Phylota: My Mind is Blown

In the June issue of Systematic Biology, Sanderson et al. report the availability of the PhyLoTA browser. If you haven't checked this out yet, do - it can be a real boon to phylogenetic analyses in the age of Bioinformatics. For clades in the Tree of Life, PhyLoTA identifies clusters, which are sets of sequences for the same gene across sets of taxa. For example, here are some clusters for the geckos. You can see the big hitters in there: c-mos, 12s, 16s, cytochrome b. There are also a few decent data sets for other genes as well. You can then download preliminary alignments for the clusters for your phylogenetic analyses.

If you've every tried to do this sort of thing directly in GenBank, the value of this will be immediately apparent. This is particularly useful if you, like me, suck at sequencing.

As a side note, I talked to a colleague who got harassed at the Ichs and Herps meeting for... gasp... downloading sequences from GenBank and using them without asking the author's permission! Good lord, what is the world coming to? I'm surprised to hear of such active resistance to public availability of information.

UPDATE: Further discussion of the final paragraph at <bbgm>.

Highlights (or Lack Thereof) from Ichthyology & Herpetology 2008

I'm just back from the Ichs and Herps meetings in Montreal. Overall, the meetings were a bit of a let-down. They suffered in particular by comparison to the Evolution meetings just a few weeks previously. At Evolution, I saw lots of phylogenies reconstructed with 10-20 nuclear loci as well as a range of exciting new phylogenetic and comparative methods. At Ichs and Herps, phylogenies from mitochondrial DNA plus 0-5 nuclear loci were the norm and hardly anybody was doing innovative or novel analyses.

The coolest science talk I saw was Todd Castoe's talk about mtDNA evolution in snakes. Apparently, the remarkably rapid rate of mtDNA evolution in snakes is due primarily to non-synonymous substitutions in cytochrome oxidase (a transmembrane protein complex that is esstential for cellular respiration). In their recent PLoS One paper, Todd and his colleagues reasonably suggested that this is due to the radical shift in niche and diet that accompanied snake evolution, and their tendency to endure long fasts punctuated by the occasional very large meal in particular.

Structurama: Revisiting models for the inference of population structure

We've previously highlighted updates of Structure, commonly used for inferring population structure, and Distruct, the sister package used for pretty result plotting . Specifically, Structure uses a fixed number of populations (K) to assign posterior probabilities of assigning individuals to populations. It's worth pointing out that Huelsenbeck and Andolfatto (2007) have implemented a nice modification (originally suggested by Pella and Masuda 2006), which can consider K as a random variable that follows a Dirichlet process prior. In other words, it's no longer necessarily fixed to some arbitrary value. The Dirichlet process is nicely explained in the

Structurama manual.

In another homage to a previous post, it's also worth highlighting that it is remarkably easy to use R to manipulate the resulting plots (results are arrayed in columns) and create output very similar to that obtained in Distruct.

R Tip: Indicating Tree Support

I can't take any more of the tiny, unreadable posterior probability and bootstrap support values that I've been seeing on phylogenetic trees at the Ichs and Herps Meeting. Wouldn't it be easier to to put some easy-to-read symbols on the nodes instead of text in 4 point font? I understand why people haven't done this in the past -- it would have required individually replacing text with symbol at each node. Thanks to R, however, this tedious process is no longer necessary. Below are some simple instructions for doing this with posterior probability values included in the '.con' trees that are output from MrBayes using the sumt command (see further details in Paradis' book on R for phylogenetics). If you've never used R for phylogenetics before, you might also want to start at the new R-phylo Wiki.

#First, load the required library.
library(ape)
#Next, get your consensus tree from MrBayes into R.
read.nexus("your_file.con") -> your_tree
#Then, simplify matters by using only the tree with PP values.
your_tree[[1]] -> your_tree
#Tell R to save the resulting tree file in PDF format.
pdf(file="labeled_tree.pdf")
#Generate the vector required to store values for background colors for symbols.
p <- character(length(your_tree$node.label))
#The following three lines define your labeling scheme. p[your_tree$node.label >= 0.95] <- "black"
p[your_tree$node.label < 0.95 & your_tree$node.label >= 0.75] <- "gray"
p[your_tree$node.label < 0.75] <- "white"
#Almost done, you're ready to plot your tree
plot(your_tree)
#Now label your tree:'pch' tells R to use filled circles, 'cex' defines the size of the circles, and 'bg' tells it the name of the vector including the fill colors.
nodelabels(pch=21, cex = .75, bg = p)
#Finally, turn off the PDF writing
dev.off()

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.

