Population Differentiation: Measures

Abstract The genetic divergence between populations or accumulated by a single population from an ancestral group can be quantified using different measures. None of them can be considered better than others in all respects. The type of marker(s) or gene(s) analysed, the temporal scale considered and the level of variation are differentially affecting the quality of an index, and standardisation for comparisons across groups of populations or species is important. Some commonly used measures of population differentiation are briefly discussed, and it is argued that these measures or related quantities can be used to estimate crucial evolutionary and demographic parameters such as divergence times and migration rates, and to identify genes affected by natural or artificial selection processes. Key Concepts: Several measures of population differentiation can be computed and their comparison may provide useful insights into the evolutionary history of populations. F st and related indices are moment estimators that measure the degree of population differentiation. F st computed from multi‐allelic markers usually under‐estimates population differentiation; some alternative indices do not show this behaviour. Measures of differentiation can be used to define conservation units. Differentiation measures can be used both to estimate demographic parameters and to detect genomic regions under selection. The Lewontin–Krakauer and related tests are based on the idea that loci showing particularly high or low values of population differentiation have been shaped by selective processes. Demographic parameters can be estimated from measures of population differentiation or using likelihood/Bayesian methods.