June 15, 2017

Online-Only Material in Am Nat

If you are looking at online-only material and wondering how The American Naturalist might handle it, here is a quick guide:
  1. Is it essential to telling the article’s story clearly? Then it should be part of the article (or possibly be a separate print appendix). Papers can be as long as they need to be—but not any longer.
  2. Is it essential for replicating the paper? Is it something a reader will want to see 30 years from now? Then it should be in the appendix—in the source file, edited, and typeset.
  3. Is it nice but not necessary? Is it a format that can’t be printed on a piece of standard paper? Is it so extensive that it’s prohibitively expensive? Is it laid out in such a way that redoing it makes little sense? Then it should be in author-supplied file formats.
  4. Is it code? Then it’s in author-supplied files. Is it data? Then it’s in Dryad.

Here's why we do what we do...

We handle online-only material differently from many other journals, so it seemed like a good idea to explain why we do what we do. First though, it’s useful to look at the 20 years I’ve been managing editor and see the problems I've already witnessed. We had supplementary files in Excel back in 1998. Microsoft no longer supports Excel 1993 so proprietary software is a liability. We have moved every file (thousands of them) to new platforms three times. Files that aren’t integrated can be misplaced. We have systems to track them down and repost them, but over time, inevitably, this will be harder and harder. Data archiving policies have been developed, and alternative workflows for scientists, particularly with commercial sites, have developed, so the landscape is more complicated. Commercial sites (e.g., GitHub or FigShare), even if they aren’t particularly oriented toward profit, are financed by venture capital and are at the mercy of market forces and may not have the same kind of institutional commitment to long-term access and preservation, so they aren't a clear alternative.

So here is a breakdown of how we handle online-only material.

Appendixes

Back in 2003, we had a terrible backlog of papers. To try to squeeze in more papers into our print page budget, we decided to move the appendixes for papers from print, where they had always been, to be online-only appendixes. However, often these appendixes are essential for replication or for understanding the breakdown of the math. The University of Chicago Press was one of the first presses to have an electronic edition, and it had worked up its definition of the best practices for preservation. The Press determined that online-only appendixes had to be in the same source file as the main text, they should be edited and typeset for consistency with the article and for clarity, and they would be preserved for as long as the article itself would be preserved. The journal hopes to still be publishing for the next 150 years. The questions we ask about supplementary material, therefore, are, Does this material need to be preserved? What is the consequence if this material became unusable or lost 30 years from now? Will editing and typesetting this material make it less clear? Because figures are processed for the best quality possible, the tables are edited, and the math typeset, appendixes use up expensive and limited resources (people) and so there are page charges for appendixes (which can be waived with the other page charges). An appendix, if it is short or very useful, may still be printed in the journal. We may also print a short essential appendix (e.g., a table defining the variables) and put other appendix material online only.

Other Supplementary Materials

Supplementary materials generally are nice but not necessary. Separate files supplied by the authors, particularly separate files in proprietary formats, are detachable and “losable,” may not be usable as the owner of the proprietary software upgrades, and are not always well edited and well presented. However, in the time since 2003, authors have gotten used to the idea of putting all kinds of materials related to a paper online at no cost, so it’s sometimes not clear what needs very long-term preservation (i.e., appendix style) or what is informative but not as necessary. In addition, there are items such as massive excel tables, code that is better in its original file format, or files that are just not typesettable, like video or sound files. Material may also be at other locations (e.g., GitHub or FigShare) but the best practice is to have information, especially code essential for replicating the paper, together in one place with the article. Our goal is preservation that is as long-term as possible and that is not dependent on the vagaries of the venture capital marketplace. We post any author-supplied files (posted in the original format supplied) at no charge.

Data Archiving

In 2010, journals in ecology and evolutionary biology agreed to enforce the Data Archiving policy, originally proposed by the NSF and made possible by the development of Dryad. See the announcement of the policy here: http://www.journals.uchicago.edu/doi/full/10.1086/650340. I happened to attend the initial meeting launching the project in 2005—so I remember that the idea was two-fold: providing the necessary information so that a study could be replicated and preserving data into the future. The image they kept using in 2005 was the researcher who retired, turned off her computer, and lost a life-time of irreplaceable information. As a result, the journal requires that data be archived in Dryad or a noncommercial data repository that is open (or accessible) and that is designed for long-term preservation. Dryad can also host other materials related to the article. The journal article has an active link to Dryad and Dryad has an active link to the article so the connection is clear. Data files may also be stored with the article at UCP but they must be archived at Dryad. The American Society of Naturalists covers the costs (via a change in the page charge structure).

