Phylogenetic tree of the green plants incorporating all species used in this study, with the exception of N. nucifera, which as a public annotation was not yet available upon completion. In total, sequence information from 38 full genome sequences and three transcriptome assemblies was used (see Supplemental Table S1). Bars indicate all known WGDs. Black bars indicate WGD age estimates from the literature and are not to scale (see Supplemental Information for justification and corresponding references). (Green bars) Estimates for WGDs dated in this study, with right and left boundaries corresponding to the youngest and oldest 90% confidence interval boundary found in the complete set of species-specific WGD age estimates that descend from each independent WGD (see Table 1). Some WGDs in woody species such as G. raimondii (Malvales), P. trichocarpa, and M. esculenta (Malpighiales), and the WGD shared by both M. domestica and P. bretschneideri (Rosales), are most likely underestimated through strong rate deceleration that is not fully corrected for (see Results and Discussion; Supplemental Information). The fading brown bars for the WGD in P. trichocarpa, and the WGD shared by M. domestica and P. bretschneideri, indicate corrected WGD age suggestions based on fossil evidence and/or other dating studies (see Results and Discussion). The green bar for M. acuminata most likely represents two separate WGDs in close succession (D’Hont et al. 2012). A possible WGD at the base of the monocots is not indicated because its exact phylogenetic placement remains unclear (Paterson et al. 2004). Branch lengths are truncated after 150 mya to improve clarity.
