A practical genome scan for population-specific strong selective sweeps that have reached fixation.
A practical genome scan for population-specific strong selective sweeps that have reached fixation.
复制标题
实用的基因组扫描已达到固定的人群特异性强选择性扫描。
DOI：
10.1371/journal.pone.0000286
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发表时间：
2007-03-14
期刊：
影响因子：
3.7
通讯作者：
Ohashi, Jun
中科院分区：
文献类型：
--
作者：
Kimura, Ryosuke;Fujimoto, Akihiro;Tokunaga, Katsushi;Ohashi, Jun
在过去的10万年里，由于对当地环境的遗传适应，现代人类种群之间的表型差异已经发展起来。为了鉴定涉及群体特异性表型的基因，有必要检测人类基因组中最近正选择的特征。虽然延长连锁不平衡（LD）的检测已成为进化遗传学领域的一个强大的工具，目前的LD为基础的方法不适用于已经固定的基因座。在这里，我们报告了一种方法，扫描特定人群的强选择性扫描，已达到固定。在该方法中，全基因组SNP数据用于分析单倍型频率、核苷酸多样性和LD在群体之间的差异，使用群体之间的单倍型纯合性比率。为了估计本研究中使用的统计数据的检测能力，我们进行了计算机模拟，发现如果有利等位基因已达到固定，则这些测试对分型SNP和人口统计参数的密度相对稳健。因此，我们可以确定保持高检测能力的阈值，而不管SNP密度和人口统计学历史。当这种方法应用于HapMap数据时，它能够比依赖于经验分布的离群值方法更有效地识别群体特异性强选择性扫描的候选者。这项研究证实了先前报道的与特定表型相关的基因的强阳性选择，还确定了可能导致人类群体之间表型差异的其他候选人。
Phenotypic divergences between modern human populations have developed as a result of genetic adaptation to local environments over the past 100,000 years. To identify genes involved in population-specific phenotypes, it is necessary to detect signatures of recent positive selection in the human genome. Although detection of elongated linkage disequilibrium (LD) has been a powerful tool in the field of evolutionary genetics, current LD-based approaches are not applicable to already fixed loci. Here, we report a method of scanning for population-specific strong selective sweeps that have reached fixation. In this method, genome-wide SNP data is used to analyze differences in the haplotype frequency, nucleotide diversity, and LD between populations, using the ratio of haplotype homozygosity between populations. To estimate the detection power of the statistics used in this study, we performed computer simulations and found that these tests are relatively robust against the density of typed SNPs and demographic parameters if the advantageous allele has reached fixation. Therefore, we could determine the threshold for maintaining high detection power, regardless of SNP density and demographic history. When this method was applied to the HapMap data, it was able to identify the candidates of population-specific strong selective sweeps more efficiently than the outlier approach that depends on the empirical distribution. This study, confirming strong positive selection on genes previously reported to be associated with specific phenotypes, also identifies other candidates that are likely to contribute to phenotypic differences between human populations.
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影响因子：
9.8
作者：
Akey JM;Eberle MA;Rieder MJ;Carlson CS;Shriver MD;Nickerson DA;Kruglyak L
通讯作者：
Kruglyak L
DOI：
10.1073/pnas.0401720101
发表时间：
2004-07-20
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作者：
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作者：
Bustamante, CD;Fledel-Alon, A;Clark, AG
通讯作者：
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