February 15, 2019

Reproduction

Recent Papers on Reproduction

Open Access
Edward J. Almond, Timothy J. Huggins, Liam P. Crowther, Joel D. Parker, and Andrew F. G. Bourke


Open Access, Natural History Note
Mohamed Abdelaziz, Mohammed Bakkali, José M. Gómez, Enrica Olivieri, and Francisco Perfectti


James L. L. Lichtenstein, Ambika Kamath, Sarah Bengston, Leticia Avilés, and Jonathan N. Pruitt

Note
Carolyn M. Bauer, Jessica L. Graham, Mikus Abolins-Abols, Britt J. Heidinger, Ellen D. Ketterson, and Timothy J. Greives

Pluck or Luck: Does Trait Variation or Chance Drive Variation in Lifetime Reproductive Success?
Robin E. Snyder and Stephen P. Ellner
Lay summary: https://www.amnat.org/an/newpapers/AprSnyder.html

The Energetic Cost of Reproduction and Its Effect on Optimal Life-History Strategies
Asta Audzijonyte and Shane A. Richards
Lay summary: https://www.amnat.org/an/newpapers/OctAudzijonyte.html

Mating Opportunity Increases with Synchrony of Flowering among Years More than Synchrony within Years in a Nonmasting Perennial
Amy Waananen, Gretel Kiefer, Jennifer L. Ison, and Stuart Wagenius
Lay summary: https://www.amnat.org/an/newpapers/SepWaananen.html

Sex Allocation Theory for Facultatively Sexual Organisms Inhabiting Seasonal Environments: The Importance of Bet Hedging
Nina Gerber, Isobel Booksmythe, and Hanna Kokko

Adaptive Foraging of Pollinators Can Promote Pollination of a Rare Plant Species
Gita Benadi and Robert J. Gegear
Lay summary: https://www.amnat.org/an/newpapers/AugBenadi.html

A Physiological Signature of the Cost of Reproduction Associated with Parental Care
Melinda A. Fowler and Tony D. Williams
Lay summary: https://www.amnat.org/an/newpapers/DecFowler.html

Multivariate Sexual Selection on Ejaculate Traits under Sperm Competition
Rowan A. Lymbery, W. Jason Kennington, and Jonathan P. Evans
Lay summary: http://amnat.org/an/newpapers/JulyLymbery.html

Collector Motion Affects Particle Capture in Physical Models and in Wind Pollination
Dori McCombe and Josef D. Ackerman
Lay summary: http://amnat.org/an/newpapers/JulyMcCombe.html

Natural History Miscellany Note
Dispensing Pollen Via Catapult: Explosive Pollen Release in Mountain Laurel (Kalmia latifolia)
Callin M. Switzer, Stacey A. Combes, and Robin Hopkins
Lay summary: http://amnat.org/an/newpapers/JuneSwitzer.html

Selfing Can Facilitate Transitions between Pollination Syndromes
Carolyn A. Wessinger and John K. Kelly
Abstract: http://amnat.org/an/newpapers/MayWessinger-A.html

Open Access
The Consequences of Polyandry for Sibship Structures, Distributions of Relationships and Relatedness, and Potential for Inbreeding in a Wild Population
Ryan R. Germain, Peter Arcese, and Jane M. Reid
Lay summary: http://amnat.org/an/newpapers/MayGermain.html

The Behavior and Reproductive Physiology of a Solitary Progressive Provisioning Vespid Wasp: Evidence for a Solitary-Cycle Origin of Reproductive Castes
Hans C. Kelstrup, Klaus Hartfelder, Tiago Falcon Lopes, and Theresa C. Wossler

Offspring Size and Reproductive Allocation in Harvester Ants
Diane C. Wiernasz and Blaine J. Cole
Lay summary: http://amnat.org/an/newpapers/JanWiernasz.html

Synthesis
Mechanisms of Assortative Mating in Speciation with Gene Flow: Connecting Theory and Empirical Research
Michael Kopp, Maria R. Servedio, Tamra C. Mendelson, Rebecca J. Safran, Rafael L. Rodríguez, Mark E. Hauber, Elizabeth C. Scordato, Laurel B. Symes, Christopher N. Balakrishnan, David M. Zonana, and G. Sander van Doorn
Abstract: http://amnat.org/an/newpapers/JanKopp-A.html

