Caetano Daniel S, Quental Tiago B
Department of Biological Sciences, Towson University, 8000 York Road, Towson, MD 21252, USA.
Department of Ecology, University of São Paulo, Rua do Matão, 321 - Trav. 14, São Paulo, SP, 05508-090, Brazil.
Syst Biol. 2023 Dec 30;72(6):1443-1453. doi: 10.1093/sysbio/syad050.
The acknowledgment of evolutionary dependence among species has fundamentally changed how we ask biological questions. Phylogenetic models became the standard approach for studies with 3 or more lineages, in particular those using extant species. Most phylogenetic comparative methods (PCMs) translate relatedness into covariance, meaning that evolutionary changes before lineages split should be interpreted together whereas after the split lineages are expected to change independently. This clever realization has shaped decades of research. Here, we discuss one element of the comparative method often ignored or assumed as unimportant: if nodes of a phylogeny represent the dissolution of the ancestral lineage into two new ones or if the ancestral lineage can survive speciation events (i.e., budding). Budding speciation is often reported in paleontological studies, due to the nature of the evidence for budding in the fossil record, but it is surprisingly absent in comparative methods. Here, we show that many PCMs assume that divergence happens as a symmetric split, even if these methods do not explicitly mention this assumption. We discuss the properties of trait evolution models for continuous and discrete traits and their adequacy under a scenario of budding speciation. We discuss the effects of budding speciation under a series of plausible evolutionary scenarios and show when and how these can influence our estimates. We also propose that long-lived lineages that have survived through a series of budding speciation events and given birth to multiple new lineages can produce evolutionary patterns that challenge our intuition about the most parsimonious history of trait changes in a clade. We hope our discussion can help bridge comparative approaches in paleontology and neontology as well as foster awareness about the assumptions we make when we use phylogenetic trees.
对物种间进化依赖性的认识从根本上改变了我们提出生物学问题的方式。系统发育模型成为研究三个或更多谱系（特别是那些使用现存物种的研究）的标准方法。大多数系统发育比较方法（PCMs）将亲缘关系转化为协方差，这意味着谱系分裂前的进化变化应一起解释，而分裂后谱系预计会独立变化。这一巧妙的认识塑造了数十年的研究。在这里，我们讨论比较方法中一个经常被忽视或认为不重要的元素：系统发育树的节点是代表祖先谱系分裂成两个新谱系，还是祖先谱系能够在物种形成事件中存活下来（即出芽）。由于化石记录中出芽证据的性质，出芽物种形成在古生物学研究中经常被报道，但在比较方法中却令人惊讶地缺失。在这里，我们表明许多PCMs假设分歧是以对称分裂的方式发生的，即使这些方法没有明确提及这一假设。我们讨论了连续和离散性状的性状进化模型的性质及其在出芽物种形成情况下的适用性。我们讨论了在一系列合理的进化情景下出芽物种形成的影响，并展示了这些影响何时以及如何影响我们的估计。我们还提出，通过一系列出芽物种形成事件存活下来并产生多个新谱系的长寿谱系可以产生挑战我们对一个分支中最简约性状变化历史直觉的进化模式。我们希望我们的讨论能够帮助弥合古生物学和现代生物学中的比较方法，以及提高我们在使用系统发育树时对所做假设的认识。