Origin of Flatfishes: The Eyes Have It!

Flatfishes (Pleuronectiformes) are unusual in that they are asymmetrical, having both eyes on the same side of the head. The placement of eyes in young flatfishes is symmetrical, and the origin of this bizarre morphology has puzzled evolutionary biologists dating back to Charles Darwin. Unfortunately, the apparent lack of flatfish species that exhibit an intermediate morphology with regard to the placement of eyes has been a favorite of creationists as yet another example of "no intermediate form. " A paper published yesterday in Nature by Matt Friedman, a graduate student at the University of Chicago, blows this creationist example away by showing that fossil flatfish species dating from the Eocene (approx. 50 Ma) have an intermediate placement of the eyes on the head. Another important aspect of this study is that the evolution of this was not saltatory, but gradual. The work presented in this paper is an outstanding example of integrating fossil and extant lineages to discover the course of diversification in a trait, and how information from fossil lineages can inform phylogeny. There is some news buzz about this paper, and I was interviewed by the Chicago Tribune (my home town paper). Philippe Janvier wrote a very nice News & Views for this paper in Nature.

G-Day!

Raise your hand if you're trying to get a grant in for today's NSF target. (Mine's up). Out of curiosity, how many days does your institution's granting bureaucracy require to review your proposal before formal submission? Mine wants five days, but permits some revisions made while they're looking it over.

New SSU Alignment and Phylogenetic Pipeline: STAP

Ok, here's where I, as the "microbial" person on this blog start speaking another language: most microbiologists, especially those who conduct large-scale environmental sampling for novel lineages of bacteria, archaea, and microbial eukaryotes, still use (gasp!) small subunit ribosomal RNA sequences for identifying organisms and analyzing communities. The reason is simple - primers to amplify these genes are almost completely universal so can be counted on to pick out even rare ("unculturable" almost goes without saying) microbes and, perhaps more importantly, these genes rarely undergo horizontal gene transfer and so are thought to be reliable for identifying truly new bugs out there. The problem has been that the process of taking a slew of these sequences and cranking them through available software to see who was living in your favorite type of sludge was a tedious process involving many different programs. The slowest part of this process was often manual editing of the matrix to adjust alignments. Recently, Wu et al. developed a new pipeline that can completely automate this process, called "Small Subunit rRNA Taxonomy and Alignment Pipeline" or STAP, for short. Although getting this pipeline going requires that you have a basic bioinformatics toolkit installed and compiled (including ClustalW, PhyML and some BioPerl scripts), once this thing is up and running, it is fast (& parallelizable), reliable (more reliable than BLASTN as you approach finer taxonomic scales - see figure above), and open source. Kudos to fellow blogger Jonathan Eisen and his crew for making the lives of Venter-ites everywhere a little easier - and bacterial taxonomy and systematics a lot more solid at the same time.

Welcome iPhylo Readers

Thanks to a nice plug from Rod Page, we've been seeing quite a few visitors from his iPhylo blog today. Welcome! Most of you seem to be coming for the porn, but we hope you'll run across some other interesting material while you're here.

If you haven't checked out iPhylo yet, you should head over there. Those interested in on-line databases of phylogenetic trees and taxonomic information - including Page's own iSpecies initiative - will find his posts particularly enlightening (including several recent posts on potential problems with these databases [1], [2]). We're also glad to see that somebody else shares our tendency to rant about inefficient commercial reference databases! His rant, however, actually elicited a response from the offending parties.

Software Review: Structure 2.2 GUI

The structure method introduced by Pritchard et al. in 2000 has quickly become one of the most widely-used analytical methods in population genetics and phylogeography (more than 1,000 citations in seven years!). It's popularity is sure to grow as extensions are developed and the type of multi-locus genetic data it requires accumulates for non-model organisms. With the release of a cross-platform graphical front-end in 2007, users who were scared of by its somewhat cumbersome command-line interface are out of excuses. Although veteran users may prefer to stick with the command line interface, I've found the graphical front-end to be a helpful supplement. It's particularly useful for visualizing the results of structure analyses, including generation of the iconic structure diagrams that previously required Noah Rosenberg's complementary distruct package. Don't trash your copy of distruct just yet though, you're still going to need it to produce high quality images for publication; the structure GUI produces low quality JPG images and has limited options for custom labeling. OK, now go play!

