Lineage Divergence and Historical Gene Flow in the Chinese Horseshoe Bat (Rhinolophus sinicus)

Abstract

Closely related taxa living in sympatry provide good opportunities to investigate the origin of barriers to gene flow as well as the extent of reproductive isolation. The only two recognized subspecies of the Chinese rufous horseshoe bat Rhinolophus sinicus are characterized by unusual relative distributions in which R. s. septentrionalis is restricted to a small area within the much wider range of its sister taxon R. s. sinicus. To determine the history of lineage divergence and gene flow between these taxa, we applied phylogenetic, demographic and coalescent analyses to multi-locus datasets. MtDNA gene genealogies and microsatellite-based clustering together revealed three divergent lineages of sinicus, corresponding to Central China, East China and the offshore Hainan Island. However, the central lineage of sinicus showed a closer relationship with septentrionalis than with other lineages of R. s. sinicus, in contrary to morphological data. Paraphyly of sinicus could result from either past asymmetric mtDNA introgression between these two taxa, or could suggest septentrionalis evolved in situ from its more widespread sister subspecies. To test between these hypotheses, we applied coalescent-based phylogenetic reconstruction and Approximate Bayesian Computation (ABC). We found that septentrionalis is likely to be the ancestral taxon and therefore a recent origin of this subspecies can be ruled out. On the other hand, we found a clear signature of asymmetric mtDNA gene flow from septentrionalis into central populations of sinicus yet no nuclear gene flow, thus strongly pointing to historical mtDNA introgression. We suggest that the observed deeply divergent lineages within R. sinicus probably evolved in isolation in separate Pleistocene refugia, although their close phylogeographic correspondence with distinct eco-environmental zones suggests that divergent selection might also have promoted broad patterns of population genetic structure.

Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia

“…6). Evidence for a number of these postulated glacial refugia has been reported in previous studies for many organisms, including bats (Flanders et al 2011;Khan et al 2010;Lin et al 2014;Mao et al 2013). Accordingly, we propose that the contraction of woody bamboo forests into different glacial refugia had fragmented the distribution of the Pliocene ancestors of both T. pachypus s. lat.…”

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

“…Because Rhinolophus spp. are recognized as forest‐interior specialists (Kingston, Francis, Akbar, & Kunz, ), contraction and expansion of forests during Plio‐Pleistocene have been regarded as major factors driving their biogeographical history (Flanders, Wei, Rossiter, & Zhang, ; Mao, He et al., ; Mao, Zhu, Zhang, & Rossiter, ; Rossiter, Benda, Dietz, Zhang, & Jones, ; Tu et al., ). For the R. macrotis group, we suggest that the vicariance of the most common ancestors of recent taxa might have taken place due to the persistence of different allopatric refugia across the region during Pleistocene glacial periods (Bird, Taylor, & Hunt, ; Gathorne‐Hardy, Syaukani Davies, Eggleton, & Jones, ; Lin et al., ; Morgan, Somboon, & Walto, ; Tu et al., , ).…”

“…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., ).…”