Wednesday, March 2, 2016

What explains persistent species' rarity in communities?

Someone asked me what is the most important or lingering issue in community ecology recently. (There’s probably a whole post to answer that question (to come...)). One answer is the mystery of species coexistence: for more than 50 years (from Hutchinson’s paradox of the plankton through today) we have tried to explain the immense and variable diversity on earth by understanding what allows two or more species to coexist. There are many ways to explain coexistence, and yet the details and the specifics for any given system are also still usually incompletely understood.

A good and fascinating example is that of persistent rarity. Why are so many species in communities rare? What allows species to remain rare for long periods of time, given that small populations should be at greater risk for stochastic extinction? A new preprint from Yenni et al. (1) considers the empirical evidence for one potential explanation for persistent rarity: asymmetric negative frequency dependence (see also Yenni et al. 2012 (2)).

Coexistence theory (Chesson 2000) considers stabilizing mechanisms to be those that allow intraspecific competition to be greater than interspecific competition (often defined as ‘niche’ mechanisms). The strength of such stabilizing mechanisms can be estimated by looking at how a species’ population growth rate is limited by the frequency of conspecifics compared to the frequency of heterospecifics in the community. Negative frequency dependence is expected when stabilizing mechanisms are strong. This allows species to increase when rare, since limitation by conspecifics is low, followed by a decline in growth rates as conspecific frequency increases.

Asymmetric negative frequency dependence may explain persistent rarity, since it suggests especially strong conspecific limitation. As a species’ frequency increases, their growth rate greatly declines and intraspecific interactions, rather than interspecific competition, determine abundances. Species are rare, but also less likely to experience extinctions through competition with other species. The authors suggest that as a result of this, we should expect rare species to have stronger negative frequency dependence, in comparison to more common species. They look for evidence for asymmetric frequency dependence using data from 148 communities collected across multiple taxonomic groups (birds, fish, herpetofauna, invertebrates, mammals, and plants), 5 continents, and 3 trophic levels. The data represented time series of species abundances, which the authors used to estimate negative frequency dependence as the relationship between a species’ frequency in the community and their annual per capita population growth rate.

Several aspects of the results are particularly interesting. First, the authors had to omit rare species that are not persistent, since other processes likely explain the presence of such ephemeral members of communities. The frequency of ephemeral species (not stably coexisting at a local scale), for example, was quite high, particularly in plant communities (average of 82 species per community, of which only 22.6 species were on average identified as ‘persistent’). This may suggest the importance of spatial mechanisms for coexistence or co-occurrence. Their overall prediction of stronger negative frequency dependence in rare species appeared to holds in 46% of the communities they examined, consistently for all of the taxonomic groups but one (herps!). Additionally, the opposite pattern (common species having stronger negative frequency dependence) was never observed.

Rarity in nature is common :-) but not well predicted using most coexistence theory. Many interesting and important questions arise from it, and from results like those shown in Yanni et al. For example, do rare species have rare traits or rare niches? Is the frequency dependent growth rate context dependent (i.e. can a species be strongly limited by conspecifics in one environment but not another)?

*Note I haven’t reproduced any figures here, since this is a preprint. However, it is openly available, so do have a look (link 1 below). I’m not certain if there is a rule of thumb on blogging about preprints, but I imagine it is much like blogging about conference talks. The work may not have been peer reviewed/published yet, but the broad results and ideas remain interesting to discuss.


1. Glenda Yenni, Peter Adler, Morgan Ernest. Do persistent rare species experience stronger negative frequency dependence than common species? doi: Preprint.

2. Yenni, Glenda, Peter B. Adler, and S. K. Ernest. "Strong self‐limitation promotes the persistence of rare species." Ecology 93.3 (2012): 456-461.


Ben Haller said...

After some head-scratching, I have decided that what is actually being talked about here is negative density-dependence, not negative frequency-dependence, no? Not your mistake – the authors themselves seem to have made this mistake. But the terms "frequency-dependent selection" and "density-dependent selection" have distinct meanings, and they seem to have gotten them mixed up. Either that, or ecologists use the terms in a completely different way than evolutionary biologists – but I certainly hope that that is not the case, as there's enough confusion in the world already. :->

Caroline Tucker said...

Hi Ben - I also did some head scratching about the density versus frequency dependent selection terminology. The original literature (Chesson) typically refers to density-dependence. So I actually re-read a few papers, and from what I can tell, Peter Adler et al. specifically refers to frequency-dependence in 2007 (

"Our use of relative frequency on the x-axis in Fig. 1 should not imply that density-dependent processes are unimportant for coexistence. In fact, frequency dependence is almost always the product of density-dependence. The problem is that density dependence will emerge in any system with limited resources, but it will only translate into negative frequency dependence if species limit themselves more than they limit others. When community size is fixed, as in the neutral model, density and frequency are interchangeable, but as this case is rare, frequency is the appropriate metric for detecting stabilization."

So it is different than the evolutionary sense. There may be some argument as to whether this is hairsplitting or not, but for empirical data it where spatial extents may differ, I think it makes sense?

Gavin Simpson said...

Regarding your footnote about the preprint status of the paper you are discussing, the very fact that the authors posted this to a preprint server would indicate their desire to see the work discussed by people as part of a broader review process. Your discussion of the paper here is exactly how this is supposed to work.

A conference talk is different, because unfortunately many conference still require explicit permission be given to use social media to discuss a talk.

Caroline Tucker said...

Hi Gavin - I was actually wondering specifically about the reproduction of figures from preprints. Any thoughts?

Gavin Simpson said...

HI Caroline. According to that particular paper, the authors have retained all copyright and have not licensed re-use (which I find odd given the open-science ethos of the lab that two of the three authors are part of). Fair use could apply if you wanted to, for purposes of comment or discussion. But this is all copyright.

The broader point is that I can't imagine why anyone would post a preprint and *not* want it discussed nor parts thereof reproduced (even just for purpose of commentary on a blog). I'd say using a figure would be fine as long as copyright law allows you fair use rights; the authors have already removed the cloak of secrecy by posting the preprint.

Caroline Tucker said...

Right, I saw the copyright as well and (unlike published papers, where I consider reproducing figures fair use) wasn't sure.

Re: the general question of preprints - absolutely, if they've published it as such, the authors clearly aren't worried about the work being shared and discussed :)