Previous molecular phylogenetic studies of Pelargonium have remained inconclusive with respect to branching patterns of major infrageneric lineages, with the exception of a basalmost generic split that reflects chromosome length differences. Because of this and the lack of clearly distinguishing morphological characters, no subgeneric classification has been undertaken so far. Here, we present increased phylogenetic signal using chloroplast atpB-rbcL spacer and trnL-F sequences including additional taxa (110 taxa in total) and character sampling. All analyses confirmed the previously recognised first split into two clades characterised by chromosome size, and also converged on four major clades (two within each chromosome size group). The four major clades are further supported by synapomorphic length mutations from both intergenic spacers. The evolution of characters from flower morphology and phenolic constituents was examined for usefulness for clade delimitation. Although character state distributions did not generally reveal clear synapomorphies for the respective lineages, differences in state distributions of floral characters and leaf phenols support the circumscription of these major clades. In particular, nectar guides and petal-ratios indicate character state shifts among clades. The leaf flavonoids, myricetin and prodelphinidin, exhibit differing evolutionary trends in Pelargonium species with small chromosomes. In summary, all results favour the recognition of four, morphologically diagnosable, lineages as subgenera and support a revised subgeneric classification of Pelargonium. In addition, a new section (stat. nov.) including two subsections (comb. nov.) is segregated from an otherwise paraphyletic section Polyactium.

Geraniaceae are known for their unusual plastid genomes (plastomes), with the genus Pelargonium being most conspicuous with regard to plastome size and gene organization as judged by the sequenced plastomes of P. x hortorum and P. alternans. However, the hybrid origin of P. x hortorum and the uncertain phylogenetic position of P. alternans obscure the events that led to these extraordinary plastomes. Here, we examine all plastid reconfiguration hotspots for 60 Pelargonium species across all subgenera using a PCR and sequencing approach. Our reconstruction of the rearrangement history revealed four distinct plastome types. The ancestral plastome configuration in the two subgenera Magnipetala and Pelargonium is consistent with that of the P. alternans plastome, whereas that of the subgenus Parvulipetala deviates from this organization by one synapomorphic inversion in the trnNGUU–ndhF region. The plastome of P. x hortorum resembles those of one group of the subgenus Paucisignata, but differs from a second group by another inversion in the psaI–psaJ region. The number of microstructural changes and amount of repetitive DNA are generally elevated in all inverted regions. Nucleotide substitution rates correlate positively with the number of indels in all regions across the different subgenera. We also observed lineage- and species-specific changes in the gene content, including gene duplications and fragmentations. For example, the plastid rbcL–psaI region of Pelargonium contains a highly variable accD-like region. Our results suggest alternative evolutionary paths under possibly changing modes of plastid transmission and indicate the non-functionalization of the plastid accD gene in Pelargonium.

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