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: 28
Seasonal sampling for freshwater mussel environmental DNA at Bennett Island in the Clinch River, Virginia, USA 2020-2022 Seasonal sampling for freshwater mussel environmental DNA at Bennett Island in the Clinch River, Virginia, USA 2020-2022
We tested eDNA metabarcoding as a monitoring tool to detect freshwater mussel assemblages at the Bennett Island site on the Clinch River. Sampling occurred seasonally from July 2020 through October 2022. We filtered 1L water samples 100 meters upstream and 100 meters downstream of the known mussel assemblage. We amplified and sequenced data at the ND1 and COI markers (Klymus et al., 2021...
Seasonal detection and collection method comparison of Cumberlandia monodonta and Ortmanniana ligamentina female mitotype eDNA from the Big Piney River, MO, USA, June 2020 - April 2023 (ver. 3.0, April 2026) Seasonal detection and collection method comparison of Cumberlandia monodonta and Ortmanniana ligamentina female mitotype eDNA from the Big Piney River, MO, USA, June 2020 - April 2023 (ver. 3.0, April 2026)
Data describe the detection of female mitotypes from spectaclecase (Cumberlandia monodonta) and mucket (Ortmanniana ligamentina) freshwater mussel environmental DNA (eDNA) from water samples collected from the Big Piney River in Pulaski County, MO, U.S.A. Water samples were collected from 3 sites known to contain the target species. Sampling transects spanned from 100 meters upstream of...
Invasive carp environmental DNA data from the Blackwater and Lamine rivers, Missouri, 2015 Invasive carp environmental DNA data from the Blackwater and Lamine rivers, Missouri, 2015
Data describe environmental DNA (eDNA) concentrations from invasive silver and bigheaded carp (Hypophthalmichthys spp.) in Missouri’s Blackwater and Lamine Rivers in 2015. Two, 3-day sampling trips were conducted in March and September 2015 (winter and summer samples, respectively) to collect water samples and associated water quality data. Parameters include locations of collected water...
Environmental DNA shedding and degradation rates of Epioblasma capsaeformis in a laboratory setting Environmental DNA shedding and degradation rates of Epioblasma capsaeformis in a laboratory setting
Data describe designed environmental DNA (eDNA) experiments for the estimation of eDNA shedding and degradation rates for the Oyster Mussel (Epioblasma capsaeformis) at different biomass densities from water samples collected in the laboratory. A total of 12 experimental tanks (3 per biomass treatment) were used and randomly assigned one of the following biomass treatments: control = 0...
Data on the detection of Epioblasma capsaeformis using a designed environmental DNA (eDNA) survey upstream and downstream of known populations in the Clinch River, Virginia and Tennessee, 2020 to 2022 (ver 2.0, February 2026) Data on the detection of Epioblasma capsaeformis using a designed environmental DNA (eDNA) survey upstream and downstream of known populations in the Clinch River, Virginia and Tennessee, 2020 to 2022 (ver 2.0, February 2026)
These 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...
Limits of detection and quantification for several invasive carp environmental DNA (eDNA) assays Limits of detection and quantification for several invasive carp environmental DNA (eDNA) assays
Data describe the limits of detection (LOD), limits of quantification (LOQ), and associated quality assurance measurements of several environmental DNA (eDNA) assays for invasive black carp (Mylopharyngodon piceus), bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), bigheaded carps (Hypophthalmichthys spp.), and grass carp (Ctenopharyngodon idella)...
Seasonal detection and collection method comparison of Cumberlandia monodonta and Ortmanniana ligamentina male mitotype eDNA from the Big Piney River, MO, U.S.A. from July 2020 to April 2023 Seasonal detection and collection method comparison of Cumberlandia monodonta and Ortmanniana ligamentina male mitotype eDNA from the Big Piney River, MO, U.S.A. from July 2020 to April 2023
Data describe the detection of spectaclecase (Cumberlandia monodonta) and mucket (Ortmanniana ligamentina) freshwater mussel environmental DNA (eDNA) from water samples collected from the Big Piney River in Pulaski County, MO, U.S.A. Water samples were collected from 2 sites known to contain the target species by previously surveyed mussel beds. Sampling transects spanned from 100 meters...
