Saturday, June 20, 2009

Are You Down with DPP?

What's on the horizon for phylogenetic analyses? One answer was nicely illustrated by two presentations in the Ernst Mayr awards symposium at Evolution 2009. Jamie Oaks and Charles Linkem - both graduate students in Rafe Brown's group at the University of Kansas - teamed up on two papers about the Dirichlet Process Prior (DPP) and its application to Bayesian phylogenetic inference.

DPP, which is sometimes referred to as the "Chinese restaurant" process, is a nonparametric Bayesian approach used in clustering problems where the data elements are assigned to a set of discrete clusters. Importantly, under the DPP, the number of clusters and the assignment of data elements to clusters are treated as random variables. Phylogenetic applications of the DPP include detecting positive selection in protein-coding DNA sequences (by assigning nucleotide sites to various dn/ds classes: Huelsenbeck et al., 2006), and accommodating among-site variation in substitution rates (by assigning nucleotide sites to various substitution-rate classes Huelsenbeck & Suchard, 2007).

This latter application was the subject of the talks by Oaks and Linkem, who presented results on the ability of the DPP approach for accommodating among-site substitution rate variation (ASRV) using both empirical and simulated data sets. Their results demonstrate that accommodating ASRV under the DPP can significantly improve the marginal likelihood scores relative to conventional methods that assign data partitions to substitution rate classes a priori (such as those based on codon position, etc.). In some cases, estimates under the DPP surpassed those of conventional approaches by hundreds or thousands of log likelihood units! As is well known, the studies by Oaks and Linkem also confirmed that more adequately capturing ASRV can lead to substantially different topologies.

Given that this is the case, why aren't more people using DPP? One issue emphasized by Oaks and Linkem relates to the substantial computational burden associated with inference under the DPP. For example, their analysis of two ~30 taxon data sets required more than two months of run time! Computational expense not withstanding, John Huelsenbeck (and affiliated phylo-geeks at Berkeley...Yeah, I'm looking at you Brian Moore) are working to provide faster, more user-friendly implementation of DPP-based methods that are bound to change our lives forever. Stay tuned for the latest...

Friday, June 19, 2009

Report from Moscow: Susan

It was nice to be back at the Evolution meetings! This was my first in a few years (since Stony Brook) as I've mostly been hitting the taxonomic-based ones (ASIH, Parasitology). First, kudos to everyone at Idaho for putting on a great show. Logistically, I thought things worked out very well - the rooms were good-sized and once we learned our way between the buildings, it was straight-forward to flit around between sessions and get to most talks. I definitely found myself doing more flitting this year - perhaps that's a reflection of my expanding interests - I was in lots of co-evolution talks, but also saw several phylogeography talks, some methodological talks, and of course tried to hit as many lizard talks as I could! Some of my highlights were the two ASN Young Investigator Award talks (Luke Harmon and Jason Kolbe) and Matt Brandley's head-scratching report of a very old skink on Bermuda. It was fascinating to see Jonathan Losos deliver his summary of mainland anole radiation in about 5 breaths and very exciting to be one of the first to own his book. I went to the first half of Doug Schemske's symposium on the "Origin" 150 years later and he, Hopi Hoekstra, and Daven Presgraves all gave excellent talks that both included historical tidbits about Darwin, but also really cool new data. And finally, I have to give a big "shout out" to Robin Hopkins from Duke. After Erica Bree Rosenblum's talk (on white sands lizards - very cool stuff itself), I stayed for Robin's talk on phlox because I was too food-coma'ed out from lunch to move -- and it was one of the best I saw all week. She blended field data and molecular genetics for a really nice study of phenotype evolution in flowers. Sadly, I did not make it to the Appaloosa Museum - perhaps next time I'm out there.

The photo is of my grad student, Bryan Falk, and another AMNH student, Antonia Florio, resting in the grass at the end of a long day of attending talks.

Thursday, June 18, 2009

Evolution 2009 Postmortem Open Thread

You can expect a few posts in the coming days that summarize the major findings we've taken away from the Evolution 2009 meetings in Moscow, Idaho. In the meantime, I'm posting a few photos that might give people who weren't there a flavor for the venue, and to everyone a chance to drop random thoughts they might have in the meeting's immediate aftermath. Moscow was a lovely little town and campus was beautiful. Thanks to all those who made the meeting possible, and the conference's local organizers in particular! Special thanks also to One World Cafe and it's staff, without whom myself and other members of the Dechronization crew may not have lasted more than a day. Photo legend (top to bottom): (1) Craig Moritz's SSE presidential address in the Kibbie Dome, an airplane hanger-like venue that is also the venue for the University of Idaho's home football games, (2) Luke Harmon on stage for his ASN Young Investigator Award lecture on "Causes and Effects o f Adaptive Radiation" (note: not picking, clearly scratching), (3) caffeine addicts trying in vain to get a fix during the meeting's first few days, (4) the court-room venue that was located in the U of I's law school and was complete with a judges stand and jury box.

