Geographical distribution and diversity of current plant species have been strongly shaped by climatic oscillations during the Quaternary. Analyzing the resulting divergence among species and differentiation within species is crucial to understand the evolution of taxa like the Vitis genus, which provides very useful genetic resources for grapevine improvement and might reveal original recolonization patterns due to growth habit and dispersal mode. Here, we studied the genetic structure in natural populations of three species from eastern North America: Vitis aestivalis, V. cinerea and V. riparia using different marker types. V. aestivalis and V. cinerea showed higher diversity than V. riparia. The two former species are less differentiated, confirming an earlier divergence of V. riparia. V. aestivalis and V. riparia exhibited different genetic groups on both sides of the Appalachian Mountains that could mirror different recolonization routes from southern refugia. Genetic structure was stronger in V. cinerea, for which two varieties (var. berlandieri  and var. cinerea) are morphologically recognized. Our results confirm this distinction and suggest the existence of three other lineages within var. cinerea. These discontinuities appear linked to adaptation of var. berlandieri to dry and limy areas of Texas and partially to the Mississippi River Valley. Rapid range expansions from refugia upon climate warming are also suggested by the low linkage disequilibrium values observed. Furthermore, large variation for downy mildew resistance was observed in the three species. Our findings appeared consistent with the vegetation history of eastern North America.

Natural populations of three Vitis species were collected in North America. DNA was extracted from leaves using the DNeasy Plant Mini Kit (Qiagen). Nuclear and chloroplast markers were genotyped with ABI Prism 3700 XL (Applied Biosystems). SNPs were discovered in Sanger sequences and genotyping was undertaken using 384-plex oligo pool assays (OPAs), according to Illumina^®GoldenGate^® VeraCode^®assay protocols (Genotoul plateform, Toulouse, France).

- nSSR_3sp_467.csv : Diploid genotypes of 123 V. aestivalis, 113 V. cinerea and 231 V. riparia (rows) for 26 nuclear microsatellite markers (columns). Genotypes are coded on six digits and missing genotypes are indicated by 0. V. cinereais divided in two varieties : var. berlandieriand var. cinerea, identified as CIN-B and CIN-C in column Pop2. Each species comprises a discovery panel of 15-16 genotypes, identified as AESReseq, CINReseq and RIPReseq in columns Pop1 and Pop2.

- cpSSR_3sp_421.csv : Haploid genotypes of 108 V. aestivalis, 98 V. cinerea and 216 V. riparia (rows) for 15 chloroplast microsatellite markers (columns). Genotypes are coded on three digits and there is no missing data.

-Table Amplicon SNP Aestivalis.csv : Table of 619 SNPs (rows) discovered in Sanger sequences of a panel of 16 genotypes of V. aestivalis. The position of each SNP is given on Vitis vinifera cv. PN40024 genome 12x. V0 and V2, with the reference allele, the MAF values and the sequences provided to Illumina to design the array (columns).

-Table Amplicon SNP Cinerea.csv : Table of 620 SNPs (rows) discovered in Sanger sequences of a panel of 15 genotypes of V. cinerea. The position of each SNP is given on Vitis vinifera cv. PN40024 genome 12x. V0 and V2, with the reference allele, the MAF values and the sequences provided to Illumina to design the array (columns).

-Table Amplicon SNP Riparia.csv : Table of 615 SNPs (rows) discovered in Sanger sequences of a panel of 15 genotypes of V. riparia. The position of each SNP is given on Vitis vinifera cv. PN40024 genome 12x. V0 and V2, with the reference allele, the MAF values and the sequences provided to Illumina to design the array (columns).

- AES_619_80_ATCG.csv : Diploid genotypes of 80 V. aestivalis (rows) for 619 SNPs (columns). Genotypes are given with the two alleles coded as ATGC and missing genotypes are indicated by 0.

- CIN_620_88_ATCG.csv : Diploid genotypes of 88 V. cinerea (rows) for 620 SNPs (columns). Genotypes are given with the two alleles coded as ATGC and missing genotypes are indicated by 0.

- RIP_615_199_ATCG.csv : Diploid genotypes of 199 V. riparia (rows) for 615 SNPs (columns). Genotypes are given with the two alleles coded as ATGC and missing genotypes are indicated by 0.