More Proof that Parasites Rule the World

This week's Nature has an article by Kuris et al. [1] that presents the results of a long-term study of a California estuary that quantified biomass of various groups of organisms. Although as a percentage of the total, parasites are only about 1% of the animal biomass, but it turns out that parasitic trematodes can reach biomasses greater than the birds and fishes in the ecosystem! Some of these parasites are host castrators, thus if one considers these hosts as extended phenotypes of the parasites, the effective biomass of parasites is even higher. One of the things that I found most interesting, though, is that in some snails, the trematode parasites can be 22% of the animal' soft-tissue body weight, a stat published by several members of the same group this year [2]. There has already been a much-hyped instance of researchers accidentally sequencing a gene from a trematode parasite instead of that of the frog they were working on. Now these data are a big caution that the potential for sequencing parasite instead of host can be very high in many invertebrates. Potential for parasite contamination might be very high in EST libraries made from organisms that might be hosts, too...yikes!!

1. Kuris, A.M., R. F. Hechinger, J. C. Shaw et al. 2008. Ecosystem energetic implications of parasite and free-living biomass in three estuaries. Nature 454:515-518.
2. Hechinger, R.F., K. D. Lafferty, F. T. Mancini III, R. R. Warner, and A. M. Kuris. 2008. How large is the hand in the puppet? Ecological and evolutionary factors affecting body mass of 15 trematode parasitic castrators in their snail host. Evolutionary Ecology, in press.

Photo credit: Rodrigo Mexas, on http://nikoninstruments.mediaroom.com/index.php?s=13

Ichthyology & Herpetology 2008

Anybody else headed to Montreal this week for the 2008 Joint Meetings of Ichthyologists and Herpetologists? I'm driving up today. Something tells me I'll be the only one trying to live blog from the Cottonmouth symposium...

New Uses for Old Thermalcyclers (and Scientists?)

I know we don't usually re-post blogs, but this one struck me as funny. Perhaps if I don't get tenure at the same time an older thermalcycler is being disposed of, I could have a new career forming the third "DNA dating" company. Here is a blog discussing the latest and cheapest company that will use your DNA to help you find your perfect match. The service is available to both singles, who can use their database of other people who have also submitted their DNA samples to find a match, and couples where both members submit samples to find out if their genes spell fairy tale ending or divorce court (won't the lawyers have fun with this??). From the GenePartner website it appears that they base compatibility on HLA or immune loci but this sounds more like testing for can we go on a trip to Cabo together and come back speaking to each other. Maybe my new company will use microarrays to screen for "remote hogging" and "Gray's Anatomy tolerance" genes...that might be more effective.

Do Mammal Species Avoid Living with Their Relatives?

As the reconstructed tree of life grows, phylogeneticists increasingly find themselves revisiting classic questions in ecology and evolutionary biology. Among the most interesting of these questions involve evolution's contribution to the composition of ecological communities. Two studies published a few months ago use the recently-completed mammalian supertree to ask whether communities tend to consist of particularly distantly-related species. This pattern of "phylogenetic overdispersion" has long been considered a symptom of strong competitive interactions among closely-related -- and presumably ecologically similar -- species.

Cardillo et al. (2008) address overdispersion by asking whether a global dataset of island assemblages tend to consist of phylogenetically overdispersed samples from their putative source populations. Although a few communities exhibited overdispersion, the overwhelming majority of their samples consisted of random samples (see figure). A subsequent study by Cooper et al. (2008) [subscription required] took a closer look at monkey, squirrel, and possum communities over large geographic regions. They found evidence for overdispersion in five of eight analyses of pooled samples, but never in individual communities.

The absence of general conclusions from these studies mirrors earlier results from studies of plant communities, where both overdispersion and its converse (i.e., phylogenetic clustering) have been recorded (see papers by Silvertown, Caveder-Bares, etc). Together these observations suggest that -- at least for the time being -- the phylogenetic contribution to community composition must be evaluated on a case by case basis. Perhaps more importantly, the inability of broad scale analyses to distinguish among the many possible alternative explanations for the diverse patterns they observe should be seen as a call for detailed, biological-informed studies of specific examples.

