Saturday, February 27, 2010

Toe Pads & Tails

The adhesive toepads of lizards are one of life's most spectacular inventions. Humans are even using this innovation as the inspiration for new adhesive nanostructures. Did you know that some geckos have similar adhesive structure on the tips of their prehensile tails, as well as on their toes? I caught one such gecko in northern Australia a number of years ago during an expedition to Arnhem Land with Jane Melville and Museum Victoria. The species we found - Pseudothecadactylus lindneri - is closely related to geckos on New Caledonia and could be found wandering Arnhem Land's impressive rock outcrops at night. The photo above is of a juvenile P. lindneri and close-ups of the toepads (top) and tailtip (bottom) of an adult animal. It seems likely that the tailpad results from similar genetic and developmental mechanisms to the toepads found in the same animal, but this has yet to be investigated in any detail. Remarkably similar toepads are known to have evolved independently in geckos, anoles, and skinks.

Wednesday, February 17, 2010

One Year of Stimulating Science

Last year was a good year for science. Thanks to a $3 billion dollar windfall from the American Recovery and Reinvestment Act, the NSF enjoyed a 50% increase in its expected level of funding for 2009. Scientific American just published an nice piece on the ARRA's impact on science over the past year (this article is the source for most of the facts mentioned below) . Anyone who's applied for funding from the NSF over the year and half doesn't need an article in Scientific American to tell them that the NSF devoted the bulk of its boost to grants. At the evolution meetings in Moscow Idaho last summer it wasn't hard to find others like me who had just been awarded ARRA funds. Those of us receiving these funds were told that our prosposals were deemed worthy of funding by the NSF's review process, but wouldn't have received funds in an ordinary year due to budgetary constraints.

For years, the NSF has received many more worthy proposals than it was able to fund, resulting in a logjam of high quality proposals and stifling progress in many important disciplines. Indeed, nearly 80% of the NSF's ARRA funds went to clearing the NSF's backlog, being used to fund highly rated, but unfunded, awards that were submitted the previous year. Although those who didn't submit proposals eligible for ARRA support might feel like they've been left out, the clearing of NSF's backlog is sure to result in higher funding for proposals submitted more recently.

Short-sighted politicians are likely to find fault with the fact that the NSF ranks second to last among federal agencies in spending their stimulus funds (only $136 million of the NSF's ARRA award has been spent). The reason for this are clear - most grants from NSF are multi-year awards and are going to sit in the bank accounts of awardee's institutions as they are allocated over the years to come. This does not mean, of course, that these awards are not having an immediate impact. The bulk of the money associated with my award is going directly to salaries of PhD students and undergraduate employees. My collaborator is using his share of the funds to hire two post-doctoral scholars. Our award, therefore, will directly fund three-four full time positions and a number of additional part-time positions for the next two and half years. Perhaps more importantly than providing jobs today, our award is also contributing tremendously to training the next generation of scientists. While it may not have the same immediate impact as other worthy investments like hiring jobless construction workers to build bridges and roads, the ARRA's gift to the NSF is likely to be a gift that keeps on giving both to the academic community and the country at large for many years to come.

Monday, February 15, 2010

In Memoriam: John Thorbjarnarson

We are sad to report that John Thorbjarnarson passed away yesterday morning. John was a Conservation Officer for the Wildlife Conservation Society, based in Gainesville, Florida. He was a PhD student of Wayne King and then spent the next nineteen years leading in situ conservation efforts of reptiles for WCS. He was a noted expert on the conservation biology of crocodiles worldwide --- having led efforts in the recovery of both Orinoco crocodiles in Venezuela and Chinese alligators in Anhui, China. He is also well know for his long term efforts focused on capacity building and conservation of crocodiles in Cuba and Black caiman in Brazil. John was in India to give a course at the Wildlife Institute when he succumbed to a severe case of falciparum malaria. He will be sadly missed by his colleagues and friends who will always remember his dedication to learning more about crocs and other herps and doing everything he could to protect them.

The photo came from this website, which has a nice interview with John about his work.

You may also see John in action in the Amazon in this National Geographic clip.

Friday, February 12, 2010

Darwin Day at Case Western Reserve University

Happy 201st birthday Charles Darwin!

