Nathan Thompson
Nathan is a Biologist at the Columbia Environmental Research Center.
His focus is environmental DNA (eDNA). He uses qPCR to measure the amount of eDNA of Asian carp in water samples for the purpose of detecting changes between conditions and/or time. Nathan is also involved in a project using eDNA for species detection via metagenomics in Arizona.
Professional Experience
July 2014 - present, Biologist, CERC, Columbia, MO
May 2013 - July 2014, Student services contractor, CERC, Columbia, MO
March 2011 - May 2013, Senior laboratory technician, University of Missouri, Columbia, MO
Education and Certifications
B.S. in Biological Science, University of Missouri, 2012
Science and Products
Filter Total Items: 14
Laboratory estimates of eDNA degradation rates for Actinionais ligamentina eDNA
Data describe a designed environmental DNA (eDNA) experiment for the estimation of eDNA degradation rates for the mucket (Actinonaias ligamentina) from water samples collected in the laboratory. Samples were collected from experiments performed from November 01, 2019 to November 15, 2019 at the USGS Columbia Environmental Research Center, Missouri
Development and testing of a qPCR assay for Lampsilis siliquoidea eDNA
Data describe specificity and sensitivity testing for the L.sil2 assay. This assay is used to amplify eDNA from the freshwater mussel Lampsilis siliquoidea.
Development, testing and use of four species-specific qPCR assays for freshwater mussel eDNA detection in the Niobrara River
This data consists of information on the specificity and sensitivity of 4 species specific qPCR assays for the detection of eDNA from 4 species of freshwater mussels, specifically Lampsilis cardium, Lampsilis siliquoidea, Pyganodon grandis, and Anodontoides ferussacianus. The data also contain the results of eDNA sampling in Niobrara River at Niobrara National Scenic River and Agate Fossil Beds Na
Environmental DNA shedding rates in laboratory conditions for Cumberlandia monodonta, Actinonaias ligamentina, and Lampsilis siliquoidea.
Data describe designed environmental DNA (eDNA) experiments for the estimation of eDNA shedding rates for the spectaclecase (Cumberlandia monodonta), mucket (Actinonaias ligamentina), and fatmucket (Lampsilis siliquoidea) from water samples collected in the laboratory under differing laboratory conditions. Shedding rates were tested under variable mussel biomass, diet, and temperature. Parameters
Water chemistry and molecular eDNA data observed in experimental laboratory mesocosms exposed to different nitrogen amendments in the presence or absence of a nitrifier enriched microbial community
Data describe the results of a controlled laboratory mesocosm experiment evaluating the influence of a nitrifier enriched microbial community on silver carp (Hypophthalmichthys molitrix) milt eDNA degradation. Parameters described include the concentration results, limit of detection, and limit of quantification of two silver carp specific quantitative PCR assays and water chemistry results of exp
Data on the detection of Epioblasma capsaeformis using a designed environmental DNA (eDNA) survey upstream and downstream of known populations in the Clinch River, Tennessee (2019 to 2021)
Data describe a designed environmental DNA (eDNA) survey for the detection of oyster mussel (Epioblasma capsaeformis) from field collected water samples. Parameters described include the limit of detection and limit of quantification of the assay; a list of freshwater mussel species tissue samples that were used to test specificity of the assay; and field collected water samples that were tested t
Data on the detection of Cumberlandia monodonta using a designed environmental DNA (eDNA) survey upstream and downstream of known populations in the Big Piney River, Missouri 2020 – 2022 (ver. 2.0, August 2024)
Data describe a designed environmental DNA (eDNA) survey for the detection of Spectaclecase (Cumberlandia monodonta, also referred to as Margaritifera monodonta) from field collected water samples. Parameters described include the limit of detection and limit of quantification of the assay; a list of freshwater mussel species tissue samples that were used to test specificity of the assay; and fiel
Degradation of Cumberlandia monodonta environmental DNA over time in laboratory conditions using the C.monCOI assay
Data describe a designed environmental DNA (eDNA) experiment for the estimation of eDNA degradation rates for the spectaclecase (Cumberlandia monodonta) from water samples collected in the laboratory. Parameters described include laboratory collected water samples that were tested to estimate concentration of spectaclecase DNA and associated quality assurance data. Samples were collected from expe
Genomic variation in the genus Pimephales: raw sequence data and single-nucleotide polymorphisms
The fathead minnow (Pimephales promelas) is a key model of vertebrate toxicity. Standardized tests of toxicity in fathead minnow have been developed to support regulatory science, and much is known about the response of the species to various environmental pollutants. However, there is little data on genetic variation within the species, despite the potential influence of genetic background on tox
Longnose darter (Percina nasuta) eDNA survey results from the St. Francis River, Missouri 2018
Data describe a designed environmental DNA (eDNA) survey for the detection of longnose darter (Percina nasuta) in field collected water samples. Parameters described include the limit of detection and limit of quantification of the assay; a list of freshwater fish species tissue samples that were used to test specificity of the assay; and field collected water samples that were tested to detect th
Metabarcoding data from freshwater mussel eDNA collected in Clinch River, Virginia 2017
Data from metabarcoding assays to detect a suite of mussel species using mitochondrial DNA regions of the cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit (ND1) genes sequences.
