Phylogenetic relatedness and the determinants of competitive outcomes

Godoy et al. 2014 Phylogenetic relatedness and the determinants of competitive outcomes. Ecology Letters 17 (7): 836-844

Figure 3 from Godoy et al. How fitness, demographic, and competitive differences vary with phylogenetic distance.

Figure 3 from Godoy et al. How fitness, demographic, and competitive differences vary with phylogenetic distance.

Will Pearse

In a fantastic follow-up to the many criticisms of the community phylogenetic approach, Godoy et al. fit a form of the Chesson framework to ecological data, and find that while fitness differences are greater among distant relatives, competitive differences are not. Being phylogenetically dissimilar did not mean that species were more likely to co-exist.

This is an excellent demonstration of a point that many have suspected for some time, but few (none?) have been able to conclusively show in a field experiment. This probably has something to do with the work involved in doing it…! Of course, that it’s been found once does not mean it’s a general pattern, but along with other work from the same authors decomposing traits into niche and fitness components, it seems empirical ecology is now matching its theoretical counterpart. Some are going to take papers such as these as the first nails in the coffin of community phylogenetics: personally, I think they open the door to a whole world of new approaches that we’ve been wanting to explore for some time.

Generating hypotheses about the kinds of traits that map onto different kinds of evolutionary processes means we can ask more sophisticated questions about evolutionary ecology. We don’t need to just stop at declaring that a trait shows ‘phylogenetic signal’, we can ask what model of evolution generated these traits, and (more importantly) how the evolution of those traits interacts with how they play out in species’ modern ecology. Indeed, that’s what many community phylogeneticists have been trying to do since the very beginning.

Now we can start asking more nuanced questions about the kinds of evolutionary models we are fitting. Measuring the traits that enable co-existence in one area is fantastic, but it’s unlikely that only the eighteen species in this study evolved in isolation. How did the surrounding flora (and interactions in other environments) affect the evolution of these interaction components? If (as the authors rightly argue) Brownian motion gives us very little predictive power for deeper phylogenetic structure, are there alternative models that might? Is it ever truly possible for competitive interactions and hierarchy to be strongly conserved, if diffuse competition among many competitors is frequent? If competitive hierarchies change over time, does it make sense to ask if a particular snapshot of them, in particular environmental conditions, is evolutionarily stable? Personally, I think it’s a good time to be a community phylogeneticist…

Lynsey McInnes

Lynsey Bunnefeld

Unlike Will, I’m not a community phylogeneticist (still not sure I buy into communities) and haven’t been following the recent developments in community phylogenetics that seem to be making it a much more robust field (see Will’s post above). Instead, I just jumped into this paper without previously ever having thought of the way you could split up species’ differences into stabilising niche- and average fitness- differences. What a good idea and what a shame that distinction wasn’t recognised long ago.

The authors then go on to see if they can untangle how these two features relate to phylogenetic distance using some nifty field experiments with 18 plant species. Again, I got overwhelmed by the fanciness of the experimental design and the work involved in it. And am happy to believe their findings that only average fitness differences show phylogenetic structure (more distant relatives have bigger differences) and that increased variance over longer phylogenetic distances mean that communities as a whole don’t show phylogenetic structure.

Being the macro person I am, I wonder how these results generalise to other communities and how you might go about finding out without having to conduct an epic field experiment every time you want to try. I think these authors have already published theory for these ideas so it is definitely time to get out of the computer and into the community (haha) but just how might you do it? Early community phylogeneticists went to town fitting models to species presence/absence in areas and giant phylogenies, clearly we need to be more nuanced than that. Could we go a roundabout way and find the traits that underlie the average fitness and the stabilising niche differences and use these in a similar framework to Godoy et al. advocate here? Has this been done already?

The authors find that variance increases with increasing phylogenetic distance, does this mean that clear patterns will not be found as we zoom out from narrowly defined communities? Is this OK?

Will sees these developments as a kind of new dawn for community phylogenetics. I just wonder whether the new dawn is not just tearing the field apart in increasingly nuanced ways. I for one am not confident that we can use phylogeny to robustly predict how communities will respond to change or use snapshots of current communities to work out how they got put together. At least not without a lot of knowledge of the system in hand and then who needs these phylogenetic metrics anyway?


