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

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.

本研究借助高通量基因组测序数据，对北极熊（Ursus maritimus）、棕熊（U. arctos）与美洲黑熊（U. americanus）的演化关系进行了评估，各物种的测序平均覆盖度为25X。本研究以北极熊基因组与已注释的大熊猫（Ailuropoda melanoleuca）基因组序列作为参考，对总计14亿条100碱基对双端测序读段进行了组装。在比对至北极熊基因组的三个熊类物种中，共鉴定出1380万个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）。上述数据分析结果表明，北极熊与棕熊之间共享的SNP数量均多于二者任意一方与美洲黑熊的共享SNP数量。对核基因组中约100万碱基对的超保守元件（Ultra-Conserved Element, UCE）共有序列开展串联分析与基于溯祖理论的系统发育分析后，得到的系统发育树显示：美洲黑熊为棕熊与北极熊的姊妹群，且所有棕熊均与北极熊各自构成独立演化支。对采自阿拉斯加州与蒙大拿州的336头熊的162个SNP位点进行基因分型的结果显示，三个熊类物种在遗传层面存在分化；棕熊与美洲黑熊存在地理种群结构，而北极熊未表现出此类地理种群结构。