Chloroplast capture and paralogous copies of barcoding markers matK and psbA-trnH explain phylogenetic inconsistencies in pines. Barcoding in pines

With more than one hundred species, the genus Pinus is the largest genus of conifers and the most widespread genus of trees in the northern hemisphere. Complete phylogenies relying on chloroplast gene sequences are now available for the entire genus. However, they remain unresolved for certain lineages, which are also inconsistent in terms of biogeography. One such inconsistent lineage is within subsection Pinus and includes five phylogenetically closely related species: Pinus densiflora, Pinus nigra, Pinus resinosa, Pinus sylvestris and Pinus uncinata. In this study, we explore the reasons for weak support for this clade in phylogenetic analyses and show that some of the most popular genetic markers, namely the chloroplastic matK, psbA- trnH and rbcL, are not suitable for barcoding and resolving phylogenies in closely related pine species.