Measure of the frequency spectrum from Tajima (1989a).

N

Diploid effective population size.

r

Sex-averaged recombination rate per base pair per generation.

ρ

4Nr.

Estimate of ρ from sequence data (C_{HRM}, cf.Wall 2000).

r̂

Laboratory-based estimate of r (see methods).

N̂_{ρ}

.

H

Number of distinct haplotypes.

R_{M}

Minimum number of inferred recombination events (cf.Hudson and Kaplan 1985). N_{x} One-half of the haploid effective population size for the X chromosome.

N_{a}

Diploid (i.e., one-half of the haploid) effective population size for the autosomes.

N̂_{ρ}_{x}

Estimate of N_{x} for the actual data using H, R_{M}, and r̂ (see methods).

N̂_{ρ}_{a}

Estimate of N_{a} for the actual data using H, R_{M}, and r̂ (see methods).

μ

Sex-averaged mutation rate per base pair per generation.

Estimate of μ of 1.5 × 10^{-9} per base pair per generation (see methods).

θ

4Nμ.

S

The observed number of segregating sites.

(1 -δ_{θ})

The decrease in diversity due to hitchhiking (or bottlenecks).

Λ_{r}

The rate of selective sweeps (cf.Bravermanet al. 1995).

T_{0}

Time (scaled in units of 2N generations) of the bottleneck.

N_{b}

Effective population size at time T_{0}.

n_{r}

Ratio of N_{x}/N_{a} used for diversity estimates and timescaling of bottleneck simulations.

D¯

Average D value (for all X-linked loci or all autosomal loci).

R

Likelihood-ratio statistic (see methods).

N̂_{ρ}_{x0}

Maximum-likelihood estimate of N_{x} from H, R_{M}, and r̂ for simulated data with N_{x} = N_{0} (see methods).

N̂_{ρ}_{a1}

Maximum-likelihood estimate of N_{a} from H, R_{M}, and r̂ for simulated data with N_{a} = N_{1} (see methods).

R^{*}

Likelihood that N̂_{x} and N̂_{a} from simulated data equal the actual population size estimates, assuming the null model.