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Anagnostou P, Capocasa M, Brisighelli F, Battaggia C, Destro Bisol G. The emerging complexity of Open Science: assessing Intelligent Data Openness in Genomic Anthropology and Human Genomics. J Anthropol Sci 2021; 99:135-152. [PMID: 34951605 DOI: 10.4436/jass.99016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In recent decades, the scientific community has become aware of the importance of science being effectively open in order to speed up scientific and technological progress. In this context, the achievement of a robust, effective and responsible form of data sharing is now widely acknowledged as a fundamental part of the research process. The production and resolution of human genomic data has steadily increased in recent years, mainly due to technological advances and decreasing costs of DNA genotyping and sequencing. There is, however, a downside to this process due to the huge increase in the complexity of the data and related metadata. This means it is advisable to go beyond traditional forms of sharing analysis, which have focused on data availability only. Here we present a pilot study that aims to complement a survey on the availability of data related to peer-reviewed publications with an analysis of their findability, accessibility, useability and assessability (according to the "intelligent data openness" scheme). Sharing rates in genomic anthropology (73.0%) were found to be higher than human genomics (32.4%), but lower than closely related research fields (from 96.8% to 79.2% for paleogenetics and evolutionary genetics, respectively). We discuss the privacy and methodological issues that could be linked to this finding. Comparisons of sharing rates across a wide range of disciplines has suggested that the idea of human genomics as a forerunner for the open data movement should be questioned. Finally, both in genomic anthropology and human genomics, findability and useability were found to be compliant with the expectations of an intelligent data openness, whereas only a minor part of studies met the need to make the data completely assessable.
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Affiliation(s)
- Paolo Anagnostou
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, Italy; Istituto Italiano di Antropologia, Piazzale Aldo Moro 5, Rome, Italy,
| | - Marco Capocasa
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, Italy; Istituto Italiano di Antropologia, Piazzale Aldo Moro 5, Rome, Italy
| | - Francesca Brisighelli
- Forensic Genetics Laboratory, Department of Health Surveillance and Bioethics, F. Policlinico Gemelli IRCCS Roma, Universitá Cattolica del Sacro Cuore, Italy
| | - Cinzia Battaggia
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, Italy
| | - Giovanni Destro Bisol
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, Italy; Istituto Italiano di Antropologia, Piazzale Aldo Moro 5, Rome, Italy, giovanni.
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Raveane A, Aneli S, Montinaro F, Athanasiadis G, Barlera S, Birolo G, Boncoraglio G, Di Blasio AM, Di Gaetano C, Pagani L, Parolo S, Paschou P, Piazza A, Stamatoyannopoulos G, Angius A, Brucato N, Cucca F, Hellenthal G, Mulas A, Peyret-Guzzon M, Zoledziewska M, Baali A, Bycroft C, Cherkaoui M, Chiaroni J, Di Cristofaro J, Dina C, Dugoujon JM, Galan P, Giemza J, Kivisild T, Mazieres S, Melhaoui M, Metspalu M, Myers S, Pereira L, Ricaut FX, Brisighelli F, Cardinali I, Grugni V, Lancioni H, Pascali VL, Torroni A, Semino O, Matullo G, Achilli A, Olivieri A, Capelli C. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe. Sci Adv 2019; 5:eaaw3492. [PMID: 31517044 PMCID: PMC6726452 DOI: 10.1126/sciadv.aaw3492] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/10/2019] [Accepted: 08/06/2019] [Indexed: 05/10/2023]
Abstract
European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.
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Affiliation(s)
- A. Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Department of Zoology, University of Oxford, Oxford, UK
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - S. Aneli
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - F. Montinaro
- Department of Zoology, University of Oxford, Oxford, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - G. Athanasiadis
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - S. Barlera
- Department of Cardiovascular Research, Istituto di Ricovero e Cura a Carattere Scientifico–Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - G. Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - G. Boncoraglio
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- PhD Program in Neuroscience, University Milano-Bicocca, Monza, Italy
| | - A. M. Di Blasio
- Istituto Auxologico Italiano, IRCCS, Centro di Ricerche e Tecnologie Biomediche, Milano, Italy
| | - C. Di Gaetano
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - L. Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- APE lab, Department of Biology, University of Padua, Padua, Italy
| | - S. Parolo
- Computational Biology Unit, Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - P. Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - A. Piazza
- Department of Medical Sciences, University of Turin, Turin, Italy
- Academy of Sciences, Turin, Italy
| | - G. Stamatoyannopoulos
- Department of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - A. Angius
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - N. Brucato
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - G. Hellenthal
- University College London Genetics Institute (UGI), University College London, London, UK
| | - A. Mulas
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Lanusei, Italy
| | - M. Peyret-Guzzon
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - A. Baali
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - C. Bycroft
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Cherkaoui
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - J. Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - J. Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - C. Dina
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - J. M. Dugoujon
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - P. Galan
- Equipe de Recherche en Epidémiologie Nutritionnelle (EREN), Centre de Recherche en Epidémiologie et Statistiques, Université Paris 13/Inserm U1153/Inra U1125/ Cnam, COMUE Sorbonne Paris Cité, F-93017 Bobigny, France
| | - J. Giemza
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - T. Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Herestraat 49, box 604, Leuven 3000, Belgium
| | - S. Mazieres
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - M. Melhaoui
- Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco
