Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub-Saharan Africa

Fabian et al. (2015). Journal of Evolutionary Biology. Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub-Saharan Africa

Various kinds of Drosophila melanogaster mutants. I don't think any of these show clinal variation across Africa!

Various kinds of Drosophila melanogaster mutants. I don’t think any of these show clinal variation across Africa… Taken from D’Avila et al. (2008)


Lynsey McInnes

Lynsey Bunnefeld

I picked this paper on a whim as it looked like it dealt in genetics and ecology, but not in the phylogeographic sense that I am usually drawn to. I liked it a lot, mostly for the approach it outlined rather than any specific results.

In brief, the authors are looking to see if they find evidence for adaptive differentiation in life history traits among tropical populations of Drosophila melanogaster as a function of altitude or longitude, arguing that such clines are seen as a function of latitude, and longitude, and particularly altitude, could be considered parallel gradients in environmental conditions. Indeed, they purport to find evidence for this differentiation.

I had some doubts about aspects of their methodology, particularly the mismatch in the genetic resources they assign to each population (i.e., they do not come from the populations they sampled for life history variation), but I am also happy to believe that irrespective of some potentially dodgy leaps of faith, the results they uncover do reflect reality.

And so, I really enjoyed this paper. My brain is still wired in as a macroecologist and any paper I read that tried to tackle some of the many assumptions of macroecological analyses is an impressive one to me. Here, the authors have taken a small(ish) dataset from a band of tropical populations and measured a ton of stuff in order to test a specific hypothesis on differentiation expected as a function of a geographic cline. Sounds so simple, but is not really that common in macroecology despite its concern with spatial diversity patterns. Oops.

And then you come to the next macroecological qualm. OK, Drosophila melanogaster is a wide-ranging species, so intraspecific variation is to be expected, but so are many other species and it is not so often (although things are definitely improving) that macro scale studies consider this intraspecific variation in life history or ecological or behavioural traits. We need more of this!

One could argue that the scale that macroecology operates on means that this kind of variation is not important, that it gets swamped by interspecific variation, but I doubt it. Because, on the flip side, there IS a general consensus that processes acting at multiple scales matter to understand species diversity patterns, so finer (and conversely broader) scales than species-as-unit analyses are relevant.
Don’t worry, I don’t think I am the only person to think this way, I am just still in the beating myself up about how late these things have dawned on me phase.
So, what to do? We probably need more sampling, more genetic resources, more models and better formulation of testable hypotheses. But the hardest thing will be (at least for me) accepting that really interesting insights can be made using model systems or subsets of a taxonomic group, gone is the possibility to use ‘all mammals’, ‘all birds’, etc. (Yes, I am that kind of dirty charismatic vertebrate macro person).  Perhaps general patterns/rules of thumb will emerge quite quickly, along the lines of you need a range of this size to show X and a body size of this size to show Y, or you need to live in environment A to show Z. And then the really interesting part will be piecing together how well intraspecific diversity patterns might predict speciation or extinction probabilities.
Interesting times.

Will Pearse

It’s hard to argue with a paper that does exactly what it says on the tin. This is a nice demonstration of variation within a species across environmental gradients, and an excellent demonstration of how to set up a question and then just go right ahead and answer it.

I was struck by the lack of variation in viability despite the variation in what many people would call life history traits. It’s sobering to consider that there can be this much variation in how a species operates, and yet no general variation in something that’s quite an important component of fitness. Traits play out in their environmental context, and if there can be this much variation within a species we should all be a little more careful when interpreting the importance of very slight differences across species. Of course the authors get at this with their trade-off analysis, but for me (at any rate) it was a nice reminder. I liked that the authors linked all of this variation to climatic variables, but unless I missed something I didn’t see where they explicitly tested climatic factors vs. geographical summaries. I do buy their argument from parsimony that temperature (not altitude + latitude + longitude), and I imagine co-linearities made testing things difficult, but somehow I wanted to see it.

Speaking of variation, staring at the regressions and their oddly high r2 values (I’m becoming a pastiche of myself), I noticed that mixed effects models they used detect a lot of within-line variation. I’m not saying this as a criticism; rather, I think it’s incredible how they were able to partition this out so neatly. It really drives home the importance of variation within species (and populations!), and definitely got me thinking about how biased our measures of trait values are going to be if we can’t grow species in culture like the authors were able to do. I really do just take gene-environment interactions for granted, and completely ignore the micro-processes that Lynsey is now studying. Maybe we do need to start more explicitly linking micro-processes to the macro-ones that I tend to think about.

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Climatic niche shifts between species native and naturalized ranges raise concern for ecological forecasts during invasions and climate change

Early & Sax (in press). Global Ecology and Biogeography DOI: 10.1111/geb.12208. Climatic niche shifts between species native and naturalized ranges raise concern for ecological forecasts during invasions and climate change

regan_niche_shifts

Come to America – fame, fortune, and the chance for a fresh niche! Figure 3 from Regan & Sax.


Lynsey McInnes

Lynsey Bunnefeld

I like this paper a lot. It plays to all my new found interests in, what I like to call, intelligent macroecology. It takes a small subset of species (50 or so plants that are native to Europe and naturalised in the United States) and conducts a suite of well thought out analyses on them in order to ascertain if there are any general patterns in niche shifts following facilitated expansion of the native range. Sure, not all European plants naturalised in the US have been looked at, but that doesn’t matter one bit.

