TABLE 1

Definitions of symbols

SymbolMeaning
DMeasure of the frequency spectrum from Tajima (1989a).
NDiploid effective population size.
rSex-averaged recombination rate per base pair per generation.
ρ4Nr.
Embedded Image Estimate of ρ from sequence data (CHRM, cf. Wall 2000).
Laboratory-based estimate of r (see methods).
ρEmbedded Image .
HNumber of distinct haplotypes.
RMMinimum number of inferred recombination events (cf. Hudson and Kaplan 1985). Nx One-half of the haploid effective population size for the X chromosome.
NaDiploid (i.e., one-half of the haploid) effective population size for the autosomes.
ρxEstimate of Nx for the actual data using H, RM, and (see methods).
ρaEstimate of Na for the actual data using H, RM, and (see methods).
μSex-averaged mutation rate per base pair per generation.
Embedded Image Estimate of μ of 1.5 × 10-9 per base pair per generation (see methods).
θ4Nμ.
SThe observed number of segregating sites.
(1 -δθ)The decrease in diversity due to hitchhiking (or bottlenecks).
ΛrThe rate of selective sweeps (cf. Braverman et al. 1995).
T0Time (scaled in units of 2N generations) of the bottleneck.
NbEffective population size at time T0.
nrRatio of Nx/Na used for diversity estimates and timescaling of bottleneck simulations.
Average D value (for all X-linked loci or all autosomal loci).
RLikelihood-ratio statistic (see methods).
ρx0Maximum-likelihood estimate of Nx from H, RM, and for simulated data with Nx = N0 (see methods).
ρa1Maximum-likelihood estimate of Na from H, RM, and for simulated data with Na = N1 (see methods).
R*Likelihood that x and a from simulated data equal the actual population size estimates, assuming the null model.
Embedded Image Estimate of θ from Watterson (1975).
θaEstimate of N from Embedded Image (for the autosomes) and Embedded Image .
θxEstimate of N from Embedded Image (for the X) and Embedded Image .