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Parasitic Copepod Evolution Open Access

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The Copepoda is a diverse, monophyletic group of 14,194 species of small crustaceans that have colonized virtually all major aquatic habitat types around the world and have evolved to be parasitic on multiple occasions. The dominance of copepods in the largest habitat on earth, the open ocean that constitutes 99% of habitable space, makes them one of the most abundant, if not the most abundant, groups of animals on the planet. Despite their abundance and ecological importance, we know relatively little about the evolutionary history of copepods, both in terms of interrelationships within the Copepoda and their phylogenetic relationship with the rest of the Pancrustacea (i.e., the “Crustacea” and Hexapoda). Yet this evolutionary history is key to understanding fundamental features of copepod diversity, such as the evolution of parasitism and morphological evolution. Here, I seek to review what is known about copepod evolutionary relationships, identify and describe new copepod diversity, develop NGS techniques for large, multigene phylogenomic analyses to improve our understanding of copepod phylogeny, and complete a phylogenomic analysis of the Pancrustacea to better understand the relationship of copepods and the other major groups of pancrustaceans.In this study I first (Chapter 2) complete a literature review and synthesis phylogeny of the Copepoda, which reveals that copepods have evolved to be parasitic on at least 12 occasions and indicates that only 3% (427/14,194) of copepod species have been included in published molecular phylogenetic analyses. I identify and describe three new species of copepods (Chapters 3 and 4) from the two largest clades of parasitic copepods in order to document copepod diversity and better understand the morphology and identification of these parasites. Next, a phylogenomic analysis of copepods (Chapter 5) is completed to examine the relationship among the four largest copepods orders, and to identify new genes for future phylogenomic work in copepods. To better understand relationships between the major constituent clades of pancrustaceans and to identify the appropriate outgroup for copepods, I complete a phylogenomic analysis of the Pancrustacea (Chapter 6) with the most robust taxon sampling to date and a tree-based approach to identify orthologs, which reveals a number of novel phylogenetic relationships. Finally, to facilitate studies of pancrustacean evolution and genomics, I present one of the most complete and contiguous crustacean reference genomes (Chapter 7): a chromosome-level assembly of the gooseneck barnacle Pollicipes pollicipes.

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