Data from: Molecular phylogeny of an ancient rodent family (Aplodontiidae)

Currently, 7 described subspecies are recognized based on morphological taxonomic studies. In this study, mitochondrial and nuclear genes were sequenced to infer molecular phylogenies of A. rufa. One of the goals of this study was to test the current taxonomic hypothesis based on morphology with molecular data.

Another goal was to incorporate geographic information to elucidate distributions of major clades. Our results support the previously held subspecies designations based on morphological taxonomy, with 1 main exception: we determined that within A. rufa, the subspecies A. rufa rainieri and A. rufa rufa north of the Columbia River represent a single lineage and should revert to the name A. rufa olympica. Although we revised geographic boundaries for some groups (A. r. rufa, A. r. olympica, A. r. pacifica), only the conservation status and management of A. r. olympica (previously 2 subspecies) in Canada may be affected.

Our findings support the continued conservation efforts for the isolated and endangered lineages present in coastal California. Usage notes all nuc.TXT BEAST input file:GHR nuclear DNA sequences cytb prior root stdev mean CA BEAST inout file: Mitochondrial DNA cytochrome b sequences Appendix 1 cytb 1050bp 080612 Haplotype Table whole cytochrome b sequences Appendix 2 cytb 450bp 080612 Haplotype table partial cytochrome b Appendix 3 CR 080612 Haplotype table control region mitochondrial DNA Appendix 4 GHR 080612 Haplotype table nuclear DNA GHR sequences