Phylogeography: DNA reveals evolutionary history of species


dispersal, vicariance, range expansion, extinction, introgression, secondary contact, ice age, refuge, evolutionary significant unit, subspecies, geological history

Study species

Japanese crayfish, white-spotted charr, Dolly Varden, Luciogobius gobies, Japanese tree frog, freshwater leeches, crayfish worms, Ural owl

DNA in wild populations contains much information about the evolutionary history of species over thousands or millions of years. For example, Japanese crayfish, the only native crayfish in Japan, shows two lineages that had diverged 3-5 million years ago (Koizumi et al. 2012). Interestingly, these lineages have different range expansion histories: the eastern lineage had spread rapidly relatively recently, whereas gradual stepwise range expansion was inferred in the western lineage. Data from the western lineage also suggests the presence of land bridges between Hokkaido and Honshu and between Hokkaido and its small surrounding islands. Thus, the endemic, endangered crayfish are considered historical footprints for geology and climatology. This kind of genetic analysis, called phylogeography, could provide important information that cannot be revealed by fieldwork.


  • Hashimoto S., Koizumi I., Takai K. and Higashi S. (2014) Different habitat salinity between two divergent groups of a worm-like goby Luciogobius guttatus: an indication of cryptic species. Environmental Biology of Fishes, 97, 1169-1177
  • Koizumi I., Usio N., Kawai T., Azuma N. and Masuda R. (2012) Loss of genetic diversity means loss of geological information: the endangered Japanese crayfish possessed remarkable historical footprints. PLoS ONE, 7, e33986
  • Yamamoto S., Kitano S., Maekawa K., Koizumi I. & Morita K. (2006) Introgressive hybridization between Dolly Varden Salvelinus malma and white-spotted charr Salvelinus leucomaenis on Hokkaido Island, Japan. Journal of Fish Biology, 68 (Supplement A), 68-85
  • Yamamoto S., Morita K., Kitano S., Watanabe K., Koizumi I., Maekawa K. & Takamura K. (2004) Phylogeography of white-spotted charr (Salvelinus leucomaenis) inferred from mitochondrial DNA sequences. Zoological Science, 21, 229-240.