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

the eastern sylvestris is more questionable than the identity of the western sylvestris because
eastern sylvestris clusters more closely with vinifera in genetic space (Figures S7) and because it
is safe to assume that there was a much longer period of potential contact between sylvestris and
vinifera in the east than in the west. We therefore performed the LD decay and haplotype
diversity analyses with only the western sylvestris samples instead of the full sylvestris sample.
Our results remain unchanged and this demonstrates that our conclusions are robust to this
potential source of misidentification. Moreover, it is clear that levels of haplotype diversity are
very high in vinifera regardless of the diversity observed in our sample of sylvestris (median
haplotype diversity of 5 SNP haplotypes = 0.80, Figure 3), which is consistent with a weak
domestication bottleneck. Finally, it is worth noting that our model of a weak domestication
bottleneck is consistent with the widespread use of vegetative propagation during the history of
grapevine breeding [11] and the relatively minor morphological changes between sylvestris and
vinifera [6].
Our analysis using the 3-population test [12] supports a scenario in which vinifera from western
Europe are the result of an admixture event between vinifera from the east and sylvestris from
western Europe. Using this same test, we find no support for a scenario in which our “western
sylvestris” sample is influenced by gene flow from vinifera. To our knowledge, this is the most
robust statistical framework we can employ to test models of the admixture history of vinifera
and sylvestris. This test, in conjunction with the PCA results (Figure 4), provides strong support
for the unique, unadmixed identity of the western sylvestris sample. Because the eastern
sylvestris sample is almost indistinguishable from the vinifera (Fst < 0.06 to all vinifera
populations, which is the pattern we expect if domestication occurred in the east and there was a
weak population bottleneck), the identity of the eastern sylvestris will necessarily rely on the
morphological criteria used for its identification. However, the identity of the eastern sylvestris
is extraneous to our main conclusion that western vinifera experienced introgression from
western sylvestris: the 3-population test used to test this hypothesis does not include eastern
sylvestris.