Aim: Identifying how climate change, habitat loss, and corridors interact to influence species survival or extinction is critical to understanding macro-scale biodiversity dynamics under changing environments. In North America, the ice-free corridor was the only major pathway for northward migration by megafaunal species during the last deglaciation. However, the timing and interplay among the late Quaternary megafaunal extinctions, climate change, habitat structure, and the opening and reforestation of the ice-free corridor have been unclear. Location: North America. Time period: 15–10 ka. Major taxa studied: Woolly mammoth (Mammuthus primigenius). Methods: For central North America and the ice-free corridor between 15 and 10 ka, we used a series of models and continental-scale datasets to reconstruct habitat characteristics and assess habitat suitability. The models and datasets include biophysical and statistical niche models Niche Mapper and Maxent, downscaled climate simulations from CCSM3 SynTraCE, LPJ-GUESS simulations of net primary productivity (NPP) and woody cover, and woody cover based upon fossil pollen from Neotoma. Results: The ice-free corridor may have been of limited suitability for traversal by mammoths and other grazers due to persistently low productivity by herbaceous plants and quick reforestation after opening 14 ka. Simultaneously, rapid reforestation and decreased forage productivity may have led to declining habitat suitability in central North America. This was possibly amplified by a positive feedback loop driven by reduced herbivory pressures, as mammoth population decline led to the further loss of open habitat. Main conclusions: Declining habitat availability south of the Laurentide Ice Sheet and limited habitat availability in the ice-free corridor were contributing factors in North American extinctions of woolly mammoths and other large grazers that likely operated synergistically with anthropogenic pressures. The role of habitat loss and attenuated corridor suitability for the woolly mammoth extinction reinforce the critical importance of protected habitat connectivity during changing climates, particularly for large vertebrates.

Humans evolved in a world of giant creatures. Current evidence suggests that most ice age megafauna went extinct around the transition to our current Holocene epoch. The ecological reverberations associated with the loss of over 65% of Earth’s largest terrestrial animals transformed ecosystems and human lifeways forever thereafter. However, there is still substantial debate as to the cause of this mass extinction. Evidence variously supports climate change and anthropogenic factors as primary drivers in the restructuring of the terrestrial biosphere. Much of the ongoing debate is driven by the insufficient resolution accessible via macro-remains. To help fill in the gaps in our understandings of the Pleistocene-Holocene transition, I utilized the growing power of sedimentary ancient DNA (sedaDNA) to reconstruct shifting signals of plants and animals in central Yukon. To date, sedaDNA has typically been analyzed by amplifying small, taxonomically informative regions. However, this approach is not ideally suited to the degraded characteristics of sedaDNA and ignores most of the potential data. Means of isolating sedaDNA have also suffered from the use of overly aggressive purification techniques resulting in substantial loss. To address these limitations, I first experimentally developed a novel means of releasing and isolating sedaDNA. Secondly, I developed a novel environmental bait-set designed to simultaneously capture DNA informative of macro-scale ecosystems. When combined, we identify a substantial improvement in the quantity and breadth of biomolecules recovered. These optimizations facilitated the unexpected discovery of horse and mammoth surviving thousands of years after their supposed extirpation. I followed up these results by extracting DNA from multiple permafrost cores where we confirm the late survival signal and identify a far more complex and high-resolution dataset beyond those identifiable by complementary methods. I was also able to reconstruct mitochondrial genomes from multiple megafauna simultaneously solely from sediment, demonstrating the information potential of sedaDNA. / Dissertation / Doctor of Philosophy (PhD) / A new addition to the rapidly growing field of palaeogenetics is environmental DNA (eDNA) with its immense wealth of biomolecules preserved over millennia outside of biological tissues. Organisms are constantly shedding cells, and while most of this DNA is metabolized or otherwise degraded, some small fraction is preserved through sedimentary mineral-binding. I experimentally developed new ancient eDNA methods for recovery, isolation, and analysis to maximize our access to these biomolecules and demonstrate that this novel approach outperforms alternative protocols. Thereafter, I used these methods to extract DNA from ice age permafrost samples dating between 30,000–6,000 years before present. These data demonstrate the power of ancient eDNA for reconstructing ecosystem change through time, as well as identifying evidence for the Holocene survival of caballine horse and woolly mammoth in continental North America. This late persistence of Pleistocene fauna has implications for understanding the human ecological and climatological factors involved in the Late Pleistocene mass extinction event. This effort is paralleled with megafaunal mitogenomic assembly and phylogenetics solely from sediment. This thesis demonstrates that environmental DNA can significantly augment macro-scale buried records in palaeoecology.