Differentiation measures for conservation genetics

Abstract

We compare the two main classes of measures of population structure in genetics: (i) fixation measures such as FST,GST, and θ and (ii) allelic differentiation measures such as Jost's D and entropy differentiation. These two groups of measures quantify complementary aspects of population structure, which have no necessary relationship with each other. We focus especially on empirical aspects of population structure relevant to conservation analyses. At the empirical level, the first set of measures quantify nearness to fixation, while the second set of measures quantify relative degree of allelic differentiation. The two sets of measures do not compete with each other. Fixation measures are often misinterpreted as measures of allelic differentiation in conservation applications; we give examples and theoretical explanations showing why this interpretation can mislead. This misinterpretation has led to the mistaken belief that the absolute number of migrants determines allelic differentiation between demes when mutation rate is low; we show that in the finite island model, the absolute number of migrants determines nearness to fixation, not allelic differentiation. We show that a different quantity, the factor that controls Jost's D, is a good predictor of the evolution of the actual genetic divergence between demes at equilibrium in this model. We also show that when conservation decisions require judgments about differences in genetic composition between demes, allelic differentiation measures should be used instead of fixation measures. Allelic differentiation of fast‐mutating markers can be used to rank pairs or sets of demes according to their differentiation, but the allelic differentiation at coding loci of interest should be directly measured in order to judge its actual magnitude at these loci.

metapop2: Re‐implementation of software for the analysis and management of subdivided populations using gene and allelic diversity

“…For example, the number of alleles is more sensitive to changes in population size and bottlenecks (Luikart, Allendorf, Cornuet, & Sherwin, ), and it is more correlated with long‐term responses to selection than heterozygosity (Caballero & García‐Dorado, ; Vilas, Pérez‐Figueroa, Quesada, & Caballero, ). Thus, allelic diversity should also be considered as a criterion for the analysis and management of endangered populations using molecular markers (Jost, ; Jost et al., ; Novel et al., ; Ramljak et al., ; Zhang, Peng, Hu, Zhao, & Yang, ).…”

Genetic diversity and population structure of burbot Lota lota in Germany: Implications for conservation and management

“…In addition, pairwise Jost's D were calculated for both marker types and statistical significances were tested with two‐sided Monte Carlo simulations with 10,000 permutations using packages “mmod” v1.3.3 (Winter, ), “ade4” v1.7‐6 (Dray & Dufour, ) and “adegenet” v2.1.0 (Jombart, ; Jombart & Ahmed, ) in R v3.3.3 (R Core Team, ). Whereas F ST is dependent on the variability of the markers, D is a heterozygosity measure independent of the within‐population diversity and, therefore, describing true allelic differentiation (Jost et al, ).…”

Next‐generation conservation genetics and biodiversity monitoring

“…Regarding genetic analysis, Jost et al. () provide a description and comparison of two complementary measures of population structure which are sometimes confused in the literature: fixation indices and allelic differentiation metrics. Fixation measures (G st , F st , and theta) estimate proximity to fixation in demes as opposed to the degree of differentiation of allele frequencies.…”