Overcoming the morphology problem of phylogenetics

进化树是重建进化史和检验进化假说的基础。因此，它们解决了主要问题，例如，我们的现代生物群是如何以及何时形成的，生物多样性和灭绝的形状和分布是什么？在获取和分析遗传序列数据方面的进展导致了对分子系统发育的日益重视和依赖，但表型证据(形态学)仍然至关重要。它使我们能够将有机体和它们的环境联系起来，从而展示进化变化的机制。这也是包括已灭绝的类群的唯一方法，因此提供了一个深刻的时间视角；化石打破了退化的现代动物之间的巨大差距，解开了进化变化的序列(所谓的“缺失环节”)，并为估计进化速度提供了一个时间表，包括校准分子时钟。虽然形态被认为是系统发育的关键，但它也被广泛认为是本质上的问题。发育和功能连锁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性的模式。这些有问题的现象被承认是存在的，但它们在很大程度上被忽视了；形态数据通常被视为‘表面价值’，并被分子和古生物学研究视为等同。此外，我们对这些现象的分布或影响一无所知。因此，我们对一系列进化事件的理解受到了破坏，我们重建进化历史的能力也是有限的。为了直接解决形态的局限性，我们将：1)量化问题在整个生命树和形态模块中的范围和分布；2)开发方法工具包，以独立的分子和地层数据作为基准，使用形态进行可靠的系统发育推断；3)将这些方法应用于依赖于对形态的解释但迄今被证明是棘手或模棱两可的重要进化事件，例如人类起源。结果将解决具体的进化假说，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。这个项目将把形态从19世纪带入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.