Fig. 5

Acceleration of substitution rates in accD, clpP and ycf1. a Synonymous (dS) and nonsynonymous (dN) divergence in the IRLC species for four chloroplast genes: accD, clpP, ycf1 and matK. Shown are dN (upper) and dS (lower) trees resulting from a codon-based maximum likelihood (ML) analyses performed by RAxML, rooted using three Robinioid sequences (non-IRLC species): Lotus japonicus, Sesbania grandiflora and Robinia pseudoacacia. All trees are drawn to the same scale. The species are in the same order from top to bottom in dN and dS trees of each gene, to the greatest extent possible, and are named in full in Fig. S11. Pink branches in the trees for accD, clpP, and ycf1 represent species in our study. Trees for matK do not show comparable rate heterogeneity at either synonymous or nonsynonymous sites. b-e Significance test for nonsynonymous (dN) (upper) and synonymous (dS) (lower) substitution rates of clpP, accD and ycf1 compared to matK for all the comparisons within both IRLC taxa used in this study (left) and our own 20 species (right). ****, P < 0.0001 (T-test). Detailed information can be found in Tables S8-S11