Midwest Fish & Wildlife Conference 2019

AUTHORS: Austen Thomas, Smith-Root; Samantha Stanton, Michigan State University; Jake Ponce, Smith-Root; Mieke Sinnesael, Biomeme; Phong Nguyen, Smith-Root; Caren Goldberg, Washington State University

ABSTRACT: Environmental DNA (eDNA) detection of aquatic invasive species using PCR is a powerful new tool for resource managers, but laboratory results often take weeks to be produced which limits options for rapid management response. To circumvent laboratory delay, we combined a purpose-built eDNA filtration system (ANDe) with a field DNA extraction and handheld qPCR platform (Biomeme) to form a complete field eDNA sampling and detection process. A lab study involving serial dilution of New Zealand mudsnail eDNA was conducted to compare the detection capabilities of the field system with traditional bench qPCR. Two field validation studies were also conducted to determine if the on-site eDNA process can be used to map mudsnail eDNA distribution and quantify temporal fluctuations. Both platforms (Biomeme, bench qPCR) lost the ability to reliably detect mudsnail eDNA at the same dilution level (10^-4), with SQ values as low as 21 DNA copies/reaction. A strong relationship was observed between the average Cq values of the two platforms (slope = 1.101, intercept = - 1.816, R²= 0.997, P < 0.001). Of the 80 field samples collected, 44 (55%) tested positive for mudsnail eDNA with Biomeme, and results identified both spatial and temporal fluctuations in mudsnail eDNA/L. However, the PCR inhibition rate (no IPC amplification) with Biomeme was 28% on average for field samples, and up to 48% in the temporal dataset. With additional optimization of the DNA extraction process, the ANDe-Biomeme system has potential to be a rapid and highly effective detection/quantification tool for aquatic invasive species.

AUTHORS: Mark Davis, Illinois Natural History Survey; Amanda Curtis, University of Illinois; Jeremy Tiemann, Illinois Natural History Survey; Sarah Douglass, Illinois Natural History Survey; Eric Larson, University of Illinois

ABSTRACT: The efficacy of environmental DNA to assay the presence of invasive species hinges upon understanding the covariates influencing fate and transport. In lotic systems, these covariates may include biotic (e.g. invasive species density, seasonal activity patterns, etc.) and abiotic (e.g. stream discharge, temperature, ultraviolet irradiation, pH, etc.) factors, as well as their complex interactions. To better understand fate and transport of eDNA in complex lotic systems, we assessed eDNA copy number for invasive Asian clams (Corbicula spp.) in paired freshwater streams in central Illinois via a primer/probe assay. We collected eDNA samples approximately every two weeks for one year, as well as during periods of high and low discharge. At each sampling period, we collected data for a number of water quality variables (including pH, temperature, turbidity, conductivity, total dissolved solids, and salinity), and we also conducted mid-summer quadrat sampling at each site to estimate Corbicula densities. Importantly, we placed our two sampling sites at USGS stream gages in order to access continuous discharge data. We anticipated that high stream flow events could either dilute eDNA concentrations or increase eDNA concentrations by mobilizing Corbicula DNA from the sediments. We found abundance of Corbicula eDNA as copy number increased with increasing water temperatures, likely reflecting a late spring and early summer reproductive peak for this species. However, we found a weak and non-significant negative relationship between stream flow and Corbicula eDNA abundance, despite having sampled at base flow and high flow conditions across multiple seasons. As such, we conclude that stream discharge may have little effect on estimates of eDNA abundance for common stream and river species like the invasive Asian clam, although more studies should seek to evaluate the role of stream and river flow regimes on eDNA performance.

AUTHORS: Christopher M. Merkes, US Geological Survey; Katy E. Klymus, US Geological Survey; Richard F. Lance, US Army Corps of Engineers; Emy Monroe, US Fish & Wildlife Service; Catherine A. Richter, US Geological Survey; Caren S. Goldberg, Washington State University; Antoinette J. Piaggio, USDA Animal and Plant Health Inspection Service; Chris C. Wilson, Ontario Ministry of Natural Resources; Joel P. Stokdyk, Margaret E. Hunter, Nathan L. Thompson, Craig A. Jackson, Jon J. Amberg – US Geological Survey

ABSTRACT: Many advances have been made over the last ten years in the field of environmental DNA, and new assays exist for a wide range of target species of interest.  As this technology matures, it is necessary to make methods more standardized to allow better comparisons across studies and enable meta-analysis of species distributions.  One key aspect where this may be possible is with assay sensitivity.  Sensitivity is a critical measure especially when comparing data from multiple markers, and it can be easily described in two measurements: Limit of Detection (LoD; the lowest concentration that can reliably be detected) and Limit of Quantification (LoQ; the lowest concentration that can reliably be quantified).  To facilitate this, an R script has been developed to allow a person with minimal R-coding ability to easily and reliably analyze their data to determine LoD and LoQ of their assays as well as automatically generate plots of their data that puts the values into context for easy understanding.  Putting eDNA assay results into a standardized framework and enabling end users to understand the results more clearly will enhance the value of eDNA data and facilitate its wider application.

