PDF(Sci-hub)
Abstract：
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.
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.
摘要：
地球上曾经存在的所有生命中的绝大多数现在已经灭绝，它们的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。蛇纹虫爬行动物是一个典型的例子，至少有2.3亿年的进化史，但目前由一个单一的生物物种（斑节）代表。因此，必须改进概率模型的开发和实现，以从形态数据估计进化树(例如，形态时钟)，这对理解化石和生物物种的关系和进化模式有直接的好处。然而,模型选择对仅形态学数据集的影响研究甚少。
这里,我们使用新的数据矩阵研究了一系列模型选择对进化树和宏观进化参数（发散时间和进化率）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,分类单元抽样策略，为祖先取样，以及化石生死（FBD）树模型参数随时间的变化。当应用广泛使用的方法时，我们发现对发散时间和背景进化率有很大的影响，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。我们将这些结果与先前关于模型选择对分子数据分析的影响的研究进行了比较，并为改进形态时钟的实施提供了建议。最佳模型组合发现，在三叠纪中，蝶骨的大多数主要谱系的辐射都在三叠纪，并且在整个群体的历史中，表型的不同区域的形态进化速率逐渐但持续下降。
我们提供了一种新的蝶齿分类假设，以及该群体进化史中详细的宏观进化模式。重要的是,我们提供建议，以避免使用形态时钟高估的发散时间和有偏差的参数估计。划分宽松的时钟提供了方法上的限制，但是，这些至少可以部分规避，以揭示整个表型和进化镶嵌测试的进化率的详细评估。
这里,我们使用新的数据矩阵研究了一系列模型选择对进化树和宏观进化参数（发散时间和进化率）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,分类单元抽样策略，为祖先取样，以及化石生死（FBD）树模型参数随时间的变化。当应用广泛使用的方法时，我们发现对发散时间和背景进化率有很大的影响，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。我们将这些结果与先前关于模型选择对分子数据分析的影响的研究进行了比较，并为改进形态时钟的实施提供了建议。最佳模型组合发现，在三叠纪中，蝶骨的大多数主要谱系的辐射都在三叠纪，并且在整个群体的历史中，表型的不同区域的形态进化速率逐渐但持续下降。
我们提供了一种新的蝶齿分类假设，以及该群体进化史中详细的宏观进化模式。重要的是,我们提供建议，以避免使用形态时钟高估的发散时间和有偏差的参数估计。划分宽松的时钟提供了方法上的限制，但是，这些至少可以部分规避，以揭示整个表型和进化镶嵌测试的进化率的详细评估。
