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Stolarek I, Zenczak M, Handschuh L, Juras A, Marcinkowska-Swojak M, Spinek A, Dębski A, Matla M, Kóčka-Krenz H, Piontek J, Figlerowicz M. Genetic history of East-Central Europe in the first millennium CE. Genome Biol 2023; 24:173. [PMID: 37488661 PMCID: PMC10364380 DOI: 10.1186/s13059-023-03013-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND The appearance of Slavs in East-Central Europe has been the subject of an over 200-year debate driven by two conflicting hypotheses. The first assumes that Slavs came to the territory of contemporary Poland no earlier than the sixth century CE; the second postulates that they already inhabited this region in the Iron Age (IA). Testing either hypothesis is not trivial given that cremation of the dead was the prevailing custom in Central Europe from the late Bronze Age until the Middle Ages (MA). RESULTS To address this problem, we determined the genetic makeup of representatives of the IA Wielbark- and MA Slav-associated cultures from the territory of present-day Poland. The study involved 474 individuals buried in 27 cemeteries. For 197 of them, genome-wide data were obtained. We found close genetic affinities between the IA Wielbark culture-associated individuals and contemporary to them and older northern European populations. Further, we observed that the IA individuals had genetic components which were indispensable to model the MA population. CONCLUSIONS The collected data suggest that the Wielbark culture-associated IA population was formed by immigrants from the north who entered the region of contemporary Poland most likely at the beginning of the first millennium CE and mixed with autochthons. The presented results are in line with the hypothesis that assumes the genetic continuation between IA and MA periods in East-Central Europe.
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Affiliation(s)
- Ireneusz Stolarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Michal Zenczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Luiza Handschuh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | | | - Anna Spinek
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Artur Dębski
- Department of Archaeology, Collegium Historicum, Adam Mickiewicz University, Poznan, Poland
| | - Marzena Matla
- Department of History, Collegium Historicum, Adam Mickiewicz University, Poznan, Poland
| | - Hanna Kóčka-Krenz
- Department of Archaeology, Collegium Historicum, Adam Mickiewicz University, Poznan, Poland
| | - Janusz Piontek
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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Wagner JK, Yu JH, Fullwiley D, Moore C, Wilson JF, Bamshad MJ, Royal CD. Guidelines for genetic ancestry inference created through roundtable discussions. HGG ADVANCES 2023; 4:100178. [PMID: 36798092 PMCID: PMC9926022 DOI: 10.1016/j.xhgg.2023.100178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
The use of genetic and genomic technology to infer ancestry is commonplace in a variety of contexts, particularly in biomedical research and for direct-to-consumer genetic testing. In 2013 and 2015, two roundtables engaged a diverse group of stakeholders toward the development of guidelines for inferring genetic ancestry in academia and industry. This report shares the stakeholder groups' work and provides an analysis of, commentary on, and views from the groundbreaking and sustained dialogue. We describe the engagement processes and the stakeholder groups' resulting statements and proposed guidelines. The guidelines focus on five key areas: application of genetic ancestry inference, assumptions and confidence/laboratory and statistical methods, terminology and population identifiers, impact on individuals and groups, and communication or translation of genetic ancestry inferences. We delineate the terms and limitations of the guidelines and discuss their critical role in advancing the development and implementation of best practices for inferring genetic ancestry and reporting the results. These efforts should inform both governmental regulation and self-regulation.
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Affiliation(s)
- Jennifer K. Wagner
- School of Engineering Design and Innovation, Pennsylvania State University, University Park, PA 16802, USA
- Institute for Computational and Data Science, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Rock Ethics Institute, Pennsylvania State University, University Park, PA 16802, USA
- Penn State Law, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Joon-Ho Yu
- Department of Pediatrics and Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA 98101, USA
| | - Duana Fullwiley
- Department of Anthropology, Stanford University, Stanford, CA 94305, USA
| | | | - James F. Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland
| | - Michael J. Bamshad
- Department of Pediatrics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98101, USA
| | - Charmaine D. Royal
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health, Duke University, Durham, NC 27708, USA
| | - Genetic Ancestry Inference Roundtable Participants
- School of Engineering Design and Innovation, Pennsylvania State University, University Park, PA 16802, USA
- Institute for Computational and Data Science, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Rock Ethics Institute, Pennsylvania State University, University Park, PA 16802, USA
- Penn State Law, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Pediatrics and Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA 98101, USA
- Department of Anthropology, Stanford University, Stanford, CA 94305, USA
- The DNA Detectives, Dana Point, CA, USA
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland
- Department of Pediatrics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98101, USA
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health, Duke University, Durham, NC 27708, USA
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Gretzinger J, Sayer D, Justeau P, Altena E, Pala M, Dulias K, Edwards CJ, Jodoin S, Lacher L, Sabin S, Vågene ÅJ, Haak W, Ebenesersdóttir SS, Moore KHS, Radzeviciute R, Schmidt K, Brace S, Bager MA, Patterson N, Papac L, Broomandkhoshbacht N, Callan K, Harney É, Iliev L, Lawson AM, Michel M, Stewardson K, Zalzala F, Rohland N, Kappelhoff-Beckmann S, Both F, Winger D, Neumann D, Saalow L, Krabath S, Beckett S, Van Twest M, Faulkner N, Read C, Barton T, Caruth J, Hines J, Krause-Kyora B, Warnke U, Schuenemann VJ, Barnes I, Dahlström H, Clausen JJ, Richardson A, Popescu E, Dodwell N, Ladd S, Phillips T, Mortimer R, Sayer F, Swales D, Stewart A, Powlesland D, Kenyon R, Ladle L, Peek C, Grefen-Peters S, Ponce P, Daniels R, Spall C, Woolcock J, Jones AM, Roberts AV, Symmons R, Rawden AC, Cooper A, Bos KI, Booth T, Schroeder H, Thomas MG, Helgason A, Richards MB, Reich D, Krause J, Schiffels S. The Anglo-Saxon migration and the formation of the early English gene pool. Nature 2022; 610:112-119. [PMID: 36131019 PMCID: PMC9534755 DOI: 10.1038/s41586-022-05247-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 08/17/2022] [Indexed: 11/09/2022]
Abstract
The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture1. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate2-4. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans-including 278 individuals from England-alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France5,6.
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Affiliation(s)
- Joscha Gretzinger
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | | | - Maria Pala
- University of Huddersfield, Huddersfield, UK
| | - Katharina Dulias
- University of Huddersfield, Huddersfield, UK
- Institute of Geosystems and Bioindication, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ceiridwen J Edwards
- University of Huddersfield, Huddersfield, UK
- University of Oxford, Oxford, UK
| | | | - Laura Lacher
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Susanna Sabin
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Åshild J Vågene
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wolfgang Haak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN Inc., Reykjavík, Iceland
- Department of Anthropology, School of Social Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Rita Radzeviciute
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Martina Abenhus Bager
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nick Patterson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Luka Papac
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Éadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Frank Both
- Landesmuseum Natur und Mensch, Oldenburg, Germany
| | | | | | - Lars Saalow
- Landesamt für Kultur und Denkmalpflege Mecklenburg-Vorpommern, Schwerin, Germany
| | - Stefan Krabath
- Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
- Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, Cranfield, UK
- Melbourne Dental School, University of Melbourne, Melbourne, Victoria, Australia
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
| | - Neil Faulkner
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
| | - Chris Read
- The Atlantic Technological University, Sligo, Ireland
| | | | | | | | | | | | - Verena J Schuenemann
- University of Zurich, Zurich, Switzerland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | | | - Andrew Richardson
- Canterbury Archaeological Trust, Canterbury, UK
- Isle Heritage CIC, Sandgate, UK
| | | | | | | | | | - Richard Mortimer
- Oxford Archaeology East, Cambridge, UK
- Cotswold Archaeology, Needham Market, UK
| | - Faye Sayer
- University of Birmingham, Birmingham, UK
| | - Diana Swales
- Centre for Anatomy and Human Identification (CAHID), University of Dundee, Dundee, UK
| | | | | | - Robert Kenyon
- East Dorset Antiquarian Society (EDAS), West Bexington, UK
| | - Lilian Ladle
- Department of Archaeology and Anthropology, Bournemouth University, Poole, UK
| | - Christina Peek
- Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany
| | | | | | | | | | | | | | | | | | - Anooshka C Rawden
- Fishbourne Roman Palace, Fishbourne, UK
- South Downs Centre, Midhurst, UK
| | - Alan Cooper
- BlueSkyGenetics, Adelaide, South Australia, Australia
| | - Kirsten I Bos
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Agnar Helgason
- deCODE Genetics/AMGEN Inc., Reykjavík, Iceland
- Department of Anthropology, School of Social Sciences, University of Iceland, Reykjavík, Iceland
| | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Stephan Schiffels
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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Timmers PRHJ, Wilson JF. Limited Effect of Y Chromosome Variation on Coronary Artery Disease and Mortality in UK Biobank-Brief Report. Arterioscler Thromb Vasc Biol 2022; 42:1198-1206. [PMID: 35861954 PMCID: PMC9394501 DOI: 10.1161/atvbaha.122.317664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The effect of genetic variation in the male-specific region of the Y chromosome (MSY) on coronary artery disease and cardiovascular risk factors has been disputed. In this study, we systematically assessed the association of MSY genetic variation on these traits using a kin-cohort analysis of family disease history in the largest sample to date. METHODS We tested 90 MSY haplogroups against coronary artery disease, hypertension, blood pressure, classical lipid levels, and all-cause mortality in up to 152 186 unrelated, genomically British individuals from UK Biobank. Unlike previous studies, we did not adjust for heritable lifestyle factors (to avoid collider bias) and instead adjusted for geographic variables and socioeconomic deprivation, given the link between MSY haplogroups and geography. For family history traits, subject MSY haplogroups were tested against father and mother disease as validation and negative control, respectively. RESULTS Our models find little evidence for an effect of any MSY haplogroup on cardiovascular risk in participants. Parental models confirm these findings. CONCLUSIONS Kin-cohort analysis of the Y chromosome uniquely allows for discoveries in subjects to be validated using family history data. Despite our large sample size, improved models, and parental validation, there is little evidence to suggest cardiovascular risk in UK Biobank is influenced by genetic variation in MSY.
