October 23, 2020

Data archiving

The following is a guest post by Bob Montgomerie, Queens University

The text was posted, lightly edited, and approved by the Editor In Chief, Dan Bolnick

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. 
 
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.
 
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:
•         no README (or any other) file explaining the variable names in data files
•         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
•         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
•         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.
•         no R, Python or other scripts or notebooks to replicate the analyses
•         analysis code not well-enough annotated to be comprehensible
•         code that does not run, presumably created in earlier versions of the software with unknown packages and package versions
 
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.
 
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.

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.,daniel.bolnick@uconn.edu). 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. 

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.

October 16, 2020

Behavioral Ecology

Recent Papers

Chun Lan Mai (麦春兰), Wen Bo Liao (廖文波), Stefan Lüpold, and Alexander Kotrschal

FREE
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

FREE, AMERICAN SOCIETY OF NATURALISTS ADDRESS
Ellen D. Ketterson

Quinn M. R. Webber, Michel P. Laforge, Maegwin Bonar, Alec L. Robitaille, Christopher Hart, Sana Zabihi-Seissan, and Eric Vander Wal

Juan Gabriel Martínez, Mercedes Molina-Morales, Marta Precioso, and Jesús Miguel Avilés

Note
Alyssa Laney Smith, Daniel Z. Atwater, and Ragan M. Callaway

Eva M. A. Kok, Joseph B. Burant, Anne Dekinga, Petra Manche, Darren Saintonge, Theunis Piersma, and Kimberley J. Mathot

Rémi Patin, Daniel Fortin, Cédric Sueur, and Simon Chamaillé-Jammes

October 15, 2020

Adaptation

Recent Papers 


FREE
Zepeng Sun, Kalle Parvinen, Mikko Heino, Johan A. J. Metz, André M. de Roos, and Ulf Dieckmann

Miguel Gómez-Llano, Aaditya Narasimhan, and Erik I. Svensson

Matthew R. Jones, L. Scott Mills, Jeffrey D. Jensen, and Jeffrey M. Good

Stano Pekár, Yun-Yun Tsai, and Radek Michalko


FREE
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

Sarah Guindre-Parker and Dustin R. Rubenstein

HISTORICAL PERSPECTIVE
Thomas J. Givnish

Tim Burton, Njal Rollinson, Simon McKelvey, David C. Stewart, John D. Armstrong, and Neil B. Metcalfe


SYNTHESIS
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

SYNTHESIS
Anna L. Hargreaves, Rachel M. Germain, Megan Bontrager, Joshua Persi, and Amy L. Angert


Judith C. Bachmann, Alexandra Jansen van Rensburg, Maria Cortazar-Chinarro, Anssi Laurila, and Josh Van Buskirk

NATURAL HISTORY NOTE
Xu-Li Fan, Guillaume Chomicki, Kai Hao, Qiang Liu, Ying-Ze Xiong, Susanne S. Renner, Jiang-Yun Gao, and Shuang-Quan Huang
ORCIDs: Fan, https://orci



FREE
Andrew D. Clark, Dominik Deffner, Kevin Laland, John Odling-Smee, and John Endler

FREE
Pedro Branco, Martijn Egas, Spencer R. Hall, and Jef Huisman


Introduction to Special Feature on Maladaptation
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

Free Access, Special Feature on Maladaptation
Olivier Cotto, Linnea Sandell, Luis-Miguel Chevin, and Ophélie Ronce

Free Access, Special Feature on Maladaptation
Mark C. Urban, Alice Scarpa, Justin M. J. Travis, and Greta Bocedi

Special Feature on Maladaptation
Andrew G. McAdam, Stan Boutin, Ben Dantzer, and Jeffrey E. Lane

Special Feature on Maladaptation
Jeffrey E. Lane, Zenon J. Czenze, Rachel Findlay-Robinson, and Erin Bayne


James H. Peniston, Michael Barfield, and Robert D. Holt

Christopher J. Dibble and Volker H. W. Rudolf



Free Access, Synthesis
Yvonne Willi and Josh Van Buskirk

Historical Comment
Raymond B. Huey, Theodore Garland Jr., and Michael Turelli

Free Access
Hanna ten Brink, André M. de Roos, and Ulf Dieckmann

American Society of Naturalists Address
Kathleen Donohue


Olof Leimar, Sasha R. X. Dall, John M. McNamara, Bram Kuijper, and Peter Hammerstein

Open Access
Sidney F. Gouveia, Rafael P. Bovo, Juan G. Rubalcaba, Fernando Rodrigues Da Silva, Natan M. Maciel, Denis V. Andrade, and Pablo Ariel Martinez


Life History

Recent Papers

NATURAL HISTORY NOTE
Adam E. Mitchell, Jordan Boersma, Anthonio Anthony, Kanehiro Kitayama, and Thomas E. Martin


Christopher Blackford, Rachel M. Germain, and Benjamin Gilbert

Patrick M. Barks and Robert A. Laird

Juan Gabriel Martínez, Mercedes Molina-Morales, Marta Precioso, and Jesús Miguel Avilés


