Data from: Hybrid incompatibilities, local adaptation, and the genomic distribution of natural introgression between species

Under allopatric speciation, geographic barriers eliminate gene flow between eventual species at all loci in the genome simultaneously. There is increasing evidence, however, that speciation can be complex, with some loci experiencing gene flow during speciation or during bouts of secondary contact. In taxa with heteromorphic sex chromosomes— birds, butterflies, mammals and Drosophila— the X (or Z) chromosome generally shows reduced levels of gene flow compared to autosomes. To investigate why, we develop population genetic models of secondary contact and gene flow at a neutral locus that is genetically linked to selected loci involved in hybrid incompatibilities and/or local adaptation. Using models that assume weak migration and strong selection, we compare gene flow at X-linked versus autosomal neutral loci as a function of linkage, dominance, selection, sex-specific selection, and sex-specific recombination. For most cases, gene flow at neutral loci on the X is reduced relative to autosomes, as the greater efficacy of hemizygous selection in XY hybrids reduces the opportunity for neutral migrant alleles to escape their genetically linked, locally disfavored alleles via recombination. There are some circumstances, however, involving sex-limited selection and sex-limited recombination that allow neutral loci on the X to introgress more readily than those on autosomes.

在异地物种形成（allopatric speciation）过程中，地理屏障可同时阻断最终形成的物种间基因组所有基因座的基因流。然而，越来越多的证据表明，物种形成过程往往更为复杂：部分基因座可在物种形成期间或二次接触阶段仍发生基因流。在带有异型性染色体的类群（如鸟类、蝴蝶、哺乳类及果蝇）中，X（或Z）染色体的基因流水平通常低于常染色体。为探究该现象的成因，我们构建了种群遗传模型，针对与参与杂交不亲和性和/或局部适应的选择基因座存在遗传连锁的中性基因座，分析其二次接触与基因流情况。本研究采用弱迁移、强选择的模型假设，对比了X连锁与常染色体中性基因座的基因流水平，并分析其与连锁程度、显性效应、选择强度、性别特异性选择及性别特异性重组的相关性。多数情形下，X染色体上中性基因座的基因流水平低于常染色体，这是由于XY型杂交个体的半合子选择作用更强，削弱了中性迁移等位基因通过重组摆脱与其遗传连锁的、在当地受排斥的等位基因的机会。但在部分涉及性别限制性选择与性别限制性重组的特定场景中，X染色体上的中性基因座可比常染色体上的基因座更易发生渐渗。