The effective population size (N e ) quantifies the effectiveness of genetic drift in finite populations. When generations overlap, theoretical expectations for N e typically assume that the sampling of offspring genotypes from a given individual is independent among successive breeding events, even though this is not true in many species, including humans. To explore the effects on N e of nonindependent mate pairing across breeding events, we simulated the genetic drift of mitochondrial DNA, autosomal DNA, and sex chromosome DNA under three mating systems. Nonindependent mate pairing across breeding seasons has no effect when all adults mate pair for life, a small or moderate effect when females reuse stored sperm, and a large effect when there is intense malemale competition for reproduction in a harem social system. If adult females reproduce at a constant rate irrespective of the type of mate pairing, the general effect of nonindependent mate pairing is to decrease N e for paternally inherited components of the genome. These findings have significant implications for the relative N e values of different genomic regions, and hence for the expected levels of DNA sequence diversity in these regions.T HE effective population size (N e ) is a fundamental parameter of population genetics, which quantifies the effect of genetic drift, the stochastic change in allele frequencies over time in a population of finite size (Wright 1931). The magnitude of N e affects both the level of genetic variability within a population and the efficiency with which populations retain mildly beneficial mutations and purge mildly deleterious ones. This influences a myriad of genetic phenomena, such as the level of DNA sequence polymorphism, the rate of substitution of nonsynonymous and functional noncoding nucleotide positions, the abundance of transposable elements, levels of variation, and the rate of evolution of gene expression, the persistence of duplicate genes, and genome size and organization (Lynch 2007;Charlesworth 2009). There are a variety of definitions of N e ; here we use the definition in terms of the mean coalescence time of a pair of neutral alleles, which is given by 2N e (Charlesworth 2009). This definition has the useful feature that the expected pairwise nucleotide site diversity under the widely used infinite sites model is equal to 4N e m, where m is the neutral mutation rate (Kimura 1971).As a result of differences in their ploidy level and mode of inheritance, autosomal DNA (aDNA), the X chromosome (xDNA), the Y chromosome (yDNA), and maternally transmitted organelle DNA such as mitochondrial DNA (mtDNA) generally have a different N e values. Under certain conditions, such as constant population size, discrete generations, a Poisson distribution of reproductive success, and a sex ratio equal to one, the relative N e values of these genomic regions (N e-a , N e-x , N e-mt , and N e-y ) are expected to be 4:3:1:1 (Charlesworth 2009). This is because aDNA is biparentally inherited and diploid; xDNA is b...