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Affiliation(s)
- Paul R H J Timmers
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer (P.R.H.J.T., J.F.W.), University of Edinburgh, United Kingdom.,Centre for Global Health Research, Usher Institute (P.R.H.J.T., J.F.W.), University of Edinburgh, United Kingdom
| | - James F Wilson
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer (P.R.H.J.T., J.F.W.), University of Edinburgh, United Kingdom.,Centre for Global Health Research, Usher Institute (P.R.H.J.T., J.F.W.), University of Edinburgh, United Kingdom
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5
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Cox SL. A geometric morphometric assessment of shape variation in adult pelvic morphology. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:652-671. [PMID: 34528241 DOI: 10.1002/ajpa.24399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/13/2021] [Accepted: 07/29/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVES In humans, the pelvis is the most sexually dimorphic skeletal element and is often utilized in aging and sexing remains. The pelvis has become greatly relied upon in anthropological research (e.g., forensics, demographics, obstetrics, evolutionary history); however, pelvis morphology is highly variable, and very little is known about the nature, sources, patterning, and interpretation of this variation. This study aims to quantify pelvis shape variation, document sexual shape variation, and estimate the plasticity of morphology. This will ultimately give greater ability to interpret modern, archaeological, and evolutionary patterns to gain deeper insight into processes which shape human anatomy. MATERIALS AND METHODS Using a sample of 129 Medieval Danish skeletons, shape variation is documented in the greater sciatic notch (GSN), iliac crest (IC), arcuate line (AL), and sub-pubic angle (SPA) using 3D geometric morphometrics. The landmarking method applied here has the advantage of being applicable to fragmentary remains, rather than requiring whole bones. This allows it to be easily applied to archaeological samples and for the interpretation of separate bone features. Differences in shape were statistically analyzed by principle component analysis, linear discriminate analysis, and morphological disparity. Relationships between maximum femur length, body mass, and shape centroid size were also test by allometric regression. RESULTS Results quantify the sexual dimorphism and shape variation present in these features. The GSN shape is the most variable, while the AL is the least. Similarly, the IC is the only feature which shows almost no dimorphism in shape, and instead best reflects lifestyle/activity patterns. Evidence of dimorphism in the IC is likely a result of cultural labor patterns rather than genetic and hormonal influence. Finally, the shapes of the GSN, AL, and SPA are more related to body mass than to femur length, such that individuals with increased mass exhibit more classically "male" shapes and those with less mass have more "female" shapes. DISCUSSION The results have important implications for the evolution of pelvic anatomy, and sexual dimorphism, but also highlight the plasticity inherent in pelvic morphology. Analyzing pelvis features separately in a clearly defined, relatively genetically homogenous population gives insight into the determinants of bone morphology, which are not readily observable by other means. The relationship between body mass and shape suggests dimorphism in body size and composition may affect bone shape.
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Affiliation(s)
- Samantha L Cox
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Physical Anthropology, Penn Museum, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,University of Cambridge, Department of Archaeology, Cambridge, UK
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Calò CM, Vona G, Robledo R, Francalacci P. From old markers to next generation: reconstructing the history of the peopling of Sardinia. Ann Hum Biol 2021; 48:203-212. [PMID: 34459339 DOI: 10.1080/03014460.2021.1944312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
CONTEXT For many years the Sardinian population has been the object of numerous studies because of its unique genetic structure. Despite the extreme abundance of papers, various aspects of the peopling and genetic structure of Sardinia still remain uncertain and sometimes controversial. OBJECTIVE We reviewed what has emerged from different studies, focussing on some still open questions, such as the origin of Sardinians, their relationship with the Corsican population, and the intra-regional genetic heterogeneity. METHODS The various issues have been addressed through the analysis of classical markers, molecular markers and, finally, genomic data through next generation sequencing. RESULTS AND CONCLUSIONS Although the most ancient human remains date back to the end of the Palaeolithic, Mesolithic populations brought founding lineages that left evident traces in the modern population. Then, with the Neolithic, the island underwent an important demographic expansion. Subsequently, isolation and genetic drift contributed to maintain a significant genetic heterogeneity, but preserving the overall homogeneity on a regional scale. At the same time, isolation and genetic drift contributed to differentiate Sardinia from Corsica, which saw an important gene flow from the mainland. However, the isolation did not prevent gene flow from the neighbouring populations whose contribution are still recognisable in the genome of Sardinians.
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Affiliation(s)
- Carla Maria Calò
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Giuseppe Vona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Renato Robledo
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Paolo Francalacci
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
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7
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Geary DC. Evolution and Sex Differences in Political Engagement. PSYCHOLOGICAL INQUIRY 2021. [DOI: 10.1080/1047840x.2021.1930766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- David C. Geary
- Department of Psychological Sciences, University of Missouri, Columbia, Missouri, USA
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8
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Phylogeographic review of Y chromosome haplogroups in Europe. Int J Legal Med 2021; 135:1675-1684. [PMID: 34216266 DOI: 10.1007/s00414-021-02644-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Europe, with numerous migrations and invasions, has turned this continent into a melting pot. For this reason, it is interesting to study the Y chromosome variability and how it has contributed to improving our knowledge of the distribution and development of European male genetic pool as it is today. The analysis of Y lineages in Europe shows the predominance of four haplogroups, R1b-M269, I1-M253, I2-M438 and R1a-M420. However, other haplogroups have been identified which, although less frequent, provide significant evidence about the paternal origin of the populations. In addition, the study of the Y chromosome in Europe is a valuable tool for revealing the genetic trace of the different European colonizations, mainly in several American countries, where the European ancestry is mostly detected by the presence of the R1b-M269 haplogroup. Therefore, the objective of this review is to compile the studies of the Y chromosome haplogroups in current European populations, in order to provide an outline of these haplogroups which facilitate their use in forensic studies.
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9
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Plomp KA, Dobney K, Collard M. A 3D basicranial shape-based assessment of local and continental northwest European ancestry among 5th to 9th century CE Anglo-Saxons. PLoS One 2021; 16:e0252477. [PMID: 34161340 PMCID: PMC8221467 DOI: 10.1371/journal.pone.0252477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/14/2021] [Indexed: 12/05/2022] Open
Abstract
The settlement of Great Britain by Germanic-speaking people from continental northwest Europe in the Early Medieval period (early 5th to mid 11th centuries CE) has long been recognised as an important event, but uncertainty remains about the number of settlers and the nature of their relationship with the preexisting inhabitants of the island. In the study reported here, we sought to shed light on these issues by using 3D shape analysis techniques to compare the cranial bases of Anglo-Saxon skeletons to those of skeletons from Great Britain that pre-date the Early Medieval period and skeletons from Denmark that date to the Iron Age. Analyses that focused on Early Anglo-Saxon skeletons indicated that between two-thirds and three-quarters of Anglo-Saxon individuals were of continental northwest Europe ancestry, while between a quarter and one-third were of local ancestry. In contrast, analyses that focused on Middle Anglo-Saxon skeletons suggested that 50–70% were of local ancestry, while 30–50% were of continental northwest Europe ancestry. Our study suggests, therefore, that ancestry in Early Medieval Britain was similar to what it is today—mixed and mutable.
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Affiliation(s)
- Kimberly A. Plomp
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Archaeology, Classics, Egyptology, University of Liverpool, Liverpool, United Kingdom
- * E-mail: (KAP); (MC)
| | - Keith Dobney
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Archaeology, Classics, Egyptology, University of Liverpool, Liverpool, United Kingdom
- School of Historical and Philosophical Inquiry, University of Sydney, Sydney, NSW, Australia
| | - Mark Collard
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail: (KAP); (MC)
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Halachev M, Meynert A, Taylor MS, Vitart V, Kerr SM, Klaric L, Aitman TJ, Haley CS, Prendergast JG, Pugh C, Hume DA, Harris SE, Liewald DC, Deary IJ, Semple CA, Wilson JF. Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions. PLoS Genet 2019; 15:e1008480. [PMID: 31765389 PMCID: PMC6901239 DOI: 10.1371/journal.pgen.1008480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/09/2019] [Accepted: 10/15/2019] [Indexed: 01/03/2023] Open
Abstract
Human population isolates provide a snapshot of the impact of historical demographic processes on population genetics. Such data facilitate studies of the functional impact of rare sequence variants on biomedical phenotypes, as strong genetic drift can result in higher frequencies of variants that are otherwise rare. We present the first whole genome sequencing (WGS) study of the VIKING cohort, a representative collection of samples from the isolated Shetland population in northern Scotland, and explore how its genetic characteristics compare to a mainland Scottish population. Our analyses reveal the strong contributions played by the founder effect and genetic drift in shaping genomic variation in the VIKING cohort. About one tenth of all high-quality variants discovered are unique to the VIKING cohort or are seen at frequencies at least ten fold higher than in more cosmopolitan control populations. Multiple lines of evidence also suggest relaxation of purifying selection during the evolutionary history of the Shetland isolate. We demonstrate enrichment of ultra-rare VIKING variants in exonic regions and for the first time we also show that ultra-rare variants are enriched within regulatory regions, particularly promoters, suggesting that gene expression patterns may diverge relatively rapidly in human isolates.