SYNTHESIS
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

NOTE
Cynthia J. Downs, Ned A. Dochtermann, Ray Ball, Kirk C. Klasing, and Lynn B. Martin


FREE
Adam T. Bakewell, Katie E. Davis, Robert P. Freckleton, Nick J. B. Isaac, and Peter J. Mayhew

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


Special Feature on Maladaptation
Andrew G. McAdam, Stan Boutin, Ben Dantzer, and Jeffrey E. Lane




Michał Bogdziewicz, Magdalena Żywiec, Josep M. Espelta, Marcos Fernández-Martinez, Rafael Calama, Mateusz Ledwoń, Eliot McIntire, and Elizabeth E. Crone

Alycia C. R. Lackey, Michael P. Moore, Jacqueline Doyle, Nicole Gerlanc, Ashley Hagan, Morgan Geile, Chris Eden, and Howard H. Whiteman

Open Access, Special Feature on Maladaptation
Olivier Cotto, Linnea Sandell, Luis-Miguel Chevin, and Ophélie Ronce

Synthesis
Nathan I. Wisnoski, Mathew A. Leibold, and Jay T. Lennon

Lea M. Callan, Frank A. La Sorte, Thomas E. Martin, and Vanya G. Rohwer

E. Keith Bowers, Jonathan B. Jenkins, Alexander J. Mueller, Kelly D. Miller, Charles F. Thompson, and Scott K. Sakaluk


Oscar Vedder, He Zhang, Andreas Dänhardt, and Sandra Bouwhuis

Note (an F1000 recommendation as Exceptional)
David T. Iles, Robert F. Rockwell, and David N. Koons

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

Evolutionary Dynamics

Recent Papers

Louis Paul Decena-Segarra, Lilijana Bizjak-Mali, Aleš Kladnik, Stanley K. Sessions, and Sean M. Rovito

FREE
Zepeng Sun, Kalle Parvinen, Mikko Heino, Johan A. J. Metz, André M. de Roos, and Ulf Dieckmann


FREE; AMERICAN SOCIETY OF NATURALISTS ADDRESS
Ellen D. Ketterson


Kristin L. Sikkink, Reilly Hostager, Megan E. Kobiela, Nathan Fremling, Katherine Johnston, Amod Zambre, and Emilie C. Snell-Rood




Open Access
Diana Jessie Rennison, Kira E. Delmore, Kieran Samuk, Gregory L. Owens, and Sara E. Miller

Note
Alyssa Laney Smith, Daniel Z. Atwater, and Ragan M. Callaway

Maxime Deforet, Carlos Carmona-Fontaine, Kirill S. Korolev, and Joao B. Xavier

Alycia C. R. Lackey, Michael P. Moore, Jacqueline Doyle, Nicole Gerlanc, Ashley Hagan, Morgan Geile, Chris Eden, and Howard H. Whiteman



Open Access


Open Access

Open Access
Hanna ten Brink, André M. de Roos, and Ulf Dieckmann




American Society of Naturalists Address
Kathleen Donohue


Natural Selection

Recent Papers

Chiara Morosinotto, Jon E. Brommer, Atte Lindqvist, Kari Ahola, Esa Aaltonen, Teuvo Karstinen, and Patrik Karell





Synthesis
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

Synthesis
Anna L. Hargreaves, Rachel M. Germain, Megan Bontrager, Joshua Persi, and Amy L. Angert


Andrew D. Clark, Dominik Deffner, Kevin Laland, John Odling-Smee, and John Endler


Emily M. McLean, Elizabeth A. Archie, and Susan C. Alberts

Special Feature on Maladaptation
Andrew G. McAdam, Stan Boutin, Ben Dantzer, and Jeffrey E. Lane





Open Access


American Society of Naturalists Address

Host-Parasite Interactions

Recent Papers

Jessica F. Stephenson, Martin Stevens, Jolyon Troscianko, and Jukka Jokela

Simon Maccracken Stump, James H. Marden, Noelle G. Beckman, Scott A. Mangan, and Liza S. Comita

Miguel Gómez-Llano, Aaditya Narasimhan, and Erik I. Svensson


Open Access
Amber Gigi Hoi, Benjamin Gilbert, and Nicole Mideo

Celina B. Baines, Salma Diab, and Shannon J. McCauley

Open Access
Elin Videvall, Vaidas Palinauskas, Gediminas Valkiūnas, and Olof Hellgren

Nathalie Feiner, Sueli de Souza-Lima, Fátima Jorge, Soraya Naem, Fabien Aubret, Tobias Uller, and Steven A. Nadler


Joseph R. Mihaljevic, Carlos M. Polivka, Constance J. Mehmel, Chentong Li, Vanja Dukic, and Greg Dwyer


Jiang Jiang, Karen C. Abbott, Mara Baudena, Maarten B. Eppinga, James A. Umbanhowar, and James D. Bever

