DOI: 10.5061/dryad.7cr0c76
title: Data from: Geographic range dynamics drove ancient hybridization in a lineage of angiosperms

description: Elucidating the dynamic distribution of organismal lineages has been
 central to biology since the nineteenth century, yet the difficulty of
 combining biogeographic methods with shifts in habitat suitability remains
 a limitation. This integration, however, is critical to understanding
 geographic distributions, present and past, as well as the time-extended
 trajectories of lineages. Here, we link previous advances in phyloclimatic
 modeling to develop a framework that overcomes existing methodological
 gaps by predicting potential ecological and geographic overlap directly
 from estimated ancestral trait distributions. We show the utility of this
 framework by focusing on a clade in the montane angiosperm genus Heuchera,
 which is noteworthy in that it experienced ancient introgression from
 circumboreally distributed species of Mitella, lineages now ~1,300 km
 disjunct. Using this system, we demonstrate an application of ancestral
 state reconstruction to assess geographic range dynamics in a lineage
 lacking a fossil record. We test hypotheses regarding inferred past
 geographic distributions and examine the potential for ancient geographic
 contact. Application of this multifaceted approach suggests potential past
 contact between species of Heuchera and Mitella in western North America
 during cooler periods of the Pleistocene. Integration of niche models and
 phylogenetic estimates suggests that climatic cooling may have promoted
 range contact and gene flow between currently highly disjunct species. Our
 approach has wide applicability for testing hypotheses concerning
 organismal co-occurrences in deep time.
description: Occurrence
 recordsA zip archive of all
 occurrence records used in this study in Maxent format, one file per
 species.all_occurrences.zipAncestral reconstruction -- narrow-buffer modelsAncestral reconstruction results (point estimates and credibility intervals) for narrow-buffer models. This is in BEAST-compatible NEXUS format and can be read by FigTree.narrowbuffer_tree_labels_midpointsandtips.treAncestral reconstruction -- wide-buffer modelsAncestral reconstruction results (point estimates and credibility intervals) for wide-buffer models. This is in BEAST-compatible NEXUS format and can be read by FigTree.widebuffer_tree_labels_ranges_clean.treAncestral reconstruction -- distance-buffer modelsAncestral reconstruction results (point estimates and credibility intervals) for distance-buffer models. This is in BEAST-compatible NEXUS format and can be read by FigTree.distancebuffer_tree_labels_midpointsandtips.treAncestral reconstruction pooled, thinned MCMC -- narrow-buffer modelsPooled MCMC chains for ancestral reconstruction results, thinned as discussed in the manuscript, for narrow-buffer models. These are TSV files in BayesTraits format; for variable numbering see the translation table in this deposition.thinned_MCMC_narrowbuffer.zipAncestral reconstruction pooled, thinned MCMC -- wide-buffer modelsPooled MCMC chains for ancestral reconstruction results, thinned as discussed in the manuscript, for wide-buffer models. These are TSV files in BayesTraits format; for variable numbering see the translation table in this deposition.thinned_MCMC_widebuffer.zipAncestral reconstruction pooled, thinned MCMC -- distance-buffer modelsPooled MCMC chains for ancestral reconstruction results, thinned as discussed in the manuscript, for distance-buffer models. These are TSV files in BayesTraits format; for variable numbering see the translation table in this deposition.thinned_MCMC_distancebuffer.zipFull nuclear phylogenomic analysis -- best tree with bipartition frequenciesAnalysis of all taxa (i.e., in some cases multiple accessions per species), from which a pruned one-tip-per-species tree was used for all downstream ancestral reconstruction analyses. Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).RAxML_bipartitions.277locipartitionednointronnolakelae.treFull nuclear phylogenomic analysis -- bootstrap treesAnalysis of all taxa (i.e., in some cases multiple accessions per species), from which a pruned one-tip-per-species tree was used for all downstream ancestral reconstruction analyses. Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).RAxML_bootstrap.277locipartitionednointronnolakelaeFull nuclear phylogenomic analysis -- concatenated alignmentAnalysis of all taxa (i.e., in some cases multiple accessions per species), from which a pruned one-tip-per-species tree was used for all downstream ancestral reconstruction analyses. Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).277lociNewTaxa_modifiedalignment_extensivelyfixed.phy.excludefile.txt.reduced.nolakelaeBEAST dating analysis -- chloroplast data, lognormal priorBEAST analysis of the chloroplast genome with a lognormal calibration prior. For analytical details see the manuscript. Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).lognormal_cp_BEAST.treBEAST dating analysis -- chloroplast data, truncated normal priorBEAST analysis of the chloroplast genome with a truncated normal calibration prior. For analytical details see the manuscript. Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).truncated_cp_BEAST.treBEAST dating analysis -- nuclear data, lognormal priorBEAST analysis of the nuclear genes with a lognormal calibration prior. For analytical details see the manuscript. Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).BEAST_nuc_lognormal_reps1to6.treBEAST dating analysis -- nuclear data, truncated normal priorBEAST analysis of the nuclear genes with a truncated normal calibration prior. For analytical details see the manuscript. Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).BEAST_nuc_truncated_reps1to6.trePredicted niche occupancy profiles -- narrow-buffer modelsPredicted niche occupancy profiles for narrow-buffer models. These are CSV files where the second column represents the variable value for a left-hand bin break-point, and the third column represents the weight for the bin to the right of this. For variable numbering see the translation table in this deposition. Each file represents one variable for one species.pnos_narrowbuffer.zipPredicted niche occupancy profiles -- wide-buffer modelsPredicted niche occupancy profiles for wide-buffer models. These are CSV files where the second column represents the variable value for a left-hand bin break-point, and the third column represents the weight for the bin to the right of this. For variable numbering see the translation table in this deposition. Each file represents one variable for one species.pnos_widebuffer.zipPredicted niche occupancy profiles -- distance-buffer modelsPredicted niche occupancy profiles for distance-buffer models. These are CSV files where the second column represents the variable value for a left-hand bin break-point, and the third column represents the weight for the bin to the right of this. For variable numbering see the translation table in this deposition. Each file represents one variable for one species.pnos_distancebuffer.zipModel suitability ASC files -- narrow-buffer modelsModel suitability rasters for narrow-buffer models from Maxent. These were the rasters used for predicted niche occupancy calculations.all_asc_narrowbuffer.zipModel suitability ASC files -- distance-buffer modelsModel suitability rasters for distance-buffer models from Maxent. These were the rasters used for predicted niche occupancy calculations.all_asc_distancebuffer.zipModel suitability ASC files -- wide-buffer modelsModel suitability rasters for wide-buffer models from Maxent. These were the rasters used for predicted niche occupancy calculations.all_asc_widebuffer.zipVariable numbering translate tableAn excel sheet explaining variable numbering for ancestral reconstruction analyses. A column also describes the native units of these, which in some cases differ by a factor of 10 from publication figures in order to save space in ASCII representations.ryan_heucheraoriginal_explain.xlsxBinary suitability prediction for Mitella MRCA: Holocene climatic optimum, narrow-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Holocene climatic optimum (6k years ago), using narrow-buffer models and binary maps.BINARY_final_range_product_source.tifBinary suitability prediction for California Heuchera MRCA: Holocene climatic optimum, narrow-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Holocene climatic optimum (6k years ago), using narrow-buffer models and binary maps.BINARY_final_range_product_hybrid.tifBinary suitability prediction for Mitella MRCA: Last Glacial Maximum, narrow-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Last Glacial Maximum (22k years ago), using narrow-buffer models and binary maps.BINARY_final_range_product_source.tifBinary suitability prediction for California Heuchera MRCA: Last Glacial Maximum, narrow-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Last Glacial Maximum (22k years ago), using narrow-buffer models and binary maps.BINARY_final_range_product_hybrid.tifBinary suitability prediction for Mitella MRCA: Last interglacial, narrow-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the last interglacial (120k-140k years ago), using narrow-buffer models and binary maps.BINARY_final_range_product_source.tifBinary suitability prediction for California Heuchera MRCA: Last interglacial, narrow-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the last interglacial (120k-140k years ago), using narrow-buffer models and binary