Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: A genealogical approach
Résumé
A new genetic estimator of the effective population size (N-e) is introduced. This likelihood-based (LB) estimator uses two temporally spaced genetic samples of individuals from a population. We compared its performance to that of the classical F-statistic-based N-e estimator ((N-eFk) over cap) by using data from simulated populations with known N-e and real populations. The new likelihood-based estimator ((N-eLB) over cap )showed narrower credible intervals and greater accuracy than ((N-cFk) over cap) when genetic drift was strong, but performed only slightly better when genetic drift was relatively weak. When drift was strong (e.g., N-e = 20 for five generations), as few as similar to10 loci (heterozygosity of 0.6; samples of 30 individuals) are sufficient to consistently achieve credible intervals with an upper limit <50 using the LB method. In contrast, similar to20 loci are required for the same precision when using the classical F-statistic approach. The (N-eLB) over cap estimator is much improved over the classical method when there are many rare alleles. It will be especially useful in conservation biology because it less often overestimates N-e than does (N-eFk) over cap and thus is less likely to erroneously suggest that a population is large and has a low extinction risk.