UC Santa Cruz

Bison are iconic mammals that have enormous ecological and cultural significance, and face several current threats to their existence. Despite their abundance in the fossil record throughout Eurasia and North America over the past several hundred thousand years, many aspects of their evolutionary history are unresolved. A diversity of skeletal morphologies exist, recorded in Paleolithic cave paintings and in the bones bison left behind, but it is unclear how these forms correspond at the genetic level. Deep divergences between bison mitochondrial haplotypes, along with discordance between nuclear and mitochondrial phylogenies which groups European bison with cattle, also hint at complex bison population dynamics. No ancient bison nuclear genomes have yet been sequenced to provide insight into past bison populations. The recent demographic history of bison also obscures the past. Bison in both Europe and North America underwent drastic, human-mediated population collapses over the past couple of centuries, with tens to hundreds of individuals remaining in each region. The extreme nature of these events makes it difficult to fully understand the effect they had on bison populations, and it is likely that present bison diversity incompletely represents what existed before. This dissertation aims to recover bison population dynamics across the Northern Hemisphere over the Late Pleistocene and Holocene. In the following chapters, I discuss the creation of genomic tools for making bison a model system studying evolution using large-scale whole genome ancient DNA datasets. First, I summarize recent molecular and computational advances which allow for generating and analyzing population-scale ancient genomic data, and discuss the insights that may be gained in doing so. Then, I describe generating a high quality bison reference genome, which is used to mitigate reference bias, a pervasive problem in ancient DNA. Next, I examine population dynamics in Eurasian and North American bison in the Late Pleistocene. I then focus on the recent effects of the population crash undergone by North American bison, describing extensive connectivity over large geographic distances which has been disrupted by the bottleneck and subsequent management. There were, however, specific human-facilitated gene flow events between bison subspecies and between bison and cattle, though the extent of the latter has been widely overstated. Finally, I show that most Beefalo, a cattle breed which supposedly originated through cross-breeding between bison and cattle, have no bison ancestry.