Genomics of the California vole (Microtus californicus) and related rodents
Chris Conroy, Staff Curator
Museum of Vertebrate Zoology
Applications for Spring 2024 are closed for this project.
The California vole is a common species of rodent in California, with some interesting complexity. There are two distinct groups within the species that come into contact in Southern California. We have been studying this contact zone from various morphological, climatic and genetic perspectives. The species is also found in many isolated patches in the desert. We have a project on the nuclear and mitochondrial genomes in one of the most isolated populations.
Role: The student(s) involved could help in several areas. This project has already involved assembling the draft genome and obtaining similar sequence data for other rodents. We are now in the phase of running tests of relative rates and positive selection (e.g. with PAML, PhyML), inferring genomic architecture and other comparative genomic analyses. Some of this is directed at the genes underlying certain morphologies, but much of it will be done in bulk (e.g. over many thousands of genes) to look for outliers. There is also the possibility of investigating RAD-Seq data for this species.
Qualifications: The student(s) who might be involved in the genomics project should have the interest in examining genomic data, have programming skills especially for automation of analyses, a willingness to research the current literature and discuss with Conroy, and show some interest in coming up with unique hypotheses to test. More important than anything is the ability to communicate well through emails, and to stay on task throughout the semester.
Hours: 6-8 hrs
Related website: http://mvz.berkeley.edu
Related website: https://www.ccgproject.org/species/microtus-californicus-california-vole