Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis

• Published in: Molecular phylogenetics and evolution 2023-09, Vol.186, p.107866-107866, Article 107866
• Main Authors: Talavera, Alicia, Nie, Ze-Long, Ma, Zhi-Yao, Johnson, Gabriel, Ickert-Bond, Stefanie M., Zimmer, Elizabeth A., Wen, Jun
• Format: Article
• Language: English
• Subjects: Grapes; Hyb-Seq; Phylogenomics; Targeted enrichment; Vitis
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2023.107866

[Display omitted] •New 1013-gene bait set helps resolve phylogenetic relationships in Vitis;•The Eurasian Vitis clade is nested within North American Vitis;•Within North American subgenus Vitis nine main groups can be recognized;•There is strong cytonuclear discordance in Vitis;•Concordance analyses suggest discordant signals across the phylogeny. A set of newly designed Vitaceae baits targeting 1013 genes was employed to explore phylogenetic relationships among North American Vitis. Eurasian Vitis taxa including Vitis vinifera were found to be nested within North American Vitis subgenus Vitis. North American Vitis subgenus Vitis can be placed into nine main groups: the Monticola group, the Occidentales group, the Californica group, the Vinifera group (introduced from Eurasia), the Mustangensis group, the Palmata group, the Aestivalis group, the Labrusca group, and the Cinerea group. Strong cytonuclear discordances were detected in North American Vitis, with many species non-monophyletic in the plastid phylogeny, while monophyletic in the nuclear phylogeny. The phylogenomic analyses support recognizing four distinct species in the Vitis cinerea complex in North America: V. cinerea, V. baileyana, V. berlandieri, and V. simpsonii. Such treatment will better serve the conservation of wild Vitis diversity in North America. Yet the evolutionary history of Vitis is highly complex, with the concordance analyses indicating conflicting signals across the phylogeny. Cytonuclear discordances and Analyses using the Species Networks applying Quartets (SNaQ) method support extensive hybridizations in North American Vitis. The results further indicate that plastid genomes alone are insufficient for resolving the evolutionary history of plant groups that have undergone rampant hybridization, like the case in North American Vitis. Nuclear gene data are essential for species delimitation, identification and reconstructing evolutionary relationships; therefore, they are imperative for plant phylogenomic studies.