Geology topics

Margaret Hunter

Publications and source records attributed to Margaret Hunter.

At least 19 recordsLinked to original sources

USGS2026

An evaluation of next-generation biological control methods for the invasive brown treesnake in the Mariana Islands

The brown treesnake (BTS) invasion in Guam continues to cause extensive ecological and economic damage, yet existing control tools cannot achieve islandwide suppression or eradication, highlighting the need for new strategies. This review evaluates the feasibility of classical and genetic biocontrol approaches for BTS and identifies priority knowledge gaps. Classical biocontrol, which relies on pathogens or parasites from a pest’s native range, has had limited success in vertebrates, though certain viruses may hold potential. For BTS, prior work has identified candidate agents, including hemogregarines and paramyxoviruses, but major uncertainties remain in transmission, specificity, long term efficacy, and ecological risk. Theoretical models suggest that moderately virulent pathogens may offer the strongest potential for sustained suppression, with Ophidian paramyxoviruses emerging as a leading prospect, though substantial empirical research is still required. Genetic biocontrol offers additional possibilities, including gene drives that could bias inheritance, reduce fertility, or skew sex ratios. Self sustaining homing and shredding drives could theoretically produce long term reductions, while “enhanced” self limiting systems may provide geographically restricted alternatives. Approaches involving genetically modified prey and toxic males that shorten female lifespan through mating may have future relevance but require major development and validation. Risks across genetic strategies include unintended spread, ecological side effects, technical constraints such as producing engineered snakes, potential resistance, and regulatory complexity. Because feasibility depends on societal acceptance, the review emphasizes the need for early engagement with Guam’s local and Indigenous communities, whose perspectives will shape future development and implementation. Key research priorities include improved modeling, native range genomic characterization of BTS, expanded pathogen surveys, advances in BTS genetic tools and captive rearing methods, and further exploration of both classical pathogen candidates and genetically engineered prey systems. Collectively, the review concludes that classical and genetic biocontrol hold promise for long term, cost effective BTS suppression, but substantial scientific, ethical, ecological, and social groundwork remains before deployment.

Hawai’i Cooperative Fishery Research Unit Technica↗

USGS2026

A practical framework for identifying genetic subpopulations and ESUs: Insights for IUCN assessments and broader management

Species conservation assessments evaluate extinction risk, and recovery potential, advancing species persistence through guiding resource prioritization and planning. Assessment frameworks, including the International Union for Conservation of Nature Red List and Green Status of Species, typically focus on species as a whole. Importantly, they do not routinely account for genetically distinct units or do not have standardized methods of unit delineation. This limits the representation of genetically distinct components, including adaptive genetic diversity that underpins long-term resilience and recovery. Incorporating standardized within-species units like subpopulations and Evolutionarily Significant Units (ESUs) into species assessments could help address this oversight. However, identifying and delineating such units remain challenging, particularly when molecular data are limited. Here, we propose a flexible framework that integrates molecular and non-molecular evidence to identify both subpopulations and ESUs across taxa, providing a practical tool to incorporate within-species diversity into conservation assessments.

BioScience↗

USGS2025

Sparse genetic data limit biodiversity assessments in protected areas globally

Global conservation targets include protecting genetic diversity within species. Yet few studies have assessed whether protected areas (PAs) include genetically diverse populations across species globally. A first step is understanding the availability of population genetic data that could be used in these assessments. We surveyed georeferenced population-level nuclear (as opposed to mitochondrial or plastid-based) genetic data across continents and marine biomes (36,354 populations, 2809 species) and found substantial geographic and taxonomic gaps. Most data were concentrated in Europe and North America, with major gaps in Africa and Asia. For most taxonomic groups, data were available for <1% of described species. Globally, 52.08% of the total areal extent of PAs lacked genetically sampled populations. These gaps in data availability highlight the need for targeted genetic data collection, harmonization, and sharing to improve genetic diversity monitoring and conservation planning. Combined with proxy-based genetic indicators, such data are needed to inform PA assessments, bolster area-based conservation initiatives like 30 × 30, and support achievement of global genetic conservation targets.

