April 7, 2018

Methods papers in The American Naturalist

We Editors often hear prospective authors say things like “but AmNat doesn’t publish ______”  (fill in whatever the author does in the blank space). Most often, I’ve heard that The American Naturalist does not publish Methods Papers, or does not publish genomics. 
 I’m here to say that in general, those statements are incorrect. I can’t think of subject areas in organismal biology that we exclude a priori.  Quite the contrary, a key goal of this journal is to attract a diverse readership. To do that, we like to publish on diverse topics. Or better yet, to publish papers that bring together multiple topics. 
So what DO we publish? Simple: we like to publish conceptually innovative papers (data, theory, or both), which make our readers think differently about a far-reaching topic. These could be in genomics, ecosystem, ecology, ecoimmunology, or neuroethology, as long as they push us to see an idea in a new light. This can be done by proposing a new idea (and following through to support it), or by providing the best-available evidence for a long-standing but poorly supported idea. Some papers put an innovative new twist on a classic concept. There are papers I call “Reese’s Pieces” science, after the candy made from peanut butter wrapped in chocolate. The advertisements for this candy used to make a big deal out of taking two great but familiar things and putting them together to make something new. Lastly, there are Methods papers.
It is true that The American Naturalist does not often publish purely methodological papers. Partly that’s because we don’t get many submissions. Partly it is because we keep a high bar for conceptual innovation. Often, methods papers provide new tools to solve known problems in a new way, maybe with greater precision. That’s a very useful and important service, but does not necessarily lead us to think about a subject in a new way, or to think about an entirely new subject. But sometimes Methods papers do just that. Joe Felsenstein’s 1985 paper on Independent Contrasts was fundamentally built around a new point of view, that launched the field of phylogenetic comparative methods. Masatoshi Nei proposed his famous Nei’s D in our pages, which launched a new way of thinking about molecular evolution.
What made these Methods papers so effective is that they gave us a tool to solve a problem we didn’t even know we had. By introducing their methods, they made us think differently about old problems, or revealed new questions. Not that we expect all methods submissions to compete with Felsenstein 1985.  But, we do believe there are actually many methods papers out there that fit this criteria of pointing us towards substantially new questions. These may present software or new technology or new protocols. But what should bind these together is an emphasis on opening up new questions, and providing tools to get answers that we couldn’t previously ask, maybe hadn’t even thought to ask, and which expand our conceptual horizons. 

So, Yes, we publish Methods Papers.  To use an analogy: we aren't so interested in tools for their own sake, but rather for what they can help us build. If the tool helps us build a sufficiently interesting new edifice, we might be interested in publishing it. Keep in mind that a paper describing a new method (e.g., a mathematical proof of an equation used in inference), may be most helpful to readers when accompanied by software, or a worked example to illustrate its utility. These are not strict requirements, but do tend to help the audience relate to the method. Conversely, papers describing new software for existing methods will not likely fare well because they are not advancing new kinds of questions, so much as enabling existing questions (which is important of course, but not what we look for).

 If you aren’t sure whether your Methods paper measures up, email the journal office or Editor (daniel.bolnick@uconn.edu) with a succinct pre-submission inquiry. 

April 3, 2018

Climate and Climate Change

Recent Papers

Lauren M. Smith-Ramesh, Adam E. Rosenblatt, and Oswald J. Schmitz

Natural History Note
François S. Becker, Krystal A. Tolley, G. John Measey, and Res Altwegg

Jeanne Tonnabel, Frank M. Schurr, Florian Boucher, Wilfried Thuiller, Julien Renaud, Emmanuel J. P. Douzery, and Ophélie Ronce

Thomas R. Anderson, Dag O. Hessen, James J. Elser, and Jotaro Urabe

Open Access
Derek Karssenberg, Marc F. P. Bierkens, and Max Rietkerk

Open Access
Tim Coulson, Bruce E. Kendall, Julia Barthold, Floriane Plard, Susanne Schindler, Arpat Ozgul, and Jean-Michel Gaillard

Open Access
Anieke Brombacher, Paul A. Wilson, Ian Bailey, and Thomas H. G. Ezard

Kévin Tougeron and Paul K. Abram

Hannah K. Frank, Luke O. Frishkoff, Chase D. Mendenhall, Gretchen C. Daily, and Elizabeth A. Hadly

Synthesis, Open Access
Rachael A. Bay, Noah Rose, Rowan Barrett, Louis Bernatchez, Cameron K. Ghalambor, Jesse R. Lasky, Rachel B. Brem, Stephen R. Palumbi, and Peter Ralph


American Society of Naturalists Address

Viktor Nilsson-Örtman and Frank Johansson

March 27, 2018

Evolutionary Genetics

Recent Papers 

Artificial Selection to Increase the Phenotypic Variance in gmax Fails
Jacqueline L. Sztepanacz and Mark W. Blows
Lay summaryhttp://amnat.org/an/newpapers/NovSztepanacz.html

Open Access
Modeling Adaptive and Nonadaptive Responses of Populations to Environmental Change
Tim Coulson, Bruce E. Kendall, Julia Barthold, Floriane Plard, Susanne Schindler, Arpat Ozgul, and Jean-Michel Gaillard
Lay summary: http://amnat.org/an/newpapers/SepCoulson.html

Most Colorful Example of Genetic Assimilation? Exploring the Evolutionary Destiny of Recurrent Phenotypic Accommodation
Alexander V. Badyaev, Ahva L. Potticary, and Erin S. Morrison
Lay summary: http://amnat.org/an/newpapers/AugBadyaev.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

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

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