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.

近年来的基因组学研究表明，渐渗（introgression）可在近期分化的类群间以全基因组规模发生。然而，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得到充分阐明。中华菊头蝠（Rhinolophus sinicus）在中国大陆存在三个独立类群：亚种北中华菊头蝠（R. s. septentrionalis）以及两个邻域支系的中华菊头蝠指名亚种（R. s. sinicus，分别为中部中华菊头蝠和东部中华菊头蝠）。此前的研究提示这些类群间存在广泛的mtDNA渐渗，但未检测到ncDNA渐渗。本研究对中华菊头蝠的三个类群的编码基因组进行了采样，以期在预期的ILS背景下对ncDNA渐渗开展更灵敏的检测。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（nuclear protein-coding genes），并通过最大似然法（maximum likelihood）与贝叶斯一致性分析法（Bayesian concordance methods）构建了高置信度的物种树。系统发育分析显示，中部中华菊头蝠存在由北中华菊头蝠与东部中华菊头蝠演化而来的镶嵌基因组（mosaic genome）。三项不同的分析均支持中部中华菊头蝠与北中华菊头蝠间存在ncDNA渐渗，而ILS无法被完全排除。我们的研究结果与其他近期研究一致，表明近期分化的类群可发生大规模的次生渐渗，且该过程可能与ILS共同作用，进而引发系统基因组学冲突（phylogenomic discordances）甚至形成镶嵌基因组。