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<p><i>Pseudorhodeus tanago</i>, the Tokyo bittering (Miyakotanago), is a small cyprinid endemic to the Kanto region, eastern Honshu, Japan. The species is threatened by habitat loss and population decline due to various human activities. Hence, several <i>ex situ</i> conservation programs have been implemented since the 1970s. To achieve <i>ex situ</i> conservation programs that maximize the preservation of historical population diversity, conservation units must be appropriately identified. For this purpose, previous studies have employed genetic analyses using a limited number of markers, such as mitochondrial DNA (mtDNA) and microsatellites. In this study, we utilized nuclear single nucleotide polymorphisms (SNPs) to conduct a more detailed re-assessment of the genetic population structure of this species, with particular emphasis on historical and artificial population admixtures. We obtained 935 SNPs using the multiplexed inter-simple sequence repeat genotyping by sequencing method (MIG-seq; 203 individuals), as well as partial mtDNA sequences (534 bp; 500 individuals, including data from database), from 37 wild and captive populations collected from 1991 to 2023. <i>F</i><sub><i>ST</i></sub> values for SNP and mtDNA data suggested a high degree of differentiation among local populations. Principal component analysis, admixture analysis, and phylogenetic analysis based on SNP data identified five geographically separated genetic groups, which encompassed the grouping in previous studies using mtDNA and microsatellites. Two wild and five captive populations were suggested to be admixtures of multiple population components. These were inferred to include historical admixture with geohistorical backgrounds and artificial mixing during captive management. Future reintroductions should be pursued with continued <i>ex situ</i> conservation for each local population separately, with appropriate monitoring to ensure genetic authenticity of local populations.</p>

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The genetic population structure and diversity of the endangered bittering Pseudorhodeus tanago revealed by SNP markers

  • 期刊论文

  • 发表日期：

    2025年6月4日

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  • Yoshimitsu Takada,
  • Takahiro Morosawa,
  • Masaki Asano,
  • Ryoichi Tabata,
  • Hitoshi Kubota,
  • Katsutoshi Watanabe

摘要

Pseudorhodeus tanago, the Tokyo bittering (Miyakotanago), is a small cyprinid endemic to the Kanto region, eastern Honshu, Japan. The species is threatened by habitat loss and population decline due to various human activities. Hence, several ex situ conservation programs have been implemented since the 1970s. To achieve ex situ conservation programs that maximize the preservation of historical population diversity, conservation units must be appropriately identified. For this purpose, previous studies have employed genetic analyses using a limited number of markers, such as mitochondrial DNA (mtDNA) and microsatellites. In this study, we utilized nuclear single nucleotide polymorphisms (SNPs) to conduct a more detailed re-assessment of the genetic population structure of this species, with particular emphasis on historical and artificial population admixtures. We obtained 935 SNPs using the multiplexed inter-simple sequence repeat genotyping by sequencing method (MIG-seq; 203 individuals), as well as partial mtDNA sequences (534 bp; 500 individuals, including data from database), from 37 wild and captive populations collected from 1991 to 2023. FST values for SNP and mtDNA data suggested a high degree of differentiation among local populations. Principal component analysis, admixture analysis, and phylogenetic analysis based on SNP data identified five geographically separated genetic groups, which encompassed the grouping in previous studies using mtDNA and microsatellites. Two wild and five captive populations were suggested to be admixtures of multiple population components. These were inferred to include historical admixture with geohistorical backgrounds and artificial mixing during captive management. Future reintroductions should be pursued with continued ex situ conservation for each local population separately, with appropriate monitoring to ensure genetic authenticity of local populations.