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<p>Most Atlantic salmon (<i>Salmo salar</i>) populations across the North Atlantic have declined in recent decades, increasingly prompting consideration of supplementation activities and their genetic consequences. Paramount to any potential intervention is a robust understanding of the scale of remaining genetic diversity within a given habitat and an exploration of potential causes of decline. Atlantic salmon within the Conne River in southern Newfoundland, Canada, once one of the largest populations in the region, have declined by more than 90% since the late 1980s with no definitive explanation. Here we evaluate the fine-scale genetic structure of Atlantic salmon across the Conne River watershed (drainage area ~ 602 km<sup>2</sup>) using a 220&#xa0;K single nucleotide polymorphism (SNP) array, explore evidence for a role of domestic introgression in population decline, and reconstruct demographic trends in this population over the last 1000 years. Despite ongoing declines, our analysis suggests structuring across the watershed remains (average <i>F</i><sub>ST</sub> = 0.013) with a significant pattern of isolation by distance detected (R<sup>2</sup> = 0.75, <i>p</i> &lt; 0.0001). Furthermore, comparison with representative aquaculture samples suggest that the introgression of aquaculture salmon of both North American and European ancestry has occurred in the lower portion of the watershed. Genomic reconstructions of temporal trends in effective population size suggest pervasive watershed-wide declines over recent decades consistent with demographic monitoring. Our results demonstrate the utility of genomic tools to directly inform restoration efforts in this and other threatened species allowing a characterization of population spatial and temporal status as well as informing on potential causes of decline.</p>

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Fine-scale genomic differentiation remains despite massive demographic decline in an endangered Atlantic salmon (Salmo salar) population

  • 期刊论文

  • 发表日期：

    2025年11月27日

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  • I. R. Bradbury,
  • T. Kess,
  • B. Langille,
  • S. Duffy,
  • S. J. Lehnert,
  • M Van Wyngaarden,
  • Beth Watson,
  • R. Hinks,
  • T. Van Leeuwen,
  • J. B. Dempson

摘要

Most Atlantic salmon (Salmo salar) populations across the North Atlantic have declined in recent decades, increasingly prompting consideration of supplementation activities and their genetic consequences. Paramount to any potential intervention is a robust understanding of the scale of remaining genetic diversity within a given habitat and an exploration of potential causes of decline. Atlantic salmon within the Conne River in southern Newfoundland, Canada, once one of the largest populations in the region, have declined by more than 90% since the late 1980s with no definitive explanation. Here we evaluate the fine-scale genetic structure of Atlantic salmon across the Conne River watershed (drainage area ~ 602 km2) using a 220 K single nucleotide polymorphism (SNP) array, explore evidence for a role of domestic introgression in population decline, and reconstruct demographic trends in this population over the last 1000 years. Despite ongoing declines, our analysis suggests structuring across the watershed remains (average FST = 0.013) with a significant pattern of isolation by distance detected (R2 = 0.75, p < 0.0001). Furthermore, comparison with representative aquaculture samples suggest that the introgression of aquaculture salmon of both North American and European ancestry has occurred in the lower portion of the watershed. Genomic reconstructions of temporal trends in effective population size suggest pervasive watershed-wide declines over recent decades consistent with demographic monitoring. Our results demonstrate the utility of genomic tools to directly inform restoration efforts in this and other threatened species allowing a characterization of population spatial and temporal status as well as informing on potential causes of decline.