Heat freezes niche evolution

Araújo, Ferri-Yañez et al. Heat freezes niche evolution. Ecology Letters, early view.


Some pretty exciting datasets used in this study (above)

Will Pearse

Will Pearse

I’m sorry everyone, because a number of work commitments (including preparing for ESA) mean I haven’t been able to spend the time I would normally devote to PEGE this week. I’m particularly annoyed, because this paper has a story, and stories require sitting in a quiet room with a beer and thinking, which I really don’t have right now.

Let’s assume that the tropical origin theories are right, and that the tropics are a huge source of diversity. If so, I completely buy more variability in cold tolerance – that’s what allowing species to spread towards the poles, and that’s what’s allowing species to radiate out into new niches. We should expect variation, because it’s that variation that’s driving speciation / it’s speciation that’s driving that variation.

When I look at the evolution of species traits, I assume I can measure them fairly accurately, and describe them with a single value. Well, this paper (and in particular figure 7a) really makes me think I should stop doing that, because tolerances seem to be things that are described by distributions with long (or at least variable) tails, and quite strong asymmetries. Perhaps even some kind of linkage with the traits that underly cold tolerance, and how those work physiologically, might help. So, maybe it’s time to crack out that dusty old physiology textbook!

Lynsey McInnes

Lynsey McInnes

Oops, I’ve managed to pick a paper that merits more consideration than either Will and I have had time to give it this week. But in the spirit of publishing PEGE more or less on time each week (less this week given Latvian wifi collapse), here are some initial thoughts on this paper.

Well, it looks like we are finally beginning the next generation of niche conservatism type analyses and that physiology is about to take centre stage. For a while now, we have been bandying about the notion that we can’t really look at niches by summarising the different climates found within species’ range polygons, that really niches relate to physiology and that we need to address physiological mechanisms head on. However, physiological traits are way harder to measure! The authors here do a great job of collating all available date on physiological tolerances and asking some interesting questions with this dataset (as an aside, I am extremely fond of papers that dare to use data from variety of sources and measuring slightly different things, rather than restricting themselves to more ‘perfect’ homogeneous datasets).

They conclude that upper thermal limits are much less variable than lower ones and that this indicates that upper limits are much more conserved. This in turn suggests that species living in regions close to these limits are most likely to be most screwed in the face of increasing temperatures. I really need more time to think about this, but on first glance, this sounds pretty reasonable and sits well with similar assessments of latitudinal gradients of climate change risk that have not used real physiological data.

I really appreciated that authors tackled head on what their results mean for all those studies (mine included) that make loose handwavey gestures that realised niches should be correlated in some nicely linear way with fundamental niches. I also liked the way they highlight how their findings deal (another) blow to using bioclimatic modelling to make robust assessments of species likely responses/range movements in the face of climate change.

Some thoughts that popped into my head…

How are these results affected by there just not being higher temperatures around at the moment? And by there being more species in the tropics, with smaller ranges? Is there any conflation going on?

Are there any experimental evolution studies around that have selected for increased temperature tolerance/looked at the genetic mechanisms behind this? (I expect yes!)

What is the relationship between upper and lower thermal limits and the absolute range of thermal tolerance for each species? (Not sure what I mean here, but I think I mean what about the physiology analogue of the effect of range size/intraspecific variation?).

How would these results change if studied in an explicitly phylogenetic context (harping back to my musings on what is niche conservatism without the ‘phylogenetic’ bit?).

Given the apparent complexity in species’ (thermal) niches is there any real hope that we are able to make accurate predictions of species’ likely responses to climate change (and then go on to use these predictions to take useful conservation decisions)? The typical trio – move, evolve, perish – still stand but how much progress have we made in working out what is more likely (my feeling is most species will have a bit of all three in different/overlapping parts of the range). Pragmatically, maybe we need to give up on these species by species assessments and instead look at emergent community/ecosystem assessments to insure healthy ecosystems (whatever that might mean) rather than persistence of individual species. I.e. go more macro instead of less?

Alternatively, if our aim is not necessarily to conserve, but just to understand what on earth is going on and how niches ‘work’, it looks like we are going to have heat up a lot more organisms on hot plates and digitise a few less maps…

Phylogenetic niche conservatism: what are the underlying evolutionary and ecological causes?

