Experimental assessment of optimal lotic eDNA sampling and assay multiplexing for a critically endangered fish
Abstract Designing eDNA tools to detect and quantify rare species includes inherent assumptions about the spatial distribution of the organism, spatial nature of eDNA dynamics, and the real‐world performance of alternate assays under field conditions. Here, we use cage experiments with small numbers...
Published in: | Environmental DNA |
---|---|
Main Authors: | , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Wiley
2020
|
Subjects: | |
Online Access: | https://doi.org/10.1002/edn3.64 https://doaj.org/article/65898899eb0c442895323131918704d6 |
id |
ftdoajarticles:oai:doaj.org/article:65898899eb0c442895323131918704d6 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:65898899eb0c442895323131918704d6 2023-05-15T15:32:31+02:00 Experimental assessment of optimal lotic eDNA sampling and assay multiplexing for a critically endangered fish Zachary T. Wood Bradley F. Erdman Geneva York Joan G. Trial Michael T. Kinnison 2020-10-01T00:00:00Z https://doi.org/10.1002/edn3.64 https://doaj.org/article/65898899eb0c442895323131918704d6 EN eng Wiley https://doi.org/10.1002/edn3.64 https://doaj.org/toc/2637-4943 2637-4943 doi:10.1002/edn3.64 https://doaj.org/article/65898899eb0c442895323131918704d6 Environmental DNA, Vol 2, Iss 4, Pp 407-417 (2020) eDNA multiplexing environmental DNA population abundance Salmo salar species detection stream eDNA Environmental sciences GE1-350 Microbial ecology QR100-130 article 2020 ftdoajarticles https://doi.org/10.1002/edn3.64 2022-12-31T11:29:31Z Abstract Designing eDNA tools to detect and quantify rare species includes inherent assumptions about the spatial distribution of the organism, spatial nature of eDNA dynamics, and the real‐world performance of alternate assays under field conditions. Here, we use cage experiments with small numbers of Atlantic salmon (Salmo salar), to reveal that eDNA detection rates and eDNA quantities follow a predictable, but nonlinear relationship with distance from a point source. In contrast to the common assumption of consistent eDNA degradation moving away from a source, eDNA detections and concentrations increased up to roughly 70 m downstream before declining steadily. We apply our eDNA distance functions to selection of stream sampling intervals for detecting fish without known locations and find that even a single juvenile salmon can be reliably detected with intervals up to 400 m spacing. Finally, we show that two different qPCR eDNA assays provide very different detection probabilities in nature despite similar efficiency in laboratory testing, demonstrating the importance of experimentally assessing assay efficiencies in the wild as well as the capacity for multiplexing as a strategy to ensure high detection efficiency when monitoring rare species. Article in Journal/Newspaper Atlantic salmon Salmo salar Directory of Open Access Journals: DOAJ Articles Environmental DNA 2 4 407 417 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
eDNA multiplexing environmental DNA population abundance Salmo salar species detection stream eDNA Environmental sciences GE1-350 Microbial ecology QR100-130 |
spellingShingle |
eDNA multiplexing environmental DNA population abundance Salmo salar species detection stream eDNA Environmental sciences GE1-350 Microbial ecology QR100-130 Zachary T. Wood Bradley F. Erdman Geneva York Joan G. Trial Michael T. Kinnison Experimental assessment of optimal lotic eDNA sampling and assay multiplexing for a critically endangered fish |
topic_facet |
eDNA multiplexing environmental DNA population abundance Salmo salar species detection stream eDNA Environmental sciences GE1-350 Microbial ecology QR100-130 |
description |
Abstract Designing eDNA tools to detect and quantify rare species includes inherent assumptions about the spatial distribution of the organism, spatial nature of eDNA dynamics, and the real‐world performance of alternate assays under field conditions. Here, we use cage experiments with small numbers of Atlantic salmon (Salmo salar), to reveal that eDNA detection rates and eDNA quantities follow a predictable, but nonlinear relationship with distance from a point source. In contrast to the common assumption of consistent eDNA degradation moving away from a source, eDNA detections and concentrations increased up to roughly 70 m downstream before declining steadily. We apply our eDNA distance functions to selection of stream sampling intervals for detecting fish without known locations and find that even a single juvenile salmon can be reliably detected with intervals up to 400 m spacing. Finally, we show that two different qPCR eDNA assays provide very different detection probabilities in nature despite similar efficiency in laboratory testing, demonstrating the importance of experimentally assessing assay efficiencies in the wild as well as the capacity for multiplexing as a strategy to ensure high detection efficiency when monitoring rare species. |
format |
Article in Journal/Newspaper |
author |
Zachary T. Wood Bradley F. Erdman Geneva York Joan G. Trial Michael T. Kinnison |
author_facet |
Zachary T. Wood Bradley F. Erdman Geneva York Joan G. Trial Michael T. Kinnison |
author_sort |
Zachary T. Wood |
title |
Experimental assessment of optimal lotic eDNA sampling and assay multiplexing for a critically endangered fish |
title_short |
Experimental assessment of optimal lotic eDNA sampling and assay multiplexing for a critically endangered fish |
title_full |
Experimental assessment of optimal lotic eDNA sampling and assay multiplexing for a critically endangered fish |
title_fullStr |
Experimental assessment of optimal lotic eDNA sampling and assay multiplexing for a critically endangered fish |
title_full_unstemmed |
Experimental assessment of optimal lotic eDNA sampling and assay multiplexing for a critically endangered fish |
title_sort |
experimental assessment of optimal lotic edna sampling and assay multiplexing for a critically endangered fish |
publisher |
Wiley |
publishDate |
2020 |
url |
https://doi.org/10.1002/edn3.64 https://doaj.org/article/65898899eb0c442895323131918704d6 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Environmental DNA, Vol 2, Iss 4, Pp 407-417 (2020) |
op_relation |
https://doi.org/10.1002/edn3.64 https://doaj.org/toc/2637-4943 2637-4943 doi:10.1002/edn3.64 https://doaj.org/article/65898899eb0c442895323131918704d6 |
op_doi |
https://doi.org/10.1002/edn3.64 |
container_title |
Environmental DNA |
container_volume |
2 |
container_issue |
4 |
container_start_page |
407 |
op_container_end_page |
417 |
_version_ |
1766363011567583232 |