Tuesday, August 26, 2008

Dawkins' Hate Mail

This short video of Richard Dawkins doesn't exactly conjure up anything related to phylogenetics, but I couldn't resist it.

(originally courtesy of boingboing, latest version from bligbi)

Monday, August 25, 2008

Bioinformatics Pays - Literally

Congratulations to Vince Smith of the National History Museum in London, the talented biodiversity bioinformatician with "Cybertaxonomist" on his business cards. Vince is the 2008 winner of the Ebbe Nielsen Prize, an award given by GBIF to "a researcher who is combining biosystematics and biodiversity informatics research in an exciting and novel way." And, it's not just a plaque and a handshake - the prize carries with it a cheque in the amount of 30,000 euros (which seems like something like 2 million U.S. dollars to those of us traveling abroad and dealing with the current exchange rates). Vince will use this money to help continue the work on his Scratchpads project, but I bet just a wee bit might go for a celebratory beer. Guess I can forgive him for swapping around his seminar date at the AMNH because of having to go to Tanzania to collect his prize as long as he buys a round for me when he does come to town.

Sunday, August 24, 2008

A Teacher on the Front Line (NYT)

A splendid New York Times article is making the evolution blog rounds. While we chose to not concentrate on the complex political issues surrounding the education curriculum, this piece is simply too good and inspiring to miss.

Amy Harmon describes a day in the life of David Campbell, a Jacksonville area biology teacher, who puts us to shame with his commitment to Florida's schools and reason. While this is no doubt a reality for many teachers, I find it difficult to fathom calmly teaching evolution in my classroom as my colleague undermines me next door. 

And if you get to reading, you'll find to this passage, pure gold:
When he was 5, Mr. Campbell’s aunt took him on a trip from his home in Connecticut to the American Museum of Natural History in New York City. At the end of the day, she had to pry him away from the Tyrannosaurus rex.

Tuesday, August 19, 2008

Hot Off the Press: Evolution 62(8)

Although the article layout still looks like a 13-year-old kid spilled a bag of bad ideas onto a page, a new issue of Evolution arrived in the mail. (Take a look at that crisp and readable 1980s article design.) At least the contents seem unaffected by style.

Liu et al. augment the approach initially outlined most recently in Edwards et al. (2007) and Liu and Pearl (2007; see previous post), and hinted elsewhere, for estimating species trees with multiple-allele sequence data. Brandley et al. argue that reconstructions of ancestral states alone can reveal important insights into the evolutionary history of morphological changes--their number and directionality, for example. Although, they employ a nifty model, it is likely that ignoring some well known violations of the models of character evolution yield spurious results (in this and hundreds of other studies). In other words, I don't buy the regain of limbs in squamates. Still, the regression analyses of traits associated with lizard- or snake-like body form make for nice lecture material. I wonder if they could post the data and code for R instruction? (they did!Hansen et al. expand the earlier models of quantitative character evolution by giving consideration to the shifts in trait optima, in addition to character state shifts themselves. Strasburg and Rieseberg, and Currat et al. examine the magnitude of introgression in an empirical multi-gene study of sunflowers and in simulations of invading/local populations, respectively. Finally, Rabosky and Lovette develop a method for estimating speciation and extinction rates that vary continuously through time, and find that the common slow-down in species accumulations are driven by lower speciation, not higher extinction rates.

Sunday, August 17, 2008

Dominican Transportation

In our efforts to sample anoles from across the Dominican Republic we've been doing lots of driving. While on the road we've been constantly entertained by the things Dominicans manage to move around on motorcycles. The photos above are only a small sampling of what we've seen: eggs, cases of beer, a steel gate, and five (!) people. Believe it or not, this was the first of three five-tops we've seen. Remarkabely, that's not even the record -- a few years ago I spotted seven-top that included three adults and four children.

Saturday, August 16, 2008

Maldito Fowleri

The rarest anole in the Dominican Republic has been spotted once more! Anolis fowleri is a montane species found only in the Dominican Republic's Cordillera Central that has been seen alive by less than twenty naturalists. The last sighting was six years ago when Steve Poe, Paul Hime and I found three animals south of Constanza. I've tried to find it a few times since, most recently in 2006 with a group that included the Dominican naturalist and photographer Eladio Fernandez, who was left cursing "maldito fowleri" when our efforts failed. A few nights ago, Luke Mahler of Harvard University snagged another animal from the type locality. Seen in these pictures is Luke with his prize, as well as our new friend Miguel Landestoy with the same animal. Miguel is the first Dominican of his generation to see this species and will hopefully be posting some beautiful photos on his Flickr pages soon. Almost nothing is known of fowleri's ecology or life history, a deficiency that Luke hopes to remedy by spending a few weeks on the hunt this summer.

