Mulvey Laura P A, May Michael R, Brown Jeremy M, Höhna Sebastian, Wright April M, Warnock Rachel C M
GeoZentrum Nordbayern, Department of Geography and Geosciences, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Loewenichstraße 28, 91054 Erlangen, Germany.
Department of Evolution and Ecology, University of California Davis, Davis, 2320 Storer Hall, One Shields Avenue Davis, CA 95616, USA.
Syst Biol. 2025 Feb 10;74(1):34-52. doi: 10.1093/sysbio/syae055.
Reconstructing the evolutionary history of different groups of organisms provides insight into how life originated and diversified on Earth. Phylogenetic trees are commonly used to estimate this evolutionary history. Within Bayesian phylogenetics a major step in estimating a tree is in choosing an appropriate model of character evolution. While the most common character data used is molecular sequence data, morphological data remains a vital source of information. The use of morphological characters allows for the incorporation fossil taxa, and despite advances in molecular sequencing, continues to play a significant role in neontology. Moreover, it is the main data source that allows us to unite extinct and extant taxa directly under the same generating process. We therefore require suitable models of morphological character evolution, the most common being the Mk Lewis model. While it is frequently used in both palaeobiology and neontology, it is not known whether the simple Mk substitution model, or any extensions to it, provide a sufficiently good description of the process of morphological evolution. In this study we investigate the impact of different morphological models on empirical tetrapod datasets. Specifically, we compare unpartitioned Mk models with those where characters are partitioned by the number of observed states, both with and without allowing for rate variation across sites and accounting for ascertainment bias. We show that the choice of substitution model has an impact on both topology and branch lengths, highlighting the importance of model choice. Through simulations, we validate the use of the model adequacy approach, posterior predictive simulations, for choosing an appropriate model. Additionally, we compare the performance of model adequacy with Bayesian model selection. We demonstrate how model selection approaches based on marginal likelihoods are not appropriate for choosing between models with partition schemes that vary in character state space (i.e., that vary in Q-matrix state size). Using posterior predictive simulations, we found that current variations of the Mk model are often performing adequately in capturing the evolutionary dynamics that generated our data. We do not find any preference for a particular model extension across multiple datasets, indicating that there is no "one size fits all" when it comes to morphological data and that careful consideration should be given to choosing models of discrete character evolution. By using suitable models of character evolution, we can increase our confidence in our phylogenetic estimates, which should in turn allow us to gain more accurate insights into the evolutionary history of both extinct and extant taxa.
重建不同生物群体的进化历史有助于深入了解地球上生命的起源和多样性。系统发育树通常用于估计这种进化历史。在贝叶斯系统发育学中，估计一棵树的一个主要步骤是选择合适的性状进化模型。虽然最常用的性状数据是分子序列数据，但形态学数据仍然是重要的信息来源。形态学性状的使用允许纳入化石分类群，并且尽管分子测序技术有所进步，但在现代生物学中仍继续发挥重要作用。此外，它是使我们能够在同一生成过程下直接将已灭绝和现存分类群统一起来的主要数据源。因此，我们需要合适的形态学性状进化模型，最常见的是Mk刘易斯模型。虽然它在古生物学和现代生物学中都经常使用，但尚不清楚简单的Mk替代模型或其任何扩展是否能对形态进化过程提供足够好的描述。在本研究中，我们调查了不同形态学模型对经验性四足动物数据集的影响。具体而言，我们将未划分的Mk模型与按观察到的状态数量划分性状的模型进行比较，同时考虑了位点间的速率变化和考虑抽样偏差的情况。我们表明，替代模型的选择对拓扑结构和分支长度都有影响，突出了模型选择的重要性。通过模拟，我们验证了使用模型充分性方法（后验预测模拟）来选择合适模型的有效性。此外，我们比较了模型充分性与贝叶斯模型选择的性能。我们证明了基于边际似然的模型选择方法不适用于在具有不同性状状态空间划分方案（即Q矩阵状态大小不同）的模型之间进行选择。使用后验预测模拟，我们发现当前Mk模型的变体在捕捉生成我们数据的进化动态方面通常表现良好。我们在多个数据集中未发现对特定模型扩展的偏好，这表明在形态学数据方面不存在“一刀切”的情况，在选择离散性状进化模型时应仔细考虑。通过使用合适的性状进化模型，我们可以增加对系统发育估计的信心，这反过来应该使我们能够更准确地洞察已灭绝和现存分类群的进化历史。
