Data from: Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos) and black bears (U. americanus) derived from genome sequences

• Main Authors: Cronin, Matthew A., Rincon, Gonzalo, Meredith, Robert W., MacNeil, Michael D., Islas-Trejo, Alma, Canovas, Angela, Medrano, Juan F.
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: 2013
• Subjects: Phylogeny; Polar; brown; black Bears; Ultra-conserved elements; molecular clock; single nucleotide polymorphism SNP; Genomics and gene mapping; Molecular systematics and phylogenetics; Ursus maritimus; Alaska
• Online Access: http://hdl.handle.net/10255/dryad.57431; https://doi.org/10.5061/dryad.1qp80

We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25X for each species. A total of 1.4 billion 100-bp paired-end reads was assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 13.8 million single nucleotide polymorphisms (SNP) in the three species aligned to the polar bear genome. These data indicate that polar bears and brown bears share more SNP with each other than either does with black bears. Concatenation and coalescence-based analysis of consensus sequences of approximately one million base pairs of ultra-conserved elements (UCE) in the nuclear genome resulted in a phylogeny with black bears as the sister group to brown and polar bears, and all brown bears are in a separate clade from polar bears. Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears.