FIG. 3.
Two models for the evolution of the RD13 chromosomal region and the Vr. The trees were constructed by the neighbor-joining algorithm based on the number of synonymous substitutions per synonymous site (dS). A comparison of phylogenetic trees constructed from individual set gene nucleotide data and a concatenated sequence representing the conserved genes of RD13 indicated that the topologies were cognate. Thus, the extent of recombination present was insufficient to disrupt the underlying phylogenetic signal. The set9 gene tree is shown. Bootstrap confidence limits are shown under the major nodes. The proposed ancestral state of the Vr is indicated at the hypothetical root. The gain and loss of set genes necessary to explain the extant state of each strain are indicated in red. (A) Evolution of RD13 and the Vr explained solely by the loss of set genes over time. This (preferred) model is supported by the observation that the proportion of silent mutations (synonymous substitution) within each set gene is the same. (B) Evolution of RD13 explained by both the gain and loss of set genes over time (alternative model). This model is not supported by an analysis of the proportion of polymorphic synonymous sites present in each set gene. While other models are possible, they require a larger number of evolutionary events (i.e., gain or loss), making them less likely. (C) Recombination has occurred within RD13. A Happlot analysis of the orf2, set1, and res genes in six representative strains is shown. Polymorphic nucleotide sites based upon pairwise comparisons are represented by vertical lines. Putative areas of recombination, regions of similar nucleotide sequence in different genetic backgrounds, are represented in red.