Gene sequences evolve at different rates due to different constraints, either due to chromosome position, functional constraint, and status as a single-copy or multi-copy gene. In a recent paper, Allen Rodrigo (the new NESCent director by the, way, congrats!) the authors hypothesize that correlation in branch lengths of gene trees suggest they operate in the same pathway or have a similar function. To do this they took alignments of orthologous genes from 10 bacterial species which were seeded with E. coli as the target species. The alignments were used to build trees with MrBayes and only those which recovered the known species topology were retained. The ortholog groups were assigned GO terms via similarities.
They then looked at the branch lengths of gene trees and found a correlation between GO categories and rates of gene evolution/shape of the tree. I’ll not go into more details here but I think this is an interesting finding that is probably not so surprising when you think about it. I’m be very curious to see if this held up much in multi-domained proteins as well and of course taking this approach for a drive in fungal orthologs would be an interesting project for someone to try.