Margaret Hunter, Ph.D.
Margaret Hunter is a Research Geneticist at the USGS Wetland and Aquatic Research Center.
Margaret Hunter attended the University of Florida where she received a B.Sc. in Microbiology and Cellular Sciences and minored in Chemistry and Plant Molecular and Cellular Biology. Following her bachelor degree, she received a PhD in Veterinary Medical Sciences researching Sirenia (manatee and dugong) cytogenetics and conservation genetics. Affiliations: USGS Sirenia Project USGS Genetics and Genomics Research Courtesy Assistant Professor, University of Florida, College of Veterinary Medicine, Department of Large Animal Clinical Sciences Affiliated faculty member, University of Florida Aquatic Animal Health Program Affiliated faculty member, University of Florida Genetics Institute.
Education and Certifications
Ph.D., Veterinary Medical Sciences, University of Florida
B.S., Microbiology and Cell Sciences (Minor: Chemistry, Plant Molecular and Cellular Biology), University of Florida
Science and Products
Statistical Models for the Design and Analysis of Environmental DNA (eDNA) Surveys of Invasive and Imperiled Species
Trojan Y Invasive Species Control - Sex Marker Identification
Asian Tiger Shrimp Distribution and Genetics
Developing Detection Probabilities and Quantifying the Effects of Flowing Water to Improve Asian Carp Environmental DNA (eDNA) Surveys
Efficacy of eDNA as an Early Detection and Rapid Response Indicator for Burmese Pythons in the Northern Greater Everglades Ecosystem
Genetic Analysis of the Invasive Burmese Python to Aid Management and Population-Control Decision-Making
Genetic Analysis of Wild and Captive Black Carp in the Mississippi River Basin
Using Environmental DNA for Burmese Python Detection Probabilities and Range-Delimitation in Southern Florida
Moose Health in a Changing Environment
Novel protocol for moose DNA extraction from Tempus blood tube supernatant following RNA extraction
Manatee environmental DNA data, and associated attributes, collected from the United States, Cuba, and Cameroon, from 2013-2015
Reduction of paraoxonase expression followed by inactivation across independent semiaquatic mammals suggests stepwise path to pseudogenization
Community for data integration 2019 project report
Genetic diversity and IUCN Red List status
Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework
Burmese pythons in Florida: A synthesis of biology, impacts, and management tools
Gaining decision-maker confidence through community consensus: Developing environmental DNA standards for data display on the USGS Nonindigenous Aquatic Species database
The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba
Environmental DNA metabarcoding read numbers and their variability predict species abundance, but weakly in non-dominant species
Environmental DNA methods for ecological monitoring and biodiversity assessment in estuaries
Using structured decision making to evaluate potential management responses to detection of dreissenid mussel (Dreissena spp.) environmental DNA
A framework to integrate innovations in invasion science for proactive management
Global genetic diversity status and trends: Towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition
Science and Products
- Science
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Statistical Models for the Design and Analysis of Environmental DNA (eDNA) Surveys of Invasive and Imperiled Species
Detecting invasive species at low densities or prior to population establishment is critical for successful control and eradication. For example, Burmese pythons occupy thousands of square kilometers of mostly inaccessible habitats.Trojan Y Invasive Species Control - Sex Marker Identification
To control or possibly eliminate non-native species without harm to native fauna, a genetic technique using sex-reversed females with two Y chromosomes (Trojan Y) is being developed to reduce the breeding success of the species, ultimately resulting in population decline or loss.Asian Tiger Shrimp Distribution and Genetics
The Asian tiger shrimp began appearing in commercial shrimp catches in 2006. They grow larger than native shrimp and are known to be fierce predators - so shrimpers and managers are concerned about the potential effects this species might have.Developing Detection Probabilities and Quantifying the Effects of Flowing Water to Improve Asian Carp Environmental DNA (eDNA) Surveys
Invasive Asian carp are problematic for native species, and managers are implementing control measures without well-quantified detection limits or a means to assess the accuracy and precision of existing or future survey data for the fish. Environmental DNA - eDNA - is already used to detect the presence of invasive species, and can be used to identify locations to focus carp control efforts.Efficacy of eDNA as an Early Detection and Rapid Response Indicator for Burmese Pythons in the Northern Greater Everglades Ecosystem
Traditional approaches to locating Burmese pythons - including visual searches and trapping - have resulted in low detection. Environmental DNA - or eDNA - is increasingly being used to detect the presence of non-native species, particularly when traditional methods may not be adequate.Genetic Analysis of the Invasive Burmese Python to Aid Management and Population-Control Decision-Making