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Affiliation(s)
- Mihail Halachev
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Alison Meynert
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Martin S. Taylor
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Shona M. Kerr
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Lucija Klaric
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | | | - Timothy J. Aitman
- Centre for Genomic and Experimental Medicine, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Chris S. Haley
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - James G. Prendergast
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Carys Pugh
- Centre for Clinical Brain Sciences, Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - David A. Hume
- Mater Research Institute, University of Queensland, Woolloongabba, Australia
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, George Square, Edinburgh, United Kingdom
| | - David C. Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, George Square, Edinburgh, United Kingdom
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, George Square, Edinburgh, United Kingdom
| | - Colin A. Semple
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - James F. Wilson
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom
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11
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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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12
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An actionable KCNH2 Long QT Syndrome variant detected by sequence and haplotype analysis in a population research cohort. Sci Rep 2019; 9:10964. [PMID: 31358886 PMCID: PMC6662790 DOI: 10.1038/s41598-019-47436-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/17/2019] [Indexed: 12/12/2022] Open
Abstract
The Viking Health Study Shetland is a population-based research cohort of 2,122 volunteer participants with ancestry from the Shetland Isles in northern Scotland. The high kinship and detailed phenotype data support a range of approaches for associating rare genetic variants, enriched in this isolate population, with quantitative traits and diseases. As an exemplar, the c.1750G > A; p.Gly584Ser variant within the coding sequence of the KCNH2 gene implicated in Long QT Syndrome (LQTS), which occurred once in 500 whole genome sequences from this population, was investigated. Targeted sequencing of the KCNH2 gene in family members of the initial participant confirmed the presence of the sequence variant and identified two further members of the same family pedigree who shared the variant. Investigation of these three related participants for whom single nucleotide polymorphism (SNP) array genotypes were available allowed a unique shared haplotype of 1.22 Mb to be defined around this locus. Searching across the full cohort for this haplotype uncovered two additional apparently unrelated individuals with no known genealogical connection to the original kindred. All five participants with the defined haplotype were shown to share the rare variant by targeted Sanger sequencing. If this result were verified in a healthcare setting, it would be considered clinically actionable, and has been actioned in relatives ascertained independently through clinical presentation. The General Practitioners of four study participants with the rare variant were alerted to the research findings by letters outlining the phenotype (prolonged electrocardiographic QTc interval). A lack of detectable haplotype sharing between c.1750G > A; p.Gly584Ser chromosomes from previously reported individuals from Finland and those in this study from Shetland suggests that this mutation has arisen more than once in human history. This study showcases the potential value of isolate population-based research resources for genomic medicine. It also illustrates some challenges around communication of actionable findings in research participants in this context.
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13
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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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14
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Kandt J, Cheshire JA, Longley PA. Regional surnames and genetic structure in Great Britain. TRANSACTIONS (INSTITUTE OF BRITISH GEOGRAPHERS : 1965) 2016; 41:554-569. [PMID: 27708455 PMCID: PMC5032893 DOI: 10.1111/tran.12131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Indexed: 06/06/2023]
Abstract
Following the increasing availability of DNA-sequenced data, the genetic structure of populations can now be inferred and studied in unprecedented detail. Across social science, this innovation is shaping new bio-social research agendas, attracting substantial investment in the collection of genetic, biological and social data for large population samples. Yet genetic samples are special because the precise populations that they represent are uncertain and ill-defined. Unlike most social surveys, a genetic sample's representativeness of the population cannot be established by conventional procedures of statistical inference, and the implications for population-wide generalisations about bio-social phenomena are little understood. In this paper, we seek to address these problems by linking surname data to a censored and geographically uneven sample of DNA scans, collected for the People of the British Isles study. Based on a combination of global and local spatial correspondence measures, we identify eight regions in Great Britain that are most likely to represent the geography of genetic structure of Great Britain's long-settled population. We discuss the implications of this regionalisation for bio-social investigations. We conclude that, as the often highly selective collection of DNA and biomarkers becomes a more common practice, geography is crucial to understanding variation in genetic information within diverse populations.
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Affiliation(s)
- Jens Kandt
- Department of GeographyUniversity College LondonLondonWC1E 6BT
| | | | - Paul A Longley
- Department of GeographyUniversity College LondonLondonWC1E 6BT
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15
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Schiffels S, Haak W, Paajanen P, Llamas B, Popescu E, Loe L, Clarke R, Lyons A, Mortimer R, Sayer D, Tyler-Smith C, Cooper A, Durbin R. Iron Age and Anglo-Saxon genomes from East England reveal British migration history. Nat Commun 2016; 7:10408. [PMID: 26783965 PMCID: PMC4735688 DOI: 10.1038/ncomms10408] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/09/2015] [Indexed: 12/14/2022] Open
Abstract
British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern samples from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.
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Affiliation(s)
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Pirita Paajanen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Elizabeth Popescu
- Oxford Archaeology East, 15 Trafalgar Way, Bar Hill, Cambridge CB23 8SQ, UK
| | - Louise Loe
- Oxford Archaeology South, Janus House, Osney Mead, Oxford OX2 0ES, UK
| | - Rachel Clarke
- Oxford Archaeology East, 15 Trafalgar Way, Bar Hill, Cambridge CB23 8SQ, UK
| | - Alice Lyons
- Oxford Archaeology East, 15 Trafalgar Way, Bar Hill, Cambridge CB23 8SQ, UK
| | - Richard Mortimer
- Oxford Archaeology East, 15 Trafalgar Way, Bar Hill, Cambridge CB23 8SQ, UK
| | - Duncan Sayer
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | | | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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16
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Martiniano R, Caffell A, Holst M, Hunter-Mann K, Montgomery J, Müldner G, McLaughlin RL, Teasdale MD, van Rheenen W, Veldink JH, van den Berg LH, Hardiman O, Carroll M, Roskams S, Oxley J, Morgan C, Thomas MG, Barnes I, McDonnell C, Collins MJ, Bradley DG. Genomic signals of migration and continuity in Britain before the Anglo-Saxons. Nat Commun 2016; 7:10326. [PMID: 26783717 PMCID: PMC4735653 DOI: 10.1038/ncomms10326] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/25/2015] [Indexed: 11/09/2022] Open
Abstract
The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (∼ 1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.
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Affiliation(s)
- Rui Martiniano
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Anwen Caffell
- York Osteoarchaeology Ltd, 75 Main Street, Bishop Wilton, York YO42 1SR, UK.,Department of Archaeology, Dawson Building, Durham University, South Road, Durham DH1 3LE, UK
| | - Malin Holst
- York Osteoarchaeology Ltd, 75 Main Street, Bishop Wilton, York YO42 1SR, UK.,BioArCh, Biology, S Block, Wentworth Way, York YO10 5DD, UK
| | - Kurt Hunter-Mann
- York Archaeological Trust for Excavation and Research Limited, 47 Aldwark, York YO1 7BX, UK
| | - Janet Montgomery
- Department of Archaeology, Dawson Building, Durham University, South Road, Durham DH1 3LE, UK
| | - Gundula Müldner
- Department of Archaeology, University of Reading, Whiteknights PO Box 227, Reading RG6 6AB, UK
| | - Russell L McLaughlin
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Matthew D Teasdale
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Wouter van Rheenen
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Jan H Veldink
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin 2, Ireland
| | - Maureen Carroll
- Department of Archaeology, University of Sheffield Northgate House, West Street, Sheffield S1 4ET, UK
| | - Steve Roskams
- BioArCh, Biology, S Block, Wentworth Way, York YO10 5DD, UK
| | | | - Colleen Morgan
- BioArCh, Biology, S Block, Wentworth Way, York YO10 5DD, UK
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Christine McDonnell
- York Archaeological Trust for Excavation and Research Limited, 47 Aldwark, York YO1 7BX, UK
| | | | - Daniel G Bradley
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
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17
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Simpson S, Mina S, Morris H, Mahendran S, Taylor B, Boggild M. The epidemiology of multiple sclerosis in the Isle of Man: 2006-2011. Acta Neurol Scand 2015; 132:381-8. [PMID: 25891133 DOI: 10.1111/ane.12405] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2015] [Indexed: 11/30/2022]
Abstract
BACKGROUND We sought to determine the prevalence of MS on the Isle of Man in 2006 and 2011, and the incidence and mortality rates over this interval. METHODS Cases were identified by hospital medical record review, General Practitioners and the local MS Society. The significance of the change in prevalence over time and the significance of differences in frequencies by sex and place of birth were assessed by Poisson regression. RESULTS The 2006 prevalence was 153.64 per 100,000 persons and the 2011 prevalence was 179.89. The prevalence was higher among females and persons born in the Isle of Man at both time points. The 2006-2011 incidence rate was 6.86 per 100,000 person-years, much higher among females and persons born in the Isle of Man. The prevalence sex ratios in 2006 and 2011, 2.77 and 2.59, respectively, and the incidence sex ratio, 2.19, are similar to others found in the region. The mortality rate over the study period was 2.84 per 100,000 person-years, this solely among persons born overseas. CONCLUSIONS This is the first study of MS epidemiology in the Isle of Man, finding this area to be of high prevalence and to have one of the highest incidence rates in the UK region.
