Chen Guanjie, Yuan Ao, Shriner Daniel, Tekola-Ayele Fasil, Zhou Jie, Bentley Amy R, Zhou Yanxun, Wang Chuntao, Newport Melanie J, Adeyemo Adebowale, Rotimi Charles N
Center for Research on Genomics and Global Health, NHGRI, NIH, Bethesda, Maryland, United States of America.
Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University, Washington, DC, United States of America.
PLoS One. 2015 Aug 28;10(8):e0135368. doi: 10.1371/journal.pone.0135368. eCollection 2015.
The fixation index F(st) plays a central role in ecological and evolutionary genetic studies. The estimators of Wright ([Formula: see text]), Weir and Cockerham ([Formula: see text]), and Hudson et al. ([Formula: see text]) are widely used to measure genetic differences among different populations, but all have limitations. We propose a minimum variance estimator [Formula: see text] using [Formula: see text] and [Formula: see text]. We tested [Formula: see text] in simulations and applied it to 120 unrelated East African individuals from Ethiopia and 11 subpopulations in HapMap 3 with 464,642 SNPs. Our simulation study showed that [Formula: see text] has smaller bias than [Formula: see text] for small sample sizes and smaller bias than [Formula: see text] for large sample sizes. Also, [Formula: see text] has smaller variance than [Formula: see text] for small Fst values and smaller variance than [Formula: see text] for large F(st) values. We demonstrated that approximately 30 subpopulations and 30 individuals per subpopulation are required in order to accurately estimate F(st).
固定指数F(st)在生态和进化遗传学研究中起着核心作用。赖特（[公式：见原文]）、韦尔和科克伦（[公式：见原文]）以及哈德森等人（[公式：见原文]）提出的估计方法被广泛用于测量不同种群之间的遗传差异，但都存在局限性。我们使用[公式：见原文]和[公式：见原文]提出了一种最小方差估计量[公式：见原文]。我们在模拟中对[公式：见原文]进行了测试，并将其应用于来自埃塞俄比亚的120名无亲缘关系的东非个体以及国际人类基因组单体型图计划（HapMap）3中的11个亚群，这些亚群有464,642个单核苷酸多态性（SNP）。我们的模拟研究表明，对于小样本量，[公式：见原文]的偏差比[公式：见原文]小，对于大样本量，其偏差比[公式：见原文]小。此外，对于小的Fst值，[公式：见原文]的方差比[公式：见原文]小，对于大的F(st)值，其方差比[公式：见原文]小。我们证明，为了准确估计F(st)，大约需要30个亚群，每个亚群30个个体。
