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The removal of apex predators is widely recognized to have broad ecological consequences for terrestrial and aquatic communities. In marine systems, the direct effects of fisheries exploitation include altering the community standing stock (biomass), species composition, and size- structure of the fish assemblage. Although the direct effects of fisheries exploitation are well documented, there is increasing evidence that the non-lethal effects of predation can also strongly influence the structure and function of ecological communities. In this dissertation I set out to increase our understanding of the effects of predators on coral reef fish assemblages by conducting a series of large-scale natural experiments across groups of Pacific islands spanning gradients of human population density and oceanographic productivity within four distinct geopolitical regions. My dissertation research reveals striking evidence for the effects of fisheries exploitation and oceanographic productivity on coral reef fish assemblages in three key areas. First, I found strong evidence that the effects of fisheries exploitation are not restricted to large-bodied species from higher-trophic levels but are realized throughout the entire fish assemblage and across multiple trophic groups. Importantly, I show that multiple forms of fisheries exploitation may be present on coral reefs, indicating the complex nature of coral reef fisheries. Second, I show strong evidence of biophysical coupling with gradients of oceanographic productivity and alterations in predatory fish abundance on the body condition, growth rates, maximum size, and longevity of coral reef fishes. I also observe a breakdown of natural coupling at inhabited islands, suggesting that local human impacts are capable of homogenizing life history traits of fishes even when strong environmental gradients are present. Third, I show that the trophic structure of coral reef fish assemblages are more tightly linked to changes in oceanographic productivity than to predatory fish abundance. I observed trophic channeling, a process by which different basal sources of energy entering the system can remain isolated on coral reefs forming distinct pathways up through the food web to top- level carnivores. In summary, my dissertation provides important insight into the mechanisms that structure marine communities and the direct and indirect effects of removing predators from marine ecosystems

Contains fulltext : 136075.pdf (Publisher’s version ) (Open Access) Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.