Conflicting phylogenetic signals obscure the taxonomic position of <i>Ferula heuffelii</i> (Apiaceae), a rare Southeast European endemic

ABSTRACT Ferula heuffelii (Apiaceae) is a rare endemic species of the Balkan Peninsula, with herbarium specimens collected from a few localities, often during the 19th and early 20th centuries. To determine the phylogenetic position of this species within the genus, we extracted DNA from a few fruits collected in the late 19th century and assembled nearly the entire plastid genome and the complete nrDNA cistron from sequence data obtained through genome skimming. These newly acquired markers were integrated into two previously published datasets: the first comprised three plastid and two nuclear markers, while the second included complete plastid genomes. Using maximum likelihood and Bayesian methods, we found that according to the nuclear data, F. heuffelii clustered with a clade containing species with proliferating compound umbels. This modification, also shared by F. heuffelii, involves a new compound umbel developing in place of a central umbellet, thus forming a pseudoverticillate inflorescence and continuing its monopodial growth. However, this relationship was obscured by incongruence between plastid and nuclear datasets, attributed to poor phylogenetic signal and hybridization. Furthermore, the analysis of complete plastid genomes revealed discrepancies between phylogenetic trees constructed from different parts of the plastid genome. Considering these results, along with additional challenges such as unclear species boundaries and misidentifications, we discuss the difficulties in reconstructing the phylogeny of the genus Ferula.