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: Jeffrey A. Stein, University of Illinois; Solomon R. David, Nicholls State University; Sarah M. King, University of Illinois

ABSTRACT: Gars (Lepisosteidae) and Bowfin (Amiidae), collectively known as holosteans, are among the most ancient fish lineages native to North American waters. Understudied and historically disliked relative to other North American fisheries, many holostean populations have declined due to habitat loss, overfishing, and eradication efforts. Furthermore, knowledge regarding the basic biology and life history of these species is limited. As anglers’ perception of these ancient species begins to transform from “rough fish” to “sport fish,” the need for a better understanding of the ecology and conservation status of holostean populations is fundamental to their effective management. This lightning talk will provide an overview of the Ancient Sport Fishes Project, a collaboration among researcher at the University of Illinois and Nicholls State University that explores the spatial ecology, population dynamics, genetics, and human dimensions of Gars and Bowfin.

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: 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: 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.

AUTHORS: Kellie N. Hanser, Cassi Moody-Carpenter, Jordan Pesik – Eastern Illinois University; Dan Roth, Indiana Department of Natural Resources; Aaron Schrey, Gerogia Southern University-Armstrong Campus; Anthony Porreca, Kaskaskia Biological Station: Illinois Natural History Survey; Robert E. Colombo, Eastern Illinois University

ABSTRACT: Catostomidae, the third largest freshwater fish family, comprises a high percentage of fish biomass in river systems throughout North America. Despite their presence, there is little information on the reproductive life history for this family in large, midwestern rivers and their tributaries. To address this, we sampled larval fish in three tributaries of both the Illinois River and Wabash River in conjunction with environmental data collected on factors thought to be important for reproduction. Between 2016 and 2017, we collected 130 and 2626 catostomid larvae from the Illinois and Wabash River tributaries, respectively. Due to the morphological difficulty of identifying catostomid larvae past family taxonomic level, Next Generation Sequencing (NGS) was used to identify catostomid larvae to either genus or species. Results of larvae identification are still pending due to processing time. We expect Wabash River tributaries to have a higher abundance of Moxostoma(Redhorse) while the Illinois River tributaries will have a higher abundance in Ictiobus(Buffalo) due to differences in connectivity between the systems. Future research will examine the relationship between larval and adult catostomid abundance in the Illinois and Wabash River systems.   

AUTHORS: Samuel Schaick, Eastern Illinois University; Cassi Moody-Carpenter, Eastern Illinois University; Aaron Schrey, Georgia Southern University; Katie Miller, Georgia Southern University; David Wahl, Illinois Natural History Survey; Robert Colombo, Eastern Illinois University

ABSTRACT: Silver Carp are a non-native fish species that have deleterious effects on the ecosystems they invade. Because of their destructive nature, fisheries managers devote substantial time and effort to limit the spread of these fishes. Better understanding patterns of Silver Carp reproduction and dispersal can help to better manage this invader. To determine spawning locations, we used drift nets and larval push nets in three tributaries the Wabash River to capture larval Hypophthalmichthys (Silver and Bighead Carp) in 2016 and 2017. Further, we used microsatellite loci to determine if genetic differences existed between larval Hypophthalmichthys in our three study tributaries. In total, 1,246 Hypophthalmichthys were collected from three tributaries, with the Little Wabash River and Embarras River producing roughly 83% and 16% of larvae. Having large enough sample sizes at two sites on the Little Wabash River and one site on the Embarras River, we performed genetic analyses and found all three sites had high levels of genetic diversity. Additionally, we found minimal inbreeding or outbreeding present. The middle Little Wabash and lower Embarras River samples were found to be genetically different. We expect this research to improve our understanding of Asian carp reproduction and help fisheries professionals to better mediate their spread.

AUTHORS: Megan Niner, University of Toledo; Dr. Carol Stepien, NOAA Pacific Marine Environmental Lab; Dr. Doug Leaman, Wright State University

ABSTRACT: The viral hemorrhagic septicemia virus (VHSv) is a fish virus responsible for occasional fish kills in the Laurentian Great Lakes in the last fifteen years. Substrain IVb is a recently emerged pathogen with an unusually large host range of over 30 species of fish, both of native and non-native status. With new outbreaks once again occurring, more insight into the evolutionary trends of this fish pathogen could help predict future trends. This study provides a unique examination of a wildlife pathogen in a natural setting. We sequenced the full genome of multiple VHSv-IVb isolates collected in the fifteen years following its emergence to examine evolutionary trends. For these 30 isolates, we compare and contrast differences in nucleotides, amino acids, mutation sites, and the number of transvisions and transversions to elucidate possible patterns across time. To understand how observed changes in sequences may affect the course of infection, further testing of three selected full genomes from Lake Erie were used in a variety of cell culture studies. Our selected isolates were haplotypes “v” (H31, round goby, 2015), “w” (B09, gizzard shad, 2016), and “w4” (G61, smallmouth bass, 2016). Cell experiments included testing for differences in pathogenicity from the original isolate haplotype “a” (MI03GL, 2003), examining cytopathogenicity, virus production, and immune response stimulation. All three new isolates appeared to behave similarly to “a” despite being recovered more than a decade later.