Monday, November 24, 2008

My New Favorite Plant

Botanists everywhere rejoice! Along the lines of the leafy sea dragon, we now have another plant-like animal to admire, the sea slug Elysia chlorotica.

It seems that this sea slug, which feeds on filamentous algae (Vaucheria sp.), intracellularly sequesters algal chloroplasts. Simple enough, right? No. The algae are secondary photosynthesizers, ancient heterotrophs whose ancestors acquired that ability from other algae. Their chloroplasts only encode a small fraction of genes required for their function, while the rest are ordinarily encoded by the nuclear genome. So, how does the sea slug maintain functioning chloroplasts without the supporting cast of nuclear genes? Horizontal gene transfer.

The authors find that at least one gene (psbO)  is encoded by the sea slug's own nuclear genome. It is nearly identical to the algal gene. This strongly argues for the horizontal transfer of photosynthetic ability from prey to predator. Amazing! 

Thursday, November 20, 2008

"Museomics" May Make Mammoths

For the first time, the "complete" genome of an extinct species has been generated. This week, the wooly mammoth, Mammuthus primigenius, had its DNA decoded by a team of researchers, with the results published in Nature. "Complete" was in quotes back there because without a modern species, like the African elephant's genome to compare it to, generated from intact chromosomes, the team can't be totally sure that they have the whole thing. Nonetheless, it's very exciting that a combination of some hair from the long-dead beast and next-generation sequencing technologies (oh, and $10 million) may one day allow a mammoth to walk the Earth again. It's also created the next in line of "-omics" - "Museomics" where natural history specimens, ancient DNA technology and pyrosequencing combine.

Tuesday, November 18, 2008

The World Like You've Never Seen It Before: Worldmapper

A colleague just sent me a link to this cool website that has a slew of world maps with countries drawn in proportion to various categories. A few of these are biological and pretty cool. The one shown here is a map of species at risk.

Thursday, November 13, 2008

A Tangled Bank of Genes - and Methods

The identification of orthologous genes is a fundamental process in many fields of biology. For systematists, sequencing and analyzing orthologs is critical for accurately recovering the right phylogenetic tree. Molecular biologists hoping to understand protein function and evolution similarly need to be looking at orthologs. The trouble is that gene duplication and differentiation is rampant in genomes and many, many genes exist as members of gene families. Start looking at more than one species and now speciation and the genetic processes and consequences of that will make things even messier still. In the most recent Trends in Genetics, Kuzniar et al. present an ambitious review of what I can only hope are all of the currently available methods for identifying orthologous genes. No fewer than 25 different methods, algorithms, and/or programs (that collectively created a jumble that made me feel a lot like I'd fallen into a bowl of Alphabits) are listed along with their pros and cons. These programs are grouped into tree-based methods, graph-based methods and hybrid methods that use a little of both. The authors attempt to give a few simple examples of how different methods can produce different conclusions and also show how hybrid proteins can really mess with the various algorithms. Fortunately, they do a nice job creating a decision tree at the end of the paper that is based on just 3 simple questions to help one choose what ortholog detection method is right for the job at hand. Still, reading the paper made me wonder why so, so many of these programs are out there - why hasn't natural selection pared a few of these out?

Kuzniar, A., R.C.H.J. van Ham, S. Pongor, and J.A.M. Leunissen. 2008. The quest for orthologs: finding the corresponding genes across genomes. Trends in Genetics 24:539-551.

Sunday, November 9, 2008

Now There's a Country that Appreciates Science!

Dan Rabosky just sent me this scan of England's ten pound note, expressing the hope that the United States might someday be so bold. Although such an appreciation for science may seem a long way off in a country where 55 million people just voted for a politician who believes humans walked with dinosaurs, there is already talk about undoing some of the anti-scientific legislation enacted over the past eight years. Obamanos!

Wednesday, November 5, 2008

The Latest Word on Metazoan Phylogenetics

The architect of the latest Metazoan phylogeny - Casey Dunn - was in Rochester this week talking about everything from siphonophore development to basal metazoan relations. Fans of his recent Nature paper on metazoan phylogenetics will be delighted to learn that Casey and his colleagues are dramatically expanding their EST data set. In addition to adding data from a few new taxa, the number of genes has increased by an order of magnitude to around 1,500. Their preliminary matrix is around 20% complete and they're now very actively re-evaluating the patterns recovered by the previously published dataset.

Although preliminary results largely agree with the previously published phylogeny, there is one interesting new pattern: acoel worms+xenoturbella as the basal bilaterians. Along with other organisms lacking a true coelem, acoel worms were traditionally united with platyhelminthes and placed at the base of the metazoan tree. Although rapid rates of evolution and long-branch attraction complicated molecular phylogenetic analyses these acoelemate forms, a string of studies -- including Dunn et al.'s previous analysis -- rejected the basal position of the platyhelminthes and acoels and suggested instead that they form a clade nested within the lophotrochozoa. Nevertheless, the phylogenetic distinctness of acoels and platyhelminthes, and a return of the acoels to the base of bilaterians recovered by the new dataset and preliminary analsyes, is not entirely unexpected; indeed, this conclusion brings the Dunn et al. tree in line with the conclusions of a carefully implemented 18S study. Xenoturbella (see image above), which has long been one of the greatest phylogenetic mysteries in the tree of life, is another story. As recently as the late 1990s, it was hypothesized that these almond-looking creatures were protostomes allied with molluscs. Although this story fell apart rather dramatically, I'm not aware of previous studies that have united these creatures with the aceols at the base of the bilaterians.

In addition to addressing specific phylogenetic hypotheses -- which, in Dunn's own words basically amounts to figuring out how all the various types of worms are related -- his group is also devoting attention to general systematic issues related to data-sampling and analysis efficiency. He makes a convincing case for the idea that a revolution in analytical techniques will be needed as we enter an era during which computational capabilities will be more limiting than data availability. Exciting times. If you want to get involved, you should drop Casey a line, I know he's looking for bright students and post-docs to populate his new lab.

Monday, November 3, 2008

Snake Versus Frog

The amazing photo at top is one of the winners in the BBC's annual Wildlife Photographer of the Year competition. Photographer David Maitland sat for three hours watching a frog battle for its life against the snake that was trying to eat it. Unfortunately, we don't know how things ended because the frog and snake were still locked in this position when he bailed. Although my photo is an embarrassment relative to Maitland's, I captured a similar moment a few years back when I saw a Hispaniolan vine snake (Uromacer) trying to eat a tree frog (Osteopilus) in the Dominican Republic. In this battle the frog managed to escape, due in part to flipping his legs over the snakes head and shoving off from the palm leaf as the snake tried to pull it in the other direction.

Sunday, November 2, 2008

Economic post-Darwinism?

Stanley, Gould, & Co. have earned a popular blog endorsement. A recent article about the proposed GM-Chrysler megamerger in the Daily Kos puts itself squarely into the species selection corner. It argues that species selection for body size in dinosaurs can be instructive in consideration of state-aided large corporate mergers. While clearly meant for a layperson, it is surprisingly lucid and on the mark.

The units and levels of selection, as well as the emergent properties within and among state-aided corporations remain unclear, however.