I'm spending Darwin day at Case Western Reserve University as one of several folks speaking on the topic of phylogenetics and evolution. The event's two headliners just wrapped up their talks. University of Michigan paleontologist Philip Gingerich gave an enlightening talk about evolutionary rates. Discussing a result that dates back to his famous debate with Stephen Jay Gould over punctuated equilibrium in early 1980s, Dr. Gingerich showed why the dramatic inverse correlation between rates of evolution and the interval of time over which they are measured is a simple mathematical artifact. For those interested in more on this work, Dr. Gingerich published a nice review in the Annual Review of Ecology, Evolution and Systematics. Gingerich also provided an interesting anecdote about Gould. Early in his talk today, Gingerich asked the audience how many figures were in the Origin. As any phylogeneticist knows, the answer is one: Darwin's classic illustration of the branching tree of life. Apparently when Gingerich asked this same question when Gould was in the audience Gould quickly, and incorrectly, blurted out "two!"

The other headliner today was the godfather of phylogeography, John Avise. This is the first time I've seen him speak, so it was nice that he provided a 22 point retrospective on the lessons learned from phylogeography. It's amazing to think that his first papers on this topic were published over 30 years ago now!

Thanks to Case Western's Institute for the Science of Origins for sponsoring today's event!

Sunday, February 7, 2010

The End of Adaptive Radiation?

In a provocative new Bioessays article, Olson and Arroyo-Santos attempt to kill the term "adaptive radation." Olson and Arroyo-Santos are certainly correct when they suggest that interest in adaptive radiation is paradoxical: although it is almost universally regarded as an important (if not the most important) mode of biological diversification, evolutionary biologists have argued for decades about how to diagnose and define it. Olson and Arroyo-Santos suggest that this century-old debate stems fundamentally from the fact that "adaptive radiation cannot be winnowed to any core meaning, because there is no phenomenon in nature to which the term corresponds, simply arbitrary divisions of continua."

The problem with this argument is that it focuses exclusively on the one feature of adaptive radiation that is controversial - namely, whether extraordinary diversification is intrinsic to adaptive radiation. While I agree with Olson and Arroyo-Santos's suggestion that efforts to define adaptive radiation on the basis of the extraordinary levels of diversity are hopelessly ambiguous and arbitrary, I disagree with the fundamental premise that extraordinary diversification, in any form, is intrinsic to adaptive radiation. If we focus on the shared features of modern definitions of adaptive radiation, we find that it can be universally defined as a response to natural selection and ecological opportunity involving divergence of species and associated adaptive features. In this sense, adaptive radiation is analogous to the ‘principle of divergence’ that Darwin introduced in the Origin by suggesting that “the more diversified the descendants from any one species become in structure, constitution, and habits, by so much will they be better enabled to seize on many and widely diversified places in the polity of nature, and so be enabled to increase in numbers.” Perhaps we should replace 'adaptive radiation' with 'principle of divergence,' but abandoning efforts to label the profoundly important evolutionary phenomenon that underlies these terms seems like a bad idea to me.

Friday, February 5, 2010

Phriday Phun with Photoshop

It seems like everyone blogging about the bat alcohol tolerance story in PLoS One has come up with their own Photoshopped image of a bat getting drunk. This is your chance to vote for your favorite! For a larger version of this image, go here.

Which is the best photoshopped image of a bat getting drunk?

Thursday, February 4, 2010

Designated Fliers

In a "is it Friday yet?" kind of way, I thought I would share this little post. A recent paper in PLoS One by Orbach et al. presents results showing that frugivorous and nectarivorous bats do not appear to be affected by consuming alcohol. The authors fed bats either a sugar solution or sugar+alcohol (strawberry daquiri?) solution. They then gave the bats an aerial obstacle course to test their speed and agility. They also recorded the bats' echolocation calls. Although there were differences between the species that they tested, there were no observed effects of treatment - the "drunk" bats did just as well as the "sober" bats. This was true, even though the estimated BAC's of the bats were sometimes very high - more than 0.3%. Thus, these bats seem perfectly capable of utilizing rotting fruits as food sources with no chiropteran "slurred speech" and little or no danger to themselves or others. Large, virtually hairless primates such as ourselves, do not appear so well adapted and should exercise caution.

I give thanks to Sam Crane who patiently walked me through PhotoShop again so I could make this picture.

