A new dynamic null model for phylogenetic community structure

Pigot & Eitenne 2015 A new dynamic null model for phylogenetic community structure. Ecology Letters 18(2) 153-163

Figure 2 from Pigot & Etienne. Plots of likelihood of community membership under low (top) and high (bottom) rates of local extinction. Or, if you prefer, a series of variously coloured and not-coloured phylogenies.

Figure 2 from Pigot & Etienne. Plots of likelihood of community membership under low (top) and high (bottom) rates of local extinction.

Will Pearse

As if by magic, the ‘new’ approaches I hoped would appear last post have done so. It’s almost as if I know the posting schedule ahead of time!… Alex Pigot and Rampal Etienne have produced an analytical framework within which we can distingush between speciation, extinction, and colonisation in structuring an assemblage’s phylogenetic structure. Beyond that, they have developed a method that uses phylogeny to its true potential: not a proxy but unique data that helps us estimate evolutionary (speciation and extinction) and ecological (migration) processes of interest.

This is an important contribution because the problem of dispersal is one that has vexed many for some time, yet (with notable exceptions) received relatively little attention. Dispersal from a wider source pool provides an important link between ecological and evolutionary time-scales that we need to model. A species ‘appearing’ can either have an evolutionary (speciation) or ecological (dispersal) origin, and that their DAMOCLES model can at least start getting at that distinction is important. It is of little surprise to anyone who has followed these sorts of studies that phylogenetically overdispersed communities can result from something other than competition, but linking its origin to evolutionary and dispersal events outside a community is interesting.

There are, of course, additional complexities that could be built on top of this model, and I’m not going to bore you by rambling on about traits because I think you all know where we want that to be going. However, I think it’s important to explicitly consider the meta-community (or source pool, if you prefer) from which these species are being drawn. Focusing on one assemblage is useful, but the reality is that speciation and extinction dynamics are happening at biogeographic scales, and we desperately need to link community-scale models such as these with those. Considering multiple assemblages undergoing these kinds of dynamics could be a good place to start. I wonder if the limiting factor may be finding something analytically tractable; while simulating individual communities linked within a wider system is reasonably feasible, doing so analytically (as the authors seem to have started doing) is more difficult.

Lynsey McInnes

Lynsey Bunnefeld

Alex Pigot has a way with null models. He’s already shown that the arc of species’ range size over the course of a species’ lifetime is not necessarily the result of deterministic processes and now he (and Rampal Etienne) have shown that common patterns of community assembly need not be the result of negative biotic interactions if an appropriate null model is used. Wow.

This paper is a great example of a couple of key points that I am most definitely guilty of ignoring. 1. taking time to think whether your null model is biologically as well as statistically null is important. 2. important insights can be made even before your model includes every last contributing factor (see Will’s post above). 3. data examples are important to illustrate your method. Nice.

I’m now going to largely disregard all those things I just said were important and wonder how you might extend this model and wonder what pesky real world effects might topple the null expectation.

I wonder how biotic interactions with non-clade members affect community assembly, i.e., competitors, predators, prey, hosts, etc. I wonder what a null model for this might look like? Should hosts/parasites (for example) evolve in tight coevolution, or not? I wonder what repeat processes of community assembly look like? Always the same, or not (I’m sure this has been treated in microcosms and by Gould). How would phylogenies help with these questions? In the same vein, I wonder how what happens to the new sister species that does not enter the community of his ancestor? I guess I am pondering the effects of space. I have no doubt the authors have too, and would not be surprised if they already have the answers up their sleeve. The authors deal elegantly with variation in a quantitative trait (or traits) meant, I think, the characterise niche. I wonder what happens when you throw in variation in other traits, probably dispersal ability (haha, with all the trauma that goes with defining and measuring that!).


Is dispersal neutral?

Winsor Lowe & Mark McPeek. Trends in Ecology & Evolution 29(8): 444-450. Is dispersal neutral?

Eadweard Muybridge’s "Bird in Flight". He was a pioneer of photography (particularly of animals), and was acquitted of shooting his wife's lover for 'justifiable homicide'. This is all over the Internet and I think past copyright.

Eadweard Muybridge’s “Bird in Flight”. He was a pioneer of photography (particularly of movement), and was acquitted of shooting his wife’s lover for ‘justifiable homicide’. This is all over the Internet and I think past copyright.

Lynsey McInnes

Lynsey Bunnefeld

I picked this paper because I don’t think dispersal is neutral and I had a hunch that the authors didn’t think so either. Perhaps because I already agreed with the main thrust of their argument – that we need to consider how intrinsic traits affect dispersal propensity and movement as well as intra-specific variation in these traits – I came away from the paper a bit disappointed. I know, I know, I am hard to please. Let me explain.

The authors systematically undermine the notion that dispersal might be a neutral process. They note that thinking of it as a neutral process makes it a lot easier to think about and to model as you just need one dispersal parameter that specifies something like average dispersal distance per species (or if you are getting swanky, a parameter to characterise a dispersal kernel for each species). On top of this you can add in dispersal barriers and spatial structure of population patches, but, throughout, you are buying into the idea that all individuals of all populations of a species behave the same way. They go on to outline experimental and field evidence that this is not the case, that individuals vary in their dispersal propensity as a function of intrinsic traits, trade-offs with other traits as well as geographically as a function of intrinsic traits interacting with the extrinsic environment. In short, dispersal is nastily complicated and thinking of it in neutral terms is just too simplistic to be useful.

A few problems with thinking about it more realistically. Data is notoriously hard to come by, and even if you could collect whatever data you wanted, what would you collect? You’d need wide sampling across and within populations, you’d need to account for extrinsic factors and you’d have to have some clear ideas on what traits might influence which bits of dispersal (propensity, distance, establishment).

