A species-specific digital PCR assay for the endangered blue racer ( Coluber constrictor foxii ) in Canada
The only population of the endangered blue racer ( ) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including habitat degradation and loss, road mortality, persecution, and potentially predation. We designed and evaluated the performance of an environmental...
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Published in | Genome Vol. 66; no. 9; pp. 251 - 260 |
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Main Authors | , , , , |
Format | Journal Article |
Language | English |
Published |
Canada
NRC Research Press
01.09.2023
Canadian Science Publishing NRC Research Press |
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Abstract | The only population of the endangered blue racer (
) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including habitat degradation and loss, road mortality, persecution, and potentially predation. We designed and evaluated the performance of an environmental DNA droplet digital PCR assay that can be used for multiple facets of conservation of this species. We tested the assay
and
using DNA of blue racers and co-occurring snake species and estimated the LOD and LOQ using synthetic DNA. As wild turkey predation has been suggested to negatively affect racers, we tested the assay on eight wild turkey faecal samples. Our assay is specific, can detect the target species at very low levels of concentration (0.002 copies/µL), and can accurately quantify copy numbers ≥ 0.26 copies/µL. We detected no racer DNA in any wild turkey faecal sample. More faecal samples collected at strategic locations during snake peak activity on Pelee Island would enable a more thorough assessment of the possibility of turkey predation. Our assay should be effective for other environmental samples and can be used for investigating other factors negatively affecting blue racers, for example, helping to quantify blue racer habitat suitability and site occupancy. |
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AbstractList | The only population of the endangered blue racer ( Coluber constrictor foxii) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including habitat degradation and loss, road mortality, persecution, and potentially predation. We designed and evaluated the performance of an environmental DNA droplet digital PCR assay that can be used for multiple facets of conservation of this species. We tested the assay in silico and in vitro using DNA of blue racers and co-occurring snake species and estimated the LOD and LOQ using synthetic DNA. As wild turkey predation has been suggested to negatively affect racers, we tested the assay on eight wild turkey faecal samples. Our assay is specific, can detect the target species at very low levels of concentration (0.002 copies/µL), and can accurately quantify copy numbers ≥ 0.26 copies/µL. We detected no racer DNA in any wild turkey faecal sample. More faecal samples collected at strategic locations during snake peak activity on Pelee Island would enable a more thorough assessment of the possibility of turkey predation. Our assay should be effective for other environmental samples and can be used for investigating other factors negatively affecting blue racers, for example, helping to quantify blue racer habitat suitability and site occupancy. The only population of the endangered blue racer (Coluber constrictor foxii) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including habitat degradation and loss, road mortality, persecution, and potentially predation. We designed and evaluated the performance of an environmental DNA droplet digital PCR assay that can be used for multiple facets of conservation of this species. We tested the assay in silico and in vitro using DNA of blue racers and co-occurring snake species and estimated the LOD and LOQ using synthetic DNA. As wild turkey predation has been suggested to negatively afect racers, we tested the assay on eight wild turkey faecal samples. Our assay is specific, can detect the target species at very low levels of concentration (0.002 copies/[micro]L), and can accurately quantify copy numbers [greater than or equal to] 0.26 copies/[micro]L. We detected no racer DNA in any wild turkey faecal sample. More faecal samples collected at strategic locations during snake peak activity on Pelee Island would enable a more thorough assessment of the possibility of turkey predation. Our assay should be effective for other environmental samples and can be used for investigating other factors negatively affecting blue racers, for example, helping to quantify blue racer habitat suitability and site occupancy. The only population of the endangered blue racer (Coluber constrictor foxii) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including habitat degradation and loss, road mortality, persecution, and potentially predation. We designed and evaluated the performance of an environmental DNA droplet digital PCR assay that can be used for multiple facets of conservation of this species. We tested the assay in silico and in vitro using DNA of blue racers and co-occurring snake species and estimated the LOD and LOQ using synthetic DNA. As wild turkey predation has been suggested to negatively afect racers, we tested the assay on eight wild turkey faecal samples. Our assay is specific, can detect the target species at very low levels of concentration (0.002 copies/[micro]L), and can accurately quantify copy numbers [greater than or equal to] 0.26 copies/[micro]L. We detected no racer DNA in any wild turkey faecal sample. More faecal samples collected at strategic locations during snake peak activity on Pelee Island would enable a more thorough assessment of the possibility of turkey predation. Our assay should be effective for other environmental samples and can be used for investigating other factors negatively affecting blue racers, for example, helping to quantify blue racer habitat suitability and site occupancy. Key words: environmental DNA, reptile, conservation, droplet digital PCR The only population of the endangered blue racer ( ) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including habitat degradation and loss, road mortality, persecution, and potentially predation. We designed and evaluated the performance of an environmental DNA droplet digital PCR assay that can be used for multiple facets of conservation of this species. We tested the assay and using DNA of blue racers and co-occurring snake species and estimated the LOD and LOQ using synthetic DNA. As wild turkey predation has been suggested to negatively affect racers, we tested the assay on eight wild turkey faecal samples. Our assay is specific, can detect the target species at very low levels of concentration (0.002 copies/µL), and can accurately quantify copy numbers ≥ 0.26 copies/µL. We detected no racer DNA in any wild turkey faecal sample. More faecal samples collected at strategic locations during snake peak activity on Pelee Island would enable a more thorough assessment of the possibility of turkey predation. Our assay should be effective for other environmental samples and can be used for investigating other factors negatively affecting blue racers, for example, helping to quantify blue racer habitat suitability and site occupancy. |
Audience | Academic |
Author | McCurdy-Adams, Hannah Chabot, Amy A Lougheed, Stephen C Tournayre, Orianne Wolfe, Ryan |
Author_xml | – sequence: 1 givenname: Orianne orcidid: 0000-0002-0260-8189 surname: Tournayre fullname: Tournayre, Orianne organization: Biology Department, Queen's University, Kingston, ON K7L 3N6, Canada – sequence: 2 givenname: Ryan surname: Wolfe fullname: Wolfe, Ryan organization: Natural Resource Solutions Inc., Waterloo, ON N2L 3X2, Canada – sequence: 3 givenname: Hannah surname: McCurdy-Adams fullname: McCurdy-Adams, Hannah organization: Wildlife Preservation Canada, Guelph, ON N1H 6J2, Canada – sequence: 4 givenname: Amy A surname: Chabot fullname: Chabot, Amy A organization: African Lion Safari, Cambridge, ON N1R 5S2, Canada – sequence: 5 givenname: Stephen C surname: Lougheed fullname: Lougheed, Stephen C organization: Biology Department, Queen's University, Kingston, ON K7L 3N6, Canada |
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Snippet | The only population of the endangered blue racer (
) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including... The only population of the endangered blue racer ( Coluber constrictor foxii) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple... The only population of the endangered blue racer (Coluber constrictor foxii) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple... |
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SubjectTerms | Assaying Biochemical assays Coluber constrictor Colubrids Endangered species Environmental degradation Environmental DNA Feces Genetic aspects Methods Polymerase chain reaction Predation Protection and preservation Snakes Target detection Threatened species Wildlife conservation |
Title | A species-specific digital PCR assay for the endangered blue racer ( Coluber constrictor foxii ) in Canada |
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