Invasive Burmese pythons threaten the success of Everglades restoration efforts. To assist with management and population control decision making, USGS scientists are implementing genetic studies to identify potential new entry pathways and to help quantify the size of the breeding population.Genetic Analysis of Wild and Captive Black Carp in the Mississippi River Basin
Black carp have likely been present in the Mississippi River since the 1990s, but their current distribution and spread is not well understood. Genetics is helping to shed light on this species, including its diversity, the relatedness of wild and captive fish, and its introduction history.Using Environmental DNA for Burmese Python Detection Probabilities and Range-Delimitation in Southern Florida
Current tools for detection of Burmese pythons in South Florida have resulted in low detection rates. Environmental DNA - eDNA - has shown to be effective at detecting these invasive snakes, and can help to determine range limits for the species, information that is critical for management and control efforts.Moose Health in a Changing Environment
There have been increasing concerns regarding the decline in moose numbers along the southern range of their North American distribution. This has prompted varied research efforts to determine the factors contributing to the reduced local populations. Although heat stress from increasing temperatures could be a potential factor for declining populations in Minnesota, temperature increases have als - Data
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Novel protocol for moose DNA extraction from Tempus blood tube supernatant following RNA extraction
Data were collected to validate the use of supernatant from the isolation of RNA from Tempus blood RNA tubes to obtain genomic DNA in the associated blood sample from moose. Data represent the metrics measured to validate the novel technique for isolating DNA from the supernatant of an RNA isolation protocol using blood collected into Tempus blood RNA tubes.Manatee environmental DNA data, and associated attributes, collected from the United States, Cuba, and Cameroon, from 2013-2015
Environmental DNA (eDNA) detection is a rapidly expanding technique used to non-invasively detect cryptic, low density, or logistically difficult-to-study species, such as imperiled manatees. Genetic material shed into the environment through tissue and body fluids is concentrated from water samples and analyzed for the presence of targeted eDNA. To help delineate manatee habitat ranges, high use - Multimedia
- Publications
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Reduction of paraoxonase expression followed by inactivation across independent semiaquatic mammals suggests stepwise path to pseudogenization
Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We prevAuthorsAllie M. Graham, Jerrica M. Jamison, Marisol Bustos, Charlotte Cournoyer, Alexa Michaels, Jason S. Presnell, Rebecca Richter, Daniel E. Crocker, Ari Fustukjian, Margaret Hunter, Lorrie D. Rea, Judit Marsillach, Clement E. Furlong, Wynn K. Meyer, Nathan L. ClarkCommunity for data integration 2019 project report
The U.S. Geological Survey Community for Data Integration annually supports small projects focusing on data integration for interdisciplinary research, innovative data management, and demonstration of new technologies. This report provides a summary of the 14 projects supported in fiscal year 2019 and outlines their goals, activities, and accomplishments. Proposals in 2019 were encouraged to addreAuthorsAmanda N. Liford, Caitlin M. Andrews, Aparna Bamzai, Joseph A. Bard, David S. Blehert, John B. Bradford, Wesley M. Daniel, Sara L. Caldwell Eldridge, Frank Engel, Jason A. Ferrante, Amy K. Gilmer, Margaret E. Hunter, Jeanne M. Jones, Benjamin Letcher, Frances L. Lightsom, Richard R. McDonald, Leah E. Morgan, Sasha C. Reed, Leslie HsuByEcosystems Mission Area, Water Resources Mission Area, Science Synthesis, Analysis and Research Program, Science Analytics and Synthesis (SAS) Program, Volcano Hazards Program, Community for Data Integration (CDI), Geology, Geophysics, and Geochemistry Science Center, Geosciences and Environmental Change Science Center, National Wildlife Health Center, Oklahoma-Texas Water Science Center, Southwest Biological Science Center, Volcano Science Center, Western Geographic Science Center, Wetland and Aquatic Research Center , Woods Hole Coastal and Marine Science Center, Science Data ManagementGenetic diversity and IUCN Red List status
The International Union for Conservation of Nature (IUCN) Red List is an important and widely used tool for conservation assessment. The IUCN uses information about a species’ range, population size, habitat quality and fragmentation levels, and trends in abundance to assess extinction risk. Genetic diversity is not considered, although it affects extinction risk. Declining populations are more stAuthorsChloe Schmidt, Sean M. Hoban, Margaret Hunter, Ivan Paz-Vinas, Colin J. GarrowayGenetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework
Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how gAuthorsSean M. Hoban, Michael W. Bruford, Jessica M. da Silva, W. Chris Funk, Richard Frankham, Michael J. Gill, Catherine E. Grueber, Myriam Heuertz, Margaret Hunter, Francine Kershaw, Robert C. Lacy, Caroline Lees, Margarida Lopes-Fernandes, Anna J. MacDonald, Alicia Mastretta-Yanes, Philip J. K. McGowan, Mariah H. Meek, Joachim Mergeay, Katie L. Millette, Cinnamon S. Mittan-Moreau, Laetitia M. Navarro, David O'Brien, Rob Ogden, Gernot Segelbacher, Ivan Paz-Vinas, Cristiano Vernesi, Linda LaikreBurmese pythons in Florida: A synthesis of biology, impacts, and management tools