AUTHORS: Emy Monroe, Erica Mize – U.S. Fish and Wildlife Service; Richard Erickson, Christopher Merkes – US Geological Survey; Nicholas Berndt, Katherine Bockrath, Jeena Credico, Nikolas Grueneis, Jenna Merry, Kyle Mosel, Maren Tuttle-Lau, Kyle Von Ruden, Zebadiah Woiak, Kelly Baerwaldt, Sam Finney – U.S. Fish and Wildlife Service; Jon Amberg, US Geological Survey

ABSTRACT: Natural resource managers use data from survey or monitoring efforts that use a wide variety of tools. Environmental DNA (eDNA) is a genetic surveillance tool for detecting species and holds potential as a tool for large-scale monitoring programs.  Two challenges of eDNA-based studies are imperfect capture of eDNA in collection samples (e.g., water field samples) and imperfect detection of eDNA using molecular methods (e.g., quantitative PCR), which create uncertainty about sample designs for eDNA-based monitoring.  We used an occurrence model to address these challenges and determine how many  samples were required to detect species using eDNA and to examine when and where to take samples.  Water samples were collected 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 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.  Additionally, we found statistical artifacts where sample eDNA capture probabilities would artificially inflate estimates of molecular detection probabilities.  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 as well as aspects of different physical environments that impact the implementation of these methods.

AUTHORS: Christopher B. Rees, Theodore W. Lewis, Sandra Keppner, Joshua Newhard, Aaron P. Maloy, Meredith L. Bartron – U.S. Fish & Wildlife Service

ABSTRACT: Populations of Northern snakehead (Channa argus) have been introduced in the Lower Hudson, Bronx, and Rondout watersheds of New York, Lower Delaware watershed of Pennsylvania and New Jersey, and the Lower Susquehanna watershed of Pennsylvania and Maryland. Because these observations are in close proximity to Great Lakes tributaries, Northern snakehead constitute a species of high invasion concern for natural resource agencies of Great Lakes connected waters. Traditional gear capture of Northern snakehead at low densities in their established range can be difficult due to the shallow, vegetation-rich habitat they typically occupy. As a result, significant environmental DNA (eDNA) detection efforts by the U.S. Fish and Wildlife Service and partner agencies in portions of the Oswego River drainage and canal system of New York have been explored. In any eDNA detection effort, it is important to have confidence in the accuracy of the markers used, and particularly when the effort involves the detection of aquatic invasive species where management and/or response actions may be taken. Here we highlight results from validation and comparative performance testing of several eDNA markers designed to detect Northern snakehead DNA and detection results of the 2018 environmental sampling efforts.

AUTHORS: Richard F Lance, Environmental Laboratory, US Army Engineer Research & Development Center; Xin Guan, Bennett Aerospace; Emy M. Monroe, Katherine D. Bockrath, Erica L. Mize – Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service; Chris B. Rees, Northeast Fishery Center, U.S. Fish and Wildlife Service; Kelly L. Baerwaldt, Midwest Fisheries Center, U.S. Fish and Wildlife Service

ABSTRACT: The Black Carp, Mylopharyngodon piceus, is an invasive species within the Mississippi River drainage that appears to be undergoing population growth and range expansion. Black carp are molluscivores that potentially threaten significant components of North America's rich indigenous diversity of freshwater bivalves. In order to help determine the presence of black carp in various waters and habitats, and to help track its spread, we have developed a suite of environmental DNA (eDNA) markers for this species. The markers were developed using whole mitochondrial genomes from 29 black carp from three countries and target three different mitochondrial DNA genes. The markers were further tested for reliability with a total of 41 black carp DNA samples and for specificity against DNA from numerous co-occurring fish species and against samples of natural waters free of black carp. Further tests to detect black carp in natural waters proved challenging, but ultimately successful. We further report on studies of which water fractions contain the bulk of black carp eDNA (the answer appears to be largely habitat dependent) and on the efficiency of different sampling options.

