Towards whole plastome phylogeography: resolving small genetic distances among European Arnica montana L. with the PlastidPipeline

Abstract Arnica montana L. is a medicinal plant endemic to Europe and declining in large parts of its range. Low sequence diversity in genetic marker regions caused biogeographic patterns and the phylogenetic relationship between A. montana and its Holarctic congeners to remain obscure. We therefore evaluated entire chloroplast genomes of A. montana and related species as complex markers. To reliably detect even small genetic distances, we developed the PlastidPipeline, which consistently and repeatably provides structurally standardized and annotated, ready-to-analyze plastomes from short-read sequences.Complementing publicly available data, we obtained plastid genomes for eight A. montana accessions across Europe, four further species of Arnica and three outgroup species. All A. montana plastomes formed a well-supported clade. In contrast with the current circumscription of A. montana ssp. atlantica, both A. montana plastomes from the Iberian Peninsula were differentiated from those of Central and Northern Europe. Very low genetic distances among the Central European samples imply a common ancestor much more recent than the split from the Iberian lineage. Several plastome SNPs within A. montana further showed potential heteroplasmy. Rather than individual marker regions, phylogeographic studies in Arnica should use complete plastid genomes, including microstructural variation and intra-individual polymorphism in their analyses.