U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2012–3017

August 2012

Using Genetic Research to Inform Imperiled and Invasive 

Species Management 

Printed on recycled paper

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. 

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. 

USGS geneticists are using 

molecular markers to confirm the identity of invasive species and to determine 

the source populations for these species. 

By assessing these 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.

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. 

For definitions of the bold terms, please see 

 Genetic Research for Wildlife and Fisheries Management—A Primer:

 U.S. Geological Survey Fact Sheet 2012-3110

Invasive Burmese python in Everglades 

National Park, National Park Service

Young wild-caught black carp taken by 

commercial fishers in the Red-Atchafalaya 

River system, Dr. Leo G. Nico, USGS
Manatees are netted and brought into a boat for 

health assessments and tracking studies in Brazil, 

Michael Lusk, USFWS 

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.

Research on Imperiled West Indian Manatee 

Populations

Extensive USGS studies of the West Indian manatee provide an example of the various types of management-oriented 

questions that can be addressed through genetic research. The 

Florida manatee is an endangered marine mammal found in the 

coastal waters of Florida and is one of two subspecies of the 

West Indian manatee. Little systematic information was previously available to determine the genetic connectivity among 

various populations of the Florida manatee or whether they bred 

with the other West Indian subspecies, the Antillean manatee. 

USGS molecular research has helped species managers understand the following issues:

• Coastal Concerns—Conservation genetic studies in the 

Florida manatee have found little population sub-structuring 

and low overall nuclear genetic diversity. This has helped the 

U.S. Fish and Wildlife Service better evaluate management 

approaches. Additionally, pedigree studies can be used to 

determine family units and the number of successfully breeding 

males in the population. 

• Caribbean Cousins—USGS geneticists surveyed 

microsatellite markers to help determine the genetic relationships between the Antillean Puerto Rico manatee and Florida 

manatee for the first time - a major question, given that both 

populations are currently listed and managed together under the 

U.S. Endangered Species Act. 

• Trending Techniques—Understanding trends in survival is 

crucial for estimating overall mortality and recruitment rates 

in manatee populations. A new Florida manatee modeling 

approach based on mark-recapture methods is being designed 

to jointly analyze photo-identification and genetic data. Unlike 

visually-based documentation, genetic data does not require 

marks on a manatee’s body to follow its life history. For the 

first time, unscarred individuals, unaffected by encounters with 

boats, can be factored into the analysis of population trends. 

This will lead to more encompassing survival estimates and 

better assessment of the population size and extinction risk.

• Recovery and Release—Brazil is home to approximately 

500 manatees that belong to the Antillean subspecies and are 

classified as critically endangered. Marine mammal managers 

in that country have begun rehabilitation programs, similar to 

those in Florida, for injured manatees and calves that have been 

found stranded alive. USGS studies are using mitochondrial and 

microsatellite markers to understand their phylogeography. The 

results will allow managers making recovery plans to take into 

account genetic relatedness and determine how to strategically 

release rehabilitated individuals in a way that supports ongoing 

genetic mixing, diversity, and fitness. USGS is using genetic techniques on both the 

Florida manatee and invasive armored catfish, 

James Reid, USGS
Genetic Research on Invasive Species

Genetic research provides molecular tools that can be 

used to rapidly identify and monitor non-native species and 

make informed decisions about invasive species control and 

management. USGS geneticists are using molecular markers 

to distinguish genetic differences among groups of non-native 

species existing in the wild, in order to determine whether there 

are distinct populations. This can be crucial if there is one main 

breeding population (a source population) that is dispersing to 

other areas. Managers seeking to control or remove invasive 

species can use this information to focus their efforts on source 

populations. The same tools that provide information about the 

origin of non-native species may also be useful for determining whether these species were brought into the environment 

intentionally through known channels, or were unintentionally 

released or escaped from captivity.

Carp Conundrum—The black carp is a large (> 1 m long) 

riverine fish, the most recent of the four Asian carps to be 

introduced and become established in U.S. open waters. In their 

native range black carp feed heavily on mussels and snails, and 

are therefore considered a threat to North America’s imperiled 

native mollusks. The species has been used in aquaculture for 

more than two decades and wild populations likely originated as 

escapes or releases from aquaculture facilities. Genetic analyses 

will compare black carp from both wild and captive populations 

to assess black carp population structure, relatedness, and 

genetic diversity. These results may provide information on 

introduction pathways and subsequent dispersal patterns of wild 

black carp populations in the Mississippi River Basin. 

Lionfish Larvae—To support managers working to protect the 

habitat of native reef fishes, mitochondrial markers are providing information to track the genetic relatedness of lionfish 

throughout the Caribbean. This information can be used to help 

determine the source populations of larvae.

Asian tiger shrimp—Recently, there has been a 10 fold increase 

in reports of this non-native shrimp in coastal waters from North 

Carolina to Texas. The shrimp can grow up to one foot in length 

and its potential for negatively impacting native ecosystems is 

currently being studied. In the meantime, the source of these 

shrimp is uncertain, and no one knows the specific pathways 

or number of initial introduction events leading to their presence in U.S. waters. It is also unclear whether the increase in 

numbers throughout the region is due to local breeding, dispersal by ocean currents, or other mechanisms. Molecular studies 

are helping to understand the introduction pathways and genetic 

relatedness of individuals found throughout the southeast U.S. 

to begin piecing together the source of the invasion and to better 

understand the non-native range expansion. 

