Genomic enrichment data illuminate rapid and reticulate evolution of Ampelopsis (Vitaceae) in East Asia
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 intra-generic 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. Comparison of nuclear and plastid trees are also highly incongruent. 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.