Overcoming the morphology problem of phylogenetics

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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.