Edwards, Scott V.Grayson, Phillip D.2020-01-072019-052019-05-102019Grayson, Phillip D. 2019. The Comparative and Developmental Genomics of Flightlessness in Birds (Palaeognathae). Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences.http://nrs.harvard.edu/urn-3:HUL.InstRepos:42106928Convergent evolution results in shared, analogous phenotypes among evolutionarily distinct lineages. Thus, vertebrates have evolved flight independently in pterosaurs, bats, and birds, an event that requires the co-occurrence of many physiological and morphological changes. Flight has also been lost across diverse avian taxa. With a minimum of three convergent losses of flight, the Palaeognathae, a clade containing the flight-capable tinamous and iconic ratites, including the emu (Dromaius novaehollandiae) and ostrich (Struthio camelus), offers a unique opportunity to study the genomic and developmental processes underlying convergent evolution of a complex trait. In this thesis, I utilize comparative genomics, epigenomics, transcriptomics, and developmental biology to identify the evolutionary signatures that arise during the repeated loss of avian flight. In Chapter 1, I highlight the methods I utilized to sequence ten high-quality paleognath genomes, and outline the value of de novo genomes for evo-devo research. In Chapter 2, I examine the regulatory landscape of developing flight-associated tissues, validating putative regulatory elements that have experienced evolutionary rate shifts associated with convergent loss of flight. By functionally testing these elements, I determine that one is a novel enhancer in the developing chicken limb and that convergent acceleration of this enhancer in the ratites has resulted in functional divergence. In Chapter 3, using epigenomic and transcriptomic analyses, I identify regulatory changes associated with the vestigial forelimb of the developing emu, and discover a novel enhancer with altered accessibility between chicken and emu. Finally, in Chapter 4, I build upon my previous work to test whether convergent signals of regulatory evolution are present across the limbs of ratites. First, I determine that unlike the flightless paleognaths, which possess reduced forelimbs during early development, the tinamous produce a robust forelimb at the same embryonic stage as other flight-capable species. Next, I generate and analyze epigenomic and transcriptomic data for the limbs of two flight-capable and three flightless species. I demonstrate that both convergent and lineage-specific regulatory evolution likely shape the flightless avian forelimb. Overall, this integrative work indicates that convergent phenotypic evolution within this group results from both shared and lineage-specific genomic and epigenomic changes.application/pdfenconvergent evolutionPalaeognathaeflightless birdsgenomicsregulatory evolutionepigenomicstranscriptomicsATAC-seqenhancersevolutionary developmental biologyheterochronyembryologyThesis or Dissertation2020-01-070000-0002-3680-2238