We performed a simulation study of several estimators of the effective population size (Ne) (Ne based on rate of decrease in heterozygosity, NeH ; Ne based on the temporal method, NeT, and linkage disequilibrium-based method, NeLD). We first focused on NeH, which presented an increase in the variability of values over time. The distance from the mean and the median to the true Ne increased over time too. This was caused by the fixation of alleles through time due to genetic drift and changes in the distribution of allele frequencies. We compared the three estimators of Ne under scenarios of 3 and 20 bi-allelic loci. Increasing the number of loci largely improved the performance of NeT and NeLD. We highlight the value of NeT and NeLD when large numbers of bi-allelic loci are available, which is nowadays the case for SNPs markers.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Genetic Improvement Programs: Selection for harsh environments and management of animal genetic resources (Posters), , 440, 2014
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