Ichthyological Research

, Volume 65, Issue 1, pp 115–126 | Cite as

Phylogeography of the eight-barbel loach Lefua nikkonis (Cypriniformes: Nemacheilidae): how important were straits in northern Japan as biogeographical barriers?

  • Akira Ooyagi
  • Daniel F. Mokodongan
  • Javier Montenegro
  • Ixchel F. Mandagi
  • Noriyuki Koizumi
  • Yoshiyasu Machida
  • Nobuyuki Inomata
  • Sergey V. Shedko
  • Arief A. Hutama
  • Renny K. Hadiaty
  • Kazunori Yamahira
Full Paper


Many straits in the Japanese archipelago have been proposed as biogeographical boundaries, but there is disagreement regarding their importance as historic barriers against dispersal of terrestrial and freshwater taxa. Mitochondrial DNA haplotype and phylogenetic analyses of Lefua nikkonis, a primary freshwater fish inhabiting northern Japan and descendent from Siberia, revealed that the species is genetically structured within its geographic range, but that two major haplotypes are widely distributed across the Ishikari Lowland of Hokkaido Island as well as across the Tsugaru Strait between Hokkaido and Honshu Islands, two well-known biogeographical boundaries of northern Japan. The two major haplotypes were separated from each other by only one mutational step, and many other haplotypes, including those endemic to the region south of these barriers, have diverged from the major haplotypes, suggesting rapid range expansion and local differentiation. Divergence-time estimates, based on vicariance of the Honshu endemic congener L. echigonia via uplift of the Central Highlands, demonstrated that the southward dispersal of L. nikkonis from Hokkaido Island to Honshu Island occurred less than 0.08–0.19 Mya, suggesting that a land bridge emerged at the Tsugaru Strait during the Riss glaciation. Given that other freshwater taxa crossed the strait earlier (during the Middle Pleistocene), it is likely that land bridges in the strait have repeatedly emerged. The fact that L. nikkonis invaded only the northern part of Honshu, and that many other freshwater species also have the limit of their distribution ranges in this area as well, indicates that a faunal transition zone might persist even without the Tsugaru Strait. Thus, straits and lowlands in northern Japan are likely to have been less important as dispersal barriers to freshwater taxa than is currently thought.


Blakiston Line Dispersal Riss Glacial Land bridge Primary freshwater fish 



We thank Goto A, Kuwahara T, Miyazaki Y, Matsubara H, Miyazaki J, Koizumi I, Watanabe K, Takehana Y, Mukai T, Sakai T, Mishina T, Nakajima J, Takami Y, and Toda M for their valuable comments on this project. We also thank Yamaha E, Komazawa M, Takahashi H, Ichimura M, Azuma N, Takeda S, Kishida O, Mochida K, Ohbayashi K, Kanno T, Mori T, and Usui T for kindly helping with our field collections or for providing samples. This research was partially supported by a Kuromatsunai Biodiversity Conservation Research Grant to AO and KY.

Supplementary material

10228_2017_597_MOESM1_ESM.pdf (544 kb)
Supplementary material 1 (PDF 544 kb)
10228_2017_597_MOESM2_ESM.fas (77 kb)
Supplementary material 2 (FAS 77 kb)
10228_2017_597_MOESM3_ESM.docx (108 kb)
Supplementary material 3 (DOCX 108 kb)


