My new open access paper: Should we expect species’ traits to predict their abundances? (UPDATEDx2)

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.

10 thoughts on “My new open access paper: Should we expect species’ traits to predict their abundances? (UPDATEDx2)

  1. I’m the reviewer who didn’t back out and I’m not entirely happy with Frontiers either. When I agreed to review, I wasn’t told that I’d be entering into an extended dialogue with the author: I thought I’d be writing a review and then I was done. And while I now see that I was warned that my name would be published as a reviewer, that notice was at the very end of the invitation email, with nothing to call attention to it. (And yes, the website is hard to use, but frankly that’s the least of my beef.)

    Happily, I liked Jeremy’s paper, so there wasn’t much of a back-and-forth needed for me, and I think what he’s said here is not only correct but important, so I’m not concerned about having my name associated with the piece. But what about other papers I’ve reviewed, where I think the science is correct but ho-hum. Do I want my name associated with that? Not necessarily. And it’s hard enough to get reviewers without committing them to an unlimited back-and-forth with the author. I’m going to have to be very excited about a manuscript to review for Frontiers in the future.

    • Some of these issues could be alleviated by better communication from Frontiers. They do a poor job of explaining to everyone, not just reviewers, how they want their journals to work. The guest editor handling this special issue got no guidance as to how the review system was supposed to work. And their website is not only a mess, a fair bit of what’s on it reads more like promotional material than formal guidance about the journal’s policies and procedures. Frontiers doesn’t seem to realize that, if you insist on doing things differently than everyone else, you’re going to have to work hard to explain what you’re doing and why, because it’s not going to be obvious to others.

      Clearly, referees in particular need better guidance. Is the idea that authors and referees are supposed to go back and forth until the referees are satisfied? If so, referees need to be clear on that from the get-go, so they can decide whether to accept the invitation to review, and there needs to be an explicit way of dealing with impasses. Or is the online back-and-forth just an attempt to speed up or tweak what’s basically supposed to be a normal review process? If so, that too needs to be made clear to referees. And what is publishing the names of referees intended to accomplish or indicate? That the referees agree with every last detail of the ms? Is it just
      openness for the sake of openness?

      While I’m glad to have had an opportunity to get a little idea out there that I hope will grow into a bigger idea, I don’t know that I’d be involved with Frontiers in future. I don’t know if you noticed, but they’ve already published a massive volume of papers, including a lot of guest-edited “research topics”. I wouldn’t call them a predatory or vanity open-access publisher. But for the moment, a lot of their “innovative” ways of doing things look to me rather like attempts to just do things cheaply and capture a lot of author fees. I’m curious what their rejection rate is–I bet it’s low–and I’m also curious why Cyrille decided to put together a research topic for them in the first place (will have to ask him that…). Now, it could well be that they’re operating in the only economically-viable way for an open access, author-pays publisher to operate (even if they’re just trying to break even). But old codger that I am, I just don’t see much value in this kind of operation (not zero value, but not much value). The publisher isn’t doing any filtering (and so is publishing lots of stuff hardly anyone wants to read), and the post-publication “alt-metrics” and comment systems aren’t doing any filtering, and so I have no idea how readers are supposed to filter through all this stuff.

      Plus, the author fees just function as an added cost for me that sucks up money I could otherwise spend on science. I actually cried poverty and got my university’s open access author fees fund to pay for it, saying my grant was committed to other purposes. But if everyone did that (because there’s always something besides author fees that you could spend your grant money on), the university would basically need to take that part of the library budget devoted to journal subscriptions and devote it to paying author fees. And even then I have no idea if that would be enough money…

      • I’ll play devil’s advocate here for a minute. Disclosure: I am also a co-author on a paper in this journal issue. While I agree that the review system has the possibility for long, drawn-out back-and-forths, the time to publication here was far shorter than any other paper I’ve been invovled with. But I can definitely see how people might be unaccustomed and put off by the forum-style review and seemingly endless dropdown menus. I also disagree with your assertion that the journal is publishing “lots of stuff hardly anyone wants to read.” Although ecologists may not be interested in much of the subject matter here, I see a lot of cool-sounding papers that seem like they’d be at home in many other microbiology journals besides this one. Finally, the cost for publishing (at least in a “special issue”) is equivalent to journals like EcoSphere and PLoS ONE. I guess time will tell whether this thing succeeds or not. I just hope they don’t start spamming me.

      • All fair points Dave. My time to publication was indeed quick as well. And as I said, some of the issues I have with Frontiers could probably be fixed by better communication from them and a more informative, easier-to-navigate website.

        To clarify one point, I wonder whether they’re publishing lots of stuff no one wants to read simply because they’re publishing so much stuff, not because it’s stuff ecologists mostly don’t want to read. As I said, they’re mostly publishing in neuroscience, microbiology, and some other non-ecological fields. But if you say a lot of the material is of wide interest to microbiologists and would be at home in older, highly-selective microbiology journals, then I’m happy to take your word for it.

        In terms of costs, I intentionally avoided comparisons with journals that have a single per-article price, since Frontiers has so many different prices for so many different article types, and because Frontiers is priced in euros while EcoSphere and PLoS ONE are (if memory serves) priced in USD, making the (fluctuating) exchange rate a further complicating factor in pricing comparisons. Broadly speaking, I don’t find Frontiers either especially costly or especially cheap overall.

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  6. I know this blog isn’t active anymore (RIP) but I was wondering if you ever followed up with this idea. I thought it was a neat demonstration at the time and I thought there were plans to take this further.

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