From the Editor’s Desk of The American Naturalist: October 2020

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

State-Dependent Decision-Making by Predators and Its Consequences for Mimicry

Thomas G. Aubier and Thomas N. Sherratt

Spite and the Geometry of Negative Relatedness

Philip G. Madgwick

Blog: https://www.amnat.org/an/newpapers/Nov-Madgwick.html

Host Plant Choice Determined by Reproductive Interference between Closely Related Butterflies

Naota Ohsaki, Masaaki Ohata, Yoshibumi Sato, and Mark D. Rausher

Blog: https://www.amnat.org/an/newpapers/Oct-Ohsaki.html

Relative Brain Size Is Predicted by the Intensity of Intrasexual Competition in Frogs

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

Blog: https://www.amnat.org/an/newpapers/Aug-Mai.html

FREE

Metabolic Rate Interacts with Resource Availability to Determine Individual Variation in Microhabitat Use in the Wild

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

What Do Ecology, Evolution, and Behavior Have in Common? The Organism in the Middle

Ellen D. Ketterson

The Ecology of Individual Differences Empirically Applied to Space-Use and Movement Tactics

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

Blog: https://www.amnat.org/an/newpapers/July-Webber.html

Maternal Investment, Ecological Lifestyle, and Brain Evolution in Sharks and Rays

Christopher G. Mull, Kara E. Yopak, and Nicholas K. Dulvy

Blog: https://www.amnat.org/an/newpapers/June-Mull.html

Age-Related Brood Parasitism and Egg Rejection in Magpie Hosts

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

Blog: https://www.amnat.org/an/newpapers/May-Martinez.html

FREE

Reinforcement Learning Theory Reveals the Cognitive Requirements for Solving the Cleaner Fish Market Task

Andrés E. Quiñones, Olof Leimar, Arnon Lotem, and Redouan Bshary

Blog: https://www.amnat.org/an/newpapers/Apr-Quinones.html

Safety Cues Can Give Prey More Valuable Information Than Danger Cues

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

Blurb: https://www.amnat.org/an/newpapers/Apr-Luttbeg.html

Note

Early Sibling Conflict May Ultimately Benefit the Family

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

Blurb: https://www.amnat.org/an/newpapers/Oct-Smith.html

Within-Individual Canalization Contributes to Age-Related Increases in Trait Repeatability: A Longitudinal Experiment in Red Knots

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

Blog: https://www.amnat.org/an/newpapers/Sep-Kok.html

Individual Variation in the Social Plasticity of Water Dragons

Kasha Strickland and Céline H. Frère

Assessing Behavioral Associations in a Hybrid Zone through Social Network Analysis: Complex Assortative Behaviors Structure Associations in a Hybrid Quail Population

David M. Zonana, Jennifer M. Gee, Eli S. Bridge, Michael D. Breed, and Daniel F. Doak

Blog: https://www.amnat.org/an/newpapers/JuneZonana.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

Lay summary: https://www.amnat.org/an/newpapers/JanPatin.html

October 15, 2020

Adaptation

Recent Papers

A Comparative Test for Divergent Adaptation: Inferring Speciation Drivers from Functional Trait Divergence

Sean A. S. Anderson and Jason T. Weir

Blurb: https://www.amnat.org/an/newpapers/Oct-Anderson.html

FREE

Evolution of Reproduction Periods in Seasonal Environments

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

Male-Male Competition Causes Parasite-Mediated Sexual Selection for Local Adaptation

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

Blog: https://www.amnat.org/an/newpapers/Sep-Gomez-Llano.html

The Origin and Spread of Locally Adaptive Seasonal Camouflage in Snowshoe Hares

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

Transformational Mimicry in a Myrmecomorphic Spider

Stano Pekár, Yun-Yun Tsai, and Radek Michalko

Selection and Constraints in the Ecomorphological Adaptive Evolution of the Skull of Living Canidae (Carnivora, Mammalia)

Fabio Andrade Machado

FREE

Metabolic Rate Interacts with Resource Availability to Determine Individual Variation in Microhabitat Use in the Wild

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

Survival Benefits of Group Living in a Fluctuating Environment

Sarah Guindre-Parker and Dustin R. Rubenstein

Blog: https://www.amnat.org/an/newpapers/June-Guindre-Parker.html

HISTORICAL PERSPECTIVE

The Adaptive Geometry of Trees Revisited

Thomas J. Givnish

Adaptive Maternal Investment in the Wild? Links between Maternal Growth Trajectory and Offspring Size, Growth, and Survival in Contrasting Environments

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

Blurb: https://www.amnat.org/an/newpapers/Apr-Burton.html

Belowground Competition Can Influence the Evolution of Root Traits

Sara M. Colom and Regina S. Baucom

Blog: https://www.amnat.org/an/newpapers/Apr-Colom.html

SYNTHESIS

Context Dependence of Local Adaptation to Abiotic and Biotic Environments: A Quantitative and Qualitative 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

