DOI: 10.5061/dryad.6hm4p
title: Data from: Parallel Pleistocene amphitropical disjunctions in a parasitic plant and its host

description: PREMISE OF THE STUDY: Aphyllon is a clade of holoparasites that includes
 closely related North American and South American species parasitic on
 Grindelia. Both Aphyllon (Orobanchaceae) and Grindelia (Asteraceae) have
 amphitropical disjunctions between North America and South America;
 however, the timing of these patterns and the processes to explain them
 are unknown. METHODS: Chronograms for the Orobanchaceae and Grindelia and
 their relatives were constructed using fossil and secondary calibration
 points, one of which was based on the inferred timing of horizontal gene
 transfer from a papilionoid legume into the common ancestor of Orobanche
 and Phelipanche. Elevated rates of molecular evolution in the
 Orobanchaceae have hindered efforts to determine reliable divergence time
 estimates in the absence of a fossil record. However, using a horizontal
 gene transfer event as a secondary calibration overcomes this limitation.
 These chronograms were used to reconstruct the biogeography of Aphyllon,
 Grindelia, and relatives using a DEC+J model implemented in RevBayes. KEY
 RESULTS: Aphyllon had two amphitropical dispersals from North America to
 South America, while Grindelia had a single dispersal. The dispersal of
 the Aphyllon lineage that is parasitic on Grindelia (0.40 Ma) took place
 somewhat after Grindelia began to diversify in South America (0.93 Ma).
 Using a secondary calibration based on horizontal gene transfer, we infer
 more recent divergence dates of holoparasitic Orobancheae than previous
 studies. CONCLUSIONS: Parallel host–parasite amphitropical disjunctions in
 Grindelia and Aphyllon illustrate one means by which ecological
 specialization may result in nonindependent patterns of diversity in
 distantly related lineages. Although Grindelia and Aphyllon both dispersed
 to South America recently, Grindelia appears to have diversified more
 extensively following colonization. More broadly, recent Pleistocene
 glaciations probably have also contributed to patterns of diversity and
 biogeography of temperate northern hemisphere Orobancheae. We also
 demonstrate the utility of using horizontal gene transfer events from
 well-dated clades to calibrate parasite phylogenies in the absence of a
 fossil record.
description: ETS.fastaETS alignment for the Orobanchaceae analysis.ITS.fastaITS alignment for the Orobanchaceae analysis.PhyA.fastaPhytochrome A alignment for the Orobanchaceae analysis.PhyB.fastaPhytochrome B alignment for the Orobanchaceae analysis.Orobanchaceae_concatenated.fastaConcatenated sequence alignment of ETS, ITS, Phytochrome A, and Phytochrome B, used for the Orobanchaceae analysis.Orobanchaceae_chronogram.RevRevBayes script for the chronogram analysis of the Orobanchaceae.Orobanchaceae_chrono_starting_tree.treStarting tree for the chronogram analysis of the Orobanchaceae.Orobanchaceae_chronogram.treesSet of trees resulting from the chronogram analysis of the Orobanchaceae.Orobanchaceae_chronogram_MAP.treMaximum a posteriori chronogram of the Orobanchaceae (the basis of Figure 1).Orobancheae_biogeography.RevRevBayes script for the biogeography analysis of the Orobancheae.Orobancheae_biogeography_starting_tree.nexStarting tree for the biogeography analysis of the Orobancheae.Orobancheae_ranges.nexTaxon range file used in the biogeography analysis of the Orobancheae.Orobancheae_biogeography.treesSet of trees resulting from the biogeography analysis of the Orobancheae.Orobancheae_bioeography_ase.treAncestral state estimation of Orobancheae biogeography (the basis of Figure 3).Supplemental Appendix 1.csvGenBank numbers for the sequences used in the Orobanchaceae analyses.EIGB20170224.faGrindelia sequence alignment, with ETS first (positions 1-416), followed by ITS (positions 419-1036).Grindelia_chronogram_script.RevRevBayes script for the chronogram analysis of Grindelia.RaxML_bestTree.EIGB20170224_umUltrametric starting tree for the Grindelia chronogram analysis.RAxML_bestTree.EIGB20170224_umMAP4.treeMaximum a posteriori chronogram for Grindelia (the basis of Figure 2).Grindelia_biogoegraphy_script.RevRevBayes script for the biogeography analysis of Grindelia.EIGB_BioGeo2.nexFile showing collection localities for use in the biogeographic analysis of Grindelia.EIGB_DECJ_map4.ase.treAncestral state estimation for Grindelia biogeography (the basis of Figure 4).Grindelia_vouchers.txtTab-delimited table with voucher information and GenBank numbers for the sequences used in the Grindelia analyses.