Monday, September 29, 2008

Job Hunters, Don't Overlook This Opportunity!

Job hunting can be a fickle, frustrating process. Thankfully the good people at the Institute for Creation Research offer an excruciatingly detailed account of the requirements for their open Assistant Professor position. On top of the basic degree requirements, applicants must also agree with the ICR doctrinal statements and tenets. I love that they have a such a direct mechanism for preventing anyone from doing actual science at the ICR. Even more than this list, I love the header photo on their 'science' page, which shows a girl staring into some green water through an Erlenmeyer flask. Recalling the famous Peanut Butter principle, I can't help but imagine a room full of young scholars staring at such flasks to prove that evolution doesn't happen.

Sunday, September 28, 2008

Is Local Adaptative Variation Tied to Mate Choice?

With the growing popularity of ecological speciation, instances of local adaptation have taken on added significance. In addition to being powerful examples of natural selection in action, local adaptation is now recognized as a potential starting point for the process of speciation. In order to invoke speciation or incipient speciation, however, it's necessary to show that some degree of reproductive isolation exists among local variants. Although this hypothesis is often tested indirectly with molecular markers, relatively few authors have succeeded in conducting direct behavioral assays of reproductive isolation in nature.

In the latest issue of Journal of Herpetology, Erica Bree Rosenblum uses a series of relatively simple behavioral experiments to examine reproductive isolation between the light and dark color morphs of the Lesser Earless Lizard (Holbrookia maculata). These forms evolved over the last 6,000 years to match substrate variation in the southwestern United States. While she found that light individuals are more likely to court other light individuals, this decision does not appear to be the result of body coloration: similar results were obtained even when light individuals were painted to resemble dark individuals. She suggests that behavioral signals or other aspects of the animal's coloration that are not obviously associated with crypsis (e.g., throat coloration) may be the mechanisms driving mate choice in Holbrookia.

The conclusion that the trait involved in adaptive divergence for improved crypsis is decoupled from the trait(s) involved in mate choice is surprising because it requires a more complicated model of speciation than when the same trait is filling both roles. Specifically, successful speciation under this scenario requires linkage between two traits that likely have distinct genetic foundations. Because the evolution of such linkage has always been viewed as one of the main impediments to ecological speciation it's going to be interesting to see how this story plays out, and how general this pattern is among other putative examples of ecological speciation.

Saturday, September 27, 2008

What the Hell is Niche Conservatism?

Niche conservatism is all the rage; virtually unheard of at the turn of the Millenium, 2008 has already seen nearly 30 papers on the subject. The only problem? Nobody seems to agree on what it is!

In a recent exchange in Ecological Letters, Jonathan Losos and John Wiens try to cut through the confusion. Let's begin with Losos' definition of niche conservatism as a pattern that "results when closely related species are more ecologically similar that [sic] would be expected based on their phylogenetic relationships" (emphasis mine). In advocating this definition, Losos argues strongly against the view that niche conservatism is a synonym for phylogenetic signal (i.e., the tendency for related species to be more similar than species drawn at random from a phylogeny). To make this equation, he argues, would defy the original meaning of the term niche conservatism and expands its scope so broadly as to render it meaningless. As Losos notes, some degree of ecological similarity is expected among closely related species even under the simplest models of evolution (e.g., Brownian motion resulting from shifting selective pressures or drift). Niche conservatism, meanwhile, results when species are more similar than expected under this simple model due to constraint by natural (stabilizing) selection, gene flow, pleiotropy or the absence of variation. Although Wiens agrees on this point, many recent studies claiming to support niche conservation involve nothing more than simple tests of phylogenetic signal. In Losos' view, these studies provide evidence that is necessary, but not sufficient, for the identification of niche conservation.

Although I've previously confounded niche conservatism and phylogenetic signal in my own work, I've come around to the view shared by Wiens and Losos. Another influential voice in the field -- Michael Donoghue (2008) -- seems to straddle the fence when he says "strictly speaking, it is not necessary to link PNC with the view that there are constraints on niche evolution, [but] I believe that it is the relative difficulty of making major ecological shifts that explains [patterns of niche conservation]." What do you all think?

