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Genetic Variation of the X Chromosome and the Genomic

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Genetic Variation of the X Chromosome and the Genomic Genetic variation of the X chromosome and the genomic regions of Coagulation Factors VII and XII in human populations: Epidemiological and evolutionary considerations Georgios Athanasiadis ADVERTIMENT. La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del servei TDX (www.tdx.cat) i a través del Dipòsit Digital de la UB (diposit.ub.edu) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposició des d’un lloc aliè al servei TDX ni al Dipòsit Digital de la UB. No s’autoritza la presentació del seu contingut en una finestra o marc aliè a TDX o al Dipòsit Digital de la UB (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona autora. ADVERTENCIA. La consulta de esta tesis queda condicionada a la aceptación de las siguientes condiciones de uso: La difusión de esta tesis por medio del servicio TDR (www.tdx.cat) y a través del Repositorio Digital de la UB (diposit.ub.edu) ha sido autorizada por los titulares de los derechos de propiedad intelectual únicamente para usos privados enmarcados en actividades de investigación y docencia. No se autoriza su reproducción con finalidades de lucro ni su difusión y puesta a disposición desde un sitio ajeno al servicio TDR o al Repositorio Digital de la UB. No se autoriza la presentación de su contenido en una ventana o marco ajeno a TDR o al Repositorio Digital de la UB (framing). Esta reserva de derechos afecta tanto al resumen de presentación de la tesis como a sus contenidos. En la utilización o cita de partes de la tesis es obligado indicar el nombre de la persona autora. WARNING. On having consulted this thesis you’re accepting the following use conditions: Spreading this thesis by the TDX (www.tdx.cat) service and by the UB Digital Repository (diposit.ub.edu) has been authorized by the titular of the intellectual property rights only for private uses placed in investigation and teaching activities. Reproduction with lucrative aims is not authorized nor its spreading and availability from a site foreign to the TDX service or to the UB Digital Repository. Introducing its content in a window or frame foreign to the TDX service or to the UB Digital Repository is not authorized (framing). Those rights affect to the presentation summary of the thesis as well as to its contents. In the using or citation of parts of the thesis it’s obliged to indicate the name of the author. Genetic variation of the X chromosome and the genomic regions of Coagulation Factors VII and XII in human populations: Epidemiological and evolutionary considerations Doctoral thesis presented by Georgios Athanasiadis in solicitation of the degree of Doctor of Philosophy awarded by the University of Barcelona Directed by Dr. Pedro Moral Castrillo, Professor of Physical Anthropology at the Unit of Anthropology, Department of Animal Biology University of Barcelona Doctorate Programme of Biodiversity Department of Animal Biology – Faculty of Biology Pedro Moral Castrillo Georgios Athanasiadis Director Doctorate student Variación genética en el cromosoma X y las regiones genómicas de los Factores de Coagulación VII y XII en poblaciones humanas: Consideraciones epidemiológicas y evolutivas Tesis doctoral presentada por Georgios Athanasiadis para optar al grado de Doctor por la Universidad de Barcelona Dirigida por el Dr. Pedro Moral Castrillo, Profesor Titular de Antropología Física de la Unidad de Antropología del Departmento de Biología Animal de la Universidad de Barcelona Programa de Doctorado de Biodiversidad Departmento de Biología Animal – Facultad de Biología Pedro Moral Castrillo Georgios Athanasiadis Director Doctorando Αφιερωμένο στη μνήμη του παππού μου, Παύλου Δαμιανού Dedicated to the memory of my grandfather, Pavlos Damianos O princípio da ciência é sabermos Que ignoramos. Fernando Pessoa, A Hora do Diabo ACKNOWLEDGEMENTS Barcelona, 11 April 2010 It has been more than five years since I left my life in Thessaloniki for Barcelona. Looking back, I can see in myself of those days some of the qualities that brought me where I am today: innocence, effortless optimism and decisiveness. I am so grateful that reason was not my foremost consultant back then! Had it been so, I would never have renounced the comfort of my Greek lifestyle (my compatriots should know exactly what I mean). I now am one step before finishing my doctoral studies and I feel the need to thank all the people who had something to do with it. The first person to thank could be no other but my supervisor, Pedro Moral. With his positive answer to my first