Development and Implementation of Environmental DNA (eDNA) Tools to Aid Listing and Recovery Efforts for Imperiled and Common Freshwater Mussels
Researchers will develop and optimize an eDNA assay to delineate the current distribution of P. inflatus. The assay will then be used to provide up-to-date distributional information and detection rates for P. inflatus in the Pearl River basin.
The Science Issue and Relevance: Locating rare, stream-dwelling animals like freshwater mussels is much like looking for a needle in a haystack. Traditional survey methods used to find freshwater mussels are labor-intensive and often fail to locate target species (known as imperfect detection). Accurate distribution data of rare mussels can provide resource agencies, like the U.S. Fish and Wildlife Service (USFWS) and state fish and game agencies, with critical information for species management and recovery efforts. A recent technology known as environmental DNA, or eDNA, enables researchers to detect genetic material of rare and common aquatic species from water samples. The use of eDNA sampling techniques can complement traditional sampling methods, mitigating limitations due to imperfect detection of high-priority species that are at low abundance. Additionally, eDNA technologies offer us the opportunity to screen vast areas of historically occupied habitat to determine whether previously undetected viable populations persist or if these areas are suitable for reintroducing the species and reestablishing populations.
Research underway at the U.S. Geological Survey’s Wetland and Aquatic Research Center aims to develop eDNA tools to improve distributional information for the federally protected Inflated Heelsplitter, Potamilus inflatus (Figure 1). By using eDNA to detect P. inflatus, we can reduce the size of the “haystack” by focusing survey crews in areas where eDNA from the target species has been detected. Furthermore, eDNA allows us to rapidly evaluate the presence of P. inflatus in previously occupied areas to either a) locate natural, self-sustaining populations, or b) increase confidence that the species has been extirpated to better inform listing and recovery actions.
Currently, only three viable, self-sustaining populations remain for this species. Populations in the Amite River (Louisiana) are disjunct, and its loss would decrease the number of viable P. inflatus populations to a critical level. A historical population in the Pearl River (Louisiana and Mississippi) has been long considered extirpated due to a lack of detection in more than 26 years of tactile surveys. The USFWS recovery plan prioritizes the Pearl River population and provides strategies that could help remove the species from the Endangered Species Act. This makes confirming P. inflatus occurrence in the Pearl River a crucial piece of the conservation strategy.
Methodology for Addressing the Issue: Our project is comprised of two key segments. First, we will develop and optimize an eDNA assay to delineate the current distribution of P. inflatus utilizing molecular data for P. inflatus from the Lake Pontchartrain (Louisiana) and Mobile River (Alabama) basins. Using DNA libraries and a sound understanding of unionid taxonomy and DNA-based identification, we are designing and testing species-specific eDNA tools to detect the presence of P. inflatus DNA in water samples. Initial testing will utilize a traditional polymerase chain reaction (PCR). Once effective primers have been developed, we will migrate our assay to a quantitative real-time PCR assay (qPCR), and finally to a Droplet Digital PCR (ddPCR) system. The ddPCR technology increases the sensitivity of detection using absolute quantification, which enables us to count individual DNA molecules from our target species to better understand the proximity and densities of animals at each eDNA sampling location.
Secondly, we will use the optimized eDNA assay to provide up-to-date distributional information and detection rates for P. inflatus in the Pearl River basin. We will validate our assay at sites where P. inflatus is found and sample areas where contemporary distributions are unknown. Results from eDNA sampling will be used to update distribution maps for P. inflatus, which will be a useful tool for guiding management actions of federal and state wildlife management agencies and future eDNA or tactile survey sampling.
Future Steps: Our research will be an invaluable resource toward future conservation, management, and recovery strategies for populations of P. inflatus and can be used as a model study for other imperiled aquatic species. The USFWS is considering captive propagation and reintroduction as a strategy to increase abundance and expand the current range to assist in delisting P. inflatus. Our project facilitates the establishment of effective captive propagation and reintroduction programs by delineating the current distribution of P. inflatus, identifying areas suitable for reestablishment of populations, and providing baseline genetic characterization of wild populations for genetic management planning.
