Phylogenomics of <i>Fargesia</i> and <i>Yushania</i> reveals a history of reticulate evolution

Reticulate evolution is a common and important driving force in angiosperm evolution. In this study, we analyzed the phylogenetic signals of genomic regions with different inheritance patterns to understand evolutionary process organisms using species-rich Himalaya–Hengduan taxa bamboos (Fargesia Franchet Yushania Keng). We constructed trees sampling strategies reconstruction methods based on genome skimming double digest restriction-site-associated DNA sequencing data. assessed congruence topologies generated from datasets employed several approaches reveal causes incongruence, including detection hybridization introgression PhyloNetworks D-statistic test (ABBA-BABA test). found that, plastome-based phylogeny, Fargesia can be clustered into three groups was nested within one them, which contradicts nuclear–double sequencing-based phylogeny. Moreover, genetic variation chloroplast significantly correlated geographical distribution. The strong signal incomplete lineage sorting, hybridization, introgression, cytoplasmic gene flow among genera species suggests that reticulate main cause for incongruence between nuclear datasets. Our results add evidence genomes distinct histories suggest prevalent rapidly diversifying groups.