Fig. 3.

Estimation of effective population size by comparison between observed and simulated haplotype block structures. (A) Frequency distribution of haplotype blocks; length is measured in number of concordant SNPs. The red line is the distribution observed from the three-way alignment of the two haplotypes of the sequenced individual and ≈200 kb of finished BAC sequence from unrelated individuals. The blue line is the distribution observed when the order of alignment columns is randomized. (B) Distribution of the proportion of total SNPs contained at each haplotype block length from 1 to 10. Colored bars show the distributions from population recombination simulations for a range of discrete population sizes (N_e). The red line is the observed distribution as in A. (C) Similarity of observed distribution of haplotype block lengths to each simulated distribution. Each data point represents the mean similarity of the observed haplotype block distribution to 1,000 independent simulated distributions at the specified N_e. Black standard error bars are barely visible. The arrow indicates the point of maximum similarity, at an N_e of 1.5 million individuals.