Identifying the effects of the Pleistocene on the greater horseshoe bat, Rhinolophus ferrumequinum, in East Asia using ecological niche modelling and phylogenetic analyses

Abstract

Aim The extent to which the ranges of temperate biota in East Asia have been shaped by geological and climatic changes during the Pleistocene remains poorly understood. Previous molecular-based studies of the greater horseshoe bat (Rhinolophus ferrumequinum), which is widespread across China and Japan, suggest that this species was able to persist in multiple refugia in this region. However, limited availability of samples precluded a detailed analysis of past distributions. By integrating ecological niche modelling with phylogenetic analyses, we aim to resolve the impact of past events on the population genetic structure of R. ferrumequinum and provide detailed descriptions of potential distribution patterns during this time.Location Central/East China and Japan.Methods Phylogenetic analyses were carried out using 1098 bp of the mitochondrial ND2 gene and 13 microsatellite loci from bats sampled at 26 localities across China and Japan. Haplotype data were used in isolation-withmigration models (IMa) to estimate divergence dates between different lineages, and mismatch distribution analyses were undertaken to test for signs of population expansion. Geographical structuring of the microsatellite data was examined by spatial clustering. Ecological niche modelling was performed based on highresolution palaeoclimate data inferred for the Last Glacial Maximum (LGM).Results Phylogenetic analyses identified deep levels of divergence between three major lineages broadly corresponding to Central China, East China and Japan. The divergence of all three lineages was estimated to have occurred before the LGM. A strong correlation was observed between the ecological niche model and phylogenetic data, with both methods inferring that R. ferrumequinum populations in Central China did not undergo significant range contractions during glacial episodes. The impact of glacial cycles on East China would have been more severe, with some locations being unable to support viable populations. Zones of secondary contact were identified between Central/East China and East China/Japan, which probably result from some historical gene flow between isolated populations.Main conclusions Integrating ecological niche modelling within phylogeographical studies provides support for a complex demographic history for R. ferrumequinum in East Asia, as well as persistence during glacial episodes in multiple refugia across their range.

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

“…Thus the Yangtze plains region was likely to be a glacial refuge, supporting our hypothesis that such refugia existed in eastern China during the Pleistocene. Other studies have also confirmed that mountainous areas of this region had relatively stable climatic conditions during the Pleistocene glaciation, providing probable glacial refugia for many species [14,28]. Our study identifies that intra-specific divergence within M. pilosus first occurred in 0.25-0.19 Myr BP (Clade A), which corresponds to a relatively warm interglacial period in mainland China [29].…”

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.…”

Little genetic divergence of the greater horseshoe bat Rhinolophus ferrumequinum from far-eastern Asia, with a preliminary report on genetic differentiation of R. ferrumequinum from Eurasia and northern Africa examined from cytochrome b sequences

“…Экземпляры из четырех популяций восточной Азии (Чеджу, континентальная Корея, севе-ро-восточный Китай и Япония) образуют одну слабо подразделенную дальневосточную кладу, were recognized from mtDNA ND2 gene and microsatellite analyses (Flanders et al, 2009). The further study of the same markers (Flanders et al, 2011) reported three lineages in East Asia: central China lineage from Shaanxi, Sichuan, Yunnan, and Hubei; eastern China lineage from Anhui, Jiangxi, Shandong, Henan, Hubei, and Beijing; and Japan lineage from Japan, Jilin, and Shandong. We found that both results are not consistent in the designation of the eastern China and Japan lineages (i.e., from their successive studies the Beijing sample, recognized initially as the Japan lineage, moved to the eastern China lineage, and the Shandong samples, found initially as the eastern China lineage, moved to both eastern China and Japan lineages).…”

“…On the other hand, Lopez et al (1997) reported that regarding evolutionary rates, the cytochrome b gene vary at a slower rate than the control region and ND2, and Flanders et al (2009Flanders et al ( , 2011 noted that further sampling of R. ferrumequinum from northern China and Korea is needed before colonization pattern in fareastern Asia can be fully resolved. Thus, it is necessary to obtain sequences of conservative cytochrome b gene from Korean R. ferrumequinum specimens in order to reexamine population differentiation of R. ferrumequinum from far-eastern Asia and other regions as well.…”