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.