Effective population size of current human population

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1.

Introduction

Effective population size (N_e) is a crucial parameter in population genetics. It plays a vital role in studying the mutation rate, recombination rate, selection pressure and genetic diversity (Palstra & Ruzzante, 2008; Charlesworth, 2009). Recent estimates based on linkage disequilibrium (LD) indicated that the effective population size of humans is much less than the previous estimates and the usually quoted value of 10 000 (Tenesa et al., 2007). It has been suggested that the differences resulted from the different timescales and methods in N_e estimation. The fluctuation of N_e is important and the estimated harmonic mean (N_e) tends to be dominated by the smallest N_e (Hartl & Clark, 2007). Therefore, both long-term and short-term estimates of N_e are important for understanding evolution, and estimating the N_e of the current population could be an important step towards studying various past N_e values.

There are three different kinds of effective population size based on measuring magnitude: (1) the change in probability of identity by descent (inbreeding effective size); (2) the change in variance in allele frequency (variance effective size); and (3) the rate of loss of heterozygosity (eigenvalue effective size) (Hartl & Clark, 2007). Various estimation methods have been developed to determine effective population sizes (Wang, 2005; Waples, 2005; Nomura, 2009), many of which have proven useful for estimating the short-term N_e. The temporal method was developed based on the properties of the variance of gene frequency changes (Nei & Tajima, 1981; Waples, 1989). This method requires the collection of at least two samplings of a population, which would usually be more difficult than collecting a single sampling of a population. Therefore, two particular short-term methods, the LD method (Hill, 1981) and the heterozygote-excess method (Pudovkin et al., 1996), were examined in this study, which can estimate N_e from a single sampling of a population.

Recent advances in genetic technologies have enabled the N_e estimation of human populations using LD (Tenesa et al., 2007). The estimation of N_e from LD is primarily based on the tightly linked loci and requires the separate or concurrent estimation of recombination rates....