Investigating faunal responses to climate and environmental change using ancient DNA from ursids

Abstract

The Late Quaternary Period (the past ~1.0 million years) is characterised by cyclical growth and retraction of glaciers and polar ice caps driven by periods of cooler and warmer global temperatures. Ancient DNA has emerged as a key tool for unravelling the impacts of climate and environmental change as it enables detection of population and species level changes that would otherwise be undetectable. Ursids (bears) have shown potential as a model taxon for investigating faunal responses to climate and environmental change during the Late Quaternary, especially brown bears (Ursus arctos), which have an extensive subfossil record, Holarctic distribution, and well-studied mitochondrial phylogeography. My PhD research uses ancient DNA techniques to investigate the evolutionary history of ursids during the Late Quaternary. In Chapters 2 and 5 I use analyses of new mitochondrial genome sequences from 217 ancient brown bears to investigate phylogeographic structure across their Holarctic distribution and refine their mitochondrial phylogeny, revealing striking patterns of migration and population turnover that correlate with drastic changes in the climate and environment during the Pleistocene. In Chapter 2 I also demonstrate that population changes observed in North American brown bears are paralleled by changes in lion populations, suggesting analogous drivers of phylogeographic structure and population dynamics between these two carnivorans. In Chapter 3 I use 31 mitochondrial genomes from the extinct North American giant shortfaced bear, Arctodus simus, to investigate their phylogeography and taxonomy, revealing striking sexual dimorphism and a lack of evidence for previously described subspecies. Finally, in Chapter 4 I use whole genome data from extinct short-faced bears to investigate the evolutionary history of Tremarctinae and find evidence for extensive hybridisation resulting in phylogenetic discordance between the mitochondrial and nuclear genomes. My research demonstrates the usefulness of ancient DNA datasets for understanding the evolutionary history of species and populations. Further, I argue that my data provide added evidence for the suitability of ursids as model taxa for studying Quaternary biogeography, as they appear to have exhibited pronounced responses to past climate and environmental change, have undergone extensive hybridisation among species within the family (including extinct lineages), and comprise species that both survived and went extinct during the Pleistocene-Holocene transition.