Thursday, June 23, 2011

On the Use of Terms 'Phylogenetic Comparative Methods' and 'Neontologist'

Some boring discussion of terminology.

I've heard the phrase "Phylogenetic Comparative Methods" or "Comparative Methods" get used for everything from just analyses for assessing evolutionary correlations (independent contrasts or phylogenetic general least squares), to all phylogeny-based analyses of trait evolution, to even include birth-death modelling of lineage diversification and phylogenetic community analyses. I'm actually a bit surprised that things in the past, like Pete Wagner's work on evolutionary rates, hasn't been subsumed under this phrase yet. I think using this phrase so vaguely, to refer to anything in which a phylogeny is somehow involved, contributes to some confusion among newcomers and increasingly removes any ability of ours to refer to a cohesive distinction among analytical methods.

It would be better and clearer if we used PCM to only refer to studies of evolutionary correlation. That's what comparative methods meant, prior to Felsenstein (1985), from what I understand. If I can be so forward, why not the term 'macroevolutionary analysis'? Of course, that term would also include many of the analyses done in evolutionary paleobiology, but well, as I was stating earlier, these methods largely differ in data used, not the question addressed. Maybe we can differentiate with 'phylogenetic macroevolutionary analysis' if we really want.

To finally shut my trap on things that Evolution 2011 has made me think about, I'd like to mention that the meeting caused me to have mixed feelings about the use of the word neontologist. I never really used it until I came to Chicago, it has become a useful addition to my lexicon to make the distinction between those using fossil data and those not using fossil data. However, biologists don't know they are 'neontologists' and in trying to explain why we would give such a label when I accidentally say it, I feel like I am just perpetuating bad feelings from several decades ago. But if neontologist is a poor word, than maybe paleontologist is too. Hrm.

Paleontology, Evolution 2012: Ottawa and the Future

So... with all that discussion about the meeting that just happened out the way, let's talk bigger picture here.

Next year, it will be a giant joint meeting in Ottawa with the European version of SSE. I think (and some other people are too) that it might be a pretty neat idea to lure as many paleontologists as possible to this meeting. Why? Well, based on what I observed at this meeting, evolutionary biologists and paleontologists are now asking essentially the same questions, just with different data and methods. How does trait diversity evolve? What controls lineage diversification? How do traits affect speciation and extinction (i.e. species selection or species sorting)? We definitely cannot afford to ignore one another!

This new interest in quantitative macroevolutionary analysis among evolutionary biologists means we that we should act to synthesize our efforts and learn from each other. The number of talks that were trying to use both sorts of data, either to compare or integrate, was striking. (Obviously) I think there's a lot that can be done by combining paleontological and biological data and methods. This is a very exciting time.

There are some hurdles, of course. I know some paleontologists remember earlier times, when biologists were not kind to the suggestion that paleontology could inform evolutionary biology and thus ignored paleontologists. I really don't think that is the case anymore; the relatively positive response I saw to Gene's talk on PuncEq suggested to me that biologists no longer remembered that a rift had even once existed. I see that a clear appreciation for deep time and historical factors is growing over there in biology, and we as paleontologists should be acting to nurture this.

Other hurdles, particularly limitations of money, are not as easy to fix. I don't have any great ideas on how to fix that one yet (Any ideas?). There's also time limitations. Many paleontologists do field work or museum work over the summer and there are also some early summer conferences around the same time. Nothing can be done about that.

Still, I think if evolutionary paleontologists can go and they are willing to do a little learning about how biologists do what they do and teach a little about how the fossil record works and what it means for evolution, I think they should go. I think its an opportunity that can't be missed.

Overall, I think some integration of the two communities needs to happen, but I admit that it isn't just about this Ottawa meeting next year. In discussion with some people, it was mentioned that maybe the annual SICB meeting might be a good bridge, as both paleontologist and evolutionary biologist communities partially attend. Also, Emily King and I are trying our best to try to get evolutionary biologists to come to GSA, where paleontologists generally go, but I do not know how successful we will be yet. (I'm keeping my fingers crossed!) In the long run, integration will require aisle-crossing from both sides, with paleo people going to bio meetings more frequently and bio-people coming to paleo meetings.