maps.BINARY_final_range_product_hybrid.tifBinary suitability prediction for Mitella MRCA: Holocene climatic optimum, wide-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Holocene climatic optimum (6k years ago), using wide-buffer models and binary maps.BINARY_final_range_product_source.tifBinary suitability prediction for California Heuchera MRCA: Holocene climatic optimum, narrow-buffer modelsData from: Geographic range dynamics drove ancient hybridization in a lineage of angiosperms.This is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Holocene climatic optimum (6k years ago), using wide-buffer models and binary maps.BINARY_final_range_product_hybrid.tifBinary suitability prediction for Mitella MRCA: Holocene climatic optimum, wide-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Last Glacial Maximum (22k years ago), using wide-buffer models and binary maps.BINARY_final_range_product_source.tifBinary suitability prediction for California Heuchera MRCA: Last Glacial Maximum, wide-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Last Glacial Maximum (22k years ago), using wide-buffer models and binary maps.BINARY_final_range_product_hybrid.tifBinary suitability prediction for Mitella MRCA: Last interglacial, wide-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the last interglacial (120k-140k years ago), using wide-buffer models and binary maps.BINARY_final_range_product_source.tifBinary suitability prediction for California Heuchera MRCA: Last interglacial, wide-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the last interglacial (120k-140k years ago), using wide-buffer models and binary maps.BINARY_final_range_product_hybrid.tifBinary suitability prediction for Mitella MRCA: Holocene climatic optimum, distance-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Holocene climatic optimum (6k years ago), using distance-buffer models and binary maps.BINARY_final_range_product_source.tifBinary suitability prediction for California Heuchera MRCA: Holocene climatic optimum, distance-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Holocene climatic optimum (6k years ago), using distance-buffer models and binary maps.BINARY_final_range_product_hybrid.tifBinary suitability prediction for Mitella MRCA: Last Glacial Maximum, distance-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Last Glacial Maximum (22k years ago), using distance-buffer models and binary maps.BINARY_final_range_product_source.tifBinary suitability prediction for California Heuchera MRCA: Last Glacial Maximum, distance-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Last Glacial Maximum (22k years ago), using distance-buffer models and binary maps.BINARY_final_range_product_hybrid.tifBinary suitability prediction for Mitella MRCA: Last interglacial, distance-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the last interglacial (120k-140k years ago), using distance-buffer models and binary maps.BINARY_final_range_product_source.tifBinary suitability prediction for California Heuchera MRCA: Last interglacial, distance-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the last interglacial (120k-140k years ago), using distance-buffer models and binary maps.BINARY_final_range_product_hybrid.tifBinned-probabilities suitability prediction for Mitella MRCA: Holocene climatic optimum, narrow-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Holocene climatic optimum (6k years ago), using narrow-buffer models and normalized binned-probabilities maps.final_range_product_source.normalized.tifBinned-probabilities suitability prediction for California Heuchera MRCA: Holocene climatic optimum, narrow-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Holocene climatic optimum (6k years ago), using narrow-buffer models and normalized binned-probabilities maps.final_range_product_hybrid.normalized.tifBinned-probabilities suitability prediction for Mitella MRCA: Last Glacial Maximum, narrow-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Last Glacial Maximum (22k years ago), using narrow-buffer models and normalized binned-probabilities maps.final_range_product_source.normalized.tifBinned-probabilities suitability prediction for California Heuchera MRCA: Last Glacial Maximum, narrow-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Last Glacial Maximum (22k years ago), using narrow-buffer models and normalized binned-probabilities maps.final_range_product_hybrid.normalized.tifBinned-probabilities suitability prediction for Mitella MRCA: Last interglacial, narrow-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the last interglacial (120k-140k years ago), using narrow-buffer models and normalized binned-probabilities maps.final_range_product_source.normalized.tifBinned-probabilities suitability prediction for California Heuchera MRCA: Last