Chris Conroy, Staff Curator

Closed (1) Genomics of the California vole (Microtus californicus) and related rodents

Applications for fall 2021 are now 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.

The student(s) involved could help in several areas. This project has already involved assembling the draft genome using raw Illumina data, cleaning the alignments, annotating the 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., Staff Researcher

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.

Weekly Hours: 6-8 hrs

Related website: http://mvz.berkeley.edu

Closed (2) Evolution of the Trowbridge shrew

Applications for fall 2021 are now closed for this project.

The Trowbridge shrew, Sorex trowbridgii, is a common small mammal across middle to northern California, extending into Oregon and Washington. Deep genetic divergence within the species suggests incipient speciation is underway. This project has two current goals. 1) Develop more, and novel molecular data to investigate depth of divergence and test for gene flow between genetic groups. 2) Examine the relationship between morphological variation (skull morphometrics, coloration) and genetic data. Morphology was used to elevate the current subspecies, and will aid in understanding the divergence of these groups. The morphometric research involves photographing shrew skulls, using software to measure various parts, and file manipulation. Looking at images for characters would also be useful beyond just measurements. Students can work with Conroy to whatever degree they choose.

For the genetic work, the student would assist with DNA extraction, PCR, and sequencing in the MVZ molecular lab. This work would likely involve sequewncing a portion of the mtDNA cyt b gene from existing samples, but also experimenting with extractions, primer design, PCR and sequencing from museum skins. For the morphometric work, the student initially would conduct photographing skulls and saving to a server, but can also be involved in data analysis if they are interested and have the background in statistics.

Qualifications: For the morphometric work, a background in statistics would be great. We might also consider reading field notes to better understand habitat characteristics and coding that. If someone has GIS skills, we might consider doing niche modeling.

Weekly Hours: 6-8 hrs

Related website: https://en.wikipedia.org/wiki/Trowbridge%27s_shrew