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 paleosystematists 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 (FBD) process 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, the FBD tree prior 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，是理解进化基本模式的核心基础，同时也是生物学与古生物学（paleontology）领域几乎所有研究计划的重要支撑。然而，古生物学家常用的多数系统发育推断（phylogenetic inference）方法无法适配化石数据的特有属性，因此未能充分挖掘化石记录所蕴含的全部信息。
贝叶斯末端定年（Bayesian tip-dating）系统发育估计方法的出现，对古生物分类学家（paleosystematists）而言极具应用前景：带时间戳的比较数据可与专为化石类群（fossil taxa）研究设计的概率模型（probabilistic models）相结合。
在贝叶斯框架（Bayesian framework）下，近年提出的化石出生-死亡（fossilized birth–death, FBD）过程，为包含化石的系统发育树推断提供了更贴合古生物数据的树先验模型（tree prior model），该模型可在系统发育树推断过程中纳入宏观进化动态（macroevolutionary dynamics）、化石保存与采样过程。此外，FBD树先验还支持对祖先形态类群（ancestral morphotaxa）进行采样。
尽管古生物学家对概率系统发育方法的接纳度与日俱增，但这类新近发展的方法尚未被应用于深时无脊椎动物化石记录（deep-time invertebrate fossil record）的相关研究。
本研究采用贝叶斯末端定年方法，对奥陶纪至泥盆纪海百合（crinoids）的系统发育关系展开分析。
分析结果既支持了此前仅基于奥陶纪类群（Ordovician taxa）的多项演化支（clades）结论，同时也揭示出部分类群的系统发育亲缘关系更为复杂，亟需进行大规模修订，尤其是枝海百合目（Cladida）类群。
我们为一支得到强力支持的奥陶纪‘杯心海百合类’枝海百合与合海百合类群，提出拟孔海百合超科（Porocrinoidea）这一新的演化支名称。
此外，我们将柔海百合亚纲（Flexibilia）的姊妹群命名为真枝海百合目（Eucladida），该演化支包含了被其他学者分别归类为‘杯心海百合类’‘树状海百合类’以及‘茎杯海百合类’的各类枝海百合。