The authors are most interested in how dispersal affects community assembly, I think by this they mean how does variation in dispersal affect what individual genotypes/phenotypes make it into different communities and is this predictable? This is an interesting question and one that seems to have had only a hazy treatment so far in the literature because, as the authors note, researchers prefer to concentrate on the spatial structure of populations rather than the nature of the individuals in their population set. I agree wholeheartedly with the authors and therefore think this is the point where I felt unsatisfied. I wanted the authors to tell me more about what there expectations were for how non-neutral dispersal might affect community assembly. For instance, will peripheral populations (at continent edges? on islands?) be really different ecologically (services? function?) because only far dispersing phenotypes make it there (far dispersing but rubbish competitors?). Will central populations be more transient than peripheral ones as they have higher flux of different phenotypes coming in and out? Can divergence of one species due to limited dispersal affect divergence of species at another trophic level (who might otherwise have maintain one large range)? And so on, and so on.

OK, maybe I was too harsh to be disappointed and the paper provided ample food for thought without providing a coherent framework for moving forward. Perhaps that will be paper #2 or a result of other researchers picking up the baton and moving forward in this notoriously complicated field.

Will Pearse

Will Pearse

This review really spoke to me. I think it’s hard (if not impossible) to argue that all species have the same dispersal abilities, and almost as hard to argue that variation in dispersal ability shouldn’t interact with other ecological processes. It’s a great essay – go read it. I vote for Lynsey picking all of our papers 😀

It is clearly very hard to get good data on dispersal, and I think it’s clear that there’s unlikely to be a single “dispersal” process to be modelled (long-distance vs. short-distance, etc.). Personally, I also think there’s a continuum between migration and dispersal, and the emphasis on permanent movement isn’t as important as we might think (that’s another rant for another day). Evolutionary biologists have to be very careful with dispersal; larger range sizes make speciation more likely, and if species are dispersing widely across an area I’d argue that makes character displacement a bigger deal for trait evolution. Dispersal on the ecological scale is harder to model in some ways, because it interacts with so many other processes – that’s why I think it’s excellent that the authors have stuck their necks out on the line and made definitive hypotheses about what ecological processes will be linked to dispersal. By finding ways that incorporating it into our models improves their fit, we have a better chance of detecting the influence of dispersal, and determining how, why, and when individuals disperse.

The authors flit across scales (community –> individual), and I wonder if there are two modelling approaches where dispersal could help in each. The first is meta-community modelling: the authors make a good case for how dispersal trades off against other ecological processes, and if this is the case modelling the entire system should simplify things. The source and sink dynamics they describe would simply be an emergent property of the model. The second is agent-based modelling. If individuals are making decisions to disperse based on their surroundings and preferences, then modelling that decision process is the only way to generalise across environments and (potentially) species. Maybe it would be a pain in the neck to do, but it would definitely be useful.

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!

Macroecology: Does it ignore or can it encourage further ecological syntheses based on spatially local experimental manipulations?

Macroecology: Does it ignore or can it encourage further ecological syntheses based on spatially local experimental manipulations?

"Macroecology... is not a fruitful path for thoe of us seeking to understand how ecosystems are sutrcutred and function" - Paine (2010). Image from seaotters.com

Macroecology… is not a fruitful path for those of us seeking to understand how ecosystems are structured and function” – Paine (2010). Image from seaotters.com

Will Pearse

Will Pearse

This paper made  a real impression on me; I also think it wins the ‘most polite knock-down of a field’ award, in that the first two paragraphs make it clear he doesn’t like the field but somehow he does it so politely I want to read on.

Paine is right; marine ecosystems are different, and since they’re the largest part of our planet we shouldn’t be so terrestrially-focused. I feel that much of what a terrestrial ecologist means by ‘history’ is really ‘dispersal limitation’; at evolutionary timescales vicariance and/or distance leads to speciation where we wouldn’t otherwise expect it, and in ecology it leads to species with identical environmental tolerances not co-existing. Thus when Paine identifies marine ecosystems as having huge dispersal distances (particularly in the larval stages), he’s essentially pointing us towards how terrestrial and marine ecologists are always going to view history differently. If everything truly can be everywhere, then historical contingency is a very different thing in water.

Paine is also right when he says that a species list is no end-goal for a field. Yet, for all the importance of local-scale contingency (Paine did invent the keystone species concept!), it’s worth remembering that species distribution models (SDMs) do actually work (some/most of the time). That’s not to say that they always work – trophic cascades and other biotic interactions are always mentioned but seldom modelled in SDMs – but if everything can be everywhere in water, can that change how they should be modelled? Can trophic cascades be captured by understanding the environmental conditions that enable those keystone species to survive there?

I think Paine is missing an important trick when he discusses comparative experiments. He wants comparative experiments on taxonomically similar species to identify underlying rules, and macroecology is the search for those same principles that determine a system’s rules of engagement. We study the species pool because, particularly on land, that determines what smaller-scale communities look like; maybe fundamental differences in dispersal mean the kind of macroecology Paine discusses is more appropriate for terrestrial systems. I’m always harping on about the importance of changing the phylogenetic, spatial, and temporal scales at which we examine an assemblage to help us better understand ecology. Perhaps terrestrial ecology has shifted too far in favour of laptop-jockeys like me who re-analyse datasets, and maybe we do need more local-scale experiments where we can test ecological mechanisms. Yet if broad brush-strokes without detail will never help us understand mechanism, detailed work without a context will never help us predict.

Lynsey McInnes

Lynsey McInnes

This paper is great. I think my fellow commuters were perplexed by what I was reading that was making me smile so much. As a macroecologist, I’d never heard of this man Paine until this paper came out in Am Nat a couple of years ago. But Paine is no macroecologist, so perhaps that’s OK. In fact, he is a vocal marine microecologist (I think) and is attempting in this address to argue the dual points that ‘micro’ ecology has a lot of insights to give that are impossible from macroecological techniques (fair enough, really) and then a slightly weirder, this might be my fault because I know more about terrestrial than marine systems, but not really that much about either, that macroecology is better suited to terrestrial than marine systems?

