Levels of polymorphism were quantified using two different estimators of the neutral mutation rate θ: θ̂_S , which uses the number of polymorphic sites, and θ̂_P , which uses the average number of pairwise differences [3].

(A) Results from Structure under different assumptions about the number of clusters (K = 2,…, 8). Each individual is represented by a line, which is partitioned into K colored segments according to the individual's estimated membership fractions in each of the K clusters. The assignment of each individual is the average across the genome.
(B) Results from Structure across Chromosome 1 for K = 3. Each chromosomal segment is colored according to the cluster in which it had the highest probability of membership.
(C) A plot showing those fragments that appear to be monophyletic with respect to each of the three clusters identified by Structure.
(D) F_ST with respect to the same three clusters (blue solid line) and the lower 95th percentile of F_ST obtained through 1,000 random permutations of the accessions (red dotted line).
(E) θ̂_P within each of the three clusters.
(F) Tajima's D statistic within each of the three clusters.
(G) Results from Structure across Chromosome 1 for K = 8.
(H) A plot showing those fragments that appear to be monophyletic with respect to each of these eight clusters.
(I) F_ST with respect to these eight clusters.

Each pie chart represents an accession, and is placed on the map according to origin (some of the population samples were too densely sampled and have been shifted for clarity). Accessions sampled outside Europe have been placed at the correct latitude. The exact origin of the standard lab accession Col-0 is not known. The colors and proportions within each pie chart correspond to the output of Structure in Figure 2. (A) K = 3; (B) K = 8.

(A) An example of the distribution we would expect to see in the absence of population structure, obtained by randomizing genotypes with respect to individuals for each sequenced fragment.
(B) The observed distribution.
(C) The observed distribution with accessions Cvi-0 and Mr-0 removed.

The lines indicate regions where the particular pair of accessions share at least five identical adjacent fragments. Within-population comparisons are highlighted in red. The patterns in southern Sweden and in the UK are similar to that in central Europe.

(A) The allele frequency distribution for synonymous and nonsynonymous SNPs using a sample size of 90 individuals (loci with less than 90 individuals were not used; loci with greater than 90 individuals were randomly culled). For a sample of size n, the expected frequency of SNP loci with a minor allele frequency of i under a standard constant-size population genetics model is . The excess of rare alleles is largely limited to frequencies one and two.
(B) The distribution of Tajima's D statistic [27] across the sequenced fragments, along with its expected distribution in a constant population (estimated by simulating 1,000 datasets matching the real one in terms of exon/nonexon composition and sample size).
(C) The distribution of the level of polymorphism (θ̂_S ) across the sequenced fragments along with its expected distribution (estimated the same way).
(D) The level of polymorphism in nonexon sequences as a function of the local gene density (measured in open reading frames per centimorgan).
(E) The level of polymorphism in nonexon sequences as a function of the degree of duplication in each fragment (measured as the negative log₁₀ of the BLAST significance for the second-best hit in the genome).
The patterns in (D) and (E) are also seen in exons.