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Fig. S1 Sliding window analysis of Ka/Ks ratio comparing haplogroups A and B for the 684 bp GL1 coding region, with ratio plotted against window midpoint (in bp).

Fig. S2 The range and distribution of natural variation for trichome density in the screened set of 94 accessions.

Fig. S3 Heat map of linkage disequilibrium (LD) analysis (r2) of 40 kb centered on the GL1 locus based on SNP polymorphisms from the 250 k dataset (v3.06) and 1307 accessions.

Table S1 Information on all Arabidopsis thaliana accessions and panels of accessions used in this study; stock no. refers to the ABRC/TAIR identification number (http://www.arabidopsis.org).

Table S2 Primers used for PCR and sequencing GL1.

Table S3 Resequence set of 261 accessions analyzed for GL1.

Table S4 Discrepancies between GL1 sequences from Sanger- and reseqeunce derived data.

Table S5 Comparison between GL1 datasets for tests of molecular evolution.

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