Diversification of the orchid genus Tridactyle: origin of endemism on the oceanic islands of São Tomé & Príncipe in the Gulf of Guinea

Aim: Oceanic islands have played an important role in our understanding of the diversification of organisms, and phylogenetic estimates have been used in this context to investigate the origin of island diversity and its relationship to the continent. Using a typical orchid genus rich in island endemics and with widespread continental relatives, we aim to compare alternative hypotheses of diversification with a focus on island endemism. Location: Tropical Africa and the Gulf of Guinea Islands of São Tomé & Príncipe, Central Africa. Taxon: Tridactyle genus (Orchidaceae). Methods: We used genome skimming to sequence the whole chloroplast genome and nuclear ribosomal genes from 157 individuals of 34 Tridactyle species and 15 individuals of 12 other orchid genera (outgroups) to infer a time-calibrated phylogenetic tree of the genus Tridactyle. We also used multiple statistical methods to infer the geographic ranges of the ancestral nodes from the estimated phylogeny. Alternative hypotheses for the origins of endemism on the islands of São Tomé and Príncipe were investigated based on the biogeographic reconstruction of the genus. Results: The estimated phylogeny of Tridactyle and reconstruction of geographic ranges for the ancestral nodes suggested a general history of allopatric speciation for the genus, in particular via colonisation of the islands of the Gulf of Guinea that induced a long period of geographic isolation. The most parsimonious hypothesis to explain island endemism in Tridactyle involved 6 independent colonisations of the islands from the continent. Main conclusions: In contrast to other cases of oceanic island endemism that involved adaptive radiation on an island or within an archipelago, endemism in Tridactyle is better explained by multiple colonisation events from the continent to São Tomé and Príncipe, with subsequent divergences due to geographic isolation but only one potential instance of further diversification on the islands.

研究目的：海洋岛屿对于我们理解生物类群的分化进程具有重要意义，系统发育估计方法在此研究框架中被用于探究岛屿生物多样性的起源及其与大陆的关联。本研究选取一个兼具丰富岛屿特有性（island endemism）类群与广泛大陆分布近缘类群的典型兰科属类群，旨在以岛屿特有性为核心，对比验证不同的分化假说。
研究区域：非洲热带地区以及中非几内亚湾的圣多美和普林西比群岛。
研究类群：三指兰属（Tridactyle），隶属于兰科（Orchidaceae）。
研究方法：采用基因组浅层测序（genome skimming）技术，对34个三指兰物种的157个个体以及12个其他兰属类群（外类群（outgroups））的15个个体进行全叶绿体基因组（chloroplast genome）与核核糖体基因（nuclear ribosomal genes）测序，以此构建三指兰属的时间校准系统发育树（time-calibrated phylogenetic tree）。同时，基于所构建的系统发育树，运用多种统计方法推断祖先节点的地理分布范围，并基于该属的生物地理重建（biogeographic reconstruction）结果，探究圣多美和普林西比群岛特有性起源的多种假说。
研究结果：三指兰属的系统发育估计结果与祖先节点地理范围重建结果表明，该属的演化整体遵循异域成种（allopatric speciation）模式，尤其是通过对几内亚湾群岛的殖民事件形成了长期的地理隔离。解释三指兰属岛屿特有性的最简约假说为：共有6次独立的大陆向群岛的殖民事件。
主要结论：与其他在单岛或群岛内发生适应性辐射（adaptive radiation）的海洋岛屿特有性案例不同，三指兰属的岛屿特有性更适宜用多次大陆向圣多美和普林西比群岛的殖民事件来解释：后续的分化由地理隔离驱动，但群岛内仅存在1次潜在的进一步类群分化事件。