A Genomic Analysis of Two Early Christian Cemetery Communities from Sudanese Nubia Public
Sirak, Kendra (Spring 2018)
Published
Abstract
The Early Christian Period (550–800 C.E.) site of Kulubnarti, located in Sudanese Nubia, is hypothesized to have been home to two distinct subpopulations, with the landowning members of the “R community” inhabiting the west bank of the Nile River, and the more impoverished members of the semi-itinerant “S community” occupying an adjacent Nilotic island. While bioarchaeological analyses of stress-induced lesions and life expectancy consistently found that members of the S community were exposed to more stress, experienced more ill-health, and died younger than members of the R community, biodistance studies based on morphology as a proxy for genetic variation suggested that the two communities were a single, biologically-indistinguishable population. However, without direct genetic analysis, the relationship between the two communities and their biogeographic origins and affinities to present-day populations have remained poorly resolved. This dissertation uses ancient DNA to address these questions from a high-resolution genomic perspective for the first time.
By analyzing genome-wide Single Nucleotide Polymorphisms (SNPs) in 28 individuals from Kulubnarti, this dissertation 1) Explores the genetic relationship between the S and R communities by looking for evidence of community-based genetic population substructure through patterns of clustering and estimation of genetic distance; and 2) Characterizes the genetic composition of individuals from both communities and reveals any community-based differences by exploring biogeographic genetic affinities and components of ancestry and determining the mitochondrial and Y chromosome haplogroup profiles of each community.
While analyses of autosomal SNPs identify no community-based genetic population substructure at Kulubnarti and suggest that from a genomic perspective, the two communities were a single population with the most affinity to present-day populations from Northeastern Africa, analyses of uniparental markers reveal that genetic signatures of Eurasian-associated patrilineal ancestry were overrepresented in the S community and that genetic signatures of Eurasian-associated matrilineal ancestry were overrepresented in the R community. By suggesting that the genetic signatures of sex-specific gene flow were reflected at Kulubnarti in a community-based way, this dissertation reveals a previously unknown pattern of genetic variation and provides a model for interpreting patterns of genetic variation within the context of broader sociocultural dynamics.
Table of Contents
CHAPTER 1: INTRODUCTION
1.1 Dissertation Overview.............................................................................1
1.2 Background...........................................................................................2
1.2.1 Nubia...........................................................................................2
1.2.2 Kulubnarti.....................................................................................4
1.3 Research Questions and Rationale............................................................8
1.4 Kulubnarti from a Genomic Perspective....................................................11
1.5 Dissertation Outline.................................................................................13
CHAPTER 2: THEORETICAL PERSPECTIVES IN NUBIAN ARCHAEOLOGY
2.1 Chapter Overview..................................................................................16
2.2 Introduction..........................................................................................17
2.3 The First Archaeological Survey of Nubia and the Racial Determinist
Perspective...........................................................................................20
2.4 The Second Archaeological Survey of Nubia and the Racial
Typological Perspective..........................................................................23
2.5 The UNESCO Campaign and the Biocultural Approach.................................25
2.6 Kulubnarti from a New Perspective...........................................................28
2.6.1 Moving Toward a Genomic Perspective...........................................30
2.6.2 A Genomic Analysis of Kulubnarti..................................................31
CHAPTER 3: KULUBNARTI
3.1 Chapter Overview................................................................................33
3.2 Nubia.................................................................................................34
3.2.1 Physiographic Subdivisions of Nubia.............................................35
3.2.2 Corridor to Africa.......................................................................37
3.2.3 Medieval Nubia (550–1500 C.E.)..................................................38
3.3 The Batn el Hajar.................................................................................44
3.3.1 Climate and Subsistence.............................................................46
3.4 Kulubnarti...........................................................................................48
3.4.1 Subsistence and Survival at Kulubnarti.........................................49
3.4.2 Archaeology at Kulubnarti...........................................................51
3.4.3 The Cemeteries.........................................................................52
3.5 Bioarchaeology of Kulubnarti.................................................................56
3.5.1 Relatedness Between the S and R Communities.............................56
3.5.2 Social Disparity at Kulubnarti.......................................................59
3.5.3 The Underclass..........................................................................62
3.6 Kulubnarti: A Summary.........................................................................64
CHAPTER 4: ANCIENT DNA
4.1 Chapter Overview................................................................................67
4.2 DNA Overview.....................................................................................68
4.3 The Human Genome.............................................................................71
4.3.1 Sequencing the Human Genome..................................................74
4.3.2 Human Genetic Diversity.............................................................75
4.4 Single Nucleotide Polymorphisms (SNPs).................................................76
4.4.1 Quantifying Genetic Distance Using SNPs......................................79
4.4.2 Assessing Biogeographic Affinities and Ancestries Using SNPs..........81
4.5 Introduction to Ancient DNA..................................................................83
4.5.1 Ancient DNA and Anthropology....................................................85
4.6 Challenges in Ancient DNA....................................................................88
4.6.1 Contamination..........................................................................88
4.6.2 Ancient DNA Damage................................................................92
4.6.3 Environment and Temperature....................................................95
4.7 Direction of this Dissertation.................................................................97
CHAPTER 5: RESEARCH STRATEGY
5.1 Chapter Overview...............................................................................100
5.2 The Kulubnarti Skeletal Collection.........................................................101
5.3 From Bones to Bytes: The Research Strategy.........................................103
5.3.1 Use of the Osseous Labyrinth....................................................104
5.3.2 Screening...............................................................................108
5.3.3 Targeted Enrichment and SNP Capture.......................................110
