Gene and genome duplication are major sources of material for evolutionary innovations in eukaryotes that provide opportunities for novel function, increased complexity, and rapid speciation. Single gene duplications are prevalent even in eukaryotes with small genomes. Whole genome duplication plays an important role in the evolution of plants and some vertebrate groups.

I studied the origins of tetraploid gray tree frogs using molecular sequence data and advertisement calls (Holloway et al. 2006). Molecular sequence data support multiple allopolyploid origins of tetraploids with a surprising twist. Apparently, tetraploids are composed of a single interbreeding lineage that was created from at least three distinct diploid species, a paradigm of polyploid formation that has never been seen before.

The evolutionary fate of gene duplicates has been debated since the 1970s. Duplicate genes are maintained by purifying selection or evolve novel function. Drift, adaptive evolution of one duplicate, or subfunctionalization (the parsing of multiple ancestral functions between duplicates) leads to the diversification of duplicates. Empirical evidence for all four of these models exists in nature, but the relative importance of each remains to be determined.

I developed an experimental model system in bacteria that utilized the antibiotic resistance properties of the gene, B-lactamase, to test factors involved in maintenance and divergence of duplicates (Holloway et al. 2007). Native B-lactamase confers resistance to ampicillin and to very low levels of cefotaxime. Mutations in B-lactamase allow it to confer increased resistance to cefotaxime, but decrease resistance to ampicillin, creating a tradeoff. I found that the mere existence of a tradeoff between old and new functions is insufficient for retention of the second copy; the environment must be such that the copy evolving novel function is no longer able to serve the original function.

I also examined the relative roles of novel function and subfunctionalization in evolution of duplicated male reproductive genes in Drosophila (Holloway and Begun 2004). Polymorphism and divergence data from these duplicated genes suggest that protein divergence between D. melanogaster and D. simulans is a result of adaptive evolution leading to novel function. These data strengthen the conclusion that male reproductive genes may often be under directional selection in Drosophila.