Reticulate evolution and sea-level fluctuations together drove species diversification of slipper orchids (Paphiopedilum) in Southeast Asia

South-East Asia covers four of the world's biodiversity hotspots, showing high species diversity and endemism. Owing to the successive expansion and contraction of distribution and the fragmentation by geographical barriers, the tropical flora greatly diversified in this region during the Tertiary, but the evolutionary tempo and mode of species diversity remain poorly investigated. Paphiopedilum, the largest genus of slipper orchids comprising nearly 100 species, is mainly distributed in South-East Asia, providing an ideal system for exploring how plant species diversity was shaped in this region. Here, we investigated the evolutionary history of this genus with eight cpDNA regions and four low-copy nuclear genes. Discordance between gene trees and network analysis indicates that reticulate evolution occurred in the genus. Ancestral area reconstruction suggests that vicariance and long-distance dispersal together led to its current distribution. Diversification rate variation was detected and strongly correlated with the species diversity in subg. Paphiopedilum (~80 species). The shift of speciation rate in subg. Paphiopedilum was coincident with sea-level fluctuations in the late Cenozoic, which could have provided ecological opportunities for speciation and created bridges or barriers for gene flow. Moreover, some other factors (e.g. sympatric distribution, incomplete reproductive barriers and clonal propagation) might also be advantageous for the formation and reproduction of hybrid species. In conclusion, our study suggests that the interplay of reticulate evolution and sea-level fluctuations has promoted the diversification of the genus Paphiopedilum and sheds light into the evolution of Orchidaceae and the historical processes of plant species diversification in South-East Asia.

东南亚涵盖全球4处生物多样性热点（biodiversity hotspots）区域，物种多样性与特有现象均极为显著。受分布区持续扩张收缩及地理屏障引发的片段化效应影响，该区域的热带植物区系在第三纪期间发生了显著分化，但学界目前对其物种多样性的进化速率与模式仍缺乏深入研究。兜兰属（Paphiopedilum）是杓兰亚科最大的属，包含近100个物种，主要分布于东南亚地区，是探究该区域植物物种多样性形成机制的理想研究体系。本研究利用8个叶绿体DNA（cpDNA）区域与4个低拷贝核基因，解析了该属的进化历史。基因树拓扑结构不一致性与网络分析结果均证实，兜兰属存在网状进化现象。祖先区域重建结果显示，地理分异与长距离扩散共同塑造了该属当前的分布格局。研究检测到多样化速率存在异质性，且该异质性与兜兰亚属（subg. Paphiopedilum，约含80个物种）的物种多样性显著相关。兜兰亚属的物种形成速率转变节点，与晚新生代的海平面波动事件高度契合——此类波动既可提供物种形成所需的生态机遇，也可为基因交流搭建通路或构建障碍。此外，同域分布、生殖隔离不完全以及无性繁殖等其他因素，亦可能助力杂交物种的形成与繁衍。综上，本研究表明网状进化与海平面波动的协同作用推动了兜兰属的物种多样化进程，该发现为兰科（Orchidaceae）植物的进化研究，以及东南亚区域植物物种多样化的历史进程提供了重要参考。