Supplemental Data

Files in this Data Supplement:

• Supplemental Figure 1 - Phylogenetic utility of SSTM genes in comparison to ITS. (A) Dot plots of long intron sequences compared to themselves, showing that introns from three species (S. glandulosissimus, S. pallidiflorus, S. saxorum) consist of direct repeats of ~100 bp. The long SSTM1 third intron from S. thysanothus (lower right) is not repetitive. (B) Majority rule consensus of 32 most parsimonious ITS trees. Outgroup taxa are highlighted in grey, clades of Madagascan species are denoted by black bars and Clades I and II are labelled I and II. Morphology is indicated coloured type: black = caulescent, orange = unifoliate, green = rosulate. Branches that collapse in the strict consensus are marked with an asterisk. The SSTM1 clade in which sequences contain repetitive elements is indicated by an arrow, and the number of repeats shown in brackets. The sequence of the Saintpaulia ionantha SSTM intron was not determined. SSTM genes as phylogenetic markers: To compare the phylogenetic utility of SSTM genes with ITS, we compiled a reduced and re-aligned ITS data set from previously published work (Möller and Cronk 2001). These data were re-analysed as the SSTM genes. ITS Clade I, comprising caulescent species with 2n = 30 chromosomes, and ITS Clade II containing morphologically diverse species with 2n = 32 chromosomes were resolved. Madagascan species (branches marked with bars in Figures 4 and S1) diverged from African species at the most basal (deepest) nodes of both Clades I and II. For SSTM1, the presence of repetitive introns in four Clade I species prevented their inclusion in this analysis. For Clade II species, SSTM1 gave resolution similar to ITS, although with slightly different topography (Figure S1B). For SSTM2, similar taxonomic relationships were suggested. Unlike in previous ITS analyses, both Clade I and Clade II had strong (≥95%) bootstrap support (see Table 5, Supplemental Data for statistical comparisons). There was also strong support for African and Madagascan species forming separate groups within Clade I. Within Clade II, Madagascan and African acaulescent species formed separate clades, although relationships within clades were not resolved.