Environmental DNA sampling of ponds in Arizona, USA for detection of invertebrate species Environmental DNA sampling of ponds in Arizona, USA for detection of invertebrate species
We tested eDNA metabarcoding as a survey tool to examine invertebrate communities in a uranium mine containment pond. We tested samples collected from surface water near mines and from one mine containment pond using one primer set that targeted the COI gene (Leray et al. 2013). Subsequent sequencing of these amplicons was used to assess eDNA genetic signature of invertebrates living in...
Development and optimization of species-specific qPCR assays for eDNA detection of the mucket (Ortamannia ligamentina) and spectaclecase (Cumberlandia monodonta) mussels’ male mitotype Development and optimization of species-specific qPCR assays for eDNA detection of the mucket (Ortamannia ligamentina) and spectaclecase (Cumberlandia monodonta) mussels’ male mitotype
This dataset describes the sensitivity (limit of detection and limit of quantification) and specificity (list of species tested against the assays) of two qPCR assays designed to detect the male mitotype of two freshwater mussel species Ortmanniana ligamentina and Cumberlandia monodonta from water samples (eDNA).
Method comparison for the detection of environmental DNA from three species of unionid mussels in a mesocosm Method comparison for the detection of environmental DNA from three species of unionid mussels in a mesocosm
Data describe a mesocosm study for the detection of mucket (Ortmanniana ligamentina), fatmucket (Lampsilis siliquoidea), and giant floater (Pyganodon grandis) freshwater mussel environmental DNA (eDNA). Water samples were collected on two different days in September of 2022 from a CERC pond containing O. ligamentina, L. siliquoidea, and P. grandis then analyzed for the presence of eDNA...
Detection of Ortmanniana ligamentina male mitotype DNA from a mesocosm during a natural spawning event Detection of Ortmanniana ligamentina male mitotype DNA from a mesocosm during a natural spawning event
Data describe a mesocosm study for the detection of Mucket (Ortmanniana ligamentina) female and male mitotype environmental DNA (eDNA) during a spawning event. Water samples (approximately 1L) were collected every Monday and Thursday for 4 weeks during August 2021 from a pond located at Columbia Environmental Research Center containing O. ligamentina and analyzed for the presence of sex...
eDNA shedding rates for juvenile and subadult black carp fed a commercial diet or a Corbicula mussel diet in a laboratory setting eDNA shedding rates for juvenile and subadult black carp fed a commercial diet or a Corbicula mussel diet in a laboratory setting
Data describe designed environmental DNA (eDNA) experiments for the estimation of eDNA shedding rates for subadult and juvenile black carp (Mylopharyngodon piceus) at different biomass densities and fed different quantities of food from water samples collected in the laboratory. Parameters described include descriptions of laboratory collected water samples that were tested to estimate
Filter Total Items: 13
Spatial distribution and relative biomass of bigheaded carps in Lake Balaton, Hungary estimated from an environmental DNA survey Spatial distribution and relative biomass of bigheaded carps in Lake Balaton, Hungary estimated from an environmental DNA survey
Silver carp (Hypophthalmichthys nobilis), bighead carp (H. molitrix) and their hybrids, collectively known as bigheaded carps, have been introduced to Lake Balaton, Hungary. The current stock sizes are difficult to assess. We investigated environmental DNA (eDNA) techniques targeted for bigheaded carps, assessed the spatial distribution of eDNA in Lake Balaton, compared eDNA...
Authors
Nora Boross, Ardo Laszlo, Duane C. Chapman, Gergely Boros, Zoltán Vitál, Viktor Tóth, Nathan Thompson, Katy E. Klymus, Catherine A. Richter
Detection and transport of environmental DNA from two federally endangered mussels 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...
