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)

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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.

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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!

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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?

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

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

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

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Will Pearse

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

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

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

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Lynsey McInnes

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

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

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

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

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