Frontiers in Ecology and the Environment↗

USGS2025

A practical framework for identifying genetic subpopulations and ESUs: Insights for IUCN assessments and broader management

The International Union for Conservation of Nature (IUCN) sets global conservation standards, including the Red List of Threatened Species and the Green Status of Species. Recent analyses showed that genetic diversity has not been effectively considered by IUCN species assessments, despite being fundamental to species’ fitness and adaptive potential. Incorporation of genetic diversity into IUCN assessments can support its successful long-term conservation. To enhance the preservation of genetic diversity, assessments should include genetically meaningful within-species units. Subpopulations are recognized units by the IUCN for protecting natural connectivity, however infrequently evaluated. Evolutionarily Significant Units (ESUs) are currently not recognized as a formal unit by the IUCN. However, incorporating ESUs into conservation frameworks could significantly enhance our capacity to identify and protect adaptive genetic diversity. To facilitate inclusion of these units in IUCN assessments, we outline a widely applicable framework for their identification that uses non-molecular and molecular data for global accessibility.

EcoEvoRxiv↗

USGS2025

A survey of mammal and fish genetic diversity across the global protected area network

Global conservation targets aim to expand protected areas and maintain species’ genetic diversity. Whether protected areas capture genetic diversity is unclear. We examined this question using a global sample of nuclear population-level microsatellite data comprising genotypes from 2513 sites, 134,183 individuals, and 176 mammal and marine fish species. The genetic diversity and differentiation of samples inside and outside protected areas were similar, with some evidence for higher diversity in protected areas for small-bodied mammals. Mammal populations, particularly large species, tended to be more genetically diverse when near multiple protected areas, regardless of whether samples were collected in or outside protected areas. Older marine protected areas tended to capture more genetically diverse fish populations. However, limited data availability in many regions hinders the systematic incorporation of genetic diversity into protected area design. Focusing on minimizing population decline and maintaining connectivity between protected areas remain essential proxies for maintaining genetic diversity.

Conservation Letters↗

USGS2025

Exosomal micro RNA isolation in white-tailed deer (Odocoileus virginianus) for diagnostic biomarker discovery

Molecular approaches are becoming more prevalent for the diagnosis of neurodegenerative diseases in human medicine and can be extended to diagnosis of wildlife diseases such as chronic wasting disease and other prion diseases. These diseases have been associated with exosome-bound molecular biomarkers of disease progression, such as proteins and micro RNA molecules (miRNA). We tested and optimized a method for exosomal miRNA isolation from minimally invasive, small-volume serum samples obtained from white-tailed deer ( Odocoileus virginianus ). We confirmed the isolation of exosomes and optimized a commercially available benchtop kit to obtain sufficient and pure RNA for miRNA sequencing. The selected method for RNA extraction combines two 500- m L serum aliquots into one elution column and re-eluting the final product of the column. We identified 137 miRNA present in healthy white-tailed deer that can be used as a baseline to identify putative miRNA biomarkers of disease progression and mechanisms of infection in future comparative disease studies. This approach to biomarker discovery may help to inform biological processes in wildlife populations and provide alternatives to invasive or postmortem samples.

Journal of Wildlife Diseases↗

USGS2024

The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data

Environmental DNA ( eDNA ) and RNA ( eRNA ) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data and metadata makes results difficult to reproduce and synthesise. A working group of scientists have collaborated to produce a set of minimum reporting guidelines for the constituent steps of metabarcoding workflows, from the physical layout of laboratories through to data archiving. We emphasise how reporting the suite of data and metadata should adhere to findable, accessible, interoperable and reproducible ( FAIR ) data standards, thereby providing context for evaluating and understanding study results. An overview of the documentation considerations for each workflow step is presented and then summarised in a checklist that can accompany a published study or report. Ensuring workflows are transparent and documented is critical to reproducible research and should allow for more efficient uptake of metabarcoding data into management decision-making.

Metabarcoding and Metagenomics↗

USGS2024

How, what, and where you sample environmental DNA affects diversity estimates and species detection