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
Silver Chub spawning confirmed in the Maumee River, a tributary of Lake Erie Silver Chub spawning confirmed in the Maumee River, a tributary of Lake Erie
Objective Biodiversity is declining due to invasive species and other factors that can affect individual species differently. Silver Chub Macrhybopsis storeriana are declining in their native range, and their conservation status in the Great Lakes ranges from secure to possibly extirpated. Lake Erie once supported a large Silver Chub population until it crashed in the 1950s. Additionally...
Authors
Ryan E. Brown, Christine M. Mayer, Nathan Thompson, Corbin David Hilling, James J. Roberts, Catherine A. Richter
Environmental DNA dynamics of three species of unionid freshwater mussels Environmental DNA dynamics of three species of unionid freshwater mussels
North American freshwater mussels are of special conservation concern due to their high endemism and the multiple anthropogenic stressors affecting them. Of the over 300 species in North America, nearly one third of these species are federally listed as threatened or endangered. Environmental DNA (eDNA) analysis has been successful in detecting freshwater mussels and could aid in...
Authors
Dannise Ruiz-Ramos, Nathan Thompson, Catherine A. Richter, Megan C. Voshage, Theresa M. Schreier, Christopher M. Merkes, Katy E. Klymus
First documentation of grass carp spawning in Lake Erie’s Central Basin 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...
Authors
Corbin David Hilling, Adam J. Landry, James J. 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 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...
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 Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas
Background The 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...
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 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...
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 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...
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 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...
Authors
Katy E. Klymus, Dannise Vannesa Ruiz-Ramos, Nathan Thompson, Catherine A. Richter
Use of environmental DNA to detect grass carp spawning events 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...
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 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...
Authors
Katy E. Klymus, Catherine A. Richter, Nathan Thompson, Jo Ellen Hinck
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.
Spiked qPCR primary analysis Spiked qPCR primary analysis
This script is for analyzing raw eDNA qPCR data. It is designed to efficiently concatenate qPCR data from multiple plates exported as *.csv files. It will assist with completing several QA/QC checks and output documentation of these checks as well as helpful files for further review.
Science and Products
Filter Total Items: 28
Seasonal sampling for freshwater mussel environmental DNA at Bennett Island in the Clinch River, Virginia, USA 2020-2022 Seasonal sampling for freshwater mussel environmental DNA at Bennett Island in the Clinch River, Virginia, USA 2020-2022
We tested eDNA metabarcoding as a monitoring tool to detect freshwater mussel assemblages at the Bennett Island site on the Clinch River. Sampling occurred seasonally from July 2020 through October 2022. We filtered 1L water samples 100 meters upstream and 100 meters downstream of the known mussel assemblage. We amplified and sequenced data at the ND1 and COI markers (Klymus et al., 2021...
Seasonal detection and collection method comparison of Cumberlandia monodonta and Ortmanniana ligamentina female mitotype eDNA from the Big Piney River, MO, USA, June 2020 - April 2023 (ver. 3.0, April 2026) Seasonal detection and collection method comparison of Cumberlandia monodonta and Ortmanniana ligamentina female mitotype eDNA from the Big Piney River, MO, USA, June 2020 - April 2023 (ver. 3.0, April 2026)
Data describe the detection of female mitotypes from spectaclecase (Cumberlandia monodonta) and mucket (Ortmanniana ligamentina) freshwater mussel environmental DNA (eDNA) from water samples collected from the Big Piney River in Pulaski County, MO, U.S.A. Water samples were collected from 3 sites known to contain the target species. Sampling transects spanned from 100 meters upstream of...
Invasive carp environmental DNA data from the Blackwater and Lamine rivers, Missouri, 2015 Invasive carp environmental DNA data from the Blackwater and Lamine rivers, Missouri, 2015
Data describe environmental DNA (eDNA) concentrations from invasive silver and bigheaded carp (Hypophthalmichthys spp.) in Missouri’s Blackwater and Lamine Rivers in 2015. Two, 3-day sampling trips were conducted in March and September 2015 (winter and summer samples, respectively) to collect water samples and associated water quality data. Parameters include locations of collected water...
