their sequences. Researchers look for specific DNA sequences to create molecular 

markers that can be used to distinguish or 

differentiate cells, individuals, or species. 

Genetic studies often begin by compiling, comparing, and contrasting molecular 

markers in a large number of reference 

samples. Markers can then be used to 

develop more detailed analyses and 

address more complex research questions. 

Genetic markers can even be used to track 

the life histories of individual animals.

Species Identification

Genetic research can address 

logistical problems such as how to identify 

species that are very small, 

indistinguishable, cryptic, 

or otherwise hard to detect. 

Using samples of hair, 

skin, bone marrow, feathers, feces, or body fluids, 

geneticists can overcome 

limitations of traditional 

sampling methodologies. 

This is possible because 

tiny fragments can be used 

for identification, offering new techniques for 

monitoring or determining 

biological inventory. 

Genetic Diversity

Genetic diversity is, in essence, 

the variation of DNA sequences within 

a species or population. Such variation 

increases the chances that some individuals may survive stressors that adversely 

affect a population. High genetic diversity improves a species’ ability to adapt 

to change, cope with disease, or rebound 

from environmental disturbances. Once 

genetic variation is lost from a population, 

U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2012–3110

September 2012

Genetic Research for Wildlife and Fisheries Management— 

A Primer

Printed on recycled paper

Scientists at the U.S. Geological Survey (USGS) use a range of research approaches to investigate the 

genetics of native and non-native species that are being managed. This Fact Sheet outlines those approaches 

and explains the type of information they provide.

What’s in a Gene?

Genetic research helps managers 

“peer under the hood” of a species’ biology by looking into the molecular units 

that are passed down from generation 

to generation to build and maintain an 

organism’s traits. Many traits are determined by deoxyribonucleic acid (DNA), 

sequences of coded molecules inside each 

living organism that provide blueprints for 

how that individual’s cells should develop 

and grow. DNA does this by producing 

ribonucleic acid (RNA), which in turn 

codes for proteins—the building blocks of 

an organism. This process is called gene 

expression.

Studying an 

organism’s genes allows 

scientists to identify individuals, and compare and 

contrast differences in 

populations and species. 

With sufficient data, scientists can also study the 

migration and breeding patterns that affect their longterm likelihood of survival. 

Studying gene expression opens up even more 

potential research avenues 

about how a species 

responds to its environmental conditions.

Many of these research questions 

would be impossible by surveying wild 

populations. Furthermore, new techniques 

offer managers alternative ways to ask 

research questions that once required 

large-scale field investigations. 

The Importance of Markers

Genetic research examines the DNA 

and RNA sequences in an individual 

sample to decode and analyze variation in 

as is often the case with an imperiled 

species, it cannot be easily recovered. 

If diversity becomes too low, species 

can cross an inbreeding threshold and 

enter an extinction vortex—a period of 

Genetic Expressions

You’ve probably heard of DNA 

(deoxyribonucleic acid), but have you 

heard of these other genetic terms? 

Genome. An organism’s complete set of 

hereditary sequences. 

Nuclear DNA. The genetic blueprint for 

a living organism, found in the nucleus 

of a cell. 

Molecular (DNA) markers. Target 

sequences that researchers use for 

analysis. DNA markers can be microsatellites (found on nuclear DNA) or 

mitochondrial. 

Mitochondrial DNA. Remember 

mitochondria, those powerhouses that 

help your cells convert oxygen to energy? 

These contain their own genome, which 

is passed on with the mitochondria from 

mother to child. 

RNA. Copies of DNA used in actively 

expressed genes that code for proteins 

and can vary with different environmental and physiological conditions. 

Functional (protein-coding) DNA.

DNA that can be linked to a physical 

trait, such as eye color, by the RNA and 

proteins it codes for. 

“Junk” (non-protein coding) DNA.

This general term refers to any DNA 

sequence with no known gene function.

Non-invasive swabs are used to 

collect DNA from hard-to-identify, 

imperiled mussel species. 
self-reinforcing population decline that 

makes it difficult for a species to recover. 

To help managers understand the diversity issues that threatened and endangered 

species face, geneticists can quantify the 

amount of diversity. These can focus on 

an entire species or be used to compare 

and contrast specific populations. 