Wednesday, February 3, 2010

Going Rogue

If we've learned anything from US politics over the past year and half its that adding 'rogues' to an an otherwise orderly system can result in rapid descent to the lowest common denominator. In the latest issue of Systematic Biology, Thomson and Shaffer show that the same is true in phylogenetics. With the goal of reconstructing a robust phylogenetic hypothesis for turtles using existing sequence data, Thomson and Shaffer use a new pipeline and the data available via the PhyLoTA browser to assemble a dataset that is noteworthy for both its size and incompleteness: 223 taxa, 53,406 bp, 7.59% complete. Although Thomson and Shaffer explore the influence of a variety of factors on phylogenetic inference, they conclude that rogue taxa "probably represent the most insidious problem for supermatrix phylogenetics." For those unfamiliar with rogue taxa, the term is used to describe taxa whose phylogenetic position can vary dramatically without having a strong effect on a tree's overall score. Thomson and Shaffer identify rogues using the taxonomic instability index (I) calculated by Mesquite from a sample of trees generated using standard bootstrapping methods. To explore the influence of rogues on phyogenetic resolution, Thomson and Shaffer remove those taxa exhibiting the most roguish behavior and redo their analyses. The top panel of their Fig. 4 provides a compelling visual representation of the results of this exercise, with the completely unresolved tree on the left being generated before pruning rogues and the nearly fully-resolved tree on the right resulting from analysis of the same dataset subsequent to de-roguing. Although one might challenge the wisdom of deleting problematic taxa until a resolved tree is produced, this practice may be justified in some instances. How we deal with rogue taxa is sure to be a topic of debate in the years to come, but, for the time being Thomson and Shaffer's analyses suggest that simply deleting the taxa with the worst I values may be a reasonable solution.

Tuesday, February 2, 2010

Rotten Fish and the Chordate Tree of Life

The origin of vertebrates is part of a larger story involving the evolution of a more inclusive group of kin, the chordates that along with vertebrates include urochordates (tunicates) and cephalochordates (lancelets). Recent decades have been an exciting time for our understanding of chordate evolution, with the discovery and evolutionary analysis of important chordate fossils that date to the Cambrian (542 to 488 million years ago). On the basis of distinct morphological features preserved in the fossils, scientists have been able to integrate these extinct lineages into phylogenetic hypotheses of chordates, extinct early vertebrate lineages, and extant vertebrates.

In a very clever study published last week in Nature, Sanson et al. allowed specimens of lancelets and larval lampreys (ammocoetes) to decay in artificial seawater in the laboratory. The anatomical features that are the most important for distinguishing clades in the phylogeny were the most prone to decay, while the least informative (pleisiomorphic) characters were more resistant to decay. The results are striking and have important implications for the evolutionary interpretation of early chordate and vertebrate fossils. The bias in anatomical decay will result in placement of derived lineages further down the stem of the phylogeny, a phenomena the authors refer to 'stem-ward slippage.' As a result, placement of chordate and vertebrate fossil taxa on the stem of their respective phylogenies may be an artifact of character preservation. As such, the phylogenetic position of fossil taxa lacking derived features, but possessing character states of stem chordates or vertebrates, may be suspect. A video showing time lapse photography of a rotting lamprey is available on Nature's youtube channel. Picture of the cleared and stained ammocoete from

Monday, February 1, 2010

Trees in Pop Culture: The Darwin Electro-Opera

Did you ever think you'd see a phylogenetic tree displayed in laser light as the backdrop to an opera? Well, neither did I, but that's exactly what happens during an opera based on Darwin's life and works written by the Swedish synth-pop innovators and Pitchfork darlings known as The Knife. The image above is a screen capture from the 2:37 mark of a 7 minute preview video in which one of Darwin's hand-drawn trees is clearly visible. The soundtrack releases via tomorrow, but you can preview it now at NPR. Reviews and commentaries on this work are all over the place. NPR's All Songs Considered blog links to a twenty minute roundtable discussion with The Knife and their collaborators (Mt. Sims and Planningtorock) that is almost as bizarre as the video. If one thing is clear, it's that they've taken the task of learning about Darwin and his theory rather seriously. The resulting music is fascinating and full of meaning, but its also a bit abstract for the minds of most scientists.