The NIH funded parent award uses genomics of threespine stickleback to address questions about the mechanism of rapid adaptation from standing genetic variation. It focuses primarily on anadromous threespine stickleback in Alaska that have recently been transplanted into freshwater environments and exhibited major phenotypic change. An important finding from the parent grant thus far has been that the starting haplotype structure on which freshwater-adaptive alleles lie in the anadromous population is key to how rapidly alleles will evolve in a new freshwater environment. The proposed undergraduate summer research project will examine 65 whole genomes from three anadromous Stickleback populations from Alaska and the Pacific Northwest in order to elucidate patterns of haplotype sharing across marine environments. The candidate will learn how to perform the bioinformatic processing necessary to generate high coverage whole genomes that can then be analysed using various downstream data manipulation, visualization and population genetics methods. This proposed summer research is closely associated with Aim 1 of the parent NIH grant and will provide the candidate with the opportunity to develop technical skills in accessing and using remote computer clusters, processing 2nd generation sequencing data, asking biologically relevant questions and interpreting and visualizing data. In addition, the candidate will also obtain exposure to being in a lab group, interacting with students and staff at various levels and participating in lab meetings and a journal club. The candidate will also present their work at an undergraduate research symposium hosted by Stony Brook University in 2021. Due to the COVID-19-related restrictions in the state of New York, this project will be carried out remotely.
Our R01 parent grant is using a genomics approach to identify the role of standing genetic variation in the rapid adaptation of marine threespine stickleback to freshwater environments in Alaska. This supplement will enable an undergraduate to gain summer research training in how to perform bioinformatic processing of 2nd generation sequencing data from ancestral marine populations. They will also learn how to perform population genetic analysis of haplotype diversity across populations.
