30T13:27:55.479-05:00Predator-Prey Interactions<h2>
Recent Papers</h2><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710568" target="_blank">State-Dependent Decision-Making by Predators and Its Consequences for Mimicry</a></b></div><div>Thomas G. Aubier and Thomas N. Sherratt</div></div><div><br /></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/691100" target="_blank">Ecological Pleiotropy Suppresses the Dynamic Feedback Generated by a Rapidly Changing Trait</a></b></div><div><div>John P. DeLong</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Oct-DeLong.html">https://www.amnat.org/an/newpapers/Oct-DeLong.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707719" target="_blank">Prey Exploits the Auditory Illusions of Eavesdropping Predators</a></b></div><div>Henry D. Legett, Claire T. Hemingway, and Ximena E. Bernal</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/May-Legett.html">https://www.amnat.org/an/newpapers/May-Legett.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707392" target="_blank">Factors That Can Affect the Spatial Positioning of Large and Small Individuals in Clusters of Sit-and-Wait Predators</a></b></div><div>Inon Scharf</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Apr-Scharf.html">https://www.amnat.org/an/newpapers/Apr-Scharf.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707544" target="_blank">Safety Cues Can Give Prey More Valuable Information Than Danger Cues</a></b></div><div>Barney Luttbeg, Maud C. O. Ferrari, Daniel T. Blumstein, and Douglas P. Chivers</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Apr-Luttbeg.html">https://www.amnat.org/an/newpapers/Apr-Luttbeg.html</a></div><div><br /></div><div><div><b><i>VP Symposium</i></b></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706813" target="_blank">How Does Joint Evolution of Consumer Traits Affect Resource Specialization?</a></b></div><div>Paula Vasconcelos and Claus Rueffler</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/VP-Vasconcelos.html">https://www.amnat.org/an/newpapers/VP-Vasconcelos.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706913" target="_blank">Spatial Scales of Population Synchrony in Predator-Prey Systems</a></b></div><div>Javier Jarillo, Bernt-Erik Sæther, Steinar Engen, and Francisco Javier Cao-García</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Feb-Jarillo.html">https://www.amnat.org/an/newpapers/Feb-Jarillo.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705811" target="_blank">Trophic Position of Consumers and Size Structure of Food Webs across Aquatic and Terrestrial Ecosystems</a></b></div><div>Anton M. Potapov, Ulrich Brose, Stefan Scheu, and Alexei V. Tiunov</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Dec-Potapov.html">https://www.amnat.org/an/newpapers/Dec-Potapov.html</a></div><div><br /></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705381" target="_blank">False Exclusion: A Case to Embed Predator Performance in Classical Population Models</a></b></div><div><div>David J. S. Montagnes, Xuexia Zhu, Lei Gu, Yunfei Sun, Jun Wang, Rosie Horner, and Zhou Yang</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Nov-Montagnes.html">https://www.amnat.org/an/newpapers/Nov-Montagnes.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705242" target="_blank">Information about Predators Varies across an Amazonian Rain Forest as a Result of Sentinel Species Distribution</a></b></div><div>Ettore Camerlenghi, Paola Tellaroli, Matteo Griggio, and Ari E. Martínez</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Nov-Camerlenghi.html">https://www.amnat.org/an/newpapers/Nov-Camerlenghi.html</a></div><div><br /></div><div><div><b><i>Open Access</i></b></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705809" target="_blank">Patch Size as a Niche Dimension: Aquatic Insects Behaviorally Partition Enemy-Free Space across Gradients of Patch Size</a></b></div><div>William J. Resetarits, Matthew R. Pintar, Jason R. Bohenek, and Tyler M. Breech</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Dec-Resetarits.html">https://www.amnat.org/an/newpapers/Dec-Resetarits.html</a></div><div><br /></div><div><div><i><b>Open Access; Special Feature on Maladaptation</b></i></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704780" target="_blank">Maladapted Prey Subsidize Predators and Facilitate Range Expansion</a></b></div><div>Mark C. Urban, Alice Scarpa, Justin M. J. Travis, and Greta Bocedi</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Oct-Urban.html">https://www.amnat.org/an/newpapers/Oct-Urban.html</a></div><div><br /></div><div><div><b><i>Special Feature on Maldaptation</i></b></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703743" target="_blank">Seed Masting Causes Fluctuations in Optimum Litter Size and Lag Load in a Seed Predator</a></b></div><div>Andrew G. McAdam, Stan Boutin, Ben Dantzer, and Jeffrey E. Lane</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/AugMcAdam.html">https://www.amnat.org/an/newpapers/AugMcAdam.html</a></div><div><br /></div>
<div>
<div><div><b><i>Natural History Note</i></b></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704338" target="_blank">Destruction of Spiderwebs and Rescue of Ensnared Nestmates by a Granivorous Desert Ant (<i>Veromessor pergandei</i>)</a></b></div><div>Christina L. Kwapich and Bert Hölldobler</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Sep-Kwapich.html">https://www.amnat.org/an/newpapers/Sep-Kwapich.html</a></div><div><br /></div><div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704279" target="_blank">Decreasing Predator Density and Activity Explains Declining Predation of Insect Prey along Elevational Gradients</a></b></div>
<div>
Luis F. Camacho and Leticia Avilés</div>
</div>
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<br /></div>
<div>
<div>
<b><i>Natural History Note</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704169" target="_blank">Playing out Liem’s Paradox: Opportunistic Piscivory across Lake Tanganyikan Cichlids</a></b></div>
<div>
Jimena Golcher-Benavides and Catherine E. Wagner</div>
</div>
<div>
Summary: <a href="https://amnat.org/an/newpapers/Aug-Golcher-Benavides.html">https://amnat.org/an/newpapers/Aug-Golcher-Benavides.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702856" target="_blank">Higher Nest Predation Favors Rapid Fledging at the Cost of Plumage Quality in Nestling Birds</a></b></div>
<div>
Lea M. Callan, Frank A. La Sorte, Thomas E. Martin, and Vanya G. Rohwer</div>
</div>
<div>
Summary: <a href="https://amnat.org/an/newpapers/MayCallan.html">https://amnat.org/an/newpapers/MayCallan.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701780" target="_blank">Effects of Predator Avoidance Behavior on the Coexistence of Competing Prey</a></b></div>
<div>
Pacifica Sommers and Peter Chesson</div>
</div>
<div>
Summary: <a href="https://amnat.org/an/newpapers/MaySommers.html">https://amnat.org/an/newpapers/MaySommers.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702252" target="_blank">Prey Responses to Exotic Predators: Effects of Old Risks and New Cues</a></b></div>
<div>
Sean M. Ehlman, Pete C. Trimmer, and Andrew Sih</div>
</div>
<div>
Summary: <a href="https://amnat.org/an/newpapers/AprEhlman.html">https://amnat.org/an/newpapers/AprEhlman.html</a></div>
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<br /></div>
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<div>
<b><i>Open Access</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701670" target="_blank">Predator-Prey Models with Competition: The Emergence of Territoriality</a></b></div>
<div>
Henri Berestycki and Alessandro Zilio</div>
</div>
<div>
Summary: <a href="https://amnat.org/an/newpapers/MarBerestycki.html">https://amnat.org/an/newpapers/MarBerestycki.html</a></div>
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<br /></div>
<div>
<div>
<b><i>Open Access</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701632" target="_blank">Conspicuous Plumage Does Not Increase Predation Risk: A Continent-Wide Test Using Model Songbirds</a></b></div>
<div>
Kristal E. Cain, Michelle L. Hall, Illiana Medina, Ana V. Leitao, Kaspar Delhey, Lyanne Brouwer, Anne Peters, Stephen Pruett-Jones, Michael S. Webster, Naomi E. Langmore, and Raoul A. Mulder</div>
</div>
<div>
Summary: <a href="https://amnat.org/an/newpapers/MarCain.html">https://amnat.org/an/newpapers/MarCain.html</a></div>
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<br /></div>
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<div>
<b><i>Open Access</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703171" target="_blank">Species’ Range Dynamics Affect the Evolution of Spatial Variation in Plasticity under Environmental Change</a></b></div>
<div>
Max Schmid, Ramon Dallo, and Frédéric Guillaume</div>
</div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701041" target="_blank">Predator-Prey Games in Multiple Habitats Reveal Mixed Strategies in Diel Vertical Migration</a></b></div>
<div>
Jérôme Pinti and André W. Visser</div>
</div>
<div>
Summary: <a href="https://amnat.org/an/newpapers/MarPinti.html">https://amnat.org/an/newpapers/MarPinti.html</a></div>
<div>
<br /></div>
<b><i>Natural History Note</i></b><br />
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701433" target="_blank">Testing Darwin’s Hypothesis about the Wonderful Venus Flytrap: Marginal Spikes Form a “Horrid Prison” for Moderate-Sized Insect Prey</a></b><br />
Alexander L. Davis, Matthew H. Babb, Matthew C. Lowe, Adam T. Yeh, Brandon T. Lee, and Christopher H. Martin<br />
Summary: <a href="https://www.amnat.org/an/newpapers/FebDavis.html">https://www.amnat.org/an/newpapers/FebDavis.html</a><br />
<br />
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700566" target="_blank">Space Use and Leadership Modify Dilution Effects on Optimal Vigilance under Food-Safety Trade-Offs</a></b><br />
Rémi Patin, Daniel Fortin, Cédric Sueur, and Simon Chamaillé-Jammes<br />
Summary: <a href="https://www.amnat.org/an/newpapers/JanPatin.html">https://www.amnat.org/an/newpapers/JanPatin.html</a><br />
<br />
<b><i>Celebrating The American Naturalist at 150, Open Access</i></b><br />
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/695985" target="_blank">Specifying the Harsh Conditions of Life: Resource Competition and Predation in the 1970s</a></b><br />
Alita R. Burmeister and Richard E. Lenski<br />
<br />ASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-68229226563477469152020-09-29T12:40:00.000-05:002020-09-30T13:39:44.424-05:00Demography<h2>
Recent Papers</h2><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708723" target="_blank">Investigating the Dynamics of Elk Population Size and Body Mass in a Seasonal Environment Using a Mechanistic Integral Projection Model</a></b></div><div>Shelly Lachish, Ellen E. Brandell, Meggan E. Craft, Andrew P. Dobson, Peter J. Hudson, Daniel R. MacNulty, and Tim Coulson</div></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708271" target="_blank">Parental Age Effects and the Evolution of Senescence</a></b></div><div>Patrick M. Barks and Robert A. Laird</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/May-Barks.html">https://www.amnat.org/an/newpapers/May-Barks.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706811" target="_blank">Deconstructing Evolutionary Game Theory: Coevolution of Social Behaviors with Their Evolutionary Setting</a></b></div><div>Erol Akçay</div></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706904" target="_blank">Demography-Dispersal Trait Correlations Modify the Eco-Evolutionary Dynamics of Range Expansion</a></b></div><div>Brad M. Ochocki, Julia B. Saltz, and Tom E. X. Miller</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Feb-Ochocki.html">https://www.amnat.org/an/newpapers/Feb-Ochocki.html</a></div><div><br /></div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706183" target="_blank">Decreased Precipitation Predictability Negatively Affects Population Growth through Differences in Adult Survival</a></b></div><div>Guillem Masó, Arpat Ozgul, and Patrick S. Fitze</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Jan-Maso.html">https://www.amnat.org/an/newpapers/Jan-Maso.html</a></div><div><br /></div>
