Phylogenies support out-of-equilibrium models of biodiversity

Manceau et al. 2015 Phylogenies support out-of-equilibrium models of biodiversity. Ecology Letters 18 (4): 347-356

Overview of speciation underManceau et al.'s model.

Overview of the new Speciation by Genetic Differentation model of Manceau et al.


Will Pearse

It’s been a good few months for Neutral Theory in Ecology Letters (…and so, by extension, PEGE!). In this paper, Manceau et al. put forward an extension of Neutral Theory, including a new model of speciation (Speciation by Genetic Differentation), and relax the dependence upon a static metacommunity. Both are exciting extensions to the theory.

The concept of the meta-community is something that’s always troubled me about Neutral Theory, because it seems a bit much to appeal to something outside the system to keep the system stable. Yet at the same time the only thing I can think of that’s less realistic than a meta-community is not having a meta-community, since clearly no community evolves in isolation. In this model the meta-community can change through time (i.e., it’s not at equilibrium); it’s no longer a deus ex machina, and is instead a part of the ecological theatre (see what I did there? :p).

Equally, the speciation mechanism the authors put forward is a useful development. I’m a fan of protracted speciation models, but my general problem comes from fitting them onto a specific evolutionary process. I don’t doubt they describe pattern and process well, but they don’t seem to be linked to one process in particular. Thus the genetic differentation model the authors suggest is, to me, extremely exciting. As with all these exciting new models, it’s almost a shame that the cleverest bit – the maths – is too complex to present in the body of the paper (I say almost a shame, because I’m certain I wouldn’t understand it!).

To me, the most important concept in this paper is that telling phrase ‘out of equilibrium’. Arguments about whether diversification is or isn’t density-dependent are never going to go away, but there are some who are calling for the debate to happen in the context of recent ecological theory about what carrying capacities in systems look like. Personally, I think that a discussion on density-dependence has to happen with an understanding of species’ abundances, and that means individual-based models. Work like this is an important step towards this.


Lynsey McInnes

Lynsey Bunnefeld

It has indeed been a good couple of months for neutral theory at PEGE. Here, we have another tweak to Hubbell’s original theory to bring phylogenetic tree topologies more in line with empirically observed trees. Specifically, the authors tweak the speciation mechanism from point or random fission speciation (i.e., instantaneous) into ‘speciation with genetic differentiation’ such that new species form only when they have accumulated enough mutations to be distinct genetic ‘types.’ Furthermore, the authors relax the assumption of constant metacommunity size instead allowing size to vary stochastically according to the growth (birth – death) rate of the clade.

I must admit I read this paper far quicker than it merited, so my thoughts are a bit hazy and any qualms might be unfounded. On that note, here goes…

I did appreciate the positivity bouncing around in this paper. The authors were resolutely positive about the capacity of phylogenies and macroevolution in general to inform us on diversity patterns. This was nice to see as many people, myself included, often despair on the ability of phylogenies to tell us anything.

Their two tweaks to neutral theory also sound, on the whole, sensible tweaks that make sense given what we know about species and given that we agree we want to retain the simplicity of the neutral theory while identifying the key assumptions that make it fall down.

First, speciation by genetic differentiation. Indeed, closely related species generally do differ genetically. Whether this difference is just an accumulation of neutral mutations or some kind of adaptive divergence (and which of the two kinds is more common) is another question. I felt like the authors could have discussed this issue more deeply because as a naive reader I was left wondering about the biological reality of such an abstract speciation mechanism. Sure, the model does not claim to be 100% realistic, but a discussion of the different signatures expected depending on the speciation mode would have been nice. The authors talk a lot about future directions and models they would like to compare theirs too (e.g., Pigot’s biogeographic model) and I look forward to hearing about these extensions. They somewhat cryptically refer to some lineages acting like speciation hubs that presumably shoot out new species willy-nilly. What kind of lineages would these be? Large ranged? Sexually selected? Weird mating system? Host shifter?

Second, growing/shrinking metacommunity. I agree with the authors that a constant metacommunity seems unreasonable. But I would have liked to hear more about how a growing/shrinking metacommunity might come about. Are we talking about finer partitioning of a finite area or colonisation of new habitats or competitive exclusion of crappy species, or what? Is a metacommunity the right term to use when we are thinking about the interactions of ENTIRE species. Could populations of the same species occupy different metacommunities? (Meta-metacommunities!! :$).

My hunch is the authors have also thought of all of the above and this is just a first pass attempt, albeit an impressive one that (again) shows that with just a few small tweaks the overall premise of the neutral theory is really useful in understanding general diversity patterns. I remain on the fence whether all this tweaking is destroying the original premise of the neutral theory (as I see it, to provide a conceptually simple null with which we can work out which non-neutral processes really do matter).