Blog: https://www.amnat.org/an/newpapers/Mar-Briscoe-Runquist.html

SYNTHESIS

Local Adaptation to Biotic Interactions: A Meta-analysis across Latitudes

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

Blog: https://www.amnat.org/an/newpapers/Mar-Hargreaves.html

Evolution Transforms Pushed Waves into Pulled Waves

Philip Erm and Ben L. Phillips

Blurb: https://www.amnat.org/an/newpapers/Mar-Erm.html

Gene Flow Limits Adaptation along Steep Environmental Gradients

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

NATURAL HISTORY NOTE

Transitions between the Terrestrial and Epiphytic Habit Drove the Evolution of Seed-Aerodynamic Traits in Orchids

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

NOTE

Evolutionary Rescue from a Wave of Biological Invasion

J. David Van Dyken

The Evolution of Immigration Strategies Facilitates Niche Expansion by Divergent Adaptation in a Structured Metapopulation Model

Éva Kisdi, Helene C. Weigang, and Mats Gyllenberg

Blog: https://www.amnat.org/an/newpapers/Jan-Kisdi.html

FREE

Niche Construction Affects the Variability and Strength of Natural Selection

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

FREE

Why Do Phytoplankton Evolve Large Size in Response to Grazing?

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

Blurb: https://www.amnat.org/an/newpapers/Jan-Branco.html

Meta-analysis Shows That Rapid Phenotypic Change in Angiosperms in Response to Environmental Change Is Followed by Stasis

Lucas D. Gorné and Sandra Díaz

Introduction to Special Feature on Maladaptation

Understanding Maladaptation by Uniting Ecological and Evolutionary Perspectives

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

Maladaptive Shifts in Life History in a Changing Environment

Olivier Cotto, Linnea Sandell, Luis-Miguel Chevin, and Ophélie Ronce

Blurb: https://www.amnat.org/an/newpapers/AugCotto.html

Free Access, Special Feature on Maladaptation

Maladapted Prey Subsidize Predators and Facilitate Range Expansion

Mark C. Urban, Alice Scarpa, Justin M. J. Travis, and Greta Bocedi

Blog: https://www.amnat.org/an/newpapers/Oct-Urban.html

Special Feature on Maladaptation

Seed Masting Causes Fluctuations in Optimum Litter Size and Lag Load in a Seed Predator

Andrew G. McAdam, Stan Boutin, Ben Dantzer, and Jeffrey E. Lane

Special Feature on Maladaptation

Phenotypic Plasticity and Local Adaptation in a Wild Hibernator Evaluated through Reciprocal Translocation

Jeffrey E. Lane, Zenon J. Czenze, Rachel Findlay-Robinson, and Erin Bayne

(In)exhaustible Suppliers for Evolution? Epistatic Selection Tunes the Adaptive Potential of Nongenetic Inheritance

Etienne Rajon and Sylvain Charlat

Pulsed Immigration Events Can Facilitate Adaptation to Harsh Sink Environments

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

Blog: https://www.amnat.org/an/newpapers/Sep-Peniston.html

Phenotype-Environment Matching Predicts Both Positive and Negative Effects of Intraspecific Variation

Christopher J. Dibble and Volker H. W. Rudolf

Biotic Interactions Contribute to the Geographic Range Limit of an Annual Plant: Herbivory and Phenology Mediate Fitness beyond a Range Margin

John W. Benning, Vincent M. Eckhart, Monica A. Geber, and David A. Moeller

Blog: https://www.amnat.org/an/newpapers/JuneBenning.html

Adaptive Differences in Circadian Clock Gene Expression Patterns and Photoperiodic Diapause Induction in Nasonia vitripennis

Elena Dalla Benetta, Leo W. Beukeboom, and Louis van de Zande

Blog: https://www.amnat.org/an/newpapers/JuneDallaBenetta.html

Free Access, Synthesis

A Practical Guide to the Study of Distribution Limits

Yvonne Willi and Josh Van Buskirk

Blurb: https://www.amnat.org/an/newpapers/JuneWilli.html

Historical Comment

Revisiting a Key Innovation in Evolutionary Biology: Felsenstein’s “Phylogenies and the Comparative Method”

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

Free Access

The Evolutionary Ecology of Metamorphosis

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

Blog: https://www.amnat.org/an/newpapers/MayTenBrink.html

American Society of Naturalists Address

The Snail’s Charm

Kathleen Donohue

Evolutionary Consequences of Sex-Specific Selection in Variable Environments: Four Simple Models Reveal Diverse Evolutionary Outcomes

Tim Connallon, Shefali Sharma, and Colin Olito

Ecological Genetic Conflict: Genetic Architecture Can Shift the Balance between Local Adaptation and Plasticity