Open Access
Do Sperm Really Compete and Do Eggs Ever Have a Choice? Adult Distribution and Gamete Mixing Influence Sexual Selection, Sexual Conflict, and the Evolution of Gamete Recognition Proteins in the Sea
Don R. Levitan
Lay summary: http://amnat.org/an/newpapers/JanLevitan.html

Kinship and Incest Avoidance Drive Patterns of Reproductive Skew in Cooperatively Breeding Birds
Christina Riehl
Lay summary: http://amnat.org/an/newpapers/DecRiehl.html

The Roles of Sexual and Viability Selection in the Evolution of Incomplete Reproductive Isolation: From Allopatry to Sympatry
Olivier Cotto and Maria R. Servedio
Lay summary: http://amnat.org/an/newpapers/NovCotto.html

Open Access
The Evolution of Clutch Size in Hosts of Avian Brood Parasites
Iliana Medina, Naomi E. Langmore, Robert Lanfear, and Hanna Kokko
Lay summary: http://amnat.org/an/newpapers/NovMedina.html

Divorce in an Island Bird Population: Causes, Consequences, and Lack of Inheritance
Nathaniel T. Wheelwright and Céline Teplitsky
Lay summary: http://amnat.org/an/newpapers/OctWhlwrght.html

Open Access
Sex Allocation Patterns across Cooperatively Breeding Birds Do Not Support Predictions of the Repayment Hypothesis
Nyil Khwaja, Ben J. Hatchwell, Robert P. Freckleton, and Jonathan P. Green

Open Access
Effects of Clonal Reproduction on Evolutionary Lag and Evolutionary Rescue
Maria E. Orive, Michael Barfield, Carlos Fernandez, and Robert D. Holt
Lay summary: http://amnat.org/an/newpapers/OctOrive.html

Open Access
Differential Allocation Revisited: When Should Mate Quality Affect Parental Investment?
Thomas R. Haaland, Jonathan Wright, Bram Kuijper, and Irja I. Ratikainen
Lay summary: http://amnat.org/an/newpapers/OctHaaland.html

Resource Allocation and Seed Size Selection in Perennial Plants under Pollen Limitation
Qiaoqiao Huang, Martin Burd, and Zhiwei Fan
Lay summary: http://amnat.org/an/newpapers/SepHuang.html

Convergent Reversion to Single Mating in a Wasp Social Parasite
Kevin J. Loope, Federico Lopez-Osorio, and Libor Dvořák

The Evolution of Cooperation: Interacting Phenotypes among Social Partners
Mat Edenbrow, Bronwyn H. Bleakley, Safi K. Darden, Charles R. Tyler, Indar W. Ramnarine, and Darren P. Croft
Lay summaryhttp://amnat.org/an/newpapers/JunEdenbrow.html

Influence of Early Reproductive Success on Longevity and Late Reproductive Success in an Alpine Ungulate
Andrea Panagakis, Sandra Hamel, and Steeve D. Côté
Lay summary: http://amnat.org/an/newpapers/JunPanagakis.html

Mating System Evolution under Strong Pollen Limitation: Evidence of Disruptive Selection through Male and Female Fitness in Clarkia xantiana
Ryan D. Briscoe Runquist, Monica A. Geber, Michael Pickett-Leonard, and David A. Moeller
Lay summary: http://amnat.org/an/newpapers/MayBriscRunq.html

Natural History Note
Testing the Terminal Investment Hypothesis in California Oaks
Walter D. Koenig, Johannes M. H. Knops, William J. Carmen, and Mario B. Pesendorfer
Lay summary: http://amnat.org/an/newpapers/MayKoenig.html

Note
Royal Darwinian Demons: Enforced Changes in Reproductive Efforts Do Not Affect the Life Expectancy of Ant Queens
Alexandra Schrempf, Julia Giehr, Ramona Röhrl, Sarah Steigleder, and Jürgen Heinze
Lay summary: http://amnat.org/an/newpapers/AprSchrempf.html

