title: Phylogeny of the bears (Ursidae) based on nuclear and mitochondrial genes.
abstract: The taxomic classification and phylogenetic relationships within the bear family remain argumentative subjects in recent years. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence data, herein we employ two nuclear single-copy gene segments, the partial exon 1 from gene encoding interphotoreceptor retinoid binding protein (IRBP) and the complete intron 1 from transthyretin (TTR) gene, in conjunction with previously published mt data, to clarify these enigmatic problems. The combined analyses of nuclear IRBP and TTR datasets not only corroborated prior hypotheses, positioning the spectacled bear most basally and grouping the brown and polar bear together but also provided new insights into the bear phylogeny, suggesting the sister-taxa association of sloth bear and sun bear with strong support. Analyses based on combination of nuclear and mt genes differed from nuclear analysis in recognizing the sloth bears as the earliest diverging species among the subfamily ursine representatives while the exact placement of the sun bear did not resolved. Asiatic and American black bears clustered as sister group in all analyses with moderate levels of bootstrap support and high posterior probabilities. Comparisons between the nuclear and mtDNA findings suggested that our combined nuclear dataset have the resolving power comparable to mtDNA dataset for the phylogenetic interpretation of the bear family. As can be seen from present study, the unanimous phylogeny for this recently derived family was still not produced and additional independent genetic markers were in need.
authors.affiliation: Laboratory of Molecular Biology of Domestic Animals and Cellular and Molecular Evolution, Kunming Institute of Zoology, Kunming, China.
authors.forename: Li
authors.initials: L
authors.lastname: Yu
authors.forename: Qing-wei
authors.initials: QW
authors.lastname: Li
authors.forename: O A
authors.initials: OA
authors.lastname: Ryder
authors.forename: Ya-ping
authors.initials: YP
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics*; D005091:Exons / Q000235:genetics; D005136:Eye Proteins / Q000235:genetics*; D005819:Genetic Markers; D007438:Introns / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D011228:Prealbumin / Q000235:genetics*; D012177:Retinol-Binding Proteins / Q000235:genetics*; D001503:Ursidae / Q000145:classification* / Q000235:genetics*; D000099214:Retinol-Binding Proteins, Interstitial
chemical_list: D004272:DNA, Mitochondrial; D005136:Eye Proteins; D005819:Genetic Markers; D011228:Prealbumin; D012177:Retinol-Binding Proteins; D000099214:Retinol-Binding Proteins, Interstitial