Phylogenetics of Japanese Geranium (Geraniaceae) using chloroplast genome sequences and genome-wide single nucleotide polymorphisms

Eleven native Geranium species have been reported in Japan, several of which include infraspecific taxa. Although phylogenetic analyses have been conducted using conventional methods (i.e., chloroplast fragment and ribosomal DNA sequencing), relationships at the infraspecific level have not been elucidated due to a lack of genetic polymorphisms. We collected specimens of 22 Geranium taxa from Japan and peripheral areas (e.g., mainland China, South Korea, Russia, and Taiwan), and performed detailed phylogenetic analyses using chloroplast genome sequencing and genome-wide single-nucleotide polymorphisms. Some discrepancies were observed between the current taxonomy and the phylogenetic relationships elucidated in our analyses. The Geranium tripartitum complex was found to be paraphyletic, and Geranium onoei f. yezoense, which is synonym of Geranium reinii, was found to be more closely related to Geranium erianthum than to G. reinii. In particular, G. tripartitum var. hastatum located at intermediate position between Geranium thunbergii and Geranium wilfordii in the network analysis. Therefore, we suggest that G. tripartitum var. hastatum should be treated as an independent species, and that G. onoei f. yezoense should be transferred to G. erianthum.