Recommended fossil calibrators for time-scaled molecular phylogenies of Afrotheria

A phylogenetic framework provides the necessary evolutionary context for studies of comparative anatomy, life history, behavior, biogeography, systematics, and conservation. Time-scaled phylogenetic analyses require researchers to include calibration ages which are used to fit a model that transforms tree branch lengths into units of time. The inclusion of multiple calibration ages (if they are available) is a best practice that brings all the available evidence to bear on the temporal model. While selecting the appropriate ages of calibrating fossil taxa is obviously important, perhaps more relevant is where those calibrations are applied in the tree. A misattributed fossil calibrator (e.g., using a stem-taxon to set a minimum age on a tipward crown-node) can severely distort the results. Our aim is to provide a summary of fossil calibrators that can be used in molecular phylogenetic assessments of Afrotheria. The literature that documents these fossils, and discusses their ages and affiliations, is somewhat scattered. Included in this contribution are the oldest extinct species that are (in our opinion) securely attributable to stem lineages of afrotherian clades. Each informs a minimum age for the adjacent rootward tree node. We then assemble a large DNA supermatrix that includes 32 genes and 39 afrotherian genera – including recently extinct elephants and sea-cows. A time-scaled phylogenetic estimate is derived from this dataset with explicit inclusion of fossil taxa in the analysis.

系统发育框架可为比较解剖学、生活史、行为学、生物地理学、分类学以及保护生物学研究提供必要的演化背景。时间标度的系统发育分析要求研究者纳入校准年代，这类年代用于拟合将树支长度转换为时间单位的演化模型。纳入多组可用校准年代是最佳实践，可将所有可获得的证据充分应用于时间演化模型的构建。尽管选取合适的化石类群校准年代至关重要，但更关键的或许是这些校准点在系统发育树上的放置位置。错误归属的化石校准节点（例如利用茎类群（stem-taxon）为向顶的冠群节点（crown-node）设定最小年代）会严重扭曲分析结果。本研究旨在汇总可用于非洲兽总目（Afrotheria）分子系统发育评估的化石校准节点。相关文献中虽记载了这些化石并讨论了其年代与分类归属，但分布较为零散。本研究纳入的是我们认为可明确归属于非洲兽总目各演化支茎系的最古老灭绝物种，每一类物种均可为其相邻的向根节点提供最小年代约束。随后我们构建了包含32个基因与39个非洲兽总目属类的大型DNA超级矩阵，其中涵盖了近期灭绝的象类与海牛类。本数据集通过在分析中明确纳入化石类群，可得到带时间标度的系统发育估算结果。