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<b><i>Note</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704684" target="_blank">Soil Microbiomes Underlie Population Persistence of an Endangered Plant Species</a></b></div>
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Aaron S. David, Pedro F. Quintana-Ascencio, Eric S. Menges, Khum B. Thapa-Magar, Michelle E. Afkhami, and Christopher A. Searcy</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/Oct-David.html">https://www.amnat.org/an/newpapers/Oct-David.html</a></div>
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<b><i>Open Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704249" target="_blank">Ecological Release of the Anna’s Hummingbird during a Northern Range Expansion</a></b></div>
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C. J. Battey</div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703155" target="_blank">How Does the Evolution of Universal Ecological Traits Affect Population Size? Lessons from Simple Models</a></b></div>
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Peter A. Abrams</div>
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<a href="https://www.journals.uchicago.edu/doi/full/10.1086/702849" target="_blank"><b>When Do Shifts in Trait Dynamics Precede Population Declines?</b></a></div>
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Gaurav Baruah, Christopher F. Clements, Frédéric Guillaume, and Arpat Ozgul</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/MayBaruah.html">https://www.amnat.org/an/newpapers/MayBaruah.html</a></div>
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<b><i>Open Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701857" target="_blank">Stage-Structured Evolutionary Demography: Linking Life Histories, Population Genetics, and Ecological Dynamics</a></b></div>
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Charlotte de Vries and Hal Caswell</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/AprDeVries.html">https://www.amnat.org/an/newpapers/AprDeVries.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701783" target="_blank">Brood Size Affects Future Reproduction in a Long-Lived Bird with Precocial Young</a></b></div>
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Alan G. Leach, James S. Sedinger, Thomas V. Riecke, Amanda W. Van Dellen, David H. Ward, and W. Sean Boyd</div>
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<b><i>Open Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701631" target="_blank">Meeting Yield and Conservation Objectives by Harvesting Both Juveniles and Adults</a></b></div>
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Niklas L. P. Lundström, Nicolas Loeuille, Xinzhu Meng, Mats Bodin, and Åke Brännström</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/MarLundstrom.html">https://www.amnat.org/an/newpapers/MarLundstrom.html</a></div>
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<b><i>Open Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701781" target="_blank">Catastrophic Mortality, Allee Effects, and Marine Protected Areas</a></b></div>
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Emilius A. Aalto, Fiorenza Micheli, Charles A. Boch, Jose A. Espinoza Montes, C. Broch Woodson, and Giulio A. De Leo</div>
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<b><i>Note</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701043" target="_blank">Shifting Vital Rate Correlations Alter Predicted Population Responses to Increasingly Variable Environments</a></b></div>
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David T. Iles, Robert F. Rockwell, and David N. Koons</div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700698" target="_blank">Multiple Evolutionary Routes to Monogamy: Modeling the Coevolution of Mating Decisions and Parental Investment</a></b></div>
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Arne Jungwirth and Rufus A. Johnstone</div>
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Lay summary: <a href="https://www.amnat.org/an/newpapers/FebJungwirth.html">https://www.amnat.org/an/newpapers/FebJungwirth.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/698217" target="_blank">Matrix Models of Hierarchical Demography: Linking Group- and Population-Level Dynamics in Cooperative Breeders</a></b></div>
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Andrew W. Bateman, Arpat Ozgul, Martin Krkošek, and Tim H. Clutton-Brock</div>
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Lay summary: <a href="https://www.amnat.org/an/newpapers/AugBateman.html">https://www.amnat.org/an/newpapers/AugBateman.html</a></div>
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ASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-73845523709905855202020-09-29T11:37:00.000-05:002020-09-30T10:32:39.485-05:00Macroevolution<span style="background-color: white; color: #333333; font-family: cantarell;"><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><b>Open Access, Note</b></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/691100" target="_blank">Detecting the Signature of Body Mass Evolution in the Broad-Scale Architecture of Food Webs</a></b></div><div>John P. DeLong</div><div>Blurb: <a href="https://www.amnat.org/an/newpapers/Oct-DeLong.html">https://www.amnat.org/an/newpapers/Oct-DeLong.html</a></div></div><div style="font-weight: bold;"><br /></div><div style="font-weight: bold;"><a href="https://www.journals.uchicago.edu/doi/full/10.1086/710176" target="_blank">High Preservation Potential of Paleogeographic Range Size Distributions in Deep Time</a></div><div>Simon A. F. Darroch, Michelle M. Casey, Gwen S. Antell, Amy Sweeney, and Erin E. Saupe</div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Oct-Darroch.html">https://www.amnat.org/an/newpapers/Oct-Darroch.html</a></div></div><div style="font-weight: bold;"><br /></div><div style="font-weight: bold;"><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709819">Mammal Community Structure through the Paleocene-Eocene Thermal Maximum</a></div><div>Danielle Fraser and S. Kathleen Lyons</div></div><div style="font-weight: bold;"><br /></div><div style="font-weight: bold;"><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709610">Selection and Constraints in the Ecomorphological Adaptive Evolution of the Skull of Living Canidae (Carnivora, Mammalia)</a></div><div>Fabio Andrade Machado</div></div><div style="font-weight: bold;"><br /></div><div style="font-weight: bold;"><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708639">Evolutionary Pathways to Communal and Cooperative Breeding in Carnivores</a></div><div>Valentine Federico, Dominique Allainé, Jean-Michel Gaillard, and Aurélie Cohas</div></div><div style="font-weight: bold;"><br /></div><div style="font-weight: bold;"><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708273">Why Are There So Many Flowering Plants? A Multiscale Analysis of Plant Diversification</a></div><div>Tania Hernández-Hernández and John J. Wiens</div></div><div>Blog:<b style="font-style: italic;"> </b><a href="https://www.amnat.org/an/newpapers/June-Hernandez.html">https://www.amnat.org/an/newpapers/June-Hernandez.html</a></div><div><br /></div><div><b><i>Open Access</i></b></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707664">Revisiting a Landmark Study System: No Evidence for a Punctuated Mode of Evolution in <i>Metrarabdotos</i></a></b></div><div>Kjetil Lysne Voje, Emanuela Di Martino, and Arthur Porto</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/May-Voje.html">https://www.amnat.org/an/newpapers/May-Voje.html</a></div><div><br /></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707207">Does Evolutionary History Correlate with Contemporary Extinction Risk by Influencing Range Size Dynamics?</a></b></div><div>Andrew J. Tanentzap, Javier Igea, Matthew G. Johnston, and Matthew J. Larcombe</div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Mar-Tanentzap.html">https://www.amnat.org/an/newpapers/Mar-Tanentzap.html</a></div></div><div><br /></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707194">Developmental Constraints Do Not Influence Long-Term Phenotypic Evolution of Marsupial Forelimbs as Revealed by Interspecific Disparity and Integration Patterns</a></b></div><div>Alberto Martín-Serra and Roger B. J. Benson</div></div><div>Blog: <a href="https://www.amnat.org/an/newpapers/Mar-Martin-Serra.html">https://www.amnat.org/an/newpapers/Mar-Martin-Serra.html</a></div><div><b><i><br /></i></b></div><div><b><i>Open Access, Symposium</i></b></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705992">Memory in Trait Macroevolution</a></b></div><div>Emma E. Goldberg and Jasmine Foo</div></div><div><br /></div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706905">Transitions between the Terrestrial and Epiphytic Habit Drove the Evolution of Seed-Aerodynamic Traits in Orchids</a></b></div><div>Xu-Li Fan, Guillaume Chomicki, Kai Hao, Qiang Liu, Ying-Ze Xiong, Susanne S. Renner, Jiang-Yun Gao, and Shuang-Quan Huang</div></div><div style="font-size: medium;"><br /></div><div style="font-size: medium;"><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706914">Wasp Waist and Flight: Convergent Evolution in Wasps Reveals a Link between Wings and Body Shapes</a></b></div><div style="font-size: medium;">Adrien Perrard</div><div style="font-size: medium;">Blog: <a href="https://www.amnat.org/an/newpapers/Feb-Perrard.html">https://www.amnat.org/an/newpapers/Feb-Perrard.html</a></div></div><div style="font-size: medium;"><br /></div><div style="font-size: medium;"><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705294">Macroevolutionary Origin and Adaptive Function of a Polymorphic Female Signal Involved in Sexual Conflict</a></b></div><div style="font-size: medium;">Beatriz Willink, M. Catherine Duryea, and Erik I. Svensson</div><div style="font-size: medium;">Blog: <a href="https://www.amnat.org/an/newpapers/Nov-Willink.html">https://www.amnat.org/an/newpapers/Nov-Willink.html</a></div></div><div style="font-size: medium;"><span style="font-size: 14.85px;"><br /></span></div><div style="font-size: medium;"><span style="font-size: 14.85px;"><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703535">Consistent Associations between Body Size and Hidden Contrasting Color Signals across a Range of Insect Taxa</a></b></span></div><div style="font-size: medium;"><span style="font-size: 14.85px;">Karl Loeffler-Henry, Changku Kang, and Thomas N. Sherratt</span></div><div style="font-size: 14.85px; font-style: italic;">Blurb: <a href="https://www.amnat.org/an/newpapers/JulyLoefflerHenry.html">https://www.amnat.org/an/newpapers/JulyLoefflerHenry.html</a></div></div><div style="font-size: 14.85px;"><br /></div><div style="font-size: 14.85px;"><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703112">Macroevolutionary Patterning in Glucocorticoids Suggests Different Selective Pressures Shape Baseline and Stress-Induced Levels</a></b></div><div style="font-size: 14.85px;">Maren N. Vitousek, Michele A. Johnson, Cynthia J. Downs, Eliot T. Miller, Lynn B. Martin, Clinton D. Francis, Jeremy W. Donald, Matthew J. Fuxjager, Wolfgang Goymann, Michaela Hau, Jerry F. Husak, Bonnie K. Kircher, Rosemary Knapp, Laura A. Schoenle, and Tony D. Williams</div></div><div style="font-size: 14.85px;"><br /></div><div style="font-size: 14.85px;"><b><i>Historical Perspective</i></b></div><div style="font-size: 14.85px;"><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703055">Revisiting a Key Innovation in Evolutionary Biology: Felsenstein’s “Phylogenies and the Comparative Method”</a></b></div><div style="font-size: 14.85px;">Raymond B. Huey, Theodore Garland Jr., and Michael Turelli</div><div style="font-size: 14.85px;"><br /></div><div style="font-size: 14.85px;"><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706903">Detecting Mosaic Patterns in Macroevolutionary Disparity</a></b></div><div>Caroline Parins-Fukuchi</div></div><div style="font-size: 14.85px; font-style: italic; font-weight: bold;"><br /></div><div><div><div><b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701630">Speciation Rate Is Independent of the Rate of Evolution of Morphological Size, Shape, and Absolute Morphological Specialization in a Large Clade of Birds</a></b></div><div>Nicholas M. A. Crouch and Robert E. Ricklefs</div></div></div><div style="font-size: 14.85px; font-style: italic; font-weight: bold;"><br /><br /></div></span>ASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.comtag:blogger.com,1999:blog-6418000394750538816.post-71478077057781025532020-09-08T09:21:00.005-05:002020-09-08T09:21:43.833-05:00Guidelines for data on Dryad<p><span style="font-family: inherit;"> The American Naturalist has begun the process of creating a new editorial board position: 'Data Editors'. Their job will be to help facilitate and check compliance with the journal's open-data policies. We require publication of raw data and metadata on Dryad or equivalent public repositories, and we recommend including code to reproduce analyses. Exceptions can be made, to post the data but embargo public access for a set amount of time to allow authors to publish related papers, but we rarely get these requests.