| | - M. Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - S. Myers
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - L. Pereira
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - F. X. Ricaut
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Brisighelli
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - I. Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - H. Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. L. Pascali
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - A. Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - O. Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - G. Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - A. Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - A. Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - C. Capelli
- Department of Zoology, University of Oxford, Oxford, UK
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
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Martinez-Matilla M, Blanco-Verea A, Santori M, Ansede-Bermejo J, Ramos-Luis E, Gil R, Bermejo AM, Lotufo-Neto F, Hirata MH, Brisighelli F, Paramo M, Carracedo A, Brion M. Genetic susceptibility in pharmacodynamic and pharmacokinetic pathways underlying drug-induced arrhythmia and sudden unexplained deaths. Forensic Sci Int Genet 2019; 42:203-212. [PMID: 31376648 DOI: 10.1016/j.fsigen.2019.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/14/2019] [Accepted: 07/14/2019] [Indexed: 12/21/2022]
Abstract
Drug-induced arrhythmia is an adverse drug reaction that can be potentially fatal since it is mostly related to drug-induced QT prolongation, a known risk factor for Torsade de Pointes and sudden cardiac death (SCD). Several risk factors have been described in association to these drug-induced events, such as preexistent cardiac disease and genetic variation. Our objective was to study the genetic susceptibility in pharmacodynamic and pharmacokinetic pathways underlying suspected drug-induced arrhythmias and sudden unexplained deaths in 32 patients. The genetic component in the pharmacodynamic pathway was studied by analysing 96 genes associated with higher risk of SCD through massive parallel sequencing. Pharmacokinetic-mediated genetic susceptibility was investigated by studying the genes encoding cytochrome P450 enzymes using medium-throughput genotyping. Pharmacodynamic analysis showed three probably pathogenic variants and 45 variants of uncertain significance in 28 patients, several of them previously described in relation to mild or late onset cardiomyopathies. These results suggest that genetic variants in cardiomyopathy genes, in addition to those related with channelopathies, could be relevant to drug-induced cardiotoxicity and contribute to the arrhythmogenic phenotype. Pharmacokinetic analysis showed three patients that could have an altered metabolism of the drugs they received involving CYP2C19 and/or CYP2D6, probably contributing to the arrhythmogenic phenotype. The study of genetic variants in both pharmacodynamic and pharmacokinetic pathways may be a useful strategy to understand the multifactorial mechanism of drug-induced events in both clinical practice and forensic field. However, it is necessary to comprehensively study and evaluate the contribution of the genetic susceptibility to drug-induced cardiotoxicity.
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Affiliation(s)
- M Martinez-Matilla
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (A Coruña), Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.
| | - A Blanco-Verea
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (A Coruña), Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - M Santori
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - J Ansede-Bermejo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain; Centro Nacional de Genotipado-CeGen-USC-PRB3-ISCIII, Santiago de Compostela, Spain
| | - E Ramos-Luis
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (A Coruña), Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - R Gil
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (A Coruña), Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - A M Bermejo
- Instituto de Ciencias Forenses "Luis Concheiro" (INCIFOR), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - F Lotufo-Neto
- Psiquiatry Institute - Faculty of Medicine at University of São Paulo, São Paulo, Brazil
| | - M H Hirata
- Institute Dante Pazzanese of Cardiology, São Paulo, Brazil; School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - F Brisighelli
- Institute of Public Health, Section of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - M Paramo
- Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - A Carracedo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain; Centro Nacional de Genotipado-CeGen-USC-PRB3-ISCIII, Santiago de Compostela, Spain
| | - M Brion
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (A Coruña), Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain; Centro Nacional de Genotipado-CeGen-USC-PRB3-ISCIII, Santiago de Compostela, Spain
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4
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Serventi P, Panicucci C, Bodega R, De Fanti S, Sarno S, Fondevila Alvarez M, Brisighelli F, Trombetta B, Anagnostou P, Ferri G, Vazzana A, Delpino C, Gruppioni G, Luiselli D, Cilli E. Iron Age Italic population genetics: the Piceni from Novilara (8th-7th century BC). Ann Hum Biol 2018; 45:34-43. [PMID: 29216758 DOI: 10.1080/03014460.2017.1414876] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Archaeological data provide evidence that Italy, during the Iron Age, witnessed the appearance of the first communities with well defined cultural identities. To date, only a few studies report genetic data about these populations and, in particular, the Piceni have never been analysed. AIMS To provide new data about mitochondrial DNA (mtDNA) variability of an Iron Age Italic population, to understand the contribution of the Piceni in shaping the modern Italian gene pool and to ascertain the kinship between some individuals buried in the same grave within the Novilara necropolis. SUBJECTS AND METHODS In a first set of 10 individuals from Novilara, we performed deep sequencing of the HVS-I region of the mtDNA, combined with the genotyping of 22 SNPs in the coding region and the analysis of several autosomal markers. RESULTS The results show a low nucleotide diversity for the inhabitants of Novilara and highlight a genetic affinity of this ancient population with the current inhabitants of central Italy. No family relationship was observed between the individuals analysed here. CONCLUSIONS This study provides a preliminary characterisation of the mtDNA variability of the Piceni of Novilara, as well as a kinship assessment of two peculiar burials.
