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AimThe Hengduan Mountains (HDM) of southwest China is a biodiversity hotspot and harbours one of the world's richest temperate floras. However, the origin and evolution of its biota remain largely unresolved. Here we explore the impact of mountain uplift on the diversification process of biodiversity in this hotspot using alpine bamboos.LocationThe HDM region, southwest China.TaxonAlpine bamboos.MethodsWe used ddRAD‐seq data from the most complete sampling of alpine bamboos undertaken to date (79% of the species diversity), to investigate their evolutionary history. The ancestral area of these bamboos was reconstructed using a time‐calibrated phylogeny in BioGeoBEARS and diversification rates were inferred using BAMM analyses. In addition, the impact of mountain uplift on the divergence of alpine bamboos was evaluated using trait‐dependent models of diversification.ResultsThe alpine bamboos were strongly supported as monophyletic, and the relationships within them were robustly resolved. Fargesia was found to be polyphyletic and Yushania was resolved as monophyletic. Alpine bamboos originated outside the HDM region during the late Miocene, and spread to this region in the Pliocene, undergoing a significant acceleration in net diversification, which is temporally congruent with the orogeny. The speciation rate increased with altitude and a high diversification rate, estimated to be 0.75 species per million years, was detected for alpine bamboos distributed in high elevations.Main ConclusionsOur study demonstrates that heterogeneous mountain habitats and geographical isolation of alpine bamboos, which have limited dispersal ability, are important drivers for their rapid diversification. This study also highlights the power of complementary analyses in revealing the link between species diversification and past geological changes.

The temperate bamboos (tribe Arundinarieae, Poaceae) are strongly supported as monophyly in recent molecular studies, but taxonomic delineation and phylogenetic relationships within the tribe lack resolution. Here, we sampled 39 species (36 temperate bamboos and 3 outgroups) for restriction-site associated DNA sequencing (RAD-seq) with an emphasis on Phyllostachys clade and related clades. Using the largest data matrix for the bamboos to date, we were able to infer phylogenetic relationships with unparalleled resolution. The Phyllostachys, Shibataea, and Arundinaria clades defined from plastid phylogeny, were not supported as monophyletic group. However, the RAD-seq phylogeny largely agreed with the morphology-based taxonomy, with two clades having leptomorph rhizomes strongly supported as monophyletic group. We also explored two approaches, BWA-GATK (a mapping system) and Stacks (a grouping system), for differences in SNP calling and phylogeny inference. For the same level of missing data, the BWA-GATK pipeline produced much more SNPs in comparison with Stacks. Phylogenetic analyses of the largest data matrices from both pipelines, using concatenation and coalescent methods provided similar tree topologies, despite the presence of missing data. Our study demonstrates the utility of RAD-seq data for elucidating phylogenetic relationships between genera and higher taxonomic levels in this important but phylogenetically challenging group.