Environmental DNA shedding and degradation rates of Epioblasma capsaeformis in a laboratory setting Environmental DNA shedding and degradation rates of Epioblasma capsaeformis in a laboratory setting
Data describe designed environmental DNA (eDNA) experiments for the estimation of eDNA shedding and degradation rates for the Oyster Mussel (Epioblasma capsaeformis) at different biomass densities from water samples collected in the laboratory. A total of 12 experimental tanks (3 per biomass treatment) were used and randomly assigned one of the following biomass treatments: control = 0...
Data on the detection of Epioblasma capsaeformis using a designed environmental DNA (eDNA) survey upstream and downstream of known populations in the Clinch River, Virginia and Tennessee, 2020 to 2022 (ver 2.0, February 2026) Data on the detection of Epioblasma capsaeformis using a designed environmental DNA (eDNA) survey upstream and downstream of known populations in the Clinch River, Virginia and Tennessee, 2020 to 2022 (ver 2.0, February 2026)
These 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...
Limits of detection and quantification for several invasive carp environmental DNA (eDNA) assays Limits of detection and quantification for several invasive carp environmental DNA (eDNA) assays
Data describe the limits of detection (LOD), limits of quantification (LOQ), and associated quality assurance measurements of several environmental DNA (eDNA) assays for invasive black carp (Mylopharyngodon piceus), bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), bigheaded carps (Hypophthalmichthys spp.), and grass carp (Ctenopharyngodon idella)...
Seasonal detection and collection method comparison of Cumberlandia monodonta and Ortmanniana ligamentina male mitotype eDNA from the Big Piney River, MO, U.S.A. from July 2020 to April 2023 Seasonal detection and collection method comparison of Cumberlandia monodonta and Ortmanniana ligamentina male mitotype eDNA from the Big Piney River, MO, U.S.A. from July 2020 to April 2023
Data describe the detection of spectaclecase (Cumberlandia monodonta) and mucket (Ortmanniana ligamentina) freshwater mussel environmental DNA (eDNA) from water samples collected from the Big Piney River in Pulaski County, MO, U.S.A. Water samples were collected from 2 sites known to contain the target species by previously surveyed mussel beds. Sampling transects spanned from 100 meters...
Environmental DNA sampling of ponds in Arizona, USA for detection of invertebrate species Environmental DNA sampling of ponds in Arizona, USA for detection of invertebrate species
We tested eDNA metabarcoding as a survey tool to examine invertebrate communities in a uranium mine containment pond. We tested samples collected from surface water near mines and from one mine containment pond using one primer set that targeted the COI gene (Leray et al. 2013). Subsequent sequencing of these amplicons was used to assess eDNA genetic signature of invertebrates living in...
Development and optimization of species-specific qPCR assays for eDNA detection of the mucket (Ortamannia ligamentina) and spectaclecase (Cumberlandia monodonta) mussels’ male mitotype Development and optimization of species-specific qPCR assays for eDNA detection of the mucket (Ortamannia ligamentina) and spectaclecase (Cumberlandia monodonta) mussels’ male mitotype
This dataset describes the sensitivity (limit of detection and limit of quantification) and specificity (list of species tested against the assays) of two qPCR assays designed to detect the male mitotype of two freshwater mussel species Ortmanniana ligamentina and Cumberlandia monodonta from water samples (eDNA).
Method comparison for the detection of environmental DNA from three species of unionid mussels in a mesocosm Method comparison for the detection of environmental DNA from three species of unionid mussels in a mesocosm
Data describe a mesocosm study for the detection of mucket (Ortmanniana ligamentina), fatmucket (Lampsilis siliquoidea), and giant floater (Pyganodon grandis) freshwater mussel environmental DNA (eDNA). Water samples were collected on two different days in September of 2022 from a CERC pond containing O. ligamentina, L. siliquoidea, and P. grandis then analyzed for the presence of eDNA...
