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

Abstract

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 asymmetric, which is likely to have resulted from mating between R. s. septentrionalis females with smaller R. s. sinicus and R. thomasi males, although we cannot rule out other scenarios completely. Further conflicts between genetic data and accepted species arrangements across the genus, with paraphyly of members of the rouxii-group, suggest the need for a thorough systematic revision of relationships within this group.

Heteroplasmy and Ancient Translocation of Mitochondrial DNA to the Nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus) Complex

“…This structural variation suggests that the Central sinicus is more closely related to septentrionalis than to the other two sinicus taxa, a finding that is consistent with previous results based on two mtDNA protein coding genes [34]. The shared absence of repeated motifs in Central sinicus and septentrionalis could arise from introgression of the complete mitochondrial genome from septentrionalis to Central sinicus , as suggested previously [33], [34]. Alternatively, this simple structure could suggest that the Central sinicus and septentrionalis represent the ancestral form before R. sinicus diverged into several taxa, although why this has been retained whereas more complex repeated sequences have evolved in East sinicus and Hainan sinicus , is not known.…”

Integrative taxonomy of theRhinolophus macrotiscomplex (Chiroptera, Rhinolophidae) in Vietnam and nearby regions

“…As a consequence, vicariant populations adaptively evolved under different ecological selections imposed by isolated refugia which may have led to shifts in their morphology (noseleaf structure and body, skull, glans penis, and baculum morphology) and echolocation systems, and subsequently their own SMRSs. Depending on the status of SMRSs of each taxon, the restoration of connectivity between some of those during interglacial periods allowed ancient introgression events between some taxa that retained their relatedness (Mao, Zhang et al., ; Mao, He et al., ; Mao, Thong et al., ). However, to test this hypothesis, further investigations including genetic analyses of both mitochondrial and nuclear genomes are needed (Berthier et al., ; Hassanin et al., ; Mao, Zhang et al., ; Nesi et al., ; Tu et al., ).…”

The effects of cultural drift on geographic variation in echolocation calls of the Chinese rufous horseshoe bat (Rhinolophus sinicus)

“…In China, R. sinicus is widely distributed in the Southwest, Central, and Eastern regions, as well as in Hainan Island (Csorba, Ujhelyi, & Thomas, ). Previous studies based on multilocus datasets have revealed high genetic differentiation and strong phylogeographic structuring within R. sinicus (Mao, He, Zhang, Rossiter, & Zhang, ; Mao, Thong, et al., ). The bats from East China, the offshore Hainan Island and Vietnam formed a highly supported lineage, which separated from those lineages in Central China and Yunnan (Mao, Thong, et al., ).…”

“…Previous studies based on multilocus datasets have revealed high genetic differentiation and strong phylogeographic structuring within R. sinicus (Mao, He, Zhang, Rossiter, & Zhang, ; Mao, Thong, et al., ). The bats from East China, the offshore Hainan Island and Vietnam formed a highly supported lineage, which separated from those lineages in Central China and Yunnan (Mao, Thong, et al., ). Among those lineages of R. sinicus , the morphological data and echolocation call frequencies are different, although there is considerable overlap.…”

“…Our sampling range covered those provinces described by Mao et al. (Mao, He, Zhang, Rossiter, & Zhang, ; Mao, Thong, et al., ), but with four new sampling provinces and one municipality. Here, we address the patterns and causes of the geographic variation in RF.…”