DOI: 10.5061/dryad.bt5v6
title: Data from: A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae.

description: Differential adaptation to distinct niches can restrict gene flow and
 promote population differentiation within a species. However, in some
 cases the distinction between niches can collapse, forming a hybrid niche
 with features of both environments. We previously reported that
 distinctions between vineyards and oak soil present an ecological barrier
 that restricts gene flow between lineages of Saccharomyces cerevisiae.
 Vineyard isolates are tolerant to stresses associated with grapes while
 North American oak strains are particularly tolerant to freeze-thaw
 cycles. Here, we report the isolation of Saccharomyces cerevisiae strains
 from Wisconsin cherry trees, which display features common to vineyards
 (e.g. high sugar concentrations) and frequent freeze-thaw cycles. Genome
 sequencing revealed that the isolated strains are highly heterozygous and
 represent recent hybrids of the oak x vineyard lineages. We found that the
 hybrid strains are phenotypically similar to vineyard strains for some
 traits, but are more similar to oak strains for other traits. The cherry
 strains were exceptionally good at growing in cherry juice, raising the
 possibility that they have adapted to this niche. We performed
 transcriptome profiling in cherry, oak, and vineyard strains and show that
 the cherry-tree hybrids display vineyard-like or oak-like expression,
 depending on the gene sets, and in some cases the expression patterns
 linked back to shared stress tolerances. Allele-specific expression in
 these natural hybrids suggested concerted cis-regulatory evolution at sets
 of functionally regulated genes. Our results raise the possibility that
 hybridization of the two lineages provides a genetic solution to the
 thriving in this unique niche.
description: DC6.vcfSNPs identified in cherry strain DC 6 using GATK. SNPs were called on both DC 6 and DC 16, then sites for each strain were separated, and all non-SNP positions removed using VCFtools.DCM6.PASS_SNPs.NonREF.recode.vcfDC16.vcfSNPs identified in cherry strain DC 16 using GATK. SNPs were called on both DC 6 and DC 16, then sites for each strain were separated, and all non-SNP positions removed using VCFtools.DCM16.PASS_SNPs.NonREF.recode.vcfRNAseqCountsRead counts for each gene across all strains analyzed in EdgeR.Counts.txtOakvVintopTagsEdgeR output for differentially expressed genes in oak versus vineyard strains.DCtopTagsEdgeR output for DC-specific differentially expressed genes.DCvOaktopTagsEdgeR output for differentially expressed genes in DC versus oak strains.DCvVintopTagsEdgeR output for differentially expressed genes in DC versus vineyard strains.PCAsnpsVCF file containing all of the genotype data used for PCA.25Strains_latest_snp_R64-1-1_NonREF.recode.vcfPCAmap Filemap file created for PCA.25Strains.mapPCA ped fileped file used for PCA25Strains.pedPCArawraw file for PCA analysis25Strains.rawCh4 alignmentAlignment file of Chromosome 4 sanger sequencingCh4.nexChr4 tree fileMr. Bayes tree file for Chromosome 4Ch4.nex.con.treCh9 alignmentAlignment file of Chromosome 9 sanger sequencingCh9.nexCh10 alignmentAlignment file of Chromosome 10 sanger sequencingCh10.nexCh9 tree fileMrBayes tree file for Chromosome 9Ch9.nex.con.treCh10 tree fileMrBayes tree file for Chromosome 10Ch10.nex.con.tre