Vertebrate Evolution from the Perspective of the Non-coding Genome

Abstract

Vertebrates, despite having exons that align across 500 million years of divergence, have come to occupy a wide array of niches in disparate environments. Given the conservation at the exon level, the variation seen between these species must lie elsewhere. From jawless lamprey to birds and reptiles to humans and other mammals, there are many crucial transitions to account for, the driving forces of which remain largely unknown. Here, I detail my work to build tools of discovery, utilize new and old methods of detection, create computational tools to examine in depth the ancestry of regions of the non-coding genome, and develop methods to study these regions in vivo. I find that non-coding genome sequence conservation seems to align itself with major transitions in the vertebrate lineage, such as the transition to land and the advent of placental mammals. Additionally, I'm able to detect the vertebrate ancestors that first had regions similar to open chromatin regions found in over 200 human tissues. Of particular interest to me is the lack of resources applied to understanding one of the largest groups of the vertebrate lineage, avians. Part of my work has been focused on developing methods that can be utilized for all vertebrates, particularly those with more ancient branching points than humans and fewer outgroups to reference. I aim to utilize all the gathered methods to shed more light on avian adaptation, as well as how they fit into the larger story of vertebrates, while also examining how these new methods fit into the toolkit of well-studied vertebrates like humans.