Well, we picked a nothing if not provocative paper to relaunch PEGE with.

Paine’s address is packed with home truths about macroecological approaches, but regularly (at least to me) jumps off the deep end into ridiculous. Macroecology (‘the study of relationships between organisms and their environment at large spatial scales to characterise and explain statistical patterns of abundance, distribution and diversity’) is often berated for being overly concerned with documenting pattern without a thought to processing generating patterns, and I think this criticism does stand true. However, there is a. plenty of work that tries much harder to understand process and b. more fundamentally (and this is where my opinion differs from Paine’s) I think there are processes operating at these broad scales that are of interest to identify and understand (a factor that probably contributes to so many people attempting to document the patterns these processes produce).

I’d argue that an across scales approach is the most valuable. Are local scale happenings relevant to emergent broader scale patterns? Are they divergent? How do ecological responses at one trophic level affect others? How do responses on evolutionary timescales affect things? What governs turnover through time and across space? What allows invasion from one site into another? And so on. Sure, documenting yet another latitudinal diversity gradient, or an exception to it, doesn’t get us much further in any endeavour, but a comparative analysis of food web structure across continents does.

I am not sure I followed Paine’s terrestrial vs. marine arguments, but I think the crux of it might have been that ‘local’ or ‘micro’ in marine systems is already way broader than in terrestrial systems where people can more easily summarise whatever they wish in 100km grid cells (oh the horror) and go to town with their pattern documentation. I would argue that both systems have interesting and important ‘micro’ and ‘macro’ ecology and that perhaps the easier route to deeper understanding of ecology or ecological responses comes from an objective comparison of the two (like here and here).

Lastly, Paine laments the ‘niche craze era.’ What a great phrase. And so true. I, and many others, jumped on the – somewhat specialised – niche conservatism bandwagon and went a little crazy. We documented crude patterns using deficient taxonomies and didn’t get very far in working out what drives change in some dimensions’ of a species niche and not others. This was perhaps because we didn’t know what a niche was or how to quantify as we embarked on this endeavour or perhaps because we didn’t care. No doubt about it, understanding species’ roles in ecosystems is more vital than quantifying variation along some orthogonalised niche axis, but once robust methods are devised (and I don’t think they have been yet) to quantify ‘role’ (and I mean on a ‘micro’ or ‘macro’ scale), I imagine they will simply be some axis of the (again not properly defined yet) elusive niche. I see these advances as an exciting challenge for the pretty near future than a reason for contention.

I recommend this paper to all brands of ecologist. It helped me realise I did still find macroecology and the insights it seeks to identify interesting and important, while feeling chasistised that macroecologists can sometimes, in fact often, be lax in defining relevant and appropriate research goals.

The shaping of genetic variation in edge-of-range populations under past and future climate change

Razgour et al.. Ecology Letters (early view). DOI: 10.1111/ele.12158. The shaping of genetic variation in edge-of-range populations under past and future climate change

Plecotus austriacus; photo by Branko Karapandža

Plecotus austriacus; photo by Branko Karapandža (via EuroBats)

Will Pearse

Will Pearse

This is an extremely impressive set of analyses that did make me think. The authors examine the genetic structure of these bats, find that glacial refugia contain a lot of its genetic diversity, and then show that under climate change a lot of this diversity will be lost.

It had never occurred to me that hiding from glaciers and hiding from climate change involve species moving in opposite directions, and so what was a refuge before is now a death-trap with nowhere to run to. We know that species’ traits can vary (often adaptively) within their ranges, and we know that species’ past selective pressures can leave an imprint on species today (phylogenetic signal/inertia) and can cause sub-optimal phenotypes. Thus I think it’s entirely plausible that the progeny of the colonists that survived the last great climate-shift on Earth are the ones that will be worst-hit by the next, and so might do badly in it. Of course, you could invert this and say that the descendants of those who dispersed after glaciation are now in the safest spot, and so maybe we’ll be OK. Anyway, my point is to expose my own ignorance, and to wonder whether this could help us figure out a null expectation for what intraspecific variation should look like when looking at lots of species, and improve the fit of species distribution models. Perhaps this has already been done, in which case please let me know!

I like bats (I worked with them one summer as work experience), and while I’m no expert, I feel safe saying they’re very sociable animals. I wonder what effect this will have on their ability to disperse in the face of climate change, because while they are quite choosy in where they roost, they (surely) choose a new roost as a group and as such they’re more likely to find a suitable habitat. Indeed, they must also be less sensitive to allee effects because an entire group is moving at once, and in species where males roost together they’re always having to hunt around for females anyway. I must emphasise I know very little about bats, and so if any/all of the above is nonsense please call me on it right now!

A final thought: I like this paper very much, and love the story it tells, but what will the consequences be of losing these populations of diversity? Are these differences all just drift, or are there adaptations? In other words, what would we be losing? I imagine the authors know the answer to these questions, but I’d quite like to know what they are!

Lynsey McInnes

Lynsey McInnes

Wow, this paper has a bit of everything,and, weirdly, incorporates elements of most of my interests in one, pretty impressive, whole! Niche conservatism, rane shifts, climate change, barriers to movement and my persistent pet interest genetic diversity within the range and the need to consider intraspecific variation and not just treat the range as one big, homogeneous whole. Neat.

The authors do a fine job of integrating the results from a whole host of analyses to suggest that this bat species is most genetically diverse in Iberia (the site of one of its refugia in the LGM) and is showing signs of movement north westerly into England where there is evidence of decreasing population size despite conditions here seemingly spot on for population persistence. The authors emphasise that such results underline the need to conserve edge of the range populations (Iberia for diversity, England for suitable conditions for driving forth any range shift necessitated through shifting climates). Sounds reasonable.

