Abstract
The genetic population structure of the small cyprinid Hemigrammocypris rasborella, distributed widely in lowlands of western Japan, was examined using partial sequence data of mitochondrial DNA (mtDNA). Molecular phylogenetic analysis revealed that the populations of the western Kyushu region were markedly differentiated from all eastern populations, such that the groups would be comparable to different species; their divergence was inferred to have occurred in the Late Miocene–Pliocene. Also, a largely divergent mtDNA group (with divergence in the early Pleistocene) was found in the Sanyo and northeastern Shikoku regions, forming a secondary contact zone in the western Kinki with the eastern mtDNA group. To date, these aspects of the population structure of H. rasborella appear to be unique among lowland fishes in western Japan. Deeper understanding of the formation processes of freshwater faunas in western Japan will require further comparisons of the phylogeographic patterns and ecological traits of constituent species.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Abe T, Kobayashi I, Watanabe K (2013) An extant native population of the Japanese rosy bitterling, Rhodeus ocellatus kurumeus, in the Sanyo Region, western Japan. Jpn J Ichthyol 60:49–55
Akada J, Yodo T (2006) Geographical and between-habitat variations in the body shape of Hemigrammocypris rasborella. Jpn J Ichthyol 53:175–179
Aoyama J, Watanabe S, Ishikawa S, Nishida M, Tsukamoto K (2000) Are morphological characters distinctive enough to discriminate between two species of freshwater eels, Anguilla celebesensis and A. interioris? Ichthyol Res 47:157–161
Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge
Burridge CP, Craw D, Fletcher D, Waters JM (2008) Geological dates and molecular rates: fish DNA sheds light on time dependency. Mol Biol Evol 25:624–633
Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772
Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214
Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4:699–710
Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567
Fowler HW (1910) Descriptions of four new cyprinoids (Rhodeinae). Proc Acad Nat Sci Phila 62:476–486
Japan Ministry of the Environment (2003) Threatened wildlife of Japan, red data book, brackish and fresh water fishes, 2nd edn. Ministry of Environment, Tokyo
Kanagawa N, Itai T (1998) Habitat of Hemigrammocypris rasborella and river improvement. In: Mori S (ed) Sakana kara mita mizu kankyo (Freshwater environments from view of fishes). Shinzansha-Sci-Tech, Tokyo, pp 61–80
Kawabe T (1994) Biwako no oitachi (Formation of Lake Biwa). In: Research Group for Natural History of Lake Biwa (ed) Biwako no shizenshi (The natural history of Lake Biwa). Yasaka Shobo, Tokyo, pp 24–72
Komiya T, Fujita-Yanagibayashi S, Watanabe K (2013). Multiple colonizations of Lake Biwa by Sarcocheilichthys fishes and their population history. Environ Biol Fish. DOI: 10.1007/s10641-013-0176-9
Kuwashiro I (1959) Submarine topography of Japanese Inland Sea Setonaikai. Geogr Rev Jpn 32:24–34
Miyake T, Nakajima J, Onikura N, Ikemoto S, Iguchi K, Komaru A, Kawamura K (2011) The genetic status of two subspecies of Rhodeus atremius, an endangered bitterling in Japan. Conserv Genet 12:383–400
Nakajima J, Onikura N, Eguchi K, Sugimoto Y, Oikawa S (2006) Distribution and present status of golden venus chub, Hemigrammocypris rasborella (Cypriniformes, Cyprinidae), in northern Kyushu Island, Japan. Bull Biogeogr Soc Jpn 61:109–116
Nakamura M (1969) Cyprinid fishes of Japan: studies on the life history of cyprinid fishes of Japan. Research Institute for Natural Resources, Tokyo
Nishimura S (1974) Nihon-kai no seiritsu (Formation of the Sea of Japan). Tsukiji-Shokan, Tokyo
Ota Y, Naruse T, Tanaka S, Ikada A (2004) Regional geomorphology of the Japanese Islands, vol 6. Geomorphology of Kinki, Chugoku and Shikoku. University of Tokyo Press, Tokyo
Palumbi S, Martin A, Romano S, McMillian WO, Stice L, Grabowski G (1991) The simple fool’s guide to PCR. Univ Hawaii, Honolulu
Rambaut A (2009) FigTree version 1.3.1. http://tree.bio.ed.ac.uk/software/figtree/. Accessed 2 December 2010
Rambaut A, Drummond AJ (2009) Tracer version 1.5. http://tree.bio.ed.ac.uk/software/tracer/. Accessed 13 December 2010
Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, Nishida M, Miya M (2006) Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol 63:826–841
Stieler P (1907) Barilius neglectus sp.n. Blätter für Aquarien- und Terrarien-Kunde. Stuttgart 18(17):169
Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4b10a. Sinauer Associates, Sunderland
Takehana Y, Nagai N, Matsuda M, Tsuchiya K, Sakaizumi M (2003) Geographic variation and diversity of the cyto- chrome b gene in Japanese wild populations of medaka, Oryzias latipes. Zool Sci 20:1279–1291
Tang KL, Agnew MK, Hirt MV, Sado T, Schneider LM, Freyhof J, Sulaiman Z, Swartz E, Vidthayanon C, Miya M, Saitoh K, Simons AM, Wood RM, Mayden RL (2010) Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). Mol Phylogenet Evol 57:189–214
Takeuchi H, Tokuda K, Kanagawa N, Hosoya K (2011) Cephalic lateral line canal system of the golden venus chub, Hemigrammocypris rasborella (Teleostei: Cypriniformes). Ichthyol Res 58:175–179
Ueda K (1989) Phytogeography of Tokai Hilly land element I. Definition. Acta Phytotax Geobot 40:190–202
Watanabe K (1998) Parsimony analysis of the distribution pattern of Japanese primary freshwater fishes, and its application to the distribution of the bagrid catfishes. Ichthyol Res 45:259–270
Watanabe K (2012) Faunal structure of Japanese freshwater fishes and its artificial disturbance. Environ Biol Fish 94:533–547
Watanabe K, Mori S (2008) Comparison of genetic population structure between two cyprinids, Hemigrammocypris rasborella and Pseudorasbora pumila subsp., in the Ise Bay basin, central Honshu, Japan. Ichthyol Res 55:309–320 (Errata: Ichthyol Res 56:108)
Watanabe K, Takahashi H (2010) Tansuigyorui chiri no shizenshi (Natural history of freshwater fish geography). Hokkaido University Press, Sapporo
Watanabe K, Kanagawa N, Kakioka R, Itai T, Mori S (2009) Genetic diversity and conservation units in wild and captive populations of endangered freshwater fishes: a case of Hemigrammocypris rasborella in Shizuoka, Japan. Ichthyol Res 56:411–416
Watanabe K, Kawase S, Mukai T, Kakioka R, Miyazaki J-I, Hosoya K (2010a) Population divergence of Biwia zezera (Cyprinidae: Gobioninae) and the discovery of a cryptic species, based on mitochondrial and nuclear DNA sequence analyses. Zool Sci 27:647–655
Watanabe K, Kano Y, Takahashi H, Mukai T, Kakioka R, Tominaga K (2010b) GEDIMAP: a database of genetic diversity for Japanese freshwater fishes. Ichthyol Res 57:107–109
Yokoyama T (1988) Seinan Nihon no Shizenshi (Natural history of southwestern Japan). Sanwa-shobo, Kyoto
Zardoya R, Doadrio I (1999) Molecular evidence on the evolutionary and biogeographical patterns of European cyprinids. J Mol Evol 49:227–237
Zarske A (2013) Barilius neglectus Stieler, 1907 – ein Seniorsynonym von Hemigrammocypris rasborella Fowler, 1910 (Teleostei: Cypriniformes: Cyprinidae). Vert Zool 63:253–257
Acknowledgments
We thank T. Asaka, H. Egi, Z. Shimizu, M. Tsujio, N. Oshima, O. Masuda, S. Fujita, T. Tanimoto, Y. Yasui, and T. Nishioka for their help with obtaining the specimens. This study was supported in part by Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology, Japan (nos. 21370035), and the Global Center of Excellence Program “Formation of a Strategic Base for Biodiversity and Evolutionary Research: from Genome to Ecosystem” of Kyoto University).
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
About this article
Cite this article
Watanabe, K., Mori, S., Tanaka, T. et al. Genetic population structure of Hemigrammocypris rasborella (Cyprinidae) inferred from mtDNA sequences. Ichthyol Res 61, 352–360 (2014). https://doi.org/10.1007/s10228-014-0406-y
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10228-014-0406-y