Genetic distance

Measure of divergence between populations

Genetic distance is a measure of the genetic divergence between species or between populations within a species, whether the distance measures time from common ancestor or degree of differentiation. Populations with many similar alleles have small genetic distances. This indicates that they are closely related and have a recent common ancestor. Genetic distance is useful for reconstructing the history of populations, such as the multiple human expansions out of Africa. It is also used for understanding the origin of biodiversity. For example, the genetic distances between different breeds of domesticated animals are often investigated in order to determine which breeds should be protected to maintain genetic diversity.

Recent advancement in sequencing technology and the availability of comprehensive genomic databases and bioinformatics tools that are capable of storing and processing colossal amount of data generated by the advanced sequencing technology has tremendously improved evolutionary studies and the understanding of evolutionary relationships among species.

Evolutionary forces such as mutation, genetic drift, natural selection, and gene flow drive the process of evolution and genetic diversity. All these forces play significant role in genetic distance within and among species.

Different statistical measures exist that aim to quantify genetic deviation between populations or species. By utilizing assumptions gained from experimental analysis of evolutionary forces, a model that more accurately suits a given experiment can be selected to study a genetic group. Additionally, comparing how well different metrics model certain population features such as isolation can identify metrics that are more suited for understanding newly studied groups The most commonly used genetic distance metrics are Nei's genetic distance, and Reynolds, Weir and Cockerham's genetic distance.

One of the most basic and straight forward distance measures is Jukes Cantor distance. This measure is constructed based on the assumption that no insertions or deletions occurred, all substitutions are independent, and that each nucleotide change is equally likely. With these presumptions, we can obtain the following equation:

where is the Jukes Cantor distance between two sequences A, and B, and being the dissimilarity between the two sequences.

Many other measures of genetic distance have been proposed with varying success.

While these formulas are easy and quick calculations to make, the information that is provided gives limited information. The results of these formulas do not account for the potential effects of the number of codon changes between populations, or separation time between populations.

A commonly used measure of genetic distance is the fixation index (FST) which varies between 0 and 1. A value of 0 indicates that two populations are genetically identical (minimal or no genetic diversity between the two populations) whereas a value of 1 indicates that two populations are genetically different (maximum genetic diversity between the two populations). No mutation is assumed. Large populations between which there is much migration, for example, tend to be little differentiated whereas small populations between which there is little migration tend to be greatly differentiated. FST is a convenient measure of this differentiation, and as a result FST and related statistics are among the most widely used descriptive statistics in population and evolutionary genetics. But FST is more than a descriptive statistic and measure of genetic differentiation. FST is directly related to the Variance in allele frequency among populations and conversely to the degree of resemblance among individuals within populations. If FST is small, it means that allele frequencies within each population are very similar; if it is large, it means that allele frequencies are very different.