Phylogeography and diversification of Taiwanese bats

Abstract

Gene flow is a central evolutionary force that largely determines the level of differentiation among populations of organisms and thus their potential for divergence from each other. Identifying key factors that influence gene flow among populations or closely related taxa can thus provide valuable insights into how new species arise and are maintained. I undertook a comparative study of the factors that have shaped range-wide intraspecific differentiation in four related and broadly co-distributed Taiwanese bat species of the genera Murina and Kerivoula. Bats were sampled from sites across Taiwan and sequenced at two mitochondrial genes as well as genotyped at newly developed and/or existing multi-locus microsatellite markers. To improve phylogeographic inference of existing patterns of population genetic structure, I undertook spatial distribution modeling of the focal species at both the present time and at the Last Glacial Maximum. Genetic data were analysed using traditional and new methods, including Bayesian clustering, coalescent-based estimation of gene flow, and haplotype network reconstruction. My findings revealed contrasting signatures of population subdivision and demographic expansion that appear in part to reflect differences in the altitudinal ranges of the focal taxa. Mitochondrial analyses also revealed a putative sister relationship between two of the Taiwanese endemic taxa - M. gracilis and M. recondita, which - given the fact both are restricted to Taiwan - presents an unusual case of potential non-allopatric divergence. To dissect this divergence process in more detail, I used 454-Pyrosequencing to obtain ten nuclear loci sequences of these two taxa, and a third taxon from mainland Asia, M. eleryi. Based on these loci, Bayesian isolation-migration models provided no strong evidence of post-split gene flow and, therefore, did not support speciation within Taiwan. Instead, the divergence process reconstructed from ncDNA loci was found to be incompatible with the mtDNA tree, with M. recondita showing a sister relationship with M. eleryi. This conflict is best explained by the ancient introgression of mtDNA between the two insular species following their colonization of Taiwan at different times.