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Affiliation(s)
- S. Simpson
- Menzies Research Institute Tasmania; University of Tasmania; Hobart TAS Australia
| | - S. Mina
- Noble's Hospital; Douglas Isle of Man
| | - H. Morris
- Noble's Hospital; Douglas Isle of Man
| | - S. Mahendran
- Walton Centre for Neurology and Neurosurgery; Liverpool UK
| | - B. Taylor
- Menzies Research Institute Tasmania; University of Tasmania; Hobart TAS Australia
| | - M. Boggild
- Department of Neurology; Townsville Hospital; Douglas QLD Australia
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18
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Krzewińska M, Bjørnstad G, Skoglund P, Olason PI, Bill J, Götherström A, Hagelberg E. Mitochondrial DNA variation in the Viking age population of Norway. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130384. [PMID: 25487335 DOI: 10.1098/rstb.2013.0384] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland.
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Affiliation(s)
- Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden Department of Biosciences, University of Oslo, 0316 Oslo, Norway Museum of Cultural History, University of Oslo, 0130 Oslo, Norway
| | - Gro Bjørnstad
- Department of Forensic Biology, Norwegian Institute of Public Health, 0403 Oslo, Norway Department of Archaeology, Conservation and History, University of Oslo, 0315 Oslo, Norway
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Pall Isolfur Olason
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Jan Bill
- Museum of Cultural History, University of Oslo, 0130 Oslo, Norway
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Erika Hagelberg
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
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19
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Wei W, Fitzgerald TW, Fitzgerald T, Ayub Q, Massaia A, Smith BH, Smith BB, Dominiczak AF, Dominiczak AA, Morris AD, Morris AA, Porteous DJ, Porteous DD, Hurles ME, Tyler-Smith C, Xue Y. Copy number variation in the human Y chromosome in the UK population. Hum Genet 2015; 134:789-800. [PMID: 25957587 PMCID: PMC4460274 DOI: 10.1007/s00439-015-1562-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 04/28/2015] [Indexed: 11/25/2022]
Abstract
We have assessed copy number variation (CNV) in the male-specific part of the human Y chromosome discovered by array comparative genomic hybridization (array-CGH) in 411 apparently healthy UK males, and validated the findings using SNP genotype intensity data available for 149 of them. After manual curation taking account of the complex duplicated structure of Y-chromosomal sequences, we discovered 22 curated CNV events considered validated or likely, mean 0.93 (range 0–4) per individual. 16 of these were novel. Curated CNV events ranged in size from <1 kb to >3 Mb, and in frequency from 1/411 to 107/411. Of the 24 protein-coding genes or gene families tested, nine showed CNV. These included a large duplication encompassing the AMELY and TBL1Y genes that probably has no phenotypic effect, partial deletions of the TSPY cluster and AZFc region that may influence spermatogenesis, and other variants with unknown functional implications, including abundant variation in the number of RBMY genes and/or pseudogenes, and a novel complex duplication of two segments overlapping the AZFa region and including the 3′ end of the UTY gene.
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Affiliation(s)
- Wei Wei
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
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20
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Prestes PR, Mitchell RJ, Daniel R, Sanchez JJ, van Oorschot RA. Predicting biogeographical ancestry in admixed individuals – values and limitations of using uniparental and autosomal markers. AUST J FORENSIC SCI 2015. [DOI: 10.1080/00450618.2015.1022600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Leslie S, Winney B, Hellenthal G, Davison D, Boumertit A, Day T, Hutnik K, Royrvik EC, Cunliffe B, Lawson DJ, Falush D, Freeman C, Pirinen M, Myers S, Robinson M, Donnelly P, Bodmer W. The fine-scale genetic structure of the British population. Nature 2015; 519:309-314. [PMID: 25788095 DOI: 10.1038/nature14230] [Citation(s) in RCA: 232] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 01/13/2015] [Indexed: 12/22/2022]
Abstract
Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide single nucleotide polymorphism (SNP) data from a carefully chosen geographically diverse sample of 2,039 individuals from the United Kingdom. This reveals a rich and detailed pattern of genetic differentiation with remarkable concordance between genetic clusters and geography. The regional genetic differentiation and differing patterns of shared ancestry with 6,209 individuals from across Europe carry clear signals of historical demographic events. We estimate the genetic contribution to southeastern England from Anglo-Saxon migrations to be under half, and identify the regions not carrying genetic material from these migrations. We suggest significant pre-Roman but post-Mesolithic movement into southeastern England from continental Europe, and show that in non-Saxon parts of the United Kingdom, there exist genetically differentiated subgroups rather than a general 'Celtic' population.
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Affiliation(s)
- Stephen Leslie
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia.,University of Melbourne, Department of Mathematics and Statistics, Parkville, Victoria 3010, Australia
| | - Bruce Winney
- University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Garrett Hellenthal
- University College London Genetics Institute, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Dan Davison
- Counsyl, Inc. 180 Kimball Way, South San Francisco, CA 94080, USA
| | - Abdelhamid Boumertit
- University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Tammy Day
- University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Katarzyna Hutnik
- University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Ellen C Royrvik
- University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Barry Cunliffe
- University of Oxford, Institute of Archaeology, 36 Beaumont Street, Oxford, OX1 2PG, UK
| | | | | | - Daniel J Lawson
- University of Bristol, Department of Mathematics, University Walk, Bristol, BS8 1TW, UK
| | - Daniel Falush
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Colin Freeman
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Matti Pirinen
- University of Helsinki, P.O. Box 20, Helsinki, FI-00014, Finland
| | - Simon Myers
- University of Oxford, Department of Statistics, 1 South Parks Road, Oxford, OX1 3TG, UK
| | - Mark Robinson
- University of Oxford, University Museum of Natural History, Parks Road, Oxford, OX1 3PW, UK
| | - Peter Donnelly
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.,University of Oxford, Department of Statistics, 1 South Parks Road, Oxford, OX1 3TG, UK
| | - Walter Bodmer
- University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
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22
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Mays S. Mandibular morphology in two archaeological human skeletal samples from northwest Europe with different masticatory regimes. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2015; 66:203-15. [PMID: 25724125 DOI: 10.1016/j.jchb.2014.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/01/2014] [Indexed: 10/24/2022]
Abstract
Mandibular morphology, assessed osteometrically, is studied in two historic human skeletal series (N = 64 individuals) from northwest Europe, one from Zwolle, the Netherlands (19th century CE), the other from Wharram Percy, England (10th-19th century). Both groups show greater dental wear than modern Western populations, but the rate of wear is greater at Wharram Percy than at Zwolle, suggesting a more vigorous masticatory regime. The aim is to evaluate any differences in mandibular morphology between the two groups that might relate to the inferred difference in biomechanical loading upon the chewing apparatus consequent upon the different physical properties of the diets consumed. Results indicate that the mandibles from Zwolle are generally smaller than those from Wharram Percy, especially in the gonial and ramus region and in the height of the post-canine corpus. These differences are consistent with those predicted on biomechanical grounds. That clear differences were observed in two samples whose masticatory regimes were distinct but not very different is an indication of the sensitivity of mandibular morphology to biomechanical input, and supports its value for investigating differences in physical properties of diets in palaeopopulations.
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Affiliation(s)
- S Mays
- Investigation and Analysis Division, English Heritage, Fort Cumberland, Eastney, Portsmouth PO4 9LD, UK.
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Gilks WP, Abbott JK, Morrow EH. Sex differences in disease genetics: evidence, evolution, and detection. Trends Genet 2014; 30:453-63. [DOI: 10.1016/j.tig.2014.08.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/27/2014] [Accepted: 08/27/2014] [Indexed: 12/13/2022]
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No Association Between NRG1 and ErbB4 Genes and Psychopathological Symptoms of Schizophrenia. Neuromolecular Med 2014; 16:742-51. [DOI: 10.1007/s12017-014-8323-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 07/25/2014] [Indexed: 12/15/2022]
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Pardiñas AF, Roca A, García-Vazquez E, López B. Evaluation of large-scale genetic structure in complex demographic and historical scenarios: the mitochondrial DNA and Y-chromosome pools of the Iberian Atlantic façade. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 153:617-26. [PMID: 24375152 DOI: 10.1002/ajpa.22461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 12/12/2013] [Indexed: 11/11/2022]
Abstract
Genetic structural patterns of human populations are usually a combination of long-term evolutionary forces and short-term social, cultural, and demographic processes. Recently, using mitochondrial DNA and Y-chromosome loci, various studies in northern Spain have found evidence that the geographical distribution of Iron Age tribal peoples might have influenced current patterns of genetic structuring in several autochthonous populations. Using the wealth of data that are currently available from the whole territory of the Iberian Peninsula, we have evaluated its genetic structuring in the spatial scale of the Atlantic façade. Hierarchical tree modeling procedures, combined with a classic analysis of molecular variance (AMOVA), were used to model known sociocultural divisions from the third century BCE to the eighth century CE, contrasting them with uniparental marker data. Our results show that, while mountainous and abrupt areas of the Iberian North bear the signals of long-term isolation in their maternal and paternal gene pools, the makeup of the Atlantic façade as a whole can be related to tribal population groups that predate the Roman conquest of the Peninsula. The maintenance through time of such a structure can be related to the numerous geographic barriers of the Iberian mainland, which have historically conditioned its settlement patterns and the occurrence of genetic drift processes.