References in Appendixes

As of 2016, we are requiring that references cited in the appendixes be printed in the main body of the article. In pursuing a question about how the field’s reliance on the impact factor was creating its own impact on research, it became very clear that original research was not getting its just due. Lists of references in author-supplied files are not counted as citations by Google Scholar or by Web of Science. Google Scholar counts cites in our form of appendix (i.e., mining the html tagging) but Web of Science counts only the Literature Cited in the main PDF. We wish to support original research so we commit pages to printing the references. Occasionally a meta-analysis paper presents a reference list that becomes prohibitively expensive to print, but we’ve hit only one of those since this policy began.

Patricia Morse
Managing Editor

June 7, 2017

Syntheses and Perspectives

The Synthesis and Perspectives section publishes visionary re-evaluations designed to move fields of ecology, evolution, and behavior forward.


Predicting Responses to Contemporary Environmental Change Using Evolutionary Response Architectures
Rachael A. Bay, Noah Rose, Rowan Barrett, Louis Bernatchez, Cameron K. Ghalambor, Jesse R. Lasky, Rachel B. Brem, Stephen R. Palumbi, and Peter Ralph (OPEN ACCESS)

Fundamental Theorems of Evolution, David C. Queller (2017, OPEN ACCESS)


Shaping the Latitudinal Diversity Gradient: New Perspectives from a Synthesis of Paleobiology and Biogeography, David Jablonski, Shan Huang, Kaustuv Roy, and James W. Valentine (2017)

The Case of the Missing Ancient Fungal Polyploids, Matthew A. Campbell, Austen R. D. Ganley, Toni Gabaldón, and Murray P. Cox (2016) [OPEN ACCESS] 

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions (Sean Hoban, Joanna L. Kelley, Katie E. Lotterhos, Michael F. Antolin, Gideon Bradburd, David B. Lowry, Mary L. Poss, Laura K. Reed, Andrew Storfer, and Michael C. Whitlock 2016) [OPEN ACCESS] 

An Integrative Framework for the Assessment of Coloration in Nature (Kemp et al., 2015) [OPEN ACCESS]

Coevolution and the Diversification of Life (Hembry et al., 2014)

Dinosaur Energetics: Setting the Bounds on Feasible Physiologies and Ecologies (Clarke, 2013)

Enemies Maintain Hyperdiverse Tropical Forests (Terborgh, 2012)

A Unified Approach to the Evolutionary Consequences of Genetic and Nongenetic Inheritance (Day and Bonduriansky, 2011) [OPEN ACCESS]

See  http://www.journals.uchicago.edu/journals/an/instruct for details and submission instructions. A short proposal is required for Syntheses and Perspectives; it will be given full and constructive attention.

In addition to Syntheses and Perspectives, we publish Primary Research with either an empirical or theoretical focus, as well as Natural History reports. We are seeking papers with a basic orientation whose impact extends well beyond the focal system, and that address broad, novel, and conceptually oriented issues and methods in ecology, evolution and behavior.

June 6, 2017

Recent Papers on Population Genetics

Clines Arc through Multivariate Morphospace
Brian K. Lohman, Daniel Berner, and Daniel I. Bolnick

Open Access, Synthesis
Fundamental Theorems of Evolution
David C. Queller

Hormonally Mediated Increases in Sex-Biased Gene Expression Accompany the Breakdown of Between-Sex Genetic Correlations in a Sexually Dimorphic Lizard
Robert M. Cox, Christian L. Cox, Joel W. McGlothlin, Daren C. Card, Audra L. Andrew, and Todd A. Castoe
Lay summaryhttp://amnat.org/an/newpapers/MarCox.html

