An increasing number of phylogenomic studies have documented a clear “footprint” of postspeciation introgression among closely related species. Nonetheless, systematic genome‐wide studies of factors that determine the likelihood of introgression remain rare. Here, we propose an a priori hypothesis‐testing framework that uses introgression statistics—including a new metric of estimated introgression, D_p—to evaluate general patterns of introgression prevalence and direction across multiple closely related species. We demonstrate this approach using whole genome sequences from 32 lineages in 11 wild tomato species to assess the effect of three factors on introgression—genetic relatedness, geographical proximity, and mating system differences—based on multiple trios within the “ABBA–BABA” test. Our analyses suggest each factor affects the prevalence of introgression, although our power to detect these is limited by the number of comparisons currently available. We find that of 14 species pairs with geographically “proximate” versus “distant” population comparisons, 13 showed evidence of introgression; in 10 of these cases, this was more prevalent between geographically closer populations. We also find modest evidence that introgression declines with increasing genetic divergence between lineages, is more prevalent between lineages that share the same mating system, and—when it does occur between mating systems—tends to involve gene flow from more inbreeding to more outbreeding lineages. Although our analysis indicates that recent postspeciation introgression is frequent in this group—detected in 15 of 17 tested trios—estimated levels of genetic exchange are modest (0.2–2.5% of the genome), so the relative importance of hybridization in shaping the evolutionary trajectories of these species could be limited. Regardless, similar clade‐wide analyses of genomic introgression would be valuable for disentangling the major ecological, reproductive, and historical determinants of postspeciation gene flow, and for assessing the relative contribution of introgression as a source of genetic variation.

中文翻译：

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评估影响种后渗入的生物学因素

越来越多的系统生物学研究已证明密切相关物种之间物种形成渗入的明显“足迹”。尽管如此，对决定基因渗入可能性的因素的系统全基因组研究仍然很少。在这里，我们提出一个使用渐渗统计量的先验假设检验框架，其中包括估计的渐渗量新指标D _p—评估跨多个密切相关物种的渗入流行率和方向的一般模式。我们使用来自11种野生番茄的32个谱系的全基因组序列，基于“ ABBA-BABA”测试中的多个三元组，使用三个基因组来评估渗入的影响-遗传相关性，地理邻近性和交配系统差异，证明了这种方法。我们的分析表明，每个因素都会影响渗入的发生率，尽管我们检测这些渗入的能力受到当前可用比较数的限制。我们发现，在地理上“近距离”与“远距离”种群比较的14个物种对中，有13个显示出渗入的迹象。在其中10个案例中，这一点在地理上更接近的人群中更为普遍。我们还发现了一些适度的证据，即基因渗入随着谱系之间遗传差异的增加而降低，在共有相同交配系统的谱系之间更普遍，并且（如果确实发生在交配系统之间）趋向于涉及从近交系到近交系的基因流。尽管我们的分析表明，该组中最近的物种形成后渗入很频繁（在17个测试的三重奏中有15个被检测到），但估计的遗传交换水平是中等水平的（占基因组的0.2-2.5％），因此杂交在塑造进化轨迹方面的相对重要性这些物种的数量可能会受到限制。无论如何，类似的进化枝全基因组渗入分析对于区分后物种形成基因流的主要生态，生殖和历史决定因素将是有价值的，