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Affiliation(s)
- Antonio F Pardiñas
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Asturias, Spain
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An overview of the genetic structure within the Italian population from genome-wide data. PLoS One 2012; 7:e43759. [PMID: 22984441 PMCID: PMC3440425 DOI: 10.1371/journal.pone.0043759] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 07/24/2012] [Indexed: 12/21/2022] Open
Abstract
In spite of the common belief of Europe as reasonably homogeneous at genetic level, advances in high-throughput genotyping technology have resolved several gradients which define different geographical areas with good precision. When Northern and Southern European groups were considered separately, there were clear genetic distinctions. Intra-country genetic differences were also evident, especially in Finland and, to a lesser extent, within other European populations. Here, we present the first analysis using the 125,799 genome-wide Single Nucleotide Polymorphisms (SNPs) data of 1,014 Italians with wide geographical coverage. We showed by using Principal Component analysis and model-based individual ancestry analysis, that the current population of Sardinia can be clearly differentiated genetically from mainland Italy and Sicily, and that a certain degree of genetic differentiation is detectable within the current Italian peninsula population. Pair-wise F(ST) statistics Northern and Southern Italy amounts approximately to 0.001 between, and around 0.002 between Northern Italy and Utah residents with Northern and Western European ancestry (CEU). The Italian population also revealed a fine genetic substructure underscoring by the genomic inflation (Sardinia vs. Northern Italy = 3.040 and Northern Italy vs. CEU = 1.427), warning against confounding effects of hidden relatedness and population substructure in association studies.
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Niederstätter H, Rampl G, Erhart D, Pitterl F, Oberacher H, Neuhuber F, Hausner I, Gassner C, Schennach H, Berger B, Parson W. Pasture names with Romance and Slavic roots facilitate dissection of Y chromosome variation in an exclusively German-speaking alpine region. PLoS One 2012; 7:e41885. [PMID: 22848647 PMCID: PMC3407130 DOI: 10.1371/journal.pone.0041885] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 06/28/2012] [Indexed: 01/04/2023] Open
Abstract
The small alpine district of East Tyrol (Austria) has an exceptional demographic history. It was contemporaneously inhabited by members of the Romance, the Slavic and the Germanic language groups for centuries. Since the Late Middle Ages, however, the population of the principally agrarian-oriented area is solely Germanic speaking. Historic facts about East Tyrol's colonization are rare, but spatial density-distribution analysis based on the etymology of place-names has facilitated accurate spatial mapping of the various language groups' former settlement regions. To test for present-day Y chromosome population substructure, molecular genetic data were compared to the information attained by the linguistic analysis of pasture names. The linguistic data were used for subdividing East Tyrol into two regions of former Romance (A) and Slavic (B) settlement. Samples from 270 East Tyrolean men were genotyped for 17 Y-chromosomal microsatellites (Y-STRs) and 27 single nucleotide polymorphisms (Y-SNPs). Analysis of the probands' surnames revealed no evidence for spatial genetic structuring. Also, spatial autocorrelation analysis did not indicate significant correlation between genetic (Y-STR haplotypes) and geographic distance. Haplogroup R-M17 chromosomes, however, were absent in region A, but constituted one of the most frequent haplogroups in region B. The R-M343 (R1b) clade showed a marked and complementary frequency distribution pattern in these two regions. To further test East Tyrol's modern Y-chromosomal landscape for geographic patterning attributable to the early history of settlement in this alpine area, principal coordinates analysis was performed. The Y-STR haplotypes from region A clearly clustered with those of Romance reference populations and the samples from region B matched best with Germanic speaking reference populations. The combined use of onomastic and molecular genetic data revealed and mapped the marked structuring of the distribution of Y chromosomes in an alpine region that has been culturally homogeneous for centuries.
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Affiliation(s)
| | - Gerhard Rampl
- Institute of Lexicography of Austrian Dialects and Names, Austrian Academy of Sciences, Vienna, Austria
| | - Daniel Erhart
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Florian Pitterl
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Franz Neuhuber
- Institute of Legal Medicine, University of Salzburg, Salzburg, Austria
| | - Isolde Hausner
- Institute of Lexicography of Austrian Dialects and Names, Austrian Academy of Sciences, Vienna, Austria
| | - Christoph Gassner
- Central Institute for Blood Transfusion & Immunological Department, Innsbruck, Austria
- Blood Transfusion Service Zürich, SRC, Schlieren, Switzerland
| | - Harald Schennach
- Central Institute for Blood Transfusion & Immunological Department, Innsbruck, Austria
| | - Burkhard Berger
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
- * E-mail:
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
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Khusnutdinova EK, Litvinov SS, Kutuev IA, Yunusbayev BB, Khusainova RI, Ahmetova VL, Ahatova FS, Metspalu E, Rootsi S, Villems R. Gene pool of ethnic groups of the Caucasus: Results of integrated study of the Y chromosome and mitochondrial DNA and genome-wide data. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412060063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Jobling MA. The impact of recent events on human genetic diversity. Philos Trans R Soc Lond B Biol Sci 2012; 367:793-9. [PMID: 22312046 DOI: 10.1098/rstb.2011.0297] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The historical record tells us stories of migrations, population expansions and colonization events in the last few thousand years, but what was their demographic impact? Genetics can throw light on this issue, and has mostly done so through the maternally inherited mitochondrial DNA (mtDNA) and the male-specific Y chromosome. However, there are a number of problems, including marker ascertainment bias, possible influences of natural selection, and the obscuring layers of the palimpsest of historical and prehistorical events. Y-chromosomal lineages are particularly affected by genetic drift, which can be accentuated by recent social selection. A diversity of approaches to expansions in Europe is yielding insights into the histories of Phoenicians, Roma, Anglo-Saxons and Vikings, and new methods for producing and analysing genome-wide data hold much promise. The field would benefit from more consensus on appropriate methods, and better communication between geneticists and experts in other disciplines, such as history, archaeology and linguistics.
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Affiliation(s)
- Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, UK.
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30
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DeWitte SN, Hughes-Morey G. Stature and frailty during the Black Death: the effect of stature on risks of epidemic mortality in London, A.D. 1348-1350. JOURNAL OF ARCHAEOLOGICAL SCIENCE 2012; 39:10.1016/j.jas.2012.01.019. [PMID: 24363485 PMCID: PMC3868458 DOI: 10.1016/j.jas.2012.01.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Recent research has shown that preexisting health condition affected an individual's risk of dying during the 14th-century Black Death. However, a previous study of the effect of adult stature on risk of mortality during the epidemic failed to find a relationship between the two; this result is perhaps surprising given the well-documented inverse association between stature and mortality in human populations. We suggest that the previous study used an analytical approach that was more complex than was necessary for an assessment of the effect of adult stature on risk of mortality. This study presents a reanalysis of data on adult stature and age-at-death during the Black Death in London, 1348-1350 AD. The results indicate that short stature increased risks of mortality during the medieval epidemic, consistent with previous work that revealed a negative effect of poor health on risk of mortality during the Black Death. However, the results from a normal, non-epidemic mortality comparison sample do not show an association between stature and risks of mortality among adults under conditions of normal mortality. Fisher's exact tests, used to determine whether individuals who were growing during the Great Famine of 1315-1322 were more likely to be of short stature than those who did not endure the famine, revealed no differences between the two groups, suggesting that the famine was not a source of variation in stature among those who died during the Black Death.
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Affiliation(s)
- Sharon N. DeWitte
- Department of Anthropology, University of South Carolina, Columbia, SC 29208, United States
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States
| | - Gail Hughes-Morey
- Department of Anthropology, University at Albany, SUNY, Albany, NY 12222, United States
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31
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Charchar FJ, Bloomer LD, Barnes TA, Cowley MJ, Nelson CP, Wang Y, Denniff M, Debiec R, Christofidou P, Nankervis S, Dominiczak AF, Bani-Mustafa A, Balmforth AJ, Hall AS, Erdmann J, Cambien F, Deloukas P, Hengstenberg C, Packard C, Schunkert H, Ouwehand WH, Ford I, Goodall AH, Jobling MA, Samani NJ, Tomaszewski M. Inheritance of coronary artery disease in men: an analysis of the role of the Y chromosome. Lancet 2012; 379:915-922. [PMID: 22325189 PMCID: PMC3314981 DOI: 10.1016/s0140-6736(11)61453-0] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND A sexual dimorphism exists in the incidence and prevalence of coronary artery disease--men are more commonly affected than are age-matched women. We explored the role of the Y chromosome in coronary artery disease in the context of this sexual inequity. METHODS We genotyped 11 markers of the male-specific region of the Y chromosome in 3233 biologically unrelated British men from three cohorts: the British Heart Foundation Family Heart Study (BHF-FHS), West of Scotland Coronary Prevention Study (WOSCOPS), and Cardiogenics Study. On the basis of this information, each Y chromosome was tracked back into one of 13 ancient lineages defined as haplogroups. We then examined associations between common Y chromosome haplogroups and the risk of coronary artery disease in cross-sectional BHF-FHS and prospective WOSCOPS. Finally, we undertook functional analysis of Y chromosome effects on monocyte and macrophage transcriptome in British men from the Cardiogenics Study. FINDINGS Of nine haplogroups identified, two (R1b1b2 and I) accounted for roughly 90% of the Y chromosome variants among British men. Carriers of haplogroup I had about a 50% higher age-adjusted risk of coronary artery disease than did men with other Y chromosome lineages in BHF-FHS (odds ratio 1·75, 95% CI 1·20-2·54, p=0·004), WOSCOPS (1·45, 1·08-1·95, p=0·012), and joint analysis of both populations (1·56, 1·24-1·97, p=0·0002). The association between haplogroup I and increased risk of coronary artery disease was independent of traditional cardiovascular and socioeconomic risk factors. Analysis of macrophage transcriptome in the Cardiogenics Study revealed that 19 molecular pathways showing strong differential expression between men with haplogroup I and other lineages of the Y chromosome were interconnected by common genes related to inflammation and immunity, and that some of them have a strong relevance to atherosclerosis. INTERPRETATION The human Y chromosome is associated with risk of coronary artery disease in men of European ancestry, possibly through interactions of immunity and inflammation. FUNDING British Heart Foundation; UK National Institute for Health Research; LEW Carty Charitable Fund; National Health and Medical Research Council of Australia; European Union 6th Framework Programme; Wellcome Trust.
