Figure 3.

Repeated co-transfer of xapR with xapA, which it regulates. In the presence of xanthosine, xapR activates the transcription of the xapAB operon, which allows the transport and catabolism of xanthosine [65]. The gene tree shows that xapR forms a well supported clade (80/100 bootstraps) within a larger family of regulators (COG583). xapR is scattered across the γ-Proteobacteria, within which we identify four acquisition events. For each acquisition, we show the multiple independent gene losses that would otherwise be required to explain the gene's distribution across the species tree. The gene tree also places xapR from Shewanella baltica between the sequences from Vibrio spp., which suggests that it could have been acquired separately by the two groups of Vibrio. However, this potential fifth acquisition event is rejected because of several factors: the bootstrap support is low; a small change to the tree's topology (one swap) would render the gene tree congruent with the species tree; and the gene might have been transferred from an ancestor of one of these Vibrio spp. to S. baltica. The xapR tree was computed from amino acid sequences using phyml with 100 bootstraps, four classes of gamma-distributed rates (with optimized alpha), and an optimized proportion of invariant sites [55]. In the gene tree, the scale bar corresponds to 20% amino acid divergence, and the internal nodes are labeled with their bootstrap values. The gene context shows gene order only (not spacing or scale).