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?


Developmental trait evolution in Trilobites

Fusco et al. Evolution 66(2): 314-329. DOI:10.1111/j.1558-5646.2011.01447.x. Developmental trait evolution in Trilobites

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


Figure 1 from Fusco et al. – trilobite moult cycle

Tim Astrop

Tim Astrop

This paper is a wonderful example of how innovative thinking and an integrative approach to the fossil record continues to discover new keys with which to unlock the unknown biological information held within. The Trilobitomorpha is arguably the most diverse and abundant extinct arthropod subphylum, there is certainly no shortage of palaeontological research on these critters, that’s for sure. But despite such popularity and interest in the group we still know very little about them as biological organisms. In this respect it is very apparent that preserved remains are not representative of the living animal, there is much interpretation to be done (see the recent ‘spotted trilobite’ described by McRobets et al 2013).

By looking at different ontogenetic stages represented by the different instars (discrete developmental stage of arthropods ‘bookended’ by ecdysis, or molting) preserved for over 60 species of trilobite for which adequate data is available, the authors then derive new metrics to treat growth rate via average per molt growth increment (AGI) and conformity to Dyers rule (IDC), while the former metric is self explanatory, the latter is less intuitive. The IDC quantifies the fit of observed ontogeny to that of a constant growth rate, deviations from Dyers rule would be indicative of accelerated/decelerated growth at particular ontogenetic stages (readers with a thing for shape analyses may also have noted that allometry would upset this metric via modular differentiation of growth rates within an organism, well done, have a gold star).

What is particularly cool is that the authors use this info not just to look at the evolution of this group but also to shed light on early euarthropod development, as the Trilobitamorpha are basal arthropods. Euarthropod evolution is a very active area of research (see Yang et al 2013 for interesting recent discovery) and held by many as something of a rosetta stone for understanding arthropod origins and diversity.

The meat of this article has a little too much math for than I would normally elect to tackle, but after making it through the results the discussion highlighted the findings really well.

In a nutshell, it seems that trilobites conform to Dyers rule overall, with some smaller deviations occurring in early (protapsid) development. However, the particularly interesting thing, for me at least, is that there appears to be less phenotypic integration in later stages that enables very unique, differing morphologies to evolve that deviate from standard cut-and-paste metamerism (segment repetition) seen in many trilobites (but probably most evident in the familiar Myriapoda) and calls forward to the future of arthropod diversity in all it’s mis-matched-crazy-appendage glory. It also infers that that similar morphologies may be converged upon via different developmental pathways, to me this indicates that trilobite morphology is not restricted to an adaptive peak but provides a method to move between peeks via morphological lability, something the authors refer to as ‘evolutionary dynamism’, a trait that likely contributed to their success as a group.

In summary, I think this article is a wonderful example of how valuable palaeobiological approaches can be to understanding organismal evolution. Here we have a novel approach to an existing dataset using linear measurements (and complex stats) to derive new information about the evolution and biology of an extinct arthropod subphylum.

In my opinion, the true integration of biological and palaeontological principles allows fossils to be treated as the cryptic remains of biological entities that old-school paleontology can often overlook in favour of a ‘stamp-collecting’ mindset. Thankfully there appears to be something of movement among palaeobiologists at the moment back to a more synthesized ‘Simpsonian’ concept of the fossil record. Something I look forward to hearing more about, and to hopefully contribute to!

Will Pearse

Will Pearse

I normally hate people who loudly shout “yay science” on Facebook and the like, but this paper really was one of those moments for me. We can track the development of growing trilobites using fossils? We can robustly test hypotheses about the evolution of that development? Yay science!

The most parsimonious evolutionary model of these species’ traits is one where phylogeny doesn’t matter (a star phylogeny), so it’s hard to argue that there’s any constraint to trait evolution here, despite the phylogenetic signal of some of these traits. The authors suggest this reflects the influence of particular outlier clades that are biasing model fit; I completely agree. I spend much of my time doing analyses of ‘plants’, and it’s always struck me as rather strange that I lump all these diverse and divergent species under one label and then examine their evolution altogether. I imagine the same is true of trilobites – the devil is in the detail, and understanding exactly what clades are varying (and why) will probably give us a better handle on what drives the evolution of these traits.

In passing, I wonder what the consequences of doing morphological analyses on phylogenies of extinct species that have to be built from morphological data. What if some of these traits, or traits that are strongly coupled with these traits, were used to define the phylogeny of these species – after all, ‘ontology recapitulates phylogeny’, and information about how species develop would seem (to a person ignorant of paleontology) like useful data. Could this be why the authors find stronger phylogenetic signal in the earlier developmental stages, or does this actually reflect the biology of the system? Does more evolutionary constrain in juvenile growth suggest juveniles were competing more strongly than adults (mortality does tend to decrease as species get older)? The authors give very detailed supplementary information on the phylogeny’s construction, but I’m really nowhere near qualified to comment. Can anyone help me out?

Lynsey McInnes

Lynsey McInnes

You can’t deny that Will and I like to stretch ourselves in the diversity of papers that we discuss on this site. Who knew the coverage of the terms phylogeny, ecology, geography and evolution was so broad. This week we take another foray into paleo research, this time without the potential to incorporate any extant data, these things are extinct!

My first reading of this paper was definitely made while wearing a cynical hat, and I was unconvinced that the data were adequate to ask these questions, particularly regarding the patched together phylogeny. A bit more time with the paper though, and I was becoming more and more impressed with the authors’ ability to extract conclusions, all appropriately caveated given the antiquity and patchiness of the available data. Perhaps we are all becoming too obsessed with perfect datasets, Bayesianed up and with no room for interpretation based on slotting in genuinely new findings with an already amassed body of research. This paper is a great example of the latter approach. Neat!

I’m most acquainted with adaptive zones in terms of diversity dependent cladogenesis…clades diversify until a zone is full, diversification rate declines until some upstart clade pops off into a new zone to start the process again. Sadly, a lot of contemporary ‘adaptive zone’ research remains a numbers game with little detailed investigation in what adaptations a clade possesses to occupy their zone. In contrast, this paper makes a concerted attempt to actually think about the adaptations necessary to occupy different zones and finds strong evidence for these traits in the Trilobite lineages studied. Impressive given these things went extinct millions of years ago! Not only that but the authors also successfully distinguish between intrinsic and extrinsic drivers of the patterns that they find! I’m a bit obsessed with the landscape or environmental drivers of macroevolutionary patterns and was really pleased to see this angle tackled in this paper.

So, I’m no paleontologist or developmental biologist, and appreciated this paper mostly as it reminded me that science need not be all about the perfect dataset producing good model fit in a standalone clincal model, it can be messy and incomplete, but illuminating.

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