Kara Jones, PhD (Former Employee)
Science and Products
Advancing the Environmental DNA Toolkit for Ecosystem Monitoring and Management
The emerging field of Environmental DNA (eDNA) analysis allows characterization of species presence and community biodiversity by identifying trace amounts of genetic material left behind as organisms move through their environments. EESC scientists have been using eDNA technologies to detect native and rare species and as community biomonitoring tools.
Mesophotic and Deep Benthic Communities (MDBC) eDNA metabarcoding: PC2202, NOAA Ship Pisces, June 30-July 11, 2022 Mesophotic and Deep Benthic Communities (MDBC) eDNA metabarcoding: PC2202, NOAA Ship Pisces, June 30-July 11, 2022
Data from environmental DNA (eDNA) samples filtered from seawater collected in the Gulf of America during a research expedition on the NOAA Ship Pisces from June 30-July 11, 2022. Samples were collected at depths throughout the water column using Niskins mounted to rosettes on Connectivity-Temperature-Depth instruments (CTDs). Each eDNA sample was amplified using four primer sets: MiFish...
Mesophotic and Deep Benthic Communities (MDBC) eDNA metabarcoding: NF2206, R/V Nancy Foster, August 2022 Mesophotic and Deep Benthic Communities (MDBC) eDNA metabarcoding: NF2206, R/V Nancy Foster, August 2022
Data from environmental DNA (eDNA) samples filtered from seawater collected in the Gulf of America during a research expedition on the R/V Nancy Foster in August 2022. Samples were collected at depths throughout the water column using Niskins mounted to rosettes on Connectivity-Temperature-Depth instruments (CTDs) or Niskins mounted to remote operated vehicles (ROVs). Each eDNA sample...
Mesophotic and Deep Benthic Communities (MDBC) eDNA metabarcoding: PS2308, R/V Point Sur, September 2022 Mesophotic and Deep Benthic Communities (MDBC) eDNA metabarcoding: PS2308, R/V Point Sur, September 2022
Data from environmental DNA (eDNA) samples filtered from seawater collected in the Gulf of America during a research expedition on the R/V Point Sur in September 2022. Samples were collected at depths throughout the water column. Each eDNA sample was amplified using four primer sets: MiFish 12S rRNA marker targeting ray-finned fishes; 28S rRNA marker targeting corals and other cnidarians...
Genomic data from reduced representation DNA sequencing libraries of two partially fossorial salamanders Plethodon jordani and Desmognathus wrighti from Great Smoky Mountains National Park Genomic data from reduced representation DNA sequencing libraries of two partially fossorial salamanders Plethodon jordani and Desmognathus wrighti from Great Smoky Mountains National Park
This dataset contains sample information about the origin of the Desmognathus wrighti and Plethodon jordani salamanders collected from Great Smoky Mountains National Park and sequenced, and their corresponding SNP genotype data. These data were used to examine patterns of genomic structure of these two salamander species within Great Smoky Mountains National Park. The raw sequence data...
Detections of marine fauna using environmental DNA metabarcoding of seawater samples from the northern Gulf of America Detections of marine fauna using environmental DNA metabarcoding of seawater samples from the northern Gulf of America
We sampled seawater from nine mesophotic reef sites in the Pinnacles Trend and DeSoto Rim areas in the northern Gulf of America in October 2022 to complement and inform restoration investments for coral communities. Four primer sets were used to amplify environmental DNA (eDNA) from seawater, targeting metazoans, eukaryotic plankton and protists, corals, and fishes. Across all markers...
Environmental DNA detections from deep seafloor habitats in the California Current Large Marine Ecosystem Environmental DNA detections from deep seafloor habitats in the California Current Large Marine Ecosystem
Environmental DNA (eDNA) metabarcoding may have utility in biodiversity surveys of marine environments, particularly for small, rare, or cryptic taxa that are more difficult to study using traditional methods (e.g., trawling and visual surveys). For this study, we used an eDNA metabarcoding approach to characterize biodiversity in the above-seafloor water column across three West Coast...
Arthropod detections from eDNA metabarcoding of flower filtrate and DNA derived from bulk samples of insects Arthropod detections from eDNA metabarcoding of flower filtrate and DNA derived from bulk samples of insects
We compared pollinator diversity derived from environmental DNA (eDNA) extracted from flowers and DNA extracted from pulverized bulk samples of insects collected from vane traps deployed at the same sites. We used three metabarcoding primers, two of which target arthropods generally (COI-Jusino and 16S-Marquina) and one that targets bumblebees (Bombus spp., COI-Milam). Across methods, we...
Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly: Assessing Population Structure, Facilitating Supportive Breeding, and Identifying Adaptive Potential Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly: Assessing Population Structure, Facilitating Supportive Breeding, and Identifying Adaptive Potential
The purpose of this study was to collect and analyze non-invasive DNA specimens from the endangered island marble butterfly (Euchloe ausonides insulanus) to assess population structure, identify adaptive potential, facilitate captive propagation, and support translocation planning. We used DNA extracted from meconium, exuviae, and natural mortalities to generate and test thirteen new...
Metabarcoding analysis of arthropod pollinator diversity: A methodological comparison of eDNA derived from flowers and DNA derived from bulk samples of insects Metabarcoding analysis of arthropod pollinator diversity: A methodological comparison of eDNA derived from flowers and DNA derived from bulk samples of insects
Limitations of traditional insect sampling methods have motivated the development and optimisation of new non-lethal methods capable of quantifying diverse arthropod communities. Environmental DNA (eDNA) metabarcoding using arthropod-specific primers has recently been investigated as a novel way to characterise arthropod communities from the DNA they deposit on the surface of plants...
Authors
Kara Suzanne Jones, David Pilliod, Aaron Aunins
Non-USGS Publications**
Jones, KS, and DW Weisrock. 2018. Genomic data reveal lineage divergence follows geography, not phenotype, in a clade of sympatric Desmognathus salamanders. Evolution. 72:2378-2393. https://onlinelibrary.wiley.com/doi/full/10.1111/evo.13606
Weisrock, DW, Hime, PM, Nunziata, SO, Jones, K, Murphy, MO, Hotaling, S, and JD Kratovil. 2018. Surmounting the large-genome “problem” for genomic data generation in salamanders In Population Genomics: Wildlife. Eds Rajora, OP, and P Hohenlohe. Springer International Publishing. https://link.springer.com/chapter/10.1007/13836_2018_36
Murphy, MO, Jones, KS, Price, SJ, and DW Weisrock. 2018. A genomic assessment of population structure in an aquatic salamander identifies the roles of spatial scale, barriers, and river architecture. Freshwater Biology 63: 407-419. https://onlinelibrary.wiley.com/doi/full/10.1111/fwb.13071
Jones, KS and TA Tupper. 2017. Aspects of Eastern Wormsnake (Carphophis amoenus) microhabitats at two natural areas in Fairfax County, Virginia, and Anne Arundel County, Maryland. Catesbeiana 37: 99-108.
Marsh, DM, Cosentino, BJ, Jones, KS, Apodaca, JJ, Beard, KH, Bell, JM, Bozarth, C, Carper, D, Charbonnier, JF, Dantas, A, Forys, EA, Foster, M, General, J, Genet, KS, Hanneken, M, Hess, KR, Hill, SA, Iqbal, F, Karraker, NE, Kilpatrick, ES, Langen, TA, Langford, J, Lauer, K, McCarthy, AJ, Neale, Z, Patel, S, Patton, A, Southwick, C, Stearrett, N, Steijn, N, Tasleem, M, Taylor, JM and JR Vonesh. 2017. Effects of roads and land use on pond-breeding amphibians: patterns across spatial scales and regions in the Eastern and Central United States. Diversity and Distributions 23:158-170. https://onlinelibrary.wiley.com/doi/full/10.1111/ddi.12516
Jones, KS, and TA Tupper. 2015. Fowler’s Toad (Anaxyrus fowleri) occupancy in the southern mid-Atlantic, USA. Amphibian & Reptile Conservation 9: 24–33 (e97). http://amphibian-reptile-conservation.org/pdfs/Volume/Vol_9_no_1/ARC_9_1_[General_Section]_24-33_e97_low_res.pdf
Tupper, TA, Bozarth, CA, Jones, KS, and RP Cook. 2014. Detection of Batrachochytrium dendrobatidis in the Eastern Spadefoot, Scaphiopus holbrookii, at Cape Cod National Seashore, Barnstable County, Massachusetts, USA. Herpetological Review 45:445-447
Cosentino, BJ, Marsh, DM, Jones, KS, Apodaca, JJ, Bates, C, Beach, J, Beard, KH, Becklin, K, Bell, JM, Crockett, C, Fawson, G, Fjelsted, J, Forys, EA, Genet, KS, Grover, M, Holmes, J, Indeck, K, Karraker, NE, Kilpatrick, ES, Langen, TA, Mugel, SG, Molina, A, Vonesh, JR, Weaver, RJ, and A Willey. Citizen science reveals widespread negative effects of roads on amphibian distributions. Biological Conservation 180:31-38. https://www.sciencedirect.com/science/article/pii/S0006320714003449
**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
Advancing the Environmental DNA Toolkit for Ecosystem Monitoring and Management
The emerging field of Environmental DNA (eDNA) analysis allows characterization of species presence and community biodiversity by identifying trace amounts of genetic material left behind as organisms move through their environments. EESC scientists have been using eDNA technologies to detect native and rare species and as community biomonitoring tools.
