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!

A Preserved Graptolite Zooid?

It appears that scientists have finally discovered a preserved graptolite zooid! It's benthic and it's Cambrian, and its BIG (4 cm!) but the thing looks just like Rhabdopleura, just like we would expect based on phylogenetic analyses of colony structure...

http://www.cell.com/current-biology/retrieve/pii/S0960982211002776

Hou, X.-g., Richard J. Aldridge, David J. Siveter, Derek J. Siveter, M. Williams, J. Zalasiewicz, and X.-y. Ma. 2011. An Early Cambrian Hemichordate Zooid. Current Biology 21(7):612-616.

I don't quite see the fusellar banding that Hou et al. describe in the figures, but if anyone else can, let me know.

http://www2.le.ac.uk/news/blog/2011-archive/march/fossil-discovered/

An exciting time to be a graptolite worker!

Evolution, Environment and the Red Queen

So, the original prompting for this blog came from my friend, Daniel, who has recently started his own blog to explain economics, which you can find here. He challenged me to do the same and to answer questions that normal people have about paleontology but don't know anyone to ask.

I prompted him to give me such a question, believing people didn't wonder things like that. And so:

"Evolution seems more intuitive to me if you call it an environmental process rather than a biological one (ie, as environment in a location changes the things that CAN will change as well). Is it safe to think that or is there a snag there? Why do we learn about evolution in biology class, not in earth science?" - Daniel (Edited for typographical issues)

Well, Dan, that's a heck of a question! You don't know it, but that question touches on a lot of issues in biology.

The simple answer is that, no, evolution is not better attributed to environments rather than biological entities (organisms, however we should define them). We discuss evolution in biology because evolution is largely a feature of life.

I think it's important to consider what 'evolution' means, as there tends to be confusion about that. Evolution, the term, just means change (literally 'unfolding', 'unrolling' according to Wikipedia). Note that we can refer to evolution in things that are certainly not alive (minerals and economic markets are common examples), but let's just focus on the living. Generally when we want to discuss evolution in biology (as opposed to evolution of non-living things, like minerals), we define it as change in inherited characteristics. A dog that loses its leg did not 'evolve' because that change cannot be inherited.

So, in your changing environment context, the really interesting process is how organisms living in that environment evolve inheritable changes (or fail to change). Biologists are ultimately interested in how that process works, which is essentially a biotic process (although understanding how the physical environment is changing is also pretty important!) Also, we see lots of evolutionary change which can't be tied to any particular observation of environmental change, which further muddies an argument for evolution as an environmental process (although, as I get into below, defining 'environment' is difficult).

Now, let's just take a step back so I can explain how your question touches on some hot topics. So, I'm pretty sure you are using environment to mean physical environment, but actually, it's pretty damn hard to seperate physical factors of the environment (like climate, sunlight and altitude) from environmental aspects which are functions of other organisms (like how much predation there is or how much competition there is for some required resource). Organisms live in environments that are constantly changing due to both biotic and abiotic factors, and seperating those can be pretty difficult. One school of thought says they are fundamentally unseperatable, particularly when you consider organisms that greatly alter the physical aspects of their environment (like beavers, ants, many plants) which we call ecosystem engineers.

The important thing to remember is that the environment is always changing. Even if all the physical components were held constant, an organism would be living in a world full of other evolving organisms. To survive, organisms (and populations, and lineages) need to constantly evolve to keep up. This concept was introduced by Leigh Van Valen as the Red Queen Hypothesis (in reference to the Red Queen in Through the Looking Glass). Although some interpret Red Queen as the supremacy of biotic factors in influencing evolution over abiotic, Leigh was actually trying to include both. (This interpretation has led to the formulation of the "Court Jester" hypothesis, as a counter to the supposedly biotic-focused Red Queen, where ecological communities are relatively static until perturbed by sudden large-scale environmental change.)

So, to sum up:
We tend to define evolution as the process by which organisms evolve inheritable traits. Physical change in the environment does not always cause evolutionary change, and evolutionary change is not always caused by changes in the physical environment. Thus, they are treated as separate but interconnected processes.

In addition, scientists have found it difficult to always divide the physical (abiotic) components of the environment from the biotic components, such as competition and predation. Thus, it may be more right to consider study of the environment as partly biological. Understanding the interplay between the (perhaps constantly changing) environment and evolution is a primary question of evolutionary biology.

Why "Nemagraptus gracilis"?

Hello all,
I'm David Bapst, a graduate student at the University of Chicago. I'm starting this blog to answer some questions my friends have about paleontology. I'll probably also bring up more advanced topics in phylogenetic comparative methods and functional morphology, as they relate to paleobiology and topics connected to graptolite studies. Finally, I may occassionally use this to discuss a matter involving independent roleplaying game design, which is a minor hobby of mine (my main hobby being my work).

But you might ask: why name my blog after a graptolite species?

First of all, Nemagraptus gracilis is the most beautiful graptolite, in my opinion. I've made a nice little figure of it, to the right, which I've also made the background. You've gotta admit, it's a nice little shape.

Second of all, Nemagraptus represents much of what is interesting about graptoloid morphology and function. Nemagraptus regains a multi-branched form, having evolved from two-branched Dicellograptus-like ancestors, but does so via a novel constructional modification ('cladia'). Nemagraptus's form makes it instantly recognizable, which is probably also why it is a major index fossil. There may also be some Cyrtograptus species in the Silurian which converge on a Nemagraptus form (Mitchell, 1990). Work by Fortey and Bell (1987) also suggested that is form would be optimal for feeding efficiency. Its spiral form has also been of interest to those curious about graptoloid hydrodynamics (Rigby and Rickards, 1989). These connections to functional research make it a good emblem for my research into graptoloid function.

Note that Nemagraptus is also relatively well-understood in terms of its phylogenetic relationship. This is another key connection to my researching involving the phylogeny of graptoloids. Note that I also picked a branching graptolite: just like a phylogenetic tree.
-Dave