</span></p><p><span style="font-family: inherit;">It has come to our attention recently that compliance with our data policies is ... not quite as effective as we'd like. This mostly comes down to missing material in the posted data, or unclear metadata. To help authors do a better job of meeting our data publication expectations, I began a committee composed of Bob Montgomerie, Paulinha Lemos, and Rob Knell. They have produced the following <b>Data Archiving Checklist</b>, listing best-practices which authors may find useful in preparing materials for Dryad or other data archives. You may also find the <a href="https://datadryad.org/stash/best_practices">DRYAD best practices list</a> useful.</span></p><p class="Standard" style="-webkit-text-stroke-width: 0px; border: none; color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; margin: 0in 0in 0.0001pt; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><b><span style="font-family: inherit; font-size: small;">Checklist for preparing data to upload to DRYAD or other repository<o:p></o:p></span></b></p><p class="Standard" style="-webkit-text-stroke-width: 0px; border: none; color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; margin: 0in 0in 0.0001pt; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><o:p><span style="font-family: inherit; font-size: small;"> </span></o:p></p><p class="Standard" style="margin-bottom: 6.0pt; margin-left: .75in; margin-right: 0in; margin-top: 0in; mso-list: l0 level1 lfo2; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: inherit; font-size: small;"><span style="mso-list: Ignore;"><img alt="*" height="10" src="file:////Users/dbolnick/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_" width="10" /><span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]-->assemble all of your data files used to prepare your paper<o:p></o:p></span></p><p class="Standard" style="margin-bottom: 6.0pt; margin-left: .75in; margin-right: 0in; margin-top: 0in; mso-list: l0 level1 lfo2; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: inherit; font-size: small;"><span style="mso-list: Ignore;"><img alt="*" height="10" src="file:////Users/dbolnick/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_" width="10" /><span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]-->ensure that every observation is a row and every variable is a column<o:p></o:p></span></p><p class="Standard" style="margin-bottom: 6.0pt; margin-left: .75in; margin-right: 0in; margin-top: 0in; mso-list: l0 level1 lfo2; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: inherit; font-size: small;"><span style="mso-list: Ignore;"><img alt="*" height="10" src="file:////Users/dbolnick/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_" width="10" /><span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]-->if you analyzed means rather than the raw data, also supply a data file with the raw data from which those means were calculated<o:p></o:p></span></p><p class="Standard" style="margin-bottom: 6.0pt; margin-left: .75in; margin-right: 0in; margin-top: 0in; mso-list: l0 level1 lfo2; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: inherit; font-size: small;"><span style="mso-list: Ignore;"><img alt="*" height="10" src="file:////Users/dbolnick/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_" width="10" /><span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]-->from each file remove variables not analyzed<o:p></o:p></span></p><p class="Standard" style="margin-bottom: 6.0pt; margin-left: .75in; margin-right: 0in; margin-top: 0in; mso-list: l0 level1 lfo2; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: inherit; font-size: small;"><span style="mso-list: Ignore;"><img alt="*" height="10" src="file:////Users/dbolnick/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_" width="10" /><span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]-->identify each variable (column names) with a short name (no spaces or symbols), preferably <10 characters long. Use an underline (e.g. wing_length) or camel case (e.g., WingLength) to distinguish words if you think that is needed. See t<span lang="EN-CA">he Google R style guide (</span><a href="https://google.github.io/styleguide/Rguide.html" style="color: magenta; text-decoration: underline;"><span lang="EN-CA">https://google.github.io/styleguide/Rguide.html</span></a><span lang="EN-CA">) and the Tidyverse style guide (</span><a href="https://style.tidyverse.org/syntax.html#object-names" style="color: magenta; text-decoration: underline;"><span lang="EN-CA">https://style.tidyverse.org/syntax.html#object-names</span></a>) for more information<o:p></o:p></span></p><p class="Standard" style="margin-bottom: 6.0pt; margin-left: .75in; margin-right: 0in; margin-top: 0in; mso-list: l0 level1 lfo2; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: inherit; font-size: small;"><span style="mso-list: Ignore;"><img alt="*" height="10" src="file:////Users/dbolnick/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_" width="10" /><span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]-->prepare a README file that lists all of your data and code files with a brief description of the file and a list of all variable names and an explanation of each variable so that someone else could understand what that variable means (including units). See Dryad suggestions <a href="https://datadryad.org/stash/best_practices#describe" target="_blank">here</a>.<o:p></o:p></span></p><p class="Standard" style="margin-bottom: 6.0pt; margin-left: .75in; margin-right: 0in; margin-top: 0in; mso-list: l0 level1 lfo2; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: inherit; font-size: small;"><span style="mso-list: Ignore;"><img alt="*" height="10" src="file:////Users/dbolnick/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_" width="10" /><span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]-->save the README file as a text (.txt) file and all of the data files as comma-separated variable (.csv) files<o:p></o:p></span></p><p class="Standard" style="margin-bottom: 6.0pt; margin-left: .75in; margin-right: 0in; margin-top: 0in; mso-list: l0 level1 lfo2; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: inherit; font-size: small;"><span style="mso-list: Ignore;"><img alt="*" height="10" src="file:////Users/dbolnick/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_" width="10" /><span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]-->if your data are in EXCEL spreadsheets you are welcome to submit those as well (to indicate colour coding and provide additional information (formulas etc) but each worksheet of data should also be saved as a separate .csv file.<o:p></o:p></span></p><p class="Standard" style="margin-bottom: 6.0pt; margin-left: .75in; margin-right: 0in; margin-top: 0in; mso-list: l0 level1 lfo2; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: inherit; font-size: small;"><span style="mso-list: Ignore;"><img alt="*" height="10" src="file:////Users/dbolnick/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_" width="10" /><span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]-->Save each file with a short, meaningful file name (see <a href="https://datadryad.org/stash/best_practices#organize" target="_blank">DRYAD recommendations here</a>), except the README file which should just be called README.txt<o:p></o:p></span></p><p class="Standard" style="margin-bottom: 6.0pt; margin-left: .75in; margin-right: 0in; margin-top: 0in; mso-list: l0 level1 lfo2; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: inherit; font-size: small;"><span style="mso-list: Ignore;"><img alt="*" height="10" src="file:////Users/dbolnick/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_" width="10" /><span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]-->save all image, audio, and video files in formats recommended by DRYAD (<a href="https://datadryad.org/stash/best_practices#accessible">here</a>). You may wish to contact DRYAD or your Editor if the raw data files are too large.<o:p></o:p></span></p><p class="Standard" style="margin-bottom: 6.0pt; margin-left: .75in; margin-right: 0in; margin-top: 0in; mso-list: l0 level1 lfo2; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: inherit; font-size: small;"><span style="mso-list: Ignore;"><img alt="*" height="10" src="file:////Users/dbolnick/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_" width="10" /><span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]-->upload all of your files to DRYAD or other repository and fill in all of the metadata and information requested by the repository, even if this is not required as it makes your data easier to find and understand<o:p></o:p></span></p><p class="Standard" style="margin-bottom: 6.0pt; margin-left: .75in; margin-right: 0in; margin-top: 0in; mso-list: l0 level1 lfo2; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: inherit; font-size: small;"><span style="mso-list: Ignore;"><img alt="*" height="10" src="file:////Users/dbolnick/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_" width="10" /><span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]-->from the repository get a URL that can be used by editors and reviewers before your data are made public with a DOI<o:p></o:p></span></p><p class="Standard" style="-webkit-text-stroke-width: 0px; border: none; color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; margin: 0in 0in 6pt; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><o:p><span style="font-family: inherit; font-size: small;"> </span></o:p></p><p class="Standard" style="-webkit-text-stroke-width: 0px; border: none; color: black; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; margin: 0in 0in 6pt; text-align: start; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><o:p><span style="font-family: inherit; font-size: small;"> </span></o:p></p><p><style class="WebKit-mso-list-quirks-style">
