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

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‐with‐migration 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 high‐resolution 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 phylo‐geographical 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.