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The Hokkaido clade was highly divergent from the Honshu clade suggesting a history of ancient divergence. Within Honshu, there were region-related, phylogenetically significant structures. 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By using the mitochondrial COI and ND5 genes. we reconstructed the molecular phylogeography of E. niphouica in Japan. The Hokkaido clade was highly divergent from the Honshu clade suggesting a history of ancient divergence. Within Honshu, there were region-related, phylogenetically significant structures. 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