What do you guys think? Can we better unite these fields, at least meetings-wise?

(...Of course, once we get evolutionary biology and paleontology more copacetic, the next task is ecology and paleoecology... now there's a real challenge!)

A Paleontologist at Evolution 2011

This week I was lucky enough to attend Evolution 2011, this year's iteration of an annual convention held jointly between the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB) and the American Society of Naturalists (ASN). As one of the few paleontologists who attended, I'd like to spend some time discussing my expectations going in, my reaction to the general tone of the meeting and some talks that I thought were really neat.

Before I came to Evolution, more than a few people told me that the conference would be of little interest to a paleontologist. They said the talks were very focused on molecular tree-building, experimental evolution and genomics, and that paleo stuff was generally swept off to some isolated session that no one attends. I also expected it to be a very large conference, maybe the size of the Geological Society of America national meeting (the regular yearly meet-up for most paleontologists, particularly non-vertebrate workers, but mainly attended by geologists). I just thought there was a lot of evolutionary biologists in the world.

I decided to go anyway, seeing that many of the sessions last year had been titled 'diversification', and I enjoy a good story based on a phylogeny as much anyone else. I also submitted a talk. I work on phylogenetic approaches to macroevolution in an extinct group, so my research falls very nicely into the current interests of evolutionary biologists.

First off, the meeting was surprisingly small, maybe a little bit larger than the paleo portion of GSA but definitely smaller than NAPC or IPC3. I hear this was a small year, but it makes the community of evolutionary biology less intimidating.

Secondly, there were very few paleontologists. (I count no more than 13.) However, the single paleo session at the meeting appeared to be well attended, although I didn't personally see giant crowds at the back like a few sessions had. As a speaker, I sat in the front and I did not glance behind me that often, so maybe I missed this. (After my talk, I got a lot of feedback and some compliments. People even tweeted about me! Yay!)

As far as specific talks of interest to the paleo-inclined, I particularly enjoyed Gene Hunt's talk on punctuated equilibrium. There was also some intriguing work being done on clam shrimp morphometrics to elucidate sex ratios in the fossil record, presented separately by Byron Brown and Timothy Astrop (both from the same research group). Earlier in the conference, Pete Wagner and David Polly gave talks on character evolution in the big symposium room.

There was also a considerable number of talks focusing on comparing and/or integrating the information from molecular phylogenies and the fossil record: Carl Simpson compared diversification histories in corals, Graham Slater discussed putting uncertain fossil ancestors on phylogenies for trait evolution and Rampal Etienne discussed a model of diversity-dependent diversification and fit it to both fossil data and molecular data. There was also a number of mentions in other talks about the increasing realization that fossil data was necessary for testing some macroevolutionary hypotheses. I think an integration of data and methods is a very promising route as we realize the limitations of each type of data. Although they are not integrating this data just yet, there were several people at the meeting from the BITS (Bivalves in Time and Space) working group, which holds considerable promise in exploring what a combined dataset might tell us.

Thirdly, and very importantly, the meeting was full to the brim of macroevolution. All those 'diversification' sessions were full of talks where some people made a tree and THEN went on to test some neat question about diversification rates or trait evolution using some of the more recent 'comparative methods': BISSE, MEDUSA, geiger, ouch, etc. I've talked to some people who have been to more Evolution meetings than I have and they tell me this really is something new, maybe starting last year at the Portland meeting.

All of this has given me some, well, perhaps radical thoughts which I will share in the next blog post.

Indicative of a field that is growing and developing, there was also a number of talks on the analytical power of specific methods (Richard FitzJohn, Cecile Ane, Matt Davis and Carl Boettiger). Boettiger's talk was particularly interesting, presenting a new method to show us the distinction in support for different models of trait evolution more clearly and he has also placed his slides online. Liam Revell also presented new methods for estimating shifts in rates of trait evolution, which he has discussed previously on his blog.

As always, there were a few talks I wish I had not missed: Joe Felsenstein, Josef Uyeda, Chris Martins, Sam Price... Oh well. We cannot see everything at a conference! Oh well... maybe next year!