Molecular phylogenetic analyses have greatly advanced our understanding of phylogenetic relationships in Orobanchaceae, a model system to study parasitism in angiosperms. As members of this group may lack some genes widely used for phylogenetic analysis and exhibit varying degrees of accelerated base substitution in other genes, relationships among major clades identified previously remain contentious. To improve inferences of phylogenetic relationships in Orobanchaceae, we used two pentatricopeptide repeat (PPR) and three low-copy nuclear (LCN) genes, two of which have been developed for this study. Resolving power and level of support strongly differed among markers. Despite considerable incongruence among newly and previously sequenced markers, monophyly of major clades identified in previous studies was confirmed and, especially in analyses of concatenated data, strongly supported after the exclusion of a small group of East Asian genera (Pterygiella and Phtheirospermum) from the Euphrasia-Rhinanthus clade. The position of the Orobanche clade sister to all other parasitic Orobanchaceae may indicate that the shift to holoparasitism occurred early in the evolution of the family. Although well supported in analyses of concatenated data comprising ten loci (five newly and five previously sequenced), relationships among major clades, most prominently the Striga-Alectra clade, the Euphrasia-Rhinanthus clade, and the Castilleja-Pedicularis clade, were uncertain because of strongly supported incongruence also among well-resolving loci. Despite the limitations of using a few selected loci, congruence among markers with respect to circumscription of major clades of Orobanchaceae renders those frameworks for detailed, species-level, phylogenetic studies.
Sequence alignment (nuclear locus Agt1) for Orobanchaceae
Alignment of sequences from the nuclear low-copy marker Agt1 from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus format
Orobanchaceae_Agt1.nex
Sequence alignment (nuclear locus AT1G04780) for Orobanchaceae
Alignment of sequences from the nuclear low-copy marker AT1G04780 from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus format
Orobanchaceae_AT1G04780.nex
Sequence alignment (nuclear locus AT1G09680) for Orobanchaceae
Alignment of sequences from the nuclear low-copy marker AT1G09680 from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus format
Orobanchaceae_AT1G09680.nex
Sequence alignment (nuclear locus AT1G14610) for Orobanchaceae
Alignment of sequences from the nuclear low-copy marker AT1G14610 from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus format
Orobanchaceae_AT1G14610.nex
Sequence alignment (nuclear locus AT2G37230) for Orobanchaceae
Alignment of sequences from the nuclear low-copy marker AT2G37230 from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus format
Orobanchaceae_AT2G37230.nex
Sequence alignment (nuclear ITS) for Orobanchaceae
Alignment of sequences from the nuclear ITS from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus format
Orobanchaceae_ITS.nex
Sequence alignment (nuclear low-copy marker PhyA) for Orobanchaceae
Alignment of sequences from the nuclear low-copy marker PhyA from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus format
Orobanchaceae_PhyA.nex
Sequence alignment (nuclear low-copy marker PhyB) for Orobanchaceae
Alignment of sequences from the nuclear low-copy marker PhyB from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus format
Orobanchaceae_PhyB.nex
Sequence alignment (plastid gene matK) for Orobanchaceae
Alignment of sequences from the plastid gene matK from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus format
Orobanchaceae_matK.nex
Sequence alignment (plastid gene rps2) for Orobanchaceae
Alignment of sequences from the plastid gene rps2 from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus format
Orobanchaceae_rps2.nex
Sequence alignment (5 nuclear loci) for Orobanchaceae
Alignment of sequences from 5 nuclear loci (Agt1, AT1G04780, AT1G09680, AT1G14610, AT2G37230) from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus format
Orobanchaceae_5loci.nex
Sequence alignment (8 nuclear and 2 plastid loci) for Orobanchaceae
Alignment of sequences from 8 nuclear (Agt1, AT1G04780, AT1G09680, AT1G14610, AT2G37230, ITS, PhyA, PhyB) and 2 plastid loci (matK, rps2) from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus format
Orobanchaceae_10loci.nex
Maximum parsimony reconstruction of parasitism in Orobanchaceae
Evolution of parasitism (autotrophy, hemiparasitism, holoparasitism) inferred using ordered maximum parsimony on the maximum likelihood tree (using 10 concatenated loci) in Mesquite (nexus) format
Orobanchaceae_MPreconstruction_parasitism.nex