DOI: 10.5061/dryad.hm2jf
title: Data from: A population genomics insight into the Mediterranean origins of wine yeast domestication

description: The domestication of the wine yeast Saccharomyces cerevisiae is thought to
 be contemporary with the development and expansion of viticulture along
 the Mediterranean basin. Until now, the unavailability of wild lineages
 prevented the identification of the closest wild relatives of wine yeasts.
 Here, we enlarge the collection of natural lineages and employ
 whole-genome data of oak-associated wild isolates to study a balanced
 number of anthropic and natural S. cerevisiae strains. We identified
 industrial variants and new geographically delimited populations,
 including a novel Mediterranean oak population. This population is the
 closest relative of the wine lineage as shown by a weak population
 structure and further supported by genomewide population analyses. A
 coalescent model considering partial isolation with asymmetrical
 migration, mostly from the wild group into the Wine group, and population
 growth, was found to be best supported by the data. Importantly,
 divergence time estimates between the two populations agree with
 historical evidence for winemaking. We show that three horizontally
 transmitted regions, previously described to contain genes relevant to
 wine fermentation, are present in the Wine group but not in the
 Mediterranean oak group. This represents a major discontinuity between the
 two populations and is likely to denote a domestication fingerprint in
 wine yeasts. Taken together, these results indicate that Mediterranean
 oaks harbour the wild genetic stock of domesticated wine yeasts.
description: S. cerevisiae
 whole-genome SNP alignmentThis is a gzip/tar
 compressed data archive containing the concatenated SNP alignment of S.
 cerevisiae. SNP alignments for each chromosome are also provided, together
 with the corresponding list of SNP positions.Scer_SNP_alignment.tgzS. cerevisiae (large dataset) whole-genome SNP alignment with outgroup S. paradoxus, related to Figure S3This is a gzip/tar compressed data archive containing the concatenated SNP alignment of the large dataset with S. paradoxus as outgroup, related to Figure S3. SNP alignments for each chromosome are also provided, together with the corresponding list of SNP positions.SNP-alignment-largeDataset+Spar.tgzS. cerevisiae (restricted dataset) whole-genome SNP alignment with outgroup S. paradoxus, related to Figure 3This is a gzip/tar compressed data archive containing the concatenated SNP alignment of the restricted dataset with S. paradoxus as outgroup, related to Figure 3. SNP alignments for each chromosome are also provided, together with the corresponding list of SNP positions.SNP-alignment-restrictedDataset+Spar.tgzStructure input file used in Figure 2AThis is a gzip/tar compressed data archive containing the input file used to run Structure v2.3.4 (Pritchard et al. 2000), related to figure 2A. A list file with the positions of the parsimony informative sites used is also provided.Structure-input.tgzFineStructure input files used in Figure 2BThis is a gzip/tar compressed data archive containing the idfile, phase and recombination input files used to run FineSTRUCTURE Version 2.0.2 (Lawson et al. 2012), related to Figure 2B.fineStructure-input.tgzdadi input file used to infer demographic history of Wine and MO populationsThe joint allele frequency spectrum of Wine and Mediterranean oak (MO) populations used as input to run the demographic inference in dadi (Gutenkunst et al. 2009). Populations are defined as in the comment lines at the beginning of file.allChr_scer_subset_nonCDS_wine-randMO.dadiRaw results from VariScan, related to Table 3This is a gzip/tar compressed data archive containing the results of Variscan v2.0 (Hutter et al. 2006) for the whole-genome alignments considered, related to Table 3.variscan-results.tgzRaw results from compute (libsequence analysis package), related to Table S2This is a gzip/tar compressed data archive containing the results of compute from the libsequence analysis package (http://molpopgen.org/) (Thornton 2003), related to Table S2. The archive contains results for coding sequences (CDS) and non-CDS in the Mediterranean oak population (MO) and the wine population (wine), with one file per locus. The SGD systematic name is used to identify CDS and the nucleotide positions are used to identify non-CDS.libsequence-analysis-compute-results.tgzRaw results from polydNdS (libsequence analysis package), related to Table S2This is a gzip/tar compressed data archive containing the results of polydNdS from the libsequence analysis package (http://molpopgen.org/) (Thornton 2003), related to Table S2. The archive contains results for coding sequences (CDS) in the Mediterranean oak population (MO) and the wine population (wine), with one file per locus. The SGD systematic name is used to identify CDS.libsequence-analysis-polyDnDs-results.tgzde-novo draft assembliesThis is a gzip/tar compressed data archive containing the draft contig de-novo assemblies generated in this study.deNovo-draft-assemblies.tgzWhole-genome SNP phylogeny (restricted dataset), related to Figure 3RAxML phylogenetic tree obtained from the whole-genome SNP alignment of the restricted dataset and with S. paradoxus as outgroup, related to Figure 3.raxml-tree-snp-restricted-dataset.nwkWhole-genome SNP phylogeny (restricted dataset), related to Figure S3RAxML phylogenetic tree in newick format, obtained from the whole-genome SNP alignment of the restricted dataset and with S. paradoxus as outgroup, related to Figure 3.raxml-tree-snp-large-dataset.nwkMultilocus tree including the Chinese strains, related to Figure S4Neighbor-Joining tree in newick format, inferred from a concatenated alignment of 13 loci and including Chinese strains, related to Figure S4multilocus-tree-with-Chinese-isolates.nwkRaw data of microsatelite genotypes used in figure S1This table contains 3 columns indicating the strain name, the locus name and the allele values (size bins). When only one allele was found the value has been doubled as the stain is assessed to be diploid. For some strains additional values can be observed (ie Bread strains). For such cases, additional lines are added to described all values found at this loci.DTfinaleOctobre2010forArchive.xls