Pleistocene climatic cycling drives intra‐specific diversification in the intermediate horseshoe bat (Rhinolophus affinis) in Southern China

Abstract

The repeated formation and loss of land-bridges during the Pleistocene have had lasting impacts on population genetic structure. In the tropics, where island populations persisted through multiple glacial cycles, alternating periods of isolation and contact are expected to have driven population and taxonomic divergence. Here, we combine mitochondrial and nuclear sequence data with microsatellites to dissect the impact of Pleistocene climate change on intra-specific diversification in the horseshoe bat Rhinolophus affinis. This taxon shows considerable morphological and acoustic variation: two parapatric subspecies (himalayanus and macrurus) occur on mainland China and a third (hainanus) on Hainan Island. Our phylogeographic reconstruction and coalescent analyses suggest the island subspecies formed from an ancestral population of himalayanus via two colonization events c. 800,000 years before present. R. a. hainanus then recolonized the mainland, forming macrurus and thus a secondary contact zone with himalayanus. Finally, macrurus recolonized Hainan following the LGM. We found that all three biological events corresponded to known periods of land-bridge formation. Evidence of introgression was detected between macrurus and both its sister taxa, with geographical proximity rather than length of separation appearing to be the biggest determinant of subsequent genetic exchange. Our study highlights the important role of climate-mediated sea level changes have had in shaping current processes and patterns of population structure and taxonomic diversification.

Taxonomic implications of geographical variation in Rhinolophus affinis (Chiroptera: Rhinolophidae) in mainland Southeast Asia

“…The gene was selected for the analysis as its divergence rate is known and has been used in previous publications (Mao et al 2010;Chen et al 2006;Salgueiro et al 2004). Based on jModel test, HKY +I was selected as the best substitution model and relaxed-clock model with an uncorrelated lognormal distribution was used to estimate the substitution rate.…”

“…Trees were collated using Tree Annotator version 1.8 where the maximum clade credibility tree and Median heights were selected; and 10% (6,000 trees) of the sample trees were selected as burn-in. To convert the estimates scaled by mutation rate to calendar years, we used the divergence rate of 20%/Myr for control region which was previously calibrated in the noctule bat (Petit et al 1999) and used in R. affinis (Mao et al 2010) and other bats Salgueiro et al 2004).…”

“…Therefore, the rapid fall in Pleistocene sea levels (Woodruff and Turner 2009;Woodruff 2010), climatic zones (Hughes et al 2011), and phytogeographical transitions (Baker et al 1998;Good 1964;Keng 1970;Richards 1996;van Steenis 1950;Whitmore 1984;Wikranmanayake et al 2002) likely explain the genetic variation observed in R. affinis rather than the high sea level hypothesis when marine waters (100 m, 150 to 220 m above the present level) breached the peninsula during the Neogene period (Hughes et al 2003;Hutchison 1989;Woodruff 2003). Therefore, Pleistocene climate may have played an important role in shaping the genetic profile of R. affinis (Mao et al 2010) from the peninsula.…”

“…4, IS120216.8, IS110823.10, IS120214.16, IS120215.10, IS120214.17, and IS12.042 -change codes) which were available for COI analysis did not show the separation pattern (clade I). Further population research is therefore recommended to clarify this cryptic genetic variation, and fast-mutating genes such as D-loop and microsatellites would be appropriate for such studies Mao et al 2010).…”

Phylogeography of the Rickett’s big-footed bat, Myotis pilosus(Chiroptera: Vespertilionidae): a novel pattern of genetic structure of bats in China

“…In mainland China, population genetic structure can often be explained by the influence of local geographical structure. All previous studies on Chinese bats have shown that subpopulations originally existed in eastern China [11,18,19]. However, with differences among geographical structure, multiple subpopulations in the mountains of southern China region (Yungui Plateau region, Sichuan Basin region and Southeast China Hills region) have also been documented [11,19].…”