U.S. Department of Commerce


Date of this Version



Molecular Ecology (2009) 18, 1834–1847; doi: 10.1111/j.1365-294X.2009.04157.x


Evolutionary processes are routinely modeled using ‘ideal’ Wright–Fisher populations of constant size N in which each individual has an equal expectation of reproductive success. In a hypothetical ideal population, variance in reproductive success (Vk) is binomial and effective population size (Ne) = N. However, in any actual implementation of the Wright– Fisher model (e.g., in a computer), Vk is a random variable and it’s realized value in any given replicate generation (Vk*) only rarely equals the binomial variance. Realized effective size (Ne*) thus also varies randomly in modeled ideal populations, and the consequences of this have not been adequately explored in the literature. Analytical and numerical results show that random variation in Vk*and Ne*can seriously distort analyses that evaluate precision or otherwise depend on the assumption that is constant. We derive analytical expressions for Var(Vk) [4(2N – 1)(N – 1)/N3] and Var(Ne) [N(N – 1)/(2N – 1) ≈ N/2] in modeled ideal populations and show that, for a genetic metric G = f(Ne), Var(^G) has two components: VarGene (due to variance across replicate samples of genes, given a specific Ne*) and VarDemo (due to variance in Ne*). Var(^G) is higher than it would be with constant Ne= N, as implicitly assumed by many standard models. We illustrate this with empirical examples based on F (standardized variance of allele frequency) and r2 (a measure of linkage disequilibrium). Results demonstrate that in computer models that track multilocus genotypes, methods of replication and data analysis can strongly affect consequences of variation in Ne*. These effects are more important when sampling error is small (large numbers of individuals, loci and alleles) and with relatively small populations (frequently modeled by those interested in conservation).