In a previous post, I questioned whether we should ordinarily expect species’ phenotypic traits to predict their abundances. I now have a new open access paper out (UPDATE: typeset published version now available), showing that I was right to question that idea, which I think is one a lot of people intuitively buy into. In a simple competition model in which species vary in a phenotypic trait conferring “adaptedness” to the habitat, better-adapted species often are no more abundant (or even less abundant) than more poorly-adapted species. As I suggested in the original post, this is indeed because of negative frequency dependence (what Peter Chesson calls “stabilizing mechanisms”) arising from niche differentiation. Traits conferring “adaptedness” only reliably predict species’ abundances in the mostly-unrealistic limiting cases where species exhibit no niche differences whatsoever, or such large niche differences that they don’t compete at all.
One could of course examine many other models, and I plan to do so in a follow-up paper. But there’s no reason to expect the broad conclusion to change. A world with niches is a world with negative frequency dependence. In such a world, species’ realized abundances are going to depend in exceedingly complex ways on not just their own traits, but on the traits of every species with which they interact, directly or indirectly. (And by the way, no, you cannot expect to capture all that complexity with some summary measure of how “different” species are from one another in terms of their traits, for various reasons I will be exploring in that follow-up paper…)
“Trait based approaches” are hot right now in community ecology. But unfortunately, I haven’t yet seen much in the way of serious empirical attempts to link “trait-based” approaches to modern ideas about species coexistence (with some notable exceptions, a few of which I cite in the paper). I’d really like to see those links developed. Folks like Jon Levine and Amy Angert are on the case, and David Ackerly gave a great ESA talk a couple of years ago pleading for such work. Hopefully, my little paper, and the planned follow-up, will help nudge others to take up that challenge.
Below are some more notes about the paper and the process by which it came to be, which I doubt are of great interest but which I figured I’d share anyway.
The paper is coming out in Frontiers in Microbiology as part of a special issue (“Research Topic”) on the causes and consequences of microbial community structure. The editors of the special issue invited me to submit something, and since various folks I knew were also participating, I said yes. The paper is really a “general ecology” paper with microbial examples. I figured that was ok. Drawing on ideas from general ecology is a hot thing to do in microbial ecology these days, thanks in large part to the efforts of Brendan Bohannan and his students and colleagues. All of which explains why I have a paper coming out in a microbiology journal that I admit I had never heard of before I was invited to submit to it. But for the follow-up I’m planning to return to my natural habitat of ecology journals.
Frontiers is a new publisher founded by neuroscientists and now branching out into other topic areas (mostly microbiological fields; not including ecology and evolution so far). They seem to be quite keen to try new things. They have some sort of system whereby the best or most popular articles, as judged by readers, get bumped up to “higher-tier” journal (or maybe the authors of those articles get invited to submit review/perspectives-type pieces to those higher-tier journals? I’m not clear…) They have a wide range of prices charged to authors, depending on the type of article and the tier of journal in which it appears (I wrote a “perspectives” article in large part because that’s one of the cheapest types…). The peer review system requires ongoing back-and-forth between authors and reviewers: the reviewers’ comments appear online, authors reply (and upload a revised ms if necessary), reviewers can reply further (and ask for further revisions), and so on until reviewers declare themselves to be satisfied. And they seem to aspire to be some sort of social network for scientists, but I didn’t look into those features at all and if I had to guess I’d bet they’re little used.
They have some things they need to work on. Their website is really confusing, at least for an old coot like me used to the websites of conventional journals. And while the basic idea of their review system really intrigues me, it has some kinks. My back-and-forth with one of the two reviewers eventually reached something of an impasse, despite multiple rounds of revision to the ms and lengthy online discussion. At which point I thought the editor might step in and just make a decision. But before that could happen, the reviewer asked to “no longer be associated with the ms”. It turns out (I think I’m getting this right) that Frontiers publishes the names of reviewers as part of the accepted articles (before that, reviewers are anonymous), and that reviewers can only avoid this by withdrawing from the review process entirely. Which I find odd and arguably even inappropriate, since in the page proof I just corrected, there is no official mention that there even was a second reviewer, unless I totally missed it. This despite the fact that the published version of the ms includes reasonably extensive revisions in response to that reviewer’s comments. I’m not sure what the best solution to this is, since I’m not sure why Frontiers publishes the names of reviewers as part of the articles they reviewed (I can imagine various reasons…), and the best solution will depend on why they do that. But the status quo can’t possibly be optimal, as it’s actively misleading for readers. Anyway, I emailed Frontiers to raise my concerns on this.
UPDATE #2: In the time that’s past since I wrote this post, it’s become clear to me that the problems with Frontiers weren’t just growing pains. It’s a borderline predatory publisher in my view (case in point). In retrospect, I regret having published with them. I wouldn’t do so again and would advise others not to support them.
Anyway, go check out the paper (the final version will be online soon, but it won’t differ substantively from the current version). Since it’s really a general ecology paper, I think ecologists like y’all are if anything more likely to like it and “get” it than microbial ecologists are.