To be cynical, I’m actually not sure how novel such advice is. In a world where extensive range shifts to track climate are predicted (and have been observed), it seems intuitive to focus on range edges as these are the populations that are most likely to lead the movements. To be less cynical, the authors try to show this really is the case. Similarly, a whole host of studies have shown that genetic diversity is often greatest in glacial refugia, if, for no other reason, because these populations are the oldest. Nevertheless, this study is still one of the few that sample range wide populations to show this, and also find that not all refugia are similarly diverse.

The authors also take a pragmatic approach to finding evidence for niche conservatism, arguing that their ecological niche models probably are capturing the fundamental niche and not the realised niche such that their observation of temporal continuity is valid because the species already exists in sympatry with members of its genus (ie not limited by species interactions) and is absent from more arid regions adjacent to its range despite the ability to get there (if it wanted to). While these arguments seem reasonable and are better elaborated than many similar studies, I do wonder whether there are any more conclusive ways to test this assumption. Probably heating the bat on hot plates would be one way forward (dessicating it as well to test further niche axes perhaps).

I remain on the fence over the validity of ABC analyses, but really appreciated the thought that went into defining populations and models to test. I just worry a lot about the sheer amount of simulations necessary to implement such analyses. In this case, the conclusions wrought were interesting and seemed reasonable. Just out of curiousity, I wonder at what stage the ABC analysis was implemented and how much the authors had a feeling for the results already…

I’ll end this with a plea of – watch this space – our lab is working on ways to obtain analytical solutions to similar questions of demographic history and phylogeography such that there will be no need for the simulation quagmire of ABC.

In short, I was really impressed with this study, bringing together a lot of data and analyses to underline the necessary route forward to successful protection of a species. How do we now make this macro- and roll it out for more species, either across a whole clade or a whole community? Exciting times.

Will plant movements keep up with climate change?

Richard T. Corlett and David A. Westcott. Trends in Ecology and Evolution 28(8): 482-488. DOI:10.1016/j.tree.2013.04.003. Will plant movements keep up with climate change?

It's a plant moving. Look, do you have any idea how hard it is to find a picture every week?

This plant can move fast enough… From Wikipedia

Will Pearse

Will Pearse

I picked this paper (out of Lynsey’s selection) because I had a long chat with someone about this at ESA. We concluded then that we didn’t really know whether plants could move fast enough, and to be honest that’s pretty much the conclusion I came to at the end of this review.

Box 4 of the review lists outstanding problems that include “ignorance of the factors that currently limit species ranges”, “largely unknown to what extent plants can acclimate to climate change”, and a number of other factors. The section “can plants track climate change?” lasts only two paragraphs – we apparently have no idea whether plants can track climate change or not. The authors give a number of (for what it’s worth, quite reasonable) reasons they probably can’t, but I think they’d agree that we don’t actually know. Frankly, I’m slightly shocked that we don’t know more about this.

I’m not convinced that animal-dispersed species are necessarily going to fare much better in the face of climate change. This assumes that animals with larger territories are going to move more easily (not necessarily true), particularly given we don’t fully understand the mechanisms by which species would shift their ranges. An animal that eats fruits that moves when it’s hungry is not going to disperse that fruit polewards, because it’s hungry and hasn’t eaten that fruit!

Long-distance dispersal as a mechanism by which individuals trapped in a sea of bad habitat can save the species is an interesting idea. I think this would benefit from a simulation study, but I sense it would require species to be able to colonise in the face of a quite severe numerical disadvantage (small number of immigrants, lots of incumbents). Still, this is a nice idea I’d like to think about for longer…

Lynsey McInnes

Lynsey McInnes

This is a funny paper. On the one hand, a very useful, succinct review of the different factors involved in thinking about how plants might respond to climate change and why this is of interest to ecologists/conservation scientists/mankind and on the other hand, a frustratingly on-the-fence expose of plant movement research to date and its likely next steps.

The authors undoubtedly do a great job in summarizing many recent studies (check out the reference list, its stacked with refs from post 2010). This subject is most definitely timely and popular. And yet it seems we don’t know much. For example, conclusive answers are absent for questions such as what determines a plant species’ current range? How much more range could a species occupy with unlimited dispersal/removing other species/new climates? Is this period of climate change different to past ones (cities in the way, etc.)? The author’s box 4 neatly summarizes the extent of our lack of knowledge!

I got to the end of the paper and found myself wondering (a bit like last week), should we worry? Or should we worry in a more focused way? Does the identity of individual plant species matter as long as the ecosystem is still functioning healthily? If you are a ‘rubbish’ species, has your time come? Perversely, I do just find the outstanding questions listed in box 4 of interest in and of themselves, but firmly, firmly believe that for conservation purposes, they are not the correct ones to be focusing on. I’m not a conservation scientist so I’m allowed (have allowed myself) to ponder these questions, but if wanted to be practical, I reckon we need to think more about functional types (mentioned in box 1), more about corridors to facilitate movement, more about redundancy, more about … ?

Can we ever know – ‘Will plant movements keep up with climate change?’ Seems like this is not a yes or no question. It will depend on the specific set of traits the plant species has/the environment it is found in/the interactions with other species (plants, dispersers, pollinators) it has now and could have in the future? Different camps want an answer for different reasons. Generalities seem to be in place already (and are well-summarised in the paper). However, if we want to conserve species or functions, we need more than these generalities, it seems. If want to use this broad question to learn some fundamentals on the biology of plants, my suggestion would be we need more of everything: more field studies, more theory and perhaps most importantly more of a recognition and exploration of interacting forces: a bit of evolution, a few influential abiotic factors, one or two key biotic interactions, a whole host of more minor ones, across and within trophic levels, some anthropogenic effects, short- and long-distance dispersal and this whole shebang playing out against a shifting climate.

I think the paper left me unsatisfied as it was pitched too broad and thus felt too shallow. What are these authors interested in? What piece of the puzzle will they tackle? Ja, perhaps that’s unfair to ask of from a review, but I’m curious anyway.

