# Identifying climatic drivers of hybridization with a new ancestral niche reconstruction method This repository contains sequence and GIS data associated with the study "Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method," published in *Systematic Biology*. ## Description of the data and file structure **projections_ASTRAL_tifs.zip**: A ZIP archive containing ancestral reconstruction projections using the ASTRAL tree, in GEOTiff format. Bio1 interpolated across time periods based on ASTRAL analysis, with date noted in the file name in MYA **projections_concatenation_tifs.zip**: A ZIP archive containing ancestral reconstruction projections using the concatenation tree, in GEOTiff format. Bio1 interpolated across time periods based on concatenated analysis, with date noted in the file name in MYA. **trees.zip**: A ZIP archive containing various trees used in the study. * all_gene_trees_90strip.trees: 277 gene trees in Phylip format * allele_table.txt: Allele table for ASTRAL analysis * ASTRAL_90strip_alleletable.tre: ASTRAL analysis using allele table * ASTRAL_90strip.tre: ASTRAL analysis with no allele table * MCMCtree_ASTRAL_rep3.tre: Dated ASTRAL analysis * MCMCtree_chloroplast_rep3.tre: Dated chloroplast analysis * MCMCtree_concatenation_rep3.tre: Dated concatenated nuclear analysis * RAxML_bipartitions.chloroplast.renamed.tre: Chloroplast analysis, tips renamed * RAxML_bipartitions.chloroplast.tre: Chloroplast analysis, original tip names * RAxML_bipartitions.concatenated_90stripped.renamed.tre: Concatenated nuclear analysis, tips renamed * RAxML_bipartitions.concatenated_90stripped.tre: Concatenated nuclear analysis, original tip names **alignments.zip**: A ZIP archive containing various alignments used in the study. * gene_tree_alignments: Directory of 277 alignments in FASTA format * chloroplast_all_sequences.aligned.fa.reduced: Plastid genome alignment * concatenated.90strip.phy: Concatenated nuclear alignment **PaleoGenerate_bio1.zip**: A ZIP archive containing PaleoGenerate output for BIOCLIM variable 1 (mean annual temperature). The subfolder TestPlots contains files relevant to the validation of environmental data interpolation reported in the main manuscript. OGLayerInformation.xslx summarizes information on the source layers, and MeanDifference_112519.xlsx reports the predicted vs. source difference among the layers. Subfolder Figures contains PDFs for bio1 (reported in the main manuscript) and bio12 and bio17 (not used in the main manuscript), plotting the average vs. predicted difference across the study region. **supplemental.revised.final.notrackedchanges.pdf**: Online supplement to go with the article. ## Code/Software See the GitHub repository associated with this study at:

Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit.

Published here are the complete Supplements as a collated document, phylogenies, gene trees, alignments, and paleoclimatic interpolations.

Standard phylogenetic tree, alignment, and GIS software such as QGIS.