Joshua M. Miller, René M. Malenfant, L. Ruth Rivkin, Todd C. Atwood, Steven Baryluk, Erik W. Born, Rune Dietz, Kristin L. Laidre, Jodie Pongracz, Evan S. Richardson, Øystein Wiig, Corey S. Davis
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Here we describe the development, quality control, and application of the <i>Ursus maritimus V2</i> SNP chip. This 8 K SNP chip contains loci explicitly selected to assess both RAD-derived and transcriptome-derived loci, as well as SNPs to detect hybridization between species. A total of 7,239 loci (90.3% of those printed) were successfully genotyped, with over 99% genotype concordance for individuals typed in duplicate on this chip, and between individuals typed here and on the <i>Ursus maritimus V1</i> SNP chip. Using simulations, we demonstrate that the markers have high accuracy and efficiency to detect hybridization and backcrosses between polar bears and grizzly bears. However, empirical analysis of 371 polar bears, 440 grizzly bears, and 8 known hybrids found no novel instances of recent hybridization. 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引用次数: 0
摘要
北极熊(Ursus maritimus)是一种特别容易受到气候变化影响的物种。随着气候变暖,北极熊将被迫迁徙到更合适的栖息地,而这些栖息地很可能会缩小、适应新的条件,或者种群数量减少。然而,目前还不清楚北极熊所有 19 个亚群内部和之间的基因组多样性,因此也不清楚它们的适应潜力。此外,气候变暖可能导致北极熊与灰熊(U. arctos)的接触更加频繁,而灰熊可能与北极熊杂交。在此,我们介绍了海熊 V2 SNP 芯片的开发、质量控制和应用。这个 8 K SNP 芯片包含明确选择的位点,用于评估 RAD 衍生位点和转录组衍生位点,以及用于检测物种间杂交的 SNP。共有 7,239 个位点(占打印位点的 90.3%)被成功地进行了基因分型,在该芯片上重复分型的个体基因型一致性超过 99%,在这里分型的个体与在海熊 V1 SNP 芯片上分型的个体之间的基因型一致性也超过 99%。通过模拟实验,我们证明该标记在检测北极熊和灰熊之间的杂交和回交方面具有很高的准确性和效率。然而,对 371 头北极熊、440 头灰熊和 8 头已知杂交熊的实证分析没有发现近期杂交的新情况。海熊 V2 SNP 芯片为监测该物种的适应潜力以及评估北极熊的种群结构、定量基因组学和杂交提供了一个强大的工具。
Development of an 8K SNP chip to assess adaptive diversity and hybridization in polar bears
The polar bear (Ursus maritimus) is a species particularly vulnerable to the effects of climate change. As the climate warms, polar bears will be forced to move to more suitable habitats which are likely to shrink, adapt to the new conditions, or decline in population size. However, the genomic diversity within and among all 19 subpopulations of polar bears, and therefore their adaptive potential, is currently unknown. In addition, warmer climates are likely to result in more frequent contact between polar bears and grizzly bears (U. arctos), with which they can hybridize. Here we describe the development, quality control, and application of the Ursus maritimus V2 SNP chip. This 8 K SNP chip contains loci explicitly selected to assess both RAD-derived and transcriptome-derived loci, as well as SNPs to detect hybridization between species. A total of 7,239 loci (90.3% of those printed) were successfully genotyped, with over 99% genotype concordance for individuals typed in duplicate on this chip, and between individuals typed here and on the Ursus maritimus V1 SNP chip. Using simulations, we demonstrate that the markers have high accuracy and efficiency to detect hybridization and backcrosses between polar bears and grizzly bears. However, empirical analysis of 371 polar bears, 440 grizzly bears, and 8 known hybrids found no novel instances of recent hybridization. The Ursus maritimus V2 SNP chip provides a powerful tool for monitoring the adaptive potential of this species along with assessing population structure, quantitative genomics, and hybridization in polar bears.
期刊介绍:
Conservation Genetics Resources promotes the conservation of genetic diversity and advances the study of conservation genetics by providing rapid publication of technical papers and reviews on methodological innovations or improvements, computer programs, and genomic resources, as well as on the practical application of these resources towards the development of effective conservation policy and practice.