Thomas W. Franklin

Treesearch Publications

• Daniel J. Isaak, Michael Dumelle, Dona Horan, Daniel Mason, Thomas W. Franklin, David E. Nagel, Jay M. Ver Hoef, Michael K. Young. 2025. Improving species distribution models for stream networks by incorporating spatial autocorrelation in multi-sourced datasets: A range-wide assessment of Idaho giant salamander status and future risk
• Daniel Mason, Heidi A. Henderson, Thomas W. Franklin, Michael K. Young, Jennifer Hernandez, Cory L. Engkjer, Joanna Hatt, Michael K. Schwartz. 2025. Environmental DNA detects endangered Texas hornshell and its hosts
• Jennifer Helm, Taylor Wilcox, John Kronenberger, Joanna Elmore, Michael Sleeting, Thomas W. Franklin, Michael K. Schwartz. 2025. Big data on a little chip: New eDNA tools save time and money on invasive species detection and monitoring
• David R. Steward, Thomas Hafen, Dean A. Hendrickson, Andrew T. Taylor, Alejandro Varela-Romero, Daniel Mason, Joseph Dysthe, Thomas W. Franklin, Michael K. Young, Kevin S. McKelvey, Michael K. Schwartz, James M. Long. 2024. Environmental DNA mitochondrial markers to assess potential occupancy of endangered Yaqui catfish in the Yaqui River basin, Mexico
• Michael F. Sleeting, Taylor Wilcox, Daniel Mason, Thomas W. Franklin, Michael K. Schwartz. 2024. From jaguars to pathogens: Simultaneous genetic detection of diverse taxa across biodiversity hotspots in the U.S.
• Joanna Elmore, Taylor Wilcox, Michael K. Young, Steve Kopp, Kellie Carim, Daniel Mason, Thomas W. Franklin, Michael K. Schwartz. 2024. The riverscape on a chip: High-throughput qPCR enables basin-wide fishery assessments
• John Kronenberger, Taylor Wilcox, Michael K. Young, Daniel Mason, Thomas W. Franklin, Michael K. Schwartz. 2024. Large-scale validation of 46 invasive species assays using an enhanced in silico framework
• Taylor Wilcox, John Kronenberger, Michael K. Young, Daniel Mason, Thomas W. Franklin, Michael K. Schwartz. 2024. The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa
• Michael K. Young, Daniel J. Isaak, David E. Nagel, Dona Horan, Kellie Carim, Thomas W. Franklin, Victoria Zeller, Brett Roper, Michael K. Schwartz. 2022. Broad-scale eDNA sampling for describing aquatic species distributions in running waters: Pacific lamprey Entosphenus tridentatus in the upper Snake River, USA
• Jeffrey T. Morisette, Stas Burgiel, Thomas W. Franklin, Taylor Wilcox. 2022. Shedding light on shedded cells: Using eDNA sampling for surveillance of invasive species
• Thomas W. Franklin, Joseph Dysthe, Helen Neville, Michael K. Young, Kevin S. McKelvey, Michael K. Schwartz. 2022. Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) and Paiute cutthroat trout (Oncorhynchus clarkii seleniris) detection from environmental DNA samples: A dual-purpose assay
• John Kronenberger, Taylor Wilcox, Daniel Mason, Thomas W. Franklin, Kevin S. McKelvey, Michael K. Young, Michael K. Schwartz. 2022. eDNAssay: A machine learning tool that accurately predicts qPCR cross‐amplification
• Taylor Wilcox, Anthony Caragiulo, Joseph Dysthe, Thomas W. Franklin, Daniel Mason, Kevin S. McKelvey, Katherine Zarn, Michael K. Schwartz. 2021. Detection of jaguar (Panthera onca) from genetic material in drinking water
• Jeffrey T. Morisette, Stanley Burgiel, Kelsey Brantley, Wesley Daniel, John Darling, Jeanette Davis, Thomas W. Franklin, Keith Gaddis, Margaret Hunter, Richard Lance, Tracy Leskey, Yale Passamaneck, Antoinette Piaggio, Brian Rector, Adam Sepulveda, Melissa Smith, Carol Stepien, Taylor Wilcox. 2021. Strategic considerations for invasive species managers in the utilization of environmental DNA (eDNA): Steps for incorporating this powerful surveillance tool
