U.S. Department of the Interior

U.S. Geological Survey

FS 2006-3108

July 2006

Conservation genetics is the 

application of the tools and concepts 

of genetics to the conservation of 

biological resources. Once too sophisticated 

and expensive for routine use, the tools of 

conservation genetics are now widely used to 

address many complex management questions. 

These novel methods of analysis can augment 

assessments made with traditional methods 

and can bring new information to light. The 

U.S. Geological Survey (USGS) is well suited 

to provide scientific information and expertise 

using these tools to support the management of 

biological resources.

Conservation Genetics in the USGS

©Michael Milford

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In northern Montana, a 400 lb. grizzly 

bear lumbers across the rugged landscape, 

pausing now and then to claw at the ground 

in search of roots, bulbs, and other food. 

Along the way, he encounters a liquid 

scent lure consisting of rotting fish and 

cattle blood sprinkled on a plot encircled 

with a single strand of barbed wire 

attached to trees. The bear leaves behind 

clumps of hair as he negotiates under 

and around the wire to wallow in the 

irresistible odors. Although no humans 

witnessed his passage, the hair collected 

two weeks later is analyzed by a scientist 

who identifies the bear and adds another 

point to a data set indicating detection 

locations for this particular animal. This 

work is part of a collaboration involving 

the USGS and many partners to estimate 

the size and distribution of the grizzly 

bear population within an area of 8 million 

acres. DNA analysis of hair samples 

makes this possible. Traditional mark and 

recapture methods are the basis of the 

study design; however, there is no need 

to see or capture bears because the DNA 

contained in their hair is sufficient for 

species, sex, and individual identification. 

In addition to gaining a good estimate of 

the size and distribution of the grizzly 

bear population, DNA profiles of the 

individual bears allow managers to address 

future conservation issues by providing 

them with information about genetic 

variation, the suitability of individual 

bears for augmenting small and isolated 

populations, the ratio of males to females, 

and connections with other populations.

Biological Diversity

Biological diversity, the variability among 

living organisms, includes diversity within 

species, between species, and across 

ecosystems. Each species is the repository of 

an immense amount of genetic information

that determines its form, function, behavior, 

and reproductive success. A human, for 

example, has about 20,000 to 30,000 genes. 

Each species, human or otherwise, is made 

up of multiple individuals, and rarely 

are individuals genetically identical. At 

another level, many species consist of 

multiple breeding populations, with each 

population having its own pattern of genetic 

variation and ability to interact with other 

populations. Furthermore, populations of 

different species coexist in communities, which 

together with the physical environment and a 

host of interactions, constitute an ecosystem. 

Conservation of biological diversity, regardless 

of the level of organization considered, 

is important because of its significance 

in maintaining balanced, functioning systems.

Gene Defined

A gene is a discrete unit of 

hereditary information consisting 

of a specific nucleotide sequence 

of deoxyribonucleic acid (DNA), 

or in some viruses, ribonucleic 

acid (RNA). DNA and RNA 

are the molecules that enable 

living organisms to reproduce 

their complex components from 

one generation to the next. The 

DNA molecule directs its own 

replication and also directs RNA 

synthesis, which leads to protein 

synthesis. Functionally, a gene is a 

DNA sequence coding for a specific 

chain of organic molecules, which 

then forms a protein of specific 

structure and function. Proteins, 

in turn, bring about an organism’s 

visible (phenotypic) properties.

A Hairy Undertaking
All organisms play roles that are essential to the persistence of 

ecosystems, and because we are part of those ecosystems, to the 

persistence of civilization. In most cases, numerous genetically diverse 

populations are necessary to ensure the survival and evolutionary 

potential of a species in the face of environmental change. This is true 

for domesticated and wild plants and animals, including those we 

view as benign, troublesome, or beneficial. The more we know about 

genetic diversity, the more we understand what can be managed and 

conserved. Information about genetic variation is used to select units 

for management, set priorities, test observations or presumptions, and 

meet management requirements. 

Example: Spotting the Difference between Owls 

Spotted owls are mostly non-migratory, long-lived birds whose 

populations have declined in mature forests of western North 

America. They are classified as three subspecies: California, 

northern, and Mexican. Northern and Mexican spotted owls are 

listed as threatened under the U.S. Endangered Species Act, 

whereas California spotted owls are not. Using genetic information, 

we reaffirmed that the northern spotted owl is a separate subspecies 

from California and Mexican spotted owls. Genetic information 

also indicated a zone of mixing between northern and California 

spotted owls in a portion of southern Oregon. This suggests that 

the range of California spotted owls extends farther north than 

previously described. Management agencies used these findings to 

review the status of the northern spotted owl, and in combination 

with population estimates and habitat assessments, to consider 

management options for all 

three subspecies. 

Documenting Genetic Variation

Recovering 

the Rare

Fragmentation, alteration, or 

complete conversion of a habitat can 

shift a population from a rare but viable 

status to a situation where existence is threatened. 

