An empirical test of the estimation of historical effective population size using Drosophila melanogaster

The availability of a large number of high density markers (SNPs) allows the estimation of historical effective population size (Ne) from linkage disequilibrium between loci. A recent refinement of methods to estimate historical Ne has been shown to be rather accurate with simulation data. The method has also been applied to real data from a number of species. However, the simulation data cannot encompass all the complexities of real genomes, and the performance of any estimation method with real data is always uncertain, as the true demography of the populations is not known. Here we carried out an experimental design with Drosophila melanogaster in order to test the method with real data following a known demographic history. We used a population maintained in the laboratory with a constant census size of about 2,500-3,000 individuals, and subjected the population to a drastic decline to a size of 100 individuals. After a few generations, the population was expanded back to the previous size and after a few further generations again expanded to twice the initial size. Estimates of historical Ne were obtained with the software GONE both for autosomal and X chromosomes from samples of 17 individuals sequenced for the whole genome. Estimates of the historical effective size were able to infer the patterns of changes occurred in the populations showing a good performance of the method.