Mucket eDNA detection in Wallen's Bend, Clinch river, Tennessee, September 2019
The data describe the technical performance of a designed qPCR assay for the detection of mucket (Actinonaias ligamentina) eDNA from field collected water samples. Parameters described include the sequences of the primers and probes used; the limit of detection and limit of quantification for the assay; a list of freshwater mussels species that were used to test specificity of the assay; and in si
Detection and transport of environmental DNA from two federally endangered mussels
Environmental DNA (eDNA) offers a novel approach to supplement traditional surveys and provide increased spatial and temporal information on species detection, and it can be especially beneficial for detecting at risk or threatened species with minimal impact on the target species. The transport of eDNA in lotic environments is an important component in providing more informed descriptions of wher
Authors
Brandon James Sansom, Dannise Vannesa Ruiz-Ramos, Nathan Thompson, Maura O Roberts, Zachary Taylor, Katie Ortiz, Jess W. Jones, Catherine A. Richter, Katy E. Klymus
First documentation of grass carp spawning in Lake Erie’s Central Basin
Grass carp (Ctenopharyngodon idella) are non-indigenous to North America having been translocated to the United States in the 1960s as a potential non-chemical solution for nuisance aquatic vegetation. Reproductively viable grass carp now exist in many watersheds in the United States. In the Great Lakes basin, grass carp were first discovered in the 1980s with direct confirmation of successful rep
Authors
Corbin David Hilling, Adam J. Landry, James Roberts, Nathan Thompson, Cathy A. Richter, Ryan E. Brown, Christine M. Mayer, Song S. Qian
A nitrifier-enriched microbial community contributes to the degradation of environmental DNA
Environmental DNA (eDNA) surveys are a promising alternative to traditional monitoring of invasive species, rare species, and biodiversity. Detecting organism-specific eDNA reduces the need to collect physical specimens for population estimates, and the high sensitivity of eDNA assays may improve detection of rare or cryptic species. However, correlating estimated concentrations of eDNA with speci
Authors
Rachelle Elaine Beattie, Caren C. Helbing, Jacob J. Imbery, Katy E. Klymus, Jonathan Lopez Duran, Cathy A. Richter, Anita A. Thambirajah, Nathan Thompson, Thea M. Edwards
Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas
BackgroundThe fathead minnow (Pimephales promelas) is a model species for toxicological research. A high-quality genome reference sequence is available, and genomic methods are increasingly used in toxicological studies of the species. However, phylogenetic relationships within the genus remain incompletely known and little population-genomic data are available for fathead minnow despite the poten
Authors
Katy E. Klymus, Robert A. Hrabik, Nathan Thompson, Robert S. Cornman
A comparison of eDNA and visual survey methods for detection of longnose darter Percina nasuta in Missouri
The longnose darter Percina nasuta is a rare and cryptic fish that recently disappeared from much of its historic range. We developed and used an environmental DNA (eDNA) assay for longnose darter paired with visual surveys to better determine the species’ range and compare detection probability between sampling approaches in an occupancy modeling framework. We detected longnose darter eDNA furthe
Authors
Jacob Thomas Westhoff, Leah K. Berkman, Katy E. Klymus, Nathan Thompson, Cathy A. Richter
Metabarcoding assays for the detection of freshwater mussels (Unionida) with environmental DNA
Freshwater mussels of the order Unionida are a widely distributed taxon that are important in maintaining freshwater ecosystems and are also highly imperiled throughout the world. Monitoring of mussel populations with environmental DNA (eDNA) is an attractive alternative to traditional methods because it is noninvasive and requires less labor and taxonomic knowledge from field personnel. We develo
Authors
Katy E. Klymus, Catherine A. Richter, Nathan Thompson, Jo Ellen Hinck, Jess W. Jones
