Evaluating the Use of ABBA-BABA Statistics to Locate Introgressed Loci
Evaluating the Use of ABBA-BABA Statistics to Locate Introgressed Loci
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DOI：
10.1093/molbev/msu269
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发表时间：
2015-01-01
影响因子：
10.7
通讯作者：
Jiggins, Chris D.
中科院分区：
文献类型：
--
作者：
Martin, Simon H.;Davey, John W.;Jiggins, Chris D.
已经提出了几种方法来测试跨基因组的渐渗。一种方法使用帕特森D统计量测试分类群之间共享衍生等位基因的全基因组过量，但没有确定哪些基因座显示出这种过量，也没有确定这种过量是否是由于基因渗入或祖先种群结构造成的。最近的几项研究通过将统计数据应用于小的基因组区域而不是全基因组范围来扩展D的使用。在这里，我们使用模拟和Heliconius蝴蝶的全基因组数据来研究D在小基因组区域中的行为。我们发现，在这种情况下，D是不可靠的，因为它给出了膨胀的值时，有效的人口规模是低的，导致D离群值聚集在基因组区域的多样性降低。作为替代方案，我们提出了一个相关的统计量（f）的上限（d），一个修改后的版本，最初开发的统计估计全基因组的混合分数。(f)overcap（d）不受与D相同的偏差的影响，并且在鉴定渐渗基因座方面更好。最后，我们表明，D和（f）盖（d）离群值往往聚集在低绝对分歧（d（XY））的区域，这可能会混淆最近提出的测试区分基因渗入从共享的祖先变异在个别基因座。
Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson's D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole-genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic (f) over cap (d), a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. (f) over cap (d) is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and (f) over cap (d) outliers tend to cluster in regions of low absolute divergence (d(XY)), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.