Uncovering the Dynamics of Natural Populations: Genomic Studies in Drosophila pseudoobscura & Apis mellifera
Open Access
- Author:
- Fuller, Zach Lewis
- Graduate Program:
- Biology
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- January 03, 2017
- Committee Members:
- Stephen Schaeffer, Dissertation Advisor/Co-Advisor
Kateryna Makova, Committee Chair/Co-Chair
Paul Medvedev, Committee Member
Christina Grozinger, Committee Member
Christina Grozinger, Outside Member - Keywords:
- Genomics
drosophila
apis mellifera
selection
population dynamics - Abstract:
- Genetic variation can exist in a number of forms, ranging from single nucleotide changes falling in regions with no impact on fitness to large-scale structural rearrangements of chromosomes. A variety of evolutionary forces, including selection, mutation, recombination and drift, shape the structure of this genetic variation and the resulting molecular pattern can be used to infer the evolutionary dynamics of natural populations. Questions regarding the origin and maintenance of genetic traits in natural populations have historically been a central focus to the field of evolutionary biology. Traditionally however, researchers have been limited by the amount, breadth and resolution of genetic data available to address theoretical models of how variation is expected to change over time. Recent advances in high throughput sequencing technologies yield a powerful method to inexpensively generate sequence data across entire genomes, yet at the resolution of individual nucleotides. Here, a high throughput sequencing approach is used to investigate genetic variation in the model organism Drosophila pseudoobscura and the non-model organism Apis mellifera. In this work, I find that stabilizing selection acts on synonymous codon usage and shapes the nucleotide composition of gens in D. pseudoobscura. Furthermore, I develop a series of publically available tools to perform tests of positive selection in A. mellifera and identify several genes with signatures of adaptive evolution. Additionally, I demonstrate chromosomal inversions in D. pseudoobscura are likely favored because of their indirect effect of suppressed recombination. Lastly, I suggest a novel role for segregation distortion in the process of speciation and find evidence for cross-species introgression enabled by an association with a selfish genetic element. Together, this work reveals the complex interaction of different evolutionary forces that influence the structure of genetic variation across genomes and populations.