I'm just back from the Ichs and Herps meetings in Montreal. Overall, the meetings were a bit of a let-down. They suffered in particular by comparison to the Evolution meetings just a few weeks previously. At Evolution, I saw lots of phylogenies reconstructed with 10-20 nuclear loci as well as a range of exciting new phylogenetic and comparative methods. At Ichs and Herps, phylogenies from mitochondrial DNA plus 0-5 nuclear loci were the norm and hardly anybody was doing innovative or novel analyses.The coolest science talk I saw was Todd Castoe's talk about mtDNA evolution in snakes. Apparently, the remarkably rapid rate of mtDNA evolution in snakes is due primarily to non-synonymous substitutions in cytochrome oxidase (a transmembrane protein complex that is esstential for cellular respiration). In their recent PLoS One paper, Todd and his colleagues reasonably suggested that this is due to the radical shift in niche and diet that accompanied snake evolution, and their tendency to endure long fasts punctuated by the occasional very large meal in particular.
9 comments:
That's a very cool result about snake mDNA, indeed.
For me, the biggest personal let-down of the meetings was forgetting to cancel my hotel after deciding not to go and getting billed for a night for a room I wasn't in. Live and learn...
Do we really need the term "evolutionary redesign" (proposed in the Castoe et al. article). Furthermore, is it even a good term? A quick search on Google Scholar reveals that the term "evolutionary redesign" exists, but is presently used primarily in manufacturing and engineering literature (in which items are actually designed).
I'm with you on this Liam. Design is a bad term to use here, as it implies purpose in a process that we know to lack it.
This is the kind of result that makes me pause when considering many phylo-mito genomic studies that have propogated over recent years. Total evidence usually dominates, with little attention paid to the performance/pattern of individual genes/partitions. Nice study Todd.
Two rants regarding the lackluster meeting:
1. I don't know if it's a trend, but there was a definite lack of talks from established herptologists and icthyologists in the field - even ones that were there at the meeting. I think it really helps grad students and postdocs to see top professors give a 15 minute talk about some detailed study, not just a broad overview- you can get a sense of the way they think and what their lab philosophy is.
2. Regarding Rich's complaint about one or two genes versus 10 to 20: The resulting phylogenetic hypothesis is what matters (unless we want population genetic parameters) and I would trade in one RAG1 for 10 BDNF's any day - and I don't like feeling like I have to sequence a bunch of nearly useless nuclear genes just to boost my numbers.
I agree with Todd on both points. However, since I didn't give a talk myself I guess I'm a bit of a hypocrite. Frankly, I think many of the big names just decided not to come. The meeting was certainly hurt by the absence of people like Vitt, Greene, Losos, Zamudio, Shaffer, Wake and everyone from Kansas.
As far as markers, I agree that it should not be our goal merely to accumulate markers. However, it was clear at this meeting that people were getting bad trees with bad loci. Most of these studies could have been helped with a bit more (good) data.
From every simulation that I am aware of and all empirical "tests," it has always been more taxa and fewer genes (within reason) that has performed better. That is what I find so frustrating about the various "phylogenomic" studies on birds and fishes that have been published in the last year or so... Why move the arbitrary bar of gene number up without any discussion of taxon sampling? Vapid criticism of ASIH 2008.
Although phylogenomic analyses with poor sampling justly deserve your criticism, I don't see why this would lead you to defend another practice with clear deficiencies (i.e., use of one or two haphazardly chosen loci). I don't see how somebody who was present at both meetings could avoid the conclusion that the phylogenetics talks at Evolution were superior to those at ASIH/AES/HL/SSAR and that one reason for this was the tendency for the Evolution talks to include more markers.
Hey Guys, a quick comment on the "adaptive redesign" choice we made - and Rich, thanks for all the press coverage!
I do agree that it can be annoying when folks "invent" new terminology or adapt it from other places and reapply it to new fields. (I would note, however, the precedence of Dawkins use of "evolutionary design"...) In our case, however, we put quite a bit of thought into how we referred to what we observed in the snakes and think "evolutionary redesign" is actually quite precise. Typically we think of evolution being such a stochastic process (which of course it is at heart), but the degree to which we see such targeted and directional change happening in the snakes, it implied to us that natural selection was really targeting the functional redesign of proteins here. We observed sites at the core of CO function, many conserved for the ENTIRE known diversity of vertebrates, changing radically in snake CO. At the structural-functional level, we inferred that the very way CO functions has not just been altered, but completely re-engineered (or redesigned) so that function was specifically changed. It is not often in nature that we get a front row seat for such clear and strong selection - and this argument is often used by the IT folks to reject evolution as being sufficient to direct the complexity and diversity of life. Here, we get to say - a ha - here is a case where evolution has not just led to changes in a few amino acids that may change organismal complexity of diversity, but in fact it is so strong that it clearly led to the functional redesign of the protein that allows us to conduct aerobic metabolism. So, the "evolutionary redisign" choice was in a way meant to draw attention to (and celebrate) a really fun and rare example where we can so plainly see the non-random power of selection in full swing... Cheers... -TC
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