Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps.
Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps.
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DOI：
10.1016/j.tpb.2015.04.001
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发表时间：
2015-06
影响因子：
1.4
通讯作者：
Rosenberg, Noah A.
中科院分区：
文献类型：
--
作者：
Garud, Nandita R.;Rosenberg, Noah A.
软选择扫描代表了一种重要的适应形式，其中携带适应等位基因的多个单倍型上升到高频率。然而，大多数从遗传多态性数据中检测选择性扫描的统计方法都集中在识别硬选择性扫描，其中有利的等位基因出现在单个单倍型背景上;这些方法可能无法检测软扫描。其中例外的是一套单倍型纯合性统计介绍了检测软扫描。这些统计，检查多个单倍型的频率相对于彼此，包括H12，一个统计设计来识别硬和软选择性扫描，和H2/H1，一个统计的条件下，高H12值试图区分硬和软扫描。使用H2/H1的挑战在于其范围取决于H12的相关值，因此相等的H2/H1值可能在H12的不同值处为软扫描模型提供不同水平的支持。在这里，我们通过推导H2/H1的上限作为H12的函数来增强H12和H2/H1单倍型纯合性统计用于选择性扫描检测，从而生成将H2/H1归一化为0和1之间的统计。通过对果蝇近交系重测序数据的重新分析，我们发现，增强的统计量既加强了非标准化统计量的解释，又导致了不太明显的经验见解。
Soft selective sweeps represent an important form of adaptation in which multiple haplotypes bearing adaptive alleles rise to high frequency. Most statistical methods for detecting selective sweeps from genetic polymorphism data, however, have focused on identifying hard selective sweeps in which a favored allele appears on a single haplotypic background; these methods might be underpowered to detect soft sweeps. Among exceptions is the set of haplotype homozygosity statistics introduced for the detection of soft sweeps by. These statistics, examining frequencies of multiple haplotypes in relation to each other, include H12, a statistic designed to identify both hard and soft selective sweeps, and H2/H1, a statistic that conditional on high H12 values seeks to distinguish between hard and soft sweeps. A challenge in the use of H2/H1 is that its range depends on the associated value of H12, so that equal H2/H1 values might provide different levels of support for a soft sweep model at different values of H12. Here, we enhance the H12 and H2/H1 haplotype homozygosity statistics for selective sweep detection by deriving the upper bound on H2/H1 as a function of H12, thereby generating a statistic that normalizes H2/H1 to lie between 0 and 1. Through a reanalysis of resequencing data from inbred lines of Drosophila, we show that the enhanced statistic both strengthens interpretations obtained with the unnormalized statistic and leads to empirical insights that are less readily apparent without the normalization.
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影响因子：
3.4
作者：
Menozzi P;Shi MA;Lougarre A;Tang ZH;Fournier D
通讯作者：
Fournier D
影响因子：
1.4
作者：
Edge, Michael D.;Rosenberg, Noah A.
通讯作者：
Rosenberg, Noah A.
从深度种群多样性数据中估算选择性扫描的强度。
影响因子：
3.3
作者：
Messer PW;Neher RA
通讯作者：
Neher RA
DOI：
10.1073/pnas.0401720101
发表时间：
2004-07-20
影响因子：
11.1
作者：
Innan, H;Kim, Y
通讯作者：
Kim, Y
影响因子：
--
作者：
Long, JC;Kittles, RA
通讯作者：
Kittles, RA