Gene Flow and Incomplete Lineage Sorting Have Generated Gene Tree Discordance at Different Stages During the Rapid Radiation of an Alpine Lineage

The processes and mechanisms underlying rapid radiative diversification of lineages on the Qinghai-Tibetan Plateau remain poorly understood. A major challenge in studying these radiations is resolving phylogenies that are often confounded by gene flow and incomplete lineage sorting (ILS). Focusing on the alpine plant genus Rhodiola, our study reconstructed the phylogeny of the genus using various SNP datasets and orthologous single-copy nuclear gene datasets. Based on this framework, we examined phylogenetic discordance and reticulate evolution, revealing that ILS and gene flow jointly shaped phylogenetic heterogeneity at different evolutionary stages. Combined with diversification rate shifts and ancestral range reconstruction, these findings illuminate how rapid radiations proceed in the context of mountain uplift and demonstrate the power of genomic data for resolving evolutionary histories in rapidly diversifying lineages. This is the code script that completes most of the experiments.