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:He then describes this process in more detail, which he hopes "makes it more reproducible". Here is his final tree (produced by FigTree).
Unfortunately, this process can't all be collected in an R script.
- 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.
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.