Brown and Polar Bear Y Chromosomes Reveal Extensive Male-Biased Gene Flow within Brother Lineages
Brown and Polar Bear Y Chromosomes Reveal Extensive Male-Biased Gene Flow within Brother Lineages
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DOI：
10.1093/molbev/msu109
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发表时间：
2014-06-01
影响因子：
10.7
通讯作者：
Hailer, Frank
中科院分区：
文献类型：
--
作者：
Bidon, Tobias;Janke, Axel;Hailer, Frank
棕熊和北极熊已经成为系统地理学的突出例子，但以前的系统地理学研究主要依赖于母系遗传的线粒体DNA(MtDNA)，或者受到地理上的限制。男性特有的Y染色体是线粒体DNA的天然对应物，但仍未得到充分研究。虽然这种父系遗传的染色体对于全面分析系统地理模式是必不可少的，但技术上的困难和低变异性阻碍了它在大多数哺乳动物中的应用。我们从北极熊基因组中开发了13个新的Y染色体序列和微卫星标记，并在130只棕熊和北极熊的广泛地理样本中进行了筛选。我们还分析了一个390kb长的Y染色体支架，使用了已发表的雄性熊类基因组的测序数据。Y染色体证据支持了一种新的理解，即棕熊和北极熊最晚于中更新世开始分化。与mtDNA图谱相反，我们发现1)棕熊和北极熊是相互单系的姐妹(或更确切地说是兄弟)血统，没有引入的信号，2)男性偏向的基因跨大陆和系统地理时间尺度流动，以及3)将阿拉斯加ABC群岛的种群与大陆棕熊联系起来的雄性扩散。由于女性的亲缘关系，线粒体DNA对种群分化提供了高度结构化的估计，而男性偏向的基因流是核遗传变异的同质化力量。我们的发现强调了分析母系和父系遗传位点对于全面了解系统地理学历史的重要性，许多哺乳动物基于mtDNA的系统地理学研究应该得到重新评估。测序技术的最新进展使Y染色体变异的分析成为可能，即使在非模式生物中也是如此。
Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms.