| Summary: | Determining the evolutionary history and population drivers, such as past large-scale climatic oscillations, stochastic processes and ecological adaptations, represents one of the aims of evolutionary biology. <i>Hipposideros larvatus</i> is a common bat species in Southern China, including Hainan Island. We examined genetic variation in <i>H. larvatus</i> using mitochondrial DNA and nuclear microsatellites. We found a population structure on both markers with a geographic pattern that corresponds well with the structure on mainland China and Hainan Island. To understand the contributions of geography, the environment and colonization history to the observed population structure, we tested isolation by distance (IBD), isolation by adaptation (IBA) and isolation by colonization (IBC) using serial Mantel tests and RDA analysis. The results showed significant impacts of IBD, IBA and IBC on neutral genetic variation, suggesting that genetic variation in <i>H. larvatus</i> is greatly affected by neutral processes, environmental adaptation and colonization history. This study enriches our understanding of the complex evolutionary forces that shape the distribution of genetic variation in bats.
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