Fig. 4.
Genetic variation near Adh. (A) Within- and between-class nucleotide diversity when D. melanogaster haplotypes from Raleigh, NC, are classified by the amino acid at site 192. For each 250-bp window across the locus, the mean nucleotide difference over all pairs of sequences within each class (πwithin, green) and between classes (πbetween, black) is shown. Red line, K192T; rectangles, Adh exons; arrows, transcription start sites (TSS); black line, flanking regions encompassing all known natural cis-regulatory variants (68); SI Appendix, Fig. S4. (B) Distribution of excess πbetween/πwithin in the 200-kb region surrounding Adh. Each dot plots one SNP (frequency 0.25 to 0.35); πbetween/πwithin in a 250-bp window around it was calculated when haplotypes were classified based on the nucleotide at that site. Red line, K192T; orange, boundaries of Adh locus as in A; histogram, distribution of πbetween/πwithin across all SNPs; red bin, K192T. (Inset) Close view of plot across Adh locus.