The ecological dynamics of clade diversification and community assembly

Mark McPeek. The American Naturalist 172: E270-E284. The ecological dynamics of clade diversification and community assembly

Blue damselfly; McPeek has studied damselflies extensively. Taken by Umberto Salvagnin (via Wikimedia).

Blue damselfly; McPeek has studied damselflies extensively. Taken by Umberto Salvagnin (via Wikimedia).

Lynsey McInnes

Lynsey McInnes

I picked this paper because I remember reading it when it came out and being taken in by McPeek’s approach. It felt like he had built up a pile of phylogenies with negative gammas (a metric mired in controversy, but that’s for another post) and then he decided he should find out whether more or less feasible processes of ecological or non-ecological divergence generate similar distributions of gamma values.

A short background note: Pybus & Harvey’s gamma purports to detect ‘slowdowns’ in diversification by quantifying the pattern of nodes in a reconstructed phylogeny. In brief, if nodes cluster near the root of the tree, gamma is negative and this indicates that diversification has slowed as we approach the present. Positive gammas could suggest that diversification has sped up as we approach the present, but inference is complicated because of the signal left by extinction, such that a positive gamma does not unambiguously support a particular pattern. Since publication of McPeek’s paper there has been a swath of further papers documenting problems with the metric, probably the no.1 being that you get one gamma value per tree so the results will be dependent on what scope of clade you have chosen as to whether you can detect a clean slowdown or not. Again, this is not a post about the ins and outs of gamma.

Rolling with the assumption that gamma can provide a useful summary of the distribution of nodes in your tree, it can be used, as here, to quantify the different branch lengths attainable under different diversification scenarios. Regular readers will know I have a soft spot for simulation studies, so could anticipate that I liked McPeek’s setup here. Basically, he wanted to find out whether if, he enforced ecological divergence upon speciation, trees are produced that show signs of slowdowns in diversification (as ecological gradients are filled in). And this was indeed what he found. Some might argue that you get out what you put in, and presumably this is true to some extent. But I still found it a neat and tidy finding.

Now its time to go off on a tangent. Don’t get me wrong, I like this paper and appreciate this kind of study. I really believe that many clades are probably subject to slowdowns as they diversify and this might often be because they have filled some limited set of ecological niches and additional species are formed by geographic isolation without ecological divergence or some other mechanism like sexual selection or filling the niche of a species that has gone extinct. I just wonder how easy or indeed, possible, it is to detect the signal of this diversification trajectory on phylogenies. Perhaps the pattern emergent at the ‘evolutionary’ timescale is rough enough that slowdowns or equilibrial diversity dynamics are detectable and ‘real’ and the more haphazard activities occurring at ecological timescales will always be evened out and undetectable and this is OK. I’m also intrigued by methods that work ‘the other way’ and take massive phylogenies and try to delimit more restricted clades that somehow obey these slowdown patterns. It often seems like taxonomists’ brains have worked in similar ways and genera and families conform to these delimitations. Which is actually pretty cool.

In short, I am mesmerised by broad-scale patterns in phylogenies and often buy into the current trend of assigning ecological explanations to them. In some sense, ecological and evolutionary processes are all part of one continuum so must impact each other, but how often have we made ourselves believe that something more than just random spliting processes are at play. I’ve currently turned my back on macro-scale analyses, but will always have a soft spot for finding out how these crazy, very clearly real, patterns are generated and why.

Will Pearse

Will Pearse

This paper is the scientific equivalent of Samuel L  Jackson in Snakes on a Plane; an old-school “I just sat down and thought” kind of paper, and I like it. It’s probably the best example of how a simulation study can be insightful, starting with some fundamental observations from empirical data, and making a model just complicated enough to derive insight.

McPeek’s reviewer raises a very good point: what does it mean for the fossil record if his simulations shows we get species appearing and then rapidly disappearing? This reminds me strongly of raceme phylogenies, although I think it’s an open question whether these short-lived species would ever be so abundant as to swamp out the main ‘trunk’ of the tree of life. That said, most people would agree speciation is rarely instantaneous, and the shape of the simulated phylogenies would probably be different if a species only became a true species after a delay (à la protracted speciation), even if those proto-species were still ecologically different from one-another.  It makes me wonder the extent to which the diversity on Earth right now is comprised of these side-shoots, and how many of these species (ignore our influence for a moment) will be around in a few million years.

I also enjoyed the discussion of variation in structure among clades. There is no reason to assume that models of evolution are constant across a clade simply because, in the present, a researcher has decided that a particular group forms coherent ecological assemblages. As always, I’m convinced that different ecological processes should be operating in clades that have undergone different kinds of evolutionary processes, but drawing a distinction between ecology and evolution is somewhat arbitrary. The power of McPeek’s approach is that there is no disconnect between the two: in his models, evolution is just ecology over-and-over-again, and examining the two simultaneously must ultimately be the best approach.

There is one caveat to this. Many (and McPeek notes this) are quick to point out that we may never be able to estimate extinction and speciation rates using phylogenies. There are very, very few cases where the fossil record is as rich as we would like, and a molecular phylogeny necessarily misses extinct species. While modelling exercises like this are fantastically useful, I am somewhat skeptical that we can ever reliably fit models this complex to real data; of course that doesn’t mean we shouldn’t try!


About will.pearse
Ecology / evolutionary biologist

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