Early & Sax draw heavily on comparisons with another recent study by Petitpierre et al. who showed that multiple large range agricultural weed species show little evidence for niche shift following range expansion. In contrast, Early & Sax find plenty of evidence for major changes in niche position and niche breadth (alongside evidence of species with little or no niche shift).  They argue that Petitpierre’s dataset is unlikely to be representative of the majority of species which are range-restricted and have little history of human-assisted movement into a broad niche space. So, while this study does not refute their findings, it does expand them to provide a more nuanced picture of potential outcomes.

I am as guilty as the next person of glibly stating that range limits are mostly climatic at the macro scale and that, although biotic interactions probably play a role, its 100% fine to base conclusions and indeed policy on the idea that the niche that species are currently realising would be similar anywhere on the globe. This paper and a suite of others are rapidly kicking down this argument. Small scale transplant experiments and other comparative datasets are indicating time and again that a species’ realised niche is delimited by much more than just climate.

This is, of course, a problem for the massive field of predicting species’ responses to climate change.  Species are commonly expected to move, adapt or perish in the face of an altered climate regime. In fact, they might also be able to tap into an ability to occupy a wider or different niche without evolving new adaptations. Conversely, if other species ‘get there first’ they might lose niche space to a novel competitor.

These findings are both really interesting from a how do macro niches work in principle perspective as well as a what on earth is going to happen in the very near future perspective. I think they argue for an ecosystem or community (however you might choose to define either of those concepts) wide perspective. If biotic interactions or historical contingencies or even landscape barriers are really influencing the niche space that many species are currently occupying, we have no hope of predicting how species will respond to climate change (because don’t get me wrong, climate still has a major influence on occupiable niche) if we don’t also consider how species are influenced by the actions of others. Sounds simple, but it probably isn’t.

I don’t know much about network analysis at all, but it seems like this is the way forward (see last week’s post too). At the most broadest scale, one could look for the primary species with which the focal species interacts within its range, one can also focus on similar species found surrounding the focal one’s range that might be playing a similar role and thus excluding the focal one from range expansion. I think it is crucial to think more broadly than phylogenetically-close relatives but also look for functionally-similar species. And of course add in trait variation of all involved parties through space and time. Of course.

In conclusion, a great paper that adds to the growing voice among macroecologists that climate alone just won’t cut it. Not even for just understanding how spatial diversity patterns come about, let alone for conservation of these patterns into the future.


Will Pearse

Will Pearse

This paper deserves some attention. Using a quite amazing dataset, the authors (Regan has posted on PEGE!) looked at the native and introduced ranges of plants. They found that species’ introduced ranges often extend beyond the conditions of their native range (which they term niche shift).

Isolating when species distribution models fail because they don’t account for non-stationary processes like dispersal is a really, really important thing to do. Dispersal ability is the problem that a lot of people bring up time and time again – interestingly, dispersal ability had no correlation with species’ niche shift. However, time since introduction did, and the explanation given for that (time for humans to spread the species) is essentially dispersal limitation. I think another thing at work here is release from biotic controls – species evolve in a regional community, and when they get into an area with a radically different biotic community (…when they’re spread around more by us…) biotic limitations are relaxed and they can tolerate more novel environmental conditions. I think I just re-regurgitated some Ricklefs, but with maybe less of an emphasis on pathogens. The most range-restricted species seemed to show the greatest increase; assuming this isn’t some sort of artefact (lesser range –> more likely to detect increase) then I think these species should be more limited by species interactions.

Which brings me to what I think is the part of the paper most likely to annoy people – that we might have over-estimated species range change under climate change if we assume everything is niche limited. I think we almost certainly have, but I would caution that range expansion in a completely different continent is different from range change at home. Leaving aside the arguments above about species co-evolving, under climate change the entire community is being stressed, whereas in an introduction/invasion the new species is both the invader and the sole novel stressor. Moreover, there is a lot of variation in these results,: I find it quite harrowing that while the authors were able to explain some of the variation in niche shift they couldn’t explain it all. Put frankly, we still don’t know what’s going to happen to species’ ranges under climate change, and (to me) that’s terrifying.

The latitudinal species richness gradient in New World woody angiosperms is consistent with the tropical conservatism hypothesis

Kerkhoff, Moriarty & Weiser  (2014) The latitudinal species richness gradient in New World woody angiosperms is consistent with the tropical conservatism hypothesis. PNAS 111:81258130

angiosperm_trait_transitions

Figure 4 from Kerkhoff et al. Diagram of ancestral–descendent transitions among different latitudinal zones


Lynsey McInnes

Lynsey McInnes

Yet another latitudinal diversity gradient/phylogenetic niche conservatism paper I hear you cry? Oh yes! I was deeply sceptical upon opening up this paper: more LDG/PNC, patchy datasets only including woody angiosperms, a dodgy family-level phylogeny. But somehow it almost won me over. If nothing else is was pretty brave.

The paper starts with a really clear introduction to the background to the question of what drives latitudinal diversity gradients, how the tropical conservatism hypothesis (lineages originate in the tropics and very few evolve the necessary adaptations to life outside the tropics, those that do then forming a temperate flora with tropical ancestry) is nested within other hypotheses such as ‘differential diversification rates’ or ‘out of the tropics.’ The paper goes on to summarise recent analyses finding evidence for or against tropical conservatism.

