Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL, 60637, USA.
Sci Rep. 2023 Jun 7;13(1):9273. doi: 10.1038/s41598-023-35784-3.
The interrelationships of the three major dinosaur clades (Theropoda, Sauropodomorpha, and Ornithischia) have come under increased scrutiny following the recovery of conflicting phylogenies by a large new character matrix and its extensively modified revision. Here, we use tools derived from recent phylogenomic studies to investigate the strength and causes of this conflict. Using maximum likelihood as an overarching framework, we examine the global support for alternative hypotheses as well as the distribution of phylogenetic signal among individual characters in both the original and rescored dataset. We find the three possible ways of resolving the relationships among the main dinosaur lineages (Saurischia, Ornithischiformes, and Ornithoscelida) to be statistically indistinguishable and supported by nearly equal numbers of characters in both matrices. While the changes made to the revised matrix increased the mean phylogenetic signal of individual characters, this amplified rather than reduced their conflict, resulting in greater sensitivity to character removal or coding changes and little overall improvement in the ability to discriminate between alternative topologies. We conclude that early dinosaur relationships are unlikely to be resolved without fundamental changes to both the quality of available datasets and the techniques used to analyze them.
在一个大型新特征矩阵及其广泛修改的修订版恢复了相互矛盾的系统发育后，三大大恐龙类群（兽脚亚目、蜥脚形亚目和鸟臀目）之间的相互关系受到了更多的关注。在这里，我们使用来自最近系统基因组学研究的工具来研究这种冲突的强度和原因。使用最大似然法作为总体框架，我们检查了替代假设的全局支持以及原始和重新评分数据集中文本特征的分布。我们发现，在这两个矩阵中，有三种可能的方法可以解决主要恐龙谱系（蜥脚形亚目、鸟臀目和鸟脚亚目）之间的关系，它们在统计学上是不可区分的，并且得到了几乎相同数量的特征的支持。虽然对修订矩阵所做的更改增加了单个特征的平均系统发育信号，但这并没有减少而是增加了它们之间的冲突，导致对特征去除或编码变化的敏感性增加，并且对替代拓扑结构的区分能力总体上几乎没有提高。我们的结论是，如果不对现有数据集的质量和用于分析它们的技术进行根本性改变，早期恐龙的关系不太可能得到解决。