Burmese pythons (Python molurus bivittatus) are native to southeastern Asia, however, there is an established invasive population inhabiting much of southern Florida throughout the Greater Everglades Ecosystem. Pythons have severely impacted native species and ecosystems in Florida and represent one of the most intractable invasive-species management issues across the globe. The difficulty stems fAuthorsJacquelyn C. Guzy, Bryan G. Falk, Brian J. Smith, John David Willson, Robert Reed, Nicholas Aumen, Michael L. Avery, Ian A. Bartoszek, Earl Campbell, Michael Cherkiss, Natalie M. Claunch, Andrea Faye Currylow, Tylan Dean, Jeremy Dixon, Richard M. Engeman, Sarah Funck, Rebekah Gibble, Kodiak C. Hengstebeck, John S. Humphrey, Margaret Hunter, Jillian Josimovich, Jennifer Ketterlin Eckles, Michael Kirkland, Frank J. Mazzotti, Robert A. McCleery, Melissa A. Miller, Matthew F. McCollister, M. Rockwell Parker, Shannon E. Pittman, Michael R. Rochford, Christina Romagosa, Art Roybal, Ray W. Snow, McKayla M. Spencer, Hardin Waddle, Amy A. Yackel Adams, Kristen HartGaining decision-maker confidence through community consensus: Developing environmental DNA standards for data display on the USGS Nonindigenous Aquatic Species database
To advance national efforts for the detection and biosurveillance of aquatic invasive species (AIS), we employed a community consensus process to enable the incorporation of environmental DNA (eDNA) detection data into the U.S. Geological Survey’s (USGS) Nonindigenous Aquatic Species (NAS) database (https://nas.er.usgs.gov/eDNA/). Our goal was to identify minimum standards and best practices for tAuthorsJason Ferrante, Wesley Daniel, Jonathan (Contractor) Adam Freedman, Katy E. Klymus, Matthew Neilson, Yale Passamaneck, Christopher B. Rees, Adam J. Sepulveda, Margaret HunterThe first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba
The coastal waters of Cuba are home to a small, endangered population of West Indian manatee, which would benefit from a comprehensive characterization of the population’s genetic variation. We conducted the first genetic assessment of Cuban manatees to determine the extent of the population's genetic structure and characterize the neutral genetic diversity among regions within the archipelago. WeAuthorsAnmari Alvarez-Aleman, Margaret Hunter, Thomas K. Frazer, James A. Powell, Eddy G. Alfonso, James D. AustinEnvironmental DNA metabarcoding read numbers and their variability predict species abundance, but weakly in non-dominant species
Metabarcoding of environmental DNA (eDNA) provides more comprehensive, efficient, and non-invasive sampling of biological communities than conventional methods. However, limitations of metabarcoding include taxon-specific biases in amplification and sequencing that distort assessments of community composition. Further, hyper-abundant species may disproportionately affect community composition asseAuthorsJames Skelton, Allison Cauvin, Margaret HunterEnvironmental DNA methods for ecological monitoring and biodiversity assessment in estuaries
Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, anAuthorsRaman P. Nagarajan, Mallory Bedwell, Ann E. Holmes, Thiago Sanches, Shawn Acuña, Melinda R. Baerwald, Matthew A. Barnes, Scott Blankenship, Richard E. Connon, Kristy Deiner, Daphne Gille, Caren S. Goldberg, Margaret Hunter, Christopher L. Jerde, Gordon Luikart, Rachel S. Meyer, Alison Watts, Andrea M SchreierUsing structured decision making to evaluate potential management responses to detection of dreissenid mussel (Dreissena spp.) environmental DNA
Environmental (e)DNA tools are sensitive and cost-effective for early detection of invasive species. However, the uncertainty associated with the interpretation of positive eDNA detections makes it challenging to determine appropriate natural resource management responses. Multiple sources of error can give rise to positive detections of eDNA in a sample when individuals of that species are not prAuthorsAdam J. Sepulveda, David R. Smith, Katherine M O'Donnell, Nathan Owens, Brittany White, Catherine A. Richter, Christopher M. Merkes, Skylar Wolf, Mike Rau, Matthew Neilson, Wesley Daniel, Christine E. Dumoulin, Margaret HunterA framework to integrate innovations in invasion science for proactive management
Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid development of diverse technologies and approaches haAuthorsCharles B. van Rees, Brian K. Hand, Sean C. Carter, Charles Bargeron, Timothy Joseph Cline, Wesley Daniel, Jason A. Ferrante, Keith Gaddis, Margaret E. Hunter, Catherine S. Jarnevich, Melodie A. McGeoch, Jeffrey T. Morisette, Matthew E. Neilson, Helen E. Roy, Mary Ann Rozance, Adam J. Sepulveda, Rebekah D. Wallace, Diane Whited, Taylor Wilcox, John S. Kimball, Gordon LuikartGlobal genetic diversity status and trends: Towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition
Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well-being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methodAuthorsSean M. Hoban, Frederick I. Archer, Laura D. Bertola, Jason G. Bragg, Martin F. Breed, Michael W. Bruford, Melinda A. Coleman, Robert Ekblom, W. Chris Funk, Catherine E. Grueber, Brian K. Hand, Rodolfo Jaffé, Evelyn Jensen, Jeremy S. Johnson, Francine Kershaw, Libby Liggins, Anna J. MacDonald, Joachim Mergeay, Joshua M. Miller, Frank Muller-Karger, David O'Brien, Ivan Paz-Vinas, Kevin M. Potter, Orly Razgour, Cristiano Vernesi, Margaret Hunter - News