I also really appreciated that the authors were open as to the limitations of their dataset (patchy dataset, dodgy phylogeny, geographic restrictions). They conclude that these limitations do not prevent them concluding that they find robust evidence for tropical conservatism: most lineages are tropical, those that are temperate often have tropical ancestors. Done deal.

I’m trying really hard to distinguish between my hangups based on the dataset (e.g., is it ok to look at tropical-to-temperate transitions when the group you are looking at is not monophyletic (i.e., what about all the herbaceous lineages); is it ok to use an incomplete and family-level phylogeny (and only one at that)) and on the methodology (e.g., I did not understand their rerooting method for inferring ancestral states). I would have liked to have seen more extensive analyses that filled in the missing lineages or added ambiguity to their tropicality index and looked at any biases their restricted datasets might introduce. My gut feeling is that when we obtain the holy grail of ‘global, taxonomically comprehensive distributional, phylogenetic, climatic, and ecophysiological data resources ‘ (in the words of the authors), evidence for tropical conservatism will remain or will become stronger, but at the moment perhaps it is still presumptive to barge on pretending the data is adequate (at least without more comprehensive bias testing). Just so you know I also belong to the club of people that have barged on regardless. Maybe we all need to spend more time generating these better resources. Think of the questions we could ask when we get them.

Grumble, grumble.

Why is it so popular to investigate niche conservatism at the moment? Really, its a relatively new bandwagon which, if my rant above is anything to go by, is already ‘going out of fashion.’ What is going on? As the authors mention, the hypothesis has appeal because it integrates ecological and evolutionary drivers of diversity patterns and incorporates elements from a bunch of the most popular hypotheses for explanations behind the latitudinal diversity gradient. It’s delightfully vague in terms of what a niche is, falling back mostly on co-linear climatic factors and it can probably be adapted endlessly to include additional niche elements. All species have a niche, some aspects of which are likely to be conserved among closely-related species, the whole package is very satisfying.

Beyond getting complete data resources, a conclusive ‘yes’ to the tropical conservatism hypothesis also needs more sophisticated methods for ancestral state reconstruction. We get into a circular situation if we are looking for conservatism, but assumes minimal change across the phylogeny. Can fossils help? Can microevolutionary studies help? Can we ever really know?

Final note: extinction. What about extinction?


Will Pearse

Will Pearse

I’m not quite as jaded as Lynsey, but I admit I was somewhat skeptical about this paper; I’ve read so many diversity gradient papers that they’ve started merging in my head (like James Bond films). However, I liked this paper (like James Bond films): they bring their limitations out right away (of course it’s not a perfect dataset, they’re examining the world!) and by sticking to their hypotheses they are able to push the field forward.

Lynsey mentions the woody bias, but woodiness may not be as labile as I used to think. This either means that it’s not a ‘quick-fix’ trait that fluctuates to ‘allow’ species to move quickly (good for this study), or it means that it constrains species’ thermal tolerances and thus can affect long-term evolutionary dynamics (a bad thing for this study). Evolutionary biology is, to an extent, a historical science, and so whatever choices an investigator makes are always going to be pulled apart by someone being awkward and announcing that there was some other factor they didn’t take into account. Equally, there’s a real trend at the moment to be snarky about methods – my snarky comment is that attempting to reconstruct ancestral states over a tree of this size using either a Brownian motion or OU model is going to lead to problems. I’m not sure how much we can trust these ancestral states, but then again I’m not really sure how better they could have been done, because frankly I’m always concerned about ancestral state reconstruction.

However, I buy their hypothesis that younger lineages tend to be temperate. The question now is whether this is because of the general cooling of the Earth over the last 34 million years (as the authors seem to think), or whether it’s because it takes ~34 million years for clades to die out once they move out of the tropics. Paleo-ecologists have been asking questions like this for some time now, but perhaps now that they have a specific time-frame within which to look they have more hope of finding an answer. Fingers crossed!

Mammalian evolution and the Great American Interchange

Marshall et al. Science 215(4538): 1351-1357. Mammalian evolution and the Great American Interchange

Another kind of great American interchange - the ill-fated I-10 Papago Freeway's hellicoil that never was.  Taken from the US Federal Highway Administration.

Another kind of great American interchange – the ill-fated I-10 Papago Freeway’s hellicoil that never was. Taken from the US Federal Highway Administration.


Lynsey McInnes

Lynsey McInnes

Not quite sure where to start this week. What a great story! And a great textbook example of so many biogeographic and macroevolutionary phenomena. Marshall and Co. outline the evidence for the Great American Biotic Interchange (GABI) framed in terms of MacArthur and Wilson’s equilibrium theory of island biogeography and it sounds so neat, so tidy, almost unreal! We’ve got two different dynamic equilibria, we have different sized source faunas, we’ve got tropical and temperate fauna, we’ve got replicated patterns at different taxonomic patterns, we’ve even got an emergent uber trait for the North American fauna that enables them to infiltrate the niches of South American mammals (gotta have something inexplicable, right?).

The above sounds like a highlights summary of any recent macroecology journal. And this paper was published 32 years ago. Ouf. Sure the stats have moved on, but the patterns and conclusions. alongside the inexplicable bits really haven’t, have they?

