Tags

Type your tag names separated by a space and hit enter

Refinement of eDNA as an early monitoring tool at the landscape-level: study design considerations.
Ecol Appl. 2019 09; 29(6):e01951.EA

Abstract

Natural resource managers use data on the spatial range of species to guide management decisions. These data come from survey or monitoring efforts that use a wide variety of tools. Environmental DNA (eDNA) is a surveillance tool that uses genetic markers for detecting species and holds potential as a tool for large-scale monitoring programs. Two challenges of eDNA-based studies are uncertainties created by imperfect capture of eDNA in collection samples (e.g., water field samples) and imperfect detection of eDNA using molecular methods (e.g., quantitative PCR). Occurrence models can be used to address these challenges, thus we use an occurrence model to address two objectives: first, to determine how many samples were required to detect species using eDNA; second, to examine when and where to take samples. We collected water samples from three different habitat types in the Upper Mississippi River when both Bighead Carp and Silver Carp were known to be present based on telemetry detections. Each habitat type (backwater, tributary, and impoundment) was sampled during April, May, and November. Detections of eDNA for both species varied across sites and months, but were generally low, 0-19.3% of samples were positive for eDNA. Overall, we found that eDNA-based sampling holds promise to be a powerful monitoring tool for resource managers; however, limitations of eDNA-based sampling include different biological and ecological characteristics of target species such as seasonal habitat usage patterns as well as aspects of different physical environments that impact the implementation of these methods such as water temperature.

Authors+Show Affiliations

Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.Upper Midwest Environmental Sciences Center, U.S. Geological Service, 2630 Fanta Reed Road, La Crosse, Wisconsin, 54603, USA.Upper Midwest Environmental Sciences Center, U.S. Geological Service, 2630 Fanta Reed Road, La Crosse, Wisconsin, 54603, USA.Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.La Crosse Fish and Wildlife Conservation Office, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.La Crosse Fish and Wildlife Conservation Office, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.Upper Midwest Environmental Sciences Center, U.S. Geological Service, 2630 Fanta Reed Road, La Crosse, Wisconsin, 54603, USA.Midwest Region, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.La Crosse Fish and Wildlife Conservation Office, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA.

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

31188494

Citation

Mize, E L., et al. "Refinement of eDNA as an Early Monitoring Tool at the Landscape-level: Study Design Considerations." Ecological Applications : a Publication of the Ecological Society of America, vol. 29, no. 6, 2019, pp. e01951.
Mize EL, Erickson RA, Merkes CM, et al. Refinement of eDNA as an early monitoring tool at the landscape-level: study design considerations. Ecol Appl. 2019;29(6):e01951.
Mize, E. L., Erickson, R. A., Merkes, C. M., Berndt, N., Bockrath, K., Credico, J., Grueneis, N., Merry, J., Mosel, K., Tuttle-Lau, M., Von Ruden, K., Woiak, Z., Amberg, J. J., Baerwaldt, K., Finney, S., & Monroe, E. (2019). Refinement of eDNA as an early monitoring tool at the landscape-level: study design considerations. Ecological Applications : a Publication of the Ecological Society of America, 29(6), e01951. https://doi.org/10.1002/eap.1951
Mize EL, et al. Refinement of eDNA as an Early Monitoring Tool at the Landscape-level: Study Design Considerations. Ecol Appl. 2019;29(6):e01951. PubMed PMID: 31188494.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Refinement of eDNA as an early monitoring tool at the landscape-level: study design considerations. AU - Mize,E L, AU - Erickson,R A, AU - Merkes,C M, AU - Berndt,N, AU - Bockrath,K, AU - Credico,J, AU - Grueneis,N, AU - Merry,J, AU - Mosel,K, AU - Tuttle-Lau,M, AU - Von Ruden,K, AU - Woiak,Z, AU - Amberg,J J, AU - Baerwaldt,K, AU - Finney,S, AU - Monroe,E, Y1 - 2019/07/16/ PY - 2018/09/07/received PY - 2019/02/19/revised PY - 2019/05/17/accepted PY - 2019/6/13/pubmed PY - 2019/10/12/medline PY - 2019/6/13/entrez KW - Asian carp KW - bighead carp KW - environmental DNA KW - experimental design KW - invasive species KW - occupancy/occurrence models KW - silver carp SP - e01951 EP - e01951 JF - Ecological applications : a publication of the Ecological Society of America JO - Ecol Appl VL - 29 IS - 6 N2 - Natural resource managers use data on the spatial range of species to guide management decisions. These data come from survey or monitoring efforts that use a wide variety of tools. Environmental DNA (eDNA) is a surveillance tool that uses genetic markers for detecting species and holds potential as a tool for large-scale monitoring programs. Two challenges of eDNA-based studies are uncertainties created by imperfect capture of eDNA in collection samples (e.g., water field samples) and imperfect detection of eDNA using molecular methods (e.g., quantitative PCR). Occurrence models can be used to address these challenges, thus we use an occurrence model to address two objectives: first, to determine how many samples were required to detect species using eDNA; second, to examine when and where to take samples. We collected water samples from three different habitat types in the Upper Mississippi River when both Bighead Carp and Silver Carp were known to be present based on telemetry detections. Each habitat type (backwater, tributary, and impoundment) was sampled during April, May, and November. Detections of eDNA for both species varied across sites and months, but were generally low, 0-19.3% of samples were positive for eDNA. Overall, we found that eDNA-based sampling holds promise to be a powerful monitoring tool for resource managers; however, limitations of eDNA-based sampling include different biological and ecological characteristics of target species such as seasonal habitat usage patterns as well as aspects of different physical environments that impact the implementation of these methods such as water temperature. SN - 1051-0761 UR - https://www.unboundmedicine.com/medline/citation/31188494/Refinement_of_eDNA_as_an_early_monitoring_tool_at_the_landscape_level:_study_design_considerations_ L2 - https://onlinelibrary.wiley.com/resolve/openurl?genre=article&sid=nlm:pubmed&issn=1051-0761&date=2019&volume=29&issue=6&spage=e01951 DB - PRIME DP - Unbound Medicine ER -