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Scheidel W. Fitness and Power: The Contribution of Genetics to the History of Differential Reproduction. EVOLUTIONARY PSYCHOLOGY 2021; 19:14747049211066599. [PMID: 34918580 PMCID: PMC10303451 DOI: 10.1177/14747049211066599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 11/28/2021] [Indexed: 11/16/2022] Open
Abstract
Textual evidence from pre-modern societies supports the prediction that status differences among men translate to variance in reproductive success. In recent years, analysis of genetic data has opened up new ways of studying this relationship. By investigating cases that range over several millennia, these analyses repeatedly document the replacement of local men by newcomers and reveal instances of exceptional reproductive success of specific male lineages. These findings suggest that violent population transfers and conquests could generate considerable reproductive advantages for male dominants. At the same time, this does not always seem to have been the case. Moreover, it is difficult to link such outcomes to particular historical characters or events, or to identify status-biased reproductive inequalities within dominant groups. The proximate factors that mediated implied imbalances in reproductive success often remain unclear. A better understanding of the complex interplay between social power and genetic fitness will only arise from sustained transdisciplinary engagement.
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2
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Lall GM, Larmuseau MHD, Wetton JH, Batini C, Hallast P, Huszar TI, Zadik D, Aase S, Baker T, Balaresque P, Bodmer W, Børglum AD, de Knijff P, Dunn H, Harding SE, Løvvik H, Dupuy BM, Pamjav H, Tillmar AO, Tomaszewski M, Tyler-Smith C, Verdugo MP, Winney B, Vohra P, Story J, King TE, Jobling MA. Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain. Eur J Hum Genet 2020; 29:512-523. [PMID: 33139852 PMCID: PMC7940619 DOI: 10.1038/s41431-020-00747-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/08/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We find three specifically Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; star-like features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian influence within Britain. Neither shows any frequency difference between regions that have higher (≥10%) or lower autosomal contributions from Norway and Sweden, but both are significantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-specific contribution, or the influence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia.
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Affiliation(s)
| | - Maarten H D Larmuseau
- Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium.,Laboratory of Socioecology and Social Evolution, KU Leuven-University of Leuven, Leuven, Belgium.,Histories vzw, Zoutwerf 5, 2800, Mechelen, Belgium
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,School of History, Politics and International Relations, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Pille Hallast
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, 50411, Estonia
| | - Tunde I Huszar
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Daniel Zadik
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | | | - Tina Baker
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Patricia Balaresque
- UMR5288, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Université Paul Sabatier, Toulouse, France
| | - Walter Bodmer
- Department of Oncology, University of Oxford, Oxford, UK
| | - Anders D Børglum
- Department of Biomedicine & Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Hayley Dunn
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, Sutton Bonington Campus, Loughborough, UK.,Museum of Cultural History, University of Oslo, Oslo, Norway
| | | | - Berit Myhre Dupuy
- Division of Forensic Sciences, Norwegian Institute of Public Health, Oslo, Norway
| | - Horolma Pamjav
- Hungarian Institute for Forensic Sciences, Institute of Forensic Genetics, Budapest, Hungary
| | - Andreas O Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Division of Medicine and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester, UK
| | | | - Marta Pereira Verdugo
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
| | - Bruce Winney
- Department of Oncology, University of Oxford, Oxford, UK
| | - Pragya Vohra
- School of History, Politics and International Relations, University of Leicester, Leicester, UK.,Department of History, University of York, Heslington, York, UK
| | - Joanna Story
- School of History, Politics and International Relations, University of Leicester, Leicester, UK
| | - Turi E King
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
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Allen KG, Mills RD, Knudson KJ, von Cramon-Taubadel N. Biological diversity in an Islamic archaeological population: A radiogenic strontium isotope and craniometric analysis of affinity in Ottoman Romania. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171:569-583. [PMID: 31903549 DOI: 10.1002/ajpa.23999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/05/2019] [Accepted: 12/20/2019] [Indexed: 11/10/2022]
Abstract
OBJECTIVES Written accounts, as well as a previous craniometric study, indicate that migrations of non-Europeans and conversions of Europeans to Islam define Ottoman communities in Early Modern Europe. What is less clear are the roles of migration and admixture in generating intra-communal variation. This study combines craniometric with strontium isotope data to compare the cranial affinities of locally born and immigrant individuals. We predict that locally born individuals are more likely than non-locals to show evidence of admixture. MATERIALS AND METHODS Radiogenic strontium isotope data for 21 Ottomans were compared against archaeological faunal values. Sixteen individuals with intact crania were also measured and compared against two comparative source populations from Anatolia and Europe. Discriminant function analysis assigned unclassified Ottoans to either comparative group based on typicality probabilities, with potential admixture established via intermediate morphology between the two source populations. RESULTS Strontium isotope values revealed relatively high proportions of non-locals, consistent with high mobility documented historically. The sexes differed, with more males classifying as "typically Anatolian" than females. Locals and non-locals also had different cranial affinity patterns, with most classifying either as "typically Anatolian" or "typically European." Contrary to expectation, none of the locals were identified as intermediate, suggesting admixture rates were relatively low. CONCLUSIONS Consistent with historical records, the results revealed high levels of extra-regional migration, with most individuals identifiable as either typically Anatolian or European. Moreover, locals and non-locals differed craniometrically, with no signs of admixture between Anatolian migrants and European converts in locals. This suggests intra-communal divisions were maintained.