Development and testing of species-specific quantitative PCR assays for environmental DNA applications
New, non-invasive methods for detecting and monitoring species presence are being developed to aid in fisheries and wildlife conservation management. The use of environmental DNA (eDNA) samples for detecting macrobiota is one such group of methods that is rapidly becoming popular and being implemented in national management programs. Here we focus on the development of species-specific targeted as
Authors
Katy E. Klymus, Dannise Vannesa Ruiz-Ramos, Nathan Thompson, Catherine A. Richter
Use of environmental DNA to detect grass carp spawning events
The timing and location of spawning events are important data for managers seeking to control invasive grass carp populations. Ichthyoplankton tows for grass carp eggs and larvae can be used to detect spawning events; however, these samples can be highly debris-laden, and are expensive and laborious to process. An alternative method, environmental DNA (eDNA) technology, has proven effective in det
Authors
Cari-Ann Hayer, Michael F. Bayless, Amy E. George, Nathan Thompson, Catherine A. Richter, Duane Chapman
Metabarcoding of environmental DNA samples to explore the use of uranium mine containment ponds as a water source for wildlife
Understanding how anthropogenic impacts on the landscape affect wildlife requires a knowledge of community assemblages. Species surveys are the first step in assessing community structure, and recent molecular applications such as metabarcoding and environmental DNA analyses have been proposed as an additional and complementary wildlife survey method. Here, we test eDNA metabarcoding as a survey t
Authors
Katy E. Klymus, Catherine A. Richter, Nathan Thompson, Jo Ellen Hinck
Experimental observations on the decay of environmental DNA from bighead and silver carps
Interest in the field of environmental DNA (eDNA) is growing rapidly and eDNA surveys are becoming an important consideration for aquatic resource managers dealing with invasive species. However, in order for eDNA monitoring to mature as a research and management tool, there are several critical knowledge gaps that must be filled. One such gap is the fate of eDNA materials in the aquatic environme
Authors
Richard F. Lance, Katy E. Klymus, Catherine A. Richter, Xin Guan, Heather L. Farrington, Matthew R. Carr, Nathan Thompson, Duane Chapman, Kelly L. Baerwaldt
Non-USGS Publications**
Murphy, M.A., Thompson, N.L., and Schul, J., 2016, Keeping up with the neighbor: a novel mechanism of call synchrony in Neoconocephalus ensiger katydids: Journal of Comparative Physiology A, v. 202, no. 3, p. 225-234
**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.
Science and Products
Filter Total Items: 14
Laboratory estimates of eDNA degradation rates for Actinionais ligamentina eDNA
Data describe a designed environmental DNA (eDNA) experiment for the estimation of eDNA degradation rates for the mucket (Actinonaias ligamentina) from water samples collected in the laboratory. Samples were collected from experiments performed from November 01, 2019 to November 15, 2019 at the USGS Columbia Environmental Research Center, Missouri
Development and testing of a qPCR assay for Lampsilis siliquoidea eDNA
Data describe specificity and sensitivity testing for the L.sil2 assay. This assay is used to amplify eDNA from the freshwater mussel Lampsilis siliquoidea.
Development, testing and use of four species-specific qPCR assays for freshwater mussel eDNA detection in the Niobrara River
This data consists of information on the specificity and sensitivity of 4 species specific qPCR assays for the detection of eDNA from 4 species of freshwater mussels, specifically Lampsilis cardium, Lampsilis siliquoidea, Pyganodon grandis, and Anodontoides ferussacianus. The data also contain the results of eDNA sampling in Niobrara River at Niobrara National Scenic River and Agate Fossil Beds Na
Environmental DNA shedding rates in laboratory conditions for Cumberlandia monodonta, Actinonaias ligamentina, and Lampsilis siliquoidea.
