Fig. 1

Phylogenetic tree depicting evolutionary relationships among 10 sampled species of Ruellia and principle component analysis (PCA) of transcriptome data from these species. A. Maximum likelihood tree was inferred using a hybrid transcriptome-RADloci approach newly implemented in this study. Briefly, raw, unassembled transcriptome reads were mined for the subset of reads that contained the GAATTC EcoR1 overhang; these yielded a total 110,263 biallelic sites following data processing in pyRAD. The ML tree was inferred using a GTRGAMMA model of sequence evolution implemented. Shown to the right of taxon labels are: photographs of flowers of the 10 study species as well as a shorthand coding of the major anthocyanin pigments present in petal tissues of these species (C = cyanidin + derivatives; D = delphinin + derivatives; P = pelargonidins+ derivatives). B. Gene expression profiles of ten species projected onto the first two principal components, showing two clear clusters of leaf (triangle) vs. corolla (circle) transcripts as well as two subclusters of corolla transcripts separated by PC2 that correspond to Clade I vs. Clade II in Fig. 1A