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Affiliation(s)
- Patrizia Serventi
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy.,b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Chiara Panicucci
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Roberta Bodega
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Sara De Fanti
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Stefania Sarno
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Manuel Fondevila Alvarez
- c Instituto de Ciencias Forenses 'Luis Concheiro' , University of Santiago de Compostela, Santiago de Compostela , Galicia , Spain
| | - Francesca Brisighelli
- d Sezione di Medicina Legale-Istituto di Sanità Pubblica , Università Cattolica del Sacro Cuore , Roma , Italy
| | - Beniamino Trombetta
- e Department of Biology and Biotechnology 'Charles Darwin' , Sapienza University , Rome , Italy
| | - Paolo Anagnostou
- f Department of Environmental Biology , University of Rome 'La Sapienza' , Rome , Italy.,g ISItA, Istituto Italiano di Antropologia , Rome , Italy
| | - Gianmarco Ferri
- h Department of Diagnostic and Clinical Medicine and Public Health , University of Modena and Reggio Emilia , Modena , Italy
| | - Antonino Vazzana
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Chiara Delpino
- i Superintendence of Archaeological Heritage of Marche Region , Ancona , Italy
| | - Giorgio Gruppioni
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Donata Luiselli
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Elisabetta Cilli
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
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5
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Martinez-Matilla M, Blanco-Verea A, Torres M, Ramos-Luis E, Gil R, Bermejo A, H Hirata M, Brisighelli F, Paramo M, Carracedo A, Brion M. P5857Study of pharmacodynamic and pharmacokinetic-mediated genetic susceptibility to drug-induced arrhythmia and sudden cardiac death. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx493.p5857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- M. Martinez-Matilla
- Instituto de Investigaciόn Sanitaria de Santiago, Xenética de enfermidades cardiovasculares e oftalmolόxicas, Grupo de Medicina Xenόmica, USC, Santiago de Compostela, Spain
| | - A. Blanco-Verea
- Instituto de Investigaciόn Sanitaria de Santiago, Xenética de enfermidades cardiovasculares e oftalmolόxicas, Grupo de Medicina Xenόmica, USC, Santiago de Compostela, Spain
| | - M. Torres
- University of Santiago de Compostela, CeGen (Genotyping National Center), Grupo de Medicina Xenόmica, Santiago de Compostela, Spain
| | - E. Ramos-Luis
- Instituto de Investigaciόn Sanitaria de Santiago, Xenética de enfermidades cardiovasculares e oftalmolόxicas, Grupo de Medicina Xenόmica, USC, Santiago de Compostela, Spain
| | - R. Gil
- Instituto de Investigaciόn Sanitaria de Santiago, Xenética de enfermidades cardiovasculares e oftalmolόxicas, Grupo de Medicina Xenόmica, USC, Santiago de Compostela, Spain
| | - A. Bermejo
- University of Santiago de Compostela, Instituto de Ciencias Forenses “Luis Concheiro” (INCIFOR), Santiago de Compostela, Spain
| | - M. H Hirata
- Institute Dante Pazzanese of Cardiology, Sao Paulo, Brazil
| | - F. Brisighelli
- Catholic University of the Sacred Heart, Forensic Genetics Laboratory, Institute of Legal Medicine, Rome, Italy
| | - M. Paramo
- University Hospital of Santiago de Compostela, Servicio de Psiquiatría, Santiago de Compostela, Spain
| | - A. Carracedo
- Instituto de Investigaciόn Sanitaria de Santiago, University of Santiago de Compostela (USC), Grupo de Medicina Xenόmica, Santiago de Compostela, Spain
| | - M. Brion
- Instituto de Investigaciόn Sanitaria de Santiago, Xenética de enfermidades cardiovasculares e oftalmolόxicas, Grupo de Medicina Xenόmica, USC, Santiago de Compostela, Spain
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6
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Rey-González D, Gelabert-Besada M, Cruz R, Brisighelli F, Lopez-Soto M, Rasool M, Naseer M, Sánchez-Diz P, Carracedo A. Micro and macro geographical analysis of Y-chromosome lineages in South Iberia. Forensic Sci Int Genet 2017; 29:e9-e15. [DOI: 10.1016/j.fsigen.2017.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 04/27/2017] [Accepted: 04/29/2017] [Indexed: 11/25/2022]
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7
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Bertoncini S, D'Ercole J, Brisighelli F, Ramanamanjato J, Capelli C, Tofanelli S, Donati G. Stuck in fragments: Population genetics of the Endangered collared brown lemur
Eulemur collaris
in the Malagