Data from: Heterogeneity and concordance in locus-specific differentiation and introgression between species of towhees

The maintenance or breakdown of reproductive isolation are observable outcomes of secondary contact between species. In cases where hybrids beyond the F1 are formed, the representation of each species’ ancestry can vary dramatically among genomic regions. This genomic heterogeneity in ancestry and introgression can offer insight into evolutionary processes, particularly if introgression is compared in multiple hybrid zones. Similarly, considerable heterogeneity exists across the genome in the extent to which populations and species have diverged, reflecting the combined effects of different evolutionary processes on genetic variation. We studied hybridization across two hybrid zones of two phenotypically well-differentiated bird species in Mexico (Pipilo maculatus and P. ocai), to investigate genomic heterogeneity in differentiation and introgression. Using genotyping by sequencing (GBS) and hierarchical Bayesian models, we genotyped 460 birds at over 41,000 single nucleotide polymorphism (SNP) loci. We identified loci exhibiting extreme introgression relative to the genome-wide expectation using a Bayesian genomic cline model. We also estimated locus-specific FST and identified loci with exceptionally high genetic divergence between the parental species. We found some concordance of locus-specific introgression in the two independent hybrid zones (6-20% of extreme loci shared across zones), reflecting areas of the genome that experience similar gene flow when the species interact. Additionally, heterogeneity in introgression and divergence across the genome revealed another subset of loci under the influence of locally specific factors. These results are consistent with a history in which reproductive isolation has been influenced by a common set of loci in both hybrid zones, but where local environmental and stochastic factors also lead to genomic differentiation.

物种间的次级接触可观测到生殖隔离的维持与瓦解。当产生F1代之后的杂交后代时，不同基因组区域对两个亲本物种祖先组分的占比会存在显著差异。这种祖先组分与基因渐渗的基因组异质性，能够为演化过程研究提供重要视角，尤其是在多个杂交带开展渐渗对比研究时。同样，全基因组范围内，种群与物种的分化程度也存在显著异质性，这反映了不同演化过程对遗传变异的综合作用。本研究针对墨西哥境内两种表型分化显著的鸟类——斑唧鹀（*Pipilo maculatus*）和奥氏唧鹀（*P. ocai*）的两个杂交带开展杂交研究，以探究分化与渐渗过程中的基因组异质性。本研究采用测序分型（genotyping by sequencing, GBS）技术与分层贝叶斯模型，对460只鸟类的41000余个单核苷酸多态性（single nucleotide polymorphism, SNP）位点进行基因分型。通过贝叶斯基因组梯度模型，我们筛选出了相对于全基因组预期水平存在极端渐渗现象的位点；同时估算了各位点的种群分化系数（FST），并筛选出亲本物种间遗传分化程度极高的位点。我们发现，两个独立杂交带中存在一定比例的位点特异性渐渗一致性（约6%-20%的极端渐渗位点在两个杂交带中共享），这反映出当物种发生接触时，基因组中部分区域会经历相似的基因流过程。此外，全基因组范围内渐渗与分化的异质性，还揭示了另一组受局部特异性因素影响的位点。本研究结果与以下演化历史相符：两个杂交带中的生殖隔离均受一组共同的位点调控，但局部环境与随机因素也会推动基因组的分化。