Gibbons of the genus Hylobates, which inhabit Southeast Asia, show great diversity and comprise seven to nine species. Natural hybridisation has been observed in several species contact zones, but the history and extent of hybridisation and introgression in possibly historical and the current contact zones remain unclear. To uncover Hylobates species phylogeny and the extent of introgression in their evolution, genotyping by random amplicon sequencing-direct (GRAS-Di) was applied to 47 gibbons, representing seven Hylobates species/subspecies and two outgroup gibbon species. Over 200,000 autosomal single-nucleotide variant sites were identified. The autosomal phylogeny supported that divergence from the mainland species began ~3.5 million years ago, and subsequently occurred among the Sundaic island species. Significant introgression signals were detected between H. lar and H. pileatus, H. lar and H. agilis and H. albibarbis and H. muelleri, which all are parapatric and form ongoing hybrid zones. Furthermore, the introgression signals were detected in every analysed individual of these species, indicating a relatively long history of hybridisation, which might have affected the entire gene pool. By contrast, signals of introgression were either not detected or doubtful in other species pairs living on different islands, indicating the rarity of hybridisation and introgression, even though the Sundaic islands were connected during the Pliocene and Pleistocene glacial events.

栖息在东南亚的长臂猿属的长臂猿表现出极大的多样性，包括七到九种。已经在几个物种接触区观察到自然杂交，但在可能的历史和当前接触区中杂交和基因渗入的历史和程度仍不清楚。为了揭示长臂猿物种的系统发育及其进化中的基因渗入程度，通过随机扩增子直接测序 (GRAS-Di) 进行的基因分型应用于 47 只长臂猿，代表七种长臂猿物种/亚种和两个外群长臂猿物种。鉴定了超过 200,000 个常染色体单核苷酸变异位点。常染色体系统发育支持大陆物种的分化始于约 350 万年前，随后发生在巽他群岛物种中。在H. lar和H. pileatus、H. lar和H. agilis以及H. albibarbis和H. muelleri之间检测到显着的基因渗入信号, 它们都是 parapatric 并形成持续的混合区域。此外，在这些物种的每个分析个体中都检测到基因渗入信号，表明杂交的历史相对较长，这可能影响了整个基因库。相比之下，在生活在不同岛屿上的其他物种对中，基因渗入的信号要么没有被检测到，要么是可疑的，这表明杂交和基因渗入很少见，即使在上新世和更新世冰川事件期间，巽他群岛是相连的。