Recombination

In my previous post I eluded to the lack of resolution in the H. influenzae phylogeny. I have now attempted to use three different methods of phylogenetic reconstruction (maximum likelihood, distance, and parsimony) and, due to some characteristics of the datasets, only parsimony was feasible. From the whole genome alignments I had 101 alignment files. A phylogeny was inferred for each of these alignment files using parsimony and 100 bootstrap pseudoreplicates. Most clades in each of these topologies had poor bootstrap support. Then, a consensus tree was inferred from each of the 101 trees. Guess what? Absolutely no resolution of any clades, nothing, a "star" phylogeny.

Is it due to recombination? Probably. I tested for recombination using a parsimony based approach (Bruen et al. 2006. Genetics 172:2665) in each of the 101 alignment files (so within each alignment region, not between alignment files) and found that only 11 alignment files did NOT have evidence of recombination. The lack of recombination in all but one of these is probably due to the small size, most of the 11 were under 1 kb.

What does this all mean? Recombination was previously thought to be rare in H. influenzae, based on linkage between phenotypes and multi-locus enzyme electrophoresis types. But sequence data is changing what we know about the population structure of H. influenzae. MLST studies have already shown modest incongruence between gene trees and fancy Bayesian statistics have shown that the recombination rate is moderate. My work is now showing that recombination occurs often enough to obliterate phylogenetic signal. My next question is: is it mostly due to transformational recombination?