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.
Occurrence records
A zip archive of all occurrence records used in this study in Maxent format, one file per species.
all_occurrences.zip
Ancestral reconstruction -- narrow-buffer models
Ancestral 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.tre
Ancestral reconstruction -- wide-buffer models
Ancestral 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.tre
Ancestral reconstruction -- distance-buffer models
Ancestral 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.tre
Ancestral reconstruction pooled, thinned MCMC -- narrow-buffer models
Pooled 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.zip
Ancestral reconstruction pooled, thinned MCMC -- wide-buffer models
Pooled 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.zip
Ancestral reconstruction pooled, thinned MCMC -- distance-buffer models
Pooled 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.zip
Full nuclear phylogenomic analysis -- best tree with bipartition frequencies
Analysis 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.tre
Full nuclear phylogenomic analysis -- bootstrap trees
Analysis 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.277locipartitionednointronnolakelae
Full nuclear phylogenomic analysis -- concatenated alignment
Analysis 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.nolakelae
BEAST dating analysis -- chloroplast data, lognormal prior
BEAST 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.tre
BEAST dating analysis -- chloroplast data, truncated normal prior
BEAST 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.tre
BEAST dating analysis -- nuclear data, lognormal prior
BEAST 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.tre
BEAST dating analysis -- nuclear data, truncated normal prior
BEAST 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.tre
Predicted niche occupancy profiles -- narrow-buffer models
Predicted 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.zip
Predicted niche occupancy profiles -- wide-buffer models
Predicted 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.zip
Predicted niche occupancy profiles -- distance-buffer models
Predicted 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.zip
Model suitability ASC files -- narrow-buffer models
Model suitability rasters for narrow-buffer models from Maxent. These were the rasters used for predicted niche occupancy calculations.
all_asc_narrowbuffer.zip
Model suitability ASC files -- distance-buffer models
Model suitability rasters for distance-buffer models from Maxent. These were the rasters used for predicted niche occupancy calculations.
all_asc_distancebuffer.zip
Model suitability ASC files -- wide-buffer models
Model suitability rasters for wide-buffer models from Maxent. These were the rasters used for predicted niche occupancy calculations.
all_asc_widebuffer.zip
Variable numbering translate table
An 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.xlsx
Binary suitability prediction for Mitella MRCA: Holocene climatic optimum, narrow-buffer models
This 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.tif
Binary suitability prediction for California Heuchera MRCA: Holocene climatic optimum, narrow-buffer models
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 narrow-buffer models and binary maps.
BINARY_final_range_product_hybrid.tif
Binary suitability prediction for Mitella MRCA: Last Glacial Maximum, narrow-buffer models
This 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.tif
Binary suitability prediction for California Heuchera MRCA: Last Glacial Maximum, narrow-buffer models
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 Last Glacial Maximum (22k years ago), using narrow-buffer models and binary maps.
BINARY_final_range_product_hybrid.tif
Binary suitability prediction for Mitella MRCA: Last interglacial, narrow-buffer models
This 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.tif
Binary suitability prediction for California Heuchera MRCA: Last interglacial, narrow-buffer models
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 last interglacial (120k-140k years ago), using narrow-buffer models and binary maps.
BINARY_final_range_product_hybrid.tif
Binary suitability prediction for Mitella MRCA: Holocene climatic optimum, wide-buffer models
This 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.tif
Binary 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.tif
Binary suitability prediction for Mitella MRCA: Holocene climatic optimum, wide-buffer models
This 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.tif
Binary suitability prediction for California Heuchera MRCA: Last Glacial Maximum, wide-buffer models
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 Last Glacial Maximum (22k years ago), using wide-buffer models and binary maps.
BINARY_final_range_product_hybrid.tif
Binary suitability prediction for Mitella MRCA: Last interglacial, wide-buffer models
This 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.tif
Binary suitability prediction for California Heuchera MRCA: Last interglacial, wide-buffer models
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 last interglacial (120k-140k years ago), using wide-buffer models and binary maps.
BINARY_final_range_product_hybrid.tif
Binary suitability prediction for Mitella MRCA: Holocene climatic optimum, distance-buffer models
This 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.tif
Binary suitability prediction for California Heuchera MRCA: Holocene climatic optimum, distance-buffer models
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 distance-buffer models and binary maps.
