| Summary: | The Ecdysozoa is a large clade of animals comprising the vast majority of living species and some of the most studied invertebrate models, including fruitflies and nematodes. Some of the relationships between major ecdysozoan groups remain uncertain, however, undermining comparative studies and impairing our understanding of their evolution. One hotly debated problem is the position of myriapods which have been recently grouped according to molecules with chelicerates and not with insects and crustaceans as predicted by morphological evidence. Other disputed problems are the position of tardigrades, the position of hexapods within the crustaceans as well as the mutual affinities of the nematodes and priapulid worms. Molecular systematics of the ecdysozoans is complicated by rapid divergence of the main lineages (possibly evidenced in the Cambrian explosion) followed by a subsequent long period of evolution. This may have resulted in a dilution of the historical phylogenetic signal and an increased likelihood of encountering systematic errors of tree reconstruction. This problem is exacerbated by many lineages being poorly represented in current molecular datasets, as sequencing efforts have been biased toward lab models and economically relevant species. In order to overcome problems of systematic error, I have assembled various large mitochondrial and phylogenomic datasets, including new data from undersampled tardigrades, onychophorans and especially myriapods. I analysed these datasets using the most recent evolutionary models. I have developed two new models in order to describe the evolutionary processes of metazoan mitochondrial proteins more accurately. My analyses of multiple datasets suggest that the grouping of myriapods plus chelicerates found by previous authors is likely to be the result of systematic errors; I find support for a closer relationships between myriapods and a group of insects plus crustaceans (the Mandibulata hypothesis). My analyses also support a paraphyletic origin of Cycloenuralia (nematodes and priapulids) and a sister group relationships between tardigrades, onychophorans and euarthropods in accordance with a single origin of legged ecdysozoans, the Panarthropoda. Finally, results support a monophyletic group of hemimetabolan insects. The majority of the results reconcile molecules and morphology, while others shade new light onto arthropod systematics. The evolutionary implications of these systematic findings as well as methodological advances are discussed.
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