A Generalized Approach for Estimating Effective Population Size From Temporal Changes in Allele Frequency

• Published in: Genetics (Austin) Vol. 121; no. 2; pp. 379 - 391
• Main Author: Waples, R. S
• Format: Journal Article
• Language: English
• Published: Bethesda, MD Genetics Soc America 01-02-1989; Genetics Society of America
• Subjects: Alleles; Biological and medical sciences; Computer Simulation; Fundamental and applied biological sciences. Psychology; Gene Frequency; Genetic Variation; Genetics of eukaryotes. Biological and molecular evolution; Investigations; Models, Genetic; Population genetics, reproduction patterns; Theories and miscellaneous; Computer simulation; Theory; Population number; Statistical estimation; Method; Sampling design; Population genetics; Time variation; Variance; Confidence interval; Gene frequency; Models; Sampling
• ISSN: 0016-6731; 1943-2631; 1943-2631
• DOI: 10.1093/genetics/121.2.379

The temporal method for estimating effective population size (Ne) from the standardized variance in allele frequency change (F) is presented in a generalized form. Whereas previous treatments of this method have adopted rather limiting assumptions, the present analysis shows that the temporal method is generally applicable to a wide variety of organisms. Use of a revised model of gene sampling permits a more generalized interpretation of Ne than that used by some other authors studying this method. It is shown that two sampling plans (individuals for genetic analysis taken before or after reproduction) whose differences have been stressed by previous authors can be treated in a uniform way. Computer simulations using a wide variety of initial conditions show that different formulas for computing F have much less effect on Ne than do sample size (S), number of generations between samples (t), or the number of loci studied (L). Simulation results also indicate that (1) bias of F is small unless alleles with very low frequency are used; (2) precision is typically increased by about the same amount with a doubling of S, t, or L; (3) confidence intervals for Ne computed using a chi 2 approximation are accurate and unbiased under most conditions; (4) the temporal method is best suited for use with organisms having high juvenile mortality and, perhaps, a limited effective population size.