The Origins and Spread of the Neolithic in the Old World Using Ancient Genomes
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The origins and spread of the Neolithic in the Old World using Ancient Genomes UNIVERSITY OF CAMBRIDGE Marcos Gallego Llorente Selwyn College This dissertation is submitted for the degree of Doctor of Philosophy September 2017 2 Author’s Declaration This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except as declared in the Preface and specified in the text. I further state that no substantial part of my dissertation has already been submitted, or, is being concurrently submitted for any such degree, diploma, or other qualification at the University of Cambridge or any other University or similar institution. The main text does not exceed 60,000 words. 3 4 Summary One of the biggest innovations in human prehistory was the advent of food production, consisting of the ability to grow crops and domesticate animals for consumption. This wide-scale transition from hunting and gathering to food production led to more permanent settlements, and set in motion major societal changes. In western Eurasia, this revolution spread from the Near East into Europe, Africa and diverse regions of Asia. Agriculture was brought into Europe by the descendants of early Anatolian farmers starting approximately 8,000 years ago. But little was known of the people who developed agriculture in the Fertile Crescent: where they all closely related to the early Anatolian farmers, or were there multiple ethnic groups who developed agriculture in parallel? In the first data chapter, I use the first genome from a Neolithic woman from Ganj Dareh, in the Zagros Mountains (Iran), a site with evidence of early goat domestication 10,000 years ago. I showed that Western Iran wan inhabited by populations mostly similar to Hunter- gatherer populations from the Caucasus, but remarkably, very distinct from the Anatolian farmers who spread the Neolithic package into Europe. While a degree of cultural diffusion between Anatolia, Mesopotamia and the Zagros highlands likely happened, genetic dissimilarity supports a model in which Neolithic societies of that area were distinct. The second chapter deals with how Africa was affected by population movements, originating in the Near East, during the Neolithic times. Characterising genetic diversity in Africa is a crucial step for analyses reconstructing human evolution. Using Mota, an ancient genome from a male from the Ethiopian highlands, I showed a backflow into Africa by populations closely related to the Anatolian Neolithic farmers. The third chapter deals with some common problems and themes in the analysis of ancient DNA, such as merging capture datasets with diverse number of ascertained SNPs, combining capture and shotgun data in the same analysis, and the effect of UDG treatment in ancient samples. I describe the most common problems and their effect in summary statistics, and propose a guide on how to work with ancient DNA to avoid data compatibility problems. 5 6 Acknowledgements The past four years have been, without any doubt, the most enriching and exciting years of my life. I have developed myself in ways I never thought would have been possible, and that has been thanks to the people that have been around me, and have provided me with the support, trust, company, and happiness that I needed to complete my PhD. First and foremost, my thanks go to Andrea Manica, by far the best supervisor I could have ever wished for. His availability, his trust, his support in the good moments and in the difficult ones, his enthusiasm, and his vast knowledge have always been there. He has undoubtedly been the main pillar of my time in the office. I have learned so much from him, academically, professionally and personally, that he has been an inspiration for my life, and definitely will continue to be so. Thank you so much for everything, Andrea. The Evolutionary Ecology Group has been my home for the last four years, and I am grateful to have had such a great group of people in which to trust, rely upon, and generally expect the best of times while in the office and outside. Anders, Robert, Riva, Veronika, Eppie, Liisa, Pier Paolo, Marius, Tommy, Anne Sophie, Mario: it was great to work in such a great environment. Robert especially: I won’t forget our late evenings in the office discussing whatever random philosophical aspect of life while doing work. Also, those sunsets in the old office: unforgettable. Anders, Veronika and Eppie also deserve special mentions for helping me out whenever I needed a bit of bioinformatical advice – thanks so much. And thanks Riva for our occasional deep talks over coffee breaks, they were often very much needed. You all have been inspirations in one way or another, and have definitely shaped my experience here in a great way. Life in Cambridge, however, wouldn’t have been