Monday, December 16, 2013

Phylogenetics, ecologist style

Many of us are familiar with how a phylogeneticist, systematist or evolutionary biologist constructs a phylogenetic tree. However, ecologists apparently do it differently. Scott Chamberlain explains this procedure in one of his blog posts (Networks phylogeny):
There were about 500 species to make a phylogeny for, including birds and insects, and many species that were bound to end up as large polytomies. I couldn't in reasonable time make a molecular phylogeny for this group of species, so I made one ecologist style.
That is, I:
  • Created a topology using Mesquite software from published phylogenies, then
  • Got node age estimates from (p.s. Wish I could use the new, but there isn't much there quite yet), then
  • Used the bladj function in Phylocom to stretch out the branch lengths based on the node estimates.
Unfortunately, this process can't all be collected in an R script.
He then describes this process in more detail, which he hopes "makes it more reproducible". Here is his final tree (produced by FigTree).

This is an interesting bioinformatic solution to a biological problem, when empirical data collection has failed. I am not sure that I can recommend its widespread use, though.

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