Complete genomic sequences for the full set of non-redundant sequences

Genomic sequences were constructed using the genomic sequence of the reference genome and a table of SNPs

Maximum likelihood genealogy representing the relationships among non-redundant genomic sequences.

Analyses were based on full genomic sequences (i.e. including both variant and invariant sites)

SNPs used to identify redundant sequences

This files contains the SNPs that were used to identify redundant sequences. It is based on the file containing "SNPs for non-redundant European and North-American sequences", with missing data removed. It was analysed using DNADIST&NEIGHBOR programs in the PHYLIP Package, and a single representative of each clonal complex was kept in the dataset "SNPs for non-redundant European and North-American sequences" (clonal complex identified as groups of individuals with genetic distance <0.1

SNPs for non-redundant European and North-American sequences

This file contains SNPs for the European and North American isolates of PS4B. SNP-calling was performed independently for this set of sequences, for the full set of sequences and for the full set of non redundant sequences

SNPs for full set of non-redundant sequences

This file contains SNPs for the 41 isolates of taxa PS4A, PS4B and PS6. Initially the dataset was comprised of 52 isolates, but after genome sequencing a "clone correction" was carried out, i.e. only one representative of groups of genome with genetic distance below 0.1 were kept in the dataset. The file used for clone correction has also been deposited on Dryad

dom_ref_orientalis_26SSR_structure

There are three files that we used for STRUCTURE analyses with the 26SSR markers that allowed us to detect hybrids and to do the following intra-species TESS analyses. Each file include wild species individuals and 40 M. domestica reference (last 40 individuals in each input file): (1) dom_ref_orientalis_26SSR_structure: the M. orientalis samples followed by the 40 M. domestica reference (2) dom_ref_sieversii_26SSR_structure: the M. sieversii samples followed by the 40 M. domestica reference (3) dom_ref_sylvestris_26SSR_structure: the M.sylvestris samples followed by the 40 M. domestica referenc

dom_ref_sieversii_26SSR_structure

There are three files that we used for STRUCTURE analyses with the 26SSR markers that allowed us to detect hybrids and to do the following intra-species TESS analyses. Each file include wild species individuals and 40 M. domestica reference (last 40 individuals in each input file): (1) dom_ref_orientalis_26SSR_structure: the M. orientalis samples followed by the 40 M. domestica reference (2) dom_ref_sieversii_26SSR_structure: the M. sieversii samples followed by the 40 M. domestica reference (3) dom_ref_sylvestris_26SSR_structure: the M.sylvestris samples followed by the 40 M. domestica referenc

Microsatellite genotyping of Botrytis cinerea grey mold and noble rot populations in France

Microsatellite genotyping using 8 markers. Populations of B. cinerea collected in the field, in 3 wine-producing French regions, from grey mold and nobel rot symptoms. Data are given in allele size in bp (haploid data). 0 indicate missing values

Genetic SSR data

Genetic SSR dat

mainparams_no_geogr_prior

structure parameter file used with input file structure_CC_no_geogr_prior.tx