The relationship between F(ST) and the frequency of the most frequent allele.
The relationship between F(ST) and the frequency of the most frequent allele.
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DOI：
10.1534/genetics.112.144758
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发表时间：
2013-02
期刊：
影响因子：
3.3
通讯作者：
Rosenberg NA
中科院分区：
文献类型：
--
作者：
Jakobsson M;Edge MD;Rosenberg NA
FST常被用作群体间遗传分化的总结。有研究表明，FST取决于基因座上的等位基因频率，因为它表现出与遗传多样性相关的各种特性：双等位基因单核苷酸多态性（snp）的值高于多等位基因微卫星的值，在高度多样性的群体中，被认为是显著不同的群体中，FST的值较低，而在稀有等位基因谱上主要不同的群体中，FST的值较低。然而，FST对等位基因频率依赖性的完整数学理解一直难以捉摸。在这里，我们研究了FST与最常见等位基因频率之间的关系，证明FST可以取的值范围在很大程度上受到等位基因频率分布的限制。对于双种群模型，我们导出了FST的严格界，它是种群间平均频率最高的等位基因频率M的函数。利用这些界限，我们表明，在等位基因数目未指定的多等位基因位点上，M的值均匀选择在0和1之间，平均最大FST为~ 0.3585。此外，当M较低或较高时，FST被限制在远小于1的值，最常见等位基因对最大FST的贡献平均为~ 0.4485。利用我们之前作为M的函数导出的纯合子界限，我们用总体的纯合子描述了FST的严格界限，发现在这种纯合子的情况下，FST的平均最大值为1−ln2≈0.3069。我们的结果为理解FST对等位基因频率和遗传多样性的依赖，以及解释这些数量在从群体遗传数据计算FST中的作用提供了概念基础。此外，我们的分析表明，许多不同寻常的FST观测结果，包括非洲高多样性人群中相对较低的FST值，以及与snp相比，微卫星的FST估计值相对较低，都不能被理解为与不同群体或标记类相关的生物现象，而是FST对等位基因频率分布特性内在的数学依赖性的结果。
FST is frequently used as a summary of genetic differentiation among groups. It has been suggested that FST depends on the allele frequencies at a locus, as it exhibits a variety of peculiar properties related to genetic diversity: higher values for biallelic single-nucleotide polymorphisms (SNPs) than for multiallelic microsatellites, low values among high-diversity populations viewed as substantially distinct, and low values for populations that differ primarily in their profiles of rare alleles. A full mathematical understanding of the dependence of FST on allele frequencies, however, has been elusive. Here, we examine the relationship between FST and the frequency of the most frequent allele, demonstrating that the range of values that FST can take is restricted considerably by the allele-frequency distribution. For a two-population model, we derive strict bounds on FST as a function of the frequency M of the allele with highest mean frequency between the pair of populations. Using these bounds, we show that for a value of M chosen uniformly between 0 and 1 at a multiallelic locus whose number of alleles is left unspecified, the mean maximum FST is ∼0.3585. Further, FST is restricted to values much less than 1 when M is low or high, and the contribution to the maximum FST made by the most frequent allele is on average ∼0.4485. Using bounds on homozygosity that we have previously derived as functions of M, we describe strict bounds on FST in terms of the homozygosity of the total population, finding that the mean maximum FST given this homozygosity is 1 − ln 2 ≈ 0.3069. Our results provide a conceptual basis for understanding the dependence of FST on allele frequencies and genetic diversity and for interpreting the roles of these quantities in computations of FST from population-genetic data. Further, our analysis suggests that many unusual observations of FST, including the relatively low FST values in high-diversity human populations from Africa and the relatively low estimates of FST for microsatellites compared to SNPs, can be understood not as biological phenomena associated with different groups of populations or classes of markers but rather as consequences of the intrinsic mathematical dependence of FST on the properties of allele-frequency distributions.
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影响因子：
56.9
作者：
Rosenberg, NA;Pritchard, JK;Feldman, MW
通讯作者：
Feldman, MW
DOI：
10.1126/science.1172257
发表时间：
2009-05-22
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Tishkoff SA;Reed FA;Friedlaender FR;Ehret C;Ranciaro A;Froment A;Hirbo JB;Awomoyi AA;Bodo JM;Doumbo O;Ibrahim M;Juma AT;Kotze MJ;Lema G;Moore JH;Mortensen H;Nyambo TB;Omar SA;Powell K;Pretorius GS;Smith MW;Thera MA;Wambebe C;Weber JL;Williams SM
通讯作者：
Williams SM
DOI：
10.1126/science.1219240
发表时间：
2012-07-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Tennessen JA;Bigham AW;O'Connor TD;Fu W;Kenny EE;Gravel S;McGee S;Do R;Liu X;Jun G;Kang HM;Jordan D;Leal SM;Gabriel S;Rieder MJ;Abecasis G;Altshuler D;Nickerson DA;Boerwinkle E;Sunyaev S;Bustamante CD;Bamshad MJ;Akey JM;Broad GO;Seattle GO;NHLBI Exome Sequencing Project
通讯作者：
NHLBI Exome Sequencing Project
影响因子：
10.7
作者：
Charlesworth, B
通讯作者：
Charlesworth, B
影响因子：
3.3
作者：
Ryman, Nils;Leimar, Olof
通讯作者：
Leimar, Olof