Closely related taxa often exhibit mitonuclear discordance attributed to introgression of mitochondrial DNA (mtDNA), yet few studies have considered the underlying causes of mtDNA introgression. Here we test for demographic versus adaptive processes as explanations for mtDNA introgression in three subspecies of the intermediate horseshoe bat (Rhinolophus affinis). We generated sequences of 1692 nuclear genes and 13 mitochondrial protein-coding genes for 48 individuals. Phylogenetic reconstructions based on 320 exon sequences and 2217 single nucleotide polymorphisms (SNPs) both revealed conflicts between the species tree and mtDNA tree. These results, together with geographic patterns of mitonuclear discordance, and shared identical or near-identical mtDNA sequences, suggest extensive introgression of mtDNA between the two parapatric mainland subspecies. Under demographic hypotheses, we would also expect to uncover traces of ncDNA introgression, however, population structure and gene flow analyses revealed little nuclear admixture. Furthermore, we found inconsistent estimates of the timing of population expansion and that of the most recent common ancestor for the clade containing introgressed haplotypes. Without a clear demographic explanation, we also examined whether introgression likely arises from adaptation. We found that five mtDNA genes contained fixed amino acid differences between introgressed and non-introgressed individuals, including putative positive selection found in one codon, although this did not show introgression. While our evidence for rejecting demographic hypotheses is arguably stronger than that for rejecting adaptation, we find no definitive support for either explanation. Future efforts will focus on larger-scale resequencing to decipher the underlying causes of discordant mitonuclear introgression in this system.

密切相关的分类群经常表现出归因于线粒体 DNA (mtDNA) 基因渗入的线粒体核不一致，但很少有研究考虑 mtDNA 基因渗入的根本原因。在这里，我们测试了人口统计与适应过程，作为对中间马蹄蝠（Rhinolophus affinis）的三个亚种中 mtDNA 基因渗入的解释）。我们为 48 个个体生成了 1692 个核基因和 13 个线粒体蛋白编码基因的序列。基于 320 个外显子序列和 2217 个单核苷酸多态性 (SNP) 的系统发育重建都揭示了物种树和 mtDNA 树之间的冲突。这些结果，连同线粒体核不一致的地理模式，以及共享相同或几乎相同的 mtDNA 序列，表明两个旁系大陆亚种之间存在广泛的 mtDNA 基因渗入。在人口统计学假设下，我们还希望发现 ncDNA 基因渗入的痕迹，但是，种群结构和基因流分析显示几乎没有核混合物。此外，我们发现对种群扩张时间的估计与包含渗入单倍型的进化枝的最新共同祖先的估计不一致。在没有明确的人口统计解释的情况下，我们还检查了基因渗入是否可能由适应引起。我们发现五个 mtDNA 基因在基因渗入和非基因渗入个体之间包含固定的氨基酸差异，包括在一个密码子中发现的推定阳性选择，尽管这没有显示基因渗入。虽然我们拒绝人口统计假设的证据可以说比拒绝适应的证据更有力，但我们发现这两种解释都没有明确的支持。未来的努力将集中在更大规模的重测序上，以破译该系统中不协调的线粒体渗入的根本原因。我们发现五个 mtDNA 基因在基因渗入和非基因渗入个体之间包含固定的氨基酸差异，包括在一个密码子中发现的推定阳性选择，尽管这没有显示基因渗入。虽然我们拒绝人口统计假设的证据可以说比拒绝适应的证据更有力，但我们发现这两种解释都没有明确的支持。未来的努力将集中在更大规模的重测序上，以破译该系统中不协调的线粒体渗入的根本原因。我们发现五个 mtDNA 基因在基因渗入和非基因渗入个体之间包含固定的氨基酸差异，包括在一个密码子中发现的推定阳性选择，尽管这没有显示基因渗入。虽然我们拒绝人口统计假设的证据可以说比拒绝适应的证据更有力，但我们发现这两种解释都没有明确的支持。未来的努力将集中在更大规模的重测序上，以破译该系统中不协调的线粒体渗入的根本原因。