Data from: Orchid phylogenomics and multiple drivers of their extraordinary diversification

Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras), and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp−1 My−1) is 6.8 times that at the Asparagales crown.

兰科是被子植物（angiosperms）中物种多样性最高的科，现存物种超过25000种，数量超过哺乳类、鸟类与爬行类的总和。此前，由于缺乏完全解析的广域系统发育树（fully resolved broad-scale phylogeny），针对兰科物种多样性成因的相关假说检验一直难以推进。本研究基于覆盖兰科所有亚科、17个族中16个族的39个物种的75个叶绿体基因（chloroplast genes），结合17个被子植物化石进行时间校准，构建了这一广域系统发育树。本研究还通过基于3个质体基因（plastid genes）的超级矩阵分析（supermatrix analysis），将额外的144个物种纳入该系统发育框架。分析显示，兰科的起源时间约为1.12亿年前（百万年前，Mya）；兰亚科（Orchidoideae）与树兰亚科（Epidendroideae）在白垩纪末期发生分化；而高位树兰类群的8个族以及3个此前未确定分类地位的亚族，在3790万至3080万年前经历了快速分化。兰科类群中，兰亚科类群曾经历一次显著的物种净分化速率（net species diversification）提升，而高位树兰类群则经历了两次速率提升与一次速率下降。与理论预测一致，这些物种分化速率的提升与花粉块（pollinia）的演化、附生习性（epiphytic habit）、景天酸代谢光合作用（CAM photosynthesis）、热带分布格局（尤其在广袤的科迪勒拉山系（cordilleras）中），以及通过鳞翅目（Lepidoptera）或兰蜂（euglossine bees）进行的传粉密切相关。欺骗性传粉（deceit pollination）似乎使兰科物种数量增加了50%，但并未通过提升物种净分化速率实现这一效果。兰科内最高的物种净分化速率为0.382 物种·物种⁻¹·百万年⁻¹，是天门冬目（Asparagales）冠群节点处分化速率的6.8倍。