eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada
Abstract Climate change is a critical threat to northern freshwater ecosystems, yet many remote areas are data deficient in terms of biodiversity information. Generating community composition data through collection of environmental DNA (eDNA) is less labor‐intensive than traditional sampling method...
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2024-01-01
|
| Series: | Environmental DNA |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/edn3.517 |
| _version_ | 1797277043663044608 |
|---|---|
| author | Samantha E. Crowley Paul Bentzen Tony Kess Steven J. Duffy Amber M. Messmer Beth Watson J. Brian Dempson Donald G. Keefe Robert C. Perry Benjamin Marquis Mehrdad Hajibabaei Nicole Fahner Lesley Berghuis Kerry Hobrecker Ian R. Bradbury |
| author_facet | Samantha E. Crowley Paul Bentzen Tony Kess Steven J. Duffy Amber M. Messmer Beth Watson J. Brian Dempson Donald G. Keefe Robert C. Perry Benjamin Marquis Mehrdad Hajibabaei Nicole Fahner Lesley Berghuis Kerry Hobrecker Ian R. Bradbury |
| author_sort | Samantha E. Crowley |
| collection | DOAJ |
| description | Abstract Climate change is a critical threat to northern freshwater ecosystems, yet many remote areas are data deficient in terms of biodiversity information. Generating community composition data through collection of environmental DNA (eDNA) is less labor‐intensive than traditional sampling methods and is being increasingly used in areas that have been historically difficult to sample such as northern freshwater habitats. Here, we employed eDNA metabarcoding using three mitochondrial markers at 174 coastal river sites, sampled over three years (2019–2021) across a broad region in northeastern North America, Newfoundland and Labrador. We characterized current riverine fish community composition, compared it to traditional sampling records, and quantified the influence of climate on variation in fish community composition. The analysis detected 33 fish species across the region (1–13 per location), including three non‐native species, as well as several new possible range expansions. Variance partitioning with redundancy analysis indicated ~56% of the variation in community composition could be explained by spatial and climate factors (~21% and ~7%, respectively, with an additional ~28% shared). A temporal comparison across a subset of locations with both eDNA and historical records (1965–1985) revealed that more species were detected on average with eDNA sampling, and that sampling method explained a small portion of the variation (~4%) in comparison with space (~10%) and climate (~7%). Ultimately, this work is the most complete survey of freshwater and diadromous fishes present in Newfoundland and Labrador to date, highlights new detections of non‐native species including previously unknown diversity for the region, and provides future direction for the application of eDNA analysis in northern riverine habitats. |
| first_indexed | 2024-03-07T15:37:58Z |
| format | Article |
| id | doaj.art-c2ddad5c8a25434383b351855f42d84e |
| institution | Directory Open Access Journal |
| issn | 2637-4943 |
| language | English |
| last_indexed | 2024-03-07T15:37:58Z |
| publishDate | 2024-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj.art-c2ddad5c8a25434383b351855f42d84e2024-03-05T09:32:37ZengWileyEnvironmental DNA2637-49432024-01-0161n/an/a10.1002/edn3.517eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern CanadaSamantha E. Crowley0Paul Bentzen1Tony Kess2Steven J. Duffy3Amber M. Messmer4Beth Watson5J. Brian Dempson6Donald G. Keefe7Robert C. Perry8Benjamin Marquis9Mehrdad Hajibabaei10Nicole Fahner11Lesley Berghuis12Kerry Hobrecker13Ian R. Bradbury14Department of Biology Dalhousie University Halifax Nova Scotia CanadaDepartment of Biology Dalhousie University Halifax Nova Scotia CanadaNorthwest Atlantic Fisheries Centre Fisheries and Oceans Canada St. John's Newfoundland and Labrador CanadaNorthwest Atlantic Fisheries Centre Fisheries and Oceans Canada St. John's Newfoundland and Labrador CanadaNorthwest Atlantic Fisheries Centre Fisheries and Oceans Canada St. John's Newfoundland and Labrador CanadaDepartment of Biology Dalhousie University Halifax Nova Scotia CanadaNorthwest Atlantic Fisheries Centre Fisheries and Oceans Canada St. John's Newfoundland and Labrador CanadaWildlife Division, Fisheries, Forestry and Agriculture Corner Brook Newfoundland and Labrador CanadaFish and Wildlife Division, Department of Environment Government of Yukon Whitehorse Yukon CanadaGreat Lakes Forestry Center, Natural Resources