  1. Aoyagi H (1957) General notes on the freshwater fishes of the Japanese Archipelago. Taishukan, TokyoGoogle Scholar
  2. Blakiston T, Pryer H (1880) Catalogue of the birds of Japan. Trans Asiatic Soc Jpn 8:172–242Google Scholar
  3. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1659Google Scholar
  4. Crandall KA, Templeton AR (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134:959–969Google Scholar
  5. Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772Google Scholar
  6. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214Google Scholar
  7. Fujimaki Y (1994) Across the strait: fauna of mixture. In: Ishigaki K, Fukuda M (eds) Formation history of nature of Hokkaido. Hokkaido University Press, Sapporo, pp 167–179Google Scholar
  8. Goto A (1982) Freshwater fishes in Hokkaido and their origin. Tansuigyo 8:19–26Google Scholar
  9. Goto A (1994) Fishes in rivers and lakes: origin and adaptive strategy. In: Ishigaki K, Fukuda M (eds) Formation history of nature of Hokkaido. Hokkaido University Press, Sapporo, pp 150–166Google Scholar
  10. Goto A, Nakanishi T, Utoh H, Hamada K (1978) A preliminary study of the freshwater fish fauna of rivers in southern Hokkaido. Bull Fac Fish Hokkaido Univ 29:118–130Google Scholar
  11. Japan Association for Quaternary Research (1987) Quaternary maps of Japan (plus explanatory text). University of Tokyo Press, TokyoGoogle Scholar
  12. Johnson KP, Weckstein JD (2011) The Central American land bridge as an engine of diversification in New World doves. J Biogeogr 38:1069–1076Google Scholar
  13. Koizumi I, Usio N, Kawai T, Azuma N, Masuda R (2012) Loss of genetic diversity means loss of geological information: the endangered Japanese crayfish exhibits remarkable historical footprints. PLoS ONE 7:e33986Google Scholar
  14. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–187Google Scholar
  15. Kurose N, Masuda R, Yoshida MC (1999) Phylogeographic variation in two mustelines, the least weasel Mustela nivalis and the ermine M. erminea of Japan, based on mitochondrial DNA control region sequences. Zool Sci 16:971–977Google Scholar
  16. Kuwahara T (1996) The geographic distribution and reproductive biology of Lefua costata nikkonis. Master Theses, Faculty of Fisheries, Hokkaido UniversityGoogle Scholar
  17. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452Google Scholar
  18. Machida H, Matsuda T, Umitsu M, Koizumi T (2006) Regional geomorphology of the Japanese islands, vol 5. Geomorphology of Chubu Region. University of Tokyo Press, TokyoGoogle Scholar
  19. Masuda H, Amaoka K, Araga C, Uyeno T, Yoshino T (1988) The Fishes of the Japanese Archipelago, English edition. Tokai University Press, TokyoGoogle Scholar
  20. Matsui H, Tada R, Oba T (1998) Low-salinity isolation event in the Japan Sea in response to eustatic sea-level drop during LGM: reconstruction based on salinity-balance model. Daiyonki Kenkyu (Quaternary Res) 37:221–233Google Scholar
  21. Ministry of the Environment, Government of Japan (2012) The 4th version of the Japanese red lists. Ministry of the Environment, Government of Japan, TokyoGoogle Scholar
  22. Miyazaki J, Dobashi M, Tamura T, Beppu S, Sakai T, Mihara M, Hosoya K (2011) Parallel evolution in eight-barbel loaches of the genus Lefua (Balitoridae, Cypriniformes) revealed by mitochondrial and nuclear DNA phylogenies. Mol Phylogenet Evol 60:416–417Google Scholar
  23. Mayr E (1944) Wallace’s Line in the light of recent zoogeographic studies. Q Rev Biol 19:1–14Google Scholar
  24. Nakajima J (2017) Loaches of Japan–natural history and culture. Yama-kei Publishers, TokyoGoogle Scholar
  25. von Oheimb PV, Albrecht C, Riedel F, Bössneck U, Zhang H, Wilke T (2013) Testing the role of the Himalaya Mountains as a dispersal barrier in freshwater gastropods (Gyraulus spp.). Biol J Linn Soc 109:526–53Google Scholar
  26. Ohshima K (1990) The history of straits around the Japanese Island in the late-Quaternary. Daiyonki Kenkyu (Quaternary Res) 29:193–208Google Scholar
  27. Ohshima K (1991) The late-Quaternary sea-level change of the Japanese islands. J Geogr 100:967–975Google Scholar
  28. Ohtani K, Kido K (1980) Oceanographic Structure in Funka Bay. Bull Fac Fish Hokkaido Univ 31:84–114Google Scholar
  29. Ono Y (1994) A drama in the ice age: the genesis of Hokkaido. In: Ishigaki K, Fukuda M (eds) Formation history of nature of Hokkaido. Hokkaido University Press, Sapporo, pp 1–15Google Scholar