 

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A mean field model for competition: from neutral ecology to the Red Queen

O’Dwyer & Chisholm 2014 A mean field model for competition: from neutral ecology to the Red Queen. Ecology Letters 17: 961-969

I'm reliably informed that this is actually quite simple to understand! Equation 2 from O'Dwyer & Chisholm.

I’m reliably informed that this is actually quite simple to understand! Equation 2 from O’Dwyer & Chisholm.


Will Pearse

To spoil the punch-line, I’m not sure I completely agree that the model in this paper is biological defensible, but I’m quite certain this is a very important contribution. The authors have found a way to incorporate species differences into neutral theory: the most recently speciated species out-competes all others, and as a consequence phylogenetic branching times become more reasonable. Much ink has been spent suggesting Neutral Theory will form the building blocks of models that incorporate species differences, and this (finally!) is an extremely important piece of such work. My main concern is that I think, to be biologically defensible, there has to be some kind of inheritance of fitness from the new species’ ancestor. The only way I can see the youngest species being the best is if the driving force of biology is pathogens – the authors point towards this, and somewhere Ricklefs is jumping for joy – but I just can’t see it. To me, this would require that we change (again) the scope of Neutral models from covering species within the same guild to covering the same ‘pathological guild’. Moreover, I find it hard to believe that each speciation event is coupled with a magic trait that pathogens must evolve, from scratch. Surely a species in a large clade, presumably with an equally large body of pathogens, is even less likely to have such a trait evolve, and we have yet another way for diversity-dependence to rear its head. That said, all is certainly not lost, and this is an (extremely impressive) start. If a similar model could have multiple guilds nested within itself, and allow some degree of exchange between the guilds, I would have little trouble getting behind it. Using diffuse competition to approximate the competitive hierarchy was a wonderful moment in the paper, and it’s fantastic to see an argument used to defend Neutral Theory extending, not defending, it. If we can use these kind of approximations to bring even more niche-based concepts into Neutral Theory, things are looking up!


Lynsey McInnes

Lynsey Bunnefeld

I am still on the fence about this paper. On the one hand, I admire how they have taken neutral theory and changed it a bit in order to produce predictions that more closely match what we see in reality (specifically, they assume new species are fitter than all older species and that leads to more realistic distributions of species ages than the hardcore neutral theory where all individuals are equivalent). This is impressive. On the other hand, this is a bit of a weird tweak to make and doesn’t really seem to be biologically defensible, at least not generally.

I like the idea of neutral theory. I like its simplicity and the fact that it is remarkably good at predicting a lot of recurrent patterns we see in nature. I even like the way it sometimes fails and I really like that it can really irritate people. It is fun to watch people get stressed out about it. I agree that if it is to continue to have relevance, it needs to be continually scrutinised and tweaks applied and tested. This paper provides a remarkably simple and tractable tweak to deal with one of the outstanding issues with neutral theory – that is tends to predict unrealistically long species ages. By making new species fitter than older ones, the authors are able to purge communities of older species more quickly and so reproduce patterns that more closely match those observed in nature. Neat.

But wait? Are new species typically fitter than old ones? The authors’ argument for yes appears to hinge on the new species being free, or at least relatively more free, of nasties that could hold them back. I’m no expert, but my intuition is that not all, or indeed many, new species are ‘free’ in this way. Indeed, don’t most species come about through divergence in geographically or ecologically distinct arenas and might be really quite similar to their close relatives apart from in a key few traits (and not even that sometimes). Indeed, there seems to be mixed evidence at best that you shed the majority of your parasites upon speciation.

OK, but if the assumptions of this model sit uneasily, what other tweaks might be made to neutral theory to reign in unrealistically old species ages? At this is when the authors’ ideas become harder to put down. They have recognised that you need to find something that ‘gets rid’ of older species and their idea seems at least a bit better than species just having an ‘intrinsic’ life span (cycle of life style). An idea that has been bandied about, but with lots of quite robust refutation too. What else might do it? Some kind of slowing down of adaptation to changing environment? Some kind of competitive density effect? Some kind of lag in competitive interactions (your enemies catch up with you and get rid of you?). None of these sound particularly promising.

And so, while I might not agree with the authors’ model I’m pretty happy that people are producing such models and refining and refuting things further. One day we might be able to figure out where these recurrent patterns in biodiversity are coming from and the relative importance of niche and neutral processes. We won’t get there without trying.