Staying Fit 

A diverse gene pool helps a 

population adapt to its environment by 

offering a mix of potential traits for individuals. Traits that are well suited to the 

environment help organisms survive and 

pass genes down to future generations. 

In general, an organism’s propensity for 

survival and reproduction is known as 

“fitness.” Understanding how genes have 

been passed down through generations 

provides information that can be used to 

help manage a wild population. Managing for fitness involves understanding 

how gene flow influences diversity and 

affects locally adapted traits that may 

have developed in some populations. 

Therefore, it is useful to gain information 

about how different populations are 

interbreeding.

Breeding Patterns 

Depending on which type of DNA 

is sequenced, genetic studies can reveal 

deep evolutionary relationships using 

gene trees or more recent breeding patterns. Researchers use mitochondrial 

markers to study ancestry and phylogenetics. In contrast, nuclear DNA, which 

is inherited from both parents and used 

to identify specific individuals, allows 

scientists to study contemporary gene 

flow. It can be used to look at pedigrees, 

population interbreeding, hybridization, 

and genetic differences found in different 

geographic groups.

Research Capabilities and their Management Applications

•	 Functional genetics/transcriptomics. The sequencing of expressed genes that 

influence health and adaptation, often produced in response to environmental 

challenges, such as disease outbreak or climate change.

•	 Genetic diversity analysis. Studies that use molecular markers to quantify 

diversity, estimate population sizes, learn how genetic material has been passed 

down, and infer how gene flow influences diversity and fitness.

•	 Genetic population structure. The study of a group of individuals over the 

landscape to determine related (interbreeding) and non-related groups. This 

type of analysis can be used to identify genetically-unique groups for conservation measures or to find migration pathways through which genetic material is 

exchanged. 

•	 Landscape genetics. Research that examines how physical features such as 

oceans, waterfalls, dams, and culverts have influenced genetic variation across 

landscapes by interpreting movement patterns of individuals in terms of the 

biological processes that create and maintain them. This aids efforts to manage 

populations based on connectivity.

•	 Molecular marker development. Techniques used to create new, reliable 

markers for use in genetic investigations. New markers must be developed in 

situations where no existing marker offers the appropriate comparative detail 

needed for an analysis.

•	 Microsatellite marker fragment analysis. An analysis based on short, 

repeating base pairs (for example, ACTACTACT) of nuclear DNA sequence that 

are highly variable. These fragments are used to detect hybridization, evaluate 

pedigrees, identify individuals in order to predict survival rates, and characterize 

genetic population structure.

•	 Mitochondrial DNA sequencing. A study of sequences from the mitochondrial 

genome to determine the evolutionary history of a population (ancestral relatedness) through relationships in gene trees. Mitochondrial DNA is usually maternally inherited, meaning all offspring have gene copies matching their mothers. 

•	 Parentage assignment and pedigree analysis. Reconstructions of genetic relationships of individuals and their families through time. This information allows 

researchers to estimate the heritability of traits in captive and wild populations, 

minimize inbreeding in captive populations, reveal patterns of sexual selection 

and dispersal, and determine rates of gene flow within and between populations. 

•	 Phylogenetics. Studies of ancestry used to create relatedness trees on a geologic 

time scale and reveal evolutionary relationships between a species and its higher 

taxonomy (that is, Family, Order, and Class).

•	 Phylogeography. An analysis of breeding and genetic variation patterns in 

a geographic context that can reveal information about species boundaries and 

breeding not always detected by conventional taxonomic methodologies.

•	 Species identification/DNA barcoding. Identification of a species, by matching 

DNA in tissue from a specimen to a reference “barcode” sequence. This technique 

can also be used to identify prey species based on analysis of gut contents.

By Rachel J. Pawlitz, Margaret E. Hunter, 

and Nathan A. Johnson. 

For more information 

Dr. Margaret E. Hunter, Research Geneticist, 

 (352) 264-3484, mhunter@usgs.gov 

Nathan A. Johnson, Mussel Ecologist, 

 (352) 264-3574, najohnson@usgs.gov 

Laboratory Address:

USGS Southeast Ecological Science Center

7920 NW 71st Street 

Gainesville, Florida 32653

http://sesc.usgs.gov