Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid GenusCypripediumL

Abstract

Background and AimsCypripediumis the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny ofCypripediumand explore its evolutionary history using target capture data for the first time.MethodsWe used the orchid-specific bait set Orchidaceae963 in combination with transcriptomic data to reconstruct the phylogeny ofCypripediumbased on 913 nuclear loci, covering all 13 sections. Subsequently, we investigated discordance among nuclear and chloroplast trees, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies, and diversification rate shifts, and identified potential gene (genome) duplication and hybridization events.Key ResultsAll sections were recovered as monophyletic, contrary to the two subsections within sect.Cypripedium. The two subclades within this section did not correspond to its subsections but matched the geographic distribution of their species. Additionally, we discovered high levels of discordance in the short backbone branches of the genus and within sect.Cypripedium, which can be attributed to hybridization events detected based on phylogenetic network analyses, and incomplete lineage sorting caused by rapid radiation. Our biogeographic analysis suggested a Neotropical origin of the genus during the Oligocene (∼30 Ma), with a lineage of potentially hybrid origin spreading to the Old World in the Early Miocene (∼22 Ma). The rapid radiation at the backbone likely occurred in Southeast Asia around the Middle Miocene Climatic Transition (∼15–13 Ma), followed by several independent dispersals back to the New World. Moreover, the Pliocene-Quaternary glacial cycles may have contributed to further speciation and reticulate evolution withinCypripedium.ConclusionsOur study provided novel insights into the evolutionary history ofCypripediumbased on high-throughput molecular data, shedding light on the dynamics of its distribution and diversity patterns from its origin to the present.