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Affiliation(s)
- Kathryn Grow Allen
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology, University at Buffalo, Buffalo, New York
| | - Ryan D Mills
- Department of Geological Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kelly J Knudson
- Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
| | - Noreen von Cramon-Taubadel
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology, University at Buffalo, Buffalo, New York
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4
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Abstract
Britain and Ireland are known to show population genetic structure; however, large swathes of Scotland, in particular, have yet to be described. Delineating the structure and ancestry of these populations will allow variant discovery efforts to focus efficiently on areas not represented in existing cohorts. Thus, we assembled genotype data for 2,554 individuals from across the entire archipelago with geographically restricted ancestry, and performed population structure analyses and comparisons to ancient DNA. Extensive geographic structuring is revealed, from broad scales such as a NE to SW divide in mainland Scotland, through to the finest scale observed to date: across 3 km in the Northern Isles. Many genetic boundaries are consistent with Dark Age kingdoms of Gaels, Picts, Britons, and Norse. Populations in the Hebrides, the Highlands, Argyll, Donegal, and the Isle of Man show characteristics of isolation. We document a pole of Norwegian ancestry in the north of the archipelago (reaching 23 to 28% in Shetland) which complements previously described poles of Germanic ancestry in the east, and "Celtic" to the west. This modern genetic structure suggests a northwestern British or Irish source population for the ancient Gaels that contributed to the founding of Iceland. As rarer variants, often with larger effect sizes, become the focus of complex trait genetics, more diverse rural cohorts may be required to optimize discoveries in British and Irish populations and their considerable global diaspora.
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5
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Shah RR. Metamizole (dipyrone)-induced agranulocytosis: Does the risk vary according to ethnicity? J Clin Pharm Ther 2018; 44:129-133. [DOI: 10.1111/jcpt.12768] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 09/12/2018] [Accepted: 09/13/2018] [Indexed: 12/30/2022]
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6
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Krzewińska M, Kjellström A, Günther T, Hedenstierna-Jonson C, Zachrisson T, Omrak A, Yaka R, Kılınç GM, Somel M, Sobrado V, Evans J, Knipper C, Jakobsson M, Storå J, Götherström A. Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town. Curr Biol 2018; 28:2730-2738.e10. [PMID: 30146150 DOI: 10.1016/j.cub.2018.06.053] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/13/2018] [Accepted: 06/21/2018] [Indexed: 02/03/2023]
Abstract
The impact of human mobility on the northern European urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia itself are still largely unexplored. Our study of the demographics in the final phase of the Viking era is the first comprehensive multidisciplinary investigation that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier common pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 individuals from the 10th to 12th century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed variation exceeds the genetic diversity in distinct modern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople. Our results uncover the social system underlying the urbanization process of the Viking World of which mobility was an intricate part and was comparable between males and females. The inhabitants of Sigtuna were heterogeneous in their genetic affinities, probably reflecting both close and distant connections through an established network, confirming that early urbanization processes in northern Europe were driven by migration.
