Resolving the Evolutionary Relationships of Two Enigmatic Ungulates from Pleistocene North America

Ancient DNA (aDNA) data have been integral to investigation of the iconic and mostly extinct Late Pleistocene megafauna, and have provided a wealth of evolutionary and ecological insights such as the response of past populations to climate change. Despite being a major focus of more than two decades of aDNA research, however, there are still members of the Late Pleistocene megafauna whose DNA has been too degraded for use in previous studies. Recent methodological advances have the potential to unlock these difficult taxa for aDNA analysis and the suite of important questions that these data can potentially address. In this study, we focused on two extinct North American ungulate taxa, whose evolutionary relationships with closely related taxa have been controversial based on inferences from morphology. Using whole mitochondrial and low coverage nuclear genomes, derived from target capture and shotgun sequencing, we demonstrate the robust phylogenetic placement of these taxa and provide a framework for future large-scale population genomic analyses.