Data from: Bayesian estimation of genomic clines

We developed a Bayesian genomic cline model to study the genetic architecture of adaptive divergence and reproductive isolation between hybridizing lineages. This model quantifies locus-specific patterns of introgression with two cline parameters that describe the probability of locus-specific ancestry as a function of genome-wide admixture. "Outlier" loci with extreme patterns of introgression relative to most of the genome can be identified. These loci are potentially associated with adaptive divergence or reproductive isolation. We simulated genetic data for admixed populations that included neutral introgression, as well as loci that were subject to directional, epistatic or underdominant selection, and analyzed these data using the Bayesian genomic cline model. Under many demographic conditions, underdominance or directional selection had detectable and predictable effects on cline parameters and "outlier" loci were greatly enriched for genetic regions affected by selection. We also analyzed previously published genetic data from two transects through a hybrid zone between Mus domesticus and M. musculus. We found considerable variation in rates of introgression across the genome and particularly low rates of introgression for two X-linked markers. There were similarities and differences in patterns of introgression between the two transects, which likely reflects a combination of stochastic variability due to genetic drift and geographic variation in the genetic architecture of reproductive isolation. By providing a robust framework to quantify and compare patterns of introgression among genetic regions and populations, the Bayesian genomic cline model will advance our understanding of the genetics of reproductive isolation and the speciation process.本研究开发了一款贝叶斯基因组梯度模型（Bayesian genomic cline model），用于探究杂交谱系间适应性分化与生殖隔离的遗传架构。该模型通过两个梯度参数量化位点特异性的基因渐渗模式，这两个参数可描述位点特异性祖先血统概率随全基因组混合比例的变化关系。相较于基因组大部分区域，基因渐渗模式极端的“异常位点”可被识别，此类位点可能与适应性分化或生殖隔离相关。本研究对包含中性渐渗的混合种群开展遗传数据模拟，同时纳入受定向选择、上位性选择或杂合劣势选择作用的位点，并使用该贝叶斯基因组梯度模型对模拟数据进行分析。在多种种群统计条件下，杂合劣势选择或定向选择会对梯度参数产生可检测且可预测的影响，受选择作用的遗传区域在“异常位点”中显著富集。本研究同时分析了已发表的遗传数据，该数据取自家鼠（Mus domesticus）与小家鼠（Mus musculus）杂交带的两条样带。研究发现，全基因组的基因渐渗速率存在显著差异，且两个X连锁遗传标记的渐渗速率尤其低下。两条样带的基因渐渗模式既存在共性也存在差异，这大概率反映了遗传漂变带来的随机变异与生殖隔离遗传架构的地理变异共同作用的结果。该贝叶斯基因组梯度模型可为量化并比较不同遗传区域及种群间的基因渐渗模式提供稳健的分析框架，将推动我们对生殖隔离遗传学与物种形成过程的认知。