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

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

Open Access, Synthesis
The Case of the Missing Ancient Fungal Polyploids
Matthew A. Campbell, Austen R. D. Ganley, Toni Gabaldón, and Murray P. Cox
Lay summary: http://amnat.org/an/newpapers/DecCampbell.html

Recent Papers on Morphological Evolution

Natural History Note
A Sea Scorpion’s Strike: New Evidence of Extreme Lateral Flexibility in the Opisthosoma of Eurypterids
W. Scott Persons IV and John Acorn
Lay summary: http://amnat.org/an/newpapers/JulyPersons.html

How Parallel Is Parallel Evolution? A Comparative Analysis in Fishes
Krista B. Oke, Gregor Rolshausen, Caroline LeBlond, and Andrew P. Hendry
Lay summary: http://amnat.org/an/newpapers/JulyOke.html

Evolutionary Determinants of Morphological Polymorphism in Colonial Animals
Carl Simpson, Jeremy B. C. Jackson, and Amalia Herrera-Cubilla

Natural History Note
The Hawk-Eyed Songbird: Retinal Morphology, Eye Shape, and Visual Fields of an Aerial Insectivore
Luke P. Tyrrell and Esteban Fernández-Juricic

Clines Arc through Multivariate Morphospace
Brian K. Lohman, Daniel Berner, and Daniel I. Bolnick

Color Change for Thermoregulation versus Camouflage in Free-Ranging Lizards
Kathleen R. Smith, Viviana Cadena, John A. Endler, Michael R. Kearney, Warren P. Porter, and Devi Stuart-Fox
Lay summary: http://amnat.org/an/newpapers/DecSmith.html

Note
Large Brains, Small Guts: The Expensive Tissue Hypothesis Supported within Anurans
Wen Bo Liao, Shang Ling Lou, Yu Zeng, and Alexander Kotrschal
Lay Summary: http://amnat.org/an/newpapers/DecLiao.html

Natural History Note
Behavioral Plasticity and the Origins of Novelty: The Evolution of the Rattlesnake Rattle
Bradley C. Allf, Paul A. P. Durst, and David W. Pfennig
Lay summary: http://amnat.org/an/newpapers/OctAllf.html


Recent Papers in Reproductive Evolution

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

Open Access
Evolution of Inbreeding Avoidance and Inbreeding Preference through Mate Choice among Interacting Relatives
A. Bradley Duthie and Jane M. Reid
Lay summary: http://amnat.org/an/newpapers/DecDuthie.html

Open Access
The Evolution of Mutual Mate Choice under Direct Benefits
Alexandre Courtiol, Loïc Etienne, Romain Feron, Bernard Godelle, and François Rousset
Lay summary: http://amnat.org/an/newpapers/NovCourtiol.html

Effects of Prior Contest Experience and Contest Outcome on Female Reproductive Decisions and Offspring Fitness
Natalie Pilakouta, Cerian Halford, Rita Rácz, and Per T. Smiseth
Lay summary: http://amnat.org/an/newpapers/SepPilakouta.html

Tissue Specificity and Sex-Specific Regulatory Variation Permit the Evolution of Sex-Biased Gene Expression
Rebecca Dean and Judith E. Mank

Alternative Reproductive Tactics in Context: How Demography, Ecology, and Behavior Affect Male Mating Success
John T. Rotenberry and Marlene Zuk

How Have Self-Incompatibility Haplotypes Diversified? Generation of New Haplotypes during the Evolution of Self-Incompatibility from Self-Compatibility
Satoki Sakai

Sneaker Males Affect Fighter Male Body Size and Sexual Size Dimorphism in Salmon
Laura K. Weir, Holly K. Kindsvater, Kyle A. Young, and John D. Reynolds
Lay summary: http://amnat.org/an/newpapers/AugWeir.html

Intralocus Sexual Conflict and the Tragedy of the Commons in Seed Beetles
David Berger, Ivain Martinossi-Allibert, Karl Grieshop, Martin I. Lind, Alexei A. Maklakov, and Göran Arnqvist
Lay summary: http://amnat.org/an/newpapers/OctBerger.html



May 8, 2017

Recent Papers on Predator-Prey Interactions

Seasonally varying predation behavior and climate shifts are predicted to affect predator-prey cycles
Rebecca Tyson1and Frithjof Lutscher