The Evolutionary Economics of Embryonic-Sac Fluids in Squamate Reptiles
Xavier Bonnet, Guy Naulleau, and Richard Shine
Lay summary: http://amnat.org/an/newpapers/MarBonnet.html

Surviving in a Cosexual World: A Cost-Benefit Analysis of Dioecy in Tropical Trees
Marjolein Bruijning, Marco D. Visser, Helene C. Muller-Landau, S. Joseph Wright, Liza S. Comita, Stephen P. Hubbell, Hans de Kroon, and Eelke Jongejans
Lay summaryhttp://amnat.org/an/newpapers/MarBruijning.html

Ecological and Social Factors Constrain Spatial and Temporal Opportunities for Mating in a Migratory Songbird
Sara A. Kaiser, Benjamin B. Risk, T. Scott Sillett, and Michael S. Webster
Lay summary: http://amnat.org/an/newpapers/MarKaiser.html

The Evolution of Reproductive Phenology in Broadcast Spawners and the Maintenance of Sexually Antagonistic Polymorphism
Colin Olito, Dustin J. Marshall, and Tim Connallon
Lay summary: http://amnat.org/an/newpapers/FebOlito.html

Helping Relatives Survive and Reproduce: Inclusive Fitness and Reproductive Value in Brood Parasitism
Malte Andersson
Lay summary: http://amnat.org/an/newpapers/FebAndersson.html

American Society of Naturalists Address
Selfing, Local Mate Competition, and Reinforcement
Mark D. Rausher

Note
Rapid Changes in the Sex Linkage of Male Coloration in Introduced Guppy Populations
Swanne P. Gordon, Andrés López-Sepulcre, Diana Rumbo, and David N. Reznick
Lay summary: http://amnat.org/an/newpapers/FebGordon.html

February 14, 2019

Call for Special Feature Proposals

Call for Special Feature Proposals
The American Naturalist

The American Naturalist seeks to publish conceptually innovative research in all areas of organismal biology, with emphasis on ecology, evolution, and behavior.  To showcase the breadth of topics that the journal covers, we are beginning a series of Special Features.  These Features will be collections of 4-8 articles, each on a coherent theme that are published together within a monthly issue, typically with an introductory synthetic essay by the Feature organizers. Such special features often attract a larger readership and can help define the direction of a research topic. Perhaps the most famous example of such a special feature is the November 1983 issue on the role of competition in community ecology (https://www.journals.uchicago.edu/toc/an/1983/122/5).

We are inviting proposals for these special features. Successful proposals should represent innovative thought-provoking research on a topic of current interest to our broad readership. Proposals may be focused on ecology, evolution, behavior, and related subjects in organismal biology. We especially encourage proposals that integrate across disciplines. Papers within special features should present state-of-the-art research and help define future directions of the relevant field.

To submit a proposal, email the following information to the journal Editor-In-Chief, Dr. Daniel Bolnick (daniel.bolnick@uconn.edu):

1) A Special Feature Title

2) A description of and justification for the special feature (approximately 300 words), explaining the topic and why this is innovative and timely for the discipline(s) concerned.

3) A tentative list of potential papers (titles, authors), with a couple-sentence description of each. There should be a minimum of four papers to constitute a Special Feature, and no more than ten. Indicate whether the authors have confirmed their intention to write and submit the papers in question.

4) An estimated deadline for submission.

There is no submission deadline for these proposals, they will be considered on a running basis, each on their own merits. If a proposal is successful, the organizers will be asked to coordinate the submission and review process.

Special Feature manuscripts will be subject to full review. Special Feature organizers will act as Associate Editors (soliciting reviews and writing decision recommendations) and will be acknowledged as such on the manuscript and journal Table of Contents. They will be responsible for ensuring manuscripts are submitted and revised in a timely manner, so the journal can publish the accepted papers together without undue delay. Final decisions on papers will be made by a journal Editor who is independent from the Special Feature, to ensure adherence to the journal’s high standards of quality and novelty. A minimum of three papers must be accepted to make a Special Feature; if fewer are accepted they will be published as regular articles.

