Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) derived from genome sequences.
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 25× for each species. A total of 1.4 billion 100-bp paired-end reads were 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 3 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 1 million base pairs of ultraconserved elements 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.
the School of Natural Resources and Agricultural Sciences, University of Alaska Fairbanks, Palmer Research Center, 1509 South Trunk Road, Palmer, AK 99645.
Matthew A
MA
Cronin
Gonzalo
G
Rincon
Robert W
RW
Meredith
Michael D
MD
MacNeil
Alma
A
Islas-Trejo
Angela
A
Cánovas
Juan F
JF
Medrano
D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D016384:Consensus Sequence; D005260:Female; D005787:Gene Frequency; D005828:Genetics, Population; D016678:Genome / Q000235:genetics*; D056914:Genomic Structural Variation; D008297:Male; D010375:Pedigree; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D001503:Ursidae / Q000145:classification / Q000235:genetics*
Ursus; black bears; brown; molecular clock; phylogeny; polar; single nucleotide polymorphism; ultraconserved elements