Michael H. Cortez

Choosy cannibals preferentially consume siblings with relatively low fitness prospects
Matthew B. Dugas, Larkin McCormack, Alice Gadau, and Ryan A. Martin

Historical Comment
Revisiting Paine’s 1966 Sea Star Removal Experiment, the Most-Cited Empirical Article in the American Naturalist
Kevin D. Lafferty and Thomas H. Suchanek

Mimicry among Unequally Defended Prey Should Be Mutualistic When Predators Sample Optimally
Thomas G. Aubier, Mathieu Joron, and Thomas N. Sherratt
Lay summary: http://amnat.org/an/newpapers/MarAubier.html

Does Cohistory Constrain Information Use? Evidence for Generalized Risk Assessment in Nonnative Prey
Emily W. Grason
Lay summaryhttp://amnat.org/an/newpapers/MarGrason.html

Behavioral Hypervolumes of Predator Groups and Predator-Predator Interactions Shape Prey Survival Rates and Selection on Prey Behavior
Jonathan N. Pruitt, Kimberly A. Howell, Shaniqua J. Gladney, Yusan Yang, James L. L. Lichtenstein, Michelle Elise Spicer, Sebastian A. Echeverri, and Noa Pinter-Wollman

Fear Mediates Trophic Cascades: Nonconsumptive Effects of Predators Drive Aquatic Ecosystem Function
Crasso Paulo B. Breviglieri, Paulo S. Oliveira, and Gustavo Q. Romero
Lay summary: http://amnat.org/an/newpapers/MayBrevigl.html

Natural History Note
Ecological Release from Aquatic Predation Is Associated with the Emergence of Marine Blenny Fishes onto Land
Terry J. Ord, Thomas C. Summers, Mae M. Noble, and Christopher J. Fulton
Lay summary: http://amnat.org/an/newpapers/MayOrd.html

April 5, 2017

Recent Papers in Evolutionary Dynamics

Eco-Evolutionary Theory and Insect Outbreaks
David J. Páez, Vanja Dukic, Jonathan Dushoff, Arietta Fleming-Davies, and Greg Dwyer
Lay summary: http://amnat.org/an/newpapers/JunePaez.html

Open Access
What Kind of Maternal Effects Can Be Selected for in Fluctuating Environments?
Stephen R. Proulx and Henrique Teotónio
Lay summaryhttp://amnat.org/an/newpapers/JuneProulx.html

Open Access, Synthesis
Fundamental Theorems of Evolution
David C. Queller

Evolution of Thermal Reaction Norms in Seasonally Varying Environments
Priyanga Amarasekare and Christopher Johnson

Open Access
Poison Frog Colors Are Honest Signals of Toxicity, Particularly for Bird Predators
Martine E. Maan and Molly E. Cummings
Lay summary: http://amnat.org/an/newpapers/JanMaan.html

Open Access
Evolution of Inbreeding Avoidance and Inbreeding Preference through Mate Choice among Interacting Relatives
A. Bradley Duthie and Jane M. Reid
Lay summaryhttp://amnat.org/an/newpapers/DecDuthie.html

Epistasis-Induced Evolutionary Plateaus in Selection Responses
Arnaud Le Rouzic and José M. Álvarez-Castro
Lay summary: http://amnat.org/an/newpapers/DecLeRouzic.html

Open Access
The Evolution of Mutual Mate Choice under Direct Benefits
Alexandre Courtiol, Loïc Etienne, Romain Feron, Bernard Godelle, and François Rousset
Lay summary: http://amnat.org/an/newpapers/NovCourtiol.html

Adaptive Value and Costs of Physiological Plasticity to Soil Moisture Limitation in Recombinant Inbred Lines of Avena barbata
Hafiz Maherali, Christina M. Caruso, Mark E. Sherrard and Robert G. Latta

“Does genetic variation maintained by environmental heterogeneity facilitate adaptation to novel selection?”
Yuheng Huang, Ivan Tran, and Aneil F. Agrawal

“Evolutionary stability of jointly evolving traits in subdivided populations”
Charles Mullon, Laurent Keller, and Laurent Lehmann

