| dc.description.abstract | Much of wildlife research is plagued by outdated molecular methods and bison studies are no exception. The aim of this work is to push the boundaries of population genetics in bison and to update and build upon previously existing techniques to provide a more accurate assessment of population health, genetic diversity, and the level of domestic cattle introgression in the bison genome. I also aimed to develop protocols and analyses that would swiftly translate to other wildlife species. To that effect, I looked at several different genomic markers, including the whole mitochondrial genome, microsatellites, as well as genome-wide SNPs. A great deal of my research revolved around the single most important US bison herd at Yellowstone National Park. Using whole mitochondrial sequences from 25 Yellowstone bison, the levels of genetic diversity and population subdivision were established, and constructing a large dataset of 65 bison from all across North America helped reveal the signatures of the most recent historic bottleneck and how it has affected the herd. In order to conduct future experiments with a less constrained and more random way of sampling bison, the quality of DNA from fecal samples was also assessed by directly comparing them to paired blood samples from the same 50 Yellowstone bison. In addition to establishing a set of 15 markers that performed reliably with bison fecal samples, we have also shown that there is a statistically significant reduction in heterozygosity estimates from fecal samples if the paired sample method is not implemented during marker selection. This discrepancy is often overlooked by previous researchers, causing them to present data that underestimate the genetic diversity in various wildlife species. Indubitably, the biggest threat facing bison genomic integrity today is domestic cattle introgression that has left the majority of bison today riddled with domestic cattle chromosomal segments. I set out to create a SNP-based in-depth genotyping assay to differentiate cattle- and bison-like segments with high resolution.
To that effect, I analyzed 40 bison from all across North America and found that the least introgressed of the herds appears to be the one at Santa Catalina Island, a herd with known high levels of mitochondrial albeit low levels of nuclear cattle introgression. Thus, no herd could be identified to date that did not have a recent cattle influence, including herds that were previously thought to be non-introgressed, such as the herds at Yellowstone National Park, Wind Cave National Park, and the plains bison of Canada. The likely reason for introgression in many of these herds can be traced back to three male bison that were introduced into Yellowstone National Park in 1902. In addition, multiple historical hybridization events between plains and wood bison were uncovered, some of which occurred in the United States. | en |
