Fig. 4: Increased synonymous substitution rates in P. zijinensis and P. guangdongensis.
From: Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy
a, Kernel-density estimates (KDEs) of KS distributions for one-to-one orthologues between D. catenatum and three Platanthera orchids, namely P. guangdongensis, P. zijinensis and P. clavellata. As the modes (peaks) of the KDE all represent the distances between D. catenatum and the compared orchids, the differences observed among the KS values of the modes indicate substitution rate variations among these Orchidaceae lineages. The segments with arrows above the KDE denote, from bottom to top, the KS distances calculated for P. zijinensis (yellow) and P. guangdongensis (red) using P. clavellata (blue) as the reference and D. catenatum as the outgroup (Methods). The dotted lines align with the observed modes in the KDE of the ortholog KS distributions. The black dots on the segments represent the divergence between P. clavellata with the other two Platanthera orchids; hence, the lengths of segments pointed to the right show the KS accumulated in P. zijinensis and P. guangdongensis, whereas the grey segments pointed to the left show the KS distance between D. catenatum and the divergence of the three Platanthera orchids. The grey rectangles show the 95% confidence intervals of the KS inferred from 200 bootstraps. b, Boxplots showing modes of the one-to-one orthologous KS distributions between D. catenatum and P. clavellata (PC), D. catenatum and P. zijinensis (PZ) and D. catenatum and P. guangdongensis (PG) by resampling the corresponding KS distributions 200 times. The line in the middle of a box represents the median value and the top and bottom borders of the boxes denote the 75th and 25th percentiles, respectively. The upper and lower bars show the largest value within 1.5 times the interquartile range above the 75th percentile and the smallest value within 1.5 times the interquartile range below the 25th percentile, respectively. A dot shows the outside value, which is >1.5 times and <3 times the interquartile range beyond either end of the box.
