Data from: Towards a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa (SUPERSMART)

Rapidly growing biological data –including molecular sequences and fossils– hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyse these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive datasets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable.

飞速增长的生物学数据——包括分子序列与化石在内——拥有前所未有的潜力，用以揭示演化过程如何产生并维持生物多样性。然而，研究者往往需要开发个性化定制的工作流，以整合并分析此类数据，进而重建经时间校准的系统发育树。此外，基于不同方法、假设以及质量与可靠性各异的数据所估算的分歧时间，若未经过恰当校正，不应直接合并使用。我们在此介绍一款模块化框架，命名为SUPERSMART（Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa，即物种形成与迁移速率、年代及类群关系估算自更新平台），并针对演化与生物地理学研究中的动态研究对象提供了概念验证。该框架可针对任意类群整合分子与化石数据以构建综合数据集，并通过稳健的物种树方法推断带有年代信息的系统发育树，同时支持纳入下一代测序技术产出的基因组数据。我们以哺乳纲灵长目（Primates）与棕榈科（Arecaceae）的系统发育及年代分析为例，展示了本方法的应用。我们认为，该框架将为系统分类学、生物地理学及演化生物学领域诸多基于假说的研究问题提供极具价值的研究工具。SUPERSMART还将加速"Dated Tree of Life"（时间校准生命树）的构建，使所有节点年代均可直接进行比较。