Marine Biotech Fellowship: A Molecular Analysis of the Phylum Ctenophora

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Pelagic biogeography has been limited by the inability to distinguish genetic structure of a species. The problems include constant movement of local populations, unknown oceanic circulation patterns, the 3-dimensional aspect of the ocean and the difficulties inherent with oceanic sampling. This project will examine members of the Phylum Ctenophora using modern molecular techniques to help elucidate the taxonomy of this understudied group of organisms. Ctenophores are abundant in all the oceans and occur at all depths in the water column. Distribution of ctenophores is often patchy and these patches can fluctuate in time and location. The techniques developed by molecular biologists (e.g. allozymes and nucleic acid analyses) are appropriate for the marine sciences and represent novel tools for the marine scientist to examine the distribution of marine populations. These techniques have been utilized for fisheries but have not been applied to gelatinous zooplankton despite the importance and abundance of this group. There are a number of ctenophore species that occur in the Monterey Bay area, the majority of which are still undescribed. This project will consist of:: 1. Collection of specimens and the isolation of genomic DNA focused on Monterey Bay with shallow-water and deep- water collections; 2. Use of the Polymerase Chain Reaction to amplify the nuclear encoded small ribosomal subunit genes (ssRNA), spacer regions, and certain DNA segments of the mitochondrial genome; 3. Analyze the amplified DNA with restriction enzymes in order to detect any Restriction Fragment Length Polymorphisms that are present: 4. Sequencing of the amplified DNA either directly from the PCR product or after cloning the product; 5. Analysis of the sequences will be done using DOTPLOT, BESTFIT, and GAP/RANDOMIZATION; 6. Clarification of the taxonomy of the Phylum Ctenophora using a combination of the molecular data and classical data (morphology and natural history). The use of the ssRNA sequences will be most useful for the higher taxonomic levels while the sequence information from the spacer region or mtDNA regions will be useful for examining the variation within species.