The tree complexity of reticulate evolution

Dating back to Darwin, phylogenetic (evolutionary) trees have provided the primary representation of the evolutionary relationships among species. These trees are typically inferred from genomic data and are central to evolutionary biology for classifying species, dating evolutionary events, and tracing the origins, relationships, and future developments of pathogens. Yet, different genes often support contradictory evolutionary histories as a result of reticulate evolutionary processes such as lateral gene transfer and hybridisation. This has prompted increased interest in moving from phylogenetic trees to phylogenetic networks. However, although these networks can ‘display’ a set of supported trees, they typically also display many additional trees that may have no support from the data. Moreover, phylogenetic networks may hide an underlying ‘central’ tree that is supported by the data. The proposed project will take a foundational approach to these and related issues by developing new mathematical and computational techniques to explore the complex relationships between phylogenetic networks and the trees they display. In that way, the project will provide novel techniques to generate, augment, and simplify phylogenetic networks so that they provide a more efficient and explicit representation of the evolutionary history of species and the genes they carry.