Congruence with independent data will be used as a benchmark - primarily molecular trees, which are comparatively well-validated and based on abundant data. The performance of different phylogenetic techniques will be directly compared and assessed: 1) implied weighting which minimizes homoplasy, 2) clique removal to minimize character over-saturation, 3) and Bayesian inference to overcome the problems associated with traditional parsimony analysis. cranium vs post-cranium, hard vs soft, appendage vs non-appendage, flower vs leaf), and 2) investigating the distribution and prevalence of cliques of inter-dependent and ecologically linked characters as identified a posteriori. Identification of misleading morphological moieties will be achieved by 1) investigating the performance of logical a priori subdivisions and modules of morphology (e.g. This project aims to identify the scale and distribution of these problematic phylogenetic phenomena and establish new ways of working that minimize their effects. Furthermore, homoplasy is widespread due to convergence, and subjectivity of character definition. Character independence is violated due to over-saturation, and functional and developmental linkage. Morphological data are essential for phylogenetic reconstruction, but are acknowledged to be intrinsically problematic. This project will bring morphology out of the 19th century and into the 21st. The outcomes will address specific evolutionary hypotheses, and provide powerful tools, workflows and guides for future analyses by providing new ways of working. 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. As such, our understanding of a range of evolutionary events is undermined, and our ability to reconstruct evolutionary history is limited. Furthermore, we have no idea about the distribution or influence of these phenomena. 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. Developmental and functional linkage can result in suites or modules of non-independent morphological characters and thus misleading patterns with respect to phylogeny reconstruction. Although morphology is acknowledged to be essential for phylogeny, it is also widely recognized as intrinsically problematic. 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. It enables us to make the link between organisms and their environment and thus demonstrate the mechanisms of evolutionary change. 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. Phylogenetic trees underpin reconstructions of evolutionary history and tests of evolutionary hypotheses.
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