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Comparative genomics and host plant adaptation in Hawaiian Picture-wing Drosophila

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Title: Comparative genomics and host plant adaptation in Hawaiian Picture-wing Drosophila
Authors: Armstrong, Ellie
Advisor: Price, Donald K.
Keywords: Biology
Genetics
Ecology
Issue Date: May 2016
Abstract: For arthropod lineages, host-switching and differential host adaptations are commonly suggested as important ecological drivers behind diversification and co-evolution. The Hawaiian picture-wing Drosophila are an ideal lineage for investigations of the genomics of speciation because of their close relationship to D. melanogaster, their well-known phylogeny, thoroughly documented ecology, and incredible diversity. I investigated the genomic landscape changes and genome evolution in relation to host-plant adaptation in four species of Hawaiian picture-wing Drosophila. Three of these species, Drosophila sproati, Drosophila murphyi, and Drosophila ochracea were sequenced for this study using de-novo whole-genome sequencing and assembly. All of these species are endemic to Hawaii Island and considered specialist species and oviposit on the plants Cheirodendron trigynum (D. sproati and D. murphyi) and Freycinetia arborea (D. ochracea). The last species, D. grimshawi from the Maui Nui complex, was originally sequenced by the Drosophila 12 Genomes Consortia and is considered a generalist species. I also used the outgroup, Scaptomyza flava, a continental species of the Scaptomyza genera, which originated in Hawaii.
In the picture-wing lineage, there were 264 genes found to be under positive selection, notably those with chemosensory gene functions, plant detoxification functions, and inter-male aggression functions. Using all paralogs and orthologs of chemosensory genes, three genes in the odorant receptor and odorant binding protein gene families were detected to be under positive selection. It was also shown that specialists lost more chemosensory genes over time compared to the generalist species. Using 1:1 orthologs across species, I detected 12 genes under positive selection in individual picture-wing species that had a variety of functions in protein signaling, cell metabolism and division, and plant detoxification. These results highlight the genomic changes associated with host plant adaptation and sexual selection in the Hawaiian Drosophila.
In addition, the results show that repeat content is strongly correlated with genome size across the Drosophila genus. Drosophila grimshawi has a repeat content 3x higher than the other picture-wings, but this does not correspond to increases in repeat diversity. There was no notable codon bias between picture-wing species, but there was codon bias between D. grimshawi and S. flava. Picture-wings tended to favor a single codon over other codons, whereas S. flava has evenly represented codon choice for any given amino acid. Genomic synteny across picture-wing species and D. melanogaster was highly conserved at the chromosome level.
Pages/Duration: 91 pages
URI/DOI: http://hdl.handle.net/10790/2759
Appears in Collections:Tropical Conservation Biology and Environmental Science



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