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.