Genetic Investigation of Irish Ancestry and Surname History
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Genetic Investigation of Irish Ancestry and Surname History Brian Patrick McEvoy A thesis submitted to the University of Dublin for the degree of Doctor of Philosophy Department of Genetics University of Dublin Trinity College September 2004 DECLARATION I hereby certify that this thesis, submitted to the University of Dublin, Trinity College, for the degree of Doctor of Philosophy, has not been presented for examination at this or any other university. The research described herein is entirely my own unless otherwise stated and acknowledged. This thesis may be made available for consultation within the university library and may be copied or loaned to other libraries for the purposes of consultation. Brian McEvoy September 2004 ii ACKNOWLEDGEMENTS “No man is an island entire of itself; every man is a piece of the Continent, a part of the main”. Although John Donne may not have been thinking about the PhD process when he wrote this in 1624, his words sum up my feelings on the great group of people whose support and encouragement make this work possible. First and foremost to Dan Bradley, for giving me the opportunity to work in this field and, what‘s more, making sure I ploughed it thoroughly. His patient direction and creativity were crucial and this thesis would simply not have been possible without his input. A big thank you to each and every member of the lab, past and present: Caitriona, Elaine, Emma, Dave, David, Jill, Laoise, Stephen and Valeria, for their never-ending willingness to help, and for their friendship, which always made the lab such a great place to be. It was a privilege and pleasure to work with you all. A special word of gratitude to Ruth for all her help over the past four years, and to Ceiridwen for always offering the right advice at the right time. In addition, thanks to all the temporary members of the lab over the years, particularly Claire and Mindy for their part in the Viking work. My appreciation also to the members of the wider TCD Genetics Department for their help; I am particularly grateful to Professors Ken Wolfe and David McConnell, Sue, Dave, Brenda, Paul and everyone in the Gill and Wolfe labs, too numerous to mention everyone but your individual help was always appreciated. The National Millennium Committee, through the Royal Irish Academy, and the generosity of Patrick Guinness and Joseph A. Donohoe, funded this research. The interest, enthusiasm and help of Patrick and Joseph were appreciated and it was always a great encouragement to know there was a willingness to support this field of research, in every respect. I pay particular tribute to Patrick Guinness in this regard. iii I was very fortunate over the past few years to interact with the wider population genetics community and never ceased to be amazed by their willingness to help. The input of Peter Forster, and especially Martin Richards, in the mtDNA work is gratefully acknowledged and appreciated. Thanks also to all my family and friends for their support over the past few years, especially my parents, for keeping a long-term student, and Deirdre and Mike, for feeding and ―watering‖ me! Last and by no means least, a huge word of appreciation to all the volunteers who donated DNA samples and without whom this research really would not have been possible. Go raibh míle maith agaibh go