Finally – I did very much appreciate this line from the paper: ‘The involvement of government agencies, nongovernmental organizations, and citizen-science networks will be essential, given the focus of academic science on novelty.’

Climatic control of dispersal–ecological specialization trade-offs: a metacommunity process at the heart of the latitudinal diversity gradient?

Jocque et al.. Global Ecology and Biogeography 19(2): 244-252. DOI:10.1111/j.1466-8238.2009.00510.x. Climatic control of dispersal–ecological specialization trade-offs: a metacommunity process at the heart of the latitudinal diversity gradient?

Dispersal's important too, don't'cha'know. From

Dispersal’s important too, don’t’cha’know. From Jocque et al..

Yael Kisel

Yael Kisel

Though it was a nice bonus, I didn’t pick this paper because it says that dispersal (one of my pet topics) is a key process in the creation of global biodiversity patterns. I picked it because it presents an elegant central thesis that I haven’t heard before: that climate variability may modulate species richness indirectly, by deciding whether a region’s species pool will be biased towards ecological generalists that are good at dispersing (and thus have low speciation and extinction rates) or ecological specialists that are poor at dispersing (and thus have high speciation and extinction rates). To me, this idea gives me the “how intuitive and straightforward! why didn’t I ever think about it that way before?” feeling that I associate with true scientific advance and beauty. I just love how it ties together so many key factors – climate, ecological specialization, dispersal, speciation, extinction – and the authors even manage to tie in sex (well, asexual species)! From now on this idea will definitely be a part of my mental framework of how biodiversity probably works.

There are also a few smaller bits and pieces that I quite like in here. I am quite happy with the reasons the authors give for why climate variability should select for increased dispersal. Clif notes: 1) Seasonal weather with some very harsh seasons selects for seasonal migration, which involves a lot of movement and could thus lead to increased dispersal. 2) Environmental variability will likely lead to increased population extinctions, selecting for increased dispersal to recolonize those empty locations when they become habitable again. 3) Occasional harsh environmental conditions favor the evolution of dormant stages, which also make dispersal possible over longer distances. I also really like the idea that climate-driven extinction will disproportionately affect specialized, poor dispersing species. I hadn’t thought about extinction that way before; it makes sense; and it fits into my feeling that diversification over long time periods is characterized by cycles of wide-ranging generalist species budding off lots of small-ranged specialists that don’t do much speciating and eventually die out in big chunks, allowing for another burst of budding from the survivor generalists. Finally, I like how the authors put forward a lot of specific predictions that we should go out and test, like “are tropical species usually poorer dispersers than temperate/polar species?” and “are specialist/poor dispersing species less common during times of faster climate change?” (I wonder if that second question is testable with paleo data though?).

All that said, there’s also a lot that disappointed me in this paper, and I wouldn’t immediately recommend you to read it thoroughly. I felt the authors were trying too hard to sell their idea, I didn’t understand why they needed to discuss “metacommunities” and “continuity of habitat availability in time and space” so much instead of using simpler language, and there were many specific points in their reasoning that I didn’t agree with or couldn’t follow (for instance, I don’t agree that ecological specialization and competitive ability are interchangeable). I also think the central figure is a bit sloppy – it’s unclear to me why ecological specialization should itself limit gene flow, and it’s unclear whether “isolation” refers to reproductive isolation or geographic isolation – a big distinction. I also wish that they had used the latitudinal diversity gradient as one example of a possible application of their theory, rather than the main topic, as for me that focus both limited and confused the paper. Finally, just to vent for a second about typos, I found it lame that the annoying word eurytopic was spelled wrong the one time it was used!

Moving on, I think this theory deserves to be tested properly and I see some cool ways to do that. Of course, as I said, the authors lay out a number of rather specific predictions and those should be tackled (are any students reading this that need a research project for their degree?). I also had a few more ideas while reading through. First, assuming that invasive species are generally rather generalists that thrive in disturbed areas and disperse well (correct me if I’m wrong!), this would suggest that invasive species should generally come from more climatically variable regions. Is that true? Second, though the authors really focus on tropical vs. polar species/communities, what about other gradients in climate variability, for instance between coastal regions and continental interiors? Do these gradients also show the expected patterns of variation in dispersal propensity, species richness, speciation and extinction rates, etc?

I don’t have any other big thoughts about the paper to conclude with, so instead I’ll conclude with an appeal for PEGE readers to consider doing more research that would produce results useful to me. Study dispersal! Especially with comparative population genetics or new databases of dispersal related traits! It’s fascinating, I promise!

Will Pearse

Will Pearse

I’m not a dispersal person, and I’m not much of a macroecologist, so if I say something stupid below please correct me in the comments. I liked this paper; they put their heads above the parapet, whacked out some testable hypotheses, and that enables me to be constructive in my criticism (I hope) because they’ve given me something concrete to aim at.

Dispersal is complex, and I’m pretty sure it’s not just one thing. Long-distance dispersal, in my mind, is this rare process that moves individuals very long distances. Rafts carrying seeds or stems of plants across oceans are an example of it. I don’t disagree with much of what these authors say, but I think they need to be more clear about the kind of dispersal they’re considering, and I can’t actually find much of a definition of dispersal in the paper. Is long-distance dispersal relevant when talking about regional co-existence? Probably not. Is long-distance dispersal relevant when talking about the latitudinal diversity gradient and whether the tropics are cradles or graves of diversity? Probably. I think mixing in community ecological definitions of dispersal and then using them to explore long-term evolutionary trends is a bit iffy, and (I never thought I’d say this) I’d almost like to see some kind of theoretical analysis of how some of this might work. More explicit and complex incorporation of dispersal into evolutionary processes is a good thing, but we need to know what we’re putting in.