  30. Ooyagi A (2013) Distribution in the Shimokita Peninsula, Aomori Prefecture of Japanese Ezohotoke Lefua nikkonis (Cobitidae) and morphologic comparison with species of the Hokkaido Prefecture product. J Nat Hist Aomori 18:61–67Google Scholar
  31. Parenti LR, Ebach MC (2009) Comparative biogeography: discovering and classifying biogeographical patterns of a dynamic earth. University of California Press, OaklandGoogle Scholar
  32. Ronquist F, Teslenko M, van der Mark P, Ayres D, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2011) MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:1–4Google Scholar
  33. Saka R, Takehana Y, Suguro N, Sakaizumi M (2003) Genetic population structure of Lefua echigonia inferred from allozymic and mitochondrial cytochrome b variations. Ichthyol Res 50:301–309Google Scholar
  34. Sakai H, Ueda T, Yokoyama R, Safronov SN, Goto A (2014) Genetic structure and phylogeography of northern Far Eastern pond minnows, Rhynchocypris perenurus sachalinensis and R. p. mantschuricus (Pisces, Cyprinidae), inferred from mitochondrial DNA sequences. Biogeography 16:87–109Google Scholar
  35. Sato M (1969) Floristic and faunastic regions in biogeography. Ann Rep Inst Reg Stu Ibaraki Univ 1:7–27Google Scholar
  36. Shedko SV, Miroshnichenko IL, Nemkova GA (2008) On the systematics and phylogeography of eight-barbel loaches of the genus Lefua (Cobitoidea: Nemacheilidae): mtDNA typing of L. pleskei. Russian J Genet 44:817–825Google Scholar
  37. Silvestro D, Michalak I (2012) raxmlGUI: a graphical front-end for RAxML. Org Divers Evol 12:335–337Google Scholar
  38. Takeuchi M, Ohta T (1993) Distribution and a few ecological aspects of Lefua costata nikkonis (Cobitididae) in Aomori Prefecture, Japan. Bull Biogeogr Soc Japan 48:73–80Google Scholar
  39. Templeton AR, Sing CF (1993) A cladistic-analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics 134: 659–669Google Scholar
  40. Tominaga K, Nakajima J, Watanabe K (2016) Cryptic divergence and phylogeography of the pike gudgeon Pseudogobio esocinus (Teleostei: Cyprinidae): a comprehensive case of freshwater phylogeography in Japan. Ichthyol Res 63:79–93Google Scholar
  41. Wallace AR (1860) On the zoological geography of the Malay Archipelago. J Proc Linn Soc Lond Zool 4:172–184Google Scholar
  42. Watanabe K, Takahashi H, Kitamura A, Yokoyama R, Kitagawa T, Takeshima H, Sato S, Yamamoto S, Takehana Y, Mukai T, Ohara K, Iguchi K (2006) Biogeographical history of Japanese freshwater fishes: phylogeographic approaches and perspectives. Jpn J Ichthyol 53:1–38Google Scholar
  43. Watanabe K, Takahashi H (2010) Natural history of freshwater fish geography. Hokkaido University Press, SapporoGoogle Scholar
  44. Whitten AJ, Mustafa M, Henderson GS (2002) The ecology of Sulawesi. Periplus, SingaporeGoogle Scholar
  45. Yamazaki Y, Goto A, Nishida M (2003) Mitochondrial DNA sequence divergence between two cryptic species of Lethenteron, with reference to an improved identification technique. J Fish Biol 62:591–609Google Scholar
  46. Yokoyama R, Goto A (2002) Phylogeography of a freshwater sculpin, Cottus nozawae, from the northeastern part of Honshu Island, Japan. Ichthyol Res 49:147–155Google Scholar

Copyright information

© The Ichthyological Society of Japan 2017

Authors and Affiliations

  • Akira Ooyagi
    • 1
  • Daniel F. Mokodongan
    • 2
  • Javier Montenegro
    • 2
  • Ixchel F. Mandagi
    • 2
  • Noriyuki Koizumi
    • 3
  • Yoshiyasu Machida
    • 4
  • Nobuyuki Inomata
    • 5
  • Sergey V. Shedko
    • 6
  • Arief A. Hutama
    • 7
  • Renny K. Hadiaty
    • 8
  • Kazunori Yamahira
    • 2
  1. 1.Shimokita Field Science NestMutsuJapan
  2. 2.Tropical Biosphere Research CenterUniversity of the RyukyusOkinawaJapan
  3. 3.Institute for Rural Engineering, National Agriculture and Food Research OrganizationIbarakiJapan
  4. 4.Bihoro MuseumBihoroJapan
  5. 5.Department of Environmental ScienceFukuoka Women’s UniversityFukuokaJapan
  6. 6.Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of SciencesVladivostokRussia
  7. 7.Conservation International IndonesiaJakartaIndonesia
  8. 8.Museum Zoologicum Bogoriense, Research Center for Biology, LIPICibinongIndonesia

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