I have always been fascinated with DNA. My primary interests are in how DNA sequences can control development or cause disease. I am also excited to be able to use forensic DNA analysis to learn more about the natural environment. Resource managers can then use that information to implement efficient and effective management practices to keep our natural resources healthy.
I began my studies at University of Wisconsin – Stevens Point as a molecular biologist testing ticks for the Lyme disease pathogen Borellia burgdorferi and tracking the movement pattern of the spirochete through a local nature reserve. Simultaneously, I was also working as a water chemist studying the effects of agricultural runoff into streams and testing private well water for human health concerns (for example: fecal coliform bacteria, arsenic, or heavy metal contamination). I then took a job at University of Kansas (KU) as a fruit fly geneticist using recombinant inbred fruit fly lines to map genetic influences on complex traits such as caffeine, nicotine, or alcohol sensitivity. I then joined the graduate program at KU and completed a master’s project examining developmental defects in a zebrafish cancer model. My thesis work used a combination of genetic and biochemical techniques in zebrafish embryos and human cell lines to show that the Ewing’s Sarcoma Breakpoint Region 1 gene (ewsr1) helps control skeletal development by modifying the regulation of Sex Determination Region Y – Box 9 (SOX9) target genes.
I began working for the USGS – UMESC in 2013 where I use my skills in molecular biology to promote healthy ecosystems primarily in developing tools for species-specific controls and monitoring for aquatic invasive species.
Science and Products
READI-Net: Transitioning eDNA aquatic invasive species surveillance from research to actionable science
Environmental DNA (eDNA): Combining Technology and Biology to Detect Aquatic Invasive Species and Pathogens
Environmental DNA (eDNA) Data Management
Developing RNA Interference to Control Zebra Mussels
Correlating seasonal trends and occupancy of bigheaded carp eDNA to land use and stream characteristics
Developing a portable LAMP assay for detecting grass and black carp
Relationship between fish presence and abundance in Arizona standing waters measured through standard techniques and environmental DNA
Assessing the properties of RNA degradation in complex environmental water samples
Data Release for Validation of portable eDNA detection kit for Asian carps
Developmental Stages of Grass Carp (Ctenopharyngodon idella) eggs in the Sandusky River (ver. 3.0, July 2020)
Assessment of carbon dioxide piscicide treatments: Data
When are environmental DNA early detections of invasive species actionable?
Validation of a portable eDNA detection kit for invasive carps
Using structured decision making to evaluate potential management responses to detection of dreissenid mussel (Dreissena spp.) environmental DNA
Assessment of sea lamprey (Petromyzon marinus) diet using DNA metabarcoding of feces
Using environmental DNA (eDNA) to detect the endangered Spectaclecase Mussel (Margaritifera monodonta)
Robotic environmental DNA bio-surveillance of freshwater health
Reporting the limits of detection and quantification for environmental DNA assays
Refinement of eDNA as an early monitoring tool at the landscape-level: Study design considerations
Sampling designs for landscape-level eDNA monitoring programs using three-level occurrence models
Development of a quantitative PCR method for screening ichthyoplankton samples for bigheaded carps
Environmental DNA as a tool to help inform zebra mussel, Dreissena polymorpha, management in inland lakes
Correlating sea lamprey density with environmental DNA detections in the lab
Non-USGS Publications**
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Sea lamprey quantitative environmental DNA surveillance
Science and Products
- Science
READI-Net: Transitioning eDNA aquatic invasive species surveillance from research to actionable science
USGS researchers are working with the Monterey Bay Aquarium Research Institute to optimize autonomous, robotic samplers for detection of DNA fragments shed by biological threats (BT; invasive species, parasites, pathogens) in our nation’s waters. Finding DNA fragments (a method known as environmental DNA sampling) produced by an emerging BT in water is akin to finding a needle in a haystack—many...ByEcosystems Mission Area, Biological Threats and Invasive Species Research Program, Columbia Environmental Research Center, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, New York Water Science Center, Northern Rocky Mountain Science Center, Upper Midwest Environmental Sciences Center, Wetland and Aquatic Research Center , Wyoming-Montana Water Science Center, Pacific Northwest Environmental DNA LaboratoryEnvironmental DNA (eDNA): Combining Technology and Biology to Detect Aquatic Invasive Species and Pathogens
