Phylogenetic relationships of cottontails (Sylvilagus, Lagomorpha): congruence of 12S rDNA and cytogenetic data.

The genus Sylvilagus, which comprises the New World cottontail rabbits, contains several commercially important as well as endangered (or threatened) species. Understanding the evolution of this group is pertinent to their management and conservation. The purpose of this study was to examine the evolutionary history of the cottontails using sequence data from the mitochondrial 12S rRNA gene. The 12S data provide a robust phylogeny which was supported under a variety of phylogenetic approaches and transition/transversion (Ti/Tv) weighting schemes. Stem and loop regions of the gene were analyzed separately and two different methods of estimating Ti/Tv ratios were employed. The phylogeny obtained was consistent with available cytogenetic information. The 12S data indicate that separate generic status for the pygmy rabbit, Brachylagus idahoensis, is warranted based on its phylogenetic position and sequence divergence values. Additionally, the taxa which are geographically adjacent are also phylogenetically closely related; for example, the marsh rabbit, S. palustris, and the swamp rabbit, S. aquaticus, are sister taxa, as are the mountain cottontail, S. nuttallii, and desert cottontail, S. audubonii. This finding suggests that recent vicariance events might explain the diversification of several cottontail lineages.