Phylogenomic analyses sheds new light on the phylogeny and diversification of Corydalis DC. in Himalaya–Hengduan Mountains and adjacent regions

Phylogeny and divergence time estimation of Corydalis. The blue bars corresponded to the 95% HPD (highest posterior density) credibility intervals of age estimates. Oli., Oligocene; Pal., Paleocene; P., Pliocene; Q., Quaternary. Bar chart after each species indicated the elevational range. The section classification was followed with Chen et al. (2023). The lowercase letters (a-m) following the species names corresponded to the photographs of these species on the right. [Display omitted] •A robust time-calibrated phylogeny of Corydalis was reconstructed by the genome skimming data.•Phylogenomic sheds new light on the topology relationships and section classification of Corydalis.•Ongoing orogeny and climate change trigger the early divergence and recent diversification of Corydalis in HMM. The Himalaya–Hengduan Mountains (HHM), a renowned biodiversity hotspot of the world, harbors the most extensive habitats for alpine plants with extraordinary high levels of endemism. Although the general evolution pattern has been elucidated, the underlying processes driving spectacular radiations in many species-rich groups remain elusive. Corydalis DC. is widely distributed throughout the Northern Hemisphere containing more than 500 species, with high diversity in HHM and adjacent regions. Using 95 plastid genes, 3,258,640 nuclear single nucleotide polymorphisms (SNPs) and eight single-copy nuclear genes (SCNs) generated from genome skimming data, we reconstructed a robust time-calibrated phylogeny of Corydalis comprising more than 100 species that represented all subgenera and most sections. Molecular dating indicated that all main clades of Corydalis began to diverge in the Eocene, with the majority of extant species in HHM emerged from a diversification burst after the middle Miocene. Global pattern of mean divergence times indicated that species distributed in HHM were considerably younger than those in other regions, particularly for the two most species-rich clades (V and VI) of Corydalis. The early divergence and the recent diversification of Corydalis were most likely promoted by the continuous orogenesis and climate change associated with the uplift of the Qinghai-Tibetan Plateau (QTP). Our study demonstrates the effectivity of phylogenomic analyses with genome skimming data on the phylogeny of species-rich taxa, and sheds lights on how the uplift of QTP has triggered the evolutionary radiations of large plant genera in HHM and adjacent regions.