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Affiliation(s)
- Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden.
| | - Anna Kjellström
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden.
| | - Torsten Günther
- Department of Organismal Biology, Evolutionary Biology Centre, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Charlotte Hedenstierna-Jonson
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Torun Zachrisson
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Ayça Omrak
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, 06800 Tandogan, Ankara, Turkey
| | - Gülşah Merve Kılınç
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Tandogan, Ankara, Turkey
| | - Veronica Sobrado
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Jane Evans
- NERC Isotope Geosciences Laboratory British Geological Survey, Keyworth, Nottingham NG12 5GG, UK
| | - Corina Knipper
- Curt-Engelhorn-Zentrum Archäometrie, D6, 3, 68159 Mannheim, Germany
| | - Mattias Jakobsson
- Department of Organismal Biology, Evolutionary Biology Centre, Norbyvägen 18C, 752 36 Uppsala, Sweden; Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden; Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden.
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Matey-Hernandez ML, Brunak S, Izarzugaza JMG. Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. BMC Bioinformatics 2018; 19:239. [PMID: 29940840 PMCID: PMC6019707 DOI: 10.1186/s12859-018-2239-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/12/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transplantation. The cost and technical limitations of current laboratory techniques, together with advances in next-generation sequencing (NGS) methodologies, have increased the need for precise computational typing methods. RESULTS We tested two widespread HLA typing methods using high quality full genome sequencing data from 150 individuals in 50 family trios from the Genome Denmark project. First, we computed descendant accuracies assessing the agreement in the inheritance of alleles from parents to offspring. Second, we compared the locus-specific homozygosity rates as well as the allele frequencies; and we compared those to the observed values in related populations. We provide guidelines for testing the accuracy of HLA typing methods by comparing family information, which is independent of the availability of curated alleles. CONCLUSIONS Although current computational methods for HLA typing generally provide satisfactory results, our benchmark - using data with ultra-high sequencing depth - demonstrates the incompleteness of current reference databases, and highlights the importance of providing genomic databases addressing current sequencing standards, a problem yet to be resolved before benefiting fully from personalised medicine approaches HLA phenotyping is essential.
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Affiliation(s)
- Maria Luisa Matey-Hernandez
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Lyngby, Denmark
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jose M. G. Izarzugaza
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Lyngby, Denmark
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8
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Byrne RP, Martiniano R, Cassidy LM, Carrigan M, Hellenthal G, Hardiman O, Bradley DG, McLaughlin RL. Insular Celtic population structure and genomic footprints of migration. PLoS Genet 2018; 14:e1007152. [PMID: 29370172 PMCID: PMC5784891 DOI: 10.1371/journal.pgen.1007152] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/13/2017] [Indexed: 12/14/2022] Open
Abstract
Previous studies of the genetic landscape of Ireland have suggested homogeneity, with population substructure undetectable using single-marker methods. Here we have harnessed the haplotype-based method fineSTRUCTURE in an Irish genome-wide SNP dataset, identifying 23 discrete genetic clusters which segregate with geographical provenance. Cluster diversity is pronounced in the west of Ireland but reduced in the east where older structure has been eroded by historical migrations. Accordingly, when populations from the neighbouring island of Britain are included, a west-east cline of Celtic-British ancestry is revealed along with a particularly striking correlation between haplotypes and geography across both islands. A strong relationship is revealed between subsets of Northern Irish and Scottish populations, where discordant genetic and geographic affinities reflect major migrations in recent centuries. Additionally, Irish genetic proximity of all Scottish samples likely reflects older strata of communication across the narrowest inter-island crossing. Using GLOBETROTTER we detected Irish admixture signals from Britain and Europe and estimated dates for events consistent with the historical migrations of the Norse-Vikings, the Anglo-Normans and the British Plantations. The influence of the former is greater than previously estimated from Y chromosome haplotypes. In all, we paint a new picture of the genetic landscape of Ireland, revealing structure which should be considered in the design of studies examining rare genetic variation and its association with traits. A recent genetic study of the UK (People of the British Isles; PoBI) expanded our understanding of population history of the islands, using newly-developed, powerful techniques that harness the rich information embedded in chunks of genetic code called haplotypes. These methods revealed subtle regional diversity across the UK, and, using genetic data alone, timed key migration events into southeast England and Orkney. We have extended these methods to Ireland, identifying regional differences in genetics across the island that adhere to geography at a resolution not previously reported. Our study reveals relative western diversity and eastern homogeneity in Ireland owing to a history of settlement concentrated on the east coast and longstanding Celtic diversity in the west. We show that Irish Celtic diversity enriches the findings of PoBI; haplotypes mirror geography across Britain and Ireland, with relic Celtic populations contributing greatly to haplotypic diversity. Finally, we used genetic information to date migrations into Ireland from Europe and Britain consistent with historical records of Viking and Norman invasions, demonstrating the signatures of these migrations the on modern Irish genome. Our findings demonstrate that genetic structure exists in even small isolated populations, which has important implications for population-based genetic association studies.