Environmental DNA (eDNA) is a complex mixture of DNA, varying in particle sizes and distributed heterogeneously in aquatic systems. Optimizing eDNA sampling is crucial for maximizing species detection, particularly in high-risk scenarios like invasive species management. In this study, we compare two eDNA sampling methods - namely tow net and grab sample, where the tow nets process large volumes of water (3500–7000 L) through a 64 μm pore size and the grab samples process 1 L sample at a single point through 0.45–1.2 μm pore size membranes. We compared these methods to ascertain what most influences (1) the detection of invasive species ( Dreissena mussels and Burmese pythons) using qPCR or ddPCR and (2) total diversity monitoring of metazoan, protist, and fungi community using a COI marker and plant communities using the ITS marker. Sampling was conducted across a wide geography and diverse aquatic environments in Minnesota and Florida, USA, and Switzerland. The tow net samples had significantly higher eDNA yield compared to grab samples; however, they exhibited equal or lower alpha diversity of OTUs (Operational Taxonomic Units). The two sampling methods measured different beta diversity of communities detected with the COI marker across all three regions, highlighting the impact of the sampling method on the diversity of eDNA captured. In comparison, the beta diversity of plant eDNA was less impacted by the sampling method. We found no clear difference in detection for the invasive species targets based on the eDNA sampling method. These results underscore the need for pilot studies before conducting biodiversity inventory and monitoring, and a need for a greater understanding of not just how much, but also what, eDNA is captured depending on method choice, considering both spatial and particle size heterogeneity.

Florida, Minnesota↗

USGS2024

Community for Data Integration 2020 project report

The U.S. Geological Survey Community for Data Integration annually funds small projects focusing on data integration for interdisciplinary research, innovative data management, and demonstration of new technologies. This report provides a summary of the 12 projects funded in fiscal year 2020, outlining their goals, activities, and accomplishments.

Open-File Report↗

USGS2024

DNA-based studies and genetic diversity indicator assessments are complementary approaches to conserving evolutionary potential

Genetic diversity is essential for maintaining healthy populations and ecosystems. Several approaches have recently been developed to evaluate population genetic trends without necessarily collecting new genetic data. Such “genetic diversity indicators” enable rapid, large-scale evaluation across dozens to thousands of species. Empirical genetic studies, when available, provide detailed information that is important for management, such as estimates of gene flow, inbreeding, genetic erosion and adaptation. In this article, we argue that the development and advancement of genetic diversity indicators is a complementary approach to genetic studies in conservation biology, but not a substitute. Genetic diversity indicators and empirical genetic data can provide different information for conserving genetic diversity. Genetic diversity indicators enable affordable tracking, reporting, prioritization and communication, although, being proxies, do not provide comprehensive evaluation of the genetic status of a species. Conversely, genetic methods offer detailed analysis of the genetic status of a given species or population, although they remain challenging to implement for most species globally, given current capacity and resourcing. We conclude that indicators and genetic studies are both important for genetic conservation actions and recommend they be used in combination for conserving and monitoring genetic diversity.

Conservation Genetics↗

USGS2024

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

Nature Methods↗

USGS2024

Realizing the potential of eDNA biodiversity monitoring tools in the marine environment with application to offshore renewable energy

The U.S. Geological Survey (USGS) researches the biological diversity and distribution of species to support management, conservation, and resource use decisions. USGS scientists advance detection and monitoring technologies to assess changes in fish and wildlife populations, biodiversity, and the health of ecosystems. The United States is planning to install 30 gigawatts of offshore marine and wind energy by 2030. However, the effects on fish and wildlife and their habitats are not well understood. The USGS is a leader in the field of eDNA technologies and has helped advance robotic eDNA samplers, has extensive experience working in the offshore environment, and has developed novel and actionable statistical methods and standards for eDNA monitoring applications. This fact sheet presents key eDNA research and development advances needed for realizing the potential of eDNA biodiversity monitoring tools in the marine environment and applying eDNA monitoring to offshore renewable energy development. New and cost-effective tools for measuring changes in biodiversity in response to offshore renewable energy development can help to inform natural resource management and project planning and permitting decisions.

Fact Sheet↗

USGS2024

Best practices for genetic and genomic data archiving

Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible and FAIR (findable, accessible, interoperable and reusable) compliant, they could be reused for many additional purposes. We discuss the main challenges with existing genetic and genomic data archives, and suggest best practices for archiving genetic and genomic data. Recognizing that this is a longstanding issue due to little formal data management training within the fields of ecology and evolution, we highlight steps that research institutions and publishers could take to improve data archiving.

