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<p><i>Coilia brachygnathus</i> is an anchovy fish that normally inhabits lakes in the middle Yangtze River and was historically absent from the upstream region. However, after the construction of the Three Gorges Reservoir (TGR) in 2003, this species suddenly appeared around 2015 and proliferated in the reservoir. The source, pathway, and mechanisms underlying this invasion remain unclear. In this study, we used whole-genome resequencing, generating SNP data and mitochondrial <i>Cytb</i> gene sequences to investigate the invasion dynamics and proliferation of <i>Coilia brachygnathus</i> (CB) in the TGR. Our results showed that the mtDNA haplotypes of <i>C. brachygnathus</i> from the TGR population (CBT), scattering with the Poyang Lake (CBP) and Liangzi Lake (CBL) populations, and it had the lowest <i>F</i><sub><i>ST</i></sub> value with CBP, indicating its origination from the middle Yangtze River, particularly from the Poyang Lake population. Based on whole-genome resequencing data, demographic modeling and gene flow analyses revealed very recent gene flow between CBT and CBP populations. Source–sink dynamic analysis also confirmed CBP as the source population for both CBL and CBT, further supporting the origin of CBT in the TGR from CBP. The reduced nucleotide diversity, elevated Tajima’s <i>D</i>, and increased linkage disequilibrium in the TGR population support a strong founder effect and experienced bottleneck. These findings indicate that the reservoir environment, together with demographic constraints, may have contributed to the observed genetic differentiation in this newly established population, which could inform invasive species management and conservation strategies in regulated river systems.</p>

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Proliferation of an invasive fish in a large reservoir from the downstream evidenced by whole-genome resequencing data

  • 期刊论文

  • 发表日期：

    2026年1月24日

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  • Tereza M. Magati,
  • Ping Yang,
  • Ke Yang,
  • Dan Yu,
  • Qingjuan Liu,
  • Yahan Wu,
  • Qiaoling Deng,
  • Ruijin Ding,
  • Huanzhang Liu

摘要

Coilia brachygnathus is an anchovy fish that normally inhabits lakes in the middle Yangtze River and was historically absent from the upstream region. However, after the construction of the Three Gorges Reservoir (TGR) in 2003, this species suddenly appeared around 2015 and proliferated in the reservoir. The source, pathway, and mechanisms underlying this invasion remain unclear. In this study, we used whole-genome resequencing, generating SNP data and mitochondrial Cytb gene sequences to investigate the invasion dynamics and proliferation of Coilia brachygnathus (CB) in the TGR. Our results showed that the mtDNA haplotypes of C. brachygnathus from the TGR population (CBT), scattering with the Poyang Lake (CBP) and Liangzi Lake (CBL) populations, and it had the lowest FST value with CBP, indicating its origination from the middle Yangtze River, particularly from the Poyang Lake population. Based on whole-genome resequencing data, demographic modeling and gene flow analyses revealed very recent gene flow between CBT and CBP populations. Source–sink dynamic analysis also confirmed CBP as the source population for both CBL and CBT, further supporting the origin of CBT in the TGR from CBP. The reduced nucleotide diversity, elevated Tajima’s D, and increased linkage disequilibrium in the TGR population support a strong founder effect and experienced bottleneck. These findings indicate that the reservoir environment, together with demographic constraints, may have contributed to the observed genetic differentiation in this newly established population, which could inform invasive species management and conservation strategies in regulated river systems.