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Affiliation(s)
- Ross P. Byrne
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin, Republic of Ireland
- * E-mail: (RPB); (RLM)
| | - Rui Martiniano
- Population Genetics Laboratory, Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin, Republic of Ireland
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Lara M. Cassidy
- Population Genetics Laboratory, Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin, Republic of Ireland
| | - Matthew Carrigan
- Ocular Genetics Unit, Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin, Republic of Ireland
| | - Garrett Hellenthal
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Republic of Ireland
| | - Daniel G. Bradley
- Population Genetics Laboratory, Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin, Republic of Ireland
| | - Russell L. McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin, Republic of Ireland
- * E-mail: (RPB); (RLM)
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9
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The Irish DNA Atlas: Revealing Fine-Scale Population Structure and History within Ireland. Sci Rep 2017; 7:17199. [PMID: 29222464 PMCID: PMC5722868 DOI: 10.1038/s41598-017-17124-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 11/21/2017] [Indexed: 01/31/2023] Open
Abstract
The extent of population structure within Ireland is largely unknown, as is the impact of historical migrations. Here we illustrate fine-scale genetic structure across Ireland that follows geographic boundaries and present evidence of admixture events into Ireland. Utilising the 'Irish DNA Atlas', a cohort (n = 194) of Irish individuals with four generations of ancestry linked to specific regions in Ireland, in combination with 2,039 individuals from the Peoples of the British Isles dataset, we show that the Irish population can be divided in 10 distinct geographically stratified genetic clusters; seven of 'Gaelic' Irish ancestry, and three of shared Irish-British ancestry. In addition we observe a major genetic barrier to the north of Ireland in Ulster. Using a reference of 6,760 European individuals and two ancient Irish genomes, we demonstrate high levels of North-West French-like and West Norwegian-like ancestry within Ireland. We show that that our 'Gaelic' Irish clusters present homogenous levels of ancient Irish ancestries. We additionally detect admixture events that provide evidence of Norse-Viking gene flow into Ireland, and reflect the Ulster Plantations. Our work informs both on Irish history, as well as the study of Mendelian and complex disease genetics involving populations of Irish ancestry.
