title: Phylogeny and historical demography of endemic fishes in Lake Biwa: the ancient lake as a promoter of evolution and diversification of freshwater fishes in western Japan.
abstract: To elucidate the origins of the endemic fish of Lake Biwa, an ancient lake in Japan, and the role of the lake in the diversification of freshwater fish in western Japan, we established a molecular phylogenetic framework with an absolute time scale and inferred the historical demography of a large set of fish species in and around the lake. We used mtDNA sequences obtained from a total of 190 specimens, including 11 endemic species of Lake Biwa and their related species, for phylogenetic analyses with divergence time estimations and from a total of 2319 specimens of 42 species (including 14 endemics) occurring in the lake for population genetic analyses. Phylogenetic analysis suggested that some of the endemic species diverged from their closest relatives earlier (1.3-13.0 Ma) than the period in which the present environmental characteristics of the lake started to develop (ca. 0.4 Ma), whereas others diverged more recently (after 0.4 Ma). In contrast, historical demographic parameters suggested that almost all species, including endemic and nonendemic ones, expanded their populations after the development of the present lake environment. In phylogeographic analyses, common or very close haplotypes of some species were obtained from Lake Biwa and other regions of western Japan. The phylogenetic and historical demographic evidence suggests that there was a time lag between phylogenetic divergence and population establishment and that phenotypic adaptation of some endemic species to the limnetic environment occurred much later than the divergences of those endemic lineages. Population structure and phylogeographic patterns suggest that Lake Biwa has functioned not only as the center of adaptive evolution but also as a reservoir for fish diversity in western Japan.
authors.affiliation: Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan.
authors.forename: Ryoichi
authors.initials: R
authors.lastname: Tabata
authors.affiliation: Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan; Research Institute for Humanity and Nature 457-4 Kamigamo-Motoyama Kita-ku Kyoto 603-8047 Japan.
authors.forename: Ryo
authors.initials: R
authors.lastname: Kakioka
authors.affiliation: Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto606-8502 Japan; Kwansei Gakuin Senior High School 1-155 Uegahara-ichibancho Nishinomiya Hyogo 662-8501 Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Tominaga
authors.affiliation: Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan.
authors.forename: Takefumi
authors.initials: T
authors.lastname: Komiya
authors.affiliation: Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan.
authors.forename: Katsutoshi
authors.initials: K
authors.lastname: Watanabe
keywords: Ancient lake; Lake Biwa; cytochrome b; divergence time; historical demography; mtDNA