Sequencing a symbol: The genome of a California golden bear
Background: Have you ever wondered why there is a bear on California’s state flag? Did you know that he was actually a living bear who became famous? That bear’s name was Monarch and he was very special. He was one of the last of his kind, one of the last of the California grizzly bears. Monarch was captured in Ventura County in 1889 as part of a publicity stunt. He lived for for the rest of his life on display at Woodward Gardens, Golden Gate Park and the San Francisco Zoo. Monarch survived the 1906 San Francisco earthquake, becoming a symbol for the city’s reconstruction. He lived on for 22 years in captivity while the rest of his kind were hunted to extinction. Monarch’s story is not a completely happy one, but through our efforts and your kind donations, we at the UCSC Paleogenomics lab hope to raise awareness about his story and learn all that we can about this special bear through his DNA.
Bears are important members of their ecological communities in that they regulate prey populations and disperse seeds in their stools and on their coats. Grizzly bears (Ursus arctos) today are endangered. Their range once ran from Alaska down to Mexico and from California to the Great Plains. Today they are only found in Washington, Montana, Wyoming, Idaho, Alaska and western Canada. There are multiple kinds (subspecies) of grizzly bears. Since it’s extinction, very little is known about the California grizzly bear (Ursos arctos californicus). Some questions that may be answered using DNA include: How related was it to other types of grizzly bears? How related was it to other species of bears?
Morphologically, there is quite a range of phenotypes for brown bears in regards to size and fur color, and that led to their initial splitting into over 90 subspecies in the past. Miller used a segment of the control region of the mitochondria to show that this was largely taxonomic over-splitting, and that North American brown bear populations have a similar maternal ancestry (Miller et al., 2006). We do plan to compare full nuclear genomes of brown bears to see if this holds true or if this California population was divergent enough to merit a subspecies status.
North American brown bears all have polar bear nuclear ancestry within their genome, highest in the ABC Islands. This is because the ABC Islands brown bears are thought to originate from a population of polar bears that were stranded on the Alaskan coastline. As a result of generations of male biased gene flow of brown bears into this isolated polar bear population, they have increased levels of polar bear ancestry in their sex chromosomes compared to their autosomes, and share a mitochondrial lineage with polar bears. Thus ABC Island brown bears have the highest percentage polar bear nuclear content, and this percentage decreases with geographical distance from the islands. (Cahill et al., 2013 Cahill et al., 2015) We will determine the amount of polar bear ancestry in its nuclear genome using newly developed Hidden Markov Modeling techniques.
Cahill, J. A., Stirling, I., Kistler, L., Salamzade, R., Ersmark, E., Fulton, T. L., Stiller, M., Green, R. E. and Shapiro, B. (2015), Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Mol Ecol, 24: 1205–1217. doi:10.1111/mec.13038
Cahill JA, Green RE, Fulton TL, Stiller M, Jay F, Ovsyanikov N, et al. (2013) Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution. PLoS Genet 9(3): e1003345. doi:10.1371/journal.pgen.1003345
Miller, C.R., Waits, L.P., and Joyce, P. (2006). Phylogeography and mitochondrial diversity of extirpated brown bear (Ursus arctos) populations in the contiguous United States and Mexico. Molecular Ecology 15, 4477–4485.