Fig. 1. Phylogenetic tree showing divergence times and the evolution of gene family size.

The phylogenetic tree shows the topology and divergence times for 19 plant species. As expected, as a genus of the family Solanaceae, Petunia is sister to other genera; Lycium is sister to Capsicum and Solanum, indicating that woody Lycium evolved from an herb. In general, the estimated Solanaceae divergence times are in agreement with recent broad-scale Solanaceae phylogenies⁵. Divergence times are represented by light blue bars at internodes; the range of these bars indicates the 95% confidence interval of the divergence time. Numbers at branches represent the expansion and contraction of gene families (see “Methods”). MRCA most recent common ancestor. The number in parentheses is the number of gene families in the MRCA as estimated by CAFɹ⁶. The yellow pentagram means the gamma WGT shared by eudicot plants, which occurred ~130 Mya⁶⁷. The red pentagram means the Solanaceous shared WGT, which was estimated at an average of 69 Mya (Supplementary Table 12).