Phylogenomics of Lithospermum (Boraginaceae) based on genome skimming

Abstract Lithospermum (Boraginaceae) is a cosmopolitan genus of ca. 80 species native to both the Old and New Worlds. The genus has been the subject of multiple phylogenetic studies during the past 20 years, with different evolutionary relationships recovered depending on the taxon-locus combinations. Using whole plastomes and nuclear ribosomal cistrons, the phylogenetics, biogeographic patterns, and plastome selection of Lithospermum and its relatives were examined. Lithospermum is here resolved as non-monophyletic, with Ulugbekia tschimganica forming the sister group to L. hancockianum . Therefore, an expanded circumscription of Lithospermum is tentatively proposed, which aligns with other, prior studies. Based on multiple phylogenetic methods, evolutionary relationships inferred by the plastid genome are incongruent with those from the nuclear ribosomal cistron as well as prior analyses based on other nuclear DNA loci. This incongruence is likely due to incomplete lineage sorting within the nuclear genome and between nuclear and plastid markers during early diversification of the genus in the New World. Lithospermum is resolved to have originated in the Old World, with independent dispersal events to southern Africa and to North America, and a subsequent a long-distance dispersal event to the northern Andes mountain range in South America. Only six genes of the plastid genome are under positive selection, and based on prior studies, these are similar to those across Lithospermeae but differ from those among other tribes in the family.