Such populations often experience reductions in genetic 

variation; in fact, one of the biggest problems is loss of genetic diversity though 

a process called inbreeding depression. This occurs when only a few individuals interbreed in 

small groups and pass a limited array of genes, some harmful, to their offspring. Individuals 

gradually become genetic copies, lacking the built-in adaptability to environmental change that 

would occur in a diverse group through natural selection. This is particularly problematic for 

captive populations where artificial propagation occurs with a limited breeding stock. We 

routinely help managers working to recover rare populations by measuring genetic diversity 

in wild and captive-bred populations, suggesting mating assignments, and evaluating the 

origins of individuals that establish a new population. 

Example: Crown Jewel of Puerto Rico

The Puerto Rican parrot is considered one of the most endangered birds in the world. During 

Columbus’ time, the parrot population may have exceeded one million but dropped to a low 

of 13 by 1975. For over 30 years, scientists and managers have studied and nurtured the few 

remaining wild and captive parrots. Success with reproduction of birds in captivity has given 

new hope for bolstering the wild population. USGS scientists have spent the past decade 

working with federal agencies and the Puerto Rican government to establish family trees 

for the captive and wild populations. We use molecular markers to identify individuals and 

verify their lineage to model potential strategies for moving birds to and from captive and 

wild populations and to set up pairings for breeding programs to maximize genetic diversity. 

Recovery of the parrot is far from realized, but some birds are being released into the wild 

— a major step in bringing the parrot back from the brink of extinction.

Management Applications 

of Genetic Information

Evaluate threats

Identify and treat disease

Meet policy requirements

Evaluate relocation options

Identify movement patterns

Propagate wild or 

domesticated stocks

Estimate relatedness and 

reconstruct lineages

Evaluate settler (founder) stocks 

Uncover and monitor change

Identify individuals for 

estimation of population 

characteristics

Infer relationships to identify 

units of management and 

evaluate taxonomy

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Effects of Pollutants

A special form of population monitoring considers effects of 

pollutants or other contaminants on plants and animals, even 

if those effects are not visible or lethal. Many pollutants are 

carcinogens or mutating agents that affect either the structure of 

DNA, its biological expression, or both. Genetic toxicologists 

study the interaction of DNA-damaging agents with the cell’s 

genetic material in relation to subsequent effects on the health 

of the organism. The organism functions as an integrator of 

exposure. The magnitude of the change in DNA or change in 

its biological expression is used as an estimate of the severity 

of exposure. In another field called genetic ecotoxicology, 

we evaluate potential effects of pollution on the health of an 

ecosystem by assessing genetics of multiple individuals in 

populations or communities and correlate this information with 

exposure to contaminants. This field is still largely theoretical, 

but it is a fruitful area of research because it offers an opportunity 

to rapidly advance our knowledge and understanding of the 

effects of environmental pollutants. 

Example: Duck Soup 

Many lesser scaup winter in the Indiana Harbor Canal of 

southern Lake Michigan. This canal, now a “Superfund” site, 

was built to service a petroleum-based industrial corridor. The 

USGS studied wintering scaup to determine if they were exposed 

to contaminants from that site, and if so, were the contaminants 

associated with genetic damage. Some of the contaminants 

studied were a group of organic compounds called polycyclic 

aromatic hydrocarbons, which originate from fossil fuels and 

combustion residues. This was the first study of wild birds to 

demonstrate a correlation between concentrations of these 

hydrocarbons in tissues and genetic damage to red blood cells. 

The concern underlying this research was that contaminant 

exposure could compromise the welfare of lesser scaup, and the 

scaup served as an indicator for the well being of other species. 

Management agencies have used 

this information in cleanup, restoration, and 

mitigation actions.

Population Monitoring

Information about abundance, population structure, reproduction, 

survival, and movement are important in management of plant and 

animal populations. Obtaining that information is often difficult 

or impossible for wide-ranging animals using traditional methods 

that involve capture, marking, and relocation. Genes already 

contain information coded in DNA that can be used as individual 

markers, and we use these “genetic tags” to accomplish population 

monitoring. There are many advantages to this approach. We are 

not restricted to monitoring the living population because genetic 

markers contain information that is inherited across generations. 

This means that information gathered in one year can be applied to 

both subsequent and previous generations, even over evolutionary 

time frames. Also, the same genetic information is obtainable at any 

life stage and frequently with little, if any, disruption to the organism 

of interest. An additional benefit is that we can monitor movements 

of individuals or populations throughout the course of a year or 

more, even if they travel to multiple, distant locations. We can even 

take DNA from museum specimens, assess the genetic variation of 

these specimens, and use this information to evaluate variation in 

current populations relative to variation in earlier populations.

