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Comparative Phylogeography As an Integrative Approach to Understand Human and Other Mammal

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Comparative Phylogeography As an Integrative Approach to Understand Human and Other Mammal Comparative phylogeography as an integrative approach to understand human and other mammal distributions in Europe Luis Oxala García Rodríguez A thesis submitted in partial fulfilment of the requirements of Bournemouth University for the degree of Doctor of Philosophy June 2019 This page intentionally left blank II This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with its author and due acknowledgement must always be made of the use of any material contained in, or derived from, this thesis. III Comparative phylogeography as an integrative approach to understand human and other mammal distributions in Europe. Oxala García Rodríguez 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. IV 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. V Table of contents Abstract ................................................................................................................................. IV List of Figures ........................................................................................................................ IX List of Tables ......................................................................................................................... XV Acknowledgements ........................................................................................................... XVIII Author’s declaration ........................................................................................................... XXI Chapter 1. General introduction ............................................................................................ 1 1.1 Introduction and literature review ...................................................................................... 1 1.1.1 Phylogeography ............................................................................................................ 1 1.1.2 Comparative phylogeography ...................................................................................... 3 1.1.3 Climate during the last 60 kya in Europe ...................................................................... 7 1.1.4 Phylogeographic patterns in Europe after the LGM and comparison between modern humans and other mammals ................................................................................................. 9 1.1.5 Human-mediated phylogeographic patterns ............................................................. 14 1.2 Research Outline ................................................................................................................ 15 1.2.1 Research aims and objectives ..................................................................................... 15 1.2.2 Thesis structure ........................................................................................................... 17 Chapter 2. Material and Methods ....................................................................................... 19 2.1 Introduction ....................................................................................................................... 19 2.2 Genetic delimitations ......................................................................................................... 21 2.3 Species collection ............................................................................................................... 23 RODENTIA ............................................................................................................................ 26 LAGOMORPHA ..................................................................................................................... 30 EULIPOTYPHLA ..................................................................................................................... 31 CARNIVORES ........................................................................................................................ 33 ARTIODACTYLA .................................................................................................................... 39 2.4 Geographical delimitations ............................................................................................... 43 2.5 Database ............................................................................................................................ 44 2.6 Data analysis ..................................................................................................................... 48 Chapter 3. Modern mammalian genetic diversity in Europe .............................................. 51 3.1 Introduction ....................................................................................................................... 51 3.2 Materials and Methods ..................................................................................................... 52 3.2.1 Data collection ............................................................................................................ 52 3.2.2 Data analysis .............................................................................................................. 54 VI 3.3 Results ............................................................................................................................... 55 3.4 Discussion .......................................................................................................................... 61 3.5 Conclusion ......................................................................................................................... 66 Chapter 4. Identifying genetic diversity patterns shaped by the LGM in modern humans and other mammal species .................................................................................................. 67 4.1 Introduction ....................................................................................................................... 67 4.2 Methods ............................................................................................................................ 70 4.3 Results ............................................................................................................................... 72 4.3.1 Species by species ....................................................................................................... 72 RODENTIA ........................................................................................................................... 72 LAGOMORPHA .................................................................................................................... 92 EULIPOTYPHLA .................................................................................................................... 98 CARNIVORES ...................................................................................................................... 104 ARTIODACTYLA .................................................................................................................. 125 4.3.2 Phylogeographic patterns based on diversity indices for mammals in Europe ....... 146 4.4 Discussion ........................................................................................................................ 149 4.5 Conclusion ......................................................................................................................
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