Phylogenetic relationships and migration patterns of the Fargesia spathacea complex inferred from genomic data

Recent molecular research has revealed the significance of hybridization and reticulate evolution in the evolution of temperate woody bamboos at both intergeneric and intrageneric levels. Although the monophyly of Fargesia s.l. is debated, species of Fargesia s.l. with the spathe-like leaf sheath syndrome form a clade as the Fargesia spathacea complex. A previous study showed varying degrees of genetic diversity and an excess of heterozygotes across the F. spathacea complex, but phylogenetic relationships within this complex remain unclear. Here, we sampled 24 populations and 72 individuals of the F. spathacea complex and three outgroups: Yushania confusa, Fargesia setosa, and Bashania fargesii. Using phylogenomic data, we generated a robust phylogeny and explored the implications of the phylogeny for previous hybridization and introgression hypotheses. The phylogenetic analyses suggested that the 72 individuals were clustered into four major clades consistent with the genetic structure but different from the statistical results of vegetative traits. Our phylogenetic and biographical evidence demonstrate that the species in the F. spathacea complex originated outside the Hengduan Mountains region and spread to heterogeneous mountain habitats in the Daba and Qinling Mountains. In addition, adaptive radiation to cold climates and reticulate evolution may have driven species diversification within the F. spathacea complex, making it difficult to classify at the population level.