Friday, August 8, 2008

Goin' Parasite Hunting, Back in Two Weeks

On Monday, I will board a plane to Santo Domingo and hook up with Rich and crew who are down there hunting all kinds of anoles. My new graduate student, Bryan Falk, is there with them now and our goal on this trip (besides convincing Rich that field work can indeed involve fun things, too), is to sample three main types of parasites from the anoles. We'll be taking blood samples, like I always do, to extend our work on malaria parasites. Last time we were down there, I found 4 species in the Dominican anoles - one (shown in photo in a lizard erythrocyte) was originally described as a subspecies of P. fairchildi, a species originally described from Costa Rica, but our genetic data show that this relationship is not valid. We'll also be collecting a pinworm, Parapharyngodon cubensis and mites, to see if these parasites mirror the differentiation, be it at the population or the species level, of their hosts. If all goes well, we'll be back on the 24th of this month. Have a good couple of weeks, everyone!

Thursday, August 7, 2008

A great day for us all

There have been a number of monumental moments in the history of Evolutionary Biology: Darwin's publication of the Origin, the modern synthesis, the invention and development of cladistic methods... and now, we are all about to witness the next milestone. In the August 2008 issue of Systematic Biology, Bond and Stockman have published a paper describing a method for the mathematical delimitation of cohesion species.  Although this is interesting in itself, the truly monumental part of the paper is the name they have chosen for this new species: Aptostichus stephencolberti. That's right, Americans, the species has been named after the great Patriot himself. I'm hopeful that this is the first of many contributions that Mr. Colbert will make to our field.

Update: better video

There's also some other great stuff coming online as the issue is being assembled.  To me, Lemmon and Lemmon's approach to quantitative biogeography on a continuous landscape is really exciting; we've needed a method like this for some time, especially given recent criticism of nested clade analysis. There's also a dull paper in there about day geckos that you might want to check out.

Wednesday, August 6, 2008

Passive voice was used

Recently, many manuscripts from graduate students were read, and comments made by me. It was noticed that students choose to use passive voice for much of their papers (especially descriptions of sequencing and tree building). Some speculations were proposed as to why the students were doing this. It was concluded that they are trying to sound more "science-y," but that it was not really working very well. 

Please, stop!  You're all slowly killing me with these sentences. 

Saturday, August 2, 2008

Goin' Lizard Hunting, Back in September

This might be my last post for a while: tomorrow I'm off for six weeks of lizard hunting on Hispaniola, four in the Dominican Republic and two in Haiti.

Our first stop will be the Recodo Road, a locality made famous by the studies of the late Harvard Professor and and godfather of Anolis lizard biology Ernest Williams. Our first step will be to see how far up the road we can go; as Williams noted "there are no problems other than two fords, the first possible in a rented car, the second not so." In spite of this challenge, anole populations along the Recodo road have a history of yielding insight into the role of the dewlap in anole communication and speciation.

It was along the Recodo road that Williams and his students discovered some unusual trunk-ground anoles that could only be distinguished from the widespread Anolis cybotes by their striking purple and red dewlaps. They turned out to be a distinct new species - Anolis marcanoi - and one of the first whose validity was confirmed via molecular genetic analyses. Later, an experimental behavioral study - which remains one a few of its kind - suggested an important role for dewlap divergence in dictating the nature of interspecific interactions between A. cybotes and A. marcanoi, and marked a career beginning for the man who has assumed the anole throne at Harvard.

We'll be looking at an even more interesting species complex of trunk anoles that also attracted the attention of Williams and his students (see attached figure from the 1977 Anolis newsletter). Unfortunately, the main architect of this work - Preston Webster - died tragically before completing his thesis. Although incomplete, his work marked the high point of the Williams lab's foray into molecular analyses of species and speciation. Webster's preliminary field and allozymic studies were published posthumously in the third Anolis newsletter and got far enough to reveal evidence for two intriguing patterns: habitat-mediated dewlap divergence (a key to ecological speciation) and reproductive character displacement (perhaps driven by selection against hybridization events that were shown to produce sterile male offspring). Although these observations prompted Williams himself to suggest that there "are obviously several problems here crying for solution", they have remained unexplained for more than three decades.

It never hurts to go into a field trip with the blessings of the godfather...