The American Naturalist is a ‘hybrid’ journal produced by a nonprofit publisher. Accepted papers will be subject to regular author page charge system (which includes the availability of waivers and paid APC open access).

February 3, 2019

A "Best Practices" checklist to help authors and reviewers

A number of journals have introduced required or optional checklists in recent years, aimed at either reviewers or authors. The Editorial Board of The American Naturalist is adopting an optional (but recommended) checklist as well. The intent is to remind authors of items that reviewers (and readers) expect in a paper. It may also serve to remind reviewers of things they should look for, but which often get overlooked. Because we receive both a mix of theory and data and synthesis and meta-analysis papers, there is no one-size-fits-all checklist, so the list below is broken down into parts that pertain to different kinds of papers.

The following checklist is a semi-final draft, and we welcome feedback from both authors and reviewers and Associate Editors as we finalize this document. Send comments to daniel.bolnick@uconn.edu.

____________

Rationale:
A paper by Parker et al (2018. “Empowering peer reviewers with a checklist to improve transparency”, Nature Ecology and Evolution) advocated greater use of checklists in evaluating research publications. They argue that “Good checklists do not replace complex thought; they facilitate it. … by calling attention to essential elements that are often overlooked”. Here, we provide a set of checklists tailored to the diverse kinds of papers submitted to The American Naturalist. Authors and reviewers are not required to use this checklist, but it may help each identify common weaknesses that need to be fixed. Not all items in the following checklist pertain to all studies. It is the job of the authors and reviewers to judge what elements apply to any given study. The checklist is therefore not meant to be a straight-jacket, but rather a prompt to remind us what authors should aspire to do, and what reviewers should check for. The checklists below do not cover methods, syntheses, historical perspectives, and some other articles that are also welcome at this journal.

Authors:The following checklists are designed to remind you of key features that maximize transparency of your work, and that reviewers look for in evaluating your work. We encourage you to examine relevant parts of this checklist before submissionof a new manuscript, or during revision, to ensure that you are meeting our expectations. Using this checklist may help you pre-emptively avoid common reviewer critiques. Authors should also visit the journal webpage for formatting details:   https://www.journals.uchicago.edu/journals/an/instruct#data

Reviewers: You may find the checklist to be a useful reminder of manuscript features to comment on, including somewhat mundane details that authors frequently forget to include (and reviewers frequently forget to check for). 

Contents:
1:   General considerations
2:   Articles with empirical data
3:   Articles with meta-analysis
4:   Articles with theory
5:   Submission Formatting

Aspirational features that are recommended but not yet standard practice are marked with a .


GENERAL CONSIDERATIONS

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SUITABILITY FOR THE AMERICAN NATURALIST

The American Naturalist seeks papers that cause readers to consider new ideas, merge existing ideas in new ways, rethink familiar ideas, or which provide particularly compelling evidence for established ideas. Theory and data papers are welcome in equal measure.

Methods papers enable researchers to ask new questions, or address existing questions in new and particularly effective ways. 

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LITERATURE

The manuscript gives sufficient coverage to relevant existing ideas, and does not inflate its own novelty by omitting mention of relevant published studies.

Authors may cite reviews and syntheses, but when possible should also cite original sources for key new insights.

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WRITING

Length: The American Naturalist does not have a specific page length maximum. Papers should be thorough but succinct: as long as they need to be, and not one word longer. Clear enough to describe the context, methods, insights fully.

The prose is clear.

Papers should be free from typographical errors, and spelling and grammar mistakes. Text should be structured in well-organized sentences and paragraphs. But, reviewers should refrain from commenting on the presumed linguistic qualifications of authors.

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FIGURES AND TABLES

Figures avoid use of red/green that may be hard for color blind readers to see.

Figure font sizes and lines are large enough to be easily readable when reproduced on a printed page at a typical figure size.

Figures need not show all data broken down in all possible ways: figures should convey a result as simply and directly as possible, focusing readers’ attention on key trends.