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10
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Montgomery J, Grimes V, Buckberry J, Evans JA, Richards MP, Barrett JH. Finding Vikings with Isotope Analysis: The View from Wet and Windy Islands. ACTA ACUST UNITED AC 2014. [DOI: 10.3721/037.002.sp705] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Janet Montgomery
- Department of Archaeology, Durham University, Durham, DH1 3LE, UK
| | - Vaughan Grimes
- Department of Archaeology, Memorial University, St. John's, NL, A1C 5S7, Canada
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Jo Buckberry
- Archaeological Sciences, University of Bradford, Bradford, BD7 1DP, UK
| | | | - Michael P. Richards
- Department of Archaeology, Durham University, Durham, DH1 3LE, UK
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Department of Anthropology, University of British Columbia, 6303 NW Marine Drive, Vancouver, BC, V6T 1Z1, Canada
| | - James H. Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology and Anthropology, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK
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11
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Admixture Indicative Interval (AII): a new approach to assess trends in genetic admixture. Genetica 2014; 142:473-82. [PMID: 25238944 DOI: 10.1007/s10709-014-9792-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 09/13/2014] [Indexed: 10/24/2022]
Abstract
The genetic admixture is a dynamic and diachronic process, taking place during a great number of generations. Consequently, a sole admixture rate does not represent such an event and several estimates could help to take into account its dynamics. We developed an Admixture Indicative Interval (AII) which gives a mathematical key to avoid this problem by integrating several admixture estimators and their respective accuracy into a single metric and provides a trend in genetic admixture. To illustrate AIIs interests in admixture studies, AII were calculated using seven estimators on two sets of simulated SNPs data generated under two different admixture scenarios and were then calculated from several published admixed population data: a Comorian population and several Puerto-Rican and Colombian populations for recent admixture events as well as European populations representing the Neolithic/Paleolithic admixture for an older event. Our method provides intervals taking properly the variability and accuracy of admixture estimates into account. The AII lays in the intuitive interval in all actual and simulated datasets and is not biased by divergent points by the mean of a double-weighting step. The great quantity of heterogeneous parental contributions is synthesized by a few AII, which turn out to be more manageable and meaningful than aplenty variable point estimates. This offers an improvement in admixture study, allowing a better understanding of migratory flows. Furthermore, it offers a better assessment of admixture than the arithmetic mean, and enhances comparisons between regions, samples, and between studies on same population.
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12
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Boattini A, Lisa A, Fiorani O, Zei G, Pettener D, Manni F. General method to unravel ancient population structures through surnames, final validation on Italian data. Hum Biol 2013; 84:235-70. [PMID: 23020096 DOI: 10.3378/027.084.0302] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We analyze the geographic location of 77,451 different Italian surnames (17,579,891 individuals) obtained from the lists of telephone subscribers of the year 1993. By using a specific neural network analysis (Self-Organizing Maps, SOMs), we automatically identify the geographic origin of 49,117 different surnames. To validate the methodology, we compare the results to a study, previously conducted, on the same database, with accurate supervised methods. By comparing the results, we find an overlap of 97%, meaning that the SOMs methodology is highly reliable and well traces back the geographic origin of surnames at the time of their introduction (Late Middle Ages/Renaissance in Italy). SOMs results enables one to distinguish monophyletic surnames from polyphyletic ones, that is surnames having had a single geographic and historic origin from those that started to be in use, with an identical spelling, in different locations (respectively, 76.06% and 21.05% of the total). As we are interested in geographic origins, polyphyletic surnames are excluded from further analyses. By comparing the present location of each monophyletic surname to its inferred geographic origin in late Middle Ages/Renaissance, we measure the extent of the migrations having occurred in Italy since that time. We find that the percentage of individuals presently living in the very area where their surname started to be in use centuries ago is extremely variable (ranging from 22.77% to 77.86% according to the province), thus meaning that self-assessed regional identities seldom correspond to the "autochthony" they imply. For example the upper part of the Thyrennian coast (Northern Latium, Tuscany) has a strong identity but few "autochthonous" inhabitants (∼28%) having been a passageway from the North to the South of Italy.
