Patterns and Consequences of Novel Gene Origination in Arthropoda

Abstract

Characterizing the phenotypic diversity of life has been a central goal of evolutionary biology since its inception. No less important, though often underappreciated, is variation in genes and genomes across organisms. In this dissertation, I explore the origins, phylogenetic distribution, and functional consequences of evolutionarily novel genes in the largest and most diverse phylum of animals, the arthropods. In Chapter 1, I place my work in the context of the existing literature on novel gene birth via duplication, fusion, and horizontal gene transfer (HGT). In spite of substantial prior work on these mechanisms, gaps remain in our understanding of the interactions between HGT and other gene birth mechanisms, as well as in the importance of inter-animal HGT. In Chapter 2, I develop a methodology to detect the fusion of genes acquired via HGT from non-animal donors with existing arthropod genes. Deploying this methodology across 319 arthropod genomes, I uncover 104 genes that emerged via the fusion of arthropod genes with fragments acquired from bacteria, viruses, fungi, and plants. Next, I turn to the role of inter-animal HGT. In Chapter 3, I deploy a genome-wide phylogenetic screen to detect HGT from non-dipteran donors in the genome of the fungus gnat Bradysia coprophila. I discover that nearly 10% of protein-coding genes in the B. coprophila genome originated via HGT, primarily from other animals. My colleagues and I further demonstrate that horizontally acquired genes are physiologically intact and may contribute to novel stress tolerance and biosynthetic capabilities in these gnats. Finally, in Chapter 4, colleagues and I combine molecular phylogenetics with subcellular localization prediction to examine the potential for evolutionary convergence in genes born via lamin duplication. We discover evidence consistent with the hypothesis that, following their loss in the last common ancestor of panarthropods, cytoplasmic intermediate filaments have repeatedly re-evolved via lamin duplication and divergence in all subphyla of extant arthropods. Collectively, my work in this dissertation shows that new gene birth has shaped arthropod diversity at the genomic, cellular, and physiological levels.