I had two main thoughts when reading this paper. Number one was that we haven’t moved on much in the insights we are having on broad scale patterns in biodiversity. Which, in some ways, is totally fine, its not like the patterns have changed. We’ve just reinvented the wheel, sliced the cake thinner and topped it with fancy stats.

The second thought was, for me, more frustrating! Over the past couple of years, my intuitive belief in dynamic equilibria and carrying capacities and ecological limits to diversity has been thoroughly shaken. I was coming to the conclusion that these were patterns we were finding in our data because they are neat and tidy and clever and merge beautifully ecological and evolutionary time scales. My opinion was shifting that these patterns might emerge by chance and that regions are not closed enough to reach equilibrium, that biotic interactions mattered more than we gave them credit for and (meta)populations not biogeographic ranges were the appropriate units to look for the processes underlying biogeographic scale patterns, that niche construction mattered, that we were missing tons of important features in our quest to understand biodiversity patterns.

And then a paper like this comes along, and, in theory, it should do nothing to my emerging mindset as all of the above arguments could, more or less, be applied to Marshall and Co’s dataset and reasoning. But somehow the simplicity of the analyses, the merging of masses of paleo data with the explicit linking to M&W’s equilibrial theory has set me back to square one (maybe square two) in buying into equilibria in macroevolution. Wah.

Where to go from here? What data would complement what was already compiled here? What contemporary data could be added? What experiments could be conducted? What stats would we like to apply? What was the elusive North American trait?


Will Pearse

Will Pearse

I was really struck by how few papers tell as a coherent a story as this. It really is almost like a story, with remarkably little in the way of obfuscated statistics and graphs to obscure the general take-home message. In re-reading this, I think I’ve even detected a beginning, middle, and end!

I’m no expert in this field, but I was somewhat surprised how well these methods have stood the test of time. Yes, there are some who would claim rarefaction methods are outdated, but I would hope the signal in these data would overpower methodological quibbles. Equally, the equilibrium models employed here are simplistic – more sophisticated models of carrying capacities I’m sure could now be fit – but their only purpose is to demonstrate that something else is going on, and they do that very well.

What is it about North American species that makes them speciate so much more? The authors seem to come down on the side of some meta-trait, some family-level inheritance of speciation ability. I’m not someone who believes strongly in the concept of taxonomic units as real biological things (although see this, and Aelys does some great work on higher evolutionary units), but it seems there is something about these clades. Perhaps it’s related to how the South American groups have already equilibrated to a particular level of diversity – maybe there’s some kind of genetic inertia and traits associated with dispersal into a new continent give recently-moved species a radiating edge. I’m sure, somewhere, Ricklefs is screaming “parasite load” at the top of his lungs, and maybe there’s something to that. Perhaps it’s because competition is only as fierce as your competitors; the North American lineages had to fight particularly hard (more diversity crammed in? Evolutionary fluke?) and so they won out.

One thing I am certain about is that we need more stories in biogeography and evolution in general. Evolution is an inherently historical science – that doesn’t mean we can’t do comparative analyses, but it does mean that we should be a little more understanding that regressions aren’t everything. Species distributions are not stationary; different processes are operating across different spatial and  temporal scales, and there are far too many idiosyncratic events like the Great American Interchange for us to simply sweep them under the rug. More stories, fewer stats, please. I never thought I’d write that!

Climate envelope modelling reveals intraspecific relationships among flowering phenology, niche breadth and potential range size in Arabidopsis thaliana

Banta et al. Ecology Letters 15(8): 769-777. Climate envelope modelling reveals intraspecific relationships among flowering phenology, niche breadth and potential range size in Arabidopsis thaliana

Easy to forget that Arabidopsis thaliana doesn't just live in laboratories! Via Wikimedia

Easy to forget that Arabidopsis thaliana doesn’t just live in laboratories! Via Wikimedia


Lynsey McInnes

Lynsey McInnes

You guessed it, this was another of my choices. I found it a while back and was intrigued over the approach the authors would take. In brief, the paper looks at whether genotypes underlying (or rather, linked to) flowering time generate significantly different niche models (and by extensions niches) and thus can they (the authors) provide evidence that there are intraspecific differences in niche and niche breadth. A. thaliana is a great species to use to ask this question, it is an exceedingly well-known model organism and has a wide distribution.

The conclusions of the paper are far from surprising, with such a wide distribution and with known flowering time variation, it was inevitable that the authors would find evidence of intraspecific variation in niche dimensions. Nevertheless, this is really important to show! There is a whole market devoted to niche models and projections of range change due to climate change that almost exclusively treat species as a single entity. Oops. This is clearly too simplistic for species beyond a certain range size (and yes people kind of know this already). Papers like this (and the Razgour et al. paper we covered earlier) demonstrate this well. Phew.

Now here comes the issue. This paper was only possible because it builds on a ton of A. thaliana research. For instance, genetic variation in flowering time was already known and the underlying loci already characterised. The authors state themselves that defining coherent populations that might be expected to have significantly different niches to each other is really difficult (they probably could not have emphasised this enough!). Populations are rarely closed entities. They circumvent this problem here by going straight for a crude single locus genotype definition. How would you make your population buckets without this additional data? Can you? Is movement among populations (with their specific local adaptations) something that might save chunks of a species range? Probably.

