The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored. Here, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group. We provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.

中文翻译：

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蝶齿动物系统发育和模型选择对贝叶斯形态时钟估计分歧时间和进化速率的影响


地球上曾经存在的绝大多数生命现在已经灭绝，它们进化史的几个方面只能通过使用化石记录中的形态数据来评估。蝶齿象爬行动物是一个典型的例子，其进化历史至少有 2.3 亿年，但目前以单一现存物种（Sphenodon punctatus）为代表。因此，必须改进概率模型的开发和实施，以根据形态数据（例如形态时钟）估计进化树，这对于理解化石和现存物种的关系和进化模式有直接的好处。然而，模型选择对纯形态数据集的影响却鲜有探讨。在这里，我们使用蝶齿类爬行动物的新数据矩阵来研究各种模型选择对进化树和宏观进化参数（分歧时间和进化速率）推断的影响。具体来说，我们测试了不同的时钟模型、时钟分区、分类单元采样策略、祖先采样以及化石生死（FBD）树模型参数随时间的变化。我们发现，当应用广泛使用的方法时，例如允许树中的祖先以及多样化参数随时间恒定的不适当假设，会对分歧时间和背景进化率产生强烈影响。我们将这些结果与之前关于模型选择对分子数据分析影响的研究进行比较，并为改进形态时钟的实施提供建议。 最佳模型组合发现蝶齿目大多数主要谱系的辐射处于三叠纪，并且在该群体的整个历史中，不同表型区域的形态进化速率逐渐但持续下降。我们提供了蝶齿类分类的新假设，以及该群体进化史上详细的宏观进化模式。重要的是，我们提供了建议，以避免使用形态时钟高估发散时间和有偏差的参数估计。划分宽松时钟提供了方法学上的局限性，但这些至少可以部分规避，以揭示对表型进化速率的详细评估和进化嵌合体的测试。