Python Parameters—The 

invasive and exotic Burmese python is established 

and breeding in Everglades 

National Park and has the 

potential to occupy the entire 

greater Everglades region. 

Pythons may adversely affect 

populations of native and 

endangered species. Genetic 

information can aid resource 

managers in monitoring the 

invasion of this non-native 

species. Therefore, USGS 

scientists developed a suite 

of new python microsatellite 

markers using next-generation 

sequencing techniques. These 

markers make it easier for researchers to identify their genetic 

diversity, growing or declining population sizes, and breeding 

patterns over geographic areas. Additionally, there are plans to 

analyze the DNA of python gut contents to identify which species pythons feed upon in the wild.

Invasive lionfish in Puerto Rico, 

Antonio Mignucci-Giannoni, Inter American University of Puerto Rico

Burmese python swimming in Florida Bay, 

Camp Walker, Islamorada, Fla.

Gel electrophoresis visualizing 

python genomic DNA 
What is eDNA?

Environmental DNA (eDNA) is a term used to describe genetic material found in the environment. It comes from 

biological samples such as cells, microorganisms, tissue, and feces, and can originate from both living and dead organisms. Researchers identify it by sampling water, sediment, soil, or even air. In the lab, the small quantities of eDNA are 

extracted from the environmental sample and copied exponentially until there is enough material for genetic sequencing 

and species determination. 

Environmental DNA techniques can use molecular markers to target a particular species. For example, aquatic eDNA 

surveillance is useful to identify specific invasive species, particularly those that are difficult to detect because they are 

concealed or present in small numbers. However, other techniques, including metagenetics and metagenomics, can be 

used to sequence all the organisms or genetic material present in an environmental sample. A researcher might sequence 

all the microorganisms found in a soil sample to better understand soil productivity. 

USGS geneticists are developing species-specific eDNA markers that will make it possible to monitor invasive 

armored catfish. Water samples collected from rivers, lakes, and springs can be analyzed for residual eDNA to detect the 

presence of invasive catfish. Further, eDNA can also be used to track their dispersal to new areas and assist in targeting 

specific waterways for more intense monitoring.

Next-Generation Genetic Sequencing: 

Why it is Revolutionizing Conservation Genetics

Next-generation sequencing allows scientists to explore 

questions that were once limited by the time-consuming 

process of decoding individual genetic sequences. A rapidly 

evolving set of technologies now allows for automated gene 

sequencing, enabling geneticists to produce thousands or 

millions of sequences in parallel. This makes it possible to 

sequence an organism’s full genome more easily or analyze 

functional DNA, genes that code for proteins (the building 

blocks of our bodies). These genes are turned on at different times and at varying levels in response to developmental 

or environmental cues. This more comprehensive and easily 

obtainable sequence information allows geneticists to more 

readily develop molecular tools or compare differences in individual genome sequences. Additionally, changes in expressed 

genes can be used to assess a species’ ability to adapt to disease 

or environmental challenges, such as climate change. 

Perspective on Pythons— The microsatellite markers that are 

being used to analyze Burmese python population structure in 

the Everglades were developed using next-generation sequencing. Previous studies found little genetic diversity and a lack of 

differentiation among pythons from different geographic areas 

in the Everglades. Therefore, the additional nuclear microsatellite markers can provide a finer-scale resolution of genetic 

differences and enabled comparison of genetic diversity of 

pythons within and outside Everglades National Park. With the 

aid of genetic tools, managers may be able to locate breeding 

sources and prioritize areas for removal efforts. 

Manatee Adaptation— Using new techniques, USGS 

geneticists launched an innovative project to find functional 

markers that vary according to a manatee’s physilogical and 

immune state and can provide clues to how manatees adapt 

to changing environmental conditions. This is done through 

sequencing the RNA (copied from DNA) of genes that are currently in use. The suite of RNA from these actively expressed 

genes is called the transcriptome. Sequencing of RNA can also 

be used to determine the health of individual manatees and 

how they respond to disease and environmental stressors. 

Coral Diagnostics— Coral disease in the Caribbean has long 

puzzled scientists. In the U.S. Virgin Islands, next generation 

sequencing will provide crucial pieces to the puzzle by generating a large set of gene sequence transcripts. Scientists can 

then compare coral, microorganisms, and symbionts inhabiting 

healthy as well as diseased corals. 

Corals in the U.S. Virgin Islands, Caroline Rogers, USGS

For More Information

Dr. Margaret E. Hunter, 

Research Geneticist

USGS Southeast 

Ecological Science Center

7920 NW 71st Street 

Gainesville, Florida 32653

Phone: 352-264-3484, 

Email: mhunter@usgs.gov 

http://fl.biology.usgs.gov/

genetics/index.html

DNA clipart made available from 

http://www.all-about-forensicscience.com