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Affiliation(s)
- Fadi J Charchar
- School of Health Sciences, University of Ballarat, Ballarat, VIC, Australia
| | - Lisa Ds Bloomer
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Timothy A Barnes
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Mark J Cowley
- Peter Wills Bioinformatics Centre, Garvan Institute for Medical Research, Sydney, NSW, Australia
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, UK
| | - Yanzhong Wang
- Division of Health and Social Care Research, King's College London, London, UK
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Radoslaw Debiec
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | | | - Scott Nankervis
- School of Health Sciences, University of Ballarat, Ballarat, VIC, Australia
| | - Anna F Dominiczak
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Ahmed Bani-Mustafa
- School of Health Sciences, University of Ballarat, Ballarat, VIC, Australia
| | - Anthony J Balmforth
- Division of Epidemiology, LIGHT, School of Medicine, University of Leeds, Leeds, UK
| | - Alistair S Hall
- Division of Epidemiology, LIGHT, School of Medicine, University of Leeds, Leeds, UK
| | | | - Francois Cambien
- INSERM UMRS 937, Pierre and Marie Curie University and Medical School, Paris, France
| | | | - Christian Hengstenberg
- Klinik und Poliklinik für Innere Medizin II, Universität Regensburg, Regensburg, Germany
| | - Chris Packard
- College of Medicine, Veterinary and Life Sciences, and Department of Vascular Biochemistry, University of Glasgow, Glasgow, UK
| | | | - Willem H Ouwehand
- Wellcome Trust Sanger Institute, Cambridge, UK; Department of Haematology, University of Cambridge and National Health Service Blood and Transplant, Cambridge, UK
| | - Ian Ford
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK
| | - Alison H Goodall
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, UK
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, UK
| | - Maciej Tomaszewski
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, UK.
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32
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Pattison JE. Integration versus apartheid in post-Roman Britain: a response to Thomas et Al. (2008). Hum Biol 2012; 83:715-33. [PMID: 22276970 DOI: 10.3378/027.083.0604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The genetic surveys of the population of Britain conducted by Weale et al. and Capelli et al. produced estimates of the Germani immigration into Britain during the early Anglo-Saxon period, c.430-c.730. These estimates are considerably higher than the estimates of archaeologists. A possible explanation suggests that an apartheid-like social system existed in the early Anglo-Saxon kingdoms resulting in the Germani breeding more quickly than the Britons. Thomas et al. attempted to model this suggestion and showed that it was a possible explanation if all Anglo-Saxon kingdoms had such a system for up to 400 years. I noted that their explanation ignored the probability that Germani have been arriving in Britain for at least the past three millennia, including Belgae and Roman soldiers, and not only during the early Anglo-Saxon period. I produced a population model for Britain taking into account this long term, low level migration that showed that the estimates could be reconciled without the need for introducing an apartheid-like system. In turn, Thomas et al. responded, criticizing my model and arguments, which they considered persuasively written but wanting in terms of methodology, data sources, underlying assumptions, and application. Here, I respond in detail to those criticisms and argue that it is still unnecessary to introduce an apartheid-like system in order to reconcile the different estimates of Germani arrivals. A point of confusion is that geneticists are interested in ancestry, while archaeologists are interested in ethnicity: it is the bones, not the burial rites, which are important in the present context.
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Affiliation(s)
- John E Pattison
- School of EIE - Applied Physics, University of South Australia, Mawson Lakes, Adelaide, SA, Australia, 5095.
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33
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Busby GBJ, Brisighelli F, Sánchez-Diz P, Ramos-Luis E, Martinez-Cadenas C, Thomas MG, Bradley DG, Gusmão L, Winney B, Bodmer W, Vennemann M, Coia V, Scarnicci F, Tofanelli S, Vona G, Ploski R, Vecchiotti C, Zemunik T, Rudan I, Karachanak S, Toncheva D, Anagnostou P, Ferri G, Rapone C, Hervig T, Moen T, Wilson JF, Capelli C. The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269. Proc Biol Sci 2011; 279:884-92. [PMID: 21865258 DOI: 10.1098/rspb.2011.1044] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collection of R1b1b2-M269 chromosomes yet assembled. Our analysis reveals no geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis, and suggests an alternative explanation for the apparent cline in diversity recently described. We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. As a consequence, the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution.
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Gaieski JB, Owings AC, Vilar MG, Dulik MC, Gaieski DF, Gittelman RM, Lindo J, Gau L, Schurr TG. Genetic ancestry and indigenous heritage in a Native American descendant community in Bermuda. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:392-405. [PMID: 21994016 DOI: 10.1002/ajpa.21588] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 06/17/2011] [Indexed: 11/09/2022]
Abstract
Discovered in the early 16th century by European colonists, Bermuda is an isolated set of islands located in the mid-Atlantic. Shortly after its discovery, Bermuda became the first English colony to forcibly import its labor by trafficking in enslaved Africans, white ethnic minorities, and indigenous Americans. Oral traditions circulating today among contemporary tribes from the northeastern United States recount these same events, while, in Bermuda, St. David's Islanders consider their histories to be linked to a complex Native American, European, and African past. To investigate the influence of historical events on biological ancestry and native cultural identity, we analyzed genetic variation in 111 members of Bermuda's self-proclaimed St. David's Island Native Community. Our results reveal that the majority of mitochondrial DNA (mtDNA) and Y-chromosome haplotypes are of African and West Eurasian origin. However, unlike other English-speaking New World colonies, most African mtDNA haplotypes appear to derive from central and southeast Africa, reflecting the extent of maritime activities in the region. In light of genealogical and oral historical data from the St. David's community, the low frequency of Native American mtDNA and NRY lineages may reflect the influence of genetic drift, the demographic impact of European colonization, and historical admixture with persons of non-native backgrounds, which began with the settlement of the islands. By comparing the genetic data with genealogical and historical information, we are able to reconstruct the complex history of this Bermudian community, which is unique among New World populations.
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Affiliation(s)
- Jill B Gaieski
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
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35
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Winney B, Boumertit A, Day T, Davison D, Echeta C, Evseeva I, Hutnik K, Leslie S, Nicodemus K, Royrvik EC, Tonks S, Yang X, Cheshire J, Longley P, Mateos P, Groom A, Relton C, Bishop DT, Black K, Northwood E, Parkinson L, Frayling TM, Steele A, Sampson JR, King T, Dixon R, Middleton D, Jennings B, Bowden R, Donnelly P, Bodmer W. People of the British Isles: preliminary analysis of genotypes and surnames in a UK-control population. Eur J Hum Genet 2011; 20:203-10. [PMID: 21829225 PMCID: PMC3260910 DOI: 10.1038/ejhg.2011.127] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
There is a great deal of interest in a fine-scale population structure in the UK, both as a signature of historical immigration events and because of the effect population structure may have on disease association studies. Although population structure appears to have a minor impact on the current generation of genome-wide association studies, it is likely to have a significant part in the next generation of studies designed to search for rare variants. A powerful way of detecting such structure is to control and document carefully the provenance of the samples involved. In this study, we describe the collection of a cohort of rural UK samples (The People of the British Isles), aimed at providing a well-characterised UK-control population that can be used as a resource by the research community, as well as providing a fine-scale genetic information on the British population. So far, some 4000 samples have been collected, the majority of which fit the criteria of coming from a rural area and having all four grandparents from approximately the same area. Analysis of the first 3865 samples that have been geocoded indicates that 75% have a mean distance between grandparental places of birth of 37.3 km, and that about 70% of grandparental places of birth can be classed as rural. Preliminary genotyping of 1057 samples demonstrates the value of these samples for investigating a fine-scale population structure within the UK, and shows how this can be enhanced by the use of surnames.
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Affiliation(s)
- Bruce Winney
- Department of Oncology, University of Oxford, ORCRB, Headington, Oxford, UK.
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Dewitte SN. Age Patterns of Mortality During the Black Death in London, A.D. 1349-1350. JOURNAL OF ARCHAEOLOGICAL SCIENCE 2010; 37:3394-3400. [PMID: 21572598 PMCID: PMC3094018 DOI: 10.1016/j.jas.2010.08.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This paper examines adult age-specific mortality patterns of one of the most devastating epidemics in recorded history, the Black Death of A.D. 1347-351. The goal was to determine whether the epidemic affected all ages equally or if it targeted certain age groups. Analyses were done using a sample of 337 individuals excavated from the East Smithfield cemetery in London, which contains only individuals who died during the Black Death in London in 1349-1350. The age patterns from East Smithfield were compared to a sample of 207 individuals who died from non-epidemic causes of mortality. Ages were estimated using the method of transition analysis, and age-specific mortality was evaluated using a hazards model. The results indicate that the risk of mortality during the Black Death increased with adult age, and therefore that age had an effect on risk of death during the epidemic. The age patterns in the Black Death cemetery were similar to those from the non-epidemic mortality sample. The results from this study are consistent with previous findings suggesting that despite the devastating nature of the Black Death, the 14(th)-century disease had general patterns of selectivity that were similar to those associated with normal medieval mortality.