AUTHORS: Catherine A. Richter, Katy E. Klymus, Nathan Thompson, Jeffrey C. Jolley, Duane C. Chapman – U.S. Geological Survey; PRESENTER: Rick Lance

ABSTRACT: Creve Coeur Lake is a large natural floodplain lake intermittently connected to the Missouri River near St. Louis, Missouri. The lake has been invaded by Bighead Carp (Hypophthalmichthys nobilis) and Silver Carp (Hypophthalmichthys molitrix), collectively known as Bigheaded Carp. Both are native to Asia. The invasion has resulted in impairment of the native crappie (Pomoxis spp.) fishery, and hazards to recreational users. Fish can enter the lake from the Missouri River only during high water events. During the winter of 2017-2018, an intensive removal effort was conducted using the unified fishing method. A total of approximately 108,129 kg of Bigheaded Carp was removed from the lake in February 2018. Monitoring of Bigheaded Carp environmental DNA (eDNA) concentrations was conducted at intervals before and after the removal effort. Water was sampled at 53 locations equally spaced along transects covering the entire surface area of Creve Coeur Lake, a smaller upstream connected lake (Mallard Lake), and the channel between the two lakes. We measured eDNA concentrations with quantitative PCR using two marker sets specific to the genus Hypophthalmichthys, and thus able to detect and quantify DNA from both species with equal efficiency. Our results showed a decrease in eDNA concentration with decreasing water temperature over three sampling events before the removal effort, in October 2017, November 2017, and January 2018. After the removal effort, we observed an increase in eDNA in March 2018, possibly resulting from the presence of injured fish and carcasses, followed by a sharp decrease in eDNA in April 2018. Our results illustrate the utility of eDNA monitoring of management actions, the advantages of repeated sampling over time, and some challenges associated with this application of eDNA analysis.

AUTHORS: Nicholas Johnson, U.S. Geological Survey, Great Lakes Science Center; Chris Merkes, Joel Putnam – U.S. Geological Survey, Upper Midwest Environmental Sciences Center

ABSTRACT: Sea lamprey are controlled in the Great Lakes to reduce damage to valuable fisheries. Sea lamprey control is effective, but damage caused by remaining sea lamprey is poorly defined because because sea lamprey feed on blood and traditional gut content analysis has not possible.  Here, we test the concept that sea lamprey diet can be quantified by barcoding DNA in sea lamprey feces.  Specifically, we determined the percentage of fecal samples containing measureable DNA from host fishes when collected from (1) recently fed parasitic sea lamprey, (2) fasted parasitic sea lamprey transitioning to the adult stage, and (3) adult sea lamprey captured from a spawning stream.   If successful, the method could help managers better interpret lake trout wounding rates by providing insight as to how often hosts alternative to lake trout are targeted by sea lamprey. Ultimately, our vision is that adult sea lamprey assessment in each Great Lake may be able to produce an annual estimate of abundance and an estimate what fishes that cohort of adult sea lamprey were feeding on, so that fish managers could estimate damage caused to specific fish stocks.

AUTHORS: Aaron P. Maloy, Stephanie Dowell, Roman Crumpton, James Henne, Julie C. Schroeter, Christopher B. Rees, Meredith L. Bartron – U.S. Fish & Wildlife Service

ABSTRACT: Flathead catfish (Pylodictis olivaris) are large, primarily piscivorous, predators native to Gulf Coast drainages of the Mobile, Mississippi and Rio Grande River.  Intentional stockings outside of their native range were common in the early to mid-20^th century, many of which resulted in self-recruiting populations that have become invasive.  Flathead catfish alter native species communities through direct predation and are considered one of the most biologically harmful invasive fish. Obtaining detailed trophic data through traditional dietary analysis is difficult due to the lack of morphological characteristics of prey and because fish are commonly taken with empty stomachs. To address these challenges a study was undertaken on the Edisto River, South Carolina to assess the trophic ecology of invasive flathead catfish using DNA-based dietary methods. A combination of DNA barcoding and metabarcoding revealed a varied diet of crustaceans, bivalves, eggs and numerous fish species.  Traditional COI barcoding was useful for determining the identity of larger remnants of prey items of both fish and invertebrates.  Metabarcoding of the 12S rRNA gene targeted fish species and was successful at identifying prey even when morphological examination determined stomachs to be empty.  A higher rate of prey detection was observed in material collected from the stomachs than that obtained from the intestines.  Used in conjunction, the two methods provided a more complete understanding of flathead catfish predation than any one method in isolation.