interglacial, narrow-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the last interglacial (120k-140k years ago), using narrow-buffer models and normalized binned-probabilities maps.final_range_product_hybrid.normalized.tifBinned-probabilities suitability prediction for Mitella MRCA: Holocene climatic optimum, wide-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Holocene climatic optimum (6k years ago), using wide-buffer models and normalized binned-probabilities maps.final_range_product_source.normalized.tifBinned-probabilities suitability prediction for California Heuchera MRCA: Holocene climatic optimum, wide-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Holocene climatic optimum (6k years ago), using wide-buffer models and normalized binned-probabilities maps.final_range_product_hybrid.normalized.tifBinned-probabilities suitability prediction for Mitella MRCA: Last Glacial Maximum, wide-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Last Glacial Maximum (22k years ago), using wide-buffer models and normalized binned-probabilities maps.final_range_product_source.normalized.tifBinned-probabilities suitability prediction for California Heuchera MRCA: Last Glacial Maximum, wide-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Last Glacial Maximum (22k years ago), using wide-buffer models and normalized binned-probabilities maps.final_range_product_hybrid.normalized.tifBinned-probabilities suitability prediction for Mitella MRCA: Last interglacial, wide-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the last interglacial (120k-140k years ago), using wide-buffer models and normalized binned-probabilities maps.final_range_product_source.normalized.tifBinned-probabilities suitability prediction for California Heuchera MRCA: Last interglacial, wide-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the last interglacial (120k-140k years ago), using wide-buffer models and normalized binned-probabilities maps.final_range_product_hybrid.normalized.tifBinned-probabilities suitability prediction for Mitella MRCA: Holocene climatic optimum, distance-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Holocene climatic optimum (6k years ago), using distance-buffer models and normalized binned-probabilities maps.final_range_product_source.normalized.tifBinned-probabilities suitability prediction for California Heuchera MRCA: Holocene climatic optimum, distance-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Holocene climatic optimum (6k years ago), using distance-buffer models and normalized binned-probabilities maps.final_range_product_hybrid.normalized.tifBinned-probabilities suitability prediction for Mitella MRCA: Last Glacial Maximum, distance-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Last Glacial Maximum (22k years ago), using distance-buffer models and normalized binned-probabilities maps.final_range_product_source.normalized.tifBinned-probabilities suitability prediction for California Heuchera MRCA: Last Glacial Maximum, distance-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Last Glacial Maximum (22k years ago), using distance-buffer models and normalized binned-probabilities maps.final_range_product_hybrid.normalized.tifBinned-probabilities suitability prediction for Mitella MRCA: Last interglacial, distance-buffer modelsThis is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the last interglacial (120k-140k years ago), using distance-buffer models and normalized binned-probabilities maps.final_range_product_source.normalized.tifBinned-probabilities suitability prediction for California Heuchera MRCA: Last interglacial, distance-buffer modelsThis is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the last interglacial (120k-140k years ago), using distance-buffer models and normalized binned-probabilities maps.final_range_product_hybrid.normalized.tifSimplified chloroplast genome phylogenyThis is a simplified version of Supplemental Figure S4, showing the most salient clades recovered with additional phylogenomic sampling.RAxML_bipartitions.partitionedchloroplastnolakelae.tre3.reduced.pdfChloroplast phylogenomic analysis -- best tree with bipartition frequenciesAnalysis of all taxa (i.e., in some cases multiple accessions per species). Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).RAxML_bipartitions.partitionedchloroplastnolakelae.treChloroplast phylogenomic analysis -- bootstrap treesAnalysis of all taxa (i.e., in some cases multiple accessions per species). Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).RAxML_bootstrap.partitionedchloroplastnolakelaeChloroplast phylogenomic analysis -- concatenated alignmentAnalysis of all taxa (i.e., in some cases multiple accessions per species). Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).NewAndOldCpTaxa.aligned.fixed.nolakelae.phy