RUI: Collaborative Research: Adaptive Significance of Genomic Variation in a Montane Insect

Sonoma State University, Rohnert Park CA

Investigators

Abstract

As the Earth's climate becomes warmer and more variable, characteristics that help organisms cope with stress will become increasingly important. This research investigates beetles living at high elevation in the Sierra Nevada mountains of California to study how variation in genes coding for proteins that process energy and respond to stress affect metabolism and performance. The research seeks to discover the contrasting roles of oxygen, which is necessary to process metabolic fuel, and temperature, which changes the rate at which these processes occur. It is a synthesis of genomics, physiology, and animal natural history that will provide a unique opportunity to understand how organisms cope with environmental change. It will provide insight into the evolution of thermal plasticity and may unveil novel genes associated with temperature and oxygen stress. The work will increase research opportunities for students at two primarily undergraduate universities. Students will be trained in experimental design and analysis, proposal and paper writing, and in the presentation of research at scientific meetings, which will provide them with marketable skills for the modern work environment. Educational materials will be developed for K12 education, which illustrate the use of genomic tools for answering scientific questions. Outreach events detailing the results of this project will occur at public events in the San Francisco Bay Area and near field sites in Inyo County, California. This project will develop and use genomic and transcriptomic tools to gain mechanistic insights into the genetic basis of adaptation to temperature and atmospheric oxygen in the Sierra willow leaf beetle Chrysomela aeneicollis. This research will test the hypothesis that interactions between mitochondrial and nuclear genomes have pervasive effects on gene expression that scale up to differences in metabolic capacity and performance. To test this hypothesis, the stress response will be investigated in larvae from populations that differ with respect to mitochondrial and nuclear genetic background and that occur along a latitudinal and steep altitudinal temperature gradients. Larvae will be reared at a high elevation laboratory in chambers where oxygen level and temperature will be manipulated. At the end of the growth period, larvae reared under these different conditions will be exposed to different temperatures and running speed measured. Genetic variation associated with fast and slow running speed after stress will be identified using whole genome sequencing of individuals in the upper and lower tails of the running speed distribution. Differences in expression of genes of interest will be assessed using RNA sequencing for these same individuals. Genes of interest (e.g. stress, hypoxia, central metabolism) that have non-synonymous single nucleotide polymorphism (SNP) variation along natural temperature or elevation gradients will be identified in whole genome sequencing experiments and used to build 'SNP panels' in which larger numbers of individuals can be screened. Rearing conditions described above will then be used to generate larvae in which metabolic physiology will be examined. Metabolic enzyme activity, mitochondrial respiration, oxidative damage and thermal tolerance will be measured, SNP variation recorded, and differential expression of genes of interest quantified using quantitative PCR. Taken together, this research will reveal how mitochondrial and nuclear genomes interact to cope with stress in a changing environment. The project will establish a new international collaboration with world leading experts in insect genomics from Stockholm University (Sweden). International collaborators will help organize and lead a two-week hands-on workshop on genomics and bioinformatics for undergraduate and Masters students from Santa Clara University and Sonoma State University. Additionally, Masters students from Sonoma State University will travel to Stockholm University to receive training in genomics and bioinformatics. International activities and travel will be supported by funds from the International Science and Engineering section of NSF's Office of International and Integrative Activities.