在现代和古代DNA样本中基于哈普洛型推断最近有效人口大小的推断
Romain Fournier1, Zoi Tsangalidou1, David Reich2,3,4,5
1Department of Statistics, University of Oxford, Oxford, UK.
Nature communications
|December 1, 2023
概括
使用基因组数据,HapNe准确地推断出最近的人口规模的变化,改进了现代和古代DNA的现有方法. 这个新工具有助于理解人口历史和人口统计事件.
科学领域:
- 人口遗传学 人口遗传学
- 基因组分析 基因组分析
- 生物信息学是一种生物信息学.
背景情况:
- 最近有共同祖先的个体共享相同血统 (IBD) 基因组区域.
- IBD细分分布可以揭示过去的人口统计事件,如有效人口规模 (Ne) 变化.
- 精确的IBD检测在古代DNA和代表性不足的人群中具有挑战性,因为参考数据有限.
研究的目的:
- 介绍HapNe,这是一个准确的方法来推断过去2000年的有效人口大小变化.
- 提供适用于现代和古代DNA数据的工具.
- 改进现有的推断最近人口规模波动的方法.
主要方法:
- HapNe使用IBD共享 (HapNe-IBD) 或链接不平衡 (HapNe-LD) 来推断最近的人口规模波动.
- HapNe-LD不需要DNA相位,可以使用低覆盖率和时间异质数据.
- 该方法的准确性与现有的基于IBD和基于LD的推断技术进行了评估,使用模拟的人口情景.
主要成果:
- 在各种模拟的人口情景中,HapNe在推断最近的有效人口规模方面表现出更好的准确性.
- 与现有方法相比,该方法需要较少的计算资源.
- 哈普尼成功地检测到了现代种群 (1000个基因组项目,英国生物库) 和古代DNA样本 (铁器时代英国) 的最近有效种群大小变化.
结论:
- 哈普尼为推断最近有效人口大小变化提供了更准确,更有效的计算方法.
- 该方法对现代和古代DNA的适用性,包括低覆盖数据,扩大了其在人口遗传学研究中的实用性.
- 哈普尼提供了关于不同人类群体近期人口变化的宝贵见解.
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