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!

Advertisements

How does ecological disturbance influence genetic diversity?

Banks et al. TREE 28(11): 670-679. How does ecological disturbance influence genetic diversity?

How disturbed are your genetics? From Banks et al.

How disturbed are your genetics? From Banks et al.


Will Pearse

Will Pearse

Disturbance is a topic very close to my heart (that’s meant to be a physiology joke), mostly because I get very annoyed when people don’t define precisely what they mean by it. So I was very heartened to read this review, where the authors discuss the various temporal and spatial scales of disturbance, and also because it’s a very nicely written paper.

Disturbance, within certain conditions, can be part of the background homogeneity of a system, and the authors are keen to stress that in this paper. I was a little surprised to not find mention of the intermediate disturbance hypothesis (even though some find it controversial), since it’s so appropriate in this context. I found figure 1 (partially reproduced above), where the authors go through some case studies of what different kinds of disturbance look like, quite helpful in reminding me that disturbance can be lots of different things, and it can have lots of different effects (not always bad). However, that figure 1 is made up of case studies reflects our lack of a coherent framework to structure how we think about disturbance. Moreover, the right hand side of the figure (which I cropped out, sorry!) talks about two case studies that involve “metapopulation” and “patch dynamics”; this makes a lot of intuitive sense to me, but on reflection I find that kind of weird. Metapopulation theory is a concept humans have generated, it’s not a thing that biological systems recognise, and I think it might be better to categorise systems on the basis of properties they share rather than how we find it easiest to model them.

So what would such a categorisation look like? After reading this paper I think disturbance severity, duration, and extent (bear with me) are three important axes. With ‘extent’ I want to incorporate the ability to temporally and spatially escape a disturbance; spatially means whether the disturbance is everywhere and whether you can move to avoid it, and temporally that means whether the disturbance happens very often or very infrequently and would probably incorporate seed bank effects. I’m sorry ‘extent’ is such a poor descriptor; I’m decaffeinated and would appreciate better suggestions! I’ve very deliberately chosen to put space and time on the same axis; you might prefer to split them. You might also prefer to add predictability as another axis; I don’t, not because I don’t think it’s important, but because I think a system’s history (which, in turn, incorporates predictability) affects quite a lot and the other axes mostly capture what the system has been doing in the past. Not a lot about genetics in this post (sorry!), and instead a framework that almost certainly already exists somewhere and I’ve forgotten I’ve read it. Please do tell me where!


Lynsey McInnes

Lynsey McInnes

I had high hopes for this paper. I’m attracted to any paper that deals with intraspecific variation head-on and am well aware that intraspecfic variation affects and is affected by processes occurring on varying spatial and temporal scales. So, a paper dealing with how disturbance affects genetic diversity seemed right up my street. I was curious about the direction the paper would take as my feeling was genetic diversity is generally quite hard to measure particularly in non-equilibrium populations (such as those that have been disturbed) and assigning particular genetic signatures to historical events (‘disturbances’) is notoriously difficult as not only can a range of different events leave the same genetic signature, the same event can leave different signatures depending on the ecology and population structure of the species involved.

It was good for my ego to find that the authors largely confirmed my suspicions of these issues, but sad for the paper that there seems no easy way out.

It seems that the current state of understanding is that we live in an increasingly ‘disturbed’ world . Events such as tsunamis, fires and grazing impact nearby populations, reducing the number of individuals and thus most likely (at least) point estimates of genetic diversity and the challenge is to recognise the types of populations/species that will find recovery from such impacts difficult or impossible (if one is interested in conserving viable populations, otherwise all impacting populations are interesting, for instance, what kinds of species can you bombard with disturbances and they bounce right back to pre-disturbance levels of abundance and genetic diversity?). It seems however, that little research has focussed on the relationship between disturbance and genetic diversity and that there are many outstanding questions.

The second half of this paper gave a helpful overview of these outstanding questions and laid out some helpful ways forward. Namely, and understandably, the integration of multiple sources of data (event type, species’ traits, samples across the range and through time, etc.) will help to unravel the impact, or non impact, of putative disturbances on genetic diversity and, more importantly, what these effects mean for the longer term survival of species and/or communities. In fact, the paper lists FOURTEEN outstanding questions linking disturbance and genetic diversity and all of these are interesting. It would have been nice if these had been dealt with in more detail in the paper, perhaps focussing on a couple and on real routes forward to addressing them.

Maybe I missed this in the paper, but I also felt that what was missing was strong evidence that one expects any general link between disturbance and genetic diversity. As next gen sequencing gets cheaper and more accessible for non-model organisms, it will become trivial to look for these links, but, I feel, we need to know what we are looking for before we go looking for it. The general view is that more genetic diversity per population is better to ensure buffering against a variety of disturbances, but the authors show this is not always the case. Individuals can come from beyond the disturbance centre to make up for lost individuals and/or diversity. To predict this rescue effect one has to have a bigger picture encompassing knowledge of the genetic diversity of multiple populations within and beyond the disturbance centre. Are there enough individuals for recovery and do these individuals possess the desired adaptations? (So, I might differ from Will in thinking metapopulation theory might be helpful here).

I absolutely believe that intraspecific variation within and between populations in terms of genes and ecology must be considered if we hope to understand how populations will cope in the face of point disturbances and longer term environmental fluctuations. This paper drove home to me quite how difficult this endeavour is going to be.

%d bloggers like this: