Environmental Biology of Fishes

, Volume 101, Issue 5, pp 699–710 | Cite as

Hierarchical genetic structure of native masu salmon populations in Hokkaido, Japan

  • Shigeru Kitanishi
  • Toshiaki Yamamoto
  • Hirokazu Urabe
  • Kazutaka Shimoda


Identification of the spatial extent of genetic structuring that may be influenced by evolutionary, ecological and historical factors is critical for effective conservation or management strategies. Masu salmon Oncorhynchus masou is commonly distributed in Far East, however, many local populations have been under threats of decline due to habitat destruction, overexploitation, and genetic introgression. To reveal the spatial genetic structure of native masu salmon populations in Hokkaido, masu salmon samples were collected from 16 rivers in which there was no official record of artificial releases of any masu salmon stock and were analyzed using 15 microsatellite loci. A Bayesian assignment test revealed that masu salmon populations were divided into two genetically distinct groups: the northeastern and southwestern groups. For within-group genetic structure, all populations, except for geographically proximate populations, were significantly different from each other. AMOVA revealed that genetic variation at among-group level based on groups identified assignment test was greater than that of groups based on geographic locations. There was no significant IBD for the 16 populations. However, the Mantel test revealed significant IBD for the northeastern group, but did not for the southwestern group. This study suggested that native masu salmon populations in Hokkaido exhibit a hierarchical genetic structure that is largely a result of their precise homing behavior. The results of this study also highlight the importance of defining populations by using genetic data rather than by using predefined populations based on geographic locations for the correct determination of genetic structure.


Native population Genetic introgression Hatchery Microsatellite Oncorhynchus masou 



The authors are grateful to members of Salmon and Freshwater Fisheries Research Institute, Hokkaido Research Organization and members of Hokkaido Salmon Propagation Association for their helping in collecting samples. We are grateful to two anonymous reviewers for their constructive comments on this manuscript. This study was conducted with the permission of the Hokkaido Government.

Supplementary material

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© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  1. 1.Faculty of Regional StudiesGifu UniversityGifuJapan
  2. 2.Faculty of Science and TechnologyOita UniversityOitaJapan
  3. 3.Department of Veterinary Nursing and TechnologyNippon Veterinary and Life Science UniversityTokyoJapan
  4. 4.Salmon and Freshwater Fisheries Research InstituteHokkaido Research OrganizationEniwaJapan

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