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Chris M Merkes

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

Filter Total Items: 15

Assessment 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,
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Ecosystems, Great Lakes Science Center, Upper Midwest Environmental Sciences Center

Using environmental DNA (eDNA) to detect the endangered Spectaclecase Mussel (<i>Margaritifera monodonta</i>)

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 th
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Ecosystems, Upper Midwest Environmental Sciences Center

Robotic 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 sample
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Ecosystems, Idaho Water Science Center, Northern Rocky Mountain Science Center

Reporting 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 establis
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Ecosystems, Wetland and Aquatic Research Center , Upper Midwest Environmental Sciences Center, Columbia Environmental Research Center

Refinement 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 uncertaintie
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Ecosystems, Upper Midwest Environmental Sciences Center

Sampling 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 f
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Ecosystems, Upper Midwest Environmental Sciences Center

Development 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 c
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Ecosystems, Upper Midwest Environmental Sciences Center

Environmental 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 resour
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Ecosystems, Upper Midwest Environmental Sciences Center

Assessment of carbon dioxide piscicide treatments

Few chemicals are approved to control or eradicate nuisance fish populations in the United States. Carbon dioxide (CO2) is currently being developed and studied as a new piscicide option for nonselective population control. This study evaluated dry ice (solid state CO2) as a simple CO2 delivery method during winter piscicide applications. Nonnative Silver Carp Hypophthalmichthys molitrix, Bighead
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Ecosystems, Upper Midwest Environmental Sciences Center

Correlating 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 poly
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Ecosystems, Upper Midwest Environmental Sciences Center

Seasonal trends in eDNA detection and occupancy of bigheaded carps

Bigheaded carps, which include silver and bighead carp, are threatening to invade the Great Lakes. These species vary seasonally in distribution and abundance due to environmental conditions such as precipitation and temperature. Monitoring this seasonal movement is important for management to control the population size and spread of the species. We examined if environmental DNA (eDNA) approaches
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Ecosystems, Upper Midwest Environmental Sciences Center

Detecting the movement and spawning activity of bigheaded carps with environmental DNA

Bigheaded carps are invasive fishes threatening to invade the Great Lakes basin and establish spawning populations, and have been monitored using environmental DNA (eDNA). Not only does eDNA hold potential for detecting the presence of species, but may also allow for quantitative comparisons like relative abundance of species across time or space. We examined the relationships among bigheaded carp
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Ecosystems, Upper Midwest Environmental Sciences Center

Pre-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.0116627
Wiley 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
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Sealing MBARI Environmental Sample Processor (robot) into its housing

Environmental 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...
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Ecosystems, Northern Rocky Mountain Science Center
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Environmental 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...
Learn More
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A screen capture of the eDNA application home page.

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...
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Upper Midwest Environmental Sciences Center
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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...
Learn More
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Zebra Mussels, Dreissena polymorpha

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...
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Upper Midwest Environmental Sciences Center
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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...
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USGS Scientist Chris Merkes using portable detection ki

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...
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Invasive Species Program, Upper Midwest Environmental Sciences Center
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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...
Learn More
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Asian carp captured on the Wabash River

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...
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Invasive Species Program, Upper Midwest Environmental Sciences Center
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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...
Learn More
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UMESC Scientist prepares eDNA sample

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...
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Invasive Species Program, Upper Midwest Environmental Sciences Center
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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...
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Developmental 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, demonstra
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Great Lakes Science Center

Assessment 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
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Upper Midwest Environmental Sciences Center

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
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Upper Midwest Environmental Sciences Center

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