Using DNA, USGS researchers are able to detect the presence of invasive species in aquatic ecosystems. The DNA they use is literally floating around in the environment and is called environmental DNA (eDNA) and is a powerful tool for the early detection of invasive species and pathogens, which can cause serious ecological and economic damage. USGS researchers are also combining the use of eDNA...Environmental DNA (eDNA) Data Management
The environmental DNA (eDNA) samples collected, processed, and sequenced by the Upper Midwest Environmental Sciences Center (UMESC) and partner agencies are being archived in a cloud-based database application. Consolidating eDNA data will significantly improve researchers and managers ability to visualize, analyze, and integrate sequence data as a monitoring and early detection system for...Developing RNA Interference to Control Zebra Mussels
We aim to develop a control tool for eliminating zebra mussels that exploits natural gene regulation mechanisms (RNA-induced gene silencing; RNAi) to be specific to zebra mussels without non-target effects. In addition to the nuisance they pose, Pimentel et al. estimated that zebra mussels cost the U.S. economy over $1 billion annually. Zebra mussels are among the International Union for...Correlating seasonal trends and occupancy of bigheaded carp eDNA to land use and stream characteristics
The results of this study will advance our understanding of environmental DNA (eDNA) and how eDNA signatures change as fish behavior changes over the course of the open water season. This will further develop eDNA as an easy sampling method to collect information about invading populations or cryptic species that are difficult to capture so that resource managers can be given better information to...Developing a portable LAMP assay for detecting grass and black carp
Aquatic invasive species are a significant problem throughout the world. They cause millions of dollars in damages to industry, devastate natural ecosystems, and ruin outdoor recreational areas. Preventing their spread is imperative to preserving our natural resources. One potential pathway invasive fishes can spread is by harvesting and transporting baitfish. Often shipments of baitfish are...Relationship between fish presence and abundance in Arizona standing waters measured through standard techniques and environmental DNA
The unpredictability of DNA degradation in the environment has plagued the ability of scientists to interpret environmental DNA (eDNA) data since the technique has been used for early detection of aquatic invasive species (AIS) such as silver and bighead carps (Hypophthalmichthys molitrix and Hypophthalmichthys nobilis) throughout the Chicago Area Waterway System (CAWS), Des Plaines River, near...Assessing the properties of RNA degradation in complex environmental water samples
The unpredictability of nucleic acid degradation in the environment has plagued the ability of scientists to interpret environmental DNA (eDNA) data since the technique has been used for early detection of aquatic invasive species (AIS) such as silver and bighead carps (Hypophthalmichthys molitrix and Hypophthalmichthys nobilis) throughout the Chicago Area Waterway System (CAWS), Des Plaines River... - Data
Data Release for Validation of portable eDNA detection kit for Asian carps
This is the qPCR and loop-mediated isothermal amplification (LAMP) data in support of the article "Validation of a portable eDNA detection kit for invasive carps". There are four types of data contained in five files including: limit of detection analysis for each method (qPCR and LAMP), qPCR analysis and LAMP analysis of eDNA samples collected over time from ponds containing 3 or 33 Grass Carp (CDevelopmental Stages of Grass Carp (Ctenopharyngodon idella) eggs in the Sandusky River (ver. 3.0, July 2020)
Grass Carp Ctenopharyngodon idella was imported to the United States in the 1960s for research into its usefulness as a biocontrol agent for nuisance aquatic vegetation. Escapees and intentionally stocked individuals founded wild, spawning populations in the Mississippi River and tributaries to the Laurentian Great Lakes. USGS-led research on the Sandusky River, a tributary to Lake Erie, demonstraAssessment of carbon dioxide piscicide treatments: Data
Spreadsheets include data that was used to evaluate the efficacy of dry ice administered under-ice as a tool for reducing the overwinter survival of invasive carps. There are 10 CSV associated with this study - Publications
Filter Total Items: 18
When are environmental DNA early detections of invasive species actionable?