The metacommunity concept: a framework for multi-scale community ecology

Leibold et al. (2004) Ecology Letters 7: 601-612. DOI:10.1111/j.1461-0248.2004.00608.x. The metacommunity concept: a framework for multi-scale community ecology

metacommunity_types

Naughtily, this is a diagram of (roughly) the same concepts as discussed in this paper but from Logue et al. (2011). NM: Neutral Model, PD: Patch Dynamics, ME: Mass Effect, and SS: Species-Sorting.


Will Pearse

Will Pearse

What surprised me most about this paper was how much of it I feel I have absorbed, and yet I can’t consciously recall reading it. It’s a classic in the field, and I think either influenced or consolidated a lot of what people thought about metacommunity structure. It’s a great paper, and if you can’t recall reading it I suggest you go ahead and do so.

I don’t want to dig up old ground, but I was pleased to read the authors making explicit claims about how different processes would be picked up depending on the evolutionary history of the system. It’s great to see an attempt at integrating fields (when was the last time you heard someone call Neutral Theory a metacommunity model?) that doesn’t just stop at the line of ecology. Last time we discussed whether species truly neutrally dispersed, and how dispersal traits can interact with traits that we consider in a classic ‘here’s my quadrat what’s growing in it’ ecology. Metacommunity dynamics open up a whole range of additional processes and evolutionary interactions that can be simulated and estimated using empirical data – although whether we actually do that is a different question.

The authors claiming not to have covered spatially explicit models got me thinking. When we say ‘spatially explicit’, we typically mean ‘each individual has an x,y(,z) co-ordinate which we model’, and these models can be very difficult to fit. I think the authors are right that we don’t always have to use such models to capture interesting dynamics – three levels of hierarchical spatial nesting are often enough for me! However, if we were to fit a spatially explicit model over a large enough area, with different habitat types and dispersal across the entire space (perhaps separating between long-distance and short-distance dispersal), we should essentially be able to replicate metacommunity dynamics. I don’t think I’m alone in saying that, while there is a metacommunity, there’s no real such thing a community – it’s just what individuals happen to be in the unit that we’ve defined at that point in time to be useful for us to study something of interest (here’s some Vellend). It’s communities all the way down, each capturing a different scale of interactions or species, and perhaps we would have a better chance of capturing such dynamics if we examined whether we can get meta-community-like behaviour emerging natural from spatially explicit models. In passing, for every person who emails/comments screaming about how communities are real, I will donate $1 to the ‘I made a sweeping statement sorry everyone’ fund.


Lynsey McInnes

Lynsey McInnes

Contrary to Will, I found this paper tough-going. Not because it was bad, uninteresting or poorly written, probably just because it was extremely dense. And my mind constantly kept wandering and wondering – was this really published 10 years ago? How have we moved on from here?

I’ve always had a soft spot for meta- type models while never knowing many of the details. But from my ill-informed sideline position, I don’t really feel like we have moved on much from this landmark paper. Have we? Correct me if I’m wrong.

So, that nagging feeling led me to wonder why we might not have moved on much? Is it a data availability thing? A model availability thing? A every collection of ‘communities’ is different thing? Or what? Ja, ja, it’s probably just a combination of all three and more.

So, where would I like to see things go? Well, unlike me, I think we need to spend more time working out what makes a metacommunity ‘real’ before we can really tackle how it fluctuates through space and time. Maybe a good place to focus would be working out what populations within a ‘community’ interact, how stable or transient these interactions are and then add in links to neighbouring communities and quantify how strongly connected they are. I say – use genetics! Use the genome. Let the populations tell you how they are related to each other. Fit admixture models. Fit migration models. See how congruent models are among populations. Sure, this perspective is limited to a distinct time band, it won’t work for really transient metacommunities, but it will work for established ones and could help identify which populations are stable within (meta)communities and which fluctuate in importance and could lead to more informed models for faster-turnover metacommunities. If we use genetics to let populations speak for themselves, we also won’t go wrong if we add another layer of complexity and incorporate trait variation. We might be considering six communities, each with an overlapping set of species, but spatially-distributed populations of the same species will not have the same trait complement. Recognise this! Quantify it! Find out how it happens and why it matters!

No doubt these models are already been fitted, but how much crosstalk is there between pure ecologists, metacommunity ecologists and population biologists on the one hand and geneticists on the other hand. Let’s integrate!

My big dream is for us to one day understand how diversity gets organised from the scale of individual interactions through community dynamics to shifting ranges and ultimately species’ turnover. We will not get there without more communication from the people best placed to understand the processes occurring at each scale. The metacommunity concept is a great place to start as it links individuals, populations, trophic interactions and communities. We just need to use the best data to make inferences about all of these.
*Apologies for the rushed, overly exclamation-marked rant… Metacommunities are a great concept, let’s see how far we can push them. (And apologies if all this integration has happened and just passed me by…).