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Affiliation(s)
- Sharon N Dewitte
- Department of Anthropology, University at Albany, SUNY, Albany, NY 12222
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37
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Population structure and genome-wide patterns of variation in Ireland and Britain. Eur J Hum Genet 2010; 18:1248-54. [PMID: 20571510 DOI: 10.1038/ejhg.2010.87] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Located off the northwestern coast of the European mainland, Britain and Ireland were among the last regions of Europe to be colonized by modern humans after the last glacial maximum. Further, the geographical location of Britain, and in particular of Ireland, is such that the impact of historical migration has been minimal. Genetic diversity studies applying the Y chromosome and mitochondrial systems have indicated reduced diversity and an increased population structure across Britain and Ireland relative to the European mainland. Such characteristics would have implications for genetic mapping studies of complex disease. We set out to further our understanding of the genetic architecture of the region from the perspective of (i) population structure, (ii) linkage disequilibrium (LD), (iii) homozygosity and (iv) haplotype diversity (HD). Analysis was conducted on 3654 individuals from Ireland, Britain (with regional sampling in Scotland), Bulgaria, Portugal, Sweden and the Utah HapMap collection. Our results indicate a subtle but clear genetic structure across Britain and Ireland, although levels of structure were reduced in comparison with average cross-European structure. We observed slightly elevated levels of LD and homozygosity in the Irish population compared with neighbouring European populations. We also report on a cline of HD across Europe with greatest levels in southern populations and lowest levels in Ireland and Scotland. These results are consistent with our understanding of the population history of Europe and promote Ireland and Scotland as relatively homogenous resources for genetic mapping of rare variants.
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Searle JB, Kotlík P, Rambau RV, Marková S, Herman JS, McDevitt AD. The Celtic fringe of Britain: insights from small mammal phylogeography. Proc Biol Sci 2009; 276:4287-94. [PMID: 19793757 PMCID: PMC2817114 DOI: 10.1098/rspb.2009.1422] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 09/08/2009] [Indexed: 11/12/2022] Open
Abstract
Recent genetic studies have challenged the traditional view that the ancestors of British Celtic people spread from central Europe during the Iron Age and have suggested a much earlier origin for them as part of the human recolonization of Britain at the end of the last glaciation. Here we propose that small mammals provide an analogue to help resolve this controversy. Previous studies have shown that common shrews (Sorex araneus) with particular chromosomal characteristics and water voles (Arvicola terrestris) of a specific mitochondrial (mt) DNA lineage have peripheral western/northern distributions with striking similarities to that of Celtic people. We show that mtDNA lineages of three other small mammal species (bank vole Myodes glareolus, field vole Microtus agrestis and pygmy shrew Sorex minutus) also form a 'Celtic fringe'. We argue that these small mammals most reasonably colonized Britain in a two-phase process following the last glacial maximum (LGM), with climatically driven partial replacement of the first colonists by the second colonists, leaving a peripheral geographical distribution for the first colonists. We suggest that these natural Celtic fringes provide insight into the same phenomenon in humans and support its origin in processes following the end of the LGM.
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Affiliation(s)
- Jeremy B Searle
- Department of Biology, University of York, PO Box 373, York YO105YW, UK.
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Paterson AD, Lopes-Virella MF, Waggott D, Boright AP, Hosseini SM, Carter RE, Shen E, Mirea L, Bharaj B, Sun L, Bull SB. Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. Arterioscler Thromb Vasc Biol 2009; 29:1958-67. [PMID: 19729612 DOI: 10.1161/atvbaha.109.192971] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND Elevated serum soluble E-selectin levels have been associated with a number of diseases. Although E-selectin levels are heritable, little is known about the specific genetic factors involved. E-selectin levels have been associated with the ABO blood group phenotype. METHODS AND RESULTS We performed a high-resolution genome-wide association study of serum soluble E-selectin levels in 685 white individuals with type 1 diabetes from the Diabetes Control and Complications Trial (DCCT)/Epidemiology of Diabetes Intervention and Complications (EDIC) study to identify major loci influencing levels. Highly significant evidence for association (P=10(-29)) was observed for rs579459 near the ABO blood group gene, accounting for 19% of the variance in E-selectin levels. Levels of E-selectin were higher in O/O than O/A heterozygotes, which were likewise higher than A/A genotypes. Analysis of subgroups of A alleles reveals heterogeneity in the association, and even after this was accounted for, an intron 1 SNP remained significantly associated. We replicate the ABO association in nondiabetic individuals. CONCLUSIONS ABO is a major locus for serum soluble E-selectin levels. We excluded population stratification, fine-mapped the association to sub-A alleles, and also document association with additional variation in the ABO region.
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40
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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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41
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DeWitte SN. The effect of sex on risk of mortality during the Black Death in London, A.D. 1349-1350. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 139:222-34. [DOI: 10.1002/ajpa.20974] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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McEvoy BP, Montgomery GW, McRae AF, Ripatti S, Perola M, Spector TD, Cherkas L, Ahmadi KR, Boomsma D, Willemsen G, Hottenga JJ, Pedersen NL, Magnusson PKE, Kyvik KO, Christensen K, Kaprio J, Heikkilä K, Palotie A, Widen E, Muilu J, Syvänen AC, Liljedahl U, Hardiman O, Cronin S, Peltonen L, Martin NG, Visscher PM. Geographical structure and differential natural selection among North European populations. Genome Res 2009; 19:804-14. [PMID: 19265028 DOI: 10.1101/gr.083394.108] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Population structure can provide novel insight into the human past, and recognizing and correcting for such stratification is a practical concern in gene mapping by many association methodologies. We investigate these patterns, primarily through principal component (PC) analysis of whole genome SNP polymorphism, in 2099 individuals from populations of Northern European origin (Ireland, United Kingdom, Netherlands, Denmark, Sweden, Finland, Australia, and HapMap European-American). The major trends (PC1 and PC2) demonstrate an ability to detect geographic substructure, even over a small area like the British Isles, and this information can then be applied to finely dissect the ancestry of the European-Australian and European-American samples. They simultaneously point to the importance of considering population stratification in what might be considered a small homogeneous region. There is evidence from F(ST)-based analysis of genic and nongenic SNPs that differential positive selection has operated across these populations despite their short divergence time and relatively similar geographic and environmental range. The pressure appears to have been focused on genes involved in immunity, perhaps reflecting response to infectious disease epidemic. Such an event may explain a striking selective sweep centered on the rs2508049-G allele, close to the HLA-G gene on chromosome 6. Evidence of the sweep extends over a 8-Mb/3.5-cM region. Overall, the results illustrate the power of dense genotype and sample data to explore regional population variation, the events that have crafted it, and their implications in both explaining disease prevalence and mapping these genes by association.
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Affiliation(s)
- Brian P McEvoy
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia.
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43
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Y-chromosomal evidence of the cultural diffusion of agriculture in Southeast Europe. Eur J Hum Genet 2008; 17:820-30. [PMID: 19107149 DOI: 10.1038/ejhg.2008.249] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The debate concerning the mechanisms underlying the prehistoric spread of farming to Southeast Europe is framed around the opposing roles of population movement and cultural diffusion. To investigate the possible involvement of local people during the transition of agriculture in the Balkans, we analysed patterns of Y-chromosome diversity in 1206 subjects from 17 population samples, mainly from Southeast Europe. Evidence from three Y-chromosome lineages, I-M423, E-V13 and J-M241, make it possible to distinguish between Holocene Mesolithic forager and subsequent Neolithic range expansions from the eastern Sahara and the Near East, respectively. In particular, whereas the Balkan microsatellite variation associated to J-M241 correlates with the Neolithic period, those related to E-V13 and I-M423 Balkan Y chromosomes are consistent with a late Mesolithic time frame. In addition, the low frequency and variance associated to I-M423 and E-V13 in Anatolia and the Middle East, support an European Mesolithic origin of these two clades. Thus, these Balkan Mesolithic foragers with their own autochthonous genetic signatures, were destined to become the earliest to adopt farming, when it was subsequently introduced by a cadre of migrating farmers from the Near East. These initial local converted farmers became the principal agents spreading this economy using maritime leapfrog colonization strategies in the Adriatic and transmitting the Neolithic cultural package to other adjacent Mesolithic populations. The ensuing range expansions of E-V13 and I-M423 parallel in space and time the diffusion of Neolithic Impressed Ware, thereby supporting a case of cultural diffusion using genetic evidence.
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44
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Pattison JE. Is it necessary to assume an apartheid-like social structure in Early Anglo-Saxon England? Proc Biol Sci 2008; 275:2423-9; discussion 2419-21. [PMID: 18430641 PMCID: PMC2603190 DOI: 10.1098/rspb.2008.0352] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It has recently been argued that there was an apartheid-like social structure operating in Early Anglo-Saxon England. This was proposed in order to explain the relatively high degree of similarity between Germanic-speaking areas of northwest Europe and England. Opinions vary as to whether there was a substantial Germanic invasion or only a relatively small number arrived in Britain during this period. Contrary to the assumption of limited intermarriage made in the apartheid simulation, there is evidence that significant mixing of the British and Germanic peoples occurred, and that the early law codes, such as that of King Ine of Wessex, could have deliberately encouraged such mixing. More importantly, the simulation did not take into account any northwest European immigration that arrived both before and after the Early Anglo-Saxon period. In view of the uncertainty of the places of origin of the various Germanic peoples, and their numbers and dates of arrival, the present study adopts an alternative approach to estimate the percentage of indigenous Britons in the current British population. It was found unnecessary to introduce any special social structure among the diverse Anglo-Saxon people in order to account for the estimates of northwest European intrusion into the British population.
