Human population structure and its effects on sampling Y chromosome sequence variation.
Human population structure and its effects on sampling Y chromosome sequence variation.
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人类群体结构及其对 Y 染色体序列变异采样的影响。
DOI：
10.1093/genetics/164.4.1495
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发表时间：
2003
期刊：
影响因子：
3.3
通讯作者：
Wilder,JasonA
中科院分区：
文献类型：
--
作者：
Hammer,MichaelF;Blackmer,Felisa;Garrigan,Dan;Nachman,MichaelW;Wilder,JasonA
Y 染色体非重组部分 (NRY) 的全球测序研究中出现的过量罕见变异被解释为人类人口扩张影响的证据。然而，许多 NRY 多态性是地理局部的，不同地理采样对 NRY 变异模式的影响尚不清楚。我们使用两种抽样设计来检测群体结构及其对人类 NRY 多态性模式的影响。首先，我们对代表 35 个种群的 92 名分布于全球的男性的 26.5 kb 非编码 Y 染色体 DNA 进行了测序。我们发现，单例变异的多态性数量与抽样群体的数量呈正相关，并且 Tajima’sD(TD) 和 Fu 和 Li’sD(FD) 统计数据与合并群体的数量呈显着负相关。然后，我们对从 3 个不同群体中抽取的总共 73 名男性的同一区域进行测序，发现 3 个合并样本和个体群体样本的 TD 和 FD 值的负值远小于上述全局样本中的负值。合并模拟表明，在种群规模没有变化的情况下，种群结构的简单分裂模型足以产生在我们的合并样本中看到的 TD 负值。这些实证和模拟结果表明，观察到的 NRY 种群结构水平可能会导致全球调查中单例变异数量的向上偏差，并对基于全球抽样策略的种群扩张推论提出质疑。
The excess of rare variants in global sequencing studies of the nonrecombining portion of the Y chromosome (NRY) has been interpreted as evidence for the effects of human demographic expansion. However, many NRY polymorphisms are geographically localized and the effect of different geographical sampling on patterns of NRY variation is unknown. We use two sampling designs to detect population structure and its effects on patterns of human NRY polymorphism. First, we sequence 26.5 kb of noncoding Y chromosome DNA from 92 globally distributed males representing 35 populations. We find that the number of polymorphisms with singleton variants is positively correlated with the number of populations sampled and that there is a significant negative correlation of Tajima’sD(TD) and Fu and Li’sD(FD) statistics with the number of pooled populations. We then sequence the same region in a total of 73 males sampled from 3 distinct populations and find that TD and FD values for the 3 pooled and individual population samples were much less negative than those in the aforementioned global sample. Coalescent simulations show that a simple splitting model of population structure, with no changes in population size, is sufficient to produce the negative values of TD seen in our pooled samples. These empirical and simulation results suggest that observed levels of NRY population structure may lead to an upward bias in the number of singleton variants in global surveys and call into question inferences of population expansion based on global sampling strategies.
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1 号染色体 10 kb 区域中人类 DNA 序列变异的全局模式。
影响因子：
10.7
作者：
Yu,N;Zhao,Z;Fu,YX;Sambuughin,N;Ramsay,M;Jenkins,T;Leskinen,E;Patthy,L;Jorde,LB;Kuromori,T;Li,WH
通讯作者：
Li,WH
影响因子：
3.9
作者：
E. Ziętkiewicz;V. Yotova;M. Jarnik;M. Korab;K. Kidd;D. Modiano;R. Scozzari;M. Stoneking;S. Tishkoff;M. Batzer;D. Labuda
通讯作者：
D. Labuda
DOI：
10.1073/pnas.97.13.7360
发表时间：
2000-06-20
影响因子：
11.1
作者：
Thomson, R;Pritchard, JK;Feldman, MW
通讯作者：
Feldman, MW
影响因子：
10.7
作者：
Hey, J
通讯作者：
Hey, J
影响因子：
7
作者：
A. Redd
通讯作者：
A. Redd