Data from: Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content

A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4 Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.

针对具有商业价值的咖啡属（Coffea）构建全面且严谨的系统发育假说，长期以来都是咖啡研究领域的核心目标。分子相关研究的进展曾受限于较低的序列分歧水平，导致系统发育树的拓扑分辨率与统计支持度不足，这一问题在主要演化支以及马达加斯加分布的众多物种中尤为突出。本研究首次报道了咖啡属近乎完全解析、采样范围覆盖广泛的系统发育假说，该成果通过将测序分型（genotyping-by-sequencing, GBS）技术与全新开发的实验室流程相结合，实现了对少量额外样本的短读长下一代测序整合。生物地理模式分析表明，咖啡属起源的最可能祖先分布地为非洲、亚洲（或阿拉伯半岛），且该属在非洲、亚洲以及西印度洋群岛（包括马达加斯加与毛里求斯）均发生了独立辐射演化。结合本研究构建的系统发育框架，我们对咖啡因——这一对商业与社会均具有重要意义的性状——的演化历程开展了评估。仅在西非与中非赤道完全湿润环境的物种中，检测到了高且稳定的咖啡因含量，这可能是对更高害虫捕食压力的适应性响应。而中等水平的咖啡因合成能力，则在马达加斯加的一个演化支中至少独立演化过一次（距今200万至400万年前）。这一结果提示，要么咖啡属在早期演化历史中已具备咖啡因生物合成途径，要么该属内的咖啡因合成存在趋同演化——这一现象也与咖啡、茶与巧克力中的咖啡因合成趋同演化情况一致。