Color should be used where appropriate to clearly distinguish lines

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SUPPLEMENTARY MATERIALS

Supplementary Materials enrich the results but are not essential elements to understand the core message of the paper. Imagine if the Supplement were lost to history, 50 years from now, because of a server failure. Would the paper still be understandable? The answer should be yes. If not, the Supplement has elements that belong in the main text.




EMPIRICAL PAPERS

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ETHICS

For vertebrate animal research, authors describe animal care approval.

For human subjects,  authors describe institutional research approval (e.g., IRB).

The research does not pose a threat to population viability.

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FIELD STUDIES

Authors report information about collecting permits (if needed)

Authors list specific locations (e.g., coordinates) where samples were collected or experiments performed. Exceptions may be made, for instance to protect threatened populations.

Dates of the field work are reported.


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INTENT

 It is good practice to state whether the research was initially planned to address the topic reported in the paper, or whether the paper is reporting on post-hoc analyses. We are not averse to publishing post-hoc studies, because many biological discoveries arise through surprising and un-looked for results. But, we encourage authors to be open about the relationship between their initial intent and final findings

 If a study design was pre-registered, we encourage authors to state whether the study design was pre-registered. We do not require this, nor do we penalize the absence of pre-registration, or deviations from pre-registered plans. 

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SAMPLING

Authors report how study subjects were allocated to experimental treatments.

Authors state how sample sizes were chosen (e.g., describe a power analysis, or logistical constraints).

Where applicable, sources of genetic stocks are identified.


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DATA COLLECTION

Authors state the magnitude of experimental treatments (e.g., food rations, pH levels), and describe how these magnitudes were chosen.

Observers recording data were blind to the experimental treatment imposed on the research subjects.

If voucher specimens are available, authors identify where they are deposited.

Authors provide detailed protocols for non-standard methods as supplementary materials, to aid readers in exactly replicating these methods, including reagents, concentrations, plasticware, vendors, etc.)
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DATA ANALYSIS

Authors report sample sizes for all data, including subsets of data (e.g., each treatment group, other subsets), and sample size used for all statistical analyses. 

Authors identify the level of replication relevant to a given analysis.

Authors provide the precise details of data analysis (software, packages with citations to authors, and descriptions of each statistical test).

Authors provide estimates of effect size, and uncertainty in these estimates. Tests of statistical significance that omit effect sizes are omitting the biology.

If exploratory analyses were performed, then only a subset of models reported in the paper, all exploratory analyses should be acknowledged, and the choice of final focal models clearly explained.

In reporting model results, estimated effects for all model variables should be reported (this may be in Supplementary materials).

 Code to replicate data analysis should be made available for both review and for readers after publication.

 It is good practice to pre-register your planned statistical analyses. We do not require this, nor do we penalize departures from pre-registered plans. But, if your analysis was pre-registered, we encourage authors to state where the pre-registration is recorded.

 Even if you do not pre-register, it is good to acknowledge when an analysis is a post-hoc test arising from an observation of the data, versus a pre-planned analysis.



METAANALYSIS

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DATA COLLECTION

Authors identify the scope of the meta-analysis: range of dates, geography, taxonomy.

Authors  describe the search criteria used to obtain information, including databases and keywords.

Keyword searches include antonyms to catch negative effects.

Authors describe criteria for including or excluding studies.

Authors describe how data was extracted from relevant studies. Include software citations where relevant, and state whether duplicate observers obtain replicate data extracts to evaluate repeatability.

 Authors are encouraged to acknowledge whether the study design was pre-registered. There is no penalty for lack of pre-registration.


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DATA ANALYSIS

Authors state measures of effect size.

Authors state methods for weighting studies by confidence, or justify the lack thereof.

Authors state how analyses accounted for pseudoreplication arising from multiple effect size estimates within one study population or species.

Were phylogenetic corrections were applied to adjust for non-independence of study species?

Authors clearly explain statistical model choices.

Authors state whether any data points were excluded after data acquisition, and why.

How was publication bias evaluated?

Authors explain how many entries suffer from missing data, and how these missing data were handled.

