Wednesday, July 2, 2008

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.

7 comments:

sergios-orestis said...

Nice paper, indeed. I am not a bird person, but I have a thing for adaptation. Some lifestyles evolved multiple times and...

Furthermore, our results reinterpret the evolution of various adaptations (e.g., the diurnal Apodiformes evolved from nocturnal/crepuscular Caprimulgiformes, and flighted Tinamiformes arose within the flightless Struthioniformes) and biogeographic patterns (e.g., the New Caledonian kagu and Neotropical sunbittern are sister taxa).

It'd be interesting to see a chronogram supporting the explosive nature of this radiation (CIs should overlap), as well as some tests for rate diversification. Maybe someone will take a crack at the ~32kb alignment...

Glor said...

I'm glad to see that Science provided these authors the space to show the type of detailed results seen in Fig. 1. I love how everybody who samples a bunch of genes is now calling their study a 'phylogenomic analysis.' Seems silly and faddish to me, especially since the term was originally intended to imply something more than this (http://bodegaphylo.wikispot.org/Phylogenomics_%28Eisen%29).

Tom Near said...

Joseph Brown and colleagues have a nice div time study of mtDNA from a broad sampling of bird lineages.


Brown, J. W., J. S. Rest, J. Garcia-Moreno, M. D. Sorenson and D. P. Mindell 2008. Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. Bmc Biology 6:


Re phylogenomics, I agree that is the buzz word when you have a large dataset. However, I think the original definition is even more corny. If I have it right, it was coined for discovering new microbe lineages by randomly sequencing rRNA and doing an NJ analysis.

Brian R. Moore said...

I believe that the term phylogenomics—as originally defined (and coined) by Jonathan Eisen—was meant to emphasize an explicitly evolutionary approach to understanding gen(om)e function.

That is, reconstructing the evolutionary history (phylogeny) of genes should help predict the functions of uncharacterized genes. This tree-thinking approach provided an important advance over existing non-evolutionary genomic methods based on clustering algorithms.

Eisen, J.A. 1997. Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Research 3:163-167.

Accordingly, the original definition "Inferring aspects of gen(om)e evolution in light of phylogeny" is often inverted to mean simply "Inferring phylogeny from lotsa genes".

Tom Near said...

I prefer the latter.....

Glor said...

The term was coined by Eisen and I tend to agree with him that just making a phylogeny with a modest number of genes is not phylogenomics. This is especially true when you're only sampling a very small fraction of the genome (as impressive as the bird dataset is, let's not forget that it includes <30 loci). In this case, the word seems not only unnecessary, but also arbitrary. Does a phylogenetic analysis of six genes qualify as phylogenomics? How about only one gene, that's part of the genome? Enough with the semantics, I'm done with the term phylogenomics (at least until I can use it to get a paper into Science).

Glor said...

For more on Eisen and his perspective on his term see his blog (http://phylogenomics.blogspot.com/) or this link to the full article (http://www.genome.org/cgi/content-nw/full/8/3/163/)