The Pattern of Polymorphism in Arabidopsis thaliana
Figure 7
Characteristics of the Pattern of Polymorphism
(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 (θ̂S ) 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.