Molecular evolutionary genetics.

<p>(A) Sequence diversity in the genomic region centered on <i>RKS1</i>. Red, blue and orange bars indicate non-synonymous mutations, silent mutations and indels, respectively. ‘35/46’ indicates the location of the 35 SNPs in complete linkage disequilibrium. The red cross indicates the position of the stop codon at the fourth amino-acid. Arrows indicate the orientation of the genes along the genome. (B) Observed nucleotide diversity between the two intergenic haplotypes. (C) Maximum Likelihood circular tree based on nucleotide variation of <i>RKS1</i> and the intergenic region between <i>RKS1</i> and <i>At3g57720</i>. (D) Scan for association with the relative gene expression of <i>RKS1-L</i> in the sequenced region centered on <i>RKS1</i>. Red points indicate the 35 SNPs in complete LD. The <i>y</i>-axis indicates the –log¹⁰<i>p</i>-values using the EMMAX method. (E) Tajima's <i>D</i> values along the 5 kb genomic region centered on <i>RKS1</i>. The dashed line denotes the 1% significance level of an empirical distribution based on 876 short fragments obtained for the same set of accessions <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003766#pgen.1003766-Nordborg1" target="_blank">[63]</a>.