Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation

Allozyme and microsatellite data from numerous populations of Drosophila buzzatii have been used (i) to determine to what degree N e varies among generations within populations, and among populations, and (ii) to evaluate the congruence of four temporal and five single‐sample estimators of N e . Effective size of different populations varied over two orders of magnitude, most populations are not temporally stable in genetic composition, and N e showed large variation over generations in some populations. Short‐term N e estimates from the temporal methods were highly correlated, but the smallest estimates were the most precise for all four methods, and the most consistent across methods. Except for one population, N e estimates were lower when assuming gene flow than when assuming populations that were closed. However, attempts to jointly estimate N e and immigration rate were of little value because the source of migrants was unknown. Correlations among the estimates from the single‐sample methods generally were not significant although, as for the temporal methods, estimates were most consistent when they were small. These single‐sample estimates of current N e are generally smaller than the short‐term temporal estimates. Nevertheless, population genetic variation is not being depleted, presumably because of past or ongoing migration. A clearer picture of current and short‐term effective population sizes will only follow with better knowledge of migration rates between populations. Different methods are not necessarily estimating the same N e , they are subject to different bias, and the biology, demography and history of the population(s) may affect different estimators differently.