Genetic estimates of contemporary effective population size: to what time periods do the estimates apply?

Abstract

Although most genetic estimates of contemporary effective population size (Ne) are based on models that assume Neis constant, in real populations Nechanges (often dramatically) over time, and estimates (N̂e) will be influenced by Nein specific generations. In such cases, it is important to properly match N̂eto the appropriate time periods (for example, in computing Ne/N ratios). Here I consider this problem for semelparous species with two life histories (discrete generations and variable age at maturity — the ‘salmon’ model), for two different sampling plans, and for estimators based on single samples (linkage disequilibrium, heterozygote excess) and two samples (temporal method). Results include the following.Discrete generations: (i) Temporal samples from generations 0 and t estimate the harmonic mean Nein generations 0 through t − 1 but do not provide information about Nein generation t; (ii) Single samples provide an estimate of Nein the parental generation, not the generation sampled; (iii) single‐sample and temporal estimates never provide information about Nein exactly the same generations; (iv) Recent bottlenecks can downwardly bias estimates based on linkage disequilibrium for several generations.Salmon model: (i) A pair of single‐cohort (typically juvenile) samples from years 0 and t provide a temporal estimate of the harmonic mean of the effective numbers of breeders in the two parental years (Nb(0)and Nb(t)), but adult samples are more difficult to interpret because they are influenced by Nbin a number of previous years; (ii) For single‐cohort samples, both one‐sample and temporal methods provide estimates of Nbin the same years (contrast with results for discrete generation model); (iii) Residual linkage disequilibrium associated with past population size will not affect single‐sample estimates of Nbas much as in the discrete generation model because the disequilibrium diffuses among different years of breeders. These results lead to some general conclusions about genetic estimates of Nein iteroparous species with overlapping generations and identify areas in need of further research.