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Using Genetic Research to Inform Imperiled and Invasive Species Management

The long-term viability of species and populations is related to their potential to migrate, reproduce, and adapt to environmental changes. In the southeast United States, U.S. Geological Survey (USGS) scientists are providing resource managers with genetic information to improve the long-term survival and sustainability of the Nation’s aquatic species. Research focused on native and imperiled species can assess the genetic factors influencing their survival and recovery, while work on invasive species can provide information on their proliferation, dispersal, and impacts on native species.

Imperiled Native Species

Genetic diversity plays a critical role in the ability of a species to survive. A diverse gene pool can increase a population’s ability to adapt to diseases, habitat modifications, or changes in the environment, such as altered hydrology and hurricanes. Small, imperiled populations typically have reduced genetic diversity, which can increase susceptibility to disease, decrease population viability and negatively influence fitness, or the number of surviving offspring.

Manatees are netted and brought into a boat for health assessment and tracking studies in Brazil, Michael Lusk, USFWS
Manatees are netted and brought into a boat for health assessment and tracking studies in Brazil, Michael Lusk, USFWS

Quantifying the genetic diversity of a species or population is a useful first step in understanding the factors affecting imperiled species. Using nuclear DNA (deoxyribonucleic acid), scientists can identify inbred populations before physical defects are present. This type of genetic information can help managers identify whether additional conservation measures are warranted. Genetic diversity data combined with morphological data can be used to assist with taxonomic classifications, especially for species that are at risk of extinction and are undergoing conservation listing decisions, or with samples where the species is not clearly identifiable morphologically, such as in poaching cases. Another type of analysis, known as phylogenetics, can determine the evolutionary relatedness of populations, specifically useful for assisting with decisions regarding the conservation status and management of imperiled species. Similarly, geneticists can use phylogeography to address the historic processes that resulted in the geographic distribution of organisms, while landscape genetics addresses the influence of ecology and current environmental features (rivers, mountains, roads, etc.) on genetic connectivity at a finer scale.

Knowledge of population patterns across the landscape can help improve imperiled species management. For example, if populations that were once connected are now isolated or have extremely low diversity, managers may use conservation measures, such as habitat corridors, to reconnect populations and improve the viability of the species.

Genetic tools can also identify individual animals, their sex, and pedigree or familial relationships, which can provide life history information. Repeated identification of individuals over time, known as mark-recapture studies, can help with determining population sizes, trends, and survival rate estimates. This complementary approach to traditional inventory and monitoring methods can improve the time and cost effectiveness of assessing population status and trends.

Invasive Species

Genetic tools can also be used to rapidly identify, monitor, and manage non-native species. Invasive and exotic species can potentially harm native populations, disrupt natural ecosystems, and transmit nonindigenous diseases to human and native wildlife populations.

Young wild-caught black carp taken by commercial fishers in the Red-Atchafalaya River system, Dr. Leo G. Nico, USGS
Young wild-caught black carp taken by commercial fishers in the Red-Atchafalaya River system, Dr. Leo G. Nico, USGS

USGS geneticists are using molecular markers to confirm the identity of invasive species and to determine the source populations for these species.

By assessing the origins of non-native species, scientists can help managers learn more about how they may have been introduced into the environment, through intentional releases or unintentional escapes, and gauge the likelihood of the population increasing and becoming established in the ecosystem. Genetic examination of gut contents can determine the native species that are preyed upon by invasive species, which helps managers assess the impact of invasives on the environment and imperiled species.

Invasive Burmese python in Everglades National Park, National Park Service
Invasive Burmese python in Everglades National Park, National Park Service

An improved understanding of genetic population dynamics can also be used to determine whether separate populations of non-native species exist in the wild. This determination can help managers target the main breeding population of invasive species for control or removal efforts.

The "First Generation” of Conservation Genetics

Genetic studies have traditionally focused on developing DNA markers, because they are useful for phylogenetics, phylogeography, species identification (through DNA barcoding), and other types of conservation genetics research.

Molecular markers, typically mitochondrial or nuclear microsatellites, can be used to understand ancestral relationships on a long-term, geologic time scale, which is useful for making inferences about the types of conditions that a species was adapted to in the past. They can also help managers understand more recent breeding patterns among different populations and how those patterns influence the movement and mixing of individuals across waterways or other types of corridors, such as ocean migration routes.

Current Research

dot icon USGS Conservation Genetics - Mammals

dot icon USGS Genetics Science in Invasive Species Research

dot icon Research on Imperiled West Indian Manatee Populations

dot icon Genetic Research on Invasive Species

dot icon Next-Generation Genetic Sequencing: Why it is Revolutionizing Conservation Genetics