Colin H. Kyle, Jiawei Liu, Molly E. Gallagher, Vanja Dukic, and Greg Dwyer



Daniel Hanley, Karel Gern, Mark E. Hauber, and Tomáš Grim

Eleanor Tanner, Andy White, Peter W. W. Lurz, Christian Gortázar, Iratxe Díez-Delgado, and Mike Boots

Lauren L. Truitt, Scott H. McArt, Andrew H. Vaughn, and Stephen P. Ellner


September 29, 2020

Paleobiology

Recent Papers 


Open Access
Clarke A. Knight, Jessica L. Blois, Benjamin Blonder, Marc Macias-Fauria, Alejandro Ordonez, and Jens-Christian Svenning



Predator-Prey Interactions

Recent Papers


John P. DeLong

Henry D. Legett, Claire T. Hemingway, and Ximena E. Bernal


Barney Luttbeg, Maud C. O. Ferrari, Daniel T. Blumstein, and Douglas P. Chivers


Javier Jarillo, Bernt-Erik Sæther, Steinar Engen, and Francisco Javier Cao-García


David J. S. Montagnes, Xuexia Zhu, Lei Gu, Yunfei Sun, Jun Wang, Rosie Horner, and Zhou Yang


Open Access
William J. Resetarits, Matthew R. Pintar, Jason R. Bohenek, and Tyler M. Breech

Open Access; Special Feature on Maladaptation
Mark C. Urban, Alice Scarpa, Justin M. J. Travis, and Greta Bocedi

Special Feature on Maldaptation
Andrew G. McAdam, Stan Boutin, Ben Dantzer, and Jeffrey E. Lane


Natural History Note
Jimena Golcher-Benavides and Catherine E. Wagner

Lea M. Callan, Frank A. La Sorte, Thomas E. Martin, and Vanya G. Rohwer


Sean M. Ehlman, Pete C. Trimmer, and Andrew Sih

Open Access
Henri Berestycki and Alessandro Zilio

Open Access
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



Natural History Note
Testing Darwin’s Hypothesis about the Wonderful Venus Flytrap: Marginal Spikes Form a “Horrid Prison” for Moderate-Sized Insect Prey
Alexander L. Davis, Matthew H. Babb, Matthew C. Lowe, Adam T. Yeh, Brandon T. Lee, and Christopher H. Martin
Summary: https://www.amnat.org/an/newpapers/FebDavis.html

Space Use and Leadership Modify Dilution Effects on Optimal Vigilance under Food-Safety Trade-Offs
Rémi Patin, Daniel Fortin, Cédric Sueur, and Simon Chamaillé-Jammes
Summary: https://www.amnat.org/an/newpapers/JanPatin.html

Celebrating The American Naturalist at 150, Open Access
Specifying the Harsh Conditions of Life: Resource Competition and Predation in the 1970s
Alita R. Burmeister and Richard E. Lenski

Demography

Recent Papers

Shelly Lachish, Ellen E. Brandell, Meggan E. Craft, Andrew P. Dobson, Peter J. Hudson, Daniel R. MacNulty, and Tim Coulson

Patrick M. Barks and Robert A. Laird




Note
Aaron S. David, Pedro F. Quintana-Ascencio, Eric S. Menges, Khum B. Thapa-Magar, Michelle E. Afkhami, and Christopher A. Searcy



Gaurav Baruah, Christopher F. Clements, Frédéric Guillaume, and Arpat Ozgul


Alan G. Leach, James S. Sedinger, Thomas V. Riecke, Amanda W. Van Dellen, David H. Ward, and W. Sean Boyd

Open Access
Niklas L. P. Lundström, Nicolas Loeuille, Xinzhu Meng, Mats Bodin, and Åke Brännström

Open Access
Emilius A. Aalto, Fiorenza Micheli, Charles A. Boch, Jose A. Espinoza Montes, C. Broch Woodson, and Giulio A. De Leo


Arne Jungwirth and Rufus A. Johnstone

Andrew W. Bateman, Arpat Ozgul, Martin Krkošek, and Tim H. Clutton-Brock


Macroevolution


Valentine Federico, Dominique Allainé, Jean-Michel Gaillard, and Aurélie Cohas

Tania Hernández-Hernández and John J. Wiens

Open Access
Kjetil Lysne Voje, Emanuela Di Martino, and Arthur Porto

Andrew J. Tanentzap, Javier Igea, Matthew G. Johnston, and Matthew J. Larcombe

Alberto Martín-Serra and Roger B. J. Benson

Open Access, Symposium
Emma E. Goldberg and Jasmine Foo

Xu-Li Fan, Guillaume Chomicki, Kai Hao, Qiang Liu, Ying-Ze Xiong, Susanne S. Renner, Jiang-Yun Gao, and Shuang-Quan Huang

Adrien Perrard

Beatriz Willink, M. Catherine Duryea, and Erik I. Svensson

Karl Loeffler-Henry, Changku Kang, and Thomas N. Sherratt

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

Historical Perspective
Raymond B. Huey, Theodore Garland Jr., and Michael Turelli