Much of what the authors suggest comes from an intrinsic trade-off between ecological specialisation and dispersal ability. As the authors acknowledge, community ecologists have known about these sorts of trade-offs for a while, and have made them more complicated, but I buy the concept for a regional approach with the authors’ proviso that suitable habitat has to be hard to find. If you’re specialised, and your habitat is hard to find, it makes little sense to move. But that also means it makes no sense whatsoever to move, which means you’re going to be stuck as a very local-scale endemic species, unless there’s some king of long-distance dispersal process (…) that occasionally shunts you out of your local area. So, if there are rare, hard-to-find habitats, why is it that such small-ranged endemics are so rare, perhaps except for the tropics where many invoke Neutral Theory to explain how so many similar (and so not really specialised!) things are able to coexist?

Much of the above rests on my whole ‘different kinds of dispersal’ argument, and I’d be interested to hear what you all think about that. I sense I could be missing something very important!

Eighty-three lineages that took over the world: a first review of terrestrial cosmopolitan tetrapods

Şerban Procheş and Syd Ramdhani. Journal of Biogeography (early access): DOI:10.1111/jbi.12125. Eighty-three lineages that took over the world: a first review of terrestrial cosmopolitan tetrapods.

Cosmopolitan species... geddit? From Esquire magazine

Cosmopolitan species… geddit? From Esquire magazine

Will Pearse

Will Pearse

I really don’t know how I feel about this paper; I found the introduction the most interesting part because it introduced me to many things I never think about. The authors are asking why some species are found everywhere throughout the world, and they think up some pretty cool ways of looking at it. This seems very much like a first-pass at these ideas, and I’d be quite interested to see what more analyses these authors will do.

While many species are not cosmopolitan, their clade is – the authors use shrews as an example of a clade that is widespread, but the individual species within the clade are not. This paper examines how wide you have to make your definition of a clade to make it cosmopolitan; for instance, how many close relatives of the Arctic fox do we have to add before we have a widespread clade? I think looking at the number of species is much less interesting than looking at how old a clade has to be for it to be widespread. Moreover, if we know how widespread species are, can we reconstruct that as if it were (maybe it is) an ancestral state, and look at relationships between the evolution widespread-ed-ness and traits?

Their trait analysis says that flying things and big things are more cosmopolitan, which is essentially the same as saying that things that need more space (to hunt, to feed, etc.) cover a wider space. This in of itself is kind of interesting, because it makes me think about scaling. Large birds are at the top of the food chain, and as such they’re not so affected by individual aspects of ecology – they just need other birds or larger prey they can kill. They can spread across a number of ecoregions because the ecologically limiting factors for them are more abstract (some kind of bird, not just one kind of bird) and different to those for other species. Maybe there’s a relationship between trophic position and how widespread a species is.

Lynsey McInnes

Lynsey McInnes

I have mixed feelings about this paper, just like Will. It definitely felt like a first pass exploration, with lots of potential for extensions and I am totally happy to overlook some misgivings on the approach the authors took in exchange for their presenting an interesting and most definitely overlooked side to macroecological patterns.

I’ve thought a little about cosmopolitan/widespread species mostly with respect to dispersal ability. While the authors suggest good dispersal ability helps generate cosmopolitan taxa, I’d be inclined to take a more careful look at dispersal ability and what we mean by it. A good ‘disperser’ (let’s loosely define that as a species that can move ‘far’) can get to far-flung areas, but will this action produce one cosmopolitan taxon or lots of restricted range taxa? This will of course depend on other intrinsic traits, the nature of the environments the dispersed lineages find themselves in, the frequency of dispersal (continuing gene flow preventing divergence). While it feels logical that species that can reach a large area are the most likely to have large ranges, I think we also have to think long-term (evolutionary time?) to really understand how dispersal relates to distributions.

The above paragraph also relates to the authors’ attempt to define cosmopolitan with respect to single species but also w.r.t. multiple species (i.e., how many lineages do we need to make a cosmopolitan taxon?). This was an interesting element of the paper and I felt the authors could have pursued this line of reasoning more thoroughly. ‘What is a species’ is of course a controversial subject and one I won’t go into here, but, when it comes down to it, most of us are happy to recognise a ‘species’ as a special unit such that a single species cosmopolitan taxon is much more striking than a multi-species one (requiring different traits perhaps, and strong population connectivity). One route to untangling this conundrum might be to look at species’ ages. Are all single-species cosmopolitan taxa really young, and just en route to splitting up into multiple species? I imagine yes in many cases, but probably not all. What about this subset? How do they manage it? Of course, we need robust phylogenies for this. Damn.

The authors were also keen to relate their analyses back to invasion biology and there are clear parallels here. It would be fun to do analyses on cosmopolitan/non-cosmopolitan species and on invasive/non-invasive species concomitantly and see if the same set of traits (or indeed species) come up. Are cosmopolitan species already pests? Will they become so? Do we need to separate out old and young species? Do we need to pay particular attention to restricted-range species in the paths of invading cosmopolitans.

In passing, some of the discussion in this paper reminded me of this work by Purvis et al. looking at mammals on the edge of trait space. Without re-reading the paper, I think I recall the authors finding ‘weird’ species are able to make it when they occupy ‘weird’ niches. They might not diversify, but they can persist and persist because there’s nothing else like them. Are old cosmopolitan species also weird?

In short, an imperfect, but thought-provoking paper. I’d like to see these questions being pursued further in other groups and from different angles.

Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders

Wood et al. Systematic Biology 62(2): 264-284. DOI:10.1093/sysbio/sys092. Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders.

This is a guest post with April Wright. Below, we give our first impressions of this article. Please comment below, or tweet AprilWill or Lynsey (maybe use #pegejc). Think of this as a journal club discussion group!


April Wright

When I started graduate school, I envisioned doing some fusion of paleontology and molecular phylogenetics. What I didn’t envision is other researchers constantly asking me “Why?”. Why use morphology when you can have a bajillion base pairs of sequence data? Why use morphology when we have such nice, explicit models for sequence evolution?

