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Data from: Southern Iberia as a hotspot of wild grapevine genetic diversity

Rodríguez Felizzola, Juan Jacobo1; Blanco Pastor, José Luis1; Soriano Bermúdez, Jesús José1

Published Aug 07, 2026 on Dryad. https://doi.org/10.5061/dryad.sj3tx96k6

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Abstract

The commercial interest of grapevines (Vitis vinifera L.) has prompted numerous studies on their origin and genetic resources in the context of global change. However, genomic-scale information on diversity patterns and genetic structure in southwestern Europe remains scarce. This study infers the genetic structure, gene flow events between genetic groups, and genetic refugia of Vitis vinifera spp. sylvestris in the Iberian Peninsula. We reanalyzed a set of 137 complete genomes of V. vinifera spp. sylvestris. After variant calling, validation and annotation, we obtained a high-quality SNP dataset. Using these markers, we performed phylogenetic and population structure analyses to determine the number and spatial distribution of genetic groups and their contact zones. Next, we inferred the timing and directionality of gene flow events between groups. Finally, heterozygosity and allele rarity were estimated to identify populations with high conservation value. We detected three major ancestral populations and four putative genetic refugia in the south of the Iberian Peninsula. Demographic analyses indicate sustained gene flow between ~21,000 and ~7,000 years ago from a North African ancestral group into Iberian wild populations in the south. Heterozygosity and allele rarity analyses identified populations of high conservation value in a variety of areas within the Iberian Peninsula.We identify the biogeographical factors behind the long-known singularity of wild Iberian grapevines. The southern Iberian Peninsula is a hotspot of genetic diversity for wild grapevines, hosting three ancestral populations and multiple contact zones that acted as micro‑refugia. The current genetic variability of Iberian wild grapevines is best explained by natural, climate-driven gene flow between African lineages with Middle Eastern origin and Iberian groups. These contacts were favored by climatic conditions during the late Pleistocene (~21,000 years) and early Holocene (~8,300 years). Our results dismiss a significant anthropogenic influence during Neolithic domestication for explaining the genetic composition of Iberian wild grapevine genotypes.