If people are into this topic, perhaps we can try to tackle Losos and Wiens arguments about how and when niche conservatism should be studied, and whether it represents a pattern, a process, or both...

Literature Cited:
Losos, J. B. 2008. Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecology Letters 11:995-1003.

Wiens, J. J. 2008. Commentary on Losos (2008): Niche Conservatism Déjá Vu. Ecology Letters 11:1004-1005.

Losos, J. B. 2008. Rejoinder to Wiens (2008): Phylogenetic niche conservatism, its occurrence and importance. Ecology Letters 11:1005-1007.

Donoghue, M. J. 2008. A phylogenetic perspective on the distribution of plant diversity. PNAS 105:11549-11555.

Friday, September 26, 2008

Ray-finned fish phylogeny: Going nuclear!

The most recent issue of Systematic Biology has a great new phylogenetic analysis of actinopterygian fishes that uses 10 nuclear genes. Chenhong Li, Guoqing Lu, and Guillermo Orti present an excellent study of ray-finned (actinopterygian) fish phylogeny. The trees generated in this study reflect some very interesting hypotheses of actinopt relationships hypothesized by pre-cladistic evolutionary biologists and ichthyologists. Li et al. present a cutting edge analysis of a very impressive dataset, and offer a new strategy to consider when partitioning data for maximum likelihood or Bayesian phylogenetic analyses.


Our own Tom Near was prominently featured in a New York Times article. And not just peripherally mentioned, mind you--he was called "a heavy-duty gamer." Holy crap! The article is about Spore, a recently released game from Will Wright (of SimCity and The Sims fame). It's a sketch-simulation of life from the origin on. According to some of the nerdbags quoted in the article,  the game may get the tempo and mode of evolution wrong. 

Here's my favorite excerpt from the beginning of the piece:
By night, Dr. Near, an assistant professor at Yale, is a heavy-duty gamer, steering tanks or playing football on his computer. This afternoon his two lives have come together.

Wednesday, September 24, 2008

The Fisher Archive

A couple of years ago, while following up on my reading of Provine's book about Sewall Wright, I stumbled upon the University of Adelaide's Ronald A. Fisher Digital Archive. [Fisher and Wright tangled over the problem of maintenance of polymorphism at the self-incompatibility locus in plants.] I not only found what I was looking for--Fisher's unpublished manuscript on self-incompatibility--but also a trove of other manuscripts, documents, and letters.

By the way, Fisher's Erdös number is 2. I wonder if some crafty programmer-biologist out there would mind writing a Lande distance, or something similar.

Tuesday, September 2, 2008

These Lizards are Making Me Look Bad

Ok, I try to get up every morning and do a bit of a work out...but sure, sometimes I spend the half hour sipping coffee on the couch instead - and then I feel a little guilty. Now I've got lizards to make me feel even worse! A new study by Terry Ord, a postdoc in the Losos lab at Harvard shows that four species of Anolis lizards on Jamaica do their characteristic push-ups and dewlapping displays at dawn and/or at dusk. This is the first time that such a "silent dawn chorus" has been demonstrated - but shows similarities to birds and other acoustic animals who broadcast their presence in their territories. This strategy is thought to be more efficient at maintaining stable territories and communities by advertising a male's ability to defend its territory -without having to actually go through the hassle (and energy expense and danger) of doing so. Doing it at dawn and dusk sort of "bookends" this information - in the a.m. it establishes which territories are occupied and in the evening, it advertises, "Hey, I'm still here - no snake or bird - or biologist! - got me today. Going to bed - see you in the morning."

Ugh - these things are exercising twice a day! I promise to get up early tomorrow and do some push-ups of my own...and I'm leaving the shades up so the neighbors can make no mistake that this is my apartment.

Popular press picked this up, too.