But in the past year and a half, there’s been a series of really lovely papers forging a kind of truce between the morphological and molecular worlds, and I think this paper highlights why this is important: Fossil taxa are the only record we have of extinct organisms, and we can learn a lot about the world of yore from them. Seems like an obvious point, but from the sheer volume of people asking me “Why?!”, it apparently is not.

For a little bit of background, in 2011, Alexander Pyron authored a paper treating fossil taxa as tips, rather than calibration points on nodes, in a chronogram. And people, in both the molecular and morphological spheres were pretty excited about this. It’s an intuitively appealing idea. Often, fossils are placed on a tree as calibration points, but we don’t really know the fossil belongs where we’ve placed it. Treating the fossil as a tip in the tree allows the fossil to be placed with confidence. It’s a nice concept.

In discussions with coworkers, people at meetings and randos off the street, it became clear to me that not everyone was sold on the utility of idea. While many people liked the idea of treating fossils as tips conceptually, there are still questions about if this practice will actually result in any noticeable effect on tree estimation or the inferences drawn from those trees. The paper for this week is quite nice in that it makes use of real data from fossil and extant spiders that the authors want to use to make an inference about historical biogeography to test the effect of treating fossils as tips.

A challenge in integrating morphological and molecular data is the degree of asymmetry between data types. In combined analyses, often there are many species for whom molecular data is available, some species for whom morphological data is available, and only a handful of species with both. The net result of this is basically a molecular tree and a morphological tree held together by a couple of taxa. This isn’t the case with this paper, and I was impressed by the care taken with the sampling of morphological characters in extant and fossil spiders, though the fossils are not well-intercalated with the extant taxa (more on this in a moment).

One of the interesting results in this paper is that treating fossils as tips on the tree resulted in node ages that were older than when fossils were used as calibrations. This hasn’t been found in other studies (but, this is one of the first studies of its kind, so this pattern may be quite common, and we don’t know it yet). As I mentioned before, the fossils are not intercalated in with the extant taxa, instead branching from a single point. This odd result highlights that we need to do more research to understand the effects of using fossils as tips.

This study takes it one step further and uses the dated phylogeny they obtained to make a biogeographical inference about spiders. Using the software LaGrange, the authors looked at the historical ranges of the spider clades for which they had data. The authors support the conclusion that the breakup Pangaea into Laurasia and Gondwana lead to a vicariance event within spiders. This is a very cool result, though likely not very different from the one they would have received treating fossils as calibrations only.

I’m going on a bit long, so I’ll wrap up by saying that I really enjoyed this paper. I think this is a great example of going about a new type of analysis in a very thoughtful way. I think the primary result of a vicariance event in spiders at the Pangaea split is a pretty neat, punchy result, but there’s plenty in this paper for any methods dork to have fun with.

Will Pearse

Will Pearse

In theory, I’m a phylogeneticist, so I should probably have an opinion about how we best use fossil calibration points. As such, I’m not going to talk about spiders, or biogeography, and am essentially just going to talk about what I remember of Joe Felsenstein‘s talk at Evolution 2012 on this issue. I got very excited coming out of that talk, so I hope I’ve remembered the details correctly!

There is a very big problem in phylogenetics that I don’t think enough people talk about: how do we date a phylogeny? We can now build massive phylogenies with RAxML, but the output doesn’t tell us when things evolved, just what’s closely related to what. Programs like BEAST let us simultaneously estimate phylogenetic structure and timing of evolutionary divergence, but we need to calibrate our results with fossil data. Otherwise we’re just inferring dates based on molecular data, and ignoring when we know certain groups must have evolved given what we find in the fossil record.

Wood et al. argue that dating clades by using fossils to set prior distributions on how old they’re likely to be may not be the best approach. I agree with them. Instead of using fossils to date clades, they’re putting the fossils in as extinct taxa, and they building phylogenies around them. This is kind of neat; it means the species fossils represent become part of the tree, and the extant species get dated in the process of making a phylogeny with those dated fossils in it.  They argue that, when they use this method, their results are less driven by their prior distributions, and as a rather naïve Bayesian statistician (that’s a pun, stats fans), I agree with that. I want the signal in my data to drive my answer, not the constraints and assumptions I made at the beginning.

Felsenstein outlined what I view as almost an extension of this method. In it, you use morphometric measurements of the actual fossils, along with measurements of extant species, to figure out where fossils go within a clade. Essentially, this means you can figure what a fossil’s closest relatives within a clade were, what branch of a phylogeny they’re more like, and get the dating of the phylogeny for free because we know roughly when the fossil was put down. I view this as an improvement on the present method, because the fossil taxa are not left orphaned in their own sister group to the extant species (see figure 1 in the paper) – they’re nestled in there with them, which of course reflects how the clade actually evolved. The disadvantage is that (as far as I’m aware) it’s not implemented yet, and it is probably vastly more data-hungry.

Lynsey McInnes

Lynsey McInnes

First, thanks April for providing our first guest post and for picking a whopper of a paper!

Man, this paper was dense and I commend the authors whole-heartedly for steering a relatively clear path through the huge number of analyses performed and for extracting the relevant conclusions thoughtfully. These guys certainly know their methods, and their spiders!

I was convinced by their argument to include fossils as terminal taxa and liked their inclusion of uncertainty around the fossil ages. It would have been a shame to take one step forward (including fossils as terminal taxa) and one step back (pretending their age is known with certainty).  Their conclusion – use all the data – was hardly surprising but very nicely demonstrated.

I do wonder however whether the fossils would be as crucial if extinct and extant taxa had overlapping/the same ranges? While this paper is a cool example of distributions shaped by the break up of Pangaea, making the fossil information central to any valid conclusions, how important would fossil info be if it didn’t provide additional/new information about ancestral distributions? Presumably, in these cases, the terminal fossils would function more like extant taxa in the same area, lending more weight to any conclusions on distributions possible using extant taxa alone. I guess that would be a bit boring, and so Wood et al’s situation makes for a much more gripping tale.