If you need support for structure, you should consult it's outstanding user manual (it's included as the readme.pdf file in the doc folder of a standard structure installation), or the wonderful tutorial that Bob Thompson posted over at the Bodega Phylogenetics Wiki. I just added a foot-note to Bob's tutorial that you might find helpful for installation of the front-end on Mac OSX machines if you have little or no experience navigating UNIX file architecture.

New Zoo Review: "Madagascar!" at the Bronx Zoo

Today I took my annual birthday pilgrimage to the Bronx Zoo - highlighted this year with a visit to the very newly opened Madagascar exhibit, in the Zoo's historic Lion House. It's a fairly small exhibit that, of course, stars lemurs, but in addition to the very endearing sifaka who greets you as you enter and the incredible red ruffed lemurs who make the most incredible (and loud!) group calls within feet of you, other highlights included two really huge Nile crocodiles displayed in a really, really cool way and a beautiful fossa. Surprisingly missing were any chameleons, though today was a bad day for herps, apparently, many of whom got removed due to overzealous air-conditioning, so they might be part of this exhibit otherwise. There are a lot of photos and blurbs about the conservation work being done by WCS in Madagascar, though I would have liked to have seen more info on the biogeography and evolutionary relationships of these really neat animals.

Read a more detailed review here.

Independent Contrasts Rule!

Despite the explosion of various types of phylogenetic comparative methods in recent years, Joe Felsenstein's independent contrasts still play a key role in the field. These contrasts can be thought of in a few ways: as a sort of mathematical trick to do phylogenetic generalized least squares (PGLS), as a transformation of evolutionary states to evolutionary rates, or as a method to "correct" for the phylogeny in a regression framework. In any case, they are conceptually simple yet statistically powerful.

Recently there has been an exciting development published in the American Naturalist: Felsenstein has extended his method so that one can now calculate contrasts both within and among species (the conceptual figure here is taken from this paper, Felsenstein 2008). This effectively accounts for error in the estimation of species means, which can cause bias in most applications of contrasts. But there's more to this paper than measurement error, and Felsenstein waits until the end of the paper to get into what is (to me) the best bit: this new method effectively uses contrasts to link micro- and macroevolution, unifying patterns within and among species. Sound familiar? I think this is the comparative method's version of the BEST approach.

Felsenstein, J. 2008. Comparative methods with sampling error and within-species variation: contrasts revisited and revised. Am. Nat. 171:713-725.

Do Birds of a Feather Clade Together?

In a recent paper Hackett et al., present a phylogenomic analysis of birds based on 19 genes sampled from 169 species. The phylogenies are amazingly well supported and reflect many traditional groupings. However, this new phylogeny offers several surprises. For example, parrots and passeriforms (perching birds) are sister lineages.

The analyses were based on concatenated datasets. We at dechronization are sure that species tree proponents interested in birds (e.g. Scott Edwards at Harvard) will be analyzing this wonderful dataset using the new and cutting edge methods being developed to estimate species trees. These are exciting times for phylogenetics.

Hackett, S. J., R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M. J. Bruan, J. L. Chonjnowski, W. A. Cox, K.-L. Han, J. Harshman, C. J. Huddleston, B. D. Marks, K. J. Miglia, W. S. Moore, F. H. Sheldon, D. W. Steadman, C. C. Witt and T. Yuri 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320: 1763-1768.

How Old are Turtles? A Paleontological Perspective.

In a recent paper published in Journal of Vertebrate Paleontology, Danilov and Parham present an interesting analysis of two Middle Jurassic fossil turtle lineages. They estimate the phylogenetic relationships of these extinct lineages using discretely coded morphological characters, and bracket the estimated age for the crown node of all living turtles based on the oldest fossils. As the the figure from their paper shows, there has been debate as to the timing of turtle (Testudines) diversification. Previous estimates range from the Triassic-Jurassic boundary to the Late Jurassic.

Recent molecular divergence time estimates from Charles Marshall (presented at the 2008 Evolution meetings in Minnesota) and a team composed of Peter Meylan, Brad Shaffer, and yours truly result in an age for living turtles that dates to the Triassic-Jurassic boundary (our study), or well into the Triassic (Marshall's study). Regardless of this disagreement among molecular estimates and inferences from the fossil record, Danilov and Parham's paper presents a nice summary of the problem and a clever way to investigate the origin of turtles with the fossil record.

Danilov, I. G. and J. F. Parham 2008. A reassessment of some poorly known turtles from the Middle Jurassic of China, with comments on the antiquity of extant turtles. Journal of Vertebrate Paleontology 28: 306-318.