léir ! iv CONTENTS DECLARATION ii ACKNOWLEDGEMENTS iii CONTENTS v FIGURES xi TABLES xiv ABBREVIATIONS xv SUMMARY xvii CHAPTER 1 GENERAL INTRODUCTION 1 1.1 DNA and the Human Past 2 1.2 Exploring Genetic Diversity 3 1.3 Ancient DNA 6 1.4 Reconstructing the Past from the Present 7 1.5 The Male and Female Perspective 8 1.6 Genetics and Hereditary Social Traditions 9 1.7 A Brief History of Ireland 11 1.8 Genetic Variation and Irish Origins 14 1.9 Present Study 15 CHAPTER 2 GENETIC DIVERSITY ON THE ATLANTIC FAÇADE OF EUROPE 16 2.1 INTRODUCTION 17 2.1.1 Atlantic Genetic Affinities 17 2.1.2 European mtDNA Diversity 18 2.1.3 Celtic Languages 19 2.1.4 Celtic Ethnogenesis 20 2.1.5 Atlantic Celts 20 2.1.6 Present Study 21 2.2 MATERIALS AND METHODS 22 2.2.1 Subjects and Samples 22 2.2.2 DNA Extraction 23 2.2.3 mtDNA HVS-1 Sequencing 23 v 2.2.4 mtDNA SNP Genotyping 25 2.2.5 Analysis of mtDNA Phylogeography 27 2.2.6 mtDNA Population Affinities 27 2.2.7 HVS-1 Sequence Quality Checks 28 2.2.8 Inter-population Genetic Distances 29 2.2.9 Multidimensional Scaling 29 2.2.10 Y Chromosome and Autosomal Diversity 31 2.2.11 Synthetic Surface Maps 32 2.2.12 Spatial Autocorrelation 32 2.3 RESULTS 34 2.3.1 Irish mtDNA Diversity 34 2.3.2 Neolithic and Palaeolithic Haplogroups in Ireland 35 2.3.3 Phylogeography of Irish mtDNA Lineages 36 2.3.4 European mtDNA Population Affinities 40 2.3.5 European Y chromosome and Autosomal Variation 41 2.3.6 Congruence of mtDNA and other Genetic Systems 43 2.4 DISCUSSION 44 2.4.1 European mtDNA Structure 44 2.4.2 Atlantic Façade Genetic Legacy 44 2.4.3 Irish Maternal and Paternal Past 46 2.4.4 Genetic Heterogeneity in the British Isles 47 2.4.5 Close Affinity of Scotland and Ireland 48 2.4.6 Conclusions 49 CHAPTER 3 LONGITUDINAL AUTOSOMAL GENETIC VARIATION IN IRELAND 50 3.1 INTRODUCTION 51 3.1.1 Longitudinal Gradients of Variation in Ireland 51 3.1.2 Irish Blood Group Frequencies 52 3.1.3 Intra-Ireland Molecular Genetic Variation 52 3.1.4 Detecting Regional Substructure 54 3.1.5 Present Study 55 vi 3.2 MATERIALS AND METHODS 56 3.2.1 Classical Gene Frequency Analysis 56 3.2.2 Autosomal STR Markers and Samples 57 3.2.3 Analysis of Autosomal STR Allele Frequencies 58 3.2.4 Autosomal STR Model-based Clustering 60 3.3 RESULTS 61 3.3.1 Classical Gene Frequencies 61 3.3.2 Autosomal STR Genetic Distances 62 3.3.3 Structure Analysis of Autosomal STR Genotypes 65 3.4 DISCUSSION 66 3.4.1 Classical Gene Substructure within Ireland 66 3.4.2 Genome-wide Autosomal STR Variation 66 3.4.3 Model-based Clustering versus Genetic Distances 68 3.4.4 Conclusions 69 CHAPTER 4 PATRILINEAL ANCESTRY IN IRISH SURNAMES 70 4.1 INTRODUCTION 71 4.1.1 Surnames and Genetics 71 4.1.2 Y Chromosomes and Surnames 71 4.1.3 Early Irish Names 73 4.1.4 Hereditary Surnames in Ireland 74 4.1.5 Irish Genealogical Tradition 76 4.1.6 The McGuinness Surname 77 4.1.7 The Donohoe Surname 78 4.1.8 Present Study 80 4.2 MATERIALS AND METHODS 81 4.2.1 Overview of Sample Collection Strategy 81 4.2.2 McGuinness and East Ulster Sample Collection 82 4.2.3 Donohoe and Cavan Area Sample Collection 84 4.2.4 Estimation of Surname Frequency 85 4.2.5 Y Chromosome Short Tandem Repeats 85 4.2.6 Y Chromosome Unique Event Polymorphisms 88 vii 4.2.7 Median-Joining Networks 90 4.2.8 Y Chromosome STR Weighting 91 4.2.9 Y Chromosome Cluster Definition 93 4.2.10 TMRCA of Y chromosome Lineages 94 4.2.11 Congruence of Surnames and Y Chromosomes 95 4.3 RESULTS 98 