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 timetree.org (p.s. Wish I could use the new datelife.org, 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.