“The influence of evolution on population spread through patchy landscapes”
Jennifer L. Williams, Robin E. Snyder, and Jonathan M. Levine

“How the magnitude of prey genetic variation alters predator-prey eco-evolutionary dynamics”
Michael H. Cortez

Recent Papers in Behavioral Ecology

Why Have Multiple Plastic Responses? Interactions between Color Change and Heat Avoidance Behavior in Battus Philenor Larvae
Matthew E. Nielsen and Daniel R. Papaj
Lay summary: http://amnat.org/an/newpapers/JuneNielsen.html

Natural History Note
A Waterborne Pursuit-Deterrent Signal Deployed by a Sea Urchin
Hannah Sheppard-Brennand, Alistair G. B. Poore, and Symon A. Dworjanyn

Re-Examining the Causes and Meaning of the Risk Allocation Hypothesis
Barney Luttbeg

Timing of Breeding in an Ecologically Trapped Bird
Franck A. Hollander, Nicolas Titeux, Marie-Jeanne Holveck, and Hans Van Dyck
Lay summaryhttp://amnat.org/an/newpapers/MayHollander.html

Fitness Consequences of Boldness in Juvenile and Adult Largemouth Bass
Nicholas G. Ballew, Gary G. Mittelbach, and Kim T. Scribner
Lay summary: http://amnat.org/an/newpapers/AprBallew.html

Behavioral Hypervolumes of Predator Groups and Predator-Predator Interactions Shape Prey Survival Rates and Selection on Prey Behavior
Jonathan N. Pruitt, Kimberly A. Howell, Shaniqua J. Gladney, Yusan Yang, James L. L. Lichtenstein, Michelle Elise Spicer, Sebastian A. Echeverri, and Noa Pinter-Wollman

The Behavioral Type of a Top Predator Drives the Short-Term Dynamic of Intraguild Predation
Radek Michalko and Stano Pekár
Lay summaryhttp://amnat.org/an/newpapers/MarMichalko.html

From Individual to Group Territoriality: Competitive Environments Promote the Evolution of Sociality
Markus Port, Oliver Schülke, and Julia Ostner
Lay summaryhttp://amnat.org/an/newpapers/MarPort.html

Naive Juveniles Are More Likely to Become Breeders after Witnessing Predator Mobbing
Michael Griesser and Toshitaka N. Suzuki
Lay summaryhttp://amnat.org/an/newpapers/JanGriesser.html

Alternative Reproductive Tactics in Context: How Demography, Ecology, and Behavior Affect Male Mating Success
John T. Rotenberry and Marlene Zuk

Natural History Note
Busy Nights: High Seed Dispersal by Crickets in a Neotropical Forest
Flávia Delgado Santana, Fabricio Beggiato Baccaro, and Flávia Regina Capellotto Costa
Lay summary: http://amnat.org/an/newpapers/NovSantana.html

Natural History Note
Collective Response of Leaf-Cutting Ants to the Effects of Wind on Foraging Activity
Andrea Marina Alma, Alejandro G. Farji-Brener, and Luciana Elizalde
Lay summary: http://amnat.org/an/newpapers/NovAlma.html

Choosy cannibals preferentially consume siblings with relatively low fitness prospects
Matthew B. Dugas, Larkin McCormack, Alice Gadau, and Ryan A. Martin

Communication value of mistakes in dark-eyed junco song
André C. Ferreira, Jonathan W. Atwell, Danielle J. Whittaker, Ellen D. Ketterson, and Gonçalo C. Cardoso
Lay summaryhttp://amnat.org/an/newpapers/SepFerreira.html

Absolute vs. relative assessments of individual status in status-dependent strategies under stochastic environments
Yuuya Tachiki and Itsuro Koizumi

Predictably philandering females prompt poor paternal provisioning
Julia Schroeder, Yu-Hsun Hsu, Isabel Winney, Mirre Simons, Shinichi Nakagawa, and Terry Burke
Lay summaryhttp://amnat.org/an/newpapers/AugSchroeder.html

Escape distance in ground-nesting birds differs with individual level of camouflage
Jared K. Wilson-Aggarwal, Jolyon T. Troscianko, Martin Stevens, and Claire N. Spottiswoode
Natalie Pilakouta, Cerian Halford, Rita Rácz, and Per T. Smiseth

March 7, 2017

Thought-Provoking Am Nat at 150 (part 1)

On January 6, 2017, future Editor-in-Chief @DanielBolnick was inspired by a tweet by Erik Svensson to ask, Dear evolution-ecology twitterverse: what is the most influential American Naturalist paper, for your own career?