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</style></p><p class="Standard" style="margin-bottom: 6pt;"><span style="font-size: small;"><span style="font-family: inherit;">last updated 7 September 2020</span><o:p></o:p></span></p>Dan Bolnickhttp://www.blogger.com/profile/05181664810897127126noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-28466428376557860922020-09-01T11:50:00.000-05:002020-09-01T11:50:02.185-05:00<p><span style="font-family: inherit;"> The Editorial Board of The American Naturalist has completed an evaluation of a paper by Pruitt JN , Howell KA , Gladney SJ , Yang Y , Lichtenstein JLL , Spicer MElise , Echeverri SA, and Pinter-Wollman N . 2017. Behavioral Hypervolumes of Predator Groups and Predator-Predator Interactions Shape Prey Survival Rates and Selection on Prey Behavior . The American Naturalist. 189:254–266</span></p><p><span style="font-family: inherit;">https://www.journals.uchicago.edu/doi/abs/10.1086/663680</span></p><p><span style="font-family: inherit;">A committee of six individuals, including both Associate Editors and outside research community members, were appointed by the Editor, Dan Bolnick, in late February 2020. They delivered their report on this in April 2020. After several rounds of comment by Dr. Pruitt and his co-authors, the committee requested that the Dryad repository be updated. This update has been completed (https://datadryad.org/stash/dataset/doi:10.5061/dryad.8q8p7) and the committee and this Editor have no further concerns about this paper.</span></p><p><span style="font-family: inherit;">The concern identified by the committee is summarized here:</span></p><div class="" style="font-stretch: normal; line-height: normal; margin: 0px;"><div class="" style="font-stretch: normal; line-height: normal; margin: 0px;"><span style="font-family: inherit;"><i class="">Inconsistency between sea star sample sizes reported in the paper, and the data </i><i class="">provided. The paper reports a sample size of 28 sea stars. But there are only 19 lines of </i><i class="">personality data for the sea stars, although in some data files a seastar with ID #20 is listed. In </i><i class="">figures reporting sea star behavioral repeatability data, there are either 19 or 20 visible data </i><i class="">points (Figs. A2-3, and Fig. A4, respectively), and the statistics reported in the paper seem </i><i class="">consistent with a sample size of 19.</i></span></div><div class="" style="font-stretch: normal; line-height: normal; margin: 0px;"><span style="font-family: inherit;"><br class="" /></span></div></div><div class=""><span style="font-family: inherit;">Based on communications from Dr. Pinter-Wollman and Dr. Pruitt, it appears that:</span></div><div class=""><span style="font-family: inherit;"><br class="" /></span></div><div class=""><span style="font-family: inherit;">1) not all collected individuals were used, hence the difference between 28 collected individuals and the actual sample size in the study. This point is slightly confusing for readers but not significant enough to require publication of a correction, as the Methods do not state that 28 individuals were <i>used</i>.</span></div><div class=""><span style="font-family: inherit;">2) A 20th individual of unknown original provenance, obtained from a laboratory setting, was included in the study but not in the Dryad repository. The committee suggested, and the authors agreed, that this can be fixed by updating the Dryad data repository to include the 20th individual. Note that this entails the addition of a new version of the data file, not a replacement [the original version remains]. From our point of view, the correction statement is sufficient to clarify what was absent in the original data file, and why. The Dryad repository has now been corrected as of August 18 2020. The .csv file in the update has a header that reads:</span></div><div class=""><span style="font-family: inherit;">"<span style="white-space: pre-wrap;">Not all 28 sampled sea stars were used for the study. Note the 20th individual used in this study came from a teaching collection."</span></span></div><div class=""><span style="white-space: pre-wrap;"><span style="font-family: inherit;">The Editorial Board remains concerned that the use of one individual of unknown provenance, in a sample of otherwise wild-caught sea stars, is a less than optimal experimental design, as it may inflate trait variance in a study of sea star behavioral variation. The origin of the 20th individual was not made clear in the published manuscript methods, nor was the rationale for its addition explained. However, the concern was deemed relatively minor, by the committee, as we do not have grounds to believe this changed the core results of the paper. We therefore accept the correction to the Dryad repository as sufficient to satisfy the minor concerns raised regarding this paper. Unless other concerns come to light that we are not presently aware of, <b>we consider this paper to be valid and suitable for citing in future work.</b></span></span></div><div class=""><span style="white-space: pre-wrap;"><span style="font-family: inherit;"><br /></span></span></div><div class=""><span style="font-family: inherit;">Signed,</span></div><div class=""><span style="font-family: inherit;">Daniel Bolnick</span></div><div class=""><span style="font-family: inherit;">Editor-In-Chief, The American Naturalist</span></div><div class=""><span style="font-family: inherit;">September 1, 2020</span></div><br class="Apple-interchange-newline" />Dan Bolnickhttp://www.blogger.com/profile/05181664810897127126noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-39654629686773173632020-08-31T20:43:00.006-05:002020-09-01T12:31:55.587-05:00PubPeer and ongoing evaluation of past published papers<p>In my capacity as Editor-In-Chief of The American Naturalist, I sometimes receive emails criticizing already-published papers in this journal. The criticisms sometimes come in the form of anonymous emails to me. Other times they come from known emails and contain lengthy attachments with detailed criticisms. Increasingly, however, these criticisms are posted publicly on PubPeer, often by anonymous individuals. I want to take a moment to comment on this trend, from my perspective. Note that the following is not formal journal policy, and other Editors (current and future) may disagree.</p><p>The individuals posting anonymously on PubPeer are typically genuinely concerned members of the scientific community who have identified errors, or strongly suspect errors exist, in the scientific record. Their criticisms should be addressed for their technical content. Left unanswered, a cloud hangs over the paper(s) in question.</p><p>That said, there is some question about the proper procedure for answering these criticisms. Yes, PubPeer itself leaves room for comments (interestingly, journal editors like myself must pay money to reply to comments, even if to acknowledge them and state we are evaluating the issue). But, this process bypasses the journal that publishes the paper, and bypasses the normal scientific tradition of external review by experts in the field chosen by the journal editor for their knowledge and hopefully objectivity. For this reason, I want to really encourage people with substantial concerns about a paper (e.g., which may appreciably alter the results and conclusions), to submit formal "Comments" (different journals call these different things) to the journal. These Comment manuscripts get reviewed (including by the original authors), and the original authors may write a Reply. Based on the reviews and comment and reply the Editor decides whether to (1) publish just the comment, (2) publish the comment and reply, (3) request a correction or retraction, or (4) let matters lie because the criticism does not have solid ground to stand on, is deemed to be debatable, or (per COPE guidelines) if the issue has no material impact on the conclusions of the paper. </p><p>I know that the Comment approach is onerous in several ways. First, it takes time to prepare a formal manuscript formatted submission. I know of at least one instance (concerning a putative error in an equation in a theory paper) where the critic took time to write a pages-long missive, but said s/he didn't want to take the time to actually turn it into a Comment. Second, the Comment is authored and so the critic identifies him or herself to possible reprisal. Recent activity by lawyers of one author (letters, FOIA requests) illustrates the point that critics can be subjected to legal and other harassment, which is a stressful penalty for free-speech in pursuit of ensuring scientific accuracy. {Note; anonymously authored Comments are not traditional, but might possibly be considered}. Third, Comments go through review which takes time, leaving the matter behind the scenes in the meantime. Here is where things get tricky: if a criticism proves to be groundless, a PubPeer criticism can damage an author's reputation needlessly and inappropriately. On the other hand, if a criticism has merit, we'd like it to be public knowledge immediately to correct the scientific record as soon as a problem is identified. These are conflicting needs. PubPeer is on the side of rapid dissemination, and reviewing Comments behind the scenes can err on the side of perpetuating errors too long (and can also open journals to criticisms of foot-dragging and cover-ups). While perhaps such cover-ups exist, every case I am directly aware of I have been satisfied that journals are genuine in their desire for ensuring quality science, but must exercise caution in leaping to conclusions without due process (which occurs behind the scenes).</p><p>So, as a journal, our official stance is that we prefer to receive submitted Comments. This follows the scientific tradition of obtaining third-party review, and deliberate evaluation of criticisms. But, scientific traditions are fluid and we are in an era of increasing speed and openness: Preprint servers, open peer review, open data, et cetera. We therefore also recognize that PubPeer is an active tool in science conversations. The criticisms posted there can be valid identification of genuine problems that need to be evaluated formally and corrected. If valid well-justified and substantial concerns exist and are published on PubPeer, then the affected journal should respond.</p><p>There are caveats and concerns about PubPeer. Most importantly, it is important that these not be used as a mechanism for pursuing personal vendettas. Excessive targeting of an author with multiple minor complaints can constitute a kind of harassment, and may be viewed as such by University Equity officers or equivalent. The anonymous nature of many PubPeer comments makes it easier for impacted authors to feel like (and, argue that) they are the target of personal vendettas and harassment. Second, the existence of PubPeer comments can cast a long shadow over a paper whether the comments are profound or minor. This shadow can affect an author's career prospects (fellowship applications, job applications, etc) even before the matter is resolved and judged to be valid or not. The result can be inappropriate damage to an innocent authors' career, which in turn may have grave consequences for mental health. Third, there is an established mechanism for voicing complaints about papers in science: contact the author to request clarification, or contact the Editor, or submit a Comment. I realize that many complainants are nervous about revealing their identity, and these three steps I list make this harder. One can create new email accounts to anonymously contact an author, or Editor. But bear in mind that although scientific publication is in no way bound to follow legal court-style procedures, there's something to be said for the legal tradition that accused have a chance to face their accuser. Science publication is not a court of law; but it is worth considering whether we as a community want to respect that kind of tradition. That said, whistleblowers sometimes hide their identity for good reason (e.g., not trusting that whistleblower laws offer sufficient protection). With this in mind, it might be worth considering whether journals might publish anonymizied Comments. That runs counter to the growing trend towards open peer review, but can protect vulnerable individuals when their complaint is valid and they have compelling grounds to be concerned about how their career is impacted.</p><p>How should journals respond to PubPeer comments? This is something of a wild-west issue that I expect COPE (the committee on publication ethics) is grappling with to provide guidelines. First, the PubPeer comments need to be brought to the Editor's attention. Don't assume that Editors take time to search PubPeer regularly; at least I don't. Then, the journal begins an evaluation process that may include (1) forming a committee to evaluate the papers and the citicisms, and/or (2) contacting the author(s) for a response. These take time, indeed can take many months to do properly with due care for the details and reaching a scientifically defensible and just decision. So, please be patient. Sometimes there are delays due to valid extensions in recognition of health concerns, parental leave, etc, that need to be appropriately accommodated even in pursuit of ensuring scientific truth. Also, do not expect any formal journal response on the PubPeer website; they charge Editors money to make any statement as Editor (that's how they pay their bills, at least in part).</p><p>Obviously if there is compelling evidence of malpractice by authors, the investigation should ultimately result in retraction (e.g., a Comment alone ceases to be sufficient). But, some cases where a critic may reasonably suspect data have been fudged, may appear to others to be less clear-cut. A journal's job is to carefully evaluate the opposing claims and the weight of evidence. The result may end up being inaction where the journal's editor or their appointed committees are unconvinced by the criticisms. It is my belief that, if a criticism proves to be invalid, then its public airing on PubPeer can do more harm than good. Which is why I prefer such processes be handled via a formal evaluation and review.