Sunday, September 27, 2009

SVP 2009 Bristol, and the Romer Prize Session

Despite the complaints that I've heard about the hills and distances from one session to another (come on, it was only a few minutes by foot!), SVP this year was pretty good, in my opinion anyway. I noticed some really good talks with some impressive analytical methods, some really interesting posters, and I also chatted with some intelligent and enthusiastic people.

Of particular interest for me was the Romer Prize Session - not only because I was presenting, but more because Romer Session talks were almost always of high quality research, self-contained and conclusive (unlike some "on-going research", a new locality, or some more scrappy fossils...). Romer talks tend to be more analytically/numerically oriented so there are some stats and numbers to support certain ideas and claims.

There were two talks in particular that I liked, one by my very good friend Tai Kubo (Evolution of limb posture in terrestrial tetrapods inferred from Permian and Triassic trackways), and the other by the Romer Prize winner, Christian Kammerer (Effects of the Permio-Triassic mass extinction on synapsids).

Kubo's talk was on his study using trace fossils to infer limb posture in tetrapods, which on its own is quite unique already because there has been really limited efforts on using trace fossils as a potential source of data. But what makes his research truly unique was his validation of his metrics using observations of limb posture in extant reptiles and their relationship with trackways. His results are already published so I shan't go into the details but his conclusion is that the shift to an erect limb posture occurred rapidly in the Early Triassic much earlier than predicted previously by body fossils.

And on to Krammerer. I really liked his talk. The methodology was robust, statistics were sound, and above all, the sample size was just pure astonishing. One of the things I found rather exciting about his talk was that his results showed that geologically deformed skulls fall within the range of morphospace occupation (albeit perhaps at the extreme margins) expected for that species. This, I think is a significant discovery; although you'd still need a sufficient enough sample size to say that this is true for your own pet group of fossils as well... In any case, I really admire his work and his talk and I think he rightfully won the Romer Prize. So a very big congratulations to Christian Krammerer, and it is a shame I had not had the opportunity to do this in person at the conference (yes, I couldn't find half the people I wanted to meet because of the disparate locations).

All in all, a successful conference (for me): I met half the people I was meant to meet; I met some new people; I learned some new things; I caught up with a bunch of friends and colleagues that I had not seen in months, some I had not seen since our last meeting at Cleveland; and perhaps the most important aspect of the meeting for me, I disseminated my work in front of a large audience. I didn't get much feed back on my talk but I assume either no one really liked it or that no one really understood what I do...

Monday, September 7, 2009

Updates ... and SVP Romer Prize

I've just noticed that it's been about four months since I posted my last blog entry...It is rather scary how time seems to fly even when you are not necessarily having fun...

Anyway, I thought I might as well advertise this. In the upcoming SVP at Bristol, I shall be giving a talk in the Romer Session:

Myology and functional morphology of biting in avian and non-avian dinosaurs.

It's mostly about non-avian theropods now but I have a couple of birds in there for comparison; I don't know now why I emphasised birds in the title, I could have just said dinosaurs... Perhaps it's because I made much of my myological observations in birds (but also a few crocs).

I shan't write too much about it here, but the work is basically a suped-up version of my Masters thesis from way back, almost six years now... I had to come up with a way to rescue the concept if not the work, after I'd realised I had some fatal flaws in the basic assumptions of the calculations in my Masters work, and it took nearly six years to perfect.

Wednesday, September 2, 2009

Phylogenetic constraint

My coauthors and myself recently submitted a manuscript in which we deal a little with phylogenetic constraint. In the process, I came across something interesting and I thought it would be worthwhile to share it here.

Phylogenetic constraint is a concept of evolutionary biology that has had quite a lot of discussion. Mary McKitrick (1993) has a great way of introducing the concept of phylogenetic constraint:

"in some sense, all evolutionary studies implicate phylogenetic constraint, and reviewing the topic is like trying to catch a greased pig."

How eloquently put.

It means everyone loves talking about phylogenetic constraint but it just goes all over the place and there is no real consensus on what phylogenetic constraint is. So despite all this widely held discussion, phylogenetic constraint remains one of the most difficult and least understood subjects, and possibly one that is actually ill defined as well. The problem is, when we talk about phylogenetic constraint, we are actually talking about some causal factor for a way in which some trait evolves. For instance, we may see some evolutionary changes in skull morphology that is relatively consistent in closely related taxa, thus we may conclude that some phylogenetic constraint is working on this trait preventing it from evolving more disparately from one taxon to another, e.g. in a classic adaptive radiation model. But causation is always difficult to determine if not impossible to confidently assign.

We may not be able to satisfactorily determine if phylogenetic constraint actually is a plausible mechanism in some trait evolution, but we can observe its presumed effects, as phylogenetic conservatism or phylogenetic signal in your phenotypic data. Thus, when many of us say "phylogenetic constraint" we may actually just be talking about an observed phylogenetic conservatism, i.e. some trait that is showing a pattern of evolution consistent with phylogeny. In other words, some trait evolution that shows up as phenotypic difference in two or more taxa that is consistent with the amount of time (or phylogenetic distance) separating these taxa. Phylogenetic conservatism is thus shared characteristics amongst taxa that can predominantly be explained by phylogenetic distance.

The underlying mechanism of phylogenetic conservatism may be due to several causal factors, phylogenetic constraint being one of them (constraint due to developmental, structural, etc. that is shared amongst closely related taxa). But there is another possible mechanism for phylogenetic conservatism in a character, and that would be phylogenetic inertia (as defined by McKitrick (1993)). Characters evolving under phylogenetic inertia would not particularly be under strong selection, and change would be minimal, or in other words, "if it ain't broke, why fix it?". This is a slightly different case from constraint because there isn't really an active constraint working against evolutionary change; there just ain't any selection for that character to change faster than expected. But if there were any evolutionary changes then they would be due to inertia, so more consistent with a random walk model of evolution (i.e. Brownian motion). Under such circumstances, character change is directly proportional to time and thus proportional to branch length (thus differences between phenotypic traits in two or more taxa would be consistent with phylogenetic distance); or the rate of evolutionary change per unit branch length (or time) is constant.

Funnily enough, some widely used methods (maximum likelihood and independent contrasts analysis) actually assume this a priori (i.e. that character evolution conforms to Brownian motion), so before you go on and use these methods in your characters to say something about how characters changed through phylogeny, you really ought to test to see if your character actually does show a strong phylogenetic signal. Because if it doesn't then you may be violating the assumptions of the methods, or these methods aren't suitable for your character. But that's another matter all together.

Anyway, that aside, the terms I used here are probably all used in different contexts elsewhere (e.g. phylogenetic conservatism = phylogenetic inertia) but the point is, these concepts need to be defined well and used to mean specific things.