Data from: Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata)

Knowledge of phylogenetic relationships among species is fundamental to understanding basic patterns in evolution and underpins nearly all research programs in biology and paleontology. However, most methods of phylogenetic inference typically used by paleontologists do not accommodate the idiosyncrasies of fossil data and therefore do not take full advantage of the information provided by the fossil record. The advent of Bayesian “tip-dating” approaches to phylogeny estimation is especially promising for paleo-systematists because time-stamped comparative data can be combined with probabilistic models tailored to accommodate the study of fossil taxa. Under a Bayesian framework, the recently developed fossilized birth‒death process (FBD) provides a more realistic tree prior model for paleontological data that accounts for macroevolutionary dynamics, preservation, and sampling when inferring phylogenetic trees containing fossils. In addition, FBD tree prior also allows for the possibility of sampling ancestral morphotaxa. Although paleontologists are increasingly embracing probabilistic phylogenetic methods, these recent developments have not previously been applied to the deep-time invertebrate fossil record. Here, I examine phylogenetic relationships among Ordovician through Devonian crinoids using a Bayesian tip-dating approach. Results support several clades recognized in previous analyses sampling only Ordovician taxa, but also reveal instances where phylogenetic affinities are more complex and extensive revisions are necessary, particularly among the Cladida. The name Porocrinoidea is proposed for a well-supported clade of Ordovician ‘cyathocrine’ cladids and hybocrinids. The Eucladida is proposed as a clade name for the sister group of the Flexibilia herein comprised of cladids variously considered ‘cyathocrines’, ‘dendrocrines’, and/or ‘poteriocrines’ by other authors.物种间系统发育关系（phylogenetic relationships）的认知，是理解演化基本模式的核心基础，同时支撑着生物学与古生物学领域几乎所有的研究计划。然而，古生物学家常用的多数系统发育推断方法无法适配化石数据的固有特性，因此未能充分挖掘化石记录所承载的信息。用于系统发育推断的贝叶斯末端定年（tip-dating）方法的出现，对古系统分类学家而言极具应用前景，因为带时间戳的比较数据可与专为化石分类群研究定制的概率模型相结合。在贝叶斯框架下，新近提出的化石出生-死亡过程（fossilized birth‒death process, FBD）为包含化石的系统发育树推断提供了更贴合实际的树先验模型，该模型可在推断过程中纳入宏观演化动态、化石保存与采样情况。此外，FBD树先验还支持对祖先形态分类群的采样。尽管古生物学家愈发倾向于使用概率性系统发育方法，但这类新近进展尚未被应用于深时无脊椎动物化石记录的研究中。本研究采用贝叶斯末端定年法，探究奥陶纪至泥盆纪时期海百合类的系统发育关系。研究结果支持了此前仅基于奥陶纪分类群的分析所识别的多个演化支，同时也揭示了部分类群的系统发育亲缘关系更为复杂，亟需进行大范围修订，尤其是枝海百合类（Cladida）内部。本研究为一个得到充分支持的奥陶纪‘杯海百合类’枝海百合与异海百合演化支，提出了孔海百合超科（Porocrinoidea）这一名称。此外，本研究还为柔海百合亚纲（Flexibilia）的姊妹群——一类被其他学者分别归类为‘杯海百合类’‘树海百合类’和/或‘炮海百合类’的枝海百合类，提出了真枝海百合类（Eucladida）这一演化支名称。