the same without my closest friends from Selwyn. My most special and heartfelt thanks go to Michał, Jessica, Alex and Max. You have been my home. Our evenings together, our unforgettable MCR dinners, our trip to Marrakech, our summery and wintery days out, and, in short, the discovery of Cambridge we’ve made together, have constituted the memories I’ll treasure the most of my time here. 7 To everybody else that I’ve had the pleasure to call a friend: Pablo, Nathalie, Max, Melissa, Harvey, Emmy, Afnan, Lucía, Ben, Luci, Swati, Farid, Isabelle, Leanne, James, Julia, Raj, Fedir, Eva: I am glad I have had the pleasure to share my Cambridge experience with you. To the Selwyn College Boatclub: for helping me overcome every challenge I never thought would be possible, for the early winter mornings, the sunny summer evenings, the bumps, the 2016 blades, and for making me proud of being part of such a great group of people. Nick, Nigel, Sam, Harry, George, Will, DBR, JPG, Charlie & Charlie, and Felix: Been a pleasure. I would like to thank Selwyn College for being my home away from home all these years, and for helping me attend the SMBE 2016 in Gold Coast, Australia, where I presented part of this thesis. In addition, I would like to thank the BBSRC for the funding needed for this PhD. During my PhD and throughout all my education, I have been incredibly lucky to receive the trust and support from my parents, my numerous siblings, and my family: They have been such a great motivation that has allowed me to follow my dreams and aspirations. Muchísimas gracias por todo. Y por último, a mis amigos de toda la vida: Manu, Dani, Ricardo, Diego, Laus, Marina, Gabriel, Christian: no olvidaré nuestras tardes de navidades y nuestras noches de verano. Ojalá nunca me dejéis olvidar de dónde vengo. Ha sido un placer. 8 Contents Author’s Declaration 3 Summary 5 Acknowledgements 7 Contents 9 1. Introduction 11 1.1 Bioanthropology before the advent of palaeogenetics 11 1.2 Ancient DNA 21 1.3 Understanding human prehistory with ancient DNA 25 1.4 Objective and structure of this thesis 29 2. The genetics of an early Neolithic pastoralist from the Zagros, Iran 31 Abstract 31 Introduction 32 Results 35 Discussion 55 Methods 57 3. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa 63 Abstract 63 Introduction 65 Results 69 Discussion 90 Methods 92 4. Analysis of the challenges in the compatibility of ancient genetic data of different sources and their solutions 97 Abstract 97 The problem with ascertainment bias in SNP datasets 98 Introduction 98 Results 99 Discussion 103 The problem with platform bias 104 Introduction 104 Results 106 Discussion 114 Methods 116 5. General Discussion 121 References 131 9 10 Introduction | 1 1. Introduction 1.1. Bioanthropology before the advent of palaeogenetics The emergence and expansion of Anatomically Modern Humans Anatomically Modern Humans (AMHs) constitute all the humans in today’s world: members of the species Homo sapiens, with an osteological and behavioural modernity that encompasses the entirety of modern phenotypic variation. The first defining feature of AMHs in the fossil record is osteological modernity. The human archaeological record fully supports a slow, gradual accumulation of the osteological features that define AMHs, which happened more than 200k years ago (Bräuer, 2008; McDougall et al., 2005). This fossil record equally suggests that these modern morphological features evolved in Africa, while the only inhabitants of Eurasia were the Neanderthals and other archaic humans (Pearson, 2008; Weaver, 2012). There are fossils in Ethiopia (the Herto and Omo skulls), dated to 195k and 160k years ago, which start to resemble the form that AMHs would eventually acquire, although there is still a hint of robustness resembling more archaic features. There is a temporal gap between the origin of the fully anatomically modern form and the eventually successful expansion out-of-Africa between 100k and 60k years ago. This has been subject to an intense paleoanthropological debate, and it is a study area where future climate reconstructions and genetic studies will undoubtedly shed some light in the future. The second defining feature of all current humans is our current behavioural characteristics, sometimes labelled as behavioural modernity: an accumulation of a series of changes in cognition and behaviour, which include language, abstract thinking, symbolic behaviour (art, music and rites), deep planning, and the usage of inanimate natural resources for daily tasks such as hunting megafauna and toolmaking. Some of these characteristics might however been already present in more archaic humans, such as language (D’Anastasio et al., 2013). Although this suite of developments is evident from 60k years ago, Richard Klein in 1995 argued that these changes that accumulated in order to give rise to AMHs were very gradual (Klein, 1995).