Data from: Parallel Pleistocene amphitropical disjunctions in a parasitic plant and its host

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.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.Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-160150