Browsing by Author "Price, Donald K."

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    Comparative genomics and host plant adaptation in Hawaiian Picture-wing Drosophila
    (2016-05) Armstrong, Ellie; Price, Donald K.; Tropical Conservation Biology & Environmental Science
    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.
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    Food Web Analysis of Hawai‘i Island’s Blackburnia hawaiiensis (Coleoptera: Carabidae) Using Next-generation Sequencing and Stable Isotope Techniques
    (2015) Roy, Kylle; Price, Donald K.; Tropical Conservation Biology & Environmental Science
    Tropical montane forests are valuable ecosystems in Hawai‘i, providing fresh water to the people of the islands as well as acting as reservoirs of biodiversity. These forests are experiencing rapid alterations due to anthropogenic effects such as climate change, habitat degradation, invasive species, and industrialization. Some of the detrimental effects caused by these ecosystem alterations can be mitigated through understanding the genetics and ecology of the organisms within it. Despite the importance of these arthropod-dominated ecosystems, knowledge of food webs and predator-prey interactions is sparse. In order to supplement the understanding of Hawai‘i’s montane forest ecosystems, we have implemented two different methods of diet analysis on the endemic Hawaiian carabid beetle, Blackburnia hawaiiensis. This understudied carabid may provide important ecosystem functions, being a numerically dominant predatory insect and widely distributed throughout Hawai‘i Island. B. hawaiiensis populations and potential prey in similar, highly isolated geographic locations were used to employ two different yet complimentary laboratory techniques: natural abundance stable isotope analysis (SIA) and metagenomics of gut contents using next-generation sequencing (NGS). Both NGS and SIA have revealed B. hawaiiensis to be a high trophic consumer with evidence of intraguild predation in three study sites: Ka‘iholena, Thurston, and Pu‘u Maka‘ala. In a broader context, the combined SIA and NGS techniques have great potential to further our understanding of the arthropod food webs of the montane forests of Hawai‘i Island, ultimately improving conservation efforts for the entire arthropod community. These two methods in combination could potentially be implemented in any ecosystem globally to better determine the diets of species within complex food webs, enhancing ecosystem management strategies.
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    Islands within islands: The effects of habitat fragmentation, novel community interactions, and climate on Hawaiian Drosophila populations.
    (2015-12) Mueller, Matthew C.; Price, Donald K.; Tropical Conservation Biology & Environmental Science
    Habitat fragmentation, invasive species, and shifting climate regimes are major threats to island ecosystems. Hawaii's ecosystems have been largely transformed since human colonization, with fragmented upland forests remaining important refugia for native organisms. Hawaiian Drosophila represent a large radiation of nearly 1000 endemic species, including a number of endangered and declining species. These endemic flies are important indicator species for ecosystem change, tending to be sensitive niche specialists. I examined a network of 28 lava-fragmented forests ("kipuka") on Mauna Loa to determine the effect of fragment size, presence of invasive rats, and seasonal changes in microclimate on the abundances of native Drosophila tanythrix, D. silvestris, D. sproati, and D. murphyi, and the exotic D. suzukii. All flies responded positively to increasing kipuka area. Rat exclusion had a significant and mostly positive impact on both native and exotic Drosophila abundances, but the effect varied with individual species, suggesting that rats may amplify the impact of predators on Drosophila or predate them directly, but also affect other nodes in the community. Increasing kipuka isolation from surrounding forest tended to benefit Drosophila, perhaps due to release from competitors. Exotic flies represent the vast majority of Drosophilids observed in small kipuka, and significantly outnumbered natives in all kipuka before crashing in the winter. In contrast, native flies were more abundant in winter, and rare picture-wing species were found almost exclusively in kipuka larger than 2.5 hectares. Overall, it appears that habitat fragmentation and invasive species disrupt Hawaiian Drosophila communities; the rarest species require large kipuka and the absence of rats. D. suzukii may be replacing native Drosophila in smaller kipuka, but appear maladapted to Hawaii's cold winters at higher elevations. This dynamic could tip in favor of D. suzukii as temperature isoclines climb upslope with global climate change.
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    Microbial Diversity of Two Hawaiian picture wings and their Host Plants; Microbes, Mortality and Epicuticular Hydrocarbons
    (2016-05) Yakym, Christopher-James A.V.; Price, Donald K.; Tropical Conservation Biology & Environmental Science
    Although the microbiome influences numerous aspects of organismal biology and fitness, the community characterization and role in animal evolution is largely unknown. Microbial communities in insects can have a wide range of interactions from mutualistic to parasitic and can be important in host-plant adaptation. In Drosophila, microbial associations and interactions have been studied for over a century and recently have been shown to influence the fitness and evolution of their host. This study utilizes both traditional culturing methods and high-throughput next generation DNA sequencing to evaluate the bacterial and fungal communities associated with two Hawaiian Drosophila, D. sproati and D. ochracea and their host plants, Cheirodendron trigynum and Freycinetia arborea. The culture-based and high-throughput DNA sequencing approaches provided different but complementary results. Interestingly, we found some overlap between microbiomes of the Hawaiian Drosophila and their host plants. The bacterial family Enterobacteriaceae, as well as a variety of yeasts, consisted of the majority of these shared microbes. This suggests that these microbes may play a role in the fly-host plant interaction. To evaluate the effect of these microbes on Hawaiian Drosophila, we exposed a laboratory population of D. sproati to antibacterial and antifungal treatments to determine the effect on D. sproati survivorship and epicuticular hydrocarbons. Epicuticular hydrocarbons in Drosophila serve a dual function, aiding in desiccation resistance and pheromonal communication. Flies exposed to an antifungal treatment had dramatically reduced survivorship when compared to control flies, while antibacterial treated flies were not affected. This suggests that fungi are essential to Drosophila survival while bacteria are not. However, male flies that were exposed to the antibacterial treatment showed significant changes in two major epicuticular hydrocarbons. One of which, 2MeC28, has been shown to act as a contact pheromone in other insect species. This study shows that changes in microbial communities, specifically bacteria, influence epicuticular hydrocarbon production of D. sproati which can impact multiple levels of fitness.