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13
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Genealogical surveys show a high rate of non-paternal surname transmission with regional differences in Argentina. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2012; 63:43-9. [DOI: 10.1016/j.jchb.2011.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 11/22/2011] [Indexed: 11/21/2022]
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Gourjon G, Boëtsch G, Degioanni A. Gender and population history: Sex bias revealed by studying genetic admixture of Ngazidja population (Comoro Archipelago). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 144:653-60. [PMID: 21312182 DOI: 10.1002/ajpa.21474] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 11/22/2010] [Indexed: 11/09/2022]
Affiliation(s)
- Géraud Gourjon
- UMR 6578 Anthropologie bioculturelle, Université de la Méditerranée/CNRS/EFS, Faculté de Médecine-Secteur Nord Université de la Méditerranée, Bd. Pierre Dramard, Marseille Cedex 15, France
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Olsson KS, Konar J, Dufva IH, Ricksten A, Raha-Chowdhury R. Was the C282Y mutation an Irish Gaelic mutation that the Vikings helped disseminate? HLA haplotype observations of hemochromatosis from the west coast of Sweden. Eur J Haematol 2010; 86:75-82. [PMID: 20946107 DOI: 10.1111/j.1600-0609.2010.01536.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
UNLABELLED The HLA-related hemochromatosis mutation C282Y is thought to have originated in Ireland in a person with HLA-A3-B14 and was spread by Vikings. Irish people with two HLA-A3 alleles had a high risk of hemochromatosis. In this study, from west Sweden, we wanted to test these hypotheses. METHODS HFE mutations in controls, bone marrow donors with HLA-A3/A3 and patients with hemochromatosis. HLA haplotypes, extended haplotype analysis and pedigree studies. RESULTS The allelic C282Y frequency 0.04, (CI 0.01-0.07) was lower (P < 0.001) in Sweden than in Ireland 0.10 (CI 0.08-0.11), and Swedish bone marrow donors with HLA-A3/A3 (n = 77) had a low risk of hemochromatosis. HLA haplotypes available from 239/262 (91.5%) proband patients homozygous for C282Y showed a dominance of A3-B7 and A3-B14 both in linkage disequilibrium with controls (P < 0.001). Pedigree studies extended into the 17th century supported a local founder effect of A3-B14 in the county of Bohuslän. The A3-B14 haplotype may well be the original and A3-B7 the result of centromeric recombinations. The haplotype diversity and recombination events were not different from a Celtic series. These findings do not support the hypothesis of the C282Y mutation being of an Irish Celtic origin. CONCLUSIONS The C282Y frequency shows a west to east decline from Ireland through the north of Europe. Vikings may have been involved in the spread of C282Y, but the mutation is probably older and may have been spread in Europe by earlier seafarers.
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Affiliation(s)
- Karl Sigvard Olsson
- Section of Hematology and Coagulation, Department of Medicine, Sahlgrenska University Hospital, Göteborg, Sweden.
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King TE, Jobling MA. What's in a name? Y chromosomes, surnames and the genetic genealogy revolution. Trends Genet 2009; 25:351-60. [PMID: 19665817 DOI: 10.1016/j.tig.2009.06.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 06/15/2009] [Accepted: 06/15/2009] [Indexed: 01/28/2023]
Affiliation(s)
- Turi E King
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK.
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Novelletto A. Y chromosome variation in Europe: Continental and local processes in the formation of the extant gene pool. Ann Hum Biol 2009; 34:139-72. [PMID: 17558587 DOI: 10.1080/03014460701206843] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The polymorphism of the male-specific portion of the Y chromosome has been increasingly used to describe the composition of the European gene pool and to reconstruct its formation. Here the theoretical grounds and the limitations of this approach are presented, together with the different views on debated issues. The emerging picture for the composition of the male gene pool of the continent is illustrated, but local peculiarities that represent departures from the main trends are also highlighted, in order to illustrate the main unifying feature, i.e. the overlay of recent patterns onto more ancient ones. A synopsis of the main findings and conclusions obtained in regional studies has also been compiled.
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Stacey A, Sheffield NC, Crandall KA. Calculating expected DNA remnants from ancient founding events in human population genetics. BMC Genet 2008; 9:66. [PMID: 18928554 PMCID: PMC2588638 DOI: 10.1186/1471-2156-9-66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 10/17/2008] [Indexed: 11/10/2022] Open
Abstract
Background Recent advancements in sequencing and computational technologies have led to rapid generation and analysis of high quality genetic data. Such genetic data have achieved wide acceptance in studies of historic human population origins and admixture. However, in studies relating to small, recent admixture events, genetic factors such as historic population sizes, genetic drift, and mutation can have pronounced effects on data reliability and utility. To address these issues we conducted genetic simulations targeting influential genetic parameters in admixed populations. Results We performed a series of simulations, adjusting variable values to assess the affect of these genetic parameters on current human population studies and what these studies infer about past population structure. Final mean allele frequencies varied from 0.0005 to over 0.50, depending on the parameters. Conclusion The results of the simulations illustrate that, while genetic data may be sensitive and powerful in large genetic studies, caution must be used when applying genetic information to small, recent admixture events. For some parameter sets, genetic data will not be adequate to detect historic admixture. In such cases, studies should consider anthropologic, archeological, and linguistic data where possible.
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Affiliation(s)
- Andrew Stacey
- Department of Statistics, Brigham Young University, Provo, UT 84602, USA.
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