Data describe designed environmental DNA (eDNA) experiments for the estimation of eDNA shedding rates for the spectaclecase (Cumberlandia monodonta), mucket (Actinonaias ligamentina), and fatmucket (Lampsilis siliquoidea) from water samples collected in the laboratory under differing laboratory conditions. Shedding rates were tested under variable mussel biomass, diet, and temperature. Parameters
Water chemistry and molecular eDNA data observed in experimental laboratory mesocosms exposed to different nitrogen amendments in the presence or absence of a nitrifier enriched microbial community
Data describe the results of a controlled laboratory mesocosm experiment evaluating the influence of a nitrifier enriched microbial community on silver carp (Hypophthalmichthys molitrix) milt eDNA degradation. Parameters described include the concentration results, limit of detection, and limit of quantification of two silver carp specific quantitative PCR assays and water chemistry results of exp
Data on the detection of Epioblasma capsaeformis using a designed environmental DNA (eDNA) survey upstream and downstream of known populations in the Clinch River, Tennessee (2019 to 2021)
Data describe a designed environmental DNA (eDNA) survey for the detection of oyster mussel (Epioblasma capsaeformis) from field collected water samples. Parameters described include the limit of detection and limit of quantification of the assay; a list of freshwater mussel species tissue samples that were used to test specificity of the assay; and field collected water samples that were tested t
Data on the detection of Cumberlandia monodonta using a designed environmental DNA (eDNA) survey upstream and downstream of known populations in the Big Piney River, Missouri 2020 – 2022 (ver. 2.0, August 2024)
Data describe a designed environmental DNA (eDNA) survey for the detection of Spectaclecase (Cumberlandia monodonta, also referred to as Margaritifera monodonta) from field collected water samples. Parameters described include the limit of detection and limit of quantification of the assay; a list of freshwater mussel species tissue samples that were used to test specificity of the assay; and fiel
Degradation of Cumberlandia monodonta environmental DNA over time in laboratory conditions using the C.monCOI assay
Data describe a designed environmental DNA (eDNA) experiment for the estimation of eDNA degradation rates for the spectaclecase (Cumberlandia monodonta) from water samples collected in the laboratory. Parameters described include laboratory collected water samples that were tested to estimate concentration of spectaclecase DNA and associated quality assurance data. Samples were collected from expe
Genomic variation in the genus Pimephales: raw sequence data and single-nucleotide polymorphisms
The fathead minnow (Pimephales promelas) is a key model of vertebrate toxicity. Standardized tests of toxicity in fathead minnow have been developed to support regulatory science, and much is known about the response of the species to various environmental pollutants. However, there is little data on genetic variation within the species, despite the potential influence of genetic background on tox
Longnose darter (Percina nasuta) eDNA survey results from the St. Francis River, Missouri 2018
Data describe a designed environmental DNA (eDNA) survey for the detection of longnose darter (Percina nasuta) in field collected water samples. Parameters described include the limit of detection and limit of quantification of the assay; a list of freshwater fish species tissue samples that were used to test specificity of the assay; and field collected water samples that were tested to detect th
Metabarcoding data from freshwater mussel eDNA collected in Clinch River, Virginia 2017
Data from metabarcoding assays to detect a suite of mussel species using mitochondrial DNA regions of the cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit (ND1) genes sequences.
Mucket eDNA detection in Wallen's Bend, Clinch river, Tennessee, September 2019
The data describe the technical performance of a designed qPCR assay for the detection of mucket (Actinonaias ligamentina) eDNA from field collected water samples. Parameters described include the sequences of the primers and probes used; the limit of detection and limit of quantification for the assay; a list of freshwater mussels species that were used to test specificity of the assay; and in si
Detection and transport of environmental DNA from two federally endangered mussels
Environmental DNA (eDNA) offers a novel approach to supplement traditional surveys and provide increased spatial and temporal information on species detection, and it can be especially beneficial for detecting at risk or threatened species with minimal impact on the target species. The transport of eDNA in lotic environments is an important component in providing more informed descriptions of wher
Authors
Brandon James Sansom, Dannise Vannesa Ruiz-Ramos, Nathan Thompson, Maura O Roberts, Zachary Taylor, Katie Ortiz, Jess W. Jones, Catherine A. Richter, Katy E. Klymus
First documentation of grass carp spawning in Lake Erie’s Central Basin
Grass carp (Ctenopharyngodon idella) are non-indigenous to North America having been translocated to the United States in the 1960s as a potential non-chemical solution for nuisance aquatic vegetation. Reproductively viable grass carp now exist in many watersheds in the United States. In the Great Lakes basin, grass carp were first discovered in the 1980s with direct confirmation of successful rep
