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Whole‐genome sequencing reveals small genomic regions of introgression in an introduced crater lake population of threespine stickleback
Authors:Kohta Yoshida  Ryutaro Miyagi  Seiichi Mori  Aya Takahashi  Takashi Makino  Atsushi Toyoda  Asao Fujiyama  Jun Kitano
Institution:1. Division of Ecological Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan;2. Evolutionary Genetics Laboratory, Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan;3. Biological Laboratory, Gifu‐keizai University, Ogaki, Gifu, Japan;4. Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan;5. Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan;6. Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
Abstract:Invasive species pose a major threat to biological diversity. Although introduced populations often experience population bottlenecks, some invasive species are thought to be originated from hybridization between multiple populations or species, which can contribute to the maintenance of high genetic diversity. Recent advances in genome sequencing enable us to trace the evolutionary history of invasive species even at whole‐genome level and may help to identify the history of past hybridization that may be overlooked by traditional marker‐based analysis. Here, we conducted whole‐genome sequencing of eight threespine stickleback (Gasterosteus aculeatus) individuals, four from a recently introduced crater lake population and four of the putative source population. We found that both populations have several small genomic regions with high genetic diversity, which resulted from introgression from a closely related species (Gasterosteus nipponicus). The sizes of the regions were too small to be detected with traditional marker‐based analysis or even some reduced‐representation sequencing methods. Further amplicon sequencing revealed linkage disequilibrium around an introgression site, which suggests the possibility of selective sweep at the introgression site. Thus, interspecies introgression might predate introduction and increase genetic variation in the source population. Whole‐genome sequencing of even a small number of individuals can therefore provide higher resolution inference of history of introduced populations.
Keywords:Biological invasion  conservation genomics  exotic species  fisheries  hybridization  Japan Sea stickleback  next‐generation sequencer  rapid evolution
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