DOI: 10.5061/dryad.31cf160
title: Data from: Phylogenetic relationships in Orobanchaceae inferred from low-copy nuclear genes: consolidation of major clades and identification of a novel position of the non-photosynthetic Orobanche clade sister to all other parasitic Orobanchaceae

description: 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.
description: Sequence alignment
 (nuclear locus Agt1) for OrobanchaceaeAlignment of sequences
 from the nuclear low-copy marker Agt1 from Orobanchaceae and phylogenetic
 trees (maximum likelihood, Bayesian inference) in nexus
 formatOrobanchaceae_Agt1.nexSequence alignment (nuclear locus AT1G04780) for OrobanchaceaeAlignment of sequences from the nuclear low-copy marker AT1G04780 from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus formatOrobanchaceae_AT1G04780.nexSequence alignment (nuclear locus AT1G09680) for OrobanchaceaeAlignment of sequences from the nuclear low-copy marker AT1G09680 from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus formatOrobanchaceae_AT1G09680.nexSequence alignment (nuclear locus AT1G14610) for OrobanchaceaeAlignment of sequences from the nuclear low-copy marker AT1G14610 from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus formatOrobanchaceae_AT1G14610.nexSequence alignment (nuclear locus AT2G37230) for OrobanchaceaeAlignment of sequences from the nuclear low-copy marker AT2G37230 from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus formatOrobanchaceae_AT2G37230.nexSequence alignment (nuclear ITS) for OrobanchaceaeAlignment of sequences from the nuclear ITS from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus formatOrobanchaceae_ITS.nexSequence alignment (nuclear low-copy marker PhyA) for OrobanchaceaeAlignment of sequences from the nuclear low-copy marker PhyA from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus formatOrobanchaceae_PhyA.nexSequence alignment (nuclear low-copy marker PhyB) for OrobanchaceaeAlignment of sequences from the nuclear low-copy marker PhyB from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus formatOrobanchaceae_PhyB.nexSequence alignment (plastid gene matK) for OrobanchaceaeAlignment of sequences from the plastid gene matK from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus formatOrobanchaceae_matK.nexSequence alignment (plastid gene rps2) for OrobanchaceaeAlignment of sequences from the plastid gene rps2 from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus formatOrobanchaceae_rps2.nexSequence alignment (5 nuclear loci) for OrobanchaceaeAlignment of sequences from 5 nuclear loci (Agt1, AT1G04780, AT1G09680, AT1G14610, AT2G37230) from Orobanchaceae and phylogenetic trees (maximum likelihood, Bayesian inference) in nexus formatOrobanchaceae_5loci.nexSequence alignment (8 nuclear and 2 plastid loci) for OrobanchaceaeAlignment 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 formatOrobanchaceae_10loci.nexMaximum parsimony reconstruction of parasitism in OrobanchaceaeEvolution of parasitism (autotrophy, hemiparasitism, holoparasitism) inferred using ordered maximum parsimony on the maximum likelihood tree (using 10 concatenated loci) in Mesquite (nexus) formatOrobanchaceae_MPreconstruction_parasitism.nex