Developing Detection Probabilities and Quantifying the Effects of Flowing Water to Improve Invasive Carp Environmental DNA (eDNA) Surveys
Invasive carp are problematic for native species, and managers are implementing control measures without well-quantified detection limits or a means to assess the accuracy and precision of existing or future survey data for the fish. Environmental DNA - eDNA - is already used to detect the presence of invasive species, and can be used to identify locations to focus carp control efforts.
The Science Issue and Relevance: Invasive carp, by virtue of their voracious herbivorous habits and behavior, perturb habitats and cause extensive changes to aquatic macrophytes communities, leading to dramatic ecosystem alteration, detrimental effects on waterfowl populations, and changes in food-web structure of native fish, invertebrate, and plant communities. These invasive carp have also been documented to have negative impacts on native species, including imperiled species. As hosts to many pathogens that include parasites, disease-causing microorganisms, and viruses, invasive carps pose a serious threat to native species. Resource managers are implementing control measures for carp without well-quantified detection limits or a statistical framework to assess the accuracy and precision of existing or new survey data. Enhancing early detection of invasive carp in water bodies is desirable by resource managers for increasing the timeliness of eradication and/or exclusion efforts and by monitoring the success of those efforts. Being able to obtain probabilities of detection would allow scientists to place confidence values on invasive species’ presence in the environment.
Environmental DNA (eDNA) methods are widely used to detect the presence or absence of invasive species at low densities, especially when traditional field methods are inadequate or less effective. These detections are already being used in critical management actions of many aquatic species. Improved eDNA detection of carp can be used to identify locations for concentrating control measures where grass carp are illegally breeding or not approved for biocontrol use. The Invasive Carp Regional Coordinating Committee uses eDNA in the Monitoring and Rapid Response Plan as a surveillance tool to detect the presence of invasive carp throughout the Chicago Area Waterway System. Early monitoring programs and Rapid Response Plans are recommended for feral introductions and range expansions. The Invasive Carp Control Strategy Framework indicates that an important management action is eDNA technology refinement and monitoring.
Methodology for Addressing the Issue: During the course of this research, minimum eDNA detection thresholds for grass carp (Ctenopharyngodon idella) will be quantified in laboratories and mesocosms at the WARC in Gainesville, Florida. A focus will be to quantify what effects water velocity, depth, and turbidity have on eDNA detection under various flow conditions. From detection threshold data, occupancy models will be developed to evaluate the reliability of the sampling methods and obtain confidence values on the presence or absence of the grass carp. The grass carp was chosen for eDNA occupancy model development due to its high-density and broad distribution in the southeastern U.S. Genetics laboratory analyses will lead to the development of grass carp qPCR primers, eDNA detection threshold parameters in a laboratory and mesocosm setting, and determination of the parameters that influence the accuracy of detection, all necessary for an initial occupancy model that accounts for variables. Laboratory and mesocosm phases of the study will be conducted concurrently to address the detection limits and the environmental variables that influence eDNA detection.
Specifically, precise DNA concentrations and water sample volumes will be used to develop species-specific primers and experimental parameter thresholds. This phase will be conducted in controlled laboratory facilities (e.g., tanks) to avoid the confounding influence of variables found in natural settings. Experimental parameters will be manipulated during a subsequent phase in mesocosm tanks to test the reliability of the methods in near-natural conditions, with and without flowing water. Known quantities of DNA and live fish will be used in tanks of estimated volumes. In both phases, water will be filtered for eDNA, then highly-sensitive, quantitative PCR (qPCR) will be used to detect the presence of grass carp DNA.
Data from the minimum detection threshold experiments will be used to develop occupancy models. Statistical models of site-occupancy will be extended to provide estimates of the probability of occurrence of eDNA molecules, the probability of false-negatives (given eDNA presence), and the probability of false-positives (given eDNA absence). Each of these probabilities will be specified as functions of covariates so that the effects of experimental treatments on each probability can be estimated directly. In this way we will estimate the temporal persistence of eDNA and the effects of stream flow rate (moving vs. still water) on eDNA persistence. We also anticipate being able to estimate the concentration of eDNA using repeated detections -- and nondetections -- of eDNA collected in different subsample volumes. Ultimately, we expect these analyses will be useful in estimating the biomass or abundance of fish in an area, the persistence of sloughed DNA in the environment, and the distance and time that DNA can be detected downstream of the targeted species.
Future Steps: The independent variables will also be tested in the laboratory, mesocosm, and field. The depth and structure (including eddies) of the waterbody will be considered. Important parameters that will be addressed in the future include DNA degradation rates at variable temperatures and DNA release rates for fish of various sizes over time.
