DOI: 10.5061/dryad.vq83bk3rt
title: Genetic diversity and population structure in Vitis species illustrate phylogeographic patterns in eastern North America

description: 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.
description: Natural populations of three <i>Vitis </i>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<sup>®</sup>GoldenGate<sup>® </sup>VeraCode<sup>®</sup>assay protocols (Genotoul plateform, Toulouse, France).
description: - nSSR_3sp_467.csv : Diploid genotypes of 123 <i>V. aestivalis</i>, 113 <i>V. cinerea </i>and 231 <i>V. riparia </i>(rows) for 26 nuclear microsatellite markers (columns). Genotypes are coded on six digits and missing genotypes are indicated by 0. <i>V. cinerea</i>is divided in two varieties : var. <i>berlandieri</i>and var. <i>cinerea</i>, 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 <i>V. aestivalis</i>, 98 <i>V. cinerea </i>and 216 <i>V. riparia </i>(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 <i>V. aestivalis</i>. The position of each SNP is given on <i>Vitis vinifera </i>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 <i>V. cinerea</i>. The position of each SNP is given on <i>Vitis vinifera </i>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 <i>V. riparia</i>. The position of each SNP is given on <i>Vitis vinifera </i>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 <i>V. aestivalis </i>(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 <i>V. cinerea </i>(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 <i>V. riparia </i>(rows) for 615 SNPs (columns). Genotypes are given with the two alleles coded as ATGC and missing genotypes are indicated by 0.