KOEPFLI, K-P.*; WAYNE, R.K.: Genomic Tools for Molecular Systematics: A Molecular Phylogeny of the Mustelidae (Mammalia: Carnivora) Inferred from Multiple Sequence-Tagged Sites

Sequence-tagged sites (STSs) are PCR-based markers that amplify specific and homologous nuclear genes in virtually all mammalian species and were developed for the purposes of comparative genome mapping. Several characteristics make these markers attractive to studies in molecular systematics. STS loci often amplify complete introns that may contain phylogenetically informative variation as well as flanking exon sequences so that orthology can be easily established by comparison to published sequence data. Moreover, hundreds of STS primer sets spanning the complete genomes of the human and mouse have been published and thus represent hundreds of independently segregating loci. Therefore, the phylogenetic utility of STS loci to mammalian systematics is potentially enormous yet remains unexplored. We examined the phylogenetic relationships within the Mustelidae (Mammalia: Carnivora) using STS loci to evaluate the utility of these markers for resolving relationships among closely related species. DNA sequences from six STS loci were amplified and sequenced from representatives of nearly all living genera of the Mustelidae. In addition, sequences from the mitochondrial cytochrome b gene were obtained from all taxa. Phylogenetic analyses of separate and combined data sets were used to test a number of phylogenetic hypotheses and relationships within the Mustelidae spanning estimated divergence times ranging between 2 – 35 Mya. We also found that the mitochondrial and nuclear markers differed considerably in their relative utility for reconstructing phylogenies.