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Affiliation(s)
- John E Pattison
- School of EIE-Applied Physics, University of South Australia, Mawson Lakes, SA 5095, Australia.
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45
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Thomas MG, Stumpf MP, Härke H. Integration versus apartheid in post-Roman Britain: a response to Pattison. Proc Biol Sci 2008. [DOI: 10.1098/rspb.2008.0677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Mark G Thomas
- Department of Genetics, Evolution and EnvironmentUniversity College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK
| | - Michael P.H Stumpf
- Centre for Bioinformatics, Imperial College LondonWolfson Building, London SW7 2AZ, UK
| | - Heinrich Härke
- Department of Archaeology, The University of ReadingWhiteknights, Reading RG6 6AB, UK
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46
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Zalloua PA, Xue Y, Khalife J, Makhoul N, Debiane L, Platt DE, Royyuru AK, Herrera RJ, Hernanz DFS, Blue-Smith J, Wells RS, Comas D, Bertranpetit J, Tyler-Smith C. Y-chromosomal diversity in Lebanon is structured by recent historical events. Am J Hum Genet 2008; 82:873-82. [PMID: 18374297 PMCID: PMC2427286 DOI: 10.1016/j.ajhg.2008.01.020] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 01/25/2008] [Accepted: 01/28/2008] [Indexed: 11/25/2022] Open
Abstract
Lebanon is an eastern Mediterranean country inhabited by approximately four million people with a wide variety of ethnicities and religions, including Muslim, Christian, and Druze. In the present study, 926 Lebanese men were typed with Y-chromosomal SNP and STR markers, and unusually, male genetic variation within Lebanon was found to be more strongly structured by religious affiliation than by geography. We therefore tested the hypothesis that migrations within historical times could have contributed to this situation. Y-haplogroup J∗(xJ2) was more frequent in the putative Muslim source region (the Arabian Peninsula) than in Lebanon, and it was also more frequent in Lebanese Muslims than in Lebanese non-Muslims. Conversely, haplogroup R1b was more frequent in the putative Christian source region (western Europe) than in Lebanon and was also more frequent in Lebanese Christians than in Lebanese non-Christians. The most common R1b STR-haplotype in Lebanese Christians was otherwise highly specific for western Europe and was unlikely to have reached its current frequency in Lebanese Christians without admixture. We therefore suggest that the Islamic expansion from the Arabian Peninsula beginning in the seventh century CE introduced lineages typical of this area into those who subsequently became Lebanese Muslims, whereas the Crusader activity in the 11th–13th centuries CE introduced western European lineages into Lebanese Christians.
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Selectivity of black death mortality with respect to preexisting health. Proc Natl Acad Sci U S A 2008; 105:1436-41. [PMID: 18227518 DOI: 10.1073/pnas.0705460105] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Was the mortality associated with the deadliest known epidemic in human history, the Black Death of 1347-1351, selective with respect to preexisting health conditions ("frailty")? Many researchers have assumed that the Black Death was so virulent, and the European population so immunologically naïve, that the epidemic killed indiscriminately, irrespective of age, sex, or frailty. If this were true, Black Death cemeteries would provide unbiased cross-sections of demographic and epidemiological conditions in 14th-century Europe. Using skeletal remains from medieval England and Denmark, new methods of paleodemographic age estimation, and a recent multistate model of selective mortality, we test the assumption that the mid-14th-century Black Death killed indiscriminately. Skeletons from the East Smithfield Black Death cemetery in London are compared with normal, nonepidemic cemetery samples from two medieval Danish towns (Viborg and Odense). The results suggest that the Black Death did not kill indiscriminately-that it was, in fact, selective with respect to frailty, although probably not as strongly selective as normal mortality.
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48
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Contu D, Morelli L, Santoni F, Foster JW, Francalacci P, Cucca F. Y-chromosome based evidence for pre-neolithic origin of the genetically homogeneous but diverse Sardinian population: inference for association scans. PLoS One 2008; 3:e1430. [PMID: 18183308 PMCID: PMC2174525 DOI: 10.1371/journal.pone.0001430] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 12/03/2007] [Indexed: 11/19/2022] Open
Abstract
The island of Sardinia shows a unique high incidence of several autoimmune diseases with multifactorial inheritance, particularly type 1 diabetes and multiple sclerosis. The prior knowledge of the genetic structure of this population is fundamental to establish the optimal design for association studies in these diseases. Previous work suggested that the Sardinians are a relatively homogenous population, but some reports were contradictory and data were largely based on variants subject to selection. For an unbiased assessment of genetic structure, we studied a combination of neutral Y-chromosome variants, 21 biallelic and 8 short tandem repeats (STRs) in 930 Sardinian males. We found a high degree of interindividual variation but a homogenous distribution of the detected variability in samples from three separate regions of the island. One haplogroup, I-M26, is rare or absent outside Sardinia and is very common (0.37 frequency) throughout the island, consistent with a founder effect. A Bayesian full likelihood analysis (BATWING) indicated that the time from the most recent common ancestor (TMRCA) of I-M26, was 21.0 (16.0–25.5) thousand years ago (KYA) and that the population began to expand 14.0 (7.8–22.0) KYA. These results suggest a largely pre-Neolithic settlement of the island with little subsequent gene flow from outside populations. Consequently, Sardinia is an especially attractive venue for case-control genome wide association scans in common multifactorial diseases. Concomitantly, the high degree of interindividual variation in the current population facilitates fine mapping efforts to pinpoint the aetiologic polymorphisms.
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Affiliation(s)
- Daniela Contu
- Laboratorio di Immunogenetica, Ospedale Microcitemico, Cagliari, Italy
| | - Laura Morelli
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Federico Santoni
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy
| | - Jamie W. Foster
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Paolo Francalacci
- Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari, Italy
| | - Francesco Cucca
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
- * To whom correspondence should be addressed. E-mail:
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Bowden GR, Balaresque P, King TE, Hansen Z, Lee AC, Pergl-Wilson G, Hurley E, Roberts SJ, Waite P, Jesch J, Jones AL, Thomas MG, Harding SE, Jobling MA. Excavating past population structures by surname-based sampling: the genetic legacy of the Vikings in northwest England. Mol Biol Evol 2007; 25:301-9. [PMID: 18032405 DOI: 10.1093/molbev/msm255] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The genetic structures of past human populations are obscured by recent migrations and expansions and have been observed only indirectly by inference from modern samples. However, the unique link between a heritable cultural marker, the patrilineal surname, and a genetic marker, the Y chromosome, provides a means to target sets of modern individuals that might resemble populations at the time of surname establishment. As a test case, we studied samples from the Wirral Peninsula and West Lancashire, in northwest England. Place-names and archaeology show clear evidence of a past Viking presence, but heavy immigration and population growth since the industrial revolution are likely to have weakened the genetic signal of a 1,000-year-old Scandinavian contribution. Samples ascertained on the basis of 2 generations of residence were compared with independent samples based on known ancestry in the region plus the possession of a surname known from historical records to have been present there in medieval times. The Y-chromosomal haplotypes of these 2 sets of samples are significantly different, and in admixture analyses, the surname-ascertained samples show markedly greater Scandinavian ancestry proportions, supporting the idea that northwest England was once heavily populated by Scandinavian settlers. The method of historical surname-based ascertainment promises to allow investigation of the influence of migration and drift over the last few centuries in changing the population structure of Britain and will have general utility in other regions where surnames are patrilineal and suitable historical records survive.
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Affiliation(s)
- Georgina R Bowden
- Department of Genetics, University of Leicester, Leicester, United Kingdom
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50
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Thomas MG, Barnes I, Weale ME, Jones AL, Forster P, Bradman N, Pramstaller PP. New genetic evidence supports isolation and drift in the Ladin communities of the South Tyrolean Alps but not an ancient origin in the Middle East. Eur J Hum Genet 2007; 16:124-34. [PMID: 17712356 DOI: 10.1038/sj.ejhg.5201906] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The Alps are one of the most significant geographical barriers in Europe and several isolated Swiss and Italian valleys retain the distinctive Ladin and Romansch languages, alongside the modern majority of Italian and German languages. Linguistically, Ladin belongs to the Romance languages, but some studies on mitochondrial DNA (mtDNA) variation have suggested a major Middle Eastern component to their genealogical origin. Furthermore, an observed high degree of within-population diversity has been interpreted as reflecting long-standing differentiation from other European populations and the absence of a major bottleneck in Ladin population history. To explore these issues further, we examined Y chromosome and mtDNA variation in two samples of Ladin speakers, two samples of German speakers and one sample of metropolitan Italian speakers. Our results (1) indicate reduced diversity in the Ladin-speaking and isolated German-speaking populations when compared to a sample of metropolitan Italian speakers, (2) fail to identify haplotypes that are rare in other European populations that other researchers have identified, and (3) indicate different Middle Eastern components to Ladin ancestry in different localities. These new results, in combination with Bayesian estimation of demographic parameters of interest (population size, population growth rate, and Palaeolithic/Neolithic admixture proportions) and phylogeographic analysis, suggest that the Ladin groups under study are small genetically isolated populations (subject to strong genetic drift), having a predominantly European ancestry, and in one locality, may have a greater Palaeolithic component to that ancestry than their neighbours.
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Affiliation(s)
- Mark G Thomas
- Department of Biology, University College London, London NW1 2HE, UK.
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