4.3.1 McGuinness Surname Y Chromosome Diversity 98 4.3.2 Geography and Age of McGuinness Y Chromosome Lineages 100 4.3.3 McGuinness and Putative Subsidiary Surnames 101 4.3.4 Y Chromosome Landscape of East Ulster 105 4.3.5 Congruence of Y chromosomes and Surnames in East Ulster 110 4.3.6 Origin of McGuinness in West Ulster/North Connacht 112 4.3.7 Donohoe Surname Y Chromosome Diversity 112 4.3.8 Y Chromosome Landscape of the Cavan Region 116 4.4 DISCUSSION 120 4.4.1 Surnames and Patrilineal Ancestry 120 4.4.2 Origin of the McGuinness Surname 120 4.4.3 McGuinness Family Reunion 121 4.4.4 Ancient Y Chromosome Diversity in East Ulster 123 4.4.5 Origin and History of the Donohoe Surname 124 4.4.6 Conclusions 125 CHAPTER 5 Y CHROMOSOME INVESTIGATION OF IRISH SURNAME HISTORIES 126 5.1 INTRODUCTION 127 5.1.1 Gaelic Surname Diversity 127 5.1.1.a Byrne 128 5.1.1.b Kennedy 128 5.1.1.c Ryan 128 5.1.1.d O‘Neill 129 5.1.1.e O‘Sullivan 129 5.1.1.f McCarthy 130 5.1.1.g O‘Gara and O‘Hara 130 5.1.1.h Bradley 135 viii 5.1.1.i Kelly 135 5.1.1.j Murphy 136 5.1.1.k McEvoy 136 5.2 MATERIALS AND METHODS 137 5.2.1 Sample Collection 137 5.2.2 Laboratory and Analytical Methods 138 5.3 RESULTS 139 5.3.1 Congruence of Paternal Ancestry and Surname 139 5.3.2 Y Chromosome Diversity in Individual Surnames 142 5.3.2.a Byrne 142 5.3.2.b Kennedy 146 5.3.2.c Ryan 146 5.3.2.d O‘Neill 149 5.3.2.e O‘Sullivan 149 5.3.2.f McCarthy 150 5.3.2.g O‘Gara and O‘Hara 151 5.3.2.h Bradley 157 5.3.2.i Kelly 157 5.3.2.j Murphy 160 5.3.2.k McEvoy 160 5.3.3 Inter-relationship of Major Surname Lineages 163 5.3.4 TMRCA Estimates and STR Mutation Rate 166 5.4 DISCUSSION 168 5.4.1 What is in an Irish Surname? 168 5.4.2 Agreement of Y Chromosomes and History 169 5.4.3 Surnames and Geography 170 5.4.4 The Complexity of Surname History 171 5.4.5 Variation in Surname Frequency 172 5.4.5 Conclusions 174 CHAPTER 6 SCANDINAVIAN ADMIXTURE IN AN IRISH NORSE SURNAME POPULATION 175 6.1 INTRODUCTION 176 ix 6.1.1 The Vikings and Ireland 176 6.1.2 Viking Settlement in Ireland 177 6.1.3 The Genetic Legacy of the Viking Era 178 6.1.4 Norse Surnames and Paternal Ancestry 179 6.1.5 Estimating Population Admixture 179 6.1.6 Present Study 181 6.2 MATERIALS AND METHODS 182 6.2.1 Sample Collection 182 6.2.2 Y Chromosome Genotyping 182 6.2.3 Analysis of UEP Variation 183 6.2.4 Analysis of STR Variation 184 6.2.5 Admixture Estimation 184 6.2.5.a mR 185 6.2.5.b mC 185 6.2.5.c my 186 6.2.5.d mL 186 6.2.5.e mW 187 6.2.5.f m 188 6.2.5.g Parental Populations 188 6.3 RESULTS 189 6.3.1 Phylogeography of Norse Surname Y Chromosomes 189 6.3.2 Norse Surname Group Population Affinities 190 6.3.3 Scandinavian Admixture Estimates 192 6.3.4 Parental Population in Admixture Estimates 194 6.3.5 Marker Type and Method Choice in Admixture Estimates 194 6.4 DISCUSSION 196 6.4.1 Nature of Hiberno-Norse Society 196 6.4.2 Quantitative Admixture Estimators 197 6.4.3 mL and the Neolithic Revolution 198 6.4.4 Conclusions 199 REFERENCES 200 x FIGURES CHAPTER 1 Figure 1.1 Map of the Historical Counties and Provinces of Ireland 13 CHAPTER 2 Figure 2.1 Estimated dispersal points or centres of gravity for the 146 MtDNA HVS-1 haplotypes found in Ireland 37 Figure 2.2 Multidimensional scaling (MDS) plot of inter-population ST values calculated from mtDNA control region sequence data 38 Figure 2.3 Synthetic surface maps of Europe displaying the three significantly correlated dimensions of genetic variation.