If niche models don’t die a death completely, their next incarnation is going to be models which incorporate not only intraspecific variation, but also connectivity among these chunks (this is going to have to involve dispersal among spatially discrete chunks and degree of genetic exchange among co-occurring genotypes). For such models to be successful and have ‘conservation relevance’ a lot more crosstalk is going to be needed among (macro)ecologists and landscape geneticists/phylogeographers (yay, that’s me!).

This paper is a great start and I look forward to seeing developments in the field that enable it to be useful for non-model organisms (perhaps with no genetics), using multi-locus genotypes, integrating additional ecological traits, adding depth to our understanding of how populations interact to make up a range and ultimately, one day, far into the future, what a realised niche is relative to a fundamental one?


Will Pearse

Will Pearse

A lot is said about model systems in evolution and ecology, and I think papers like this, where model systems for which we have a lot of information are used to answer questions in related fields, are great.

I wear my love of phylogeny and niche conservatism on my sleeve, but that doesn’t mean I don’t appreciate a good demonstration of intraspecific variation when I see one. Flowering time should be variable in a species that spans so much of Europe, because it’s exposed to such different environmental conditions. Whether ability to adapt to novel conditions, or the general constraints that mean the species has to vary its flowering time, are as variable within the species is a slightly different question. I’ve been spending some time thinking about the inheritance of species’ potential for intraspecific variation, and I’m not entirely sure I can come up with a bullet-proof way of deciding what should, or shouldn’t, show such variation. I’d be interested to know if you can!

When I saw figure 4, which shows that earlier-flowering genotypes have larger potential ranges, I was very happily sold. I’m often somewhat nervous when I read a paper involving niche modelling or species distribution models, simply because the things seem so damn hard to get right. Therefore that the authors found any kind of relationship (albeit one with some scatter) is extremely impressive, and indicates they’ve really found something cool. The extremely tight relationship between niche breadth and potential range size is less surprising to me, both from existing theory (that the paper cites), and from the definition of niche breadth itself. A species has a higher niche breadth if “different habitats are equally suitable” (p. 772) based on the MaxEnt suitability scores for each cell, and the potential range is also defined from the MaxEnt predictions which, presumably, incorporate habitat suitability. Thus I’m not so surprised that the relationship between these two things are so strong, because I think they’re related to one-another; that doesn’t make the conclusions any less valid, but it did leave me hoping (as the authors themselves mention) that someone will be able to quantify observed range occupancy for these genotypes. If I’ve missed something obvious about the above, please do let me know – I’m no niche modeller for sure!

Hyperdominance in the Amazonian tree flora

Hyperdominance in the Amazonian Tree Flora. ter Steeg et al. Science 342 (6156). DOI:10.1126/science.1243092. Hyperdominance in the Amazonian tree flora

I can't see the Amazon for all these tree plots - taken from ter Steege et al.

I can’t see the Amazon for all these tree plots – taken from ter Steege et al.


Jun Lim

Jun Lim

Among other things, the authors set out to try to estimate how many tree species are in the Amazon, how they are distributed in space and among habitat types. They did this in part by extrapolating the total Amazonian tree diversity by fitting the mean rank-abundance data for over half a million trees within 1,000 well-studied plots in the Amazon to Fisher’s log-series. They found that there were “hyper-dominant” tree species, which represented about 1.4% of Amazonian tree diversity while representing over half of all trees in the Amazon. On the other hand, the rarest 11,000 species accounted for a paltry 0.1% of all trees! Furthermore, as it turns out, this inequity in abundance among tree species in the Amazon had an interesting spatial pattern. These so-called “hyper-dominants”, had on average larger geographic ranges, but the majority of them were found to be dominant in only one or two out of several distinct forest types, suggesting that dominant species were habitat-specialists.

This paper, however, leaves me with an intense wanting, although these findings are clearly the first of many awesome papers to come. Firstly, it would be interesting to see how these patterns of dominance generalize to other tropical tree systems, such as the ever-wet forests of South-east Asia (where I grew up, albeit in the virtually deforested Singapore). Anybody who knows even a little of the rainforests of Malaysia and Indonesia thinks immediately of the dipterocarp trees (Dipterocarpaceae) that form much if not most of the canopy.

Another thing that really got me thinking was the idea of scalar-dependency in niche specialism. Sure, if you are a species that does well in one particular soil type, all the small-scale heterogeneity in habitat does not matter much to your distribution (kinda like generalism). But in the larger scheme of things, you start to appear much more constrained (specialism). What’s interesting is that this plays out in a consistent and similar way across many species and across many different habitats. From a community assembly standpoint, this brings up the age old question of the relative importance of dispersal limitation (high numbers of species can effectively coexist even if a habitat was homogeneous) and niche-based explanations for high species diversity, especially considering the strong role of habitat heterogeneity across many systems (which filters for different communities in different parts of the landscape). I feel it is still unlikely that the relative role of these two processes will be disentangled any time soon, although this paper was a big step towards that goal.


Will Pearse

Will Pearse

It’s hard to think of an image in ecology that represents much more blood, sweat, and tears than the one at the top of this article. 567 plots would be a lot anywhere in the world, but dense Amazonian rainforest does not make for easy fieldwork. That you can go online, register, and download much of this data right now makes this even more wonderful; thank you everyone involved in RAINFOR!

