Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveys
Sampling and sequencing marine environmental DNA (eDNA) provides a tool that can increase our ability to monitor biodiversity, but movement and mixing of eDNA after release from organisms before collection could affect our inference of species distributions. To assess how conditions at differing spa...
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PeerJ Inc.
2024-10-01
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| author | Ben Millard-Martin Kate Sheridan Evan Morien Matthew A. Lemay Margot Hessing-Lewis Rute B.G. Clemente-Carvalho Jennifer M. Sunday |
| author_facet | Ben Millard-Martin Kate Sheridan Evan Morien Matthew A. Lemay Margot Hessing-Lewis Rute B.G. Clemente-Carvalho Jennifer M. Sunday |
| author_sort | Ben Millard-Martin |
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| description | Sampling and sequencing marine environmental DNA (eDNA) provides a tool that can increase our ability to monitor biodiversity, but movement and mixing of eDNA after release from organisms before collection could affect our inference of species distributions. To assess how conditions at differing spatial scales influence the inferred species richness and compositional turnover, we conducted a paired eDNA metabarcoding and capture (beach seining) survey of fishes on the coast of British Columbia. We found more taxa were typically detected using eDNA compared to beach seining. eDNA identified more taxa with alternative habitat preferences, and this richness difference was greater in areas of high seawater movement, suggesting eDNA has a larger spatial grain influenced by water motion. By contrast, we found that eDNA consistently missed low biomass species present in seining surveys. Spatial turnover of communities surveyed using beach seining differed from that of the eDNA and was better explained by factors that vary at small (10–1000s meters) spatial scales. Specifically, vegetation cover and shoreline exposure explained most species turnover from seining, while eDNA turnover was not explained by those factors and showed a distance decay pattern (a change from 10% to 25% similarity from 2 km to 10 km of distance), suggesting unmeasured environmental variation at larger scales drives its turnover. Our findings indicate that the eDNA sample grain is larger than that of capture surveys. Whereas seining can detect differences in fish distributions at scales of 10s–100s of meters, eDNA can best summarize fish biodiversity at larger scales possibly more relevant to regional biodiversity assessments. |
| format | Article |
| id | doaj-art-316acd35888541cc8dcfacba6aeb71da |
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| language | English |
| publishDate | 2024-10-01 |
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| spelling | doaj-art-316acd35888541cc8dcfacba6aeb71da2025-08-20T02:17:10ZengPeerJ Inc.PeerJ2167-83592024-10-0112e1796710.7717/peerj.17967Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveysBen Millard-Martin0Kate Sheridan1Evan Morien2Matthew A. Lemay3Margot Hessing-Lewis4Rute B.G. Clemente-Carvalho5Jennifer M. Sunday6Department of Biology, McGill University, Montreal, Quebec, CanadaDepartment of Biology, McGill University, Montreal, Quebec, CanadaDepartment of Biodiversity, Hakai Institute, Victoria, British Columbia, CanadaDepartment of Biodiversity, Hakai Institute, Victoria, British Columbia, CanadaDepartment of Biodiversity, Hakai Institute, Victoria, British Columbia, CanadaDepartment of Biodiversity, Hakai Institute, Victoria, British Columbia, CanadaDepartment of Biology, McGill University, Montreal, Quebec, CanadaSampling and sequencing marine environmental DNA (eDNA) provides a tool that can increase our ability to monitor biodiversity, but movement and mixing of eDNA after release from organisms before collection could affect our inference of species distributions. To assess how conditions at differing spatial scales influence the inferred species richness and compositional turnover, we conducted a paired eDNA metabarcoding and capture (beach seining) survey of fishes on the coast of British Columbia. We found more taxa were typically detected using eDNA compared to beach seining. eDNA identified more taxa with alternative habitat preferences, and this richness difference was greater in areas of high seawater movement, suggesting eDNA has a larger spatial grain influenced by water motion. By contrast, we found that eDNA consistently missed low biomass species present in seining surveys. Spatial turnover of communities surveyed using beach seining differed from that of the eDNA and was better explained by factors that vary at small (10–1000s meters) spatial scales. Specifically, vegetation cover and shoreline exposure explained most species turnover from seining, while eDNA turnover was not explained by those factors and showed a distance decay pattern (a change from 10% to 25% similarity from 2 km to 10 km of distance), suggesting unmeasured environmental variation at larger scales drives its turnover. Our findings indicate that the eDNA sample grain is larger than that of capture surveys. Whereas seining can detect differences in fish distributions at scales of 10s–100s of meters, eDNA can best summarize fish biodiversity at larger scales possibly more relevant to regional biodiversity assessments.https://peerj.com/articles/17967.pdfeDNA metabarcodingBiodiversityMarineBeach seineFishSpatial scale |
| spellingShingle | Ben Millard-Martin Kate Sheridan Evan Morien Matthew A. Lemay Margot Hessing-Lewis Rute B.G. Clemente-Carvalho Jennifer M. Sunday Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveys PeerJ eDNA metabarcoding Biodiversity Marine Beach seine Fish Spatial scale |
| title | Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveys |
| title_full | Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveys |
| title_fullStr | Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveys |
| title_full_unstemmed | Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveys |
| title_short | Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveys |
| title_sort | effect of environmental dna sampling resolution in detecting nearshore fish biodiversity compared to capture surveys |
| topic | eDNA metabarcoding Biodiversity Marine Beach seine Fish Spatial scale |
| url | https://peerj.com/articles/17967.pdf |
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