Supplementary Tables from Balancing selection and introgression of newt immune-response genes

The importance of interspecific introgression as a source of adaptive variation is increasingly recognized. Theory predicts that beneficial genetic variants cross species boundaries easily even when interspecific hybridization is rare and gene flow is strongly constrained throughout the genome. However, it remains unclear whether certain classes of genes are particularly prone to adaptive introgression. Genes affected by balancing selection (BS) may constitute such a class, because forms of BS that favour novel, initially rare alleles, should facilitate introgression. We tested this hypothesis in hybridizing newts by comparing 13 genes with signatures of BS, in particular an excess of common non-synonymous polymorphisms, to the genomic background (154 genes). Parapatric hybridizing taxa were less differentiated in BS candidate genes than more closely related allopatric lineages, while the opposite was observed in the control genes. Coalescent and forward simulations that explored neutral and BS scenarios under isolation and migration showed that processes other than differential gene flow are unlikely to account for this pattern. We conclude that BS, probably involving a form of novel allele advantage, promotes introgression. This mechanism may be a source of adaptively relevant variation in hybridizing species over prolonged periods.种间渐渗作为适应性变异来源的重要性正日益受到学界的广泛认可。理论研究表明，即便种间杂交事件较为稀有、全基因组范围内的基因流（gene flow）受到强烈限制，有益的遗传变异仍可轻松跨越物种界限。然而目前学界仍未明确，是否存在特定类别的基因尤其易于发生适应性渐渗。受平衡选择（balancing selection, BS）作用的基因或可归为此类：部分平衡选择机制会青睐新出现、初始频率极低的等位基因，本应能够促进渐渗过程。我们以杂交蝾螈为研究对象验证该假说：将13个带有平衡选择特征（尤其表现为存在过量常见非同义多态性）的基因，与基因组背景中的154个对照基因进行对比分析。研究结果显示：相较于亲缘关系更为密切的异域分化支系，邻域分布的杂交类群在平衡选择候选基因间的遗传分化程度更低；而对照基因则呈现出完全相反的模式。通过在隔离与迁移模型下开展溯祖模拟与正向模拟，分别对中性情景与平衡选择情景进行探究后可知，除差异化基因流之外的其他演化过程，均难以解释上述观测结果。综上，平衡选择（大概率涉及新型等位基因优势这一作用形式）可促进种间渐渗。这一机制或可在漫长的演化周期中，为杂交类群提供具备适应性意义的遗传变异来源。