Monday, June 15, 2009

Hot Off the Press: Lizards in an Evolutionary Tree

A lucky few attendees of Evolution 2009 were able to obtain an early copy of Jonathan Losos's new book Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles. The book is being printed overseas and won't be available to the general public for a few months, but UC Press had around 10 copies for sale at their booth here in Moscow. Although you might have to wait a bit, it looks like you can still get it for the 20% pre-order discount if you order today from the UC Press page.

The Felsenstein Effect

I'm just getting back to the Dechronization suite in Moscow, Idaho after a full day of talks, discussions, and poster sessions at Evolution 2009. The meetings started yesterday, highlighted by an outstanding symposium on diversification organized by Mike Alfaro and two Dechronization contributors: Dan Rabosky and Luke Harmon (more on that in a subsequent post). Today featured presentations by winners of the American Society of Naturalist's Young Investigator prize, including Jason Kolbe and Luke Harmon. I was also witness to the sociological phenomenon known as the Felsenstein Effect, which describes the surge of people who flood into a seminar room to see Joe Felsenstein talk. I took the photos to the right before, during and immediately after his talk today. His talk was an interesting discussion of a new method to analyze morphometric data in a phylogenetic context (co-authored with Bookstein). There were certainly more people in the room than at any other talk I've ever seen on the technical nature of morphometric analysis.

Friday, June 12, 2009

Evolution Host Cities (and Towns)

How about you help us compile the list of all the hosting locations for the annual meeting of the Society for the Study of Evolution (SSE)? If you notice errors or if you can fill in the gaps, please do so!

SSB has a nice summary list on its website, while ASN and SSE lists are not exactly exhaustive.

Evolution Meeting Locations

2012: Ottawa, ON
2011: Norman, OK
2010: Portland, OR
2009: Moscow, ID
2008: Minneapolis, MN
2007: Christchurch, New Zealand
2006: Stony Brook, NY
2005: Fairbanks, AK
2004: Fort Collins, CO
2003: Chico, CA
2002: Champaign-Urbana, IL
2001: Knoxville, TN
2000: Bloomington, IN
1999: Madison, WI
1998: Vancouver, Canada
1997: Boulder, CO
1996: St. Louis, MO
1995: Montreal, Canada
1994: Athens, GA
1993: Snowbird, UT
1992: Berkeley, CA
1991: Hilo, HI
1990: College Park, MD (ASN, SSB, SSE joint meetings start here)
1989: State College, PA
1988: Asilomar, CA
1986: Durham, NH
1985: Chicago, IL
1983: St. Louis, MO?
1982: Stony Brook, NY
1981: Iowa City, IA
1980: Vancouver, Canada
1973: Houston, TX
1969: Boston, MA?
1946: Boston, MA, (SSE) and St. Louis, MO (AAAS Precursor)

[This is a modified version with added changes from the posted Comments. Contributors: Kent H.]

One Big Chronogram

S. Blair Hedges, Sudhir Kumar, and other members of the Timetree consortium have just announced the public release of results from the Timetree of Life project, an effort to provide a comprehensive evolutionary timescale for life. These results are available in the form of a free web page and a ridiculously-priced $200 book (compliments of Oxford Press). I've only done a little bit of poking around on the web page, but so far it seems like an impressive and remarkably easy-to-use resource. By inputing the names of two taxa of interest users can obtain a comprehensive list of molecular-clock based age estimates for the node connecting these taxa, including information on the data underlying these age estimates and references to original source material in the primary literature. Perhaps the most obvious limitation of this database is that it is comprised exclusively of age estimates from molecular data, with no direct information on node ages from the fossil record. Regardless of this and other limitations, there can be no denying that this project is an important step toward a deeper understanding of how and why biological diversity has accumulated over time. Ok, now go play with the Timetree!

Monday, June 8, 2009

Looking towards Moscow

Many of us are getting ready to head to Moscow later this week and I've been reading up a bit on what else is there besides thousands of salsify flowers, hundreds of evolutionary biologists, dozens of book dealers, and beer. I've discovered that the Appaloosa Museum is there - I may try to sneak in a visit, if possible (any other horsey-types want to come?) What is everyone else looking forward to - scientific and otherwise?