Overcoming the morphology problem of phylogenetics

系统发育树是重建进化历史和检验进化假说的基础。因此，它们解决了一些重大问题，比如，我们的现代生物群是如何以及何时形成的，以及生物多样性和灭绝的形态和分布是什么？在获取和分析基因序列数据的进步导致越来越重视和依赖分子系统发育，但表型证据（形态学）仍然至关重要。它使我们能够在生物体和它们的环境之间建立联系，从而展示进化变化的机制。这也是唯一的方法，包括灭绝的分类群，因此提供了一个深入的时间视角；化石打破了退化的现代动物群之间的巨大差距，解开了进化变化的序列（所谓的“缺失环节”），并为估计进化速率提供了一个时间尺度，包括分子钟的校准。虽然形态学被认为对系统发育至关重要，但它也被广泛认为是一个内在的问题。发育和功能的联系可能导致非独立形态特征的组合或模块，从而在系统发育重建方面产生误导模式。这些问题现象是公认存在的，但它们在很大程度上被忽视了；形态学数据通常被视为“表面价值”，并被分子和古生物学研究视为等同。此外，我们不知道这些现象的分布和影响。因此，我们对一系列进化事件的理解被削弱了，我们重建进化历史的能力也受到了限制。为了直接解决形态学的局限性，我们将：1)量化问题在生命之树和形态学模块中的范围和分布；2)以独立的分子和地层数据为基准，开发基于形态学的可靠系统发育推断的方法论工具包；3)将这些方法应用于依赖于形态学解释但迄今为止被证明难以解决或模棱两可的重要进化事件，例如人类起源。结果将解决特定的进化假设，并通过提供新的工作方式为未来的分析提供强大的工具、工作流程和指南。这个项目将把形态学从19世纪带到21世纪。

Phylogenetic trees underpin reconstructions of evolutionary history and tests of evolutionary hypotheses. As such, they address major questions, such as, how and when did our modern biota come into being, and what is the shape and distribution of biodiversity and extinction? Advances in the acquisition and analysis of genetic sequence data have led to an increasing emphasis and reliance on molecular phylogenies, yet phenotypic evidence (morphology) remains vital. It enables us to make the link between organisms and their environment and thus demonstrate the mechanisms of evolutionary change. It is also the only way to include extinct taxa, and therefore provide a deep time perspective; fossils break up large gaps between the depauperate modern fauna, unlock sequences of evolutionary change (so called 'missing links') and provide a timescale for estimating evolutionary rates, including calibration of molecular clocks. Although morphology is acknowledged to be essential for phylogeny, it is also widely recognized as intrinsically problematic. Developmental and functional linkage can result in suites or modules of non-independent morphological characters and thus misleading patterns with respect to phylogeny reconstruction. These problematic phenomena are acknowledged to exist, but they have been largely ignored; morphological data are routinely taken at 'face value' and are treated as equivalent by both molecular and palaeontological studies. Furthermore, we have no idea about the distribution or influence of these phenomena. As such, our understanding of a range of evolutionary events is undermined, and our ability to reconstruct evolutionary history is limited. To directly address the limitations of morphology we will: 1) Quantify the extent and distribution of the problem across the tree of life and across morphological modules; 2) develop methodological toolkits for reliable phylogenetic inference using morphology, with independent molecular and stratigraphic data acting as benchmarks; 3) apply those methods to important evolutionary events that rely on interpretations of morphology but have thus far proved intractable or equivocal, for example, human origins. The outcomes will address specific evolutionary hypotheses, and provide powerful tools, workflows and guides for future analyses by providing new ways of working. This project will bring morphology out of the 19th century and into the 21st.