The Limitations of molecular markers in phylogenetic reconstruction: the case of <i>Centaurea</i> sect. <i>Phrygia</i> (Compositae)

In this paper we seek to elucidate the phylogeny of Centaurea sect. Jacea and sect. Phrygia (= sect. Lepteranthus nom. inval.) which have long been a source of controversy. A molecular phylogenetic approach is used based on nrDNA and plastid markers. The study confirmed incongruence between datasets, which can be explained both by hybridization and the occurrence of shared ancestral polymorphisms. Both factors are critical in limiting the resolution of phylogenetic trees. Despite this, we provide an interpretation of the current European distribution of sect. Phrygia, and suggest a probable eastern center of origin for the section. Our results support previous studies in Centaurea, suggesting on molecular grounds that sect. Phrygia and sect. Jacea can not be clearly separated, particularly when C. nigra s.l. or C. jacea s.l. coexist with other taxa of sect. Phrygia and sect. Jacea