Michael Crisp and Lyn Cook, 2012. New Phytologist 196(3): 681-694. DOI:10.1111/j.1469-8137.2012.04298.x. Phylogenetic niche conservatism: what are the underlying evolutionary and ecological causes?

The multi-coloured world of phylogenetic niche conservatism (from Crisp and Cook)

The multi-coloured world of phylogenetic niche conservatism (from Crisp and Cook)

Jan Schnitzler

Jan Schnitzler

Much has been written about phylogenetic niche conservatism (PNC) over the past few years (e.g. Revell 2008, Losos 2008, Cooper et al. 2010, Wiens et al. 2010), so one might wonder what another review can add? Given that PNC still seems to be both a ‘hot’ topic, but also one of considerable disagreement, a conceptual paper might ideally help to clarify some open questions and suggest directions that research should take in the future. In my opinion, this is exactly what Crisp and Cook have done here.

Starting with the more general part, the paper provides a nice discussion of PNC, how different researchers have defined it, and how it compares to ‘niche conservatism’ and ‘phylogenetic signal’ (and continuing the discussion of whether it is a pattern or process – I admit that I tend to agree with Crisp and Cook here…). I get the impression that there is still quite a bit of uncertainty (understandably) regarding the use of these concepts in the scientific literature, so I believe this is a very good overview.

In the next part of the paper, they highlight a number of key processes and discuss how these may lead to PNC. One that caught my attention in particular was extinction, which that could lead to a pattern of PNC as an artefact. Even if the evolution of a niche-related trait is not constrained in the first place, higher extinction rates in a particular state (rainforest vs. scleophyll biomes in their example, but it could of course also be a continuous trait like body size) may result in a pattern of PNC. I think indirect processes (like extinction) have not really received much attention in the past. Also, this is a reminder again that molecular phylogenies of extant species might give a somewhat biased picture of the evolutionary history of a clade. The growing number of ‘total-evidence’ phylogenies will hopefully contribute to an improved (unbiased) understanding of trait evolution.

Another interesting section highlights the different tests that could be used to evaluate the degree of PNC. Blomberg’s K and Pagel’s λ are well known and widely used tests for phylogenetic signal, but as other studies have shown before, Crisp and Cook point out that the relationship between phylogenetic signal and phylogenetic niche conservatism is not always straightforward (especially if evolutionary dynamics diverge from the simple Brownian motion model).

Towards the end, the authors bring up some intriguing challenges for studying patterns of PNC. For example, we need to consider that transition rates between traits might be unequal, and that different traits might be linked to differential rates of speciation and/or extinction. Finally, I did like the outlook on the possibilities that incorporating genomics offers (yes, everything nowadays is done using genomics). If we do get a better understanding of how genomic processes influence phenotypic evolution, we will be a lot closer to understanding why some specific niche-related traits are conserved in some groups, but not in others.

In summary, I really enjoyed the paper, in particular the focus on identifying the underlying processes rather than just documenting the patterns of PNC. However, given the uncertainty about the best way to quantify PNC and the potentially confounding effects of different processes, I wonder how close we really are to achieving this.

Will Pearse

Will Pearse

Crisp and Cook have written a very thorough review of what can cause different levels of phylogenetic niche conservatism (PNC), and I find it hard to think of anything they haven’t covered. So, seeing as how I work on eco-phylogenetics and am always being accused of blindly accepting PNC without giving it any thought, I’m going to play devil’s advocate and try to argue that PNC isn’t that interesting, in the hope that someone will take issue with everything below and put me in my place!

The authors go to some pains to point out that PNC is both a pattern and a process, because while some processes generate PNC (and thus it is a pattern), PNC itself generates other patterns (and thus it is a process). I don’t like this argument; increased algae in a pond is caused by putting fertiliser in that pond (and thus it is a pattern), but increased algae has implications for other species in the pond (and thus it is a process). Making predictions using algae is probably fine, but if we want to understand the system we should model the cause of algae population levels – the fertiliser. In the same way, to understand the patterns generated by the PNC, I think it makes more sense to skip the middle-man and model the process that generated the PNC itself. Perhaps the only situation in which you would care only about observed PNC is when inferring something about the present-day ecology of those species, when past evolutionary dynamics matter only in the sense that they affect species today. However, in such cases why not just use the trait data used to derive PNC and cut out the phylogenetic middle-man (regular readers know I’ve been repeating this idea like a worn-out record).