BINARY_final_range_product_hybrid.tif
Binary suitability prediction for Mitella MRCA: Last Glacial Maximum, distance-buffer models
This 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.tif
Binary suitability prediction for California Heuchera MRCA: Last Glacial Maximum, distance-buffer models
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 Last Glacial Maximum (22k years ago), using distance-buffer models and binary maps.
BINARY_final_range_product_hybrid.tif
Binary suitability prediction for Mitella MRCA: Last interglacial, distance-buffer models
This 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.tif
Binary suitability prediction for California Heuchera MRCA: Last interglacial, distance-buffer models
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 last interglacial (120k-140k years ago), using distance-buffer models and binary maps.
BINARY_final_range_product_hybrid.tif
Binned-probabilities suitability prediction for Mitella MRCA: Holocene climatic optimum, narrow-buffer models
This 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.tif
Binned-probabilities suitability prediction for California Heuchera MRCA: Holocene climatic optimum, narrow-buffer models
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 narrow-buffer models and normalized binned-probabilities maps.
final_range_product_hybrid.normalized.tif
Binned-probabilities suitability prediction for Mitella MRCA: Last Glacial Maximum, narrow-buffer models
This 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.tif
Binned-probabilities suitability prediction for California Heuchera MRCA: Last Glacial Maximum, narrow-buffer models
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 Last Glacial Maximum (22k years ago), using narrow-buffer models and normalized binned-probabilities maps.
final_range_product_hybrid.normalized.tif
Binned-probabilities suitability prediction for Mitella MRCA: Last interglacial, narrow-buffer models
This 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.tif
Binned-probabilities suitability prediction for California Heuchera MRCA: Last interglacial, narrow-buffer models
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 last interglacial (120k-140k years ago), using narrow-buffer models and normalized binned-probabilities maps.
final_range_product_hybrid.normalized.tif
Binned-probabilities suitability prediction for Mitella MRCA: Holocene climatic optimum, wide-buffer models
This 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.tif
Binned-probabilities suitability prediction for California Heuchera MRCA: Holocene climatic optimum, wide-buffer models
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 normalized binned-probabilities maps.
final_range_product_hybrid.normalized.tif
Binned-probabilities suitability prediction for Mitella MRCA: Last Glacial Maximum, wide-buffer models
This 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.tif
Binned-probabilities suitability prediction for California Heuchera MRCA: Last Glacial Maximum, wide-buffer models
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 Last Glacial Maximum (22k years ago), using wide-buffer models and normalized binned-probabilities maps.
final_range_product_hybrid.normalized.tif
Binned-probabilities suitability prediction for Mitella MRCA: Last interglacial, wide-buffer models
This 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.tif
Binned-probabilities suitability prediction for California Heuchera MRCA: Last interglacial, wide-buffer models
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 last interglacial (120k-140k years ago), using wide-buffer models and normalized binned-probabilities maps.
final_range_product_hybrid.normalized.tif
Binned-probabilities suitability prediction for Mitella MRCA: Holocene climatic optimum, distance-buffer models
This 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.tif
Binned-probabilities suitability prediction for California Heuchera MRCA: Holocene climatic optimum, distance-buffer models
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 distance-buffer models and normalized binned-probabilities maps.
final_range_product_hybrid.normalized.tif
Binned-probabilities suitability prediction for Mitella MRCA: Last Glacial Maximum, distance-buffer models
This 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.tif
Binned-probabilities suitability prediction for California Heuchera MRCA: Last Glacial Maximum, distance-buffer models
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 Last Glacial Maximum (22k years ago), using distance-buffer models and normalized binned-probabilities maps.
final_range_product_hybrid.normalized.tif
Binned-probabilities suitability prediction for Mitella MRCA: Last interglacial, distance-buffer models
This 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.tif
Binned-probabilities suitability prediction for California Heuchera MRCA: Last interglacial, distance-buffer models
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 last interglacial (120k-140k years ago), using distance-buffer models and normalized binned-probabilities maps.
final_range_product_hybrid.normalized.tif
Simplified chloroplast genome phylogeny
This is a simplified version of Supplemental Figure S4, showing the most salient clades recovered with additional phylogenomic sampling.
RAxML_bipartitions.partitionedchloroplastnolakelae.tre3.reduced.pdf
Chloroplast phylogenomic analysis -- best tree with bipartition frequencies
Analysis 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.tre
Chloroplast phylogenomic analysis -- bootstrap trees
Analysis 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.partitionedchloroplastnolakelae
Chloroplast phylogenomic analysis -- concatenated alignment
Analysis 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