Genetic markers such as microsatellites can be useful in different research areas in animal ecology such as:

  • population genetic structure

  • parentage analyses

  • mating systems

  • pedigree

To extract DNA we first need to sample a piece of tissue of the targeted animal and store it in 95% ethanol.

A microsatellite is a stretch of DNA with mono-, di-, tri-, or tetranucleotide units repeated. Microsatellites are short sequences of nucleotides (typically 1–5 bp) that are tandemly repeated.

The most common way to detect microsatellites is to design PCR primers that are unique to one locus in the genome and the base pair on either side of the repeated portion. Therefore, a single pair of PCR primers will work for every individual in the species and produce different sized products for each of the different length microsatellites. The PCR products are then separated by either gel or capillary electrophoresis. The investigator can determine the size of the PCR product and thus how many times the dinucleotide “CA” was repeated for each allele. It would be nice if microsatellite data produced only two bands, but often there are minor bands in addition to the major bands; these are called stutter bands and they usually differ from the major bands by two nucleotides.

For more information on the methodology see link.

[Left] Detection of microsatellites from genomic DNA: Two PCR primers (forward and reverse gray arrows) are designed to flank the microsatellite region. By determining the size of each PCR product (in this case, 116 bp), one can calculate how many CA repeats are present in each microsatellite (there are eight CA repeats in this example).

[Right] Fictive examples of microsatellite data: Left Half: Four sets of data were produced by gel electrophoresis, including major (black) and stutter (gray) bands (MW: molecular weight standards). Right Half: The data are line graphs with the location of each peak on the X-axis representing a different sized PCR product; the height of each peak indicates the amount of PCR product. Major bands produce higher peaks than the stutter peaks.

According to link