There were a lot of responses! So, bit by bit, I'll post them on the blog.

Erik Svensson
Kirkpatrick and Barton 1997 Evolution of a Species' Range
http://www.journals.uchicago.edu/doi/abs/10.1086/286054

Jeffrey Ross-Ibarra (after pointing out that his own Am Nat paper obviously had the biggest impact on his own career!)
Multiple Paternity within the Fruits of the Wild Radish, Raphanus sativus
Norman C. Ellstrand
http://www.journals.uchicago.edu/doi/abs/10.1086/284241

Daniel Promislow – Felsenstein 1985 “hands down” [by the way, at #evol2017 there is going to be a “joefest” and in the June Am Nat a Countdown by Matt Pennell in appreciation of Felsenstein]
Phylogenies and the Comparative Method
Joseph Felsenstein
http://www.journals.uchicago.edu/doi/abs/10.1086/284325

Raul Costa Pereira "tricky question!"
Evolution of Niche Width
Jonathan Roughgarden
http://www.journals.uchicago.edu/doi/abs/10.1086/282807
AND
The Ecology of Individuals: Incidence and Implications of Individual Specialization.
Daniel I. Bolnick, Richard Svanbäck, James A. Fordyce, Louie H. Yang, Jeremy M. Davis, C. Darrin Hulsey, Matthew L. Forister
http://www.journals.uchicago.edu/doi/abs/10.1086/343878

Emilio Bruna "Janzen as in Janzen-Connell, hands down"
Which led me to go for the article that hyphenated:
Clark, D. A., and D. B. Clark. 1984. Spacing dynamics of a tropical rain forest tree: evaluation of the Janzen-Connell model.
http://www.journals.uchicago.edu/doi/abs/10.1086/284316
Here's a commentary
The Janzen-Connell Model for Tropical Tree Diversity: Population Implications and the Importance of Spatial Scale
Eugene W. Schupp
http://www.journals.uchicago.edu/doi/pdfplus/10.1086/285426
And here's Janzen himself
Herbivores and the Number of Tree Species in Tropical Forests
Daniel H. Janzen
http://www.journals.uchicago.edu/doi/abs/10.1086/282687

Chris Muir
Acquisition and Allocation of Resources: Their Influence on Variation in Life History Tactics
J. van Noordwijk, G. de Jong
http://www.journals.uchicago.edu/doi/abs/10.1086/284547
And a Countdown to 150 
Invisible Trade-offs: Van Noordwijk and de Jong and Life-History Evolution
C. Jessica E. Metcalf
http://www.journals.uchicago.edu/doi/full/10.1086/685487

Britt Koskella "one of my all-time faves"
Migration, Virulence, and the Geographic Mosaic of Adaptation by Parasites.
C. M. Lively
http://www.journals.uchicago.edu/doi/abs/10.1086/303210

Eric Watson 
The Red Queen and Fluctuating Epistasis: A Population Genetic Analysis of Antagonistic Coevolution.
A. D. Peters, C. M. Lively
http://www.journals.uchicago.edu/doi/abs/10.1086/303247
AND
The Optimal Balance between Size and Number of Offspring
Christopher C. Smith, and Stephen D. Fretwell
http://www.journals.uchicago.edu/doi/abs/10.1086/282929

Andrew Suarez
Food Web Complexity and Species Diversity
Robert T. Paine
http://www.journals.uchicago.edu/doi/abs/10.1086/282400

Two votes from Andrew Suarez and Terry McGlynn for
The Role of Neighborhood Competition in the Spacing and Diversity of Ant Communities
Randall T. Ryti, and Ted J. Case
http://www.journals.uchicago.edu/doi/abs/10.1086/285331

