Species-diagnostic markers in the genus Pinus: evaluation of the chloroplast regions matK and ycf1

Aim of study: The identification of material of forest tree species using genetic markers was carried out. Two promising chloroplast barcode markers, matK and ycf1, were tested for species identification and reconstruction of phylogenetic relationships in pines. Area of study: The present study included worldwide Pinus species, with a wide representation of European taxa. Material and methods: All matK sequences longer than 1600 base pairs and ycf1 sequences for the same species were downloaded from GenBank, aligned and subsequently analyzed to estimate alignment statistics, phylogenetic trees and substitution saturation signals. Main results: We confirm the usefulness of the ycf1 marker for barcoding purposes and phylogenetic studies in pines, especially in studies focusing at the within-genus level relationships, but caution in the use of the matK marker is recommended. Research highlights: Incongruent phylogenetic signals between these two chloroplast markers are demonstrated in pines for the first time.