Like Jun, I sense this is the first of many papers working with this dataset (and is an excellent start at that!), but I sense it may still take us some time yet to get a handle on the Amazon! I’m having some trouble getting my head around the spatial scale of this dataset, and so I’m unsure how I feel about the most common (hyperdominant) species in the Amazon being habitat specialists. In many ways I’d be shocked if species were truly generalists in the sense that they were everywhere across the Amazon, although I suppose I’d need a dataset like this to be sure! I’m particularly interested by how more diverse genera are less likely to contain hyperdominants. I’m tempted to infer that because hyper-diverse genera are more similar to one-another and have similar ranges, they are competing too strongly with one-another to become dominant. Given there’s a taxonomic effect to hyperdominance, perhaps a phylogenetic analysis would help get at these issues (…although I’d rather not be the one making a phylogeny of the Amazon…!)

I think it’s legitimate to ask how many species there are in the Amazon using this dataset, and I’m frankly amazed by how flat the middle of the rank-abundance plot in figure 2 is for the Amazon. While I agree with the authors’ general conclusions here, I am slightly concerned about extrapolating out into such low population sizes. It’s probably fair to say that no one single curve can describe both the hyperdominant and extremely rare species in the Amazon, and the extrapolation is based on assuming that a straight line that follows the medium-richness species will cover everything. I’m sure the authors would agree that this is a simplification; naively I would expect expect this estimate to be too high, yet their estimate of ~15000 species in the Amazon actually struck me as quite low when I first saw it. I guess much of this might fall back to what we’d be happy considering a species; trees are not known for playing by phylogeneticists’ rules, and maybe very rare species can survive for quite a while in the Amazon thanks to outcrossing and hybridisation.


Lynsey McInnes

Lynsey McInnes

I always open a Science paper with a slight sense of foreboding that if I want to understand even a little of what the authors have done, I’ll have to trawl through endless supplementary files. So, first things first, I really appreciate the slightly longer format of this article so that by the end of it, you have a sense of what was done, alongside the pitfalls and the potential implications. A real, whole paper; result!

And what a paper. My mind is still a bit fluffy on the spatial scale and connectedness of each plot (I was surprised there was no map figure of the interpolated richness per 1 degree cell), but that is a minor grumble. This is a massive, impressive collaborative effort to probe the distribution of trees in Amazonia. Naively, I was taken aback by a number of findings: that there are potentially >16,000 tree species (seems like a lot to me), that only 227 of them seem to dominant, that each hyper-dominant was kinda habitat-restricted. Conversely, I wasn’t surprised that species in different families were distributed differently (one or a few hyper-dominants vs. tons of restricted-range endemics) or that two well-chosen traits didn’t predict hyper-dominance.

It’s clear that such a big effort is going to generate tons of follow-on papers, many of which have been primed in this first article. There seemed to be some confusion whether to focus on the hyper-dominants and what made them so vs. the thousands of species with tiny or unknown distributions many of which the authors suggest are close to extinction. An interesting route by which the authors will follow up this paper will likely be to try to find out how important the non-dominant species are for ecosystem functioning. They seem to suggest that perhaps they are not so important. I wonder what the cut-off for usefulness vs. exciting rarity is? Does it vary among plant families? How much could we lose without having any impact at all? How much complementarity is there? How easy (and valid) will be to model ecosystem functioning or resource cycling concentrating only or mostly on the hyper-dominants?

I also found it funny that the authors did not wonder why their Maxent models predicted populations of many species in places where extensive surveys suggest they are not found. What is found in their place? Populations of phylogenetically or functionally related species? Or was some environmental or topographic variable missing? An easy (but perhaps quite dull) follow-on paper perhaps…

A final follow-on that I could think of would be to compare spatial patterns of some of the species’ patterns (a mix of hyper and non-hyper dominants) among regions and forest types (kinda like figure 4) to see if one can tease out any patterns of dispersal limitation. I think the authors conclude that many species are restricted to one or two forest types: are these generally within a region or across all or multiple regions (this might have been covered, but I missed it). If you are happy with the high levels of extrapolation (interpolation?) involved, this dataset is a treasure chest for dispersal ecologists…

So many options! And more or less freely-available online already (see link above). Let’s get going!

Achieving the convention on biological diversity’s goals for plant conservation

L. Joppa et al.. Science 341: 1100-1103. DOI:10.1126/science.1241706. Achieving the convention on biological diversity’s goals for plant conservation

joppa_hotspots

Endemic plant hotspots of the world (from Joppa et al.)


Matt Burgess

Matt Burgess

This paper, which came out 3 weeks ago in Science, assesses the feasibility of the UN Convention on Biological Diversity’s (CBD) goals of protecting 17% of the terrestrial world and, through the Global Strategy for Plant Conservation, 60% of plant species. Using data from a large database of plant species distributions, they show that: a) it is physically possible to achieve these two goals simultaneously (because they were able to find a group of regions comprising 17% of the terrestrial world containing the entire ranges of 67% of plant species); and b) that regions with the most plant species have only slightly more area protected currently than those with fewer species.

I want to start by saying that I think this paper is an important advance in the ‘hotspots’ literature. It identifies regions of high diversity and endemism using an algorithm and data that are transparent and can be updated – an important step forward from previous frameworks based more heavily on expert opinions, as the authors point out.

