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

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 Aestivali 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., ,

本研究构建了一套靶向1013个基因的全新葡萄科（Vitaceae）靶向捕获诱饵（baits），用于探究北美葡萄属（Vitis）的系统发育关系。研究结果显示，包括欧洲葡萄（Vitis vinifera）在内的欧亚葡萄属类群，嵌套于北美葡萄属葡萄亚属（subgenus Vitis）内部。北美葡萄属葡萄亚属可划分为9个主要类群：Monticola组、Occidentales组、Californica组、引自欧亚大陆的Vinifera组、Mustangensis组、Palmata组、Aestivali组、Labrusca组以及Cinerea组。本研究检测到北美葡萄属存在显著的质核基因组冲突（cytonuclear discordances）：诸多物种在质体系统发育（plastid phylogeny）树中并非单系类群，而在核系统发育（nuclear phylogeny）树中则为单系类群。系统发育组学（phylogenomic）分析支持将北美地区的Vitis cinerea复合群划分为4个独立物种：V. cinerea、V. baileyana、V. berlandieri以及V. simpsonii。该分类处理将更有效地助力北美野生葡萄属物种多样性的保护工作。