To my mind, PNC is useful to evolutionary biologists in exactly the same way that diversity measures are useful to ecologists. Diversity measures are something we can measure about a system, and help us understand the mechanisms driving that system. The authors describe how PNC has helped us understand Darwin’s ‘abominable mystery’ (the sudden radiation of the angiosperms), but in reality it is only by making models to explain PNC that we have understood it. That’s not to say that measuring PNC is not important, but understanding the origin of what we have measured is also key!

Lynsey McInnes

Lynsey McInnes

Phylogenetic niche conservatism has come up in a bunch of our posts so far, and I’m glad Jan chose this paper this week so we could tackle PNC head on. I really enjoyed reading this paper, I thought it was a well-written, balanced, but still clearly an opinionated piece that does make a useful contribution to the already overflowing literature on PNC. I thought the authors managed to cut through a lot of the confusion and controversy, but still did not sit on the fence regarding their own stance. They unreservedly come down on the side of PNC is a pattern caused by a set of processes, and the interest lies in determining what these processes are and how they do or do not generate PNC. I also appreciated their repeated emphasis that the most fruitful avenue of research is a relative approach (e.g., is this niche-related trait more conserved than this one?) rather than an absolute one.

The authors also emphasise that niche conservatism is intimately related to spatial patterns of diversity and community assembly. I feel that it is often overlooked that niches, more or less, are inherently spatial entities (this is probably debatable but most papers that purport to have looked at PNC so far are looking at conservatism in traits that have a spatial dimension like maximum climate found within a species’ range, rather than the physiological traits that actually mediate an organism being able to cope with such a temperature). Until it is easier to measure physiological traits across broad sets of taxa, these spatial proxies for niche-related traits will remain popular (and useful) so (I think) its good to explicitly realise their geographic dimension.

Clearly, you can’t cover everything in a single article, but I was surprised by some omissions/elements that were skimmed over. First, what is a niche? This was restricted to boxed text and I think the paper could have been stronger with a lengthier introduction into what a niche is, especially to get straight a definition that has relevance across clades. But perhaps this discussion has been done to death, so it was fine to keep it short and sweet. I also wonder what the authors’ views are on the difference between phylogenetic niche conservatism and niche conservatism (without the phylogenetic bit). Is there a difference? Does the concept only have meaning in the context of a phylogeny? I’m really not sure.

The authors were quite concerned with temporal scale, and the idea that some niche traits are conserved over very very long timescales and broad swaths of taxa (all angiosperms for example). There was less focus on spatial scale. I do wonder if PNC might also be interesting to study at very limited spatial scales…we often talk about tropical niche conservatism and the inability of tropical lineages to colonise temperate latitudes. But what about within tropical or temperate latitudes? There are quite some niches in both – how are they divided/shared among lineages? Are the processes that determine PNC patterns at these scales the same as those are broader spatial scales?

The authors do highlight, as did Jan, that the advent of genomic datasets might be helpful in this regard. What genes/mutations/phenotypes/selection pressures/genetic backgrounds are responsible for the patterns that we see? How does the genetic basis differ depending on the process that produces the pattern? Perhaps the only way we are going to clear up the confusion and controversy surrounding PNC is to get down to the genetic basis of the ACTUAL traits that produce these patterns? Perhaps not…?

And, I have to say it, I am really interested in the insights we might gain from looking at niche conservatism below the species level. Niche conservatism is often looked at in traits emergent at the species’ level (e.g., mean temperature across the species’ range). What can we learn if we look at geographical variation in temperatures found within in the range? Are populations within the range located adapted to temperatures they are exposed to? This is directly related to the recent paper we discussed on cosmopolitan taxa – how do they get to be/stay cosmopolitan? But probably also has relevance for species with even moderate range sizes. How does niche variation/conservatism within a species relate to conservatism among species?

I concede that this has become a bit of a ramble on thoughts in my head about PNC in general rather than related to the paper itself. Sorry about that. But thank you to paper for provoking all these, perhaps tangential, things to think about. I do wonder quite why the study of PNC has taken off in quite the way it has. It’s related to data availability for sure and bandwagons, is there anything else? The authors note that the concept was already thought about by Tansley, I wonder where its next steps are?

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