Phylogeny Friday -- 27 June 2008
I haven't done a Phylogeny Friday in about a month, but a recent paper reporting a "phylogenomic study of birds" was worth mentioning (doi:10.1126/science.1157704). Now, this isn't phylogenomics as Jonathan Eisen defined it. The bird evolution paper describes building a tree using lots of molecular markers.
I don't have much to say about the new bird phylogeny (I'll let the expert handle the details), but I wanted to post one of the trees for Phylogeny Friday. Here is one of the phylogenies they present, attempting to reconcile their results with those that had been previously published:
The three columns at the tips indicate three previously published taxonomic classifications. Those with black text are monophyletic taxa in this new study, while those with white text are paraphyletic. The different colored lineages indicate various clades that are supported by this new study (e.g., green indicates land birds, blue are water birds, etc.).
Eisen. 1998. Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis. Genome Res. 8: 163-167 [link]
Hackett et al. 2008. A Phylogenomic Study of Birds Reveals Their Evolutionary History. Science 320:1763-1768 doi:10.1126/science.1157704
Actually, I originally defined the term in a paper in Nature Medicine ( Eisen JA, Kaiser D, Myers RM. Gastrogenomic delights: a movable feast. Nat Med. 1997 Oct;3(10):1076-8. But alas, that was before my Open Access days ... and the paper is not available online except on my web site here
I'm not sure if I like the use of "phylogenomics" when it's just gluing 32kb together and wacking a tree down the middle. I realise that 32kb is the size of a mitochondrial genome, but phylogenomics should be phylogenies done at the genome level, not just lots-of-dna.
(Not that I'm saying it's a bad paper, I just don't think it's phylogenomics.)