Environmental DNA (eDNA) sampling provides sensitive early detection capabilities for recently introduced taxa. However, natural resource managers struggle with how to integrate eDNA results into an early detection rapid response program because positive eDNA detections are not always indicative of an eventual infestation. We used a structured decision making (SDM) framework to evaluate appropriatAuthorsAdam J. Sepulveda, Christine E. Dumoulin, Denise L. Blanchette, John Mcphedran, Colin Holme, Nathan Whalen, Margaret Hunter, Christopher M. Merkes, Catherine A. Richter, Matthew Neilson, Wesley Daniel, Devin Nicole Jones, David R. SmithValidation of a portable eDNA detection kit for invasive carps
Loop-mediated isothermal amplification (LAMP) is a rapid molecular detection technique that has been used as a diagnostic tool for detecting human and animal pathogens for over 20 years and is promising for detecting environmental DNA shed by invasive species. We designed a LAMP assay to detect the invasive carps, silver carp (Hypophthalmichthys molitrix), bighead carp (Hypophthalmichthys nobilis)AuthorsStacie A. Kageyama, Matthew Regh Hoogland, Tariq Tajjioui, Theresa M. Schreier, Richard A. Erickson, Christopher M. MerkesUsing structured decision making to evaluate potential management responses to detection of dreissenid mussel (Dreissena spp.) environmental DNA
Environmental (e)DNA tools are sensitive and cost-effective for early detection of invasive species. However, the uncertainty associated with the interpretation of positive eDNA detections makes it challenging to determine appropriate natural resource management responses. Multiple sources of error can give rise to positive detections of eDNA in a sample when individuals of that species are not prAuthorsAdam J. Sepulveda, David R. Smith, Katherine M O'Donnell, Nathan Owens, Brittany White, Catherine A. Richter, Christopher M. Merkes, Skylar Wolf, Mike Rau, Matthew Neilson, Wesley Daniel, Christine E. Dumoulin, Margaret HunterAssessment of sea lamprey (Petromyzon marinus) diet using DNA metabarcoding of feces
Sea lamprey (Petromyzon marinus) are invasive in the Laurentian Great Lakes, parasitize large-bodied fishes, and therefore are the focus of an international control program. However, damage caused by sea lamprey to modern day fish stocks remains uncertain because diet analysis of juvenile sea lamprey has been challenging; they feed on blood and are difficult to randomly sample in the lakes. Here,AuthorsNicholas S. Johnson, Sean A. Lewandoski, Christopher M. MerkesUsing environmental DNA (eDNA) to detect the endangered Spectaclecase Mussel (Margaritifera monodonta)
Margaritifera monodonta, or the Spectaclecase Mussel, is a federally endangered freshwater mussel species that has experienced a 55% reduction in range and is currently concentrated in 3 rivers in the Midwest region of the United States (Gasconade and Meramec rivers, Missouri, and St Croix River, Wisconsin). The detection of new populations by traditional survey methods has been limited because thAuthorsYer Lor, Theresa M. Schreier, Diane L. Waller, Christopher M. MerkesRobotic environmental DNA bio-surveillance of freshwater health
Autonomous water sampling technologies may help to overcome the human resource challenges of monitoring biological threats to rivers over long time periods and large geographic areas. The Monterey Bay Aquarium Research Institute has pioneered a robotic Environmental Sample Processor (ESP) that overcomes some of the constraints associated with traditional sampling since it can automate water sampleAuthorsAdam J. Sepulveda, Jim M. Birch, Elliott Barnhart, Christopher M. Merkes, Kevan Yamahara, Roman III Marin, Stacy Kinsey, Peter R. Wright, Christian SchmidtReporting the limits of detection and quantification for environmental DNA assays
BackgroundEnvironmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid progress in the eDNA field has resulted in numerous studies impacting conservation and management actions. However, standardization of eDNA methods and reporting across the field is yet to be fully establisAuthorsKaty E. Klymus, Christopher M. Merkes, Michael J. Allison, Caren S. Goldberg, Caren C. Helbing, Margaret Hunter, Craig Jackson, Richard F. Lance, Anna M. Mangan, Emy M. Monroe, Antoinette J. Piaggio, Joel P. Stokdyk, Chris C. Wilson, Catherine A. RichterRefinement of eDNA as an early monitoring tool at the landscape-level: Study design considerations
