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.近期基因组学研究表明，基因渐渗（introgression）可在新近分化的支系间以全基因组规模发生。然而，基因渐渗与不完全谱系分选（incomplete lineage sorting, ILS）难以区分，且这两种演化过程往往相伴出现。此外，核DNA（nuclear DNA, ncDNA）渐渗较线粒体DNA（mitochondrial DNA, mtDNA）渐渗更难被检测到，因此其流行程度尚未被充分阐明。中华菊头蝠（Rhinolophus sinicus）在中国大陆存在三个独立类群：北方亚种（R. s. septentrionalis）以及中华菊头蝠指名亚种的两个邻域支系（中部中华菊头蝠与东部中华菊头蝠）。既往研究表明这些亚种间存在广泛的线粒体DNA渐渗，但未检测到核DNA渐渗现象。本研究对中华菊头蝠的三个类群的编码基因组进行取样，以期在预期的不完全谱系分选背景下，对核DNA渐渗开展更灵敏的检测。我们从上述类群及另外3个同属物种中组装得到3548个核蛋白编码基因，并通过最大似然法和贝叶斯一致性分析法构建了高置信度的物种树。系统发育分析显示，中部中华菊头蝠拥有由北方亚种和东部中华菊头蝠基因融合形成的镶嵌基因组。三项独立检验均支持中部中华菊头蝠与北方亚种间存在核DNA渐渗，而不完全谱系分选仍无法完全排除。本研究结果与其他近期研究结论一致，表明新近分化的类群可发生大规模次生渐渗，且该过程与不完全谱系分选共同作用，进而引发系统基因组学冲突甚至镶嵌基因组的形成。