5.4 Aim 1: Analyzing Genetic Relationships at Kulubnarti..............................111
5.5 Aim 2: Characterizing Genetic Composition at Kulubnarti.........................114
5.6 Limitations........................................................................................125
5.6.1 Representativeness...................................................................125
5.6.2 Contemporaneity......................................................................127
CHAPTER 6: SAMPLE PREPARATION AND SCREENING
6.1: Chapter Overview..............................................................................128
6.2: Sample Selection and Preparation........................................................130
6.2.1 Selection of the Petrous Bone....................................................130
6.2.2 Sample Processing...................................................................133
6.2.3 DNA Extraction.........................................................................140
6.2.4 Construction of Next-Generation Sequencing Libraries...................143
6.2.5 PCR Amplification......................................................................149
6.2.6 Post-PCR Processing..................................................................150
6.3 Screening #1: Next-Generation Shotgun Sequencing...............................153
6.3.1 Preparation for Next-Generation Shotgun Sequencing....................153
6.3.2 Sequencing..............................................................................154
6.3.3 Processing of Sequencing Data...................................................157
6.3.4 Screening Results.....................................................................162
6.4 Sample Preparation and Screening #2: MTspike3k Capture.......................166
6.4.1 DNA Extraction........................................................................166
6.4.2 Construction of Libraries............................................................167
6.4.3 MTspike3k Capture....................................................................172
6.4.4 Indexing PCR and Sequencing of Capture Products........................174
6.4.5 Processing of Sequencing Data...................................................175
6.4.6 Screening Results.....................................................................178
6.5 1240K SNP Capture.............................................................................180
6.5.1 Benefits of 1240K SNP Capture...................................................181
6.5.2 1240K SNP Capture...................................................................182
6.5.3 Data Processing and Alignment...................................................182
CHAPTER 7: GENETIC RELATIONSHIPS AT KULUBNARTI
7.1 Chapter Overview................................................................................184
7.2 The 1240K Human Origins Dataset.........................................................184
7.3 Assessing Population Substructure at Kulubnarti.......................................187
7.3.1 Analytical Method: Principal Component Analysis (PCA)...................187
7.3.2 PCA of the Kulubnarti Nubians......................................................190
7.3.3 Interpretation of PCAs................................................................194
7.4 Quantifying Genetic Distance at Kulubnarti...............................................195
7.4.1 Analytical Method: FST................................................................195
7.4.2 Genetic Distance at Kulubnarti.....................................................198
7.4.3 Interpretation of FST Results........................................................202
7.5 Chapter Summary.................................................................................204
CHAPTER 8: GENETIC COMPOSITION OF THE KULUBNARTI NUBIANS
8.1 Chapter Overview.................................................................................207
8.2 Assessing Biogeographic Genetic Affinities and Components of
Ancestry at Kulubnarti..........................................................................207
8.2.1 Analytical Methods: Principal Component Analysis and
ADMIXTURE Clustering Analysis..................................................208
8.2.2 Biogeographic Genetic Affinities and Ancestry Components
of the Kulubnarti Nubians...........................................................211
8.2.3 Caveats to PCAs and ADMIXTURE Analysis...................................221
8.2.4 Interpretation of PCAs and ADMIXTURE Analysis...........................222
8.3 Determining Haplogroup Profiles at Kulubnarti........................................232
8.3.1 Analytical Method: Calling mtDNA Haplogroups............................232
8.3.2 mtDNA Haplogroups of the Kulubnarti Nubians.............................236
8.3.3 Interpretation of mtDNA Haplogroups..........................................238
8.3.4 Analytical Method: Calling Y Chromosome Haplogroups..................245
8.3.5 Y Chromosome Haplogroups of the Kulubnarti Nubians..................247
8.3.6 Interpretation of Y Chromosome Haplogroups..............................249
8.3.7 Comparing mtDNA and Y Chromosome Haplogroup Profile
of the Kulubnarti Nubians.........................................................256
8.4 Chapter Summary...............................................................................258
CHAPTER 9: A SUMMARY: KULUBNARTI FROM A GENOMIC PERSPECTIVE
9.1 Chapter Overview...............................................................................260
9.2 A Single Genetic Population.................................................................262
9.3 Biogeographic Genetic Affinity to Present-Day Northeastern
Africans............................................................................................265
9.4 Community-Based Variation in mtDNA and Y Chromosome
Haplogroup Profiles............................................................................270
9.5 A Hypothetical Scenario......................................................................277
9.6 Future Directions...............................................................................278
9.7 Concluding Thoughts..........................................................................281
REFERENCES..........................................................................................283
SUPPLEMENT 1: SAMPLE PROCESSING DATA FROM NINETY-NINE SCREENED KULUBNARTI SAMPLES.............................................................................337
SUPPLEMENT 2: NEXT-GENERATION SEQUENCING DATA FROM NINETY-NINE SCREENED KULUBNARTI SAMPLES............................................................349
SUPPLEMENT 3: MAPDAMAGE PLOTS FOR NINETY-NINE SCREENED KULUBNARTI SAMPLES..........................................................................357
SUPPLEMENT 4: SEXING PLOTS FOR NINETY-NINE SCREENED KULUBNARTI SAMPLES..............................................................................................378
SUPPLEMENT 5: PCA..............................................................................429
SUPPLEMENT 6: PAIRWISE FST ESTIMATES..............................................434
SUPPLEMENT 7: ADMIXTURE ANALYSIS...................................................448
SUPPLEMENT 8: MITOCHONDRIAL HAPLOGROUPS.....................................457
SUPPLEMENT 9: Y CHROMOSOME HAPLOGROUPS......................................471
SUPPLEMENT 10: RELATEDNESS ANALYSIS...............................................476
APPENDIX A: DABNEY EXTRACTION PROTOCOL.........................................496
APPENDIX B: MEYER AND KIRCHER LIBRARY PREPARATION PROTOCOL............................................................................................500
APPENDIX C: OLIGO SEQUENCES.............................................................507
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