Supporting Information (SI) Appendix - Proceedings of the National ...

Figure S2: Evalution of domestication bottleneck in the grape. Panels A and B describe
levels of haplotype diversity in vinifera and sylvestris. A) Median haplotype diversity in vinifera
and sylvestris across a range of non-overlapping window sizes. At window sizes < 5 SNPs,
vinifera has higher haplotype diversity than sylvestris which is likely due to ascertainment bias:
the SNPs assayed by the Vitis9KSNP genotyping array were chosen because they were highly
polymorphic within a set of vinifera cultivars. At window sizes > 5 SNPs, sylvestris shows
higher haplotype diversity than vinifera, although the difference between the two species is
relatively small. B) P value distribution from comparing haplotype diversity between vinifera
and sylvestris. For each window size, a one-sided Wilcoxon signed rank test was used to
compare haplotype diversity between the two species. Red dots represent the –log10 P value
from testing whether vinifera has higher diversity than sylvestris. Blue dots represent the –log10
P value from testing whether sylvestris has higher diversity than vinifera. At window sizes < 5
SNPs, vinifera shows significantly higher haplotype diversity than sylvestris, and the opposite is
true for window sizes > 5 SNPs. C) The decay of linkage disequilibrium (LD) in vinifera and
sylvestris. Each point represents the median r 2 value and the mean physical distance from bins of
500 pairwise SNP comparisons. LD decay is rapid in both vinifera and sylvestris. There is no
apparent difference in LD decay between vinifera and sylvestris.