Genomic enrichment data illuminate rapid and reticulate evolution of Ampelopsis (Vitaceae) in East Asia

Abstract 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 or low‐copy nuclear and chloroplast genomic data obtained by the Hyb‐Seq approach. Both nuclear and chloroplast genomic data strongly support the monophyly of Ampelopsis with its sequential division into several lineages corresponding to their biogeographic distribution from North America including Mexico, 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. The plastid tree also showed high incongruence to the nuclear trees. 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 the pattern may be present in many other plant lineages in East Asia.