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
Python Vital Rates
Standardizing, aggregating, analyzing and disseminating global wildlife genetic and genomic data for improved management and advancement of community best practices
READI-Net: A network of robotic environmental DNA samplers to enhance the early detection of aquatic biological threats
Chronic Wasting Disease (CWD) Detection in Cervids Using MicroRNA Biomarkers from Blood
Implementing FAIR practices: Storing and displaying eDNA data in the USGS Nonindigenous Aquatic Species database
Establishing standards and integrating environmental DNA (eDNA) data into the USGS Nonindigenous Aquatic Species database
Health Effects and Behavioral Response of Florida Manatees (Trichechus manatus latirostris) to Persistent Algal Bloom and Associated Loss of Seagrass Resources in Brevard County, Florida
West Indian Manatee Population Genetics
Manatee Health Assessment and Biomedical Studies
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
Fish community assessment using environmental DNA metabarcoding data after an invasive species eradication and native restocking effort in Pinecrest Gardens, FL in 2017-18
Single Nucleotide Polymorphism (SNP) genomic data of moose (Alces alces) from the contiguous United States, 2009-2017
Droplet digital PCR data for environmental DNA surveys of Burmese pythons in the Greater Everglades Ecosystem
Morphological measurements of Antillean manatees from Guantanamo Bay, Cuba
Red Lionfish DNA data collected from Florida, USA and around the invasive distribution from 2007 to 2016
Bullseye snakehead environmental DNA data, and associated attributes, collected from southeast Florida, from 2015-2018
Burmese python environmental DNA data, and environmental covariates, collected from wading bird aggregations and control sites in the Greater Everglades Ecosystem, United States, in 2017
Burmese python environmental DNA data, and associated attributes, collected from ARM Loxahatchee NWR and surrounding areas, from 2014-2016
Droplet digital PCR data from method testing to improve eDNA yield and reduce inhibitors from environmental water samples
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
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
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
The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice
Novel insights on aquatic mammal MHC evolution: Evidence from manatee DQB diversity
Biology: Integrating core to essential variables (Bio-ICE) task team report for marine mammals
Environmental DNA surveys of Burmese pythons in the Greater Everglades Ecosystem
Science and Products
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Filter Total Items: 18
Python Vital Rates
Researchers from USGS-FORT and -WARC and University of Florida are collaborating on a long-term Burmese python research program in southern Florida to address management needs of partners and stakeholders throughout the Greater Everglades.Standardizing, aggregating, analyzing and disseminating global wildlife genetic and genomic data for improved management and advancement of community best practices
Global biodiversity is rapidly declining, threatening humans, ecosystems, and the services that society relies upon. Monitoring and understanding the extent of biodiversity declines can support policy decisions. Genetic diversity is the foundation of biodiversity, determining the capacity of populations to adapt to environmental changes and to sustain function and structure in all ecosystems. WhilREADI-Net: A network of robotic environmental DNA samplers to enhance the early detection of aquatic biological threats
USGS researchers are working with the Monterey Bay Aquarium Research Institute to optimize autonomous, robotic samplers for detection of DNA fragments shed by biological threats (BT; invasive species, parasites, pathogens) in our nation’s waters. Finding DNA fragments (a method known as environmental DNA sampling) produced by an emerging BT in water is akin to finding a needle in a haystack—many...Chronic Wasting Disease (CWD) Detection in Cervids Using MicroRNA Biomarkers from Blood
WARC scientists are testing and developing methods for the isolation of cervid exosomes from blood samples, followed by microRNA extraction and next generation sequencing.Implementing FAIR practices: Storing and displaying eDNA data in the USGS Nonindigenous Aquatic Species database
We are working to incorporate environmental DNA (eDNA) data into the Nonindigenous Aquatic Species (NAS) database, which houses over 570,000 records of nonindigenous species nationally, and already is used by a broad user-base of managers and researchers regularly for invasive species monitoring. eDNA studies have allowed for the identification and biosurveillance of numerous invasive and threatenEstablishing standards and integrating environmental DNA (eDNA) data into the USGS Nonindigenous Aquatic Species database
Environmental DNA (eDNA) testing allows for high sensitivity monitoring efforts of cryptic species in large, remote systems and is performed by investigating water and soil samples for sloughed DNA. Having access to eDNA datasets across multiple taxa and ecosystems is necessary for improved coordination among researchers and management. Additionally, quality control protocols are needed to vet incHealth Effects and Behavioral Response of Florida Manatees (Trichechus manatus latirostris) to Persistent Algal Bloom and Associated Loss of Seagrass Resources in Brevard County, Florida
USGS researchers are working with partners to assess the health and foraging behavior of Florida manatees in the northern Indian River Lagoon and Banana River, areas that have experienced declining seagrasses due to an extended phytoplankton bloom.West Indian Manatee Population Genetics
Nuclear microsatellite markers have been developed and implemented on ~2,000 West Indian manatees. These markers provide individual genetic fingerprints for mark-recapture studies, population structure information for the conservation of unique or isolated populations, and pedigree and relatedness information for addressing inbreeding and breeding structure patterns.Manatee Health Assessment and Biomedical Studies
A multi-agency effort assesses the health of manatees and provides baseline information on their health, reproductive status, and nutritional condition.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. - Data
Fish community assessment using environmental DNA metabarcoding data after an invasive species eradication and native restocking effort in Pinecrest Gardens, FL in 2017-18