Nature, Ecology and Evolution↗

USGS2024

Too simple, too complex, or just right? Advantages, challenges, and guidance for indicators of genetic diversity

Measuring genetic diversity of wild species using DNA-based data remains resource intensive and time consuming for nearly all species. However, genetic assessments are needed for global conservation commitments, including the Convention on Biological Diversity, and for governments and managers to evaluate conservation progress, as well as prioritizing species and populations to preserve and recover genetic diversity (e.g., via genetic rescue). Recently, indicators were developed for tracking and reporting genetic diversity status and trends for hundreds of species. The indicators quantify two simple proxies of within-population and among-population genetic diversity and adaptive potential: small effective population size ( N e < 500) and the loss of genetically distinct populations. The indicators must balance scientific credibility, practicality, and simplicity. In the present article, we summarize the advantages of these pragmatic indicators, address critiques by scientists for simplifying assumptions and by policymakers for complexity, and propose potential solutions and next steps. We aim to support practitioners putting indicators into policy, action, legislation, and reporting.

BioScience↗

USGS2024

In vitro impacts of glyphosate on manatee lymphocytes

Exposure to contaminants, such as the herbicide glyphosate, can suppress protective immune functions. Glyphosate is the herbicide most used worldwide and has been found in the plasma of more than 50 % of the Florida manatees ( Trichechus manatus latirostris ) and all-year-round in their aquatic environment. Our objectives were to analyze the consequences of glyphosate exposure on their immune responses via T-lymphocyte proliferation assays and transcriptomics. We isolated peripheral blood mononuclear cells (mainly lymphocytes) of free-ranging manatees and performed T-cell proliferation assays. We used transcriptomics to understand the consequences of glyphosate in vitro exposure. The three doses chosen ranged from environmentally relevant concentrations at 10 to 10,000 µg.L −1 that is considered an environmental contamination scenario. Glyphosate caused a dose-dependent reduction in T-lymphocyte proliferation, with a significant mean reduction of 27.3 % at 10,000 µg.L −1 and up to 51.5 % in some individuals. Additionally, T-lymphocyte proliferation was significantly reduced in mid-winter compared to early winter. Transcriptomic analysis of peripheral blood mononuclear cells indicated that all doses of glyphosate (10, 1,000, and 10,000 µg.L −1 ) resulted in up-regulation of genes related to acute phase inflammation and inhibition of the T-lymphocyte proliferation pathway. Exposure to this contaminant along with other environmental stressors, such as extreme winters and red tide, might further affect the adaptive immune response of this threatened species.

Florida↗

USGS2024

Environmental DNA

The widespread adoption of environmental DNA (eDNA) detection tools for biodiversity monitoring has led to the need for universal data standards to inform principled eDNA data applications. Improvements in understanding the meaning and possible uncertainty of eDNA data can minimize erroneous conclusions, increase confidence in eDNA data, and maximize conservation outcomes. -Environmental DNA (eDNA) is the genetic material left by organisms in the environment. -eDNA is increasingly being used to detect the presence of species and assess biodiversity, but broad-scale best practices are still being developed. -This affects the quality, accessibility, and usefulness of data. -Non-invasive eDNA sampling can complement or enhance conventional approaches, as it can be a highly sensitive, rapid, and cost-effective tool for biodiversity monitoring. -Creating unified eDNA data best practices and developing DNA reference libraries will ensure eDNA detection methods are applied consistently to accurately inform conservation and wildlife management.

Report↗

USGS2024

National Aquatic Environmental DNA Strategy

Aquatic life is the engine of ecosystems and economies. In environments ranging from freshwater through marine, this biodiversity underpins the health, culture, opportunities, and economic wellbeing of the Nation -- from local communities to the entire country. The ability to evaluate the status, trends, and future projections of nature is key to maintaining national prosperity, and this requires timely and trusted information about the condition of aquatic biodiversity on a vast scale. With one of the largest Exclusive Economic Zones in the world and extensive estuaries, lakes, rivers and streams, it is a grand challenge for the United States to explore, monitor, and understand aquatic life.

Report↗

USGS2023

A pragmatic approach for integrating molecular tools into biodiversity conservation

Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across institutions and countries in access to technologies, funding, and training. Consequently, in many cases, more accessible traditional genetic data (e.g., microsatellites) are still utilized for making conservation decisions. Conservation approaches need to be pragmatic by tackling clearly defined management questions and using the most appropriate methods available, while maximizing the use of limited resources. Here we present some key questions to consider when applying the molecular toolbox for accessible and actionable conservation management. Finally, we highlight a number of important steps to be addressed in a collaborative way, which can facilitate the broad integration of molecular data into conservation.

Conservation Science and Practice↗