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Investigating Evolutionary Processes Using Ancient and Historical DNA of Rodent Species

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Investigating Evolutionary Processes Using Ancient and Historical DNA of Rodent Species Investigating evolutionary processes using ancient and historical DNA of rodent species Thesis submitted for the degree of Doctor of Philosophy (PhD) University of London Royal Holloway University of London Egham, Surrey TW20 OEX Selina Brace November 2010 1 Declaration I, Selina Brace, declare that this thesis and the work presented in it is entirely my own. Where I have consulted the work of others, it is always clearly stated. Selina Brace Ian Barnes 2 “Why should we look to the past? ……Because there is nowhere else to look.” James Burke 3 Abstract The Late Quaternary has been a period of significant change for terrestrial mammals, including episodes of extinction, population sub-division and colonisation. Studying this period provides a means to improve understanding of evolutionary mechanisms, and to determine processes that have led to current distributions. For large mammals, recent work has demonstrated the utility of ancient DNA in understanding demographic change and phylogenetic relationships, largely through well-preserved specimens from permafrost and deep cave deposits. In contrast, much less ancient DNA work has been conducted on small mammals. This project focuses on the development of ancient mitochondrial DNA datasets to explore the utility of rodent ancient DNA analysis. Two studies in Europe investigate population change over millennial timescales. Arctic collared lemming (Dicrostonyx torquatus) specimens are chronologically sampled from a single cave locality, Trou Al’Wesse (Belgian Ardennes). Two end Pleistocene population extinction-recolonisation events are identified and correspond temporally with - localised disappearance of the woolly mammoth (Mammuthus primigenius). A second study examines postglacial histories of European water voles (Arvicola), revealing two temporally distinct colonisation events in the UK. Two further studies of Caribbean rodent species assess DNA recovery from more recent, yet highly degraded, material. The Hispaniolan hutia (Plagiodontia aedium), one of the few remaining endemic Caribbean land mammals, is found to represent three distinct lineages, biogeographically consistent with the island’s Cenozoic origins and geographic heterogeneity. The extinct Antillean rice rats (Oryzomyini) were once endemic throughout the Lesser Antilles. Phylogenetic analysis of zooarchaeological rice rat material recovered from across the Lesser Antillean reveals a new genus of rice rat and at least two separate colonisation events, via over water dispersal, from South America. These overall findings demonstrate the utility of ancient rodent DNA in eliciting individual response patterns across rodent species and exploring topics of wider evolutionary interest. 4 Acknowledgements My foremost and heartfelt thanks go to my supervisor Ian Barnes, for his support and encouragement. I would particularly like to thank him for providing an environment that gave me freedom to learn and discover my way, but who was always available with a wealth of knowledge, ideas, discussions, coffee, beer and cigarettes whenever I needed them. My external advisors, John Stewart and Samuel Turvey were also very supportive, both with their advice and encouragement. I would also like to thank them for providing me with many of the samples required for this thesis. I appreciate your trust. This project would not have been possible without funding from NERC, I am very grateful for their generosity. Likewise for all the museums that permitted me to sample their collections: Bournemouth University; Florida Museum of Natural History; Hungarian Institute of Geology; Leiden University; Manchester University Museum; Moscow Institute of Geography; Museum of Comparative Zoology, University of Harvard; Musee national de Prehistoire; Natural History Museum, London; Royal Belgian Institute of Natural Sciences; Royal Holloway University of London; Sheffield City Museum; University of Ferrara; United States National Museum University of Southampton; Also to Danielle Shreeve and Adrian Lister for material, radiocarbon dates and helpful comments and my internal supervisor Vincent Jansen. I thank Mark Thomas and Adam Powell for carrying out the coalescent modelling utilised in the hutia chapter, and to Mark Thomas for his continued encouragement and support since my undergraduate days. Mark Ruddy sourced many of the water vole samples used in this study, but also provided helpful discussions and an appreciated sharp wit! I’d also like to thank Rebecca Pearson and Carolyn Kelday for their assistance in the laboratory and Rebecca Miller for her assistance regarding sampling details at TAW. 5 A special thanks goes to everyone who made Nevis such a memorable experience, Sam, Brad, Pam, Bee-man and the late Jim Johnson. I’d like to thank Jeremy Field for getting me started at UCL and many people at Royal Holloway who have given advice, assistance and friendship. I would particularly like to thank, Anouschka Hof, Robin Williams, Mark Brown, Nial McKeown, Jenny MacPherson, and all fellow members, both past and present from LaMP, especially: Love Dalén, Jessica Thomas and Pete Heintzman. And the ladies in Cafe Jules, for their chats and copious amounts of coffee that have kept me going. I am particularly grateful to my dear friend Meirav Meiri, who has shared the trials and tribulations of this PhD journey and whose kindness, caring spirit and support kept me on the right path. My family and friends deserve a special thank you. For reminding me of the ‘little train’, their continued belief in me and for keeping me going: Kti Naud - whose passion for science and life is inspirational, Lucas Tizon, Darren Sidaway and Andrew Ramsey – for always listening and lifting my spirits, Annie Towns, Jo Clayton, Pete Self, the MGGS gals, Mark Graindorge – for the fine cuisine and words of wisdom, and to Edwin van Leeuwen – whose patience is legend-worthy and calm, kind nature have been a rock and finally a thank you to Wilma, who won’t care if I succeed or fail. To everyone, I thank you for the laughter, tears and beers, I wouldn’t have got this far without you. 6 Contents Title page ................................................................................................................1 Declaration ..............................................................................................................2 Abstract ...................................................................................................................4 Acknowledgements..................................................................................................5 Contents...................................................................................................................7 List of Figures .......................................................................................................11 List of Tables.........................................................................................................13 List of Appendices.................................................................................................14 List of Abbreviations.............................................................................................15 Chapter 1: General Introduction .........................................................................16 1.1 Introduction..........................................................................................16 1.2 The geologic scale................................................................................16 1.3 Rodentia...............................................................................................17 1.4 Quaternary climate change ...................................................................19 1.5 Europe..................................................................................................22 1.6 Caribbean.............................................................................................24 1.7 Ancient DNA .......................................................................................27 1.8 Difficulties with an aDNA approach.....................................................30 1.8.1 small sample sizes ...................................................................30 1.8.2 aDNA degradation...................................................................30 1.8.3 aDNA contamination...............................................................32 1.9 Resolutions and precautionary measures...............................................32 1.9.1 Small sample sizes...................................................................32 1.9.2 aDNA authentication ...............................................................32 1.10 The use of mitochondrial DNA (mtDNA)...........................................33 1.11 Analyses.............................................................................................34 1.11.1 Nucleotide sequence evolution...............................................34 1.11.2 Maximum likelihood..............................................................37 1.11.3 Bootstrapping ........................................................................37 1.11.4 Bayesian ................................................................................38 7 1.11.5 Divergence dating..................................................................39 1.11.6 Coalescent modelling.............................................................40 1.12 Thesis aims.........................................................................................41
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