The world’s ecosystems are under serious threat due to ongoing stressors of the Anthropocene: notably habitat destruction, climate change, disease, and the spread of invasive species. Tracking and understanding how ecosystems change under these threats in real time is a major challenge for humanity, and one we are currently not meeting. We have no reliable way to quantify the overall health of an ecosystem, let alone identify thresholds of change beyond which an ecosystem cannot recover. Global threats are concentrated intensively on islands, allowing them to serve as harbingers of what the future may hold for the world at large. This project deploys a system we have developed to “scan” the ecological network of interacting species of an island, using high throughput next generation sequencing.
We employ a molecular alpha-taxonomy approach to rapidly assess the biodiversity of arthropods in tropical island ecosystems in Hawaii and French Polynesia. Specifically, we use a next-generation sequencing approach called metabarcoding to sequence a short region of mitochondrial DNA for a bulk collection of arthropods. The unique sequence DNA of each individual specimen helps designate each as a molecular operational taxonomic unit (MOTU) which can be used as a proxy for taxonomic species, allowing an evaluation of diversity and turnover, without traditional taxonomic classification. By sorting arthropod specimens into rough size categories and sequencing multiple overlapping molecular markers with differential amplification success in various arthropod orders, our group is applying correction factors for the ratio of tissue to amplification success that allows resultant DNA sequencing reads to illustrate not only species richness but also relative species abundances for each community. Thus, with such rapid generation of biological diversity data, we can examine hypotheses relevant to community ecology and biodiversity dynamics that are appropriately paced with the anthropogenic pressures to each community.
The student will be working in the Gillespie & Roderick “Evolab” under the supervision of PhD candidate Natalie Graham. They will be involved in the sorting of arthropod specimens into rough size categories and sequencing the molecular markers. Training in molecular ecology will be provided. Students will receive conceptual and practical training for: 1) arthropod collection and identification to order or family level, 2) sorting arthropods by size category into 96 well plates for downstream metabarcoding 3) DNA extraction 3) DNA polymerase chain reaction 4) Gel electrophoresis 5) DNA quantification & clean-up 6) NGS library prep methodology.
Preference will be given to applicants with an interest in biodiversity science and conservation. No prior lab experience is required but students must have attention to detail, be able to work carefully and rapidly, be willing to work independently as well as in a team, and have a demonstrated curiosity for the natural world. The ideal candidate will have taken Biology 1A and Biology 1B as well as one or more of the following courses: Biology and Geomorphology of Tropical Islands, Environmental Change Genetics, Conservation Biology, Insect Ecology, Spider Biology, Biogeography or the like.