Invasive carp are problematic for native species, and managers are implementing control measures without well-quantified detection limits or a means to assess the accuracy and precision of existing or future survey data for the fish. Environmental DNA - eDNA - is already used to detect the presence of invasive species, and can be used to identify locations to focus carp control efforts.
The Science Issue and Relevance: Invasive carp, by virtue of their voracious herbivorous habits and behavior, perturb habitats and cause extensive changes to aquatic macrophytes communities, leading to dramatic ecosystem alteration, detrimental effects on waterfowl populations, and changes in food-web structure of native fish, invertebrate, and plant communities. These invasive carp have also been documented to have negative impacts on native species, including imperiled species. As hosts to many pathogens that include parasites, disease-causing microorganisms, and viruses, invasive carps pose a serious threat to native species. Resource managers are implementing control measures for carp without well-quantified detection limits or a statistical framework to assess the accuracy and precision of existing or new survey data. Enhancing early detection of invasive carp in water bodies is desirable by resource managers for increasing the timeliness of eradication and/or exclusion efforts and by monitoring the success of those efforts. Being able to obtain probabilities of detection would allow scientists to place confidence values on invasive species’ presence in the environment.
Environmental DNA (eDNA) methods are widely used to detect the presence or absence of invasive species at low densities, especially when traditional field methods are inadequate or less effective. These detections are already being used in critical management actions of many aquatic species. Improved eDNA detection of carp can be used to identify locations for concentrating control measures where grass carp are illegally breeding or not approved for biocontrol use. The Invasive Carp Regional Coordinating Committee uses eDNA in the Monitoring and Rapid Response Plan as a surveillance tool to detect the presence of invasive carp throughout the Chicago Area Waterway System. Early monitoring programs and Rapid Response Plans are recommended for feral introductions and range expansions. The Invasive Carp Control Strategy Framework indicates that an important management action is eDNA technology refinement and monitoring.
Methodology for Addressing the Issue: During the course of this research, minimum eDNA detection thresholds for grass carp (Ctenopharyngodon idella) will be quantified in laboratories and mesocosms at the WARC in Gainesville, Florida. A focus will be to quantify what effects water velocity, depth, and turbidity have on eDNA detection under various flow conditions. From detection threshold data, occupancy models will be developed to evaluate the reliability of the sampling methods and obtain confidence values on the presence or absence of the grass carp. The grass carp was chosen for eDNA occupancy model development due to its high-density and broad distribution in the southeastern U.S. Genetics laboratory analyses will lead to the development of grass carp qPCR primers, eDNA detection threshold parameters in a laboratory and mesocosm setting, and determination of the parameters that influence the accuracy of detection, all necessary for an initial occupancy model that accounts for variables. Laboratory and mesocosm phases of the study will be conducted concurrently to address the detection limits and the environmental variables that influence eDNA detection.
Specifically, precise DNA concentrations and water sample volumes will be used to develop species-specific primers and experimental parameter thresholds. This phase will be conducted in controlled laboratory facilities (e.g., tanks) to avoid the confounding influence of variables found in natural settings. Experimental parameters will be manipulated during a subsequent phase in mesocosm tanks to test the reliability of the methods in near-natural conditions, with and without flowing water. Known quantities of DNA and live fish will be used in tanks of estimated volumes. In both phases, water will be filtered for eDNA, then highly-sensitive, quantitative PCR (qPCR) will be used to detect the presence of grass carp DNA.
Data from the minimum detection threshold experiments will be used to develop occupancy models. Statistical models of site-occupancy will be extended to provide estimates of the probability of occurrence of eDNA molecules, the probability of false-negatives (given eDNA presence), and the probability of false-positives (given eDNA absence). Each of these probabilities will be specified as functions of covariates so that the effects of experimental treatments on each probability can be estimated directly. In this way we will estimate the temporal persistence of eDNA and the effects of stream flow rate (moving vs. still water) on eDNA persistence. We also anticipate being able to estimate the concentration of eDNA using repeated detections -- and nondetections -- of eDNA collected in different subsample volumes. Ultimately, we expect these analyses will be useful in estimating the biomass or abundance of fish in an area, the persistence of sloughed DNA in the environment, and the distance and time that DNA can be detected downstream of the targeted species.
Future Steps: The independent variables will also be tested in the laboratory, mesocosm, and field. The depth and structure (including eddies) of the waterbody will be considered. Important parameters that will be addressed in the future include DNA degradation rates at variable temperatures and DNA release rates for fish of various sizes over time.