Fig. 6

Gene tree clusters revealed by TREESPACE landscape analyses (Robinson-Foulds) based on Maximum Likelihood (ML) tree topologies, and the comparisons of characteristics between the three clusters. a Principal coordinate analysis depicting ordinations of species trees versus 82 plastid protein-coding gene trees. Note that there are 11 genes overlapped in Cluster 3 (red dots). The gene names of each cluster can be found in Table 1. b-e Boxplots comparing three gene clusters for the variation in phylogenetic signal across the plastid genes, as identified by the TREESPACE analysis. Box-and-whisker plots indicate the median (horizontal line), 25th and 75th percentiles (bottom and top of the box), and limits of the 95% confidence intervals (lower and upper whiskers). Dots beyond the 95% confidence intervals are outliers. The asterisks indicate different levels of significant differences between clusters (*: <0.05, **: <0.01; ***: <0.001). b A comparison of the mean GC content of genes among clusters. c A comparison of the aligned sequence lengths (numbers of sites) of genes in the three clusters. d A comparison of the proportion of genetic variance for genes among clusters. e A comparison of the ratio of nonsynonymous to synonymous substitution rates for each gene in the three clusters