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)

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

Data from: Geographic range dynamics drove ancient hybridization in a lineage of angiosperms

Elucidating the dynamic distribution of organismal lineages has been central to biology since the 19th 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 genusHeuchera, noteworthy in that it experienced ancient introgression from circumboreally distributed species of Mitella, lineages now ~1300 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 suggest 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

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

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 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

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

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)

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

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)