UC Berkeley Scientists Use SDSC Resources to Study House Mice

Published April 26, 2022

 Photo by Alexas Fotos

By Kimberly Mann Bruch, SDSC External Relations

UC Berkeley scientists Michael Nachman and Elizabeth Beckman have been studying environmental adaptation of house mice for many years. Their latest project, which utilized San Diego Supercomputer Center (SDSC) resources, looked at how house mice colonize and adapt to high elevations in Ecuador and Bolivia. They discovered that several hypoxia-associated genes were different in the mice at the higher elevations and that some of these genes exhibited a threshold effect—a large shift in allele frequency at only the highest elevations. Their findings were recently published in Genetics.

“This study is a continuation of earlier work on the genetic basis of environmental adaptation in house mice, and in a paper that we published last year we identified genes underlying adaptation to cold weather,” said Nachman, UC Berkeley professor of integrative biology and director of the campus’s Museum of Vertebrate Zoology. “In our earlier study we found that there was some predictability to evolution, both at the organismal level and at the genetic level.  However, in the present study, we found mostly distinct evolutionary responses to high elevation in mice from Ecuador and mice from Bolivia, showing that adaptation to high elevations can occur through changes in many different genes and pathways.”

For their latest study titled The Genomic Basis of High-Elevation Adaptation in Wild House Mice (Mus musculus domesticus) from South America, the researchers used Extreme Science and Engineering Discovery Environment (XSEDE) allocations on Comet at SDSC. Specifically, they used a package called FastP to clean raw sequence reads and then aligned them to the M. musculus reference genome (GRCm38) with BWA (v 0.7.13) using the BWA-MEM algorithm.

The scientists used XSEDE allocations on Comet to index aligned reads in Samtools and next used the Genome Analysis Toolkit (v 4.0.11.0) to merge data across lanes, remove duplicates and recalibrate base quality.

“We were able to complete our large-scale bioinformatic analyses in a timely and robust way thanks to our XSEDE allocation and SDSC resources,” said Beckman, a postdoctoral researcher at Berkeley. “Now, we are using Expanse to continue our study of environmental adaptation across North and South America in house mice, as well as high-elevation adaptation in South American finches,” she said.

This research was supported by an NIH grant to Nachman (R01 GM127468). Computations on SDSC resources were allocated by XSEDE (TG-MCB130109).

About San Diego Supercomputer Center

SDSC, located at UC San Diego, is a leader in data-intensive computing and cyberinfrastructure, providing resources, services and expertise to the national research community, including industry and academia. SDSC supports hundreds of multidisciplinary programs spanning a wide variety of domains, from earth sciences and biology to astrophysics, bioinformatics and health IT.