Institut Des Sciences de L'Évolution de Montpellier (CNRS/UM/IRD/EPHE), Université de Montpellier, 34095, Montpellier, France.
Departamento de Paleobiología, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain.
BMC Biol. 2024 Nov 25;22(1):270. doi: 10.1186/s12915-024-02053-2.
Extinct organisms provide vital information about the time of origination and biogeography of extant groups. The development of phylogenetic methods to study evolutionary processes through time has revolutionized the field of evolutionary biology and led to an unprecedented expansion of our knowledge of the tree of life. Recent developments applying Bayesian approaches, using fossil taxa as tips to be included alongside their living relatives, have revitalized the use of morphological data in evolutionary tree inferences. Eumuroida rodents represent the largest group of mammals including more than a quarter of all extant mammals and have a rich fossil record spanning the last ~ 45 million years. Despite this wealth of data, our current understanding of the classification, major biogeographic patterns, and divergence times for this group comes from molecular phylogenies that use fossils only as a source of node calibrations. However, node calibrations impose several constraints on tree topology and must necessarily make a priori assumptions about the placement of fossil taxa without testing their placement in the tree.
We present the first morphological dataset with extensive fossil sampling for Muroidea. By applying Bayesian morphological clocks with tip dating and process-based biogeographic models, we provide a novel hypothesis for muroid relationships and revised divergence times for the clade that incorporates uncertainty in the placement of all fossil species. Even under strong violation of the clock model, we found strong congruence between results for divergence times, providing a robust timeline for muroid diversification. This new timeline was used for biogeographic analyses, which revealed a dynamic scenario mostly explained by dispersal events between and within the Palearctic and North African regions.
Our results provide important insights into the evolution of Muroidea rodents and clarify the evolutionary pathways of their main lineages. We exploited the advantage of tip dating Bayesian approaches in morphology-based datasets and provided a classification of the largest superfamily of mammals resulting from robust phylogenetic inference, inferring the biogeographical history, diversification, and divergence times of its major lineages.
灭绝生物为现存生物群体的起源和生物地理学时间提供了重要信息。通过将系统发育方法应用于进化过程的研究，推动了进化生物学领域的革命，并使我们对生命之树的认识得到了前所未有的扩展。最近，应用贝叶斯方法的发展，使用化石分类单元作为分支点，与它们的现存亲属一起纳入分析，使得形态学数据在进化树推断中的应用重新焕发生机。真鼠类啮齿动物是哺乳动物中最大的群体，包括超过四分之一的现存哺乳动物，其化石记录丰富，跨越了过去约 4500 万年。尽管有如此丰富的数据，但我们对该类群的分类、主要生物地理学模式和分化时间的理解仍然来自于使用化石仅作为节点校准来源的分子系统发育。然而，节点校准对树拓扑结构施加了若干限制，并且必须在不测试化石分类单元在树上的位置的情况下，对化石分类单元的位置做出先验假设。
我们提出了第一个具有广泛化石采样的真鼠类形态数据集。通过应用具有分支点日期的贝叶斯形态钟和基于过程的生物地理学模型，我们为真鼠类的关系提供了一个新的假说，并对包括所有化石种属位置不确定性的分支进行了修订的分化时间估计。即使在时钟模型强烈违反的情况下，我们仍然发现分化时间的结果之间存在很强的一致性，为真鼠类的多样化提供了一个稳健的时间线。这个新的时间线被用于生物地理学分析，结果表明了一个动态的情景，主要由古北界和北非地区之间和内部的扩散事件解释。
我们的结果为真鼠类啮齿动物的进化提供了重要的见解，并澄清了其主要谱系的进化途径。我们利用了基于形态的数据集分支点日期贝叶斯方法的优势，并提供了一个基于稳健的系统发育推断的哺乳动物最大超家族的分类，推断了其主要谱系的生物地理学历史、多样化和分化时间。
