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

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Abstract

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.

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Acknowledgments

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).

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Authors and Affiliations

  1. Tohoku National Fisheries Research Institute, Fisheries Research Agency, Shiogama, Miyagi, 9850001, Japan

    Masashi Sekino

  2. National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, 2368648, Japan

    Kenji Saitoh

  3. Miyako Station, National Station for Stock Enhancement, Fisheries Research Agency, Miyako, Iwate, 0270097, Japan

    Daisuke Shimizu

  4. Fukushima Prefectural Fisheries Experimental Station, Iwaki, Fukushima, 9700316, Japan

    Toshihiro Wada

  5. Souma Branch, Fukushima Prefectural Fisheries Experimental Station, Souma, Fukushima, 9760022, Japan

    Kyoichi Kamiyama

  6. Miyagi Prefectural Government, Sendai, Miyagi, 9808570, Japan

    Somei Gambe

  7. Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China

    Siqing Chen

  8. Seikai National Fisheries Research Institute, Fisheries Research Agency, Nagasaki, Nagasaki, 8512213, Japan

    Masato Aritaki

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  1. Masashi Sekino
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Correspondence to Masashi Sekino.

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Appendix 1

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Table 6 Per locus estimates of microsatellite variability
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Appendix 2

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Table 7 Polymorphic sites in CR, Cytb and ND2 segments of spotted halibut mtDNA
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Sekino, M., Saitoh, K., Shimizu, D. et al. Genetic structure in species with shallow evolutionary lineages: a case study of the rare flatfish Verasper variegatus . Conserv Genet 12, 139–159 (2011). https://doi.org/10.1007/s10592-010-0128-2

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