Genomic Changes Underlying Adaptive Traits and Reproductive Isolation Between Young Species of Cyprinodon Pupfishes Public Deposited

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  • McGirr, Joseph Alan
    • Affiliation: College of Arts and Sciences, Department of Biology
Abstract
  • Adaptive radiations showcase dramatic instances of biological diversification resulting from ecological speciation, which occurs when reproductive isolation evolves as a by-product of adaptive divergence between populations. While this process seems widespread and may account for much of life’s diversity, there is little known about genomic differences between species that influence differences in phenotypes and contribute to reproductive barriers. In my dissertation work, I used a variety of evolutionary genomic methods to study the genetic basis of rapid ecological speciation within an adaptive radiation of Cyprinodon pupfish endemic to San Salvador Island, Bahamas, which consists of a dietary generalist species and two trophic specialists – a molluscivore and a scale-eater. In my first chapter, I combined genome-wide divergence scans, selections scans, and association mapping to discover loci that were highly diverged between species, showed signs of recent selection, and were associated with variation in jaw size – the primary axis of phenotypic divergence in this system. In my second chapter, I found that the scale-eater and molluscivore species showed similar gene expression patterns compared to the generalist species, providing the first evidence of parallel changes in gene expression underling adaptation to divergent niches. These findings indicated convergent adaptation to higher trophic levels through shared genetic pathways. In my third and fourth chapters, I measured gene expression levels in F1 hybrids generated from crosses between San Salvador species. Intriguingly, many genes that were differentially expressed between sympatric species were also misregulated in their F1 hybrids. These results indicate that divergent ecological selection in sympatry can drive hybrid gene misregulation which may act as a primary reproductive barrier between nascent species. In my fifth chapter, I combined whole-genome resequencing data with total mRNA sequencing to identify candidate cis-acting genetic variation influencing rapidly evolving craniofacial phenotypes. I found very few alleles fixed between species – only 157 SNPs and 87 deletions. By measuring allele-specific expression in F1 hybrids, I found strong evidence for cis-regulatory alleles affecting expression divergence of genes with putative effects on skeletal development. These results highlight the utility of the San Salvador pupfish system as an evolutionary model for craniofacial development.
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Advisor
  • Martin, Christopher H
  • Matute, Daniel R
  • Duronio, Robert J
  • Willett, Christopher S
  • Langerhans, Bryan
Degree
  • Doctor of Philosophy
Degree granting institution
  • University of North Carolina at Chapel Hill Graduate School
Graduation year
  • 2020
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