Conservation Genetics

, Volume 12, Issue 1, pp 139–159 | Cite as

Genetic structure in species with shallow evolutionary lineages: a case study of the rare flatfish Verasper variegatus

  • Masashi Sekino
  • Kenji Saitoh
  • Daisuke Shimizu
  • Toshihiro Wada
  • Kyoichi Kamiyama
  • Somei Gambe
  • Siqing Chen
  • Masato Aritaki
Research Article


We examined the genetic population divergence of the spotted halibut Verasper variegatus. A previous report suggested two conservation units for this species along the Japanese Pacific coast. Extending the coverage of the genomes (29 microsatellites and three mitochondrial DNA segments) revealed hitherto-undetected genetic population boundaries. We screened population samples from the major habitats along the Japanese coast and the Yellow Sea coast (East Asian Continent). Significant genetic differentiation was found in every comparison between the habitats. In most cases, the nuclear and mitochondrial population divergences were incongruent, most likely caused by differences between the two genomes in the effects of genetic drift after recent population isolation and bottleneck events. We discuss the ecological and evolutionary mechanisms of the genetic structure as well as the units of conservation. The present study illustrates the merits of wider coverage of genomes in genetic population analysis especially for species with a shallow population history.


Spotted halibut Microsatellite Mitochondrial DNA Phylogeography Bottleneck Population genetics 



We thank Takeshi Onodera for his assistance in collecting fish samples from Miyagi Prefecture. Professor Qi Li and his graduate students helped MS’s expedition in China to procure the Yellow Sea sample. Many constructive comments provided by three anonymous reviewers and editors helped improve the manuscript significantly. We conducted this study in the research project ‘Research and Development Projects for Application in Promoting New Policy of Agriculture, Forestry, and Fisheries’, funded by the Ministry of Agriculture, Forestry, and Fisheries, Japan. This study is a scientific contribution from the Fisheries Research Agency of Japan (FRA-TNFRI-B125).

Supplementary material

10592_2010_128_MOESM1_ESM.doc (94 kb)
Supplementary material 1 (DOC 97 kb)


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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Masashi Sekino
    • 1
  • Kenji Saitoh
    • 2
  • Daisuke Shimizu
    • 3
  • Toshihiro Wada
    • 4
  • Kyoichi Kamiyama
    • 5
  • Somei Gambe
    • 6
  • Siqing Chen
    • 7
  • Masato Aritaki
    • 8
  1. 1.Tohoku National Fisheries Research InstituteFisheries Research AgencyShiogamaJapan
  2. 2.National Research Institute of Fisheries ScienceFisheries Research AgencyYokohamaJapan
  3. 3.Miyako Station, National Station for Stock EnhancementFisheries Research AgencyMiyakoJapan
  4. 4.Fukushima Prefectural Fisheries Experimental StationIwakiJapan
  5. 5.Souma Branch, Fukushima Prefectural Fisheries Experimental StationSoumaJapan
  6. 6.Miyagi Prefectural GovernmentSendaiJapan
  7. 7.Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
  8. 8.Seikai National Fisheries Research InstituteFisheries Research AgencyNagasakiJapan

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