Example: Monitoring the Wave 

In springtime, colorful waves of adult Atlantic salmon begin 

returning to their rivers of birth in preparation for spawning. Most 

are finishing an ocean journey that began several years before and 

spanned hundreds, even thousands of miles of open water in the 

North Atlantic Ocean. While feeding on their wintering grounds 

off western Greenland, Atlantic salmon originating from locations 

in North America and Europe have ample opportunity to intermix. 

Nonetheless, when it is time to spawn, wild populations remain 

relatively faithful to their migration routes and rivers of origin based 

on thousands of generations of local adaptation. Wild Atlantic 

salmon populations in eastern Canada and the United States have 

dropped to historic low levels, with some populations going extinct. 

Research by the USGS uses segments of DNA to accurately assign 

Atlantic salmon caught off the coast of Greenland to their continent 

of origin, and reasonably well, to their country and province of 

origin. Genetic information also is used to assess trends in the 

number of salmon being harvested in the Greenland subsistence 

fishery, and to screen fish to ensure that aquaculture escapees are 

not incorporated into brood stocks used to maintain endangered 

wild populations.
Fish and Wildlife Health Research

Infectious disease is a natural component of all ecosystems, 

affecting the health and abundance of both plants and animals. 

Understanding the role of the microbes (pathogens) causing these 

diseases enables managers to adopt strategies to modify their 

influence when necessary. Disease control can be particularly 

urgent in situations where pathogens alter the population 

structure or function within an ecosystem. In general, we strive 

to understand disease processes, develop diagnostic methods, 

describe incidence and distribution of significant pathogens, and 

develop strategies for prevention and control. Genetic techniques 

are well suited to study disease agents, especially viruses, 

bacteria, and fungi, which are structurally simple organisms and 

for many of which the sequence of the entire genome is known. 

Example: Whirling Disease

Whirling disease of salmon and trout is caused by the 

parasite, Myxobolus cerebralis. The disease, introduced in 

the United States in the 1950s, has spread to 23 states where 

it is sometimes associated with devastating declines in wild 

populations of rainbow trout. Using genetic tools, we evaluated 

the level of diversity among strains of the parasite from selected 

locations and found that genetic variation was relatively low, 

as might be expected for a recently introduced parasite. We 

also evaluated the diversity among strains of an oligochaete 

worm that is an essential alternate host during the parasite’s 

life cycle. Oligochaetes from rivers in which trout showed 

different levels of disease severity were not as closely related 

as traditional taxonomy, based on morphology, would suggest. 

In fact, some strains of the worms could be considered separate 

species based on genetic differences, and the identified genetic 

lineages have been shown to have very different abilities 

to produce the spores of the parasite that infect 

fish. This information is beneficial to 

managers seeking to understand the 

basis of variation in the severity 

of whirling disease in different 

locations or in different fish 

populations and also in 

predicting future risks 

of whirling disease 

in new locations.

Contact any of the USGS science centers at locations indicated on this 

map for additional information about conservation genetics research. Find 

contact information at www.usgs.gov.

Authors: Ruth Jacobs, Susan Haig, Sandy Talbot, James Winton, 

Tim King, Kate Kendall. 

Graphic design: Sandie Arbogast. 

Photo credits: grizzly bear, © Michael Melford; DNA, National 

Institute of Health; spotted owl, © Michael Sewell/Visualpursuit.com; 

Puerto Rican parrot, © Parrots International; Atlantic salmon, © 

Gilbert van Ryckevorsel; lesser scaup, © Richard Mittleman; whirling 

disease and lab sampling, USGS Western Fisheries Research Center.

USGS Biological Centers 

Conducting Genetics Research

Rapidly Evolving Technologies

The USGS is using new technologies to study adaptations of 

individual species and communities and to identify potential 

effects of both human-related and natural changes.

Genomics involves the study of an organism’s full 

genetic material, known as its genome. In the last decade, the 

number of sequenced genomes has grown to include mammals, birds, fishes, frogs, insects, marine organisms, plants, 

fungi, and bacteria. In addition to facilitating all molecular 

and genetics work, genomics has resulted in new technologies 

to study evolution, population structure, gene function, and 

effects of environmental change.

Success with genomics has led to proteomics, the study 

of the sets of proteins encoded by genes and their structure 

and function. This is an important step because the way that 

proteins interact with each other, with the environment, and 

with other molecules defines the organism. Furthermore, 

an organism will have radically different protein expression 

in different parts of its body, in different stages of its life 

cycle, and in different environmental conditions, whereas its 

genome is fairly constant.

A genetically modified organism, or GMO, is a plant 

or animal that has had its genetic material altered to exhibit 

new traits. These “transgenic” organisms can pass their new 

genes to close, wild relatives, and these cloned genes in wild 

organisms could tip balances within and between native 

populations, communities, and ecosystems. It is important to 

understand potential effects, positive or negative, of GMOs on 

native plants, animals, and their habitats.