Natural resource managers use data on the spatial range of species to guide management decisions. These data come from survey or monitoring efforts that use a wide variety of tools. Environmental DNA (eDNA) is a surveillance tool that uses genetic markers for detecting species and holds potential as a tool for large-scale monitoring programs. Two challenges of eDNA-based studies are uncertaintieAuthorsErica L. Mize, Richard A. Erickson, Christopher M. Merkes, N. Berndt, K.D. Bockrath, J. Credico, N. Grueneis, J. Merry, Kyle Mosel, M.T. Tuttle-Lau, K. Von Ruden, Jon Amberg, K. Baerwaldt, S.T. Finney, E.M. MonroeSampling designs for landscape-level eDNA monitoring programs using three-level occurrence models
Resource managers conduct landscape-level monitoring using environmental DNA (eDNA). These managers must contend with imperfect detection in samples and sub-samples (i.e., molecular analyses). This imperfect detection impacts their ability to both detect species and estimate occurrence. Although occurrence (synonymously occupancy) models can estimate these probabilities, most models and guidance fAuthorsRichard A. Erickson, Christopher M. Merkes, Erica L. MizeDevelopment of a quantitative PCR method for screening ichthyoplankton samples for bigheaded carps
Monitoring ichthyoplankton is useful for identifying reproductive fronts and spawning locations of bigheaded carps (Hypophthalmichthys spp.). Unfortunately, sorting and identifying ichthyoplankton to monitor for bigheaded carp reproduction is time consuming and expensive. Traditional methods require frequent egg-larvae sampling, sorting of all samples to obtain presumptively identified bigheaded cAuthorsAndrea K. Fritts, Brent C. Knights, James H. Larson, Jon Amberg, Christopher M. Merkes, Tariq Tajjioui, Steven E. Butler, Matthew J. Diana, David H. Wahl, Michael J. Weber, John D. WatersEnvironmental DNA as a tool to help inform zebra mussel, Dreissena polymorpha, management in inland lakes
Zebra mussels (Dreissena polymorpha) are an aquatic invasive species that plague much of North America and are difficult to impossible to eradicate once they become established. Therefore, prevention and monitoring are key elements in the control of these organisms. Traditional microscopy is commonly used in monitoring but requires the presence of larval veligers. This limits the times when resourAuthorsJon Amberg, Christopher M. Merkes, Wendylee Stott, Christopher B. Rees, Richard A. EricksonCorrelating sea lamprey density with environmental DNA detections in the lab
Invasive sea lamprey (Petromyzon marinus Linnaeus, 1758) are currently managed by the Great Lakes Fishery Commission in an effort to reduce pest populations below levels that cause ecological damage. One technique to improve stream population assessments could be molecular surveillance in the form of environmental DNA (eDNA) monitoring. We developed and validated four probe-based quantitative polyAuthorsNicholas A. Schloesser, Christopher M. Merkes, Christopher B. Rees, Jon Amberg, Todd B. Steeves, Margaret F. DockerNon-USGS Publications**
Merkes C, Turkalo TK, Wilder N, Park H, Wenger LW, Lewin SJ, et al. (2015) Ewing Sarcoma Ewsa Protein Regulates Chondrogenesis of Meckel’s Cartilage through Modulation of Sox9 in Zebrafish. PLoS ONE 10(1): e0116627. doi:10.1371/journal.pone.0116627Wiley EO, Fuiten AM, Doosey MH, Lohman BK, Merkes C, Azuma M. (2015) The Caudal Skeleton of the Zebrafish, Danio rerio, from a Phylogenetic Perspective: a Polyural Interpretation of Homologous Structures. Copeia. 103(4): 740-750.King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S, Broman KW, Long AD, Macdonald SJ. (2012) Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Research. Aug;22(8):1558-66. PMID: 22496517**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
- Software
Sea lamprey quantitative environmental DNA surveillance
The data set is six separate csv files. Four of which contain the quantity of DNA copy numbers and fluor used to analyze the DNA quantities collected from water samples from four separate portions of the study (adult SL field, adult SL lab, larval SL field, larval SL lab) and need to be in their own csv file. Also included is a csv with adult SL trapping data, a csv for larval SL shocking data, a - News