与格陵兰狼外群相对的犬类序列变化的地图
Anthony K Nguyen1,2, Peter Z Schall1, Jeffrey M Kidd3,4
1Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
概括
使用格陵兰狼基因组作为参考,通过减少偏差来改善犬类遗传分析. 这次对Dog10K数据的重新分析显示,与狼相比,村庄狗经历了显著的历史人口规模减少.
科学领域:
- 狗的遗传学 狗的遗传学
- 进行比较的基因组学.
- 人口遗传学 人口遗传学
背景情况:
- 狗遗传学研究历史上使用了一只来自Boxer的单一参考基因组 (canFam3.1).
- 最近的进展使各种犬类的高质量组合产生,改善了基因组的表现.
- 目前的分析经常将测序读数与特定品种的引用 (例如,德国牧羊犬的canFam4) 相匹配,可能引入偏差.
研究的目的:
- 使用外组参考基因组重新处理现有的犬类遗传数据,以减轻特定品种的偏见.
- 评估参考基因组选择对变异调用和种群结构分析的影响.
- 为了推断村庄狗相对于狼的历史人口规模变化.
主要方法:
- 从Dog10K联盟重新处理的1929年样本,使用格陵兰狼基因组 (mCanLor1.2) 作为参考.
- 采用GPU加速工具,以实现高效的重映射和变体调用.
- 进行主要成分分析 (PCA) 来评估人口结构.
主要成果:
- 新的变异呼叫集减少了样本间遗传差异的变异性.
- 主要成分分析结果无论使用何种基因组,都保持一致.
- 推断人口历史显示,与狼相比,村庄狗的历史有效人口规模减少了9-13倍.
结论:
- 使用外组参考基因组,如格陵兰狼,可以提高犬类遗传变异研究的准确性.
- 参考基因组选择不会显著改变推断出的人口结构.
- 村庄狗经历了相当大的历史人口瓶相对于他们的狼祖先.
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