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<p>Carmine shiner <i>Notropis percobromus</i> is a small minnow found throughout the eastern USA, but its known distribution in Canada is limited to southeastern Manitoba. Listed as Endangered on Canada’s <i>Species at Risk Act</i> (SARA), it has been the focus of targeted sampling by Fisheries and Oceans Canada, and continued monitoring is important to test for (1) potential range contractions due to habitat loss and pollution and (2) a northward shift in distribution with climate change. To complement traditional capture-based sampling, we developed and validated a species-specific TaqMan probe-based quantitative PCR environmental DNA (eDNA) assay targeting a 137-base pair fragment of the mitochondrial cytochrome <i>b</i> gene. Genetic sequences from 50 non-target cypriniform species were used in silico to design the putative species-specific assay, and in vitro testing using tissue-derived DNA from 15 other leuciscid species in Manitoba confirmed amplification only with carmine shiner DNA. Field testing within and adjacent to the known range of carmine shiner in the Winnipeg River system yielded results consistent with collection records of the species, with eDNA detected in the Whitemouth, Birch, and Boggy rivers and no detections outside the known range. This assay therefore offers a non-invasive method for inferring the presence of this endangered fish; it can be used in a complementary manner with capture-based sampling to inform on changes in distribution (e.g., to non-invasively survey in peripheral areas of the species’ range and at sites of greater concern for anthropogenic disturbance), with confirmatory capture-based sampling focusing on relative abundance and population trends.</p>

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Species-specific environmental DNA (eDNA) assay for monitoring the distribution of the endangered carmine shiner Notropis percobromus in Manitoba

  • 期刊论文

  • 发表日期：

    2026年4月30日

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  • Arfa A. Khan,
  • Brooklynne L. M. Keber,
  • Kasidy G. Harder,
  • Jessie L. Ogden,
  • Margaret F. Docker

摘要

Carmine shiner Notropis percobromus is a small minnow found throughout the eastern USA, but its known distribution in Canada is limited to southeastern Manitoba. Listed as Endangered on Canada’s Species at Risk Act (SARA), it has been the focus of targeted sampling by Fisheries and Oceans Canada, and continued monitoring is important to test for (1) potential range contractions due to habitat loss and pollution and (2) a northward shift in distribution with climate change. To complement traditional capture-based sampling, we developed and validated a species-specific TaqMan probe-based quantitative PCR environmental DNA (eDNA) assay targeting a 137-base pair fragment of the mitochondrial cytochrome b gene. Genetic sequences from 50 non-target cypriniform species were used in silico to design the putative species-specific assay, and in vitro testing using tissue-derived DNA from 15 other leuciscid species in Manitoba confirmed amplification only with carmine shiner DNA. Field testing within and adjacent to the known range of carmine shiner in the Winnipeg River system yielded results consistent with collection records of the species, with eDNA detected in the Whitemouth, Birch, and Boggy rivers and no detections outside the known range. This assay therefore offers a non-invasive method for inferring the presence of this endangered fish; it can be used in a complementary manner with capture-based sampling to inform on changes in distribution (e.g., to non-invasively survey in peripheral areas of the species’ range and at sites of greater concern for anthropogenic disturbance), with confirmatory capture-based sampling focusing on relative abundance and population trends.