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
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
Assessment of carbon dioxide piscicide treatments
Seasonal trends in eDNA detection and occupancy of bigheaded carps
Detecting the movement and spawning activity of bigheaded carps with environmental DNA
Environmental DNA mapping of Zebra Mussel populations
Validation of eDNA markers for New Zealand mudsnail surveillance and initial eDNA monitoring at Mississippi River Basin sites
Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data
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.
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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 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. DockerAssessment 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, BigheadAuthorsAaron R. Cupp, Justin Smerud, John Tix, Jose Rivera, Stacie A. Kageyama, Christopher M. Merkes, Richard A. Erickson, Jon Amberg, Mark P. GaikowskiSeasonal 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) approachesAuthorsRichard A. Erickson, Christopher M. Merkes, Craig Jackson, Reuben Goforth, Jon AmbergDetecting 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 carpAuthorsRichard A. Erickson, Christopher B. Rees, Alison A. Coulter, Christopher M. Merkes, S. Grace McCalla, Katherine F Touzinsky, Liza R. Walleser, Reuben R. Goforth, Jon AmbergEnvironmental DNA mapping of Zebra Mussel populations
Environmental DNA (eDNA) has become a popular tool for detecting aquatic invasive species, but advancements have made it possible to potentially answer other questions like reproduction, movement, and abundance of the targeted organism. In this study we developed a Zebra Mussel (Dreissena polymorpha) eDNA protocol. We then determined if this assay could be used to help determine Zebra Mussel biomaAuthorsJon Amberg, Christopher M. MerkesValidation of eDNA markers for New Zealand mudsnail surveillance and initial eDNA monitoring at Mississippi River Basin sites
The performance of newly developed New Zealand mudsnail (Potamopyrgus antipodarum; NZMS) genetic markers for environmental (eDNA) analysis of water were compared across two laboratories. The genetic markers were tested in four quantitative polymerase chain reaction assays targeting two regions of the NZMS mitochondrial genome, specifically the cytochrome c oxidase subunit 1 (coi) and cytochrome bAuthorsChristopher M. Merkes, Keith N. Turnquist, Christopher B. Rees, Jon J. AmbergPersistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data
The prevention of non-indigenous aquatic invasive species spreading into new areas is a goal of many resource managers. New techniques have been developed to survey for species that are difficult to capture with conventional gears that involve the detection of their DNA in water samples (eDNA). This technique is currently used to track the invasion of bigheaded carps (silver carp and bighead carp;AuthorsChristopher M. Merkes, S. Grace McCalla, Nathan R. Jensen, Mark P. Gaikowski, Jon J. AmbergNon-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.
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