Inferring the direction of introgression using genomic sequence data
Inferring the direction of introgression using genomic sequence data
复制标题
使用基因组序列数据推断基因渗入的方向
DOI：
10.1101/2023.06.16.545313
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Thawornwattana Y
中科院分区：
文献类型：
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作者：
Thawornwattana Y
基因组数据是关于物种分化和种间基因流动的历史的信息，包括基因流动的方向、时间和强度。然而，相反方向的基因流动在多位点序列数据中产生类似的模式，例如杂交物种之间的序列差异减小。因此，对基因流动方向的推断具有挑战性。在这里，我们调查的信息，基因组序列数据中存在的基因流的方向，使用基于似然的方法下的多物种结合与渐渗模型。我们分析了两个物种的情况下，并使用模拟来检查的情况下，三个或四个物种。我们发现，这是更容易推断基因流从一个小的人口比在相反的方向，更容易推断流入（基因流从外群物种到内群物种）比流出（基因流从内群物种到外群物种）。如果在最初的分歧和随后的渐渗之间有较长时间的单独进化，也更容易推断基因流动。当假定基因渗入发生在错误的方向上时，基因渗入的时间往往被正确估计，基因流的贝叶斯检验往往是显着的，而基因渗入概率的估计值甚至可能大于真实概率。我们分析了Heliconius蝴蝶的基因组序列，以证明典型的基因组数据集是关于种间基因流方向的信息，以及它的时间和强度。
Genomic data are informative about the history of species divergence and interspecific gene flow, including the direction, timing, and strength of gene flow. However, gene flow in opposite directions generates similar patterns in multilocus sequence data, such as reduced sequence divergence between the hybridizing species. As a result, inference of the direction of gene flow is challenging. Here, we investigate the information about the direction of gene flow present in genomic sequence data using likelihood-based methods under the multispecies-coalescent-with-introgression model. We analyze the case of two species, and use simulation to examine cases with three or four species. We find that it is easier to infer gene flow from a small population to a large one than in the opposite direction, and easier to infer inflow (gene flow from outgroup species to an ingroup species) than outflow (gene flow from an ingroup species to an outgroup species). It is also easier to infer gene flow if there is a longer time of separate evolution between the initial divergence and subsequent introgression. When introgression is assumed to occur in the wrong direction, the time of introgression tends to be correctly estimated and the Bayesian test of gene flow is often significant, while estimates of introgression probability can be even greater than the true probability. We analyze genomic sequences fromHeliconiusbutterflies to demonstrate that typical genomic datasets are informative about the direction of interspecific gene flow, as well as its timing and strength.