DOI: 10.5061/dryad.n5tb2rbzn
title: Identifying climatic drivers of hybridization with a new ancestral niche reconstruction method

description: 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.
description: Published here are the complete Supplements as a collated
 document, phylogenies, gene trees, alignments, and paleoclimatic
 interpolations.
description: Standard phylogenetic tree, alignment, and GIS software such as
 QGIS.
description: # 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: