Untangling the Evolution of American Wild Grapes: Admixed Species and How to Find Them

Abstract

Natural hybridization and introgression are central evolutionary processes in grape genus (Vitis). On the other hand, the interspecific relationships among grapes, the directionality of the inferred admixture events and the parents of hybrids are not yet completely clarified. The grapes are economically important crops characterized by tendrils used to climb on the trees and the fruits harvested by humans especially for the consumption or to produce wines and liquors. The American grapes (ca. 30 species) are recognized as an important resource because they show biotic and abiotic resistances. We analyzed 3,885 genomewide SNPs from 31 American Vitis species using the TreeMix software combined with the f3 and f4 tests. This approach allowed us to infer phylogenetic relationships and to explore the natural admixture among taxa. Our results confirmed the existence of all hybrid species recognized in literature (V. x champinii, V. x doaniana, V. x novae-angliae, and V. x slavinii), identifying their most likely parent species and provided evidence of additional gene flows between distantly related species. We discuss our results to elucidate the origin of American wild grapes, demonstrating that admixture events have ancient origins. We observe that gene flows have involved taxa currently spread through the southern regions of North America. Consequently, we propose that glacial cycles could have triggered the contact between interfertile taxa promoting local hybridization events. We conclude by discussing the phylogenetic implications of our findings and showing that TreeMix can provide novel insights into the evolutionary history of grapes.

Population genomics of Drosophila suzukii reveal longitudinal population structure and signals of migrations in and out of the continental United States

“…As Treemix requires genotypes to be called, PCAngsd was used to call genotypes from the GLs with a 95% posterior probability cutoff using estimated inbreeding coefficients as a prior. When looking at the distribution of fraction of missing genotypes per site, we observed a peak at 10%, and decided to exclude any sites with greater than 20% missing data across samples, consistent with cutoffs in other studies ( Brandenburg et al 2017 ; Zecca et al 2019 ). We also excluded sites for which data are completely missing within any one cluster as required by Treemix, leaving 29,145 SNPs for analysis.…”

Back to the Origins: Background and Perspectives of Grapevine Domestication

“…Hybridisation is a natural process generally attributed to taxa range changes but in certain circumstances can be imputed to human activity. In recent years, molecular studies have proved that interspecific hybridisation and introgression are central processes in the evolution of Vitis genus [ 79 , 82 , 102 , 103 ]. Introgression is considered a process mediated by the transfer of genes through repeated backcrosses and when occurring from crops to its wild relatives can have deleterious consequences on the genetic structure and conservation of populations [ 104 ].…”

Evaluation of Wild, Wine, Table, and Raisin Grapevine (Vitis spp.) Genotypes in Gedeo Zone, Southern Ethiopia

“…The result of the present study is in line with [ 13 , 14 ], that clearly and concisely reported that wild grapevines were vigorous compared to the modern grapes. This might be mainly due to genetic differences among the grapevine cultivars [ 15 ], sunlight distribution [ 9 ], and poor canopy management [ 16 ].…”