CENTRAL QUESTION. How can genetic technology be adapted to catalog Earth’s biological diversity?
Background. The waters surrounding California’s northern Channel Islands (sometimes called the Galapagos of North America) contain some of the most diverse species assemblages on the planet. Over the last several decades, human activities (including overfishing), together with disease, changing ocean conditions, and other factors, have produced habitat destruction and dramatic declines in the numbers of fishes and invertebrates in these waters. In 2003, the California Department of Fish and Game established a network of marine protected areas (MPAs) in state waters around Anacapa, Santa Cruz, Santa Rosa, San Miguel, and Santa Barbara Islands. Several years later, the National Oceanic and Atmospheric Administration extended the MPA boundaries to include the deeper waters of the sanctuary.
Apart from its spiritual and socioeconomic benefits, protecting species diversity is essential for environmental stability, for the identification of new pharmaceuticals to treat human disease, for insights into the production of environmentally benign materials that are superior to those currently produced by modern manufacturing methods, and for other potential sources of scientific information that can benefit humanity.
Field Work. To prepare for their field work, students will explore the following central issues: 1) the biogeographic factors influencing kelp forest biodiversity (e.g. global wind systems, current systems, forces that couple wind and water, bathymetry, nutrient upwelling, primary production, trophic levels, etc.); 2) the fundamental scientific issues guiding the design of the Channel Islands marine protected areas (MPAs); 3) the parameters used to assess MPA efficacy (e.g. population density, species diversity, size increase, number of offspring, rate of change, spillover and export, and recruitment); and 4) the biology/ecology of locally relevant marine indicator species. In the field, students will conduct basic underwater marine surveys modeled after those used by biologists to monitor the abundance of fish and invertebrate indicator species that provide vital signs of ecosystem health. Underwater survey data will be organized and submitted to an online database managed by REEF, a marine biodiversity monitoring project that was founded in 1990 in response to growing concerns over the health of the world’s oceans.
Background. Of the estimated 10 million species on the planet, only about 1.7 million have been named. In fact, our current knowledge of biodiversity is so incomplete that we are at risk of losing species before they can be discovered. To better catalog Earth’s biological diversity, scientists within an emerging global community are now participating in the Barcode of Life Initiative. This landmark international effort involves cataloging biodiversity using short, standardized DNA sequences (barcodes) that uniquely identify species groups in much the same way that Universal Product Code barcodes identify supermarket items. Scientists around the globe are now assembling a database that contains DNA barcodes from all species of plants and animals. The process of building this database begins by isolating DNA from a known biological specimen (i.e. a specimen that is easily identified based on its physical attributes). A 650 base pair region of the mitochondrial barcoding gene (cytochrome c oxidase I; COI) is then amplified from the specimen’s DNA and sequenced using a series of standard molecular biology-based laboratory techniques. This sequence, which constitutes the specimen’s barcode, is then electronically submitted to the Barcode of Life Data Systems (BOLD), a public-access informatics workbench and repository for reference barcode sequences (reference barcodes). As this database becomes populated with sequence information from different species, a DNA barcode sequence that is generated from a specimen that cannot be identified based on its physical characteristics (e.g. an embryo or other early life form) may be submitted and compared to all known reference barcodes contained in the database. Once a match is identified, a species name will be assigned to the unknown specimen. In addition to addressing basic issues in taxonomy research, the genetic information contained in this electronic repository is already proving to be a valuable tool to address a variety of important applied environmental problems, including protecting endangered species, controlling agricultural pests, sustaining natural resources, stopping disease vectors, and managing our coastal marine resources.
Laboratory Work. During the laboratory component of the Biomes to Genomes program, students will review the central dogma of molecular biology and participate in in-depth, interactive discussions on the scientific techniques used to generate DNA reference barcodes, including their biological origins and their ties to the natural world. In the laboratory, students will participate in the Barcode of Life Initiative by extracting genomic DNA from target marine specimens, using polymerase chain reaction (PCR) to copy and amplify a segment of the COI gene from their specimens, purifying their COI amplicon and verifying its length using gel electrophoresis, subcloning their amplicon into a plasmid vector, and submitting their DNA samples for rapid-turnaround sequencing. Students will then use a suite of bioinformatics tools to edit and upload their sequence data to BOLD. Once reviewed for accuracy, data will be submitted to the National Center for Biotechnology Information/GenBank and its mirror sites at the European Molecular Biology Laboratory and the DNA Data Bank of Japan. Importantly, students will be appropriately cited as authors for their submission of genetic data to these widely utilized scientific resources.