Tree files

Ampelopsis is a genus of the grape family Vitaceae, discontinuously distributed in the temperate to subtropical zones of the Northern Hemisphere but mostly diversified in East Asia. Previous phylogenetic studies on Ampelopsis have mainly been based on a few chloroplast markers, resulting in unresolved phylogenetic relationships for the East Asian taxa. Here, we carried out a phylogenetic reconstruction of Ampelopsis and intrageneric reticulate evolution analyses for the first time based on extensive single low-copy nuclear and chloroplast genomic data obtained by Hyb-Seq sequencing. Both nuclear and chloroplast genomic data strongly support the monophyly of Ampelopsis with its sequential division into three major lineages corresponding to their biogeographic distribution from North America, Europe to West Asia, and East Asia, respectively. The East Asian Ampelopsis is largely grouped into two major clades but characterized by extensive topological conflicts among individual nuclear gene trees. Plastid tree also showed high incongruence from the nuclear tree. Gene tree estimation error and gene flow were identified as the major source of phylogenetic conflicts within the East Asian lineage, which most likely resulted from recent and rapid divergence. Our results emphasize that rapid divergence accompanied by gene introgression played a significant role in the complex diversification pattern of Ampelopsis and many other plant lineages in East Asia.蛇葡萄属(Ampelopsis)是葡萄科(Vitaceae)下的一个属，间断分布于北半球温带至亚热带区域，物种多样性以东亚地区最为丰富。此前针对蛇葡萄属的系统发育(phylogenetic)研究多基于少量叶绿体标记(chloroplast markers)，导致东亚类群的系统发育关系始终未能得到厘清。本研究首次基于通过Hyb-Seq测序获得的大量单拷贝低拷贝核基因组(single low-copy nuclear genomic)及叶绿体基因组(chloroplast genomic)数据，开展了蛇葡萄属的系统发育重建(phylogenetic reconstruction)与属内网状进化(intrageneric reticulate evolution)分析。核基因组与叶绿体基因组数据均强力支持蛇葡萄属为单系群(monophyly)，其可依次划分为三个主要演化支(lineage)，分别对应北美、欧洲至西亚以及东亚的生物地理分布(biogeographic distribution)格局。东亚地区的蛇葡萄属类群大体可划分为两个主要演化支(clade)，但各核基因树之间存在广泛的拓扑结构冲突(topological conflict)；质体树(plastid tree)与核基因树同样表现出高度的拓扑不一致性。基因树估计误差(gene tree estimation error)与基因流(gene flow)被确定为东亚支系内系统发育冲突的主要来源，而该冲突极有可能由近期快速分化事件所导致。本研究结果表明，伴随基因渐渗(gene introgression)的快速分化过程，在东亚地区蛇葡萄属及诸多其他植物类群的复杂多样化格局(diversification pattern)形成过程中发挥了重要作用。