Developing and testing eDNA markers for the Federally endangered dwarf wedgemussel (DWM), Alasmidonta heterodon
Dates
Start Date
2017-10-01
End Date
2019-03-30
Summary
Dwarf Wedgemussel (DWM) is a federally endangered freshwater mussel with a historic range along the Atlantic coast (USFWS 1993). While DWM has declined throughout its range, substantial populations can still be found within the Connecticut and Delaware River watersheds in the northeastern United States. Knowledge of current population distribution and abundance is critical to monitor the species over time and to guide recovery actions. However, manual survey efforts (snorkel or scuba) necessary to detect new populations are intense and time consuming (Galbraith et al. 2016). Use of eDNA to identify areas in streams and rivers where DMW are currently located can increase survey efficiency by targeting areas within watersheds with positive [...]
Summary
Dwarf Wedgemussel (DWM) is a federally endangered freshwater mussel with a historic range along the Atlantic coast (USFWS 1993). While DWM has declined throughout its range, substantial populations can still be found within the Connecticut and Delaware River watersheds in the northeastern United States. Knowledge of current population distribution and abundance is critical to monitor the species over time and to guide recovery actions. However, manual survey efforts (snorkel or scuba) necessary to detect new populations are intense and time consuming (Galbraith et al. 2016). Use of eDNA to identify areas in streams and rivers where DMW are currently located can increase survey efficiency by targeting areas within watersheds with positive eDNA results. Through genetic analysis of water samples, a greater geographic area can be surveyed with less effort than traditional surveys.
Rigorous marker testing and field trials for an eDNA marker is critical to ensure the ability to make proper inferences from positive eDNA results. We will incorporate the methodology and analyses of Goldberg et al. (2016), leading researchers in the application of eDNA for conservation, in our application and interpretation of results. This study will evaluate qPCR markers that are publically available or develop new markers for use if markers are not publically available. Thorough testing of marker performance, to ensure that only the species of interest is consistently and accurately amplified when its DNA is present, is required for proper interpretation of results. Evaluation of different extraction methods can be used to streamline sample processing. Testing sample collection practices will help optimize the ability to detect DWM when present at a site, improving the knowledge of the species distribution throughout the Connecticut and Delaware River watersheds.
Objectives:
Develop a qPCR marker to detect the presence of DWM DNA in environmentally collected (water) samples (unless one becomes publically available first).
For either a new or already developed marker, conduct cross species amplification testing to ensure non-target species are not positively detected using a DWM-specific qPCR marker for eDNA analysis.
Conduct testing for DWM throughout its range to ensure consistent amplification of the DWM-specific marker.
Compare eDNA collection methods, filtration versus flocculation, to optimize sample handling. Water samples spiked with both dissolved and cellular DNA will be filtered using a variety of filter materials in common use for eDNA capture. Recovery of target DNA will be compared with that provided by the newly-developed chemical flocculation protocol (W. Schill, USGS, unpublished).
Conduct field testing of DWM-specific qPCR marker in areas of known DWM beds to assess sensitivity of eDNA testing, including evaluation of environmental parameters (temperature, flow, pH) and seasonality (i.e. correlating with reproduction) on qPCR sensitivity in order to maximize potential detection.
If markers are publicly available prior to the start of this study, the funds requested for marker development will be used to collect and analyze eDNA samples from unknown and suspected DWM locations (~100 samples) and used for Objective C.
