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<p>The endangered and endemic catfish <i>Glyptothorax stocki</i> faces mounting threats in Pakistan, yet its population genetics remain entirely uncharacterized. To address this gap and inform genetically based conservation strategies, we conducted the first genome-scale study of <i>G. stocki</i>, analyzing 24 individuals from three river systems: Swat (KPK), Poonch (KK), and upper Neelum (KN). Moreover, mitochondrial genome analysis placed <i>G. stocki</i> within a well-supported clade and provided its phylogenetic context among related Sisoridae taxa. Genome-wide SNP analysis revealed strong population structuring. Pairwise F<sub>ST</sub> values showed strong divergence between KPK and KN (F<sub>ST</sub> = 0.175) and minimal differentiation between KK and KN (F<sub>ST</sub> = 0.003). Nucleotide diversity was high in KK (0.0697) and KN (0.0646) but low in KPK (0.0256). KK and KN showed heterozygote deficits (F<sub>IS</sub> = 0.22, 0.11), whereas KPK showed excess heterozygosity (F<sub>IS</sub> = − 0.13), with genomic inbreeding highest in KK and lowest in KPK. Clustering analyses (PCA, ADMIXTURE, STRUCTURE) and a maximum likelihood tree grouped the populations into two distinct genetic clusters: one comprising KK and KN, and a second, highly divergent cluster represented by KPK. These results point to a long-term isolation of the KPK population, likely driven by geographic barriers. Therefore, we propose managing these clusters as separate management units (MUs). This study provides a genomic baseline for <i>G. stocki</i>’s genetically informed conservation and restoration plans.</p>

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Population genomic assessment of the endangered endemic catfish Glyptothorax stocki reveals distinct lineages in Pakistan

  • 期刊论文

  • 发表日期：

    2026年7月6日

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  • Mohsan Raza,
  • Arif Muhammad Khan,
  • Chenhong Li

摘要

The endangered and endemic catfish Glyptothorax stocki faces mounting threats in Pakistan, yet its population genetics remain entirely uncharacterized. To address this gap and inform genetically based conservation strategies, we conducted the first genome-scale study of G. stocki, analyzing 24 individuals from three river systems: Swat (KPK), Poonch (KK), and upper Neelum (KN). Moreover, mitochondrial genome analysis placed G. stocki within a well-supported clade and provided its phylogenetic context among related Sisoridae taxa. Genome-wide SNP analysis revealed strong population structuring. Pairwise FST values showed strong divergence between KPK and KN (FST = 0.175) and minimal differentiation between KK and KN (FST = 0.003). Nucleotide diversity was high in KK (0.0697) and KN (0.0646) but low in KPK (0.0256). KK and KN showed heterozygote deficits (FIS = 0.22, 0.11), whereas KPK showed excess heterozygosity (FIS = − 0.13), with genomic inbreeding highest in KK and lowest in KPK. Clustering analyses (PCA, ADMIXTURE, STRUCTURE) and a maximum likelihood tree grouped the populations into two distinct genetic clusters: one comprising KK and KN, and a second, highly divergent cluster represented by KPK. These results point to a long-term isolation of the KPK population, likely driven by geographic barriers. Therefore, we propose managing these clusters as separate management units (MUs). This study provides a genomic baseline for G. stocki’s genetically informed conservation and restoration plans.