Comparative phylogeography as an integrative approach to understand human and other mammal distributions in Europe.

Abstract

Phylogeography refers to the phylogenetic analysis of organisms in the context of their geographical distribution. The analytical methods build phylogenetic trees and networks from haplotypes in order to investigate the history of the organisms. Phylogeographic studies have revealed the importance of climatic oscillations and the role of the Last Glacial Maximum (27,500 to 16,000 years ago) with the formation of refugia where distinct haplotypes originate in Europe. The population expansions and contractions into these refugial areas have driven the evolution of different lineages but the similarities and differences between species are still poorly understood. This thesis aims to gain a better understanding of the phylogeographical processes of different mammals’ species in Europe. This was done by collecting published mitochondrial DNA control region sequences of 29 different species and analysing them individually and comparatively. This research presents a standardised way of understanding phylogeography from the mitochondrial DNA perspective to improve the comparison of studies in the field. The project investigates the patterns of genetic diversity by examining various diversity indices to test for trends and commonalities. To enhance knowledge in phylogeography and the importance of refugia during the Last Glacial Maximum in Europe through a comparative phylogeographic meta-analysis of mammal species. This thesis developed novel insights into the phylogeographic interactions of different mammal species, including modern humans, in the European geographical context. Modern human phylogeography pattern from the short control region has been contextualised in the patterns observed for other mammal species, showing a homogeneous distribution across the continent. Finally, the commensal species Mus musculus domesticus (western house mouse) was investigated in detail from a current and a past phylogeographic perspective in two islands, Cyprus and Britain, using ancient and modern DNA. This was done using this new knowledge as a bioproxy to understand more recent human movements associated with the transport of this species. This thesis, therefore, provides an integrated study with a new comparative framework and with results on the phylogeographical patterns of humans and other mammals in Europe.