What Is Molecular Ecology?

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Introduction to Molecular Ecology

Before the 1990s, the term “molecular ecology” was rarely used, though many studies had been done in the past that could be classified as molecular ecology studies. So exactly what is molecular ecology? Well, just as the name implies, molecular ecologists apply molecular methods and techniques to study a wide array of ecological problems.

What Kinds of Questions Does Molecular Ecology Research Address?

The use of molecular (i.e. genetic) techniques allows researchers to study ecological issues in much greater detail than was ever possible before. Ecological interactions between organisms and between organisms and their environment, kinship and parentage relationships, speciation and hybridization events, phylogeography, landscape ecology and population dynamics are some of the topics that can be addressed with the tools of the molecular ecologist.

Molecular ecology studies can:

  • help determine the size of a population and the home range of a population

  • identify migratory events

  • identify “at-risk” populations where a strong reduction in genetic variability may be driving a population towards extinction

  • identify taxonomic entities in order to plan management strategies

  • identify hybridization events to understand why they are occurring

  • help in efforts to minimize the loss of genetic variability in isolated populations or populations located in fragmented habitats

  • help to identify sites that could potentially be targets for reintroduction, based on genetic analyses of museum specimens and/or fossils

  • help to maintain and/or increase genetic diversity in captive populations

  • identify individuals and assign individuals (or genes) to their population or species of origin - useful in wildlife forensics.

Some of the most famous molecular ecology research studies involved the accurate identification of mating systems in birds. It was believed for a long time that certain bird species, such as bald eagles, formed pair bonds that mated for life and birds would only mate with their partner. Studies on eagle chicks, however, demonstrated that while adults do form pair bonds to raise young, many chicks in a nest are the result of what researchers call “extra-pair copulations”, essentially the bird equivalent of an extra-marital affair. Another popular example of the application of molecular biology, which happened early on in the emergence of the field, was the observation that there is virtually no genetic diversity among South African cheetahs (Acinonyx jubatus). Indeed, one of the main, and ongoing, debates in the field is the significance of genetic diversity and how much is needed to really consider a population “healthy” and able to withstand environmental change.

Tools of the Trade

The main reason for the increase in popularity of molecular ecology is the ever-increasing availability and efficiency of the essential tools of the trade, which are known as molecular markers or genetic markers. Today, genetic markers can be obtained through non-invasive sampling; i.e. animals are not harmed or stressed during the process. Samples can be obtained from hair, feathers, feces, bones, and ancient tissue.

Genetic markers are small areas of an organism’s genome that are assumed to be representative of the genome as a whole; they may or may not include a functional gene. Most markers must have some amount of polymorphism (variation), though the exact amount needed depends on what is being studied. For example, if scientists need to distinguish individuals, highly polymorphic markers are needed (this is essentially what is used in DNA fingerprinting), while population genetic analyses only require moderate levels of variation.

In the very early days of molecular ecology, protein variants were used; today they are still employed, though they are more useful to distinguish factors among species. When restriction endonucleases were discovered, researchers were able to cut up an organism’s genome into fragments that were specific to an individual; this ushered in a new era in the field. Once PCR was introduced, though, the field was completely revolutionized. The new preferred tool, which remains the tool of choice today, is the microsatellite.

A microsatellite is an area of a genome that is composed of a sequence of repeats of nucleotides (for example, AGAGAGAGAGAG); there are a multitude of these repeats and the number of repeats within a microsatellite varies from individual to individual. As techniques and tools are refined, it is possible to actually compare information gained from different types of markers.


C. Husseneder et al. “Multilocus DNA Fingerprinting and Microsatellite Genotyping: Complementary Molecular Approaches to Investigating Colony and Population Genetic Structure in Subterranean Termites.” Sociobiology. 2002.

R DeYoung and R Honeycutt. “The Molecular Toolbox: Genetic Techniques in Wildlife Ecology and Management.” Journal of Wildlife Management. 2005.

An Introduction to Molecular Ecology (Beebee and Rowe, 2006).