The 'next generation’ of ancient DNA research: a series of methods and approaches to improve our understanding of the evolutionary history of species in general, and European bison in particular

Abstract

Understanding the complex and dynamic processes underlying the evolutionary history of species is key for predicting how species evolve and respond to changes in their environment. This is particularly important for the development of appropriate conservation management strategies for species that are currently under threat or predicted to come under threat in the future. While modern DNA may be available, identifying long term patterns of evolutionary history in extant populations can be confounded by more recent population events (such as bottlenecks or local extinctions). Instead, DNA from ancient specimens can be used to directly observe genetic changes through the evolutionary history of a species as well as reconstruct the demographic history of both extinct and extant species or populations. However, the small number of specimens typically included in ancient DNA studies often limits their interpretations to fairly general or location specific conclusions. In this thesis, I developed approaches for the integration of genetic and nongenetic datasets, specifically combining modern and ancient DNA data, geographic and temporal information, palaeoenvironmental predictions, and historical records to improve our understanding of evolutionary processes. In order to maximise the inclusion of ancient DNA data, I have optimised techniques for sequencing and processing data (Chapters 2 & 3). Collectively these methods significantly improve the recovery of ancient DNA data from larger numbers of poor quality samples. Larger datasets subsequently facilitate the investigation of broad-scale continental patterns of species evolution and response to environmental change. European bison are a particularly good model for studying the responses of megafaunal species to environmental change. Samples are available from both modern and ancient individuals, and European bison have persisted across a broad geographic change throughout periods of dramatic Pleistocene environmental change. In addition, the evolutionary history of European bison remains unclear and relatively few ancient samples have been analysed (Chapter 4). I applied the optimised methods from Chapters 2 & 3 to a large set of European bison samples, significantly increasing the recovery of ancient genetic data and creating a much larger ancient DNA dataset for subsequent analysis. Using this comprehensive dataset comprising samples from across the temporal and geographic range of the species, I delineated patterns of genetic change through time in both mitochondrial (Chapter 5) and nuclear (Chapter 6) genomes. To identify potential drivers of evolution I combined palaeoenvironmental data (such as palaeoecology and palaeoclimate), and historical records with patterns of genetic change. Using this approach, I found that historical changes in forest cover and anthropogenic impacts were primary drivers of European bison evolution, and shaped their modern diversity and distribution (Chapters 5 & 6). Ultimately the research presented in my thesis contributes towards the ‘next-generation’ of ancient DNA research, providing a series of approaches to optimise recovery of genetic data from ancient samples, and combining genetic and non-genetic datasets in order to further our understanding of how species evolve and respond to environmental change.