Extended Data Fig. 3: Estimates of divergence time based on synonymous substitution rates (Ks).
a, The divergence time is estimated to be 58-59 million years ago (Mya) between Theobroma cacao and Gossypium. Data shown using Ks bin size of 0.001. Divergence time [T = Ks/(2r)] was estimated using the synonymous substitution rate (r) of 3.48 × 10−9 synonymous substitutions per synonymous site per year17 and 10,562 single copy orthologs between subgenomes and species. Ks values >1 were removed to eliminate saturated synonymous sites. b, The synonymous substitution rate, Ks, distribution for orthologs (n = 21,567), and estimates of divergence time between allotetraploid subgenomes and progenitor-like diploid genomes. Gh: G. hirsutum; Gb: G. barbadense; Ga: G. arboreum; Gr: G. raimondii; Gm: G. mustelium. Using a penalized-likelihood based on the concatenated nuclear tree (including branch lengths), the divergence between diploid-tetraploid clade is estimated to be 1-1.6 Mya.
