Data from: Bayesian morphological clock methods resurrect placoderm monophyly and reveal rapid early evolution in jawed vertebrates

The phylogeny of early gnathostomes provides an important framework for
understanding one of the most significant evolutionary events, the origin
and diversification of jawed vertebrates. A series of recent cladistic
analyses have suggested that the placoderms, an extinct group of armoured
fish, form a paraphyletic group basal to all other jawed vertebrates. We
revised and expanded this morphological data set, most notably by sampling
autapomorphies in a similar way to parsimony-informative traits, thus
ensuring this data (unlike most existing morphological data sets)
satisfied an important assumption of Bayesian tip-dated morphological
clock approaches. We also found problems with characters supporting
placoderm paraphyly, including character correlation and incorrect
codings. Analysis of this data set reveals that paraphyly and monophyly of
core placoderms (excluding maxillate forms) are essentially equally
parsimonious. The two alternative topologies have different root positions
for the jawed vertebrates but are otherwise similar. However, analysis
using tip-dated clock methods reveals strong support for placoderm
monophyly, due to this analysis favoring trees with more balanced rates of
evolution. Furthermore, enforcing placoderm paraphyly results in higher
levels and unusual patterns of rate heterogeneity among branches, similar
to that generated from simulated trees reconstructed with incorrect root
positions. These simulations also show that Bayesian tip-dated clock
methods outperform parsimony when the outgroup is largely uninformative
(e.g., due to inapplicable characters), as might be the case here. The
analysis also reveals that gnathostomes underwent a rapid burst of
evolution during the Silurian period which declined during the Early
Devonian. This rapid evolution during a period with few articulated
fossils might partly explain the difficulty in ascertaining the root
position of jawed vertebrates.

早期有颌脊椎动物的系统发育关系，为理解脊椎动物演化史上最重大的事件之一——有颌类的起源与辐射分化——提供了重要的研究框架。一系列近期的支系分类学分析表明，盾皮鱼类（placoderms）——一类已灭绝的带甲鱼类——构成了所有其他有颌脊椎动物的基干并系群。本研究对该形态学数据集进行了修订与扩充，最关键的改进在于以与简约信息性状一致的方式纳入了自衍征（autapomorphies），从而使得本数据集（不同于多数现有形态学数据集）满足了贝叶斯末端定年形态钟方法的一项重要前提假设。同时，本研究发现支撑盾皮鱼类并系群假说的性状存在若干问题，包括性状相关性与编码错误。对本数据集的分析显示，核心盾皮鱼类（排除具上颌骨类群）的并系群与单系群假说，在简约性分值上基本相当。这两种备选系统发育拓扑结构仅在有颌脊椎动物的根位置上存在差异，其余部分基本一致。但采用末端定年钟模型进行分析时，则得到了支持盾皮鱼类单系群的强证据，这是因为该分析更倾向于演化速率更为均衡的系统发育树。此外，强制限定盾皮鱼类为并系群时，分支间的演化速率异质性水平更高且模式异常，这与采用错误根位置重建的模拟树所产生的异质性模式相似。这些模拟实验还表明，当外类群整体信息不足时（例如因存在大量不适用性状），贝叶斯末端定年形态钟方法的表现优于简约法，而本研究的情况正符合这一点。本分析还揭示，有颌脊椎动物在志留纪期间经历了快速的演化爆发，这一爆发在早泥盆世逐渐减弱。在关联化石稀缺的志留纪发生的快速演化，或许可以部分解释为何确定有颌脊椎动物的系统发育根位置极具挑战性。