Yaniv Brandvain
The Evolution of Altruistic Behavior
W. D. Hamilton
http://www.journals.uchicago.edu/doi/abs/10.1086/497114
I’ll add in there’s a Countdown to 150 about it
Hamilton’s Rule
Andy Gardner
http://www.journals.uchicago.edu/doi/abs/10.1086/682082

March 6, 2017

Recent Papers on Physiology

Trophic Strategies of Unicellular Plankton
Subhendu Chakraborty, Lasse Tor Nielsen, and Ken H. Andersen

Hormonally Mediated Increases in Sex-Biased Gene Expression Accompany the Breakdown of Between-Sex Genetic Correlations in a Sexually Dimorphic Lizard

Robert M. Cox, Christian L. Cox, Joel W. McGlothlin, Daren C. Card, Audra L. Andrew, and Todd A. Castoe

Natural History Note
Age-Dependent Modulation of Songbird Summer Feather Molt by Temporal and Functional Constraints
Yosef Kiat, and Nir Sapir
Lay summary: http://amnat.org/an/newpapers/FebKiat.html

The Size Dependence of Phytoplankton Growth Rates: A Trade-Off between Nutrient Uptake and Metabolism
Ben A. Ward, Emilio Marañón, Boris Sauterey, Jonathan Rault, and David Claessen

Testing the Aerobic Model for the Evolution of Endothermy: Implications of Using Present Correlations to Infer Past Evolution

Roberto F. Nespolo and Derek A. Roff

Note
Large Brains, Small Guts: The Expensive Tissue Hypothesis Supported within Anurans

Wen Bo Liao, Shang Ling Lou, Yu Zeng, and Alexander Kotrschal
Lay summaryhttp://amnat.org/an/newpapers/DecLiao.html

Open Access
Synergism and Antagonism of Proximate Mechanisms Enable and Constrain the Response to Simultaneous Selection on Body Size and Development Time: An Empirical Test Using Experimental Evolution
Goggy Davidowitz, Derek Roff, and H. Frederik Nijhout
Lay summary: http://amnat.org/an/newpapers/NovDavidowitz.html

Energetic Physiology Mediates Individual Optimization of Breeding Phenology in a Migratory Arctic Seabird
Holly L. Hennin, Jöel Bêty, Pierre Legagneux, H. Grant Gilchrist, Tony D. Williams, and Oliver P. Love
Lay summaryhttp://amnat.org/an/newpapers/OctHennin.html

Multiscale Evaluation of Thermal Dependence in the Glucocorticoid Response of Vertebrates
Tim S. Jessop, Meagan L. Lane, Luisa Teasdale, Devi Stuart-Fox, Robbie S. Wilson, Vincent Careau, and Ignacio T. Moore

Arboreal Folivores Limit Their Energetic Output, All the Way to Slothfulness
Jonathan N. Pauli, M. Zachariah Peery, Emily D. Fountain, and William H. Karasov
Lay summary: http://amnat.org/an/newpapers/AugPauli.html

Foraging Activity Pattern Is Shaped by Water Loss Rates in a Diurnal Desert Rodent
Ofir Levy, Tamar Dayan, Warren P. Porter, and Noga Kronfeld-Schor

Reptile Embryos Lack the Opportunity to Thermoregulate by Moving within the Egg
Rory S. Telemeco, Eric J. Gangloff, Gerardo A. Cordero, Timothy S. Mitchell, Brooke L. Bodensteiner, Kaitlyn G. Holden, Sarah M. Mitchell, Rebecca L. Polich, and Fredric J. Janzen

Longer Food Chains in Pelagic Ecosystems: Trophic Energetics of Animal Body Size and Metabolic Efficiency
Richard McGarvey, Natalie Dowling, and Joel E. Cohen

Recent Papers on Mutualism

Countdown to 150, Open Access

Open Access
Three’s a Crowd: Trade-Offs between Attracting Pollinators and Ant Bodyguards with Nectar Rewards in Turnera
Emily M. Dutton, Elaine Y. Luo, Adam R. Cembrowski, Joel S. Shore, and Megan E. Frederickson

