Evolutionary Consequences of Gen(om)e Duplications in Animals

Abstract

My research interests can be broadly described as an attempt to explore the drivers of macroevolutionary processes and diversity patterns across taxa. One such driver is the contribution of gene and genome duplications. As the primary source of new genes in eukaryotes, duplication events are important drivers of molecular novelty and adaptation. In my first chapter, I wrote software to explore patterns of evolution following gene duplication across 77 whole vertebrate genomes. My coauthors and I discovered that duplicated genes evolve at a greater rate, more likely to diversify and acquire new functions than genes that originate from speciation events. This work demonstrates how molecular changes contribute to phenotypic evolution and the maintenance of lineages. Later in my PhD, I became further interested in the role environment has on such a dynamic. My second chapter, focusing on whole genome duplication events, explored the relationship between environment and genome copy number to test the hypothesis that species with whole genome duplications (polyploids) are more adaptable to extreme environments. Using comparisons between polyploids and diploids across five genera of South American frogs I discovered that polyploid frogs are more closely associated with environments affected by human agriculture and anthropogenic climate change. This work was expanded in my third chapter, which demonstrates the existence of a latitudinal polyploid gradient in amphibians, ray-finned fish, and insects. This pattern appears to be driven largely by glaciation cycles, further speaking to the increased capacity for polyploids in adapting to new, rapidly changing environments. As mentioned above, I am primarily motivated by a desire to explore the relationship between evolution and diversity. To me this includes the empirical inquiries mentioned above but also methodological questions related to our imperfect appreciation of biodiversity and how it can lead to misconceptions about evolution. For my fourth dissertation chapter I explored how high-throughput sequencing technology is being distributed across the tree of life and found that species evenness in high-throughput sequencing experiments has been steadily decreasing over time. My fifth chapter uses unsupervised machine learning to attempt to characterize novel protein sequences in poorly understood groups.