Detection of Ortmanniana ligamentina male mitotype DNA from a mesocosm during a natural spawning event Detection of Ortmanniana ligamentina male mitotype DNA from a mesocosm during a natural spawning event
Data describe a mesocosm study for the detection of Mucket (Ortmanniana ligamentina) female and male mitotype environmental DNA (eDNA) during a spawning event. Water samples (approximately 1L) were collected every Monday and Thursday for 4 weeks during August 2021 from a pond located at Columbia Environmental Research Center containing O. ligamentina and analyzed for the presence of sex...
eDNA shedding rates for juvenile and subadult black carp fed a commercial diet or a Corbicula mussel diet in a laboratory setting eDNA shedding rates for juvenile and subadult black carp fed a commercial diet or a Corbicula mussel diet in a laboratory setting
Data describe designed environmental DNA (eDNA) experiments for the estimation of eDNA shedding rates for subadult and juvenile black carp (Mylopharyngodon piceus) at different biomass densities and fed different quantities of food from water samples collected in the laboratory. Parameters described include descriptions of laboratory collected water samples that were tested to estimate
Filter Total Items: 13
Spatial distribution and relative biomass of bigheaded carps in Lake Balaton, Hungary estimated from an environmental DNA survey Spatial distribution and relative biomass of bigheaded carps in Lake Balaton, Hungary estimated from an environmental DNA survey
Silver carp (Hypophthalmichthys nobilis), bighead carp (H. molitrix) and their hybrids, collectively known as bigheaded carps, have been introduced to Lake Balaton, Hungary. The current stock sizes are difficult to assess. We investigated environmental DNA (eDNA) techniques targeted for bigheaded carps, assessed the spatial distribution of eDNA in Lake Balaton, compared eDNA...
Authors
Nora Boross, Ardo Laszlo, Duane C. Chapman, Gergely Boros, Zoltán Vitál, Viktor Tóth, Nathan Thompson, Katy E. Klymus, Catherine A. Richter
Detection and transport of environmental DNA from two federally endangered mussels 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...
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
Silver Chub spawning confirmed in the Maumee River, a tributary of Lake Erie Silver Chub spawning confirmed in the Maumee River, a tributary of Lake Erie
Objective Biodiversity is declining due to invasive species and other factors that can affect individual species differently. Silver Chub Macrhybopsis storeriana are declining in their native range, and their conservation status in the Great Lakes ranges from secure to possibly extirpated. Lake Erie once supported a large Silver Chub population until it crashed in the 1950s. Additionally...
Authors
Ryan E. Brown, Christine M. Mayer, Nathan Thompson, Corbin David Hilling, James J. Roberts, Catherine A. Richter
Environmental DNA dynamics of three species of unionid freshwater mussels Environmental DNA dynamics of three species of unionid freshwater mussels
North American freshwater mussels are of special conservation concern due to their high endemism and the multiple anthropogenic stressors affecting them. Of the over 300 species in North America, nearly one third of these species are federally listed as threatened or endangered. Environmental DNA (eDNA) analysis has been successful in detecting freshwater mussels and could aid in...
Authors
Dannise Ruiz-Ramos, Nathan Thompson, Catherine A. Richter, Megan C. Voshage, Theresa M. Schreier, Christopher M. Merkes, Katy E. Klymus
First documentation of grass carp spawning in Lake Erie’s Central Basin 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...
Authors
Corbin David Hilling, Adam J. Landry, James J. 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 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...
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 Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas
Background The 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...
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 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...
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 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...
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 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...
Authors
Katy E. Klymus, Dannise Vannesa Ruiz-Ramos, Nathan Thompson, Catherine A. Richter
Use of environmental DNA to detect grass carp spawning events 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...
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 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...
Authors
Katy E. Klymus, Catherine A. Richter, Nathan Thompson, Jo Ellen Hinck
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.
Spiked qPCR primary analysis Spiked qPCR primary analysis
This script is for analyzing raw eDNA qPCR data. It is designed to efficiently concatenate qPCR data from multiple plates exported as *.csv files. It will assist with completing several QA/QC checks and output documentation of these checks as well as helpful files for further review.