Just in time for winter, Stanford scientists studying genetics of hibernation in squirrels have illuminated the biology behind food intake, insulin, and slowed metabolism with potential applications in humans.

December 20, 2019. An article, written by Stanford Bustamante Lab alumni Katherine Grabek, Thomas Cooke, Shirley Sutton, and Kaitlyn Spees, and Biomedical Data Science faculty Carlos D. Bustamante and published today in Nature Communications Biology, has identified for the first time genetic variants associated with the onset of seasonal hibernation. In research funded by an EAGER grant from the National Science Foundation and support from the National Institutes of Health Heart, Lung and Blood Institute (NHLBI), investigators examined the genetics of hibernation onset using phenotype and genotype data from 13-lined ground squirrels implanted with telemeters and maintained in an environmentally-controlled laboratory setting to remove potential environmental effects.

Hibernation is a complex trait for which the genetic basis has remained elusive. As a strategy to survive cold winters when food availability is low, ground squirrels eat copious amounts of food over the summer and accumulate large amounts of fat mass. They begin hibernation in the fall and emerge from it in the spring. During hibernation, these animals deeply suppress metabolic, heart, and respiratory rates while lowering body temperature to near freezing to maximize energy savings. Additionally, they cease all food intake at the onset of hibernation and subsist solely off of their fat reserves over the winter. 

“This is a landmark study for the field of hibernation. To the best of our knowledge, a genetic-mapping approach has never been applied to this very complex trait. Here we propose candidate genes that will be of great interest for researchers studying hibernation. The methods employed here can easily be adopted to understand the effect of genetic variation on other traits related to hibernation in this and other species,” states Carlos Bustamante, senior author of the work and Professor of Biomedical Data Science at Stanford University as well as Co-Founding Director of the Center for Computational, Evolutionary and Human Genomics (CEHG).

To provide more insight into the genetics of hibernation, the researchers first tripled the contiguity of the 13-lined ground squirrel’s draft genome assembly using Dovetail’s HiRise pipeline. They next employed a genotype-by-sequencing strategy to characterize genetic variation in 153 ground squirrels, and coupled this information to datalogger records of hibernation onset.

Strikingly, the team found that the timing of hibernation onset was largely due to genetic variation, with a heritability estimate of 61-100%.

“When I started my postdoctoral fellowship with Carlos, one of the first things he asked me was how much of hibernation was heritable. Although I had studied hibernation as a graduate student, I realized that there was almost no information on heritability and how genetic variation influenced hibernation. I decided that answering this question would be a focus of my postdoctoral research,” states Katharine Grabek, lead author on the paper and a former postdoctoral scholar in the Bustamante Lab. Dr. Grabek is currently the CSO of Fauna Bio, a company started in 2018 to identify novel therapeutics using genomics from hibernators and other non-model organisms.

Applying a genome-wide scan, these researchers next identified two genetic loci significantly associated with the timing of hibernation onset. They also found that just 14 loci explained most of the variation in the timing of hibernation onset. These loci resided near genes involved in the control of food intake, insulin signaling, and the control of heart rate – all processes related to hibernation physiology.

After resequencing the whole genomes of 12 squirrels, the team identified a putative causal variant linked to the most significantly associated locus and situated within the promoter of FAM204A. The investigators confirm that this locus exerts an effect on FAM204A expression by applying an expression quantitative trait loci (eQTL) analysis using transcriptome datasets. They also identified significant gene expression associations for seven additional suggestively-associated loci.

The authors believe that the loci identified in their study may lead to better insight into the genes underlying seasonal physiology and behavior in humans, especially in the context of metabolism, body mass and control of food intake. Dr. Bustamante states, "Biology is the science of cycles and we’ve shown hibernation is a tightly controlled cycle with individual variation. For me, I won’t feel so guilty about putting on a few pounds during the holidays since I know in the spring, my metabolism is likely to naturally correct... for the squirrels, it means they can tough out the winter at 4 °C body temperatures and then emerge to eat for four months like crazy to do it all over again. It’s pretty amazing!”

The authors also emphasized that while their research is a great first step in applying genetic-mapping to hibernation, larger studies are needed to verify their suggestively-associated loci and to identify additional loci associated with hibernation onset. Finally, the authors conclude that their findings are poignant in the greater context of climate change, as warmer autumns may result in a mismatch for species relying on genetic factors to time winter dormancy.

First Author Katherine "Katie" Grabek

Co-author Carlos D. Bustamante, PhD

13-lined ground squirrel, image courtesy of Katie Grabek