Access Type

Open Access Dissertation

Date of Award

January 2012

Degree Type


Degree Name



Biological Sciences

First Advisor

Markus Friedrich


Gene duplication is an important source of evolutionary innovation. Using the publicly available genomic information, I studied lineage-specific gene duplications in Drosophila melanogaster (fruit fly), Anopheles gambiae (mosquito), Tribolium castaneum (red flour beetle), and Apis mellifera (honey bee) at three scales: eye-specific genes, developmental genes, and genome-wide. All three studies consistently show that the Drosophila genome contains an exceptionally high number of lineage-specific yet ancient gene duplicates, the majority of which must have originated during the early diversification of the higher Diptera (Brachycera) at least 100 million years ago. Genetic data suggest that gene duplication played an important role in the evolution of visual performance in the fast flying higher Diptera by spatial or intracellular subfunctionalization. Developmental gene duplications, by contrast, in many cases retained overlapping expression patterns and preserved partial to complete redundancy consistent with a role in boosting developmental robustness. Genes involved in metabolic process constantly occupy approximately 50% of all the conserved protein-coding gene families in the insect genomes, both in different species and at various evolutionary time periods, suggesting that the fraction of metabolic genes is maintained over the long term. Further, gene ontology analysis suggests that energy metabolism-related genes are significantly enriched in Brachycera-specific duplicates. My work leads to the conclusion that the early evolution of the higher Diptera was exceptionally impacted by gene duplication. This mutational mechanism apparently fueled the genetic underpinnings of energy metabolism related pathways coinciding with the emergence of the exceptionally fast flight capacities, which characterize most members of the Brachycera clade. I further propose that the retention of duplicated genes spiked during the early diversification of the higher Diptera due to an extended period of effective population size reduction.