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

Abstract

<title>Abstract</title> <italic>Arnica montana</italic> 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 <italic>A. montana</italic> and its Holarctic congeners to remain obscure. We therefore evaluated entire chloroplast genomes of <italic>A. montana</italic> 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 <italic>A. montana</italic> accessions across Europe, four further species of <italic>Arnica</italic> and three outgroup species. All <italic>A. montana</italic> plastomes formed a well-supported clade. In contrast with the current circumscription of <italic>A. montana</italic> ssp. <italic>atlantica</italic>, both <italic>A. montana</italic> 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 <italic>A. montana</italic> further showed potential heteroplasmy. Rather than individual marker regions, phylogeographic studies in <italic>Arnica</italic> should use complete plastid genomes, including microstructural variation and intra-individual polymorphism in their analyses.