Chloroplast DNA barcoding genes matK and psbA-trnH are not suitable for species identification and phylogenetic analyses in closely related pines

The largest and most economically important conifer genus Pinus is widespread in the northern hemisphere. Comprehensive phylogenies relying on complete chloroplast gene sequences are now available for the entire genus. However, phylogenetic relationships remain unresolved for certain lineages. One such example, which is also inconsistent in terms of biogeography, is within the subsection Pinus and includes five taxa: Pinus densiflora, P. nigra, P. resinosa, P. sylvestris and P. mugo / uncinata species complex. In this study, we use this clade as an example to explain weak support in phylogenetic studies of closely related pine species and show that some of the most popular genetic markers, namely the chloroplast DNA barcoding sequences matK, psbAtrnH and rbcL, are not recommended for species identification purposes in European pines. In addition, we show that matK and psbA-trnH contain contradicting phylogenetic signals in some of the most economically important pine species.