• Kristen M. Homel, Thomas W. Franklin, Kellie Carim, Kevin S. McKelvey, Joseph Dysthe, Michael K. Young. 2020. Detecting spawning of threatened chum salmon Oncorhynchus keta over a large spatial extent using eDNA sampling: Opportunities and considerations for monitoring recovery
• Torrey W. Rodgers, Joseph Dysthe, Cynthia Tait, Thomas W. Franklin, Michael K. Schwartz, Karen E. Mock. 2020. Detection of 4 imperiled western North American freshwater mussel species from environmental DNA with multiplex qPCR assays
• Daniel Mason, Joseph Dysthe, Thomas W. Franklin, Chris L. Williams, Michael K. Young, Kevin S. McKelvey, Michael K. Schwartz. 2020. Certain detection of uncertain taxa: eDNA detection of a cryptic mountain sucker (Pantosteus jordani) in the Upper Missouri River, USA
• Kellie Carim, N. J. Bean, J. M. Connor, W. P. Baker, M. Jaeger, M. P. Ruggles, Kevin S. McKelvey, Thomas W. Franklin, Michael K. Young, Michael K. Schwartz. 2020. Environmental DNA sampling informs fish eradication efforts: Case studies and lessons learned
• Anthony T. Robinson, Yvette M. Paroz, Matthew J. Clement, Thomas W. Franklin, Joseph Dysthe, Michael K. Young, Kevin S. McKelvey, Kellie Carim. 2019. Environmental DNA sampling of small-bodied minnows: Performance relative to location, species, and traditional sampling
• Thomas W. Franklin, Taylor M. Wilcox, Kevin S. McKelvey, Samuel Greaves, Joseph Dysthe, Michael K. Young, Michael K. Schwartz. 2019. Repurposing environmental DNA samples to verify the distribution of Rocky Mountain tailed frogs in the Warm Springs Creek Basin, Montana
• Kevin S. McKelvey, Jessie Golding, Daniel H. Mason, Joseph Dysthe, Kristine L. Pilgrim, John R. Squires, Thomas W. Franklin, Keith B. Aubry, Robert A. Long, Samuel Greaves, Catherine M. Raley, Scott Jackson, Paula MacKay, Joshua Lisbon, Joel D. Sauder, Michael T. Pruss, Don Heffington, Michael K. Schwartz. 2019. Using environmental DNA methods to improve winter surveys for rare carnivores: DNA from snow and improved noninvasive techniques
• Daniel H. Mason, Joseph Dysthe, Thomas W. Franklin, Joseph A. Skorupski, Michael K. Young, Kevin S. McKelvey, Michael K. Schwartz. 2018. qPCR detection of Sturgeon chub (Macrhybopsis gelida) DNA in environmental samples
• Joseph Dysthe, Thomas W. Franklin, Kevin S. McKelvey, Michael K. Young, Michael K. Schwartz. 2018. An improved environmental DNA assay for bull trout (Salvelinus confluentus) based on the ribosomal internal transcribed spacer I
• Thomas W. Franklin, Joseph Dysthe, Michael Golden, Kevin S. McKelvey, Blake R. Hossack, Kellie Carim, Cynthia Tait, Michael K. Young, Michael K. Schwartz. 2018. Inferring presence of the western toad (Anaxyrus boreas) species complex using environmental DNA
• Thomas W. Franklin, Joseph Dysthe, Erika S. Rubenson, Kellie Carim, Julian D. Olden, Kevin S. McKelvey, Michael K. Young, Michael K. Schwartz. 2018. A non-invasive sampling method for detecting non-native smallmouth bass (Micropterus dolomieu)
• Taylor Wilcox, Kellie Carim, Michael K. Young, Kevin S. McKelvey, Thomas W. Franklin, Michael K. Schwartz. 2018. The importance of sound methodology in environmental DNA sampling
• Joseph Dysthe, Kellie Carim, Thomas W. Franklin, Dave Kikkert, Michael K. Young, Kevin S. McKelvey, Michael K. Schwartz. 2018. Molecular detection of northern leatherside chub (Lepidomeda copei) DNA in environmental samples
• Joseph Dysthe, Torrey Rodgers, Thomas W. Franklin, Kellie Carim, Michael K. Young, Kevin S. McKelvey, Karen E. Mock, Michael K. Schwartz. 2018. Repurposing environmental DNA samples: Detecting the western pearlshell (Margaritifera falcata) as a proof of concept

