phylogenomics?

09 Mar phylogenomics?

While I was reading the Nature paper I was talking about in my last post I was thinking about the use of the term “phylogenomics”. It seems like there are two quite separate contexts where it is used.
(1) Integrating evolutionary biology into genomics (2) phylogenetics using a lot of data

The term “phylogenomics” was first published in 1998 by Jonathan Eisen. It is clear he was talking about option 1 not 2. In a recent blog post he says

“‘phylogenomic’ analysis in the way I think of phylogenomics — that is — a integration of evolutionary and genomic analyses. (NOTE – I think it is kind of lame that people use the term phylogenomics, which I coined by the way, to refer to “using genomes to infer evolutionary trees).”

So thats clear then? Well unfortunately not. There are so many publications now using it in the second context that irrespective of the initial meaning it looks like it now has both. The wikipedia (stub) also includes both meanings.

Web of Science reveals 92 publications in 2007 with the term phylogenomic*. I didn’t go through them and work out the split but both types of phylogenomics are there in numbers. WoS lists 272 publications with “phylogenomic*” across all years (searched 9th March 2008).

In my short description above I used “lots of data” rather than whole genomes. There are relatively few type 2 papers that actually use whole genomes. Thats understandable I guess, especially for Metazoa. The Nature paper I was talking about has a data matrix of 150 genes. Although the mean is only ~50% data representation for any taxon. Thats still a huge amount of data, but its not whole genome analysis. I wonder what the smallest dataset is that self-applies the term phylogenomics?

I am not exactly clear the difference between type 2 phylogenomics and supermatrix approaches to phylogenetics. How big does a matrix have to be before its super?Ultimately the use of the same name for different things may not matter much. I see little evidence people are very confused.

Here are some papers of interest-

Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis.
Eisen JA
Genome Res. 1998 Mar;8(3):163-7

Phylogenomics: Intersection of Evolution and Genomics
Jonathan A. Eisen and Claire M. Fraser
Science 13 June 2003 Vol. 300. no. 5626, pp. 1706 – 1707
DOI: 10.1126/science.1086292

Phylogenomics and the reconstruction of the tree of life
Delsuc F, Brinkmann H, Philippe H
NATURE REVIEWS GENETICS Volume: 6 Issue: 5 Pages: 361-375 Published: MAY 2005

The supermatrix approach to systematics
de Queiroz A, Gatesy J
TRENDS IN ECOLOGY & EVOLUTION Volume: 22 Issue: 1 Pages: 34-41 Published: JAN 2007