Data from: Using more than the oldest fossils: dating Osmundaceae with three Bayesian clock approaches

A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved –‘node dating’ (ND) in BEAST, ‘total evidence’ (TE) dating in MrBayes, and the ‘fossilized birth-death’ (FBD) in FDPPDiv – to infer divergence times in the royal ferns. Osmundaceae have 16–17 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ~17 genera. For ND, we used the five oldest fossils, whereas for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizomes and frond compression/impression fossils, which for TE dating were scored for 33 morphological characters. We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence ages were generally greater than those inferred from ND; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We prefer the FBD-derived ages because they best fit the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Paleozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, the FBD approach yielded speciation and extinction rates that overlapped those obtained from just neontological data. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling; therefore, these estimates should be treated with caution.分子钟定年（molecular clock dating）领域的核心关切之一，是如何利用化石记录信息对DNA序列（DNA sequences）推导得到的遗传距离（genetic distances）进行校准。本研究针对紫萁蕨类（royal ferns）的分化时间展开推断，采用了三种校准机制各异的贝叶斯定年方法（Bayesian dating methods）：BEAST中的节点定年（node dating, ND）、MrBayes中的总证据定年（total evidence dating, TE），以及FDPPDiv中的化石出生死亡模型（fossilized birth-death, FBD）。 紫萁科（Osmundaceae）现存4个属，共计16至17个物种，其中2个属主要分布于北半球，另外2个属见于南非及澳大拉西亚地区；该类群是其余薄囊蕨类（leptosporangiate ferns）的姊妹群。其化石记录涵盖约17个属的至少150个物种。 针对节点定年（ND），本研究仅使用了5个最古老的化石；而总证据定年（TE）与化石出生死亡模型（FBD）无需将化石强制锚定至特定系统发育节点，因此可纳入更多化石样本：共纳入多达36个根状茎（rhizomes）与叶压型/印痕化石（frond compression/impression fossils），其中针对总证据定年（TE）还为这些化石编码了33个形态学性状（morphological characters）。此外，我们对36个化石分别进行10%、25%、50%的抽样，以评估模型的敏感性。 研究结果显示：通过化石出生死亡模型（FBD）得到的分化年龄整体大于节点定年（ND）的推断结果；7个总证据定年（TE）推导的年龄中有2个与FBD结果一致，其余则与ND或FBD的年龄相差悬殊，或偏年轻或偏古老。我们更倾向于FBD方法得到的年龄，因其与紫萁目（Osmundales）的化石记录契合度最高（包括本研究未使用的三叠纪化石）。在最优模型下，涵盖现存紫萁科类群（及诸多化石类群）的分支起源于晚古生代至早三叠世；现存物种的分化则发生于新近纪。 在物种形成与灭绝速率恒定的假设下，FBD方法得到的物种形成与灭绝速率与仅基于现生生物数据（neontological data）得到的结果重合。然而，FBD对物种形成与灭绝速率的估计对“化石采样连续进行”这一假设的违背较为敏感，因此对该类估计需谨慎对待。