</p><p>To summarize, I believe that PubPeer has appealing features, but has the potential to do harm to innocent authors, or to be used for personal attacks. Our goal should be to promote its strengths while mitigating the risks. As editor I therefore <i>prefer</i> that critiques begin with direct communication with an author, and that journals be notified via submission of a Comment when those direct communications do not yield a satisfactory answer (or, go unanswered). In this way, concerns can be evaluated and questions can be answered, through a formal review process that might resolve the issue without exposing the author to public ridicule that might ultimately prove to be baseless. That said, I understand the motive for using PubPeer (anonymity, speed, openness) and will respond when made aware of PubPeer critiques that appear to have scientific merit.</p><p>I am aware of PubPeer criticisms targeting multiple papers of some authors. These cases take extra time to evaluate because they entail more work: committee members need to find time to read many papers, delve into their data, and authors need to respond to more comments. Please be patient. To the broader community, a journal may appear to be ignoring criticisms; but this may simply be the result of a careful and incomplete process. In some cases we also are awaiting COPE recommendations for how to proceed in cases that reveal new kinds of publication-ethics problems.</p><p>In particular, we are aware of cases where published papers lack complete data repositories (e.g., on Dryad). A present, we are awaiting guidance from the Committee on Publication Ethics on how to proceed in such cases. This is a new enough situation, that the recommendations are not yet clearly articulated as a scientific community. As an interim policy, our first step is to notify authors and give them a deadline for completing their files to our satisfaction. Such deadlines may take some time, for instance if hard drive forensics are needed, or if an individual is on parental or health leave. If the data files cannot be completed by the deadline, our present plan is to issue Editorial Expressions of Concern. Authors with such EoCs will have any future papers scrutinized far more closely for complete data. Authors would do well to avoid such situations by uploading complete Dryad (or equivalent) archives following best practices recommended by Dryad for thorough meta-data, ReadMe files, etc.</p><p> As an institution The American Naturalist is dedicated to publishing rigorous, well-supported research, and that rigor takes time. Every other Editor-In-Chief of other journals whom I have interacted with extensively shares that commitment. We will never sweep valid criticisms under the rug to defend our reputation, because that reputation comes not from having papers, but from the quality of the papers that we disseminate. But, sometimes the deliberate process of internal review may appear to the outside to be inaction; often nothing could be further from the truth.</p><p>Ultimately, it is journals that publish science (for now). And thus it is journals' job to correct errors in the science that they previously published. It follows that for any serious scientific error, it rests in journals' hands to evaluate the error and take suitable corrective steps. Of course, if journals truly fail to meet that obligation, that's a problem. And PubPeer represents an alternative, a safety net for criticisms, and a way of shaming journals into action. But - I'll say this again - sometimes what looks like inaction from outside is either (1) a slow deliberative process to ensure complete and fair evaluation, or (2) a completed evaluation that found nothing to move forward with. So, please give journals some time to do what they need to do. </p><p>Dan Bolnick</p><p><br /></p><p>Addendum:</p><p>A Twitter comment pointed out that PubPeer enables author responses to critiques, creating online dialogues that may resolve and clarify and issue. I appreciate and value that. The poster (Boris Barbour) also notes that most PubPeer comments are not graced with author defenses or acknowledgement. If correct (no statistics were offered in support), that is troubling. And in my view that again points to the value of journals as the enforcers whose job is to follow through and either require a response or else publish a retraction or Expression of Concern or Comment. Authors can ignore PubPeer comments because... because they can, there's no immediate penalty for engaging besides the court of public opinion.</p>Dan Bolnickhttp://www.blogger.com/profile/05181664810897127126noreply@blogger.com4tag:blogger.com,1999:blog-6418000394750538816.post-44856275120862479032020-08-13T13:59:00.003-05:002020-08-13T13:59:49.902-05:00Open letter of thanks to Associate Editors<p><span style="font-family: inherit;">The following is a letter addressing Associate Editors at The American Naturalist, but which may be of interest to readers and authors as well.</span></p><p><span style="font-family: inherit;"><br /></span></p><p><span style="font-family: inherit;">Dear Associate Editors,</span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;"><a name="_GoBack"></a></span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;"> </span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;">As I pass the two and a half year mark as Editor In Chief of The American Naturalist, I realized I have not done something long over due: saying thank you. The success of this journal is a reflection of your efforts: helping to encourage people to submit interesting work that you hear of (whether in person, at conferences, seminar visits, on BioRXiv, etc), choosing effective reviewers, and providing your own extensive insights into papers. I routinely hear praise from authors about the review experience at The American Naturalist: both the depth that we go to and the constructive thoughtful and supportive tone. Your Associate Editor recommendation letters are frequently longer and more insightful than the reviews themselves, and that leaves an excellent impression on authors. You show great thoughtfulness in crafting responses, rather than just rubber stamping the reviews you form your own opinions, sometimes disagreeing with reviews and setting aside mistaken concerns, sometimes forming your own objections that go beyond what the reviewers noticed. Authors appreciate this. I have often (as recently as days ago) heard comments like “I had the best rejection experience ever at AmNat”. Even if we do not choose to publish a paper, we give feedback that improves the authors’ chances elsewhere. I have not infrequently seen papers we declined that ended up in Evolution, Ecology, Ecology Letters, and I like to think the quality of our reviews and letters give authors a step up to get their paper into the best possible destination whether it is in our journal or not. All this effort takes work that is rarely rewarded with a ’thank you’. So here I am today, to say THANK YOU from the bottom of my heart. I value your efforts every single day, with every single paper that crosses my desk. I am often in awe of your insights and care, and frequently thankful that you have done a thorough enough job that I can more readily reach a decision. You work so hard for the journal, as volunteers, and this service cannot be underestimated. I am well aware of what effort that takes you often, and how you must balance this with many other demands on your time and attention. So, thank you and please keep up the great work.<o:p></o:p></span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;"> </span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;">I want to remind you all that, in return for your excellent work, if there is ever anything I or the other Editors can do, please let us know. We do sometimes have brief conversations with some of you about tricky decisions, by Zoom or email or other, and please do know that we are here to help you do your great job for the journal.<o:p></o:p></span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;"> </span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;">For me, one of the harder elements of this job is knowing when to nag you all about decision times. Please forgive my occasional nagging emails about particular papers. The Editorial Manager system auto-generates emails to remind you of when there are papers sitting unattended (from the software’s point of view). About a year ago I began chiming in when I saw papers that were on your desk for longer than about 10 days. Those nagging emails, while annoying for you to receive I do not doubt, did seem to help bring the time to first decision down a bit. Remember, we aspire to choose reviewers in ~5 days or so (preferably less) and we aspire to get recommendations from you within a week to 10 days at the outside of receiving reviews. Of course, COVID has upended all that. Some of us have lost family members, been sick, stressed, your attention drawn to more important epidemiological pursuits for your governments, or attention appropriately diverted to homeschooling kids over the spring and child care over the summer without summer camps. I’m right there with you, and fully sympathetic. I let my threshold for nagging emails slide to about the three week mark. Since COVID shows no sign of letting up, I’m going to keep it there for now. I’d still much prefer (in service of authors) that papers sit on AE desks for less than a week going out to review, and less than a week coming back from review. But I would also much prefer that COVID ‘magically go away’; since that is clearly not rational, I’ll just treat this as a generic reminder to keep in mind the impatience and nervousness of a graduate student or postdoc author who sees the paper is back from review and is waiting, with baited breath, for a decision that may impact their CV while applying for the next stages of their career. I fundamentally cannot balance everyone’s need here: your need for the time to do a good and thorough job (as a volunteer) while many other demands on your time exist, against authors’ needs for an answer. So, please consider this paragraph an apology for my continued nagging on slow papers; that’s my job. Your job is to take the time you need to give the thorough thoughtful and constructive comments that give this journal its good reputation for thorough (but slow) review and high quality papers. So, never feel you need to reply, explain, or apologize if you get an email from me, and please forgive me for the nagging, as I just try to find the right balance between respecting your time, and serving authors.<o:p></o:p></span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;"> </span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;">Lastly, some news:<o:p></o:p></span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;"> </span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;">Russell Bonduriansky, who has been a co-Editor for nearly three years, will be ending his service to the journal in the coming months, and will be replaced by Erol Akçay. Russell was an Associate Editor for over a half decade before becoming a member of the trio of Editors. He will be greatly missed.<o:p></o:p></span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;"> </span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;">An even greater tectonic shift is approaching: Trish Morse, our guiding light, our institutional memory, is retiring this fall (October 30). We have all come to view Trish as the bedrock on which the journal operates. We will be working to make the transition as seamless as possible and I have full faith we will move ahead in good order. Owen Cook will continue in his present role and knows the inner workings of the journal to keep us running very well. That said, please join me in thanking Trish for her two decades of incredible support and leadership. The journal would not have been the same without her, and her thoughtfulness and kindness are inspirations to us all. Trish, THANK YOU. As a token of our gratitude, the former Editors and I gave Trish a gift: original copies of the first four Volumes of The American Naturalist, 1867-1870 (photos attached).