Cardillo, M., J. L. Gittleman, and A. Purvis. 2008. Global patterns in the phylogenetic structure of island mammal assemblages. Proc. Royal Soc. B 275:1549-1556.

Cooper, N., J. Rodriguez, and A. Purvis. 2008. A common tendency for phylogenetic overdispersion in mammalian assemblages. Proc. Royal Soc. B 275:2031-2037.

Field Guide to Cladists

Many of our readers who subscribe to EvolDir probably saw the message announcing the upcoming event: "Beyond Cladistics: A Festschrift for Prof C J Humphries" a few days ago. Since the link to the program had some kind of error and since when Rich introduced me to the blog, he said he hoped I would offer some insight into the minds of Cladists, I thought I would both post the correct program link and offer a few words of (attempted) explanation. If you're wondering, "What the heck is a "festschrift?!", these are traditional amongst the Cladists, who definitely are lovers of tradition - and are simply books of collected contributions in honor of one of them presented by colleagues and former students. Oftentimes, these are accompanied by events where these authors present papers that highlight topics of relevance to said honoree. As Wikipedia points out, for those non-elitists, these usually are called "symposia" and the books are called "Essays in Honor of..." I won't be attending this festschrift, but am very curious about some of these talks - especially those that by the title seem to suggest that there's a resurgence of phenetics and of course many which seem to promise to discuss the future of cladistics. Perhaps I can get some reports from my colleagues here who might attend. I'll let you know in October.

About Science Blogs

In case you are a bit unsure what the purpose - for the bloggers, for other scientists, and for the public - of posts like these here at dechronization are all about - or maybe you aren't even quite sure what a blog is, there's a little article in the latest Trends in Ecology and Evolution by John Wilkins about scientific blogs...complete with nifty diagram of how these beasts work.

A Very Non-parsimonious Parsimony Model

There's a nifty paper in the June issue of Systematic Biology by Huelselbeck et al. The paper has a nifty title: "A Bayesian Perspective on a Non-parsimonious Parsimony Model." Basically, the authors implement a fully Bayesian equivalent to parsimony based on Tuffley and Steel's (1997) likelihood model. This "no common mechanism" model requires separate estimates of branch lengths for each branch and each site; adding one base pair to your sequence requires estimating 2n-3 new parameters for your model of sequence evolution, where n is the number of species in the tree. That's a lot of parameters; hence the title.

We knew that in a likelihood framework, the no common mechanism model's ML tree was the same as the maximum parsimony tree. It is not really surprising, given the commonalities between likelihood and Bayesian frameworks, that this equivalence holds for Huelsenbeck et al.'s new implementation (see their figure 5, above, showing a perfect negative relationship between log-likelihood and parsimony score). Still, there are a number of very interesting tidbits in this paper. First, one can now compare the "fit" of a parsimony model to other, more commonly used, Bayesian models. Second, this framework provides natural measures of support for a parsimony analysis, rather than approximations like bootstrap values. The catch here is that the paper itself provides compelling arguments against even implementing this model:

The no-common mechanism model is very peculiar, and the authors have mixed feelings about having implemented the method in a Bayesian framework. (Huelsenbeck et al., p. 415)

There's also a couple nifty new tree-searching "tricks" that the authors implement to help search tree space more efficiently under this complex model. These two (Gibbs-like TBR move and Gibbs eraser) may affect your life, some day, by making your tree searches run faster.

Branch Support Values: No Torture For You!

After the splashy courtroom shows (HIV cases and in enforcing the Endangered Species Act), it seems that phylogenetic approaches are now slated for broader constitutional considerations.

Perhaps as a sign of things to come, first there was the case of the Swiss Federal Ethics Committee on Non-human Biotechnology and their moral consideration of plants' rights. Among the natural questions that arise are: What is a plant, and why stop there? Now, a New York Times column reports, the Spanish Parliament granted limited rights to non-human primates. It seems near-certain that the extent of rights and freedoms will be weighed by phylogenetic position and the phenotypic measurement of "human qualities."