Reported here are the metabarcoding read numbers and biomass data assessed from a fish community in a southern Florida pond in Pinecrest Gardens after invasive species eradication and native restocking in 2017 and 2018 in linear regression models. This dataframe contains the number of fish of each species identified, their measured lengths estimated population surface area, and the number of metabSingle Nucleotide Polymorphism (SNP) genomic data of moose (Alces alces) from the contiguous United States, 2009-2017
We analyzed the single nucleotide polymorphisms (SNPs) present in the genomes of moose representing 3 subspecies in the contiguous United States. Blood samples were collected opportunistically from collaborators during field efforts or were supplied to our lab from collaborators' archives, and represented moose sampling occurring between 2009-2017. DNA was extracted, sequenced using next generatioDroplet digital PCR data for environmental DNA surveys of Burmese pythons in the Greater Everglades Ecosystem
Environmental DNA water samples were collected in the Greater Everglades Ecosystem between May 20-22, 2019 and analyzed to estimate Burmese python (Python bivittatus) occurrence. Twenty-eight sites were sampled in the Greater Everglades Ecosystem, with 5 field replicate samples per site, for a total of 140 water samples collected. Python eDNA was detected at 25 of the 28 sampling sites using DroplMorphological measurements of Antillean manatees from Guantanamo Bay, Cuba
The data were collected by U.S.G.S. biologists and their partners during several field trips from March 2013 to April 2014 in Guantanamo Bay, Cuba. Data were collected during the manatee health assessments. The U.S. Geological Survey's Sirenia Project is a federal research effort focusing on manatee biology and ecology with a long history of studies in the U.S., Puerto Rico, and the internationalRed Lionfish DNA data collected from Florida, USA and around the invasive distribution from 2007 to 2016
Red lionfish (Pterois volitans) have become a successful invasive predator across the Northwestern Atlantic, Caribbean, and Gulf of Mexico (GoM). Previous investigations have identified the southeast coast of Florida as the original site of introduction, but no region-wide genetic study has directly addressed the question of introduction location(s). This dataset includes previously unpublished reBullseye snakehead environmental DNA data, and associated attributes, collected from southeast Florida, from 2015-2018
Bullseye snakehead, Channa marulius, was first detected in 2000 in the southern Florida town of Tamarac and has been expanding its geographic range. Environmental DNA (eDNA) analysis is a newly-developed technique used to non-invasively detect cryptic or low-density species, or those that are logistically difficult to study. Genetic material shed into the environment through tissue and body fluidBurmese python environmental DNA data, and environmental covariates, collected from wading bird aggregations and control sites in the Greater Everglades Ecosystem, United States, in 2017
Environmental DNA (eDNA) water samples were collected at 15 tree islands containing wading bird breeding colonies (order Pelecaniformes) and 15 empty control islands in the central Everglades of Florida in spring of 2017 (April through June) and analyzed for the presence of eDNA from invasive Burmese pythons (Python bivittatus). The Burmese python is now established as a breeding population througBurmese python environmental DNA data, and associated attributes, collected from ARM Loxahatchee NWR and surrounding areas, from 2014-2016
Environmental DNA (eDNA) detection of invasive species can be used to delimit occupied ranges and estimate probabilities to inform management decisions. Environmental DNA is shed into the environment through skin cells and bodily fluids and can be detected in water samples collected from lakes, rivers, and swamps. In south Florida, invasive Burmese pythons occupy much of the Greater Everglades inDroplet digital PCR data from method testing to improve eDNA yield and reduce inhibitors from environmental water samples
Data files for manuscript "Improving eDNA yield and inhibitor reduction through increased water volumes and modified multi-filter isolation techniques". These include the results of different treatments for inhibitor removal from a water sample and DNA yield quantities from such tests. Environmental DNA (eDNA) methods detect genetic material that is shed into the environment through skin cellsNovel 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 - Publications
Filter Total Items: 70
Genetic 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 gBurmese 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 fGaining 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 tEnvironmental 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 asseEnvironmental 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, anUsing 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 prA 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 haGlobal 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 methodThe Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice
The Coalition for Conservation Genetics (CCG) brings together four eminent organizations with the shared goal of improving the integration of genetic information into conservation policy and practice. We provide a historical context of conservation genetics as a field and reflect on current barriers to conserving genetic diversity, highlighting the need for collaboration across traditional dividesNovel insights on aquatic mammal MHC evolution: Evidence from manatee DQB diversity
The low diversity in marine mammal major histocompatibility complex (MHC) appears to support the hypothesis of reduced pathogen selective pressure in aquatic systems compared to terrestrial environments. However, the lack of characterization of the aquatic and evolutionarily distant Sirenia precludes drawing more generalized conclusions. Therefore, we aimed to characterize the MHC DQB diversity ofBiology: Integrating core to essential variables (Bio-ICE) task team report for marine mammals
Marine mammals are wide-ranging, relatively long-lived organisms that play a crucial role in maintaining healthy ocean ecosystems. Often referred to as ecosystem engineers and sentinel species in marine ecosystems, these charismatic megafauna feed at a variety of trophic levels, affecting food web dynamics and cycling of chemicals and nutrients in the water column as well as in benthic habitats, bEnvironmental DNA surveys of Burmese pythons in the Greater Everglades Ecosystem
Improving the probability of detecting invasive giant snakes is vital for the management of emerging or established populations. Burmese pythons occupy thousands of square kilometers of mostly inaccessible habitats in Florida. Environmental DNA (eDNA) methods have been shown to be time and cost effective in a number of systems and may be preferable to traditional detection methods for constrictor - News