Population Genetics and Molecular Epidemiology of Infectious Diseases

Abstract

Population genetics is based on analysing the polymorphism patterns of genetic markers at different organizational levels; i.e. within and between individuals sampled among populations. From such analyses, inferences can be made on the reproductive modes of the species in question (hence, on patterns of genetic transmission along successive generations), as well as on the demographic functioning of the studied populations (i.e., population sizes, dispersal rates among populations, etc.). In this chapter, we present the main bases of population genetics theory and illustrate its interest for epidemiological issues via different case studies on parasite species.

Glossary

Bottleneck

Population bottleneck refers to drastic reduction in population sizes. This induces, at all loci, a decrease in heterozygous frequency and an even more pronounced drop in the allele numbers observed relatively to a demographical stable population with the same census size. In other words the bottlenecked population will remain away from mutation/drift equilibrium for a number of generations following the reduction in census size. The longer last the bottleneck (in term of generation) and the stronger the demographic reduction, the more intense and durable will be the genetic signature of such an event.

Epistatic effects

there are epistatic effects on selection among loci A and B whenever the intensities of selection pressures acting on the polymorphism at locus A vary among the different genotypes observed at the locus B and vice versa.

Identity by descent

two sampled alleles are said identical by descent if they result from an event of DNA replication in any ancestral generation. The alleles identical by descent are obligatory identical in state.

Identity in state

two alleles are identical in state whenever the genotyping methods used is unable to discriminate them.

Founding effect

the colonization of a new habitat is usually achieved by a few individuals relatively to the standard range of population sizes in the ancestral distribution area of the immigrating species. Therefore the colonization of a new area, habitat or host species for a parasite, usually induces a population bottleneck; such a bottleneck associated to colonization is called founding effect.

Homoplasy

there is homoplasy whenever the identity in state and the identity by descent are not synonymous. Reverse mutation and polymorphism with a finite number of distinguishable alleles (i.e. allelic sizes of microsatellite alleles) are frequent causes of homoplasy.

Fixation

an allele has reached fixation in a population when it remains the only allele present within a population. The immigration of different alleles into the population and mutation into a different allelic state are the only ways to re-create local polymorphism in a fixed population.

Mutation/drift equilibrium

let’s consider an isolated population (no immigration into it, no emigration from it) of constant finite size, and a neutral locus at which pangamy is realized so that it tends to be at HWE. At this locus along time, mutation will regularly introduce new alleles while genetic drift will regularly make existing alleles to disappear. The combined action of mutation and genetic drift will make evolving the polymorphism observed at the considered locus to evolve and reach an equilibrium where the number of distinct alleles (hence the heterozygous frequency) will remain constant even if the identity of the alleles present in the population will keep on changing.

Mantel test

The Mantel test is a statistical test of correlation between two matrices of same dimensions that is adapted to the case where the elements of any matrix are not independent from one another (such as the matrix of either geographical distances or that of genetic distances among populations). This test is performed by randomly permuting the rows and columns of one matrix multiple times.

Panmixia

random meeting of the gametes produced in a population; theoretically achieved only for species where individuals are self-compatible hermaphrodites.

Pangamy

random mating among the sexual partners present in population; theoretically achieved only for hermaphrodite species.