Although any of the following would have made the paper excessively long and I imagine may have been covered in the Pyron or Ronquist papers the authors refer to, I wonder, totally naively, if one could partition out how strongly the fossils drive the results found, how much fossil data is needed to change the story, what happens when one fossil is misplaced (in time or space), what happens if preservation biases mean that more fossils are found in one region than another so the signal is somehow skewed…hm…I am sure there already exists a whole literature on dealing with these issues when using fossils as calibration points and this could be preyed upon to find out what would happen in this ramped up fossil use case.

That was a harsh paragraph to end on when discussing an admirably thorough, thoughtful AND neat paper and came out mostly because I’m at a bit of a loss as to how to critique such a piece of work. So I’ll just stop rambling right here!

Niche incumbency, dispersal limitation and climate shape geographical distributions in a species-rich island adaptive radiation

Algar, A.C. et al., 2012. Global Ecology and Biogeography 22(4): 391-402. DOI:10.1111/geb.12003. Niche incumbency, dispersal limitation and climate shape geographical distributions in a species-rich island adaptive radiation

Below, we give our first impressions of this article. Please comment below, or tweet Will or Lynsey (maybe use #pegejc). Think of this as a journal club discussion group!

Will Pearse

Will Pearse

I saw this work presented at Imperial College London, and I remember being impressed with Algar’s honesty. I can’t remember when I last saw someone actively drawing attention to the potential pitfalls in an analysis, and it  made me trust him all the more. This paper is a neat, self-contained look at what controls Anolis distributions, and concludes (quite rightly) that a number of factors play a role. I really like the approach they take, and I think it has potential to answer a lot of ecological and evolutionary questions.

The setup of niche incumbency as whether species tend to co-exist with things that are similar to them is nice and general, and I like the creation of these ‘morphological landscapes’ of how similar species are to one another. I think that’s a great way to visualise things across a landscape, and fits in quite nicely with previous posts about using phylogenetic similarity to improve the fit of species distribution models. Perhaps the only (likely unfair) criticism I’d make is the use of phylogenetically-constrained measures of species’ traits to make this landscape. We constrain according to phylogeny when we’re trying to ask questions about evolution; I think these processes of incumbency play out in ecological time, and so I don’t think it matters if species are similar because of niche conservatism. Put another way, I don’t care how or why species are similar, I care whether they are similar, and so I don’t see the need to control for phylogeny. Following on from this, I would be interested to ask what aspects of niche we can ascribe to the traits they measure, what aspects we can ascribe to phylogenetic similarity, and then what aspects are non-overlapping between the two. This would help us understand whether phylogeny is capturing something different to the traits they used – sort of the phylogenetic middleman problem turned around the other way.

I wonder what the effect of different spatial scales of action are on these results. Plotting maps like those in figure 2 implies that we can link these processess at the same spatial scale; lizards compete with one-another on smaller scales than climate variables, and this might complicate matters. Equally, small-scale environmental variation would mess around with this even further, although I’m not sure how I would model that (anyone?). If we really think blue-sky, perhaps agent-based modeling could be used to get at this sort of thing, although given current computer constraints we’d probably end up being limited to single species-pair interactions, and one of the great strengths of this paper is that it isn’t so limited.

Lynsey McInnes

Lynsey McInnes

Algar et al. generate measures of morphological similarity of co-occurring congeners and of dispersal cost to determine whether niche incumbency (i.e., a morphological (and thus ecologically) similar species is already there) or dispersal limitation (i.e, some factor prevents a species reaching ecologically suitable habitat) contribute in determining distribution patterns of Anolis lizards in Hispaniola or whether they are totally determined by climate (or by nothing in particular (in their null model)). They find some signal strength for niche incumbency and dispersal limitation, although measures of climate are still overwhelmingly the most explanatory factors.

I liked this paper a lot. It felt like the authors had spent a great deal of effort thinking about how best to quantify some notoriously tricky factors in a bid to unpick what really underlies the distribution of a diverse group in a restricted area. They also admirably do not harp on about the stacks of papers that generate climate-only SDMs with a biotic interaction/dispersal caveat stuck in at the end (I include my own papers here!).

I’ve been wondering for ages how to go about getting a better understanding of how the ranges of members of a clade are determined in a certain area (in my head I populate a 100×100 grid with a single species in a single cell and see the lineage diversify into x number of species each with abutting ranges vying for occupancy – in a heavy-handed dismissal of climate, I over-emphasise the role of biotic interactions perhaps). I imagine you can get quite far with (much better developed) simulations of range dynamics along the lines of Pigot et al. But this paper represents an impressive attempt to get at that type of question with empirical data (sure, Hispaniolan anoles are probably the system with the most comprehensive data ever – but why not start high?). I do wonder what other systems this approach could be used in (maybe the non-adaptive radiation of salamanders where expectations might be different if many species are ecologically equivalent? A bigger effect of phylogeny perhaps?). Amassing all the necessary data is always going to be a problem when you try and look at more explanatory factors, right?

This setup might also be useful to bring more clarity to the ‘ecological limits’ explanation for the prevalence of slowdowns in diversification. The idea has taken off in recent years and is extremely intuitively appealing, but the actual mechanisms by which a large clade in a large area (whatever large might mean) actually experience ecological limits remains, perhaps surprisingly, unclear. Do members of the clade prevent further diversification through their occupation of all available niches? What determines the niche breadth of the constituent species? Does niche breadth of the constituent species change as a clade becomes more diverse? Aspects of these questions have been tackled before, but, not to my knowledge, all in one go. Perhaps these questions are relevant to a broader time-scale than what is the focus of this paper, but they run along the same lines.

The result – that there is often a significant effect of niche incumbency and dispersal limitation, but climate still matters is not at all surprising, but it is nice to see it quantified. I wonder at the usefulness of their null model – all non-null models were so obviously going to be better – perhaps comparing climate-only versus climate + extras would have been sufficient? But maybe this is a more philosophical question on the relevance of null models.

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