Recent Publications

Pimiento, C., Nifong, J. C., Hunter, M. E., Monaco, E., & Silliman, B. R. (2015). Habitat use patterns of the invasive red lionfish Pterois volitans: a comparison between mangrove and reef systems in San Salvador, Bahamas. Marine Ecology. [Journal Abstract]
Hunter ME, Oyler-McCance SJ, Reed RN, Fike JA, Smith BJ, Hunter CT, Hart KM. 2015. Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive Burmese pythons. Plos One 10(4): e0121655.
Butterfield JSS, Diaz-Ferguson, Silliman BR, Saunders JW, Buddo D, Mignucci-Giannoni AA, Searle L, Allen A, Hunter ME. (2015). Wide-ranging phylogeographic structure of invasive red lionfish in the Western Atlantic and Greater Caribbean. Marine Biology, 162:773-781. [Journal Abstract]
Foote AD, Liu Y, Thomas GWC, Vinai T, Alfoldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Quin X, Qu J, Raney BJ, Vijay N, Wolf JBW, Hahn MW, Muzny DM, Worley KC, Gilbert TM, Gibbs RA. 2015. Convergent evolution of the genomes of marine mammals. Nature Genetics, DOI: 10.1038/ng.3198. [Journal Article]
Fuller, P.L., D.M. Knott, P.R. Kingsley-Smith, J.A. Morris, C.A. Buckel, M.E. Hunter and L.D. Hartman. 2014. Invasion of Asian tiger shrimp, Penaeus monodon Fabricius, 1798, in the western north Atlantic and Gulf of Mexico. Aquatic Invasions 9(1): 59-70. DOI: 10.3391/ai.2014.9.1.05. [Journal Abstract]
Hunter, M. E., & Nico, L. G. (2014). Genetic analysis of invasive Asian Black Carp (Mylopharyngodon piceus) in the Mississippi River Basin: evidence for multiple introductions. Biological Invasions, 1-16. [Journal Abstract]
Hart KM, Hunter M, King TL. (2014). Regional differentiation among populations of the Diamondback terrapin (Malaclemys terrapin), Conservation Genetics. 15: 593-603. [Journal Abstract]
Guerreiro I, Nunes A, Woltering JM, Casaca A, Nóvoa A, Vinagre T, Hunter ME, Duboule D, Mallo M. 2013. Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine. Proc Natl Acad Sci U S A, 110(26):10682-6. [Journal Abstract]
Hunter, ME. 2013. The Silent Threat: Manatees, Genetic Diversity, and Caribbean Conservation. Livebetter Magazine, Issue 32. [Article]
Mahon, A.R., C.L. Jerde, M. Galaska, J.L. Bergner, W.L. Chadderton, D.M. Lodge, M.E. Hunter, L.G. Nico. 2013. Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments. PLoS ONE 8(3): e58316. doi:10.1371/journal.pone.0058316. [Journal Article]
Hunter ME, Hart KM. 2013. Rapid Microsatellite Marker Development Using Next Generation Pyrosequencing to Inform Invasive Burmese Python—Python molurus bivittatus—Management. International Journal of Molecular Sciences, 14(3):4793-4804. [Journal Abstract]
Tucker, K.P., M.E. Hunter, R.K. Bonde, J.D. Austin, A.M. Clark, C.A. Beck, P.M. McGuire and M.K. Oli. 2012. Low genetic diversity and minimal population substructure in the endangered Florida manatee: implications for conservation. Journal of Mammalogy 93(6):1504-1511.
Hunter, M.E. and Pawlitz, R.J., 2012, Using genetic research to inform imperiled and invasive species management: U.S. Geological Survey Fact Sheet 2012-3017, 4 p., available at
Hunter, M.E., A.A. Mignucci-Giannoni, K.P. Tucker, T.L. King, R.K. Bonde, B.A. Gray and P.M. McGuire. 2012. Puerto Rico and Florida manatees represent genetically distinct groups. Conservation Genetics 13 (6):1623-1635. DOI: 10.1007/s10592-012-0141-2. [USGS News Release] [Journal Abstract]
Pawlitz, R.J., Hunter, M.E., and Johnson, N.A., 2012, Genetic research for wildlife and fisheries management—A primer: U.S. Geological Survey Fact Sheet 2012-3110, 2 p., available at
Bonde, R.K., P.M. McGuire, and M.E. Hunter. 2012. A review of the key genetic tools to assist imperiled species conservation: analyzing West Indian manatee populations. J. Marine Animals & Their Ecology 5(1): 8-19. [Journal Article]
Luna, F.O., R.K. Bonde, F.N. Attademo, J.W. Saunders, G. Meigs-Friend, J.Z.O. Passavante, and M.E. Hunter. 2012. Phylogeographic implications for release of critically endangered manatee calves rescued in Northeast Brazil. Aquatic Conservation: Marine and Freshwater Ecosystems 22: 665-672. DOI: 10.1002/aqc.2260. [Journal Abstract]
Hunter, M. E., N. E. Auil-Gomez, K. P. Tucker, R. K. Bonde, J. Powell, P. M. McGuire. 2010. Low genetic variation and evidence of limited dispersal in the regionally important Belize manatee. Animal Conservation. DOI: 10.1111/j.1469-1795.2010.00383.x. [Journal Abstract]
Hunter, M.E., D. Broderick, J.R. Ovenden, K. Pause Tucker, R.K. Bonde, P.M. McGuire and J.M. Lanyon. 2010. Characterization of highly informative cross-species microsatellite panels for the Australian dugong (Dugong dugon) and Florida manatee (Trichechus manatus latirostris) including five novel primers. Molecular Ecology Resources, 10: 368-377. Journal Abstract

Genetics Lab

Left to right: Gaia Meigs-Friend, Michelle Davis, John Butterfield, Margaret Hunter, Bob Bonde, Lucy Keith
Left to right: Gaia Meigs-Friend, Michelle Davis, John Butterfield, Margaret Hunter, Bob Bonde, Lucy Keith (click image to enlarge)
Dr. Margaret E. Hunter, Research Geneticist
Dr. Margaret Hunter
Contact information:

USGS | WARC-FL - Genetics
Dr. Margaret E. Hunter
7920 NW 71st Street
Gainesville, FL 32653
Tel: 352-264-3484
Curriculum Vitae

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