There are, of course, other outstanding questions. Will the governments choose to go rank-free? Will they use parsimony? Will they assume that all polytomies are soft? Which species will get shafted because of the Felsenstein Zone?

As we wait for those and other answers, I recommend a perusal of the opening passage of that Times column:

"If you caught your son burning ants with a magnifying glass, would it bother you less than if you found him torturing a mouse with a soldering iron? How about a snake? How about his sister?"

Myth Busters: Chameleons are Nature's Masters of Camouflage

UPDATE - Another paper by Stuart-Fox et al. that appeared shortly after the work on social color change shows that chameleons do indeed change color in response to predators to increase their crypsis. Specifically, this paper shows that the dwarf chameleon (Bradypodion taeniabronchum) exhibits different responses to snake and bird predators, and does so in a manner that likely optimizes its camouflage in each case. As much as I hate to admit it, chameleons are obviously much better at this whole color change thing than anoles... [Thanks to commenter Michael Meadon for pointing this out]

Ask anybody why a chameleon changes its colors and you're sure to hear something about it trying to blend in with it's background. It may come as a surprise to many of you, then, that this simply isn't true. Chameleons, and most other reptiles that are into color change (e.g., Anolis carolinensis, a.k.a. "the American Chameleon"), do so almost exclusively for social reasons. Stuart-Fox and Moussali drove the nail in the coffin of this myth with a remarkable series of studies a few months back (one in American Naturalist and another in PLoS Biology). By combining data about chameleon color, the light environment in which they're displaying, and the visual systems of both chameleons and their potential predators, they were able to show that the conspicuous color-changes observed in the South African dwarf chameleon are specifically designed to stand out against their background for the purpose of social interaction. Got it? Color change in chameleons didn't evolve so that they could blend in with their background, but so that they could stand out against it! Of course, this doesn't change the fact that chameleons are still pretty damned good at being cryptic, just that the color change isn't used for this purpose.

PS - I couldn't agree more with their assertion "that quantifying signal conspicuousness to different receivers can be used to gain insights into the evolution of signal diversity in animals." In lizards, this type of work has been made possible to the remarkably thorough studies of Leo Fleishman and colleages, who have painstakingly measuring the properties of lizard visual system. Although the models remain imperfect, they're a hell of a start. Thanks Leo!

Hey Mom, Don't You Recognize Me? (or, They Must Have Had a Really Big Autoclave)

In this week's Science, Gibbs et al. report their findings of well, I don't know how else to say this, but a shit-ton of genetic screening that they did to identify the genetic basis of self-identity in a swarming bacterium (See this page for more info and photos of the bacteria in attack mode.) The bug of focus was Proteus mirabilis, a bacterium that is responsible for urinary tract infection, kidney stones and other types of infection in humans. What's cool is that if different strains of these motile bacteria come into contact on an agar plate, one can observe a visible boundary between them. Sometimes, there is even microbial warfare, with one strain secreting proteins capable of killing the other. Up until now, though, no one knew how one strain recognized another as either a "chip off the old block" or a potential enemy (they're too small to wear blue and red bandanas). Gibbs and company screened 3600 (!) mutants of a strain of P. mirabilis, each generated with transposons randomly integrated into the bacterial genome. They identified one region that was particularly war-mongering and christened it "ids" - identification of self. They mapped the mutation to a cluster of six genes and then set about doing even more screening to knock out the various individual genes and then replace them systematically on plasmids. They then go on to do even more experiments (read the article if you're having trouble falling asleep tonight) to tease apart the exact mechanism by which these genes allow the bacteria to tell what strain they are and then sequence this region in completely different isolates of P. mirabilis. In the end, though, they are unable to identify any specific products from these genes, so the mechanism is still a mystery. Nonetheless, it is an important step in understanding cell-cell signaling in microbes and a very basic process of producing and maintaining variation and no doubt will soon find its way into new genetics textbooks as a nifty example.