Authors
Corbin David Hilling, Adam J. Landry, James Roberts, Nathan Thompson, Cathy A. Richter, Ryan E. Brown, Christine M. Mayer, Song S. Qian
A nitrifier-enriched microbial community contributes to the degradation of environmental DNA
Environmental DNA (eDNA) surveys are a promising alternative to traditional monitoring of invasive species, rare species, and biodiversity. Detecting organism-specific eDNA reduces the need to collect physical specimens for population estimates, and the high sensitivity of eDNA assays may improve detection of rare or cryptic species. However, correlating estimated concentrations of eDNA with speci
Authors
Rachelle Elaine Beattie, Caren C. Helbing, Jacob J. Imbery, Katy E. Klymus, Jonathan Lopez Duran, Cathy A. Richter, Anita A. Thambirajah, Nathan Thompson, Thea M. Edwards
Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas
BackgroundThe fathead minnow (Pimephales promelas) is a model species for toxicological research. A high-quality genome reference sequence is available, and genomic methods are increasingly used in toxicological studies of the species. However, phylogenetic relationships within the genus remain incompletely known and little population-genomic data are available for fathead minnow despite the poten
Authors
Katy E. Klymus, Robert A. Hrabik, Nathan Thompson, Robert S. Cornman
A comparison of eDNA and visual survey methods for detection of longnose darter Percina nasuta in Missouri
The longnose darter Percina nasuta is a rare and cryptic fish that recently disappeared from much of its historic range. We developed and used an environmental DNA (eDNA) assay for longnose darter paired with visual surveys to better determine the species’ range and compare detection probability between sampling approaches in an occupancy modeling framework. We detected longnose darter eDNA furthe
Authors
Jacob Thomas Westhoff, Leah K. Berkman, Katy E. Klymus, Nathan Thompson, Cathy A. Richter
Metabarcoding assays for the detection of freshwater mussels (Unionida) with environmental DNA
Freshwater mussels of the order Unionida are a widely distributed taxon that are important in maintaining freshwater ecosystems and are also highly imperiled throughout the world. Monitoring of mussel populations with environmental DNA (eDNA) is an attractive alternative to traditional methods because it is noninvasive and requires less labor and taxonomic knowledge from field personnel. We develo
Authors
Katy E. Klymus, Catherine A. Richter, Nathan Thompson, Jo Ellen Hinck, Jess W. Jones
Development and testing of species-specific quantitative PCR assays for environmental DNA applications
New, non-invasive methods for detecting and monitoring species presence are being developed to aid in fisheries and wildlife conservation management. The use of environmental DNA (eDNA) samples for detecting macrobiota is one such group of methods that is rapidly becoming popular and being implemented in national management programs. Here we focus on the development of species-specific targeted as
Authors
Katy E. Klymus, Dannise Vannesa Ruiz-Ramos, Nathan Thompson, Catherine A. Richter
Use of environmental DNA to detect grass carp spawning events
The timing and location of spawning events are important data for managers seeking to control invasive grass carp populations. Ichthyoplankton tows for grass carp eggs and larvae can be used to detect spawning events; however, these samples can be highly debris-laden, and are expensive and laborious to process. An alternative method, environmental DNA (eDNA) technology, has proven effective in det
Authors
Cari-Ann Hayer, Michael F. Bayless, Amy E. George, Nathan Thompson, Catherine A. Richter, Duane Chapman
Metabarcoding of environmental DNA samples to explore the use of uranium mine containment ponds as a water source for wildlife
Understanding how anthropogenic impacts on the landscape affect wildlife requires a knowledge of community assemblages. Species surveys are the first step in assessing community structure, and recent molecular applications such as metabarcoding and environmental DNA analyses have been proposed as an additional and complementary wildlife survey method. Here, we test eDNA metabarcoding as a survey t
Authors
Katy E. Klymus, Catherine A. Richter, Nathan Thompson, Jo Ellen Hinck
Experimental observations on the decay of environmental DNA from bighead and silver carps
Interest in the field of environmental DNA (eDNA) is growing rapidly and eDNA surveys are becoming an important consideration for aquatic resource managers dealing with invasive species. However, in order for eDNA monitoring to mature as a research and management tool, there are several critical knowledge gaps that must be filled. One such gap is the fate of eDNA materials in the aquatic environme
Authors
Richard F. Lance, Katy E. Klymus, Catherine A. Richter, Xin Guan, Heather L. Farrington, Matthew R. Carr, Nathan Thompson, Duane Chapman, Kelly L. Baerwaldt
Non-USGS Publications**
Murphy, M.A., Thompson, N.L., and Schul, J., 2016, Keeping up with the neighbor: a novel mechanism of call synchrony in Neoconocephalus ensiger katydids: Journal of Comparative Physiology A, v. 202, no. 3, p. 225-234
**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.