Advances in genomic studies have revealed that hybridization in nature is pervasive and raised questions about the dynamics of different genetic and evolutionary factors following the initial hybridization event. While recent research has proposed that the genomic outcomes of hybridization might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated the genetic introgression between two divergent lineages of nine-spined sticklebacks (Pungitius pungitius) in the Baltic Sea. We found that the intensity and direction of selection on the introgressed variation has varied across different genomic elements: while functionally important regions displayed reduced rates of introgression, promoter regions showed enrichment. Despite the general trend of negative selection, we identified specific genomic regions that were enriched for introgressed variants and within these regions, we detected footprints of selection, indicating adaptive introgression. Geographically, we found the selection against the functional changes to be strongest in the vicinity of the secondary contact zone and weaken as a function of distance from the initial contact. Altogether, the results suggest that the stabilization of introgressed variation in the genomes is a complex, multi-stage process involving both negative and positive selection. In spite of the predominance of negative selection against introgressed variants, we also found evidence for adaptive introgression variants likely associated with adaptation to Baltic Sea environmental conditions.

中文翻译：

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刺鱼的二次接触、渐渗杂交和基因组稳定

基因组研究的进展表明，杂交在自然界中是普遍存在的，并提出了关于初始杂交事件后不同遗传和进化因素的动态的问题。虽然最近的研究提出杂交的基因组结果可能在某种程度上是可预测的，但仍然存在许多不确定性。利用全面的全基因组序列数据，我们研究了波罗的海九刺鱼（Pungitius pungitius）两个不同谱系之间的遗传渗入。我们发现，不同基因组元件对基因渗入变异的选择强度和方向有所不同：虽然功能重要的区域显示基因渗入率降低，但启动子区域显示富集。尽管存在负选择的总体趋势，我们还是确定了富含渐渗变体的特定基因组区域，并且在这些区域内，我们检测到了选择的足迹，表明适应性渐渗。从地理上看，我们发现针对功能变化的选择在次要接触区附近最强，并且随着距初始接触的距离而减弱。总而言之，结果表明基因组中渐渗变异的稳定是一个复杂的、多阶段的过程，涉及负选择和正选择。尽管针对渗入变体的负选择占主导地位，但我们还发现了适应性渗入变体的证据，可能与适应波罗的海环境条件有关。