However, I also feel I must briefly let my grumpy inner economist out of his cage, and reveal myself to the world as a big fan of Hugh Possingham, Steve Polasky, and others who have taken somewhat more pragmatic approaches to the problem of spatial conservation planning. While this paper does an excellent job assessing the physical feasibility of the CBD’s goals, I think it could have, without much extra work, gone much further in addressing other issues affecting the CBD’s practical feasibility.

In particular, I was very surprised to not see the words ‘cost’ or ‘economic’ anywhere in this paper (I even double checked this using command + F after I read through it the first time). As we all know well (e.g.  McCarthy’s et al. 2012), conservation initiatives run on a highly limited budget worldwide. It is critical for spatial conservation planning to take this into account if protected areas are going to maximize the biodiversity protected. As a cartoon example, suppose a country has a billion dollars to spend on protected areas and must choose between protecting one area with 30 000 species at a cost of the full billion or two areas of equal size at 500 million each with 20 000 species each. The authors’ greedy algorithm would suggest protecting the first area (with 30 000 species), but more species (40 000) would be protected with the available budget if the cheaper, lower-diversity areas were protected instead. The authors remark that the areas with highest diversity identified by their analysis are not protected in practice much more commonly than areas with lower diversity. I wonder if these lower diversity areas are chosen because they are relatively cheap. The authors’ mention, in the middle column on page 1100, of a bias in protected areas towards high, cold, dry lands that are far from people seems to support this hypothesis.

To suggest that this paper should have formally addressed costs in its analysis is perhaps a bit unfair, as no paper can address everything. However, I do think the authors should have discussed them, even if only briefly. Moreover, I think incorporating costs into the conservation prioritization framework developed here is a highly fruitful area of further research. For example, this paper estimates the minimum area needed to preserve 60% of the world’s plant species. A future study might try to estimate the minimum cost of such conservation. The similar recent analysis by McCarthy et al. on birds provides one example of how this could be done. Combining spatial planning algorithms optimizing for minimum cost and minimum area could yield estimates of an efficiency frontier balancing the two that would be highly useful for policy-makers and spatial planners (see Polasky et al. 2008 for an example of a similar analysis). Some research groups, notably Hugh Possingham’s (I told you I was a fan), have actually already made some promising strides in this direction (e.g. Wilson et al. 2006). I was also quite surprised to not see this or other similar studies cited or discussed by Joppa et al.

I apologize for this somewhat long-winded post, but to conclude, I think this is a good paper that, with a little bit more analysis or discussion of costs, could have been a classic. Nonetheless, I think this study lays the foundation for tremendously fruitful further research in spatial conservation planning.


Will Pearse

Will Pearse

I have a dirty secret: I love hotspot papers. I love staring at figures like the one above, and thinking about how we live in a world where we can pinpoint where all the world’s diversity is. So bear that in mind.

I think Matt unleashed his grumpy economist  a little too early. This is a great hotspot paper. The authors use fundamental biogeographical theory to show why regional data are untrustworthy; I don’t care what form you think the species-area relationship takes, that one exists means the resolution at which the data were collected matters. Yes, there is no explicit costing in this paper, but that is not the point of it – the paper is trying to make a map of endemism, and I think they do a pretty damn good job of it. Although I have serious issues with using endemism as a conservation prioritisation tool, Red Listing all these species would take far too long and so this is probably the best we can do. This is not a paper that is aiming to come up with a robust (economic) prioritisation of the world’s flora, this is a hotspot paper that is trying to figure out where things are and point out the areas of a priori importance. I think Lynsey (below) is right in pointing out that we have a lot of papers like this (here’s another relevant one), and maps of the world’s phyogenetic diversity are beginning to emerge. Indeed, figure 2 plots the number of species protected under various schemes: since we first have to establish whether the species in protected areas would survive without them, and also how much we value those species, I’m not sure what we can do with graphs like this.

The deeper question I think we can all ask is why we need papers like this, and why we shouldn’t just all be out in the field waving placards and setting up reserves. To answer that, I want to talk about when I (briefly) met Lucas Joppa (I think) and Stuart Pimm while doing my MSc at Silwood Park. Felix Whitton and I were running a conservation news website (Conservation Today; the site is dead but check out these talks), and Pimm gave us a ~two hour interview. I specifically remember Pimm saying that it was more important to worry about what was going on “at the coal face” than spend your time making hotspot maps of the world. So why one more hotspot paper for him? Because papers like this give conservation NGOs easy-to-interpret guides (“have you thought about parks in this country, because they have a load of endemics”), and give us an opening to get more money (“hey *insert name of rich person*, this easy-to-understand map that was published in Science says we need more parks here!”). Pimm and others are out there trying to get money to get things saved, and papers like this help them. Fundamentally, it’s not the economic efficiency of a park system that saves wildlife, it’s the product of economic efficiency and the money available.


Lynsey McInnes

Lynsey McInnes

Another permutation of sub-optimal range data, area-selection algorithms and conservation prioritisation! Rejoice! In all honesty, I wanted to dislike this paper as I feel we are all really going round in circles with these kinds of analyses, but there are things to like in this paper and things to ponder. I also love the style of Joppa, Jenkins et al. (check out this PNAS paper, they are just cutting about other methodologies in a way that is simply fun to read).

