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

Authors

Robin Waples, NOAAFollow

Date of this Version

2005

Citation

Molecular Ecology (2005) 14 , 3335 –3352; doi: 10.1111/j.1365-294X.2005.02673.x

Abstract

Although most genetic estimates of contemporary effective population size (N_e) are based on models that assume N_e is constant, in real populations N_e changes (often dramatically) over time, and estimates (^ˆN_e) will be influenced by N_e in specific generations. In such cases, it is important to properly match ^ˆN_e to the appropriate time periods (for example, in computing N_e / 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 N_e in generations 0 through t − 1 but do not provide information about N_e in generation t ; (ii) Single samples provide an estimate of N_e in the parental generation, not the generation sampled; (iii) single-sample and temporal estimates never provide information about N_e in 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 (N_b(0) and N_b(t)), but adult samples are more difficult to interpret because they are influenced by N_b in a number of previous years; (ii) For single-cohort samples, both one sample and temporal methods provide estimates of N_b in 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 N_b as 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 N_e in iteroparous species with overlapping generations and identify areas in need of further research.