Introgression events and population admixture occurred among Sus species across the Eurasian mainland in the Middle Pleistocene, which reflects the local adaption of different populations and contributes to evolutionary novelty. Previous findings on these population introgressions were largely based on extensive genome-wide single nucleotide polymorphism (SNP) information, ignoring structural variants (SVs) as an important alternative resource of genetic variations. Here, we profiled the genome-wide SVs and explored the formation of pattern-related SVs, indicating that PRE1-SS is a recently active subfamily that was strongly associated with introgression events in multiple Asian and European pig populations. As reflected by the three different combination haplotypes from two specific patterns and known phylogenetic relationships in Eurasian boars, we identified the Asian Northern wild pigs as having experienced introgression from European wild boars around 0.5 to 0.2 Mya and having received latitude-related selection. During further exploration of the influence of pattern-related SVs on gene functions, we found substantial sequence changes in 199 intron regions of 54 genes and 3 exon regions of 3 genes (HDX, TRO and SMIM1), implying that the pattern-related SVs were highly related to positive selection and adaption of pigs. Our findings revealed novel introgression events in Eurasian wild boars, providing a timeline of population admixture and divergence across the Eurasian mainland in the Middle Pleistocene.

中文翻译：

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PRE-1 揭示了中更新世欧亚公猪先前未知的基因渗入事件

Sus 中发生基因渗入事件和种群混合中更新世整个欧亚大陆的物种，这反映了不同种群的当地适应性，并有助于进化的新颖性。先前关于这些种群基因渗入的发现主要基于广泛的全基因组单核苷酸多态性 (SNP) 信息，而忽略了结构变异 (SV) 作为遗传变异的重要替代资源。在这里，我们分析了全基因组 SV 并探索了模式相关 SV 的形成，表明 PRE1-SS 是最近活跃的亚科，与多个亚洲和欧洲猪群的基因渗入事件密切相关。正如来自欧亚公猪的两种特定模式和已知系统发育关系的三种不同组合单倍型所反映的那样，我们确定亚洲北方野猪在 0.5 到 0.2 Mya 左右经历了来自欧洲野猪的基因渗入，并接受了与纬度相关的选择。在进一步探索模式相关SVs对基因功能影响的过程中，我们发现54个基因的199个内含子区域和3个基因的3个外显子区域发生了实质性的序列变化。HDX、TRO和SMIM1），暗示模式相关的 SV 与猪的正选择和适应高度相关。我们的研究结果揭示了欧亚野猪的新基因渗入事件，提供了中更新世欧亚大陆种群混合和分化的时间表。