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.

Mechanisms of maintenance of species diversity

Peter Chesson. Annual Reviews in Ecology, Evolution, and Systematics 31: 343-366. Mechanisms of maintenance of species diversity

Species' relative abundances fluctuating over time under various models of coexistence. If you just want to think of it as a pretty picture, that's probably OK too. Figure 2 from Chesson (2000).

Species’ relative abundances fluctuating over time under various models of coexistence. If you just want to think of it as a pretty picture, that’s probably OK too; we won’t tell anyone. Figure 2 from Chesson (2000).


Will Pearse

Will Pearse

I’m shocked how many people consider this a classic that “must be read” and yet haven’t read it themselves because it contains “too much math”. I don’t care if you haven’t read this (I’ve not read every paper most people consider a classic), and I think focusing on what people haven’t done is pointless, but I think this is a very readable coverage of what is (otherwise) very difficult math. I do find this field very math-heavy, but with only 9 equations (~1 per 3 pages) this is a really insightful review that for novices like me is helpful.

Chesson very nicely re-phrases coexistence around the ratio of species’ competitive differences and their niche differences; if species are sufficiently different, or compete sufficiently little, they will coexist. This came up an awful lot in the community phylogenetic talks I attended at ESA last year, in part because it torpedoes the assumption made by many that closely related species are more similar to one-another and that’s all that matters for co-existence. I manically circled the idea that species’ niches have an effect (e.g., reducing resources) and a response (e.g., ability to grow given certain resources). Chesson seems desperate for us to stop thinking of a niche as something that is solely a function of a species itself: it’s a function of the context within which we see the species, and that is always shifting. Even when we say a species’ niche involves competing with other species, we’re still missing the key component that the species is using up resources, thus warping the effect-response space that all the species around it experience and themselves modify.

Which sounds a lot like I’m saying the paper is about non-linearities and changes through time; it isn’t, and Chesson very artfully points out that a lot of insight can still be had by setting up simple models in well-considered ways. It is pretty dismissive of Neutral dynamics (…although it was written in 2000!) and the take-home from the section/paragraph “nonequilibrium coexistence” could be paraphrased as “stop using this unhelpful phrase”. I was particularly struck by how Chesson viewed the importance of Neutral Theory for exploring biogeographical dynamics; more than a decade later we’re starting to do this, and we’re even having discussions of how species can evolve, under neutral dynamics, to not be neutral today. This opens a whole can of worms as to what we can usefully call a N/neutral model, but more importantly helps us unify questions at a number of different levels of ecology. Which is a good thing!

Much of what’s in this paper is probably uncontroversial to a community ecologist (right?), but I think remarkably little of it has found its way into the mainstream evolutionary biology literature. I find that interesting because I’m often surprised by how much evolutionary biologists keep track of what ecologists are doing. I can’t think of any serious modelling studies where species’ effect and response traits are seriously modelled across a phylogeny (please correct me!), and I wonder what we would find if we looked.


Lynsey McInnes

Lynsey McInnes

I can’t imagine I am the only PEGE person to have cited this paper on the mechanisms of species’ coexistence without having carefully read it? Its been cited 1694 times! So, choosing it for this week’s PEGE was a great excuse to actually sit down and use some train time to read it through and through.

Now, I have always cited this paper when writing about macroevolution and the idea of equilibrium species numbers and turnover in ‘evolutionary’ time. Oops. Chesson sidelines this view of species’ coexistence early on in his paper and instead focuses throughout on ecological/contemporary notions of species’ coexistence in a – relevantly sized, more or less closed – patch. No matter, I am convinced that most if not all of what he talks about is also relevant or at least interesting for people working at longer timescales.

The problem perhaps is that too many people have jumped on the bandwagon of these ideas being relevant to understanding the build up and maintenance of species diversity that we have become blinkered to the possibility that ecological limits might not be constraining diversity at broad (temporal and spatial) scales. It feels so easy and so neat to extrapolate Chesson’s (and others) equations and explanations of how populations of species manage to stably coexist with each other (a delicate balancing act of getting more intraspecific than interspecific competition, with divergence along at least one relevant niche axis) to how ENTIRE species diversify in the presence of one another until their niche space (in physical or ‘hyper’ space) is full. It is also really easy to obtain patterns, for example in phylogenies, that agree with the idea of diversification slowing as niches fill up.