 Upon submission, we encourage authors to provide a copy of the statistical code used to analyze the data, along with necessary data files (see Submission Formatting)


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RESULTS

Authors state the number of studies that passed various filters for inclusion.

Authors provide measures of both effect size, variance in effect size, and confidence.

Authors describe possible sources of bias in the available data.



THEORY

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BIOLOGICAL MOTIVE

Too often, theory is developed on the back of other prior theory, without clear reference to an empirical biological motivation. All theory published in The American Naturalist should aim to explain or anticipate a biological phenomenon, and so must clearly describe the underlying biology with suitable references to empirical results.

Authors should describe specific examples of the biological phenomenon being studied.

Authors should relate model assumptions to biological examples, where possible.

Authors put results into biological context, comparing model output to relevant empirical data when possible.

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MODEL CONSTRUCTION

Authors explain rationale behind choosing analytical versus simulation methods.

Authors explain rationale behind choosing a deterministic versus stochastic model.

Authors justify choice of continuous versus discrete time as relevant to the underlying biology.

Authors define all symbols where they are first used. Tables of symbols (in the main text or supplement) are also useful, but if readers must refer repeatedly to a table it interrupts their reading.

When possible, the choice of a function for a biological relationship should be based on empirical trends. 

Assumptions and simplifications are clearly stated, and where possible are justified with reference to empirical data.

To reach an empirical audience, the meaning of each equation must be clearly summarized in writing.

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MODEL ANALYSIS

The range of parameters is clearly stated and, when possible, justified with reference to biological information.

When multiple parameters are involved, parameter space is explored sufficiently widely to evaluate interactions among key parameters.

Analytical solutions are clearly derived.

Approximations and simplifications are clearly identified, and their consequences are discussed (e.g., when assuming very weak selection to obtain an analytical result, consider what the consequences are if selection is strong).

Simulation code should be made available to reviewers, and subsequently shared on a public repository. Note that sharing your Github page can reveal your identity, so submitting a code file as an attachment with your manuscript is preferred



SUBMISSION FORMATTING
The American Naturalist places few constraints on initial submission formats, but be aware that reviewers are often pickier than the journal office. Reviewers’ opinions can be skewed by careless formatting that clearly deviates from journal style. See http://www.journals.uchicago.edu/journals/an/instruct#prepfor additional details.

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MANUSCRIPT FORMATTING

REQUIRED

Continuous line numbers or page numbers and line numbers are required for peer review.

Manuscripts must be double-spaced (some reviewers are very opinionated about this).

Fonts for math should be embedded in the pdf.

RECOMMENDED

We do not require precise American Naturalist-style citation formatting for initial submission, but we do require this for a final accepted version. However, authors should be advised that reviewers can be critical when citations clearly deviate from journal format (e.g., may criticize numbered in-text citations).

We do not adhere rigidly to Introduction-Methods-Results-Discussion formatting. Sometimes other structures are warranted, for instance when a paper includes a model, a mix of model and data, or a series of successive experiments that build upon each other. However, methods should always be described before Results.

We encourage authors to put figures and tables in the main text, where they are first mentioned, with captions on the same page. A majority of reviewers tend to prefer this arrangement. Preferably, figures should be on the same page as the caption that describes them.

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DATA AND CODE

Proof-read your code as carefully as you proof-read your manuscript prose.

Code should be carefully annotated to state dependencies, and the purpose of each step. For examples of good practices, see online summaries of Best Practices in R (https://swcarpentry.github.io/r-novice-inflammation/06-best-practices-R/)

Code should be self-contained so a user with the relevant input data files can re-create your results, without extraneous code.

 We strongly encourage authors, when feasible, to submit data tables and analytical code (e.g. an R markdown file) alongside the manuscript, so editors and reviewers can check the code with the data. These may be submitted with the paper, or provided via a link to a github repository or equivalent.  Data shared through a website that might reveal reviewer identity will not be accepted, and the paper may be returned.

 We encourage authors to have their Dryad data package (data files, metadata, and ReadMe) prepared before submission, and to make these files available for review.