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

Lay summary: https://www.amnat.org/an/newpapers/JanLeimar.html

Open Access

Biophysical Modeling of Water Economy Can Explain Geographic Gradient of Body Size in Anurans

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

Lay summary: https://www.amnat.org/an/newpapers/JanGouveia.html

Population Variation, Environmental Gradients, and the Evolutionary Ecology of Plant Defense against Herbivory

Philip G. Hahn, Anurag A. Agrawal, Kira I. Sussman, and John L. Maron

Lay summary: https://www.amnat.org/an/newpapers/JanHahn.html

American Society of Naturalists Address

From the Past to the Future: Considering the Value and Limits of Evolutionary Prediction

Ruth G. Shaw

Life History

Recent Papers

The Size, Symmetry, and Color Saturation of a Male Guppy’s Ornaments Forecast His Resistance to Parasites

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

Blog: https://www.amnat.org/an/newpapers/Nov-Stephenson.html

Resistance Genes Affect How Pathogens Maintain Plant Abundance and Diversity

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

Male-Male Competition Causes Parasite-Mediated Sexual Selection for Local Adaptation

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

Blog: https://www.amnat.org/an/newpapers/Sep-Gomez-Llano.html

Defensive Symbiosis and the Evolution of Virulence

Paul Nelson and Georgiana May

Open Access

Deconstructing the Impact of Malaria Vector Diversity on Disease Risk

Amber Gigi Hoi, Benjamin Gilbert, and Nicole Mideo

Blog: https://www.amnat.org/an/newpapers/Sep-Hoi.html

Parasitism Risk and Infection Alter Host Dispersal

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

Blog: https://www.amnat.org/an/newpapers/Aug-Baines.html

Open Access

Host Transcriptional Responses to High- and Low-Virulent Avian Malaria Parasites

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

Blog: https://www.amnat.org/an/newpapers/June-Videvall.html

Vertical Transmission of a Nematode from Female Lizards to the Brains of Their Offspring

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

Blog: https://www.amnat.org/an/newpapers/May-Feiner.html

Individual Specialization and Multihost Epidemics: Disease Spread in Plant-Pollinator Networks

Stephen P. Ellner, Wee Hao Ng, and Christopher R. Myers

Blog: https://www.amnat.org/an/newpapers/May-Ellner.html

An Empirical Test of the Role of Small-Scale Transmission in Large-Scale Disease Dynamics

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

Thermal Variability and Plasticity Drive the Outcome of a Host-Pathogen Interaction

Laura V. Ferguson and Brent J. Sinclair

Blog: https://www.amnat.org/an/newpapers/Apr-Ferguson.html

Pathogens and Mutualists as Joint Drivers of Host Species Coexistence and Turnover: Implications for Plant Competition and Succession

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

Blurb: https://www.amnat.org/an/newpapers/Apr-Jiang.html

Stochasticity and Infectious Disease Dynamics: Density and Weather Effects on a Fungal Insect Pathogen

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

Fecundity-Longevity Trade-Off, Vertical Transmission, and Evolution of Virulence in Sterilizing Pathogens

Eva Janoušková and Luděk Berec

Can Community Structure Causally Determine Dynamics of Constituent Species? A Test Using a Host-Parasite Community

Ryan E. Langendorf and Daniel F. Doak

Blurb: https://www.amnat.org/an/newpapers/Sep-Langendorf.html

Host Responses to Foreign Eggs across the Avian Visual Color Space

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

Blog: https://www.amnat.org/an/newpapers/JulyHanley.html

The Critical Role of Infectious Disease in Compensatory Population Growth in Response to Culling

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

Trait-Based Modeling of Multihost Pathogen Transmission: Plant-Pollinator Networks

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

Blog: https://www.amnat.org/an/newpapers/JuneTruitt.html

Predicting the Thermal and Allometric Dependencies of Disease Transmission via the Metabolic Theory of Ecology

Devin Kirk, Pepijn Luijckx, Andrijana Stanic, and Martin Krkošek

Blurb: https://www.amnat.org/an/newpapers/MayKirk.html

Within-Host Priority Effects Systematically Alter Pathogen Coexistence
Patrick A. Clay, Kailash Dhir, Volker H. W. Rudolf, and Meghan A. Duffy
Lay summary: https://www.amnat.org/an/newpapers/FebClay.html

Sexual Conflict and Sexually Transmitted Infections (STIs): Coevolution of Sexually Antagonistic Host Traits with an STI
Alison M. Wardlaw and Aneil F. Agrawal

From the Editor’s Desk of
The American Naturalist

October 23, 2020

Data archiving

October 16, 2020

Behavioral Ecology

Recent Papers

October 15, 2020

Adaptation

Recent Papers

Life History

Recent Papers

Evolutionary Dynamics

Recent Papers

Natural Selection

Recent Papers

Host-Parasite Interactions

Recent Papers