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.

研究目标：海洋岛屿在我们认知生物类群分化历程中扮演了重要角色，在此研究框架下，系统发育估计（phylogenetic estimates）方法被用于探究岛屿物种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海岛特有类群且拥有广泛大陆近缘类群的典型兰科（Orchidaceae）属，旨在对比多种分化假说，重点聚焦海岛特有性。
研究区域：非洲热带区域以及中非几内亚湾的圣多美和普林西比群岛（São Tomé & Príncipe）。
研究类群：Tridactyle属（兰科）。
研究方法：本研究采用基因组浅层测序（genome skimming）技术，对34个Tridactyle物种的157份样本以及12个其他兰科属的15份外类群（outgroups）样本进行全叶绿体基因组与核核糖体基因测序，以此构建Tridactyle属的时间校准系统发育树。此外，本研究借助多种统计方法，基于已构建的系统发育树推断祖先节点的地理分布范围，并通过该属的生物地理重建（biogeographic reconstruction），探究圣多美和普林西比群岛特有类群起源的多种替代假说。
研究结果：Tridactyle属的系统发育推断结果与祖先节点地理分布范围重建结果表明，该属的分化整体遵循异域成种（allopatric speciation）模式，尤其表现为通过殖民几内亚湾群岛并由此形成长期地理隔离实现分化。解释该属海岛特有性的最简约假说显示，共有6次来自大陆的独立殖民事件促成了群岛上的特有类群形成。
主要结论：与其他海岛特有类群案例（多涉及单岛或群岛内的适应性辐射（adaptive radiation））不同，Tridactyle属的海岛特有性更适合用"大陆向圣多美和普林西比群岛发生多次殖民事件，后续因地理隔离产生分化，但群岛内仅存在1次潜在的进一步类群分化"这一模型来解释。