Fig. 2. Whole-genome duplications in Laurales.
a KS age distribution for the whole paranome of L. cubeba. Two KS peaks are shown by dotted lines at KS ≈ 0.5 and 0.8 falling in two KS ranges highlighted by two gray rectangles in the background from 0.3 to 0.645 and from 0.645 to 1.1, respectively. b KS age distributions for anchor pairs of L. cubeba (dark gray histogram and line; peaks represent WGD events) and for one-to-one orthologs between L. cubeba and selected Lauralean species and V. vinifera (colored filled curves of kernel-density estimates; a peak represents a species divergence event). The arrows in different colors indicate under- (to the left) and overestimations (to the right) of the divergence events and point to the KS values after corrections of different substitution rates in the three comparisons based on that in L. cubeba (see Methods). c The phylogeny of Laurales and Magnoliales with branch lengths in KS units (left) and in absolute divergence time (right). The tree topology and absolute divergence time were retrieved. The KS ages and their 95% confidence intervals (CIs) for WGDs identified from the whole paranome (Supplementary Fig. 9) are shown in dots and rectangles, respectively, on the left phylogeny. Without considering species with only one KS peak in their KS distributions of paralogs, the blue and green rectangles highlight the ranges of 95% CIs of WGDs for the older peaks and the younger peaks, respectively. The red, light blue, and yellow rectangles show the ranges of 95% CIs for three independent WGD events in different lineages of Laurales. Correspondingly, the red, light blue, and yellow bars illustrate the independent WGD events on the right phylogenetic tree with absolute divergence time. The three WGD events occurred at about the same time of the radiation of Lauralean species within ~3 million years. In addition, the green bar denotes a lineage-specific WGD event in C. filiformis and the blue bar denotes the WGD event before the divergence of Laurales and Magnoliales.