Published this week in mBio, Jessica Hedge's new paper "Bacterial phylogenetic inference is robust to recombination but demographic inference is not" looks at a long-standing problem: why are phylogenetic trees so popular in bacterial genomics when everyone knows recombination (which is detectable in most species studied) leads to seriously misleading inference? A burst of research activity in the early 2000s showed that homologous recombination - which can result from various forms of horizontal gene transfer in bacteria - can distort phylogenetic trees and lead to false inference of positive selection and demographic growth in methods that rely on them.
In the intervening years there has been intense research in the field of population genetics into approaches that account for recombination, although the practically useful methods rely on approximations because of the inherent difficulties of learning about complex reticulated evolutionary networks that recombination generates. This has led many of my population genetics colleagues to regard - at least privately - the use of phylogenetic trees in recombining species as "bust", and the conclusions drawn from such studies as questionable. In this paper we show that this view is too simple.