Researchers will develop and optimize an eDNA assay to delineate the current distribution of P. inflatus. The assay will then be used to provide up-to-date distributional information and detection rates for P. inflatus in the Pearl River basin.
The Science Issue and Relevance: Locating rare, stream-dwelling animals like freshwater mussels is much like looking for a needle in a haystack. Traditional survey methods used to find freshwater mussels are labor-intensive and often fail to locate target species (known as imperfect detection). Accurate distribution data of rare mussels can provide resource agencies, like the U.S. Fish and Wildlife Service (USFWS) and state fish and game agencies, with critical information for species management and recovery efforts. A recent technology known as environmental DNA, or eDNA, enables researchers to detect genetic material of rare and common aquatic species from water samples. The use of eDNA sampling techniques can complement traditional sampling methods, mitigating limitations due to imperfect detection of high-priority species that are at low abundance. Additionally, eDNA technologies offer us the opportunity to screen vast areas of historically occupied habitat to determine whether previously undetected viable populations persist or if these areas are suitable for reintroducing the species and reestablishing populations.
Research underway at the U.S. Geological Survey’s Wetland and Aquatic Research Center aims to develop eDNA tools to improve distributional information for the federally protected Inflated Heelsplitter, Potamilus inflatus (Figure 1). By using eDNA to detect P. inflatus, we can reduce the size of the “haystack” by focusing survey crews in areas where eDNA from the target species has been detected. Furthermore, eDNA allows us to rapidly evaluate the presence of P. inflatus in previously occupied areas to either a) locate natural, self-sustaining populations, or b) increase confidence that the species has been extirpated to better inform listing and recovery actions.
Currently, only three viable, self-sustaining populations remain for this species. Populations in the Amite River (Louisiana) are disjunct, and its loss would decrease the number of viable P. inflatus populations to a critical level. A historical population in the Pearl River (Louisiana and Mississippi) has been long considered extirpated due to a lack of detection in more than 26 years of tactile surveys. The USFWS recovery plan prioritizes the Pearl River population and provides strategies that could help remove the species from the Endangered Species Act. This makes confirming P. inflatus occurrence in the Pearl River a crucial piece of the conservation strategy.
Methodology for Addressing the Issue: Our project is comprised of two key segments. First, we will develop and optimize an eDNA assay to delineate the current distribution of P. inflatus utilizing molecular data for P. inflatus from the Lake Pontchartrain (Louisiana) and Mobile River (Alabama) basins. Using DNA libraries and a sound understanding of unionid taxonomy and DNA-based identification, we are designing and testing species-specific eDNA tools to detect the presence of P. inflatus DNA in water samples. Initial testing will utilize a traditional polymerase chain reaction (PCR). Once effective primers have been developed, we will migrate our assay to a quantitative real-time PCR assay (qPCR), and finally to a Droplet Digital PCR (ddPCR) system. The ddPCR technology increases the sensitivity of detection using absolute quantification, which enables us to count individual DNA molecules from our target species to better understand the proximity and densities of animals at each eDNA sampling location.
Secondly, we will use the optimized eDNA assay to provide up-to-date distributional information and detection rates for P. inflatus in the Pearl River basin. We will validate our assay at sites where P. inflatus is found and sample areas where contemporary distributions are unknown. Results from eDNA sampling will be used to update distribution maps for P. inflatus, which will be a useful tool for guiding management actions of federal and state wildlife management agencies and future eDNA or tactile survey sampling.
Future Steps: Our research will be an invaluable resource toward future conservation, management, and recovery strategies for populations of P. inflatus and can be used as a model study for other imperiled aquatic species. The USFWS is considering captive propagation and reintroduction as a strategy to increase abundance and expand the current range to assist in delisting P. inflatus. Our project facilitates the establishment of effective captive propagation and reintroduction programs by delineating the current distribution of P. inflatus, identifying areas suitable for reestablishment of populations, and providing baseline genetic characterization of wild populations for genetic management planning.