Mesophotic and Deep Benthic Communities (MDBC) eDNA metabarcoding: PC2202, NOAA Ship Pisces, June 30-July 11, 2022 Mesophotic and Deep Benthic Communities (MDBC) eDNA metabarcoding: PC2202, NOAA Ship Pisces, June 30-July 11, 2022
Data from environmental DNA (eDNA) samples filtered from seawater collected in the Gulf of America during a research expedition on the NOAA Ship Pisces from June 30-July 11, 2022. Samples were collected at depths throughout the water column using Niskins mounted to rosettes on Connectivity-Temperature-Depth instruments (CTDs). Each eDNA sample was amplified using four primer sets: MiFish...
Mesophotic and Deep Benthic Communities (MDBC) eDNA metabarcoding: NF2206, R/V Nancy Foster, August 2022 Mesophotic and Deep Benthic Communities (MDBC) eDNA metabarcoding: NF2206, R/V Nancy Foster, August 2022
Data from environmental DNA (eDNA) samples filtered from seawater collected in the Gulf of America during a research expedition on the R/V Nancy Foster in August 2022. Samples were collected at depths throughout the water column using Niskins mounted to rosettes on Connectivity-Temperature-Depth instruments (CTDs) or Niskins mounted to remote operated vehicles (ROVs). Each eDNA sample...
Mesophotic and Deep Benthic Communities (MDBC) eDNA metabarcoding: PS2308, R/V Point Sur, September 2022 Mesophotic and Deep Benthic Communities (MDBC) eDNA metabarcoding: PS2308, R/V Point Sur, September 2022
Data from environmental DNA (eDNA) samples filtered from seawater collected in the Gulf of America during a research expedition on the R/V Point Sur in September 2022. Samples were collected at depths throughout the water column. Each eDNA sample was amplified using four primer sets: MiFish 12S rRNA marker targeting ray-finned fishes; 28S rRNA marker targeting corals and other cnidarians...
Genomic data from reduced representation DNA sequencing libraries of two partially fossorial salamanders Plethodon jordani and Desmognathus wrighti from Great Smoky Mountains National Park Genomic data from reduced representation DNA sequencing libraries of two partially fossorial salamanders Plethodon jordani and Desmognathus wrighti from Great Smoky Mountains National Park
This dataset contains sample information about the origin of the Desmognathus wrighti and Plethodon jordani salamanders collected from Great Smoky Mountains National Park and sequenced, and their corresponding SNP genotype data. These data were used to examine patterns of genomic structure of these two salamander species within Great Smoky Mountains National Park. The raw sequence data...
Detections of marine fauna using environmental DNA metabarcoding of seawater samples from the northern Gulf of America Detections of marine fauna using environmental DNA metabarcoding of seawater samples from the northern Gulf of America
We sampled seawater from nine mesophotic reef sites in the Pinnacles Trend and DeSoto Rim areas in the northern Gulf of America in October 2022 to complement and inform restoration investments for coral communities. Four primer sets were used to amplify environmental DNA (eDNA) from seawater, targeting metazoans, eukaryotic plankton and protists, corals, and fishes. Across all markers...
Environmental DNA detections from deep seafloor habitats in the California Current Large Marine Ecosystem Environmental DNA detections from deep seafloor habitats in the California Current Large Marine Ecosystem
Environmental DNA (eDNA) metabarcoding may have utility in biodiversity surveys of marine environments, particularly for small, rare, or cryptic taxa that are more difficult to study using traditional methods (e.g., trawling and visual surveys). For this study, we used an eDNA metabarcoding approach to characterize biodiversity in the above-seafloor water column across three West Coast...
Arthropod detections from eDNA metabarcoding of flower filtrate and DNA derived from bulk samples of insects Arthropod detections from eDNA metabarcoding of flower filtrate and DNA derived from bulk samples of insects
We compared pollinator diversity derived from environmental DNA (eDNA) extracted from flowers and DNA extracted from pulverized bulk samples of insects collected from vane traps deployed at the same sites. We used three metabarcoding primers, two of which target arthropods generally (COI-Jusino and 16S-Marquina) and one that targets bumblebees (Bombus spp., COI-Milam). Across methods, we...
Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly: Assessing Population Structure, Facilitating Supportive Breeding, and Identifying Adaptive Potential Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly: Assessing Population Structure, Facilitating Supportive Breeding, and Identifying Adaptive Potential
The purpose of this study was to collect and analyze non-invasive DNA specimens from the endangered island marble butterfly (Euchloe ausonides insulanus) to assess population structure, identify adaptive potential, facilitate captive propagation, and support translocation planning. We used DNA extracted from meconium, exuviae, and natural mortalities to generate and test thirteen new...
Metabarcoding analysis of arthropod pollinator diversity: A methodological comparison of eDNA derived from flowers and DNA derived from bulk samples of insects Metabarcoding analysis of arthropod pollinator diversity: A methodological comparison of eDNA derived from flowers and DNA derived from bulk samples of insects
Limitations of traditional insect sampling methods have motivated the development and optimisation of new non-lethal methods capable of quantifying diverse arthropod communities. Environmental DNA (eDNA) metabarcoding using arthropod-specific primers has recently been investigated as a novel way to characterise arthropod communities from the DNA they deposit on the surface of plants...
Authors
Kara Suzanne Jones, David Pilliod, Aaron Aunins
Non-USGS Publications**
Jones, KS, and DW Weisrock. 2018. Genomic data reveal lineage divergence follows geography, not phenotype, in a clade of sympatric Desmognathus salamanders. Evolution. 72:2378-2393. https://onlinelibrary.wiley.com/doi/full/10.1111/evo.13606
Weisrock, DW, Hime, PM, Nunziata, SO, Jones, K, Murphy, MO, Hotaling, S, and JD Kratovil. 2018. Surmounting the large-genome “problem” for genomic data generation in salamanders In Population Genomics: Wildlife. Eds Rajora, OP, and P Hohenlohe. Springer International Publishing. https://link.springer.com/chapter/10.1007/13836_2018_36
Murphy, MO, Jones, KS, Price, SJ, and DW Weisrock. 2018. A genomic assessment of population structure in an aquatic salamander identifies the roles of spatial scale, barriers, and river architecture. Freshwater Biology 63: 407-419. https://onlinelibrary.wiley.com/doi/full/10.1111/fwb.13071
Jones, KS and TA Tupper. 2017. Aspects of Eastern Wormsnake (Carphophis amoenus) microhabitats at two natural areas in Fairfax County, Virginia, and Anne Arundel County, Maryland. Catesbeiana 37: 99-108.
Marsh, DM, Cosentino, BJ, Jones, KS, Apodaca, JJ, Beard, KH, Bell, JM, Bozarth, C, Carper, D, Charbonnier, JF, Dantas, A, Forys, EA, Foster, M, General, J, Genet, KS, Hanneken, M, Hess, KR, Hill, SA, Iqbal, F, Karraker, NE, Kilpatrick, ES, Langen, TA, Langford, J, Lauer, K, McCarthy, AJ, Neale, Z, Patel, S, Patton, A, Southwick, C, Stearrett, N, Steijn, N, Tasleem, M, Taylor, JM and JR Vonesh. 2017. Effects of roads and land use on pond-breeding amphibians: patterns across spatial scales and regions in the Eastern and Central United States. Diversity and Distributions 23:158-170. https://onlinelibrary.wiley.com/doi/full/10.1111/ddi.12516
Jones, KS, and TA Tupper. 2015. Fowler’s Toad (Anaxyrus fowleri) occupancy in the southern mid-Atlantic, USA. Amphibian & Reptile Conservation 9: 24–33 (e97). http://amphibian-reptile-conservation.org/pdfs/Volume/Vol_9_no_1/ARC_9_1_[General_Section]_24-33_e97_low_res.pdf
Tupper, TA, Bozarth, CA, Jones, KS, and RP Cook. 2014. Detection of Batrachochytrium dendrobatidis in the Eastern Spadefoot, Scaphiopus holbrookii, at Cape Cod National Seashore, Barnstable County, Massachusetts, USA. Herpetological Review 45:445-447
Cosentino, BJ, Marsh, DM, Jones, KS, Apodaca, JJ, Bates, C, Beach, J, Beard, KH, Becklin, K, Bell, JM, Crockett, C, Fawson, G, Fjelsted, J, Forys, EA, Genet, KS, Grover, M, Holmes, J, Indeck, K, Karraker, NE, Kilpatrick, ES, Langen, TA, Mugel, SG, Molina, A, Vonesh, JR, Weaver, RJ, and A Willey. Citizen science reveals widespread negative effects of roads on amphibian distributions. Biological Conservation 180:31-38. https://www.sciencedirect.com/science/article/pii/S0006320714003449
**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.