Citations of Non-Forest Service Publications

• Young, Michael K.; Isaak, Daniel J.; McKelvey, Kevin S.; Schwartz, Michael K.; Carim, Kellie J.; Fredenberg, Wade; Wilcox, Taylor M.; Franklin, Thomas W.; Chandler, Gwynne L.; Nagel, David E.; Parkes-Payne, Sharon L.; Horan, Dona L.; Wollrab, Sherry P. 2017. Species occurrence data from the Range-Wide Bull Trout eDNA Project. Fort Collins, CO: Forest Service Research Data Archive. https://doi.org/10.2737/RDS-2017-0038.
• Schwartz, M. K., Young, M.K., McKelvey, K.S., Isaak, D.J., Nagel, D.E., Franklin, T.W., Greaves, S.E., Dysthe, J.C., Chandler, G.L., Wollrab, S.P., Carim, K.J., Wilcox, T.M., Parkes-Payne, S.L., Horan, D.L. 2018. Species occurrence data from the Aquatic eDNAtlas database. Fort Collins, CO: Forest Service Research Data Archive. DOI Pending.

Data and Tools

• Tool
  

  Aquatic eDNAtlas Project: eDNA field sampling grid for the Western U.S.

  https://research.fs.usda.gov/rmrs/products/dataandtools/aquatic-ednatlas-project-edna-field-sampling-grid-western-us
• Tool
  

  Aquatic eDNAtlas Project: Lab results map

  https://research.fs.usda.gov/rmrs/products/dataandtools/aquatic-ednatlas-project-lab-results-map

• Project
  

  Aquatic eDNAtlas

  https://research.fs.usda.gov/rmrs/projects/ednatlas
  Station

  Rocky Mountain Research Station
• Program
  

  Wildlife Ecology

  https://research.fs.usda.gov/rmrs/programs/wildlife-ecology
  Station

  Rocky Mountain Research Station
• Center or Group
  

  National Genomics Center for Wildlife and Fish Conservation

  https://research.fs.usda.gov/rmrs/centers/ngc
  Station

  Rocky Mountain Research Station
• Project
  

  Aquatic invasive species in highly disturbed riverscapes: monitoring, prediction, prevention, and eradication

  https://research.fs.usda.gov/rmrs/projects/bil-aquatic-invasive-species-highly-disturbed-riverscapes
  Station

  Rocky Mountain Research Station
• Project
  

  Bull Trout eDNA

  https://research.fs.usda.gov/rmrs/projects/bull-trout-edna
  Station

  Rocky Mountain Research Station

Articles

• Article
  

  Finding Idaho’s giant stream salamander with modern maps

  https://research.fs.usda.gov/rmrs/articles/finding-idahos-giant-stream-salamander-modern-maps

Multimedia

• Video

  A protocol for collecting environmental DNA samples from streams

  https://research.fs.usda.gov/rmrs/products/multimedia/videos/protocol-collecting-environmental-dna-samples-streams

• Appalachian State University, M.S., Ecology & Evolution, 2016
• Appalachian State University, B.S. Biology, Ecology, Evolution, and Environmental Science, 2014