Andrew J. Bibian, Jennifer A. Rudgers, and Tom E. X. Miller

Samuel Venner, Aurélie Siberchicot, Pierre-François Pélisson, Eliane Schermer, Marie-Claude Bel-Venner, Manuel Nicolas, François Débias, Vincent Miele, Sandrine Sauzet, Vincent Boulanger, and Sylvain Delzon

Hafiz Maherali, Brad Oberle, Peter F. Stevens, William K. Cornwell, and Daniel J. McGlinn



Natural History Note

Natural History Note
Selene Báez, David A. Donoso, Simon A. Queenborough, Liliana Jaramillo, Renato Valencia, and Olivier Dangles

Natural History Note
Flávia Delgado Santana, Fabricio Beggiato Baccaro, and Flávia Regina Capellotto Costa1

Natural History Note

February 1, 2017

Peer review at Am Nat


At the American Naturalist, our goal is to help papers develop. We try to give feedback even to papers that aren't a great fit for Am Nat. But we especially try to work with papers that can fit our niche to help them become the best they can be. We appreciate so much the time our reviewers take to be careful and thorough and helpful. Sometimes this aspect gets lost in discussions of peer review, so we're glad when we get positive feedback like the letter below when the author got news of the manuscript's acceptance (posted with permission).


Dear Dr. Winn,

Many thanks - this really is exciting news! ...

If you think it would be appropriate, I'd very much appreciate if you could send on the following note to Dr. Collar and to the two reviewers who commented on this manuscript. I'm always a bit hesitant to be too complimentary towards editors and reviewers during the review process for fear that it will appear that I'm trying to butter them up, but now I really want to express how grateful I am to them, and to the editorial structure at AmNat.

While most of our colleagues responded positively to the topic when we passed an early draft of the manuscript around for "friendly review", we found it difficult to get much advice on what we needed to do in order to improve it. The feedback that we got from the review process was immensely helpful in providing this. In particular, I cannot express how grateful I am for:

(1) the advice on how to address phylogenetic uncertainty that we received from Dr. Collar and from reviewer 2 (both in the reviews and in subsequent emails)

(2) the detailed description of missing links in our citations provided by reviewer 1, which importantly also included examples of papers that we could read in order to fill those gaps

and

(3) the very careful and specific critiques and suggestions for our modeling methods from reviewer 2, which made it clear that they had invested a lot of effort in going through them

But, I think the most important part of the review process for us was how incredibly encouraging the editors and reviewers were at all stages. Both of us are quite junior in our career trajectories, and while the opportunity for double-blind reviews gave us a bit more courage to "aim high" with this paper, I don't know that we would have considered ourselves capable of completing the suggested revisions without the very kind words that you, Dr. Collar, and the reviewers included at the beginning of each of your comments.

I think that the most genuine complement that I can give is that this manuscript simply wouldn't have been completed in its current state without all of this help and encouragement.

Many thanks again,
Adam Clark


January 6, 2017

Recent Papers in Biogeography

Synthesis

Shaping the Latitudinal Diversity Gradient: New Perspectives from a Synthesis of Paleobiology and Biogeography
David Jablonski, Shan Huang, Kaustuv Roy, and James W. Valentine (2017)
Lay summary: http://amnat.org/an/newpapers/JanJablonski.html

Article



Antonin Machac and Catherine H. Graham (2017)



Huijie Qiao, Erin E. Saupe, Jorge Soberón, A. Townsend Peterson, and Corinne E. Myers

Available Climate Regimes Drive Niche Diversification during Range Expansion
Rafael O. Wüest, Alexandre Antonelli, Niklaus E. Zimmermann, and H. Peter Linder (2015)

Natural History Note

Discovery of a Giant Chameleon-Like Lizard (Anolis) on Hispaniola and Its Significance to Understanding Replicated Adaptive Radiations
D. Luke Mahler, Shea M. Lambert, Anthony J. Geneva, Julienne Ng, S. Blair Hedges, Jonathan B. Losos, and Richard E. Glor
Lay summary: http://amnat.org/an/newpapers/SepMahler.html

Note

Information on Biotic Interactions Improves Transferability of Distribution Models
William Godsoe, Rua Murray, and Michael J. Plank (2015)