Natural Sciences Research Laboratory

The evolutionary relationships between Peromyscus, Habromys, Isthmomys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are poorly understood. In order to further explore the evolutionary boundaries of Peromyscus and compare potential taxonomic solutions for this diverse group and its relatives, we conducted phylogenetic analyses of DNA sequence data from alcohol dehydrogenase (Adh1-I2), beta fibrinogen (Fgb-I7), interphotoreceptor retinoid-binding protein (Rbp3), and cytochrome-b (Cytb). Phylogenetic analyses of mitochondrial and nuclear genes produced similar topologies although levels of nodal support varied. The best-supported topology was obtained by combining nuclear and mitochondrial sequences. No monophyletic Peromyscus clade was supported. Instead, support was found for a clade containing Habromys, Megadontomys, Neotomodon, Osgoodomys, Podomys, and Peromyscus suggesting paraphyly of Peromyscus and confirming previous observations. Our analyses indicated an early divergence of Isthmomys from Peromyscus (approximately 8 million years ago), whereas most other peromyscine taxa emerged within the last 6 million years. To recover a monophyletic taxonomy from Peromyscus and affiliated lineages, we detail 3 taxonomic options in which Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are retained as genera, subsumed as subgenera, or subsumed as species groups within Peromyscus. Each option presents distinct taxonomic challenges, and the appropriate taxonomy must reflect the substantial levels of morphological divergence that characterize this group while maintaining the monophyletic relationships obtained from genetic data.

The sister species Ictidomys parvidens and I. tridecemlineatus exhibit hybridization in southeastern New Mexico and western Texas. Presumably, hybridization was due to secondary contact as a result of recent anthropogenic changes to the landscape. However, recent phyloge- netic studies of Spermophilus, which previously included Ictidomys, indicated the possibility of widespread introgression due to paraphyly of haploytypes in the mitochondrial cytochrome-b (Cytb) gene. Samples of Ictidomys were obtained from 38 populations (N = 211) in the presumed zone of sympatry, as well as samples from 58 populations (N = 208) throughout the distribution of both sister species. DNA sequences from the Cytb gene (N = 419) and the Y-linked struc- tural maintenance of chromosomes (SmcY) gene (N = 129) were used to determine the origin of paraphyly among Cytb haplotypes. In addition, divergence date estimates were calculated to determine the association between hybridization and climate oscillations. Analyses of Cytb sequences indicated a unique mitochondrial haplotype in both parental types and putative hy- brids within the zone of sympatry but provided no evidence of contemporary mitochondrial introgression. However, analyses of the SmcY gene supported contemporary hybridization at six localities. These data, along with estimates of time since divergence, suggested an ancient hybridization event during the Pleistocene, followed by capture of the I. tridecemlineatus mito- chondrial haplotype by I. parvidens. Glacial oscillations during this period of time would have provided multiple opportunities for sympatry between these two species, increasing the potential for ancient hybridization. Whether contemporary hybridization is the result of a recent warm- ing climate or an ancillary effect of anthropogenic habitat alterations is yet to be determined.

A critical issue with species names derived from Linnaeus’ 10th edition of the Systema Naturae is the lack of holotypes, which in many instances has led to taxonomic confusion and uncertainty, as well as an unstable taxonomy. In the particular case of the South American cottontail, currently known as Sylvilagus brasiliensis, Linnaeus listed the type locality as “America Meridionali,” or South America. As a result, S. brasiliensis was ascribed a widespread distribution in North and South America, over an area estimated as approximately 1.09 × 107 Km2, and containing upwards of 37 named subspecies. In order to stabilize the taxonomy and initiate the process of illumination of evolutionary and biogeographic relationships among the South American cottontails, we designate herein a neotype for S. brasiliensis.