email, he opened a door of unimaginable possibilities for me. Pedro, gracias por enseñarme cómo hacer ciencia, por nunca decirme un no, por tratarme como a un hijo… I would also like to thank all the people in the Moral lab: Esther, Marc, Emili, Josep and Magda R for being next to me when I first joined the group, but also the people who came later, Magda G and Robert. Thank you for all the help you gave me and for the endless hours of conversation and exchange of ideas. You have been the best company ever and made all this worth even more! Also, many thanks to the Moral people I met throughout these years but haven’t had the opportunity to know better: Toni, Neus V, Natalia, Meri, Eva and Ares. But my doctoral studies were not all about Barcelona; in the last three years I had the rare fortune to visit three very important research centres outside Spain, which gave a real boost to my CV. I therefore am eternally grateful to Dr. Cathryn Lewis and Dr. Mike Weale from King’s College London, Dr. Mark Stoneking from the Max Planck Institute for Evolutionary Anthropology in Leipzig and Dr. John Hopper from the University of Melbourne for hosting me at their labs and making me feel like home. Also, many thanks to all the wonderful people I met in these places together with my apologies for not mentioning each one of them separately. From this section, how could there be missing a special mention to all the people from the “Unitat d’Antropologia”? Mireia, Neus M and Marta (the best representation of The Three Graces ever!); Bàrbara, Araceli, Mar, Mari, Nàdia, Sílvia and the rest of the Lourdes Girls (my apologies to Sergi!); Jordi, Bea, Ferràn, Laura and Mohammed; and last but not least the “big bosses” – Lourdes, Clara, Miquel, Alejandro and Txomin –, thank you for all the little things that spiced up our day-to-day routine at work! A més, moltes gràcies a Dr. Pons per la seva amabilitat i noblesa. Vostè és tota una inspiració per a mi! There are also so many friends who stood next to me throughout these years. Starting from the closest and oldest ones, I want to thank Christina and Panagiotis for their pure friendship, devotion and moral support. Είμαι πολύ τυχερός που είστε φίλοι μου! Also, many thanks to the rest of my friends – older and more recent – for all the happy moments we shared: Vasilis D, Vasilis B, Despoina, Modesta, Albert, Matteo, Serguei, Alessandro, Mario, Rossella, Magie, Oseas, John, Savvas… the list is endless! Special thanks to my dear friend James for reading through my thesis and making all the necessary language corrections. James, this work would not be the same without your help. Finally I feel the need to thank my family, my beloved brother and sister – Damon and Sophie –, my mum and dad – Chrysoula and Panagiotis – and my granny Kyriaki for their unconditional love and silent but constant moral and material support. It took me some time to realise it, but I now see it clearly: family is where everything starts and where everything ends. Χωρίς εσάς δε θα ήμουν ούτε το μισό από αυτό που είμαι τώρα. Contents Table of Contents Introduction 3 GENETIC VARIATION IN HUMANS 5 Processes that shape genetic variation 6 Mutation 6 Recombination 7 Genetic drift 9 Selection 11 Migration 13 Molecular markers and genetic analysis: a retrospect 15 Main types of molecular markers studied 19 Alu elements 19 Microsatellites 23 Single nucleotide polymorphisms 26 HUMAN POPULATIONS IN THE MEDITERRANEAN 29 Migration in the Mediterranean 29 The prehistoric colonisations 29 The great trading colonies of antiquity 34 The ‘Barbarian’ invasions 36 The Arab invasion 38 Genetic studies in the Mediterranean 39 Genetic studies based on neutral markers 40 Genetic studies with an epidemiological interest 43 POPULATION GENETIC STUDIES AND CARDIOVASCULAR DISEASE: EPIDEMIOLOGICAL APPLICATIONS 47 Studies of the genetic basis of complex diseases: general concepts 47 Linkage studies 47 Association studies 48 Family trios: a special case of association studies 49 The pathophysiology of cardiovascular diseases 51 Ischemic heart disease 53 Definition 53 Angina pectoris 54 Myocardial infarction 54 Risk factors 55 Mortality rates 55 Haemostasis and thrombotic risk 56 Coagulation factor VII 57 Coagulation factor XII 57 POPULATIONS STUDIED IN THIS WORK 59 General populations 60 Southwest Europe 60 Southeast Europe 61 North Africa 61 The Ivory Coast 62 Native American Bolivia 63 Samples for epidemiological studies 63 Family trios from Spain 63 Case-control from Tunisia 64 Goals 65 GOALS OF THE STUDY 67 Results 69 SUPERVISOR’S REPORT ON THE QUALITY OF THE PUBLISHED ARTICLES 71 Results I - Athanasiadis et al., 2007 73 Resumen
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