<o:p></o:p></span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;"> </span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;">Again, thank you all for your help and devotion to the journal,<o:p></o:p></span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;"> </span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;">Best wishes,<o:p></o:p></span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;"> </span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;">Dan Bolnick<o:p></o:p></span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><span style="font-family: inherit;">Editor-In-Chief, The American Naturalist</span></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><o:p><span style="font-family: inherit;"> </span></o:p></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6U2WdKazUPLFt7l2Udxr5fg9TQMuSe0iuYL5SaiYpoFWUTKYPf5sqJAib9ymSd_4Vo_1r6TuIIYIDVoTAF97U3jKzgvmgXUuizOoHoolmMcPqhwDSyrc8_dT0Z2sKt-ffL7q5_03J4no/s2048/IMG_8058.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: inherit;"><img border="0" data-original-height="1536" data-original-width="2048" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6U2WdKazUPLFt7l2Udxr5fg9TQMuSe0iuYL5SaiYpoFWUTKYPf5sqJAib9ymSd_4Vo_1r6TuIIYIDVoTAF97U3jKzgvmgXUuizOoHoolmMcPqhwDSyrc8_dT0Z2sKt-ffL7q5_03J4no/s640/IMG_8058.jpg" width="640" /></span></a></div><span style="font-family: inherit;"><br /></span><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgKyBsOpgVKZ3TrCwC_1aNxHyQaj8-3_YvC97vf2-Mu5wefvnVN2QKg0QJPJlXcWtr4vjYdm8MJlZ3HeYjjtij1ZuR8E2ekUFrHZPTpgcFTp8J2DTkrAacIYbPZtaw35AFYQCmeEnRAPkk/s2048/IMG_8059.jpeg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: inherit;"><img border="0" data-original-height="1536" data-original-width="2048" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgKyBsOpgVKZ3TrCwC_1aNxHyQaj8-3_YvC97vf2-Mu5wefvnVN2QKg0QJPJlXcWtr4vjYdm8MJlZ3HeYjjtij1ZuR8E2ekUFrHZPTpgcFTp8J2DTkrAacIYbPZtaw35AFYQCmeEnRAPkk/s640/IMG_8059.jpeg" width="640" /></span></a></div><o:p><span style="font-family: inherit;"><br /></span></o:p><p></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><o:p><span style="font-family: inherit;"><br /></span></o:p></p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt;"><o:p><span style="font-family: inherit;"><br /></span></o:p></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0in 0in 0.0001pt;"><o:p><br /></o:p></p>Dan Bolnickhttp://www.blogger.com/profile/05181664810897127126noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-3196643960947244412020-08-09T17:16:00.000-05:002020-08-10T10:55:38.899-05:00Competition<h2>
Recent Papers</h2>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709821" target="_blank">Shifts in Reproductive Investment in Response to Competitors Lower Male Reproductive Success</a></b></div>
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Foteini Spagopoulou, Regina Vega-Trejo, Megan L. Head, and Michael D. Jennions</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/Sep-Spagopoulou.html">https://www.amnat.org/an/newpapers/Sep-Spagopoulou.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709293" target="_blank">Effect of Stressors on the Carrying Capacity of Spatially Distributed Metapopulations</a></b></div>
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Bo Zhang, Donald L. DeAngelis, Wei-Ming Ni, Yuanshi Wang, Lu Zhai, Alex Kula, Shuang Xu, and J. David Van Dyken</div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708719" target="_blank">Species Differences in Phenology Shape Coexistence</a></b></div>
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Christopher Blackford, Rachel M. Germain, and Benjamin Gilbert</div>
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Blurb: <a href="https://www.amnat.org/an/newpapers/July-Blackford.html">https://www.amnat.org/an/newpapers/July-Blackford.html</a></div>
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<b><i>Free Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708513" target="_blank">Beyond Pairwise Interactions: Multispecies Character Displacement in Mexican Freshwater Fish Communities</a></b></div>
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Andrea J. Roth-Monzón, Mark C. Belk, J. Jaime Zúñiga-Vega, and Jerald B. Johnson</div>
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Blurb: <a href="https://www.amnat.org/an/newpapers/June-Roth-Monzon.html">https://www.amnat.org/an/newpapers/June-Roth-Monzon.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707747" target="_blank">Increased Levels of Perceived Competition Decrease Juvenile Kin-Shoaling Preferences in a Cichlid Fish</a></b></div>
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Timo Thünken, Saskia Hesse, and Denis Meuthen</div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707597" target="_blank">Belowground Competition Can Influence the Evolution of Root Traits</a></b></div>
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Sara M. Colom and Regina S. Baucom</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/Apr-Colom.html">https://www.amnat.org/an/newpapers/Apr-Colom.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707017" target="_blank">Stochastic Dynamics of Three Competing Clones: Conditions and Times for Invasion, Coexistence, and Fixation</a></b></div>
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Sylvain Billiard and Charline Smadi</div>
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Blurb: <a href="https://www.amnat.org/an/newpapers/Mar-Billiard.html">https://www.amnat.org/an/newpapers/Mar-Billiard.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707018" target="_blank">Nonlinear Effects of Intraspecific Competition Alter Landscape-Wide Scaling Up of Ecosystem Function</a></b></div>
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Chelsea J. Little, Emanuel A. Fronhofer, and Florian Altermatt</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/Mar-Little.html">https://www.amnat.org/an/newpapers/Mar-Little.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706813" target="_blank">How Does Joint Evolution of Consumer Traits Affect Resource Specialization?</a></b></div>
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Paula Vasconcelos and Claus Rueffler</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/VP-Vasconcelos.html">https://www.amnat.org/an/newpapers/VP-Vasconcelos.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706181" target="_blank">Evolutionary Rescue from a Wave of Biological Invasion</a></b></div>
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J. David Van Dyken</div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705826" target="_blank">Scale Both Confounds and Informs Characterization of Species Coexistence in Empirical Systems</a></b></div>
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Adam Clark, Helmut Hillebrand, and W. Stanley Harpole</div>
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Blurb: <a href="https://www.amnat.org/an/newpapers/JanGuelzow.html">https://www.amnat.org/an/newpapers/JanGuelzow.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705940" target="_blank">Combined Effects of Natural Enemies and Competition for Resources on a Forest Defoliator: A Theoretical and Empirical Analysis</a></b></div>
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Molly E. Gallagher and Greg Dwyer</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/Dec-Gallagher.html">https://www.amnat.org/an/newpapers/Dec-Gallagher.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705293" target="_blank">A Meta-analysis of Plant Interaction Networks Reveals Competitive Hierarchies as well as Facilitation and Intransitivity</a></b></div>
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Nicole L. Kinlock</div>
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Blurb: <a href="https://www.amnat.org/an/newpapers/Nov-Kinlock.html">https://www.amnat.org/an/newpapers/Nov-Kinlock.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705347" target="_blank">On the Consequences of the Interdependence of Stabilizing and Equalizing Mechanisms</a></b></div>
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Chuliang Song, György Barabás, and Serguei Saavedra</div>
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Blurb: <a href="https://www.amnat.org/an/newpapers/Nov-Song.html">https://www.amnat.org/an/newpapers/Nov-Song.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704773" target="_blank">Early Sibling Conflict May Ultimately Benefit the Family</a></b></div>
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Alyssa Laney Smith, Daniel Z. Atwater, and Ragan M. Callaway</div>
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Blurb: <a href="https://www.amnat.org/an/newpapers/Oct-Smith.html">https://www.amnat.org/an/newpapers/Oct-Smith.html</a></div>
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<b><i>Note</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/abs/10.1086/704102" target="_blank">A General Explanation for the Persistence of Reproductive Interference</a></b></div>
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Jonathan P. Drury, Christopher N. Anderson, Maria B. Cabezas Castillo, Jewel Fisher, Shawn McEachin, and Gregory F. Grether</div>
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Blurb: <a href="https://amnat.org/an/newpapers/AugDrury.html">https://amnat.org/an/newpapers/AugDrury.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/abs/10.1086/703158" target="_blank">Assessing Behavioral Associations in a Hybrid Zone through Social Network Analysis: Complex Assortative Behaviors Structure Associations in a Hybrid Quail Population</a></b></div>
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David M. Zonana, Jennifer M. Gee, Eli S. Bridge, Michael D. Breed, and Daniel F. Doak</div>
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Blurb: <a href="https://amnat.org/an/newpapers/JuneZonana.html">https://amnat.org/an/newpapers/JuneZonana.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/abs/10.1086/701780" target="_blank">Effects of Predator Avoidance Behavior on the Coexistence of Competing Prey</a></b></div>
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Pacifica Sommers and Peter Chesson</div>
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Blurb: <a href="https://amnat.org/an/newpapers/MaySommers.html">https://amnat.org/an/newpapers/MaySommers.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/abs/10.1086/702304" target="_blank">Age-Specific Offspring Mortality Economically Tracks Food Abundance in a Piscivorous Seabird</a></b></div>
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Oscar Vedder, He Zhang, Andreas Dänhardt, and Sandra Bouwhuis</div>
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Blurb: <a href="https://amnat.org/an/newpapers/AprVedder.html">https://amnat.org/an/newpapers/AprVedder.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701629" target="_blank">Limiting Similarity? The Ecological Dynamics of Natural Selection among Resources and Consumers Caused by Both Apparent and Resource Competition</a></b></div>
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Mark A. McPeek<br />
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707610" target="_blank">Competitive Exclusion and Evolution: Convergence Almost Never Produces Ecologically Equivalent Species: (A Comment on McPeek, “Limiting Similarity? The Ecological Dynamics of Natural Selection among Resources and Consumers Caused by Both Apparent and Resource Competition”)</a></b></div>
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Liz Pásztor, György Barabás, and Géza Meszéna</div>
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<b><i>Open Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701670" target="_blank">Predator-Prey Models with Competition: The Emergence of Territoriality</a></b></div>
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Henri Berestycki and Alessandro Zilio</div>
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<i>Lay summary:</i> <a href="https://www.amnat.org/an/newpapers/MarBerestycki.html">https://www.amnat.org/an/newpapers/MarBerestycki.html</a></div>
