Multiple cases of asymmetric introgression among horseshoe bats detected by phylogenetic conflicts across loci

Phylogenetic discordance among taxa can provide powerful insights into past episodes of introgressive hybridization, as well as lineage sorting. Previously, we showed that the taxonomically distinct taxon Rhinolophus sinicus septentrionalis has undergone historical introgression with its sympatric sister subspecies Rhinolophus sinicus sinicus. To examine in more detail the extent of gene flow between these two taxa, and also between these and their sister species Rhinolophus thomasi, we obtained new samples from China, Myanmar, and Vietnam, and combined new and published genetic data from these, Rhinolophus rouxii, and Rhinolophus indorouxii from India. Phylogenetic analyses revealed three separate cases of discordance: between R. s. septentrionalis and adjacent populations of R. s. sinicus, between R. s. septentrionalis and R. thomasi and between eastern populations of R. s. sinicus and a newly-identified lineage. In both former cases, the mitochondrial DNA introgression appears to be ...