Data from: Genomics of introgression in the Chinese horseshoe bat (Rhinolophus sinicus) revealed by transcriptome sequencing

Recent genomic studies show that introgression can occur at a genome-wide scale among recently diverged lineages. However, introgression is difficult to distinguish from incomplete lineage sorting (ILS), and these processes are expected to occur together. Moreover, ncDNA introgression is less easily detected than mtDNA introgression, and as such its prevalence is less well understood. The Chinese horseshoe bat (Rhinolophus sinicus) occurs as three distinct forms on mainland China: the subspecies R. s. septentrionalis and two parapatric clades of R. s. sinicus (Central and East R. s. sinicus). Previous work suggested widespread mtDNA introgression between these subspecies; however, no ncDNA introgression was detected. In this study we sampled the coding genomes of all three forms of R. sinicus in order to perform a more sensitive test for ncDNA introgression against an expected background of ILS. We assembled 3548 nuclear protein-coding genes from these and three congeneric species, and built a high-confidence species tree using maximum likelihood and Bayesian concordance methods. Phylogenetic analysis suggested a mosaic genome for Central R. s. sinicus derived from R. s. septentrionalis and East R. s. sinicus. Nuclear DNA introgression between Central R. s. sinicus and R. s. septentrionalis was supported by three different tests, whereas ILS could not be ruled out completely. Our findings, in line with other recent results, indicate that recently diverged taxa undergo large-scale secondary introgression, and that this process likely operates alongside ILS to give rise to phylogenomic discordances or even mosaic genomes.

近期的基因组学研究表明，基因渐渗（introgression）可在新近分化的类群间以全基因组规模发生。然而，基因渐渗难以与不完全谱系分选（incomplete lineage sorting, ILS）相区分，且这两种过程通常伴随发生。此外，核DNA（nuclear DNA, ncDNA）渐渗相较于线粒体DNA（mitochondrial DNA, mtDNA）渐渗更难被检测到，因此其流行程度尚未得到充分阐明。中华菊头蝠（Rhinolophus sinicus）在中国大陆存在三个分化类群：北方亚种（R. s. septentrionalis）以及中华菊头蝠中华亚种（R. s. sinicus）的两个邻域支系（中部中华亚种与东部中华亚种）。既往研究提示这些类群间存在广泛的线粒体DNA基因渐渗，但未检测到核DNA基因渐渗。本研究对中华菊头蝠全部三个类群的编码基因组进行了取样，以期在预期的不完全谱系分选背景下，对核DNA基因渐渗开展更为灵敏的检测。我们从上述类群以及3个同属物种中组装得到3548个核蛋白编码基因，并通过最大似然法与贝叶斯一致性分析法构建了高置信度的物种树。系统发育分析结果显示，中部中华亚种存在由北方亚种与东部中华亚种演化而来的嵌合基因组。三项不同的检测方法均支持中部中华亚种与北方亚种间存在核DNA渐渗，而不完全谱系分选无法被完全排除。我们的研究结果与其他近期研究一致，表明新近分化的类群会发生大规模的二次基因渐渗，且该过程可能与不完全谱系分选共同作用，进而导致系统基因组学冲突，甚至形成嵌合基因组。