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<b><i>Open Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701434" target="_blank">Priority Effects and Nonhierarchical Competition Shape Species Composition in a Complex Grassland Community</a></b></div>
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Lawrence H. Uricchio, S. Caroline Daws, Erin R. Spear, and Erin A. Mordecai</div>
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<i>Lay summary:</i> <a href="https://www.amnat.org/an/newpapers/FebUricchio.html">https://www.amnat.org/an/newpapers/FebUricchio.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701432" target="_blank">Increased Temperature Disrupts the Biodiversity–Ecosystem Functioning Relationship</a></b></div>
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Elodie C. Parain, Rudolf P. Rohr, Sarah M. Gray, and Louis-Félix Bersier</div>
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<i>Lay summary:</i> <a href="https://www.amnat.org/an/newpapers/FebParain.html">https://www.amnat.org/an/newpapers/FebParain.html</a></div>
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<b><i>Open Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700577" target="_blank">Delayed Chemical Defense: Timely Expulsion of Herbivores Can Reduce Competition with Neighboring Plants</a></b></div>
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Pia Backmann, Volker Grimm, Gottfried Jetschke, Yue Lin, Matthijs Vos, Ian T. Baldwin, and Nicole M. van Dam</div>
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<i>Lay summary:</i> <a href="https://www.amnat.org/an/newpapers/JanBackmann.html">https://www.amnat.org/an/newpapers/JanBackmann.html</a></div>
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<b><i>Celebrating Am Nat 150, Open Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/695985" target="_blank">Specifying the Harsh Conditions of Life: Resource Competition and Predation in the 1970s</a></b></div>
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Alita R. Burmeister and Richard E. Lenski</div>
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ASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-46429266993158522522020-08-09T12:00:00.000-05:002020-08-10T14:35:47.213-05:00Climate Change<h2>
Recent Papers</h2>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709019" target="_blank">Caching in or Falling Back at the Sevilleta: The Effects of Body Size and Seasonal Uncertainty on Desert Rodent Foraging</a></b></div>
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Justin D. Yeakel, Uttam Bhat, and Seth D. Newsome</div>
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<a href="https://www.amnat.org/an/newpapers/July-Yeakel.html">https://www.amnat.org/an/newpapers/July-Yeakel.html</a></div>
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<b><i>Free Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709009" target="_blank">Quantifying the Contribution of Habitats and Pathways to a Spatially Structured Population Facing Environmental Change</a></b></div>
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Christine Sample, Joanna A. Bieri, Benjamin Allen, Yulia Dementieva, Alyssa Carson, Connor Higgins, Sadie Piatt, Shirley Qiu, Summer Stafford, Brady J. Mattsson, Darius J. Semmens, Jay E. Diffendorfer, and Wayne E. Thogmartin</div>
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<a href="https://www.amnat.org/an/newpapers/July-Sample.html">https://www.amnat.org/an/newpapers/July-Sample.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709010" target="_blank">Climate Change and Thermoregulatory Consequences of Activity Time in Mammals</a></b></div>
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Timothy C. Bonebrake, Enrico L. Rezende, and Francisco Bozinovic</div>
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<a href="https://www.amnat.org/an/newpapers/July-Bonebrake.html">https://www.amnat.org/an/newpapers/July-Bonebrake.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708270" target="_blank">Dispersal Increases the Resilience of Tropical Savanna and Forest Distributions</a></b></div>
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Nikunj Goel, Vishwesha Guttal, Simon A. Levin, and A. Carla Staver</div>
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Blog <a href="https://www.amnat.org/an/newpapers/May-Goel.html">https://www.amnat.org/an/newpapers/May-Goel.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/707207" target="_blank">Does Evolutionary History Correlate with Contemporary Extinction Risk by Influencing Range Size Dynamics?</a></b></div>
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Andrew J. Tanentzap, Javier Igea, Matthew G. Johnston, and Matthew J. Larcombe</div>
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Blog <a href="https://www.amnat.org/an/newpapers/Mar-Tanentzap.html">https://www.amnat.org/an/newpapers/Mar-Tanentzap.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706259" target="_blank">Spatial Population Structure Determines Extinction Risk in Climate-Induced Range Shifts</a></b></div>
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Christopher Weiss-Lehman and Allison K. Shaw</div>
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<a href="https://www.amnat.org/an/newpapers/Jan-Weiss-Lehman.html">https://www.amnat.org/an/newpapers/Jan-Weiss-Lehman.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706183" target="_blank">Decreased Precipitation Predictability Negatively Affects Population Growth through Differences in Adult Survival</a></b></div>
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Guillem Masó, Arpat Ozgul, and Patrick S. Fitze</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/Jan-Maso.html">https://www.amnat.org/an/newpapers/Jan-Maso.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705680" target="_blank">Meta-analysis Shows That Rapid Phenotypic Change in Angiosperms in Response to Environmental Change Is Followed by Stasis</a></b></div>
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Lucas D. Gorné and Sandra Díaz</div>
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Blurb: https://www.amnat.org/an/newpapers/Dec-Gorne.html</div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705679" target="_blank">Climate Warming, Resource Availability, and the Metabolic Meltdown of Ectotherms</a></b></div>
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Raymond B. Huey and Joel G. Kingsolver</div>
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<b><i>Free Access; Special Feature on Maladaptation</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704780" target="_blank">Maladapted Prey Subsidize Predators and Facilitate Range Expansion</a></b></div>
<div>
Mark C. Urban, Alice Scarpa, Justin M. J. Travis, and Greta Bocedi</div>
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<div>
<a href="https://www.amnat.org/an/newpapers/Oct-Urban.html">https://www.amnat.org/an/newpapers/Oct-Urban.html</a></div>
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<b><i>Note, Open Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704607" target="_blank">Pollen on Stigmas of Herbarium Specimens: A Window into the Impacts of a Century of Environmental Disturbance on Pollen Transfer</a></b></div>
<div>
Anna L. Johnson, María Rebolleda-Gómez, and Tia-Lynn Ashman</div>
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<div>
Blurb: <a href="https://amnat.org/an/newpapers/Sep-Johnson.html">https://amnat.org/an/newpapers/Sep-Johnson.html</a></div>
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<br /></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704280" target="_blank">Intraspecific Variation in Worker Body Size Makes North American Bumble Bees (Bombus spp.) Less Susceptible to Decline</a></b></div>
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<div>
Matthew W. Austin and Aimee S. Dunlap</div>
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Blurb: <a href="https://amnat.org/an/newpapers/Sep-Austin.html">https://amnat.org/an/newpapers/Sep-Austin.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704208" target="_blank">Antagonistic Responses of Exposure to Sublethal Temperatures: Adaptive Phenotypic Plasticity Coincides with a Reduction in Organismal Performance</a></b></div>
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Anthony L. Gilbert and Donald B. Miles</div>
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<div>
Blurb: <a href="https://amnat.org/an/newpapers/Sep-Gilbert.html">https://amnat.org/an/newpapers/Sep-Gilbert.html</a></div>
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<br /></div>
<div>
<div>
<b><i>Special Feature on Maladaptation</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702313" target="_blank">Phenotypic Plasticity and Local Adaptation in a Wild Hibernator Evaluated through Reciprocal Translocation</a></b></div>
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Jeffrey E. Lane, Zenon J. Czenze, Rachel Findlay-Robinson, and Erin Bayne</div>
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<br /></div>
<div>
<div>
<b><i>Special Feature on Maladaptation</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702312" target="_blank">Lagging Adaptation to Climate Supersedes Local Adaptation to Herbivory in an Annual Monkeyflower</a></b></div>
<div>
Nicholas J. Kooyers, Jack M. Colicchio, Anna B. Greenlee, Erin Patterson, Neal T. Handloser, and Benjamin K. Blackman</div>
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<div>
Blurb: <a href="https://amnat.org/an/newpapers/AugKooyers.html">https://amnat.org/an/newpapers/AugKooyers.html</a></div>
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<br /></div>
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<div>
<b><i>Special Feature on Maladaptation, Open Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702716" target="_blank">Maladaptive Shifts in Life History in a Changing Environment</a></b></div>
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Olivier Cotto, Linnea Sandell, Luis-Miguel Chevin, and Ophélie Ronce</div>
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<div>
Blurb: <a href="https://amnat.org/an/newpapers/AugCotto.html">https://amnat.org/an/newpapers/AugCotto.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/703171" target="_blank">Species’ Range Dynamics Affect the Evolution of Spatial Variation in Plasticity under Environmental Change</a></b></div>
<div>
Max Schmid, Ramon Dallo, and Frédéric Guillaume</div>
</div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702590" target="_blank">Predicting Habitat Choice after Rapid Environmental Change</a></b></div>
<div>
Philip H. Crowley, Pete C. Trimmer, Orr Spiegel, Sean M. Ehlman, William S. Cuello, and Andrew Sih</div>
</div>
<div>
Blurb: <a href="https://amnat.org/an/newpapers/MayCrowley.html">https://amnat.org/an/newpapers/MayCrowley.html</a></div>
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<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702252" target="_blank">Prey Responses to Exotic Predators: Effects of Old Risks and New Cues</a></b></div>
<div>
Sean M. Ehlman, Pete C. Trimmer, and Andrew Sih</div>
</div>
<div>
Blurb: <a href="https://amnat.org/an/newpapers/AprEhlman.html">https://amnat.org/an/newpapers/AprEhlman.html</a></div>
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<br /></div>
<div>
<div>
<b><i>Note</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701043" target="_blank">Shifting Vital Rate Correlations Alter Predicted Population Responses to Increasingly Variable Environments</a></b></div>
<div>
David T. Iles, Robert F. Rockwell, and David N. Koons</div>
</div>
<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701432" target="_blank">Increased Temperature Disrupts the Biodiversity–Ecosystem Functioning Relationship</a></b></div>
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Elodie C. Parain, Rudolf P. Rohr, Sarah M. Gray, and Louis-Félix Bersier</div>
</div>
<div>
<i>Lay summary</i>: <a href="https://www.amnat.org/an/newpapers/FebParain.html">https://www.amnat.org/an/newpapers/FebParain.html</a></div>
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</div>
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</div>
ASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.com0tag:blogger.com,1999:blog-6418000394750538816.post-42597620239191698062020-08-07T17:48:00.000-05:002020-08-07T15:46:16.339-05:00Dispersal<h2>
