Population structure and the effects it has on genetic variation in a population and how population structure can be quantified

The term population structure refers the heterogeneity in allele frequencies across a population caused by limited gene flow. There are enormous indications can found in population structure for genotype and allele frequencies. According to Hardy–Weinberg assumptions, we know that mating within a large population is not uniform and for this reason there is a chance that two individuals generally mate based on their locations within a specific population and this leads to naming population structure. The basics of this structure is heterogeneity across a population in the chances that two randomly chosen individual will mate each other in a given population.

Population structure shows the violation of Hardy-Weinberg assumption of random mating and for this reason heterozygosity is reduced. The significance of population structure is the variation in the population at the genetic level which gives more specification of the species, Conservation of genetics and also identifying the adaptions during local conditions.

Population structure has strong effect on genetic variation in a population. We can find enormous indications in population structure for genotype and allele frequencies. Mating and migration are two phenomenon that can lead to differences in allele and genotype frequencies in different parts of a population. We can see the divergence of allele frequencies between two populations through genetic drift. If we consider a single panmictic population we can see that mutation to novel and neutral alleles results to increase genetic variability and random genetic drift tends to reduce this variability. If the population is subdivided genetic differences can accumulate among individuals within groups as well as among groups. In a highly subdivided population each local population may quickly reach fixation or loss, but both alleles can be maintained in the overall population since half of the subpopulations are expected to reach fixation and half loss for a given allele. Population structure also causes evolutionary changes. The genetic isolation among subpopulations caused by subdivision can prevent novel and even advantageous alleles from spreading throughout a population.

The most common way of quantify population structure is using hierarchical F-statistics statistics developed by Wright (1965). It can be thought that F-statistics is a measure of the correlation of alleles within individuals and are related to inbreeding coefficients. A measure of the nonrandom association of alleles within an individual is considered an inbreeding coefficient. As such, F- statistics describe the amount inbreeding-like effects within subpopulations FIS, among subpopulations, FST and within the entire population FIT. F-statistic can be quantify within a subpopulation from a ratio of the observed to expected heterozygosity where,

Where Hs is the average expected heterozygosity determine from each subpopulation by

and HI is the average observed heterozygosity,

We can observe Population substructure will also lead to inbreeding-like effects, i.e. when compared to expected we determine a reduction in observed heterozygosity. This effect is known as Wahlunds' effect. This relationship depicts that because the allele frequencies in two subpopulations reduced, the average expected heterozygosity in those populations will always be less than that expected from the pooled allele frequencies. Among subpopulations F-statistic can be quantified from this ratio.

Where,

Where HT is the Hardy-Weinberg expected frequency. One thing we should take in account that as allele frequencies reduce the variation in and will increase and will therefore also serve as a measure of genetic distance among subpopulations.

As a result the measure of the correlation of alleles for the whole population is thus a combination of both the within and among subpopulation effects, and can be quantified from

Eventually between the two subpopulations if there is no migration occurs then alternate alleles will become fixed and will reach 1. Alternatively, it has long been known that if the migration rate, measured in terms of Nm, is > 1 (where N is the effective population size and m is the fraction of migrants per generation), the allele frequencies in the subpopulations will be homogenised (Wright 1931). On the other hand if migration somehow is present but Nm < 1, an equilibrium based on the rate of mutation, migration, and genetic drift will be developed.