Example of intraphylum transfer: a hemolysin-like protein. This example of horizontal gene transfer was extracted from the list of data sets exhibiting conflicts with the plurality signal. This gene family has detectable homologs in other phyla, but phylogenetic analysis of an extended data set shows that cyanobacteria form a coherent phylogenetic group. Interestingly, in cyanobacteria this protein seems to have acquired a different function (Nagai et al. 2001). This suggests that this protein is probably not being exchanged with the organisms outside of cyanobacteria, which makes it a good example of intraphylum transfer. In this phylogeny Thermosynechococcus and Crocosphaera are sister taxa, which contradicts the relationships observed in the plurality tree. The arrow indicates placement of the Thermosynechococcus sequences in the consensus tree. The tree topology and branch lengths were calculated in PhyML (Guindon and Gascuel 2003) under the JTT+Gamma model. The bootstrap support values are from TREE-PUZZLE + NEIGHBOR phylogenetic analyses as described in Methods. Only bootstrap support values above 80% are shown. Additional examples of putative intraphylum transfers are available in the Supplemental material.