I have a feeling we are on the cusp of entering a new phase of macroevolutionary analyses where we break ranks with trying to match one for one ecological and evolutionary phenomena. I think it is already much more common to think of what units within species evolve (populations/metapopulations depending on gene flow) and also to think of niches as much more labile (e.g., what about niche construction or extent of niche breadth). Similarly, in both macroecology and macroevolution, biotic interactions are moving from postscript to centre stage as more data becomes available to address the effects of biotic interactions on the patterns we can observe and experimental systems are emerging where these effects can be empirically manipulated.

Turns out no matter how hard I try to leave it behind, I am still a macro-scale biologist at heart and it is fun to pull out the macro-scale implications of more or less any paper that I read.

Why abundant tropical tree species are phylogenetically old

Wang et al. PNAS 110(40): 16039-16043. Why abundant tropical tree species are phylogenetically old.


Will Pearse

Will Pearse

I’ve really come to appreciate Neutral Theory. Great conceptual leaps have come from thinking neutrally, such that drift is something a generation of ecologists now take for granted as part of orthodox ecological theory. I think this paper is a perfect example of the exciting work that can come from predicting evolution from ecology, and it’s something Neutral Theory helps make possible.

That said, I have two (slightly snarcky) criticisms. The first is I don’t think ‘species age’ is necessarily the most useful thing to be working with because a lot of things go into species age, and so it doesn’t make for the best test of many models. For example, extinction of closely related species will increase species age – if your thirty closest relatives die, you look older. The second is using a phylogeny from Phylomatic to make predictions about close relatives, because such phylogenies tend to have less resolution among congeners and close relatives. You can see this problem in the horizontal lines in figure 2a – all the congenerics have the same age because they’re within the same polytomy.

More fundamentally and less snarkily, this paper makes me think about models of speciation. What would protracted speciation look like when plotted like this? Do we find these patterns with species that undergo frequent hybridisation, like oaks? I think one of the great strengths of Neutral Theory is it lets us make predictions about the shape of present-day phylogeny, and more papers like this that move from evolutionary process to ecology are only a good thing.


Lynsey McInnes

Lynsey McInnes

First, apologies for the delay in posting PEGE this week, my fault entirely.Now, onto the paper. This was Will’s pick this week (because he loves Barro Colorado Island) and I gamely went along with it. As ever, I spent less time with the paper than I should, but found it really thought-provoking, if a bit odd in places.I like neutral theory and neutral theory predictions. It appeals to the side of me that doesn’t intuitively know what the ecological differences are among species, I like that you can start from a point where there aren’t any. And it amuses me that a theory can rile people so badly. In addition, I love most studies that attempt to bridge across scales and believe that there is a lot to be done in this area using neutral theory. Sure, we’ve come a long way since Hubbell’s hastily added speciation mechanism in the original book, but I don’t think we’ve exhausted possibilities yet.

I’ve got a confession to make. I’ve long been intrigued by range size, but never got to grips with abundance (my macroecological background rearing its ugly head again). So, the intricacies of this analysis did elude me a bit, but basically the authors find that if they add variable speciation rates to an otherwise neutral model they recover the empirical positive correlation in species age and abundance found for some tropical trees. Without the addition, the relationship should be flat or humped depending on speciation mode (mutation- or fission-, both a bit dodgy). The authors do mention that abundant species are usually also large ranged, so I could perhaps sub in range size for abundance and feel more comfortable (but would likely piss someone off).

The authors discuss how the range size-age correlation is often explained by niche differences, large range species are ecological generalists and buffered from extinction from, e.g., climatic fluctuations. They suggest their neutral model is more parsimonious than invoking niche differences and put forward ways to test this. I have a feeling their model would fall down in the face of these tests. There is also the chicken and the egg issue that there is plenty of evidence that most (all?) large range species are (at least now) more generalist than small range species…they have to be just to occupy really large ranges.

So, there is something circular at looking at ages, abundances and ranges in a neutral setting. One somehow needs to look at species as they speciate (and then they are all young) and the hunt to find reasons why some species are old (bad/unwilling to speciate) and especially how some species are old AND large ranged/abundant seems to remain unanswered. Models such as those in this paper and related ones might be the way to go, but it is going to be hard to avoid circularity.

One other thing that is dodgy and difficult to get around is how to define a species’ age. We don’t often know what species budded off from which or whether a split was more ‘even’ and this impacts on what is ‘old’ or not. Resetting age at every node of a phylogeny seems a naive (but understandable) way to go about things (and lets not even get into what extinction does to these ages).

Oops, this came out as a bit of stream of consciousness. Great paper for mulling over and I welcome all attempts to bridge macro and micro, evolutionary and ecological scales of analysis. The world is not neutral, but it seems like there is a lot to be gained from starting from the premise that it is.

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