Anyways, I am fairly sure that Matt is going to focus on the economic (un)feasability of their conservation guidelines, so I will skip that side of things altogether.

I like that they take actual established guidelines for protected areas and numbers of plant species that need protecting and try and work back from there to establish if they can find the optimal areas that would cover these species numbers in the minimum possible areas. They then show there is substantial overlap with restricted range vertebrate species. All it,well and good. Again, ignoring the economic and political side of protected area designation, do these results tell us much we didn’t know already. A bit…

My biggest concern, and this goes for most such studies, is do we really just want to protect areas with high numbers of species? Don’t we want to conserve ecosystem function or phylogenetic diversity (i.e. a variety of species and a source of new ones)? Don’t we want to make sure that there are corridors for species’ movement and that protected areas are well-connected and likely to be useful in the future? Don’t we want to square conservation goals with existing landuse scenarios and development goals? I am of the opinion that Myers’ hotspots were profoundly important in identifying to scientists and the general public that there are regions with there is a ton more biodiversity than elsewhere, that these are typically beautiful, interesting and probably contain a lot of tapped and untapped resources. Everything since then has (really) just reinforced his original set, perhaps adding a couple more outliers, or more pristine habitats that didn’t make his cut because they hadn’t been screwed up yet. But really tropical areas, islands, some outlier temperate areas are always identified. If you change your criteria, you might get a high latitude region or two. Where do we really want to go from here?

I would say, let’s get campaigning and conserving. Let’s get action happening to protect at least some of these amazing places. Let’s work out what is feasible (politically and economically) and get going.

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.

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!

Clade-specific consequences of climate change to amphibians in Atlantic Forest protected areas

Loyola et al. Ecography 36: 1-8. DOI:10.1111/j.1600-0587.2013.00396.x. Clade-specific consequences of climate change to amphibians in Atlantic Forest protected areas

amphibians_brasil

Amphibian species recent now (left) and 2080 (right). A message… from the future! From Loyola et al.


Will Pearse

Will Pearse

Lynsey gave me a wide selection of papers this week, and I picked this one because I’m thinking a lot of about the phylogenetic structure of ecological communities and biogeography. The authors predict amphibians’ distirbutions in Brasil in 2080 on the basis of their present distributions, and then examine the implications for protected areas.

I found this paper quite hard to interpret, and I’d appreciate your input! I found figure 2c, which shows phylogenetic diversity in protected areas now and in 2080, hard to read, as did the authors: “phylogenetic diversity increased under future climatic conditions, albeit such increase was not clear (Fig. 2C)”. The magnitude of the change (0.04 is the biggest I could see) seems very small, but it looks to me like those areas with the greatest diversity now have lesser diversity in 2080, and vice-versa, so could there be some kind of interaction going on? I’d love to write about the within-clade results, but I simply don’t understand figure 3 where they’re presented. The authors seem to have made a matrix that represents clade composition in the protected areas, and then plot principal components of that matrix, but figure 3 shows present and future climatic conditions plotted on the same axes as monophyletic clades, and I don’t know how that’s possible. Help!

However, the general approach of examining variation in response among clades is interesting. I think making predictions about protected areas’ future phylogenetic diversity is particularly useful if we want to understand ecosystem function, and I think approaches like these have the potential to be of conservation importance.


Lynsey McInnes

Lynsey McInnes

Ouf, this was a strange paper. I do think the premise was well-intentioned, but the execution was really quite confusing. As I understand it, the authors were interested in seeing how climate change will affect amphibian richness, diversity and phylogenetic diversity in protected areas within the Atlantic Forest of Brazil. A fair enough intention, protected areas are, debatably, the best hope for the persistence of endangered species, and amphibians, more so than other vertebrate groups are undoubtedly endangered. Furthermore, it is of interest whether protected areas protect certain amphibian species better than others, so the phylogenetic perspective could be a valid and important one in order to predict what kinds of amphibians we will be left with in the future.

But this is kind of where I lost the plot. I really struggled with the authors’ approach to defining phylogenetic diversity and similar to Will struggled to interpret figure 3. I also thought they altered between considering the traits of vulnerable species vs. their basal vs. derived status in the phylogeny. Phylogenetic diversity and its maintenance is of interest, but ultimately, I’m more interested in maintaining a diverse amphibian fauna (and I think the authors are too) so they could have devoted more discussion to the traits that help amphibians persist in warmer, drier areas. They highlight that the increase in phylogenetic diversity that they predict should be interpreted with caution given that it comes hand in hand with a decrease in species richness and the paper could have used this interesting result as a springboard into a more philosophical discussion of whether or not this is an acceptable tradeoff.

The authors are also admirably open as to the deficiencies in the methods they employ, namely that their species’ distribution models do not incorporate realistic dispersal parameters or the effects of sustained or disrupted biotic interactions. These problems plague many similar studies and it seems like the field is changing so fast that soon these omissions might make publishingsuch studies harder and harder. On the one hand, this is good, we should as a research community be tough on ourselves, and on the other, is a shame, as this study, even with its flaws and difficulties, can provoke valid discussion on how to go about conservation with limited funds.

One last grumble, I am deeply sceptical on ensemble forecasting. My understanding is, all models are quite uncertain so we should take an average of all such uncertain models and this will give us an average model with much LESS uncertainty? Hm.

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