Canada Sault Ste Marie Ontario CanadaCentre for Environmental Genomics Applications eDNAtec Inc St. Johns Newfoundland and Labrador CanadaCentre for Environmental Genomics Applications eDNAtec Inc St. Johns Newfoundland and Labrador CanadaCentre for Environmental Genomics Applications eDNAtec Inc St. Johns Newfoundland and Labrador CanadaCentre for Environmental Genomics Applications eDNAtec Inc St. Johns Newfoundland and Labrador CanadaNorthwest Atlantic Fisheries Centre Fisheries and Oceans Canada St. John's Newfoundland and Labrador CanadaAbstract Climate change is a critical threat to northern freshwater ecosystems, yet many remote areas are data deficient in terms of biodiversity information. Generating community composition data through collection of environmental DNA (eDNA) is less labor‐intensive than traditional sampling methods and is being increasingly used in areas that have been historically difficult to sample such as northern freshwater habitats. Here, we employed eDNA metabarcoding using three mitochondrial markers at 174 coastal river sites, sampled over three years (2019–2021) across a broad region in northeastern North America, Newfoundland and Labrador. We characterized current riverine fish community composition, compared it to traditional sampling records, and quantified the influence of climate on variation in fish community composition. The analysis detected 33 fish species across the region (1–13 per location), including three non‐native species, as well as several new possible range expansions. Variance partitioning with redundancy analysis indicated ~56% of the variation in community composition could be explained by spatial and climate factors (~21% and ~7%, respectively, with an additional ~28% shared). A temporal comparison across a subset of locations with both eDNA and historical records (1965–1985) revealed that more species were detected on average with eDNA sampling, and that sampling method explained a small portion of the variation (~4%) in comparison with space (~10%) and climate (~7%). Ultimately, this work is the most complete survey of freshwater and diadromous fishes present in Newfoundland and Labrador to date, highlights new detections of non‐native species including previously unknown diversity for the region, and provides future direction for the application of eDNA analysis in northern riverine habitats.https://doi.org/10.1002/edn3.517climatecommunity compositionenvironmental DNAfishmetabarcoding |
| spellingShingle | Samantha E. Crowley Paul Bentzen Tony Kess Steven J. Duffy Amber M. Messmer Beth Watson J. Brian Dempson Donald G. Keefe Robert C. Perry Benjamin Marquis Mehrdad Hajibabaei Nicole Fahner Lesley Berghuis Kerry Hobrecker Ian R. Bradbury eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada Environmental DNA climate community composition environmental DNA fish metabarcoding |
| title | eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada |
| title_full | eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada |
| title_fullStr | eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada |
| title_full_unstemmed | eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada |
| title_short | eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada |
| title_sort | edna metabarcoding reveals riverine fish community structure and climate associations in northeastern canada |
| topic | climate community composition environmental DNA fish metabarcoding |
| url | https://doi.org/10.1002/edn3.517 |
| work_keys_str_mv | AT samanthaecrowley ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT paulbentzen ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT tonykess ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT stevenjduffy ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT ambermmessmer ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT bethwatson ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT jbriandempson ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT donaldgkeefe ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT robertcperry ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT benjaminmarquis ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT mehrdadhajibabaei ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT nicolefahner ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT lesleyberghuis ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT kerryhobrecker ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada AT ianrbradbury ednametabarcodingrevealsriverinefishcommunitystructureandclimateassociationsinnortheasterncanada |