Background- Methods-

---

Microsatellites

• Introduction
• Applications
  • Genetic Diversity
  • Genetic Distance
  • Population Structure

INTRODUCTION:

What are Microsatellites?

Microsatellites are DNA sequences made up of tandemly repeated single sequence motifs no more than six bases long. For example: CACACACACACACACA. In this case the motif is CA and the allele consists of 8 repeats, with each repeat being two bases long (or 16 base pairs total). It can be written as: (CA)₈. Diploid organisms have two versions (alleles) of each gene. If the other allele for the individual mentioned above has the same number of repeats, than this individual is a homozygote, but if the number of repeats differs, say (CA)₁₀, then it is a heterozygote carrying two different alleles at the same locus (a (CA)₈ allele and a (CA)₁₀ allele). You can extend this to comparisons among individuals within populations, comparisons among populations within species, comparisons among species, and so on. We can use some measure of the number of alleles per locus as an indicator of how diverse a given population is, and differences in the frequencies of microsatellite alleles among populations to get a sense of how different two or more populations are.

Why are Microsatellites so Popular?

Microsatellites are presently the most popular genetic markers in use because they possess a series of useful properties including:

• Mutation rates are extremely high, with a value of 10^-3 mutation events per locus documented for humans being typical (Hancock, 1999).
• Levels of polymorphism in natural populations are high and the basis of the polymorphism is size, which is relatively easy to score.
• They are extremely common in genomes and have a fairly even distribution, although they tend to be less frequent in coding regions and telomeres (Hancock, 1999).
• They are codominant genetic markers, so all genotypes can be scored.

What mechanism is responsible for the high levels of polymorphism?

Slipped strand mispairing (slippage) during DNA replication is thought to be the primary mechanism responsible for the high mutation rates/polymorphism. However, recombination has also been suggested (Hancock, 1999).

APPLICATIONS:

How are microsatellites used in biology?

Microsatellites have numerous applications ranging from ecological studies of natural populations of animals to the search for genes responsible for human diseases. Below I describe applications which I use in my research related to (1)measuring levels of genetic diversity, (2)estimating genetic distances between populations, and (3)assessing population structure.

1. Measuring Genetic Diversity:

The genetic diversity of a population generally refers to the amount of DNA variation that exists in a population. Genetic diversity is important because it provides the raw material on which natural selection acts. The more genetically diverse a population is, the more likely it will be able to adapt to the changing circumstances it encounters over space and time. There are many different ways in which you can measure genetic diversity. These include (from Frankham et al., 2002):

• Ho = Observed number of heterozygotes, the total number of heterozygotes at a locus divided by the total number of individuals sampled. This can be averaged across loci for a single population measure. Remember, heterozygotes are invividuals that have two different alleles at a given locus. The more genetically diverse the population is, the more likely a given individual will be a heterozygote.
• He = Expected heterozygosity (or gene diversity), the expected number of heterozygotes in a population (a theoretical measure). The equation is:

  He = 1 - Sum(p_i²)

  where p_i is the frequency of the ith allele. This can be averaged across loci for a single population measure.

• A = Allelic diversity, defined as the total number of alleles across all loci, divided by the total number of loci. A good, simple comparative measure of genetic diversity but note that it doesn't take into account allele frequencies, so it can be overly sensitive to the presence of rare alleles.
• ne = Expected number of alleles. This is a theoretical value indicating the number of alleles there would be to provide the same heterozygosity if all were equally frequent. This measure is much less sensitive to rare alleles and is usually much less than A. The equation is:

  ne = 1 / (Sum(p_i²))

  where p_i is the frequency of the ith allele. This can be averaged across loci for a single population measure.

2. Estimating Genetic Distances Between Populations:

Genetic distances give a measure of how genetically distinct two samples (populations) are. The distinctness can arise because of a difference in the alleles present in the two samples or, more commonly, because of differences in the frequencies of alleles in the two samples. Pairwise distances can be listed in matrix form for a set of samples. Distances can be used to create trees, which are diagrams used in biology to indicate relationships among samples. The "relationships" can be either phylogenetic (i.e. indicating their evolutionary history) or simply genetic (how genetically similar samples are regardless of their evolutionary history). There are numerous different measures of genetic distances:

3. Assessing Population Structure:

Created: 28 April 2006
Last Updated: 3 July 2006