Recent Papers</h2>
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<div>
<b><i>Free Access</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709009" target="_blank">Quantifying the Contribution of Habitats and Pathways to a Spatially Structured Population Facing Environmental Change</a></b></div>
<div>
Christine Sample, Joanna A. Bieri, Benjamin Allen, Yulia Dementieva, Alyssa Carson, Connor Higgins, Sadie Piatt, Shirley Qiu, Summer Stafford, Brady J. Mattsson, Darius J. Semmens, Jay E. Diffendorfer, and Wayne E. Thogmartin</div>
</div>
<div>
Blog: <a href="https://www.amnat.org/an/newpapers/July-Sample.html">https://www.amnat.org/an/newpapers/July-Sample.html</a></div>
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<br /></div>
<div>
<div>
<b><i>Free Access</i></b></div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709479" target="_blank">Metabolic Rate Interacts with Resource Availability to Determine Individual Variation in Microhabitat Use in the Wild</a></b></div>
<div>
Sonya K. Auer, Ronald D. Bassar, Daniel Turek, Graeme J. Anderson, Simon McKelvey, John D. Armstrong, Keith H. Nislow, Helen K. Downie, Thomas A. J. Morgan, Darryl McLennan, and Neil B. Metcalfe</div>
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<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709163" target="_blank">Parasitism Risk and Infection Alter Host Dispersal</a></b></div>
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Celina B. Baines, Salma Diab, and Shannon J. McCauley</div>
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<div>
Blog: <a href="https://www.amnat.org/an/newpapers/Aug-Baines.html">https://www.amnat.org/an/newpapers/Aug-Baines.html</a></div>
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<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708806" target="_blank">Optimal Network Architectures for Spatially Structured Populations with Heterogeneous Diffusion</a></b></div>
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Alfonso Ruiz-Herrera and Pedro J. Torres</div>
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<div>
<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/709109" target="_blank">Dispersal Predicts Hybrid Zone Widths across Animal Diversity: Implications for Species Borders under Incomplete Reproductive Isolation</a></b></div>
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Jay P. McEntee, J. Gordon Burleigh, and Sonal Singhal</div>
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<div>
Blog: <a href="https://www.amnat.org/an/newpapers/July-McEntee.html">https://www.amnat.org/an/newpapers/July-McEntee.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708721" target="_blank">The Ecology of Individual Differences Empirically Applied to Space-Use and Movement Tactics</a></b></div>
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Quinn M. R. Webber, Michel P. Laforge, Maegwin Bonar, Alec L. Robitaille, Christopher Hart, Sana Zabihi-Seissan, and Eric Vander Wal</div>
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<div>
Blog: <a href="https://www.amnat.org/an/newpapers/July-Webber.html">https://www.amnat.org/an/newpapers/July-Webber.html</a></div>
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<br /></div>
<div>
<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708639" target="_blank">Evolutionary Pathways to Communal and Cooperative Breeding in Carnivores</a></b></div>
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Valentine Federico, Dominique Allainé, Jean-Michel Gaillard, and Aurélie Cohas</div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708519" target="_blank">Within Reach? Habitat Availability as a Function of Individual Mobility and Spatial Structuring</a></b></div>
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Jason Matthiopoulos, John Fieberg, Geert Aarts, Frédéric Barraquand, and Bruce E. Kendall</div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708156" target="_blank">Frequency of Occurrence and Population-Dynamic Consequences of Different Forms of Density-Dependent Emigration</a></b></div>
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Rachel R. Harman, Jerome Goddard II, Ratnasingham Shivaji, and James T. Cronin</div>
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<div>
Blog: <a href="https://www.amnat.org/an/newpapers/May-Harman.html">https://www.amnat.org/an/newpapers/May-Harman.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/708270" target="_blank">Dispersal Increases the Resilience of Tropical Savanna and Forest Distributions</a></b></div>
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Nikunj Goel, Vishwesha Guttal, Simon A. Levin, and A. Carla Staver</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/May-Goel.html">https://www.amnat.org/an/newpapers/May-Goel.html</a></div>
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<br /></div>
<div>
<b><i>Symposium</i></b></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705993" target="_blank">Evolution of Dispersal Can Rescue Populations from Expansion Load</a></b></div>
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Stephan Peischl and Kimberly J. Gilbert</div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706904" target="_blank">Demography-Dispersal Trait Correlations Modify the Eco-Evolutionary Dynamics of Range Expansion</a></b></div>
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Brad M. Ochocki, Julia B. Saltz, and Tom E. X. Miller</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/Feb-Ochocki.html">https://www.amnat.org/an/newpapers/Feb-Ochocki.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706913" target="_blank">Spatial Scales of Population Synchrony in Predator-Prey Systems</a></b></div>
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Javier Jarillo, Bernt-Erik Sæther, Steinar Engen, and Francisco Javier Cao-García</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/Feb-Jarillo.html">https://www.amnat.org/an/newpapers/Feb-Jarillo.html</a></div>
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<br /></div>
<div>
<b><i>Note</i></b></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706181" target="_blank">Evolutionary Rescue from a Wave of Biological Invasion</a></b></div>
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J. David Van Dyken</div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706258" target="_blank">The Evolution of Immigration Strategies Facilitates Niche Expansion by Divergent Adaptation in a Structured Metapopulation Model</a></b></div>
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Éva Kisdi, Helene C. Weigang, and Mats Gyllenberg</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/Jan-Kisdi.html">https://www.amnat.org/an/newpapers/Jan-Kisdi.html</a></div>
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<br /></div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/706259" target="_blank">Spatial Population Structure Determines Extinction Risk in Climate-Induced Range Shifts</a></b></div>
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Christopher Weiss-Lehman and Allison K. Shaw</div>
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<div>
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705410" target="_blank">Variability in Dispersal Syndromes Is a Key Driver of Metapopulation Dynamics in Experimental Microcosms</a></b></div>
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Staffan Jacob, Alexis S. Chaine, Michèle Huet, Jean Clobert, and Delphine Legrand</div>
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<div>
<b><i>Free Access, Note</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/705243" target="_blank">A Minimal Model for the Latitudinal Diversity Gradient Suggests a Dominant Role for Ecological Limits</a></b></div>
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Rampal S. Etienne, Juliano Sarmento Cabral, Oskar Hagen, Florian Hartig, Allen H. Hurlbert, Loïc Pellissier, Mikael Pontarp, and David Storch</div>
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Blurb: <a href="https://www.amnat.org/an/newpapers/Nov-Etienne.html">https://www.amnat.org/an/newpapers/Nov-Etienne.html</a></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704608" target="_blank">Pulsed Immigration Events Can Facilitate Adaptation to Harsh Sink Environments</a></b></div>
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James H. Peniston, Michael Barfield, and Robert D. Holt</div>
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Blog: <a href="https://www.amnat.org/an/newpapers/Sep-Peniston.html">https://www.amnat.org/an/newpapers/Sep-Peniston.html</a></div>
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<div>
<b><i>Free Access</i></b></div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704594" target="_blank">Evolution at the Edge of Expanding Populations</a></b></div>
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Maxime Deforet, Carlos Carmona-Fontaine, Kirill S. Korolev, and Joao B. Xavier</div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/704168" target="_blank">Dormancy in Metacommunities</a></b></div>
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Nathan I. Wisnoski, Mathew A. Leibold, and Jay T. Lennon</div>
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702590" target="_blank">Predicting Habitat Choice after Rapid Environmental Change</a></b></div>
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Philip H. Crowley, Pete C. Trimmer, Orr Spiegel, Sean M. Ehlman, William S. Cuello, and Andrew Sih</div>
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<i>Summary</i>: <a href="https://www.amnat.org/an/newpapers/MayCrowley.html">https://www.amnat.org/an/newpapers/MayCrowley.html</a></div>
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<br /></div>
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<b><i>Note</i></b><br />
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/702589" target="_blank">Heterogeneous Matrix Habitat Drives Species Occurrences in Complex, Fragmented Landscapes</a></b><br />
Jedediah F. Brodie and William D. Newmark<br />
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701041" target="_blank">Predator-Prey Games in Multiple Habitats Reveal Mixed Strategies in Diel Vertical Migration</a></b><br />
Jérôme Pinti and André W. Visser<br />
<i>Summary: </i><a href="https://www.amnat.org/an/newpapers/MarPinti.html">https://www.amnat.org/an/newpapers/MarPinti.html</a><br />
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/701667" target="_blank">The Evolution of Marine Larval Dispersal Kernels in Spatially Structured Habitats: Analytical Models, Individual-Based Simulations, and Comparisons with Empirical Estimates</a></b><br />
Allison K. Shaw, Cassidy C. D’Aloia, and Peter M. Buston<br />
<i>Summary:</i> <a href="https://www.amnat.org/an/newpapers/MarShaw.html">https://www.amnat.org/an/newpapers/MarShaw.html</a><br />
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<b><i>American Society of Naturalists Address</i></b><br />
<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700960" target="_blank">The Snail’s Charm</a></b><br />
Kathleen Donohue<br />
<i>Summary</i>: <a href="https://www.amnat.org/an/newpapers/FebDonohue.html">https://www.amnat.org/an/newpapers/FebDonohue.html</a><br />
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700595" target="_blank">An Empirical and Mechanistic Explanation of Abundance-Occupancy Relationships for a Critically Endangered Nomadic Migrant</a></b><br />
Matthew H. Webb, Robert Heinsohn, William J. Sutherland, Dejan Stojanovic, and Aleks Terauds<br />
<i>Summary</i>: <a href="https://www.amnat.org/an/newpapers/JanWebb.html">https://www.amnat.org/an/newpapers/JanWebb.html</a><br />
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<b><a href="https://www.journals.uchicago.edu/doi/full/10.1086/700835" target="_blank">Metaecosystem Dynamics of Marine Phytoplankton Alters Resource Use Efficiency along Stoichiometric Gradients</a></b><br />
Nils Gülzow, Yanis Wahlen, and Helmut Hillebrand<br />
<i>Summary</i>: <a href="https://www.amnat.org/an/newpapers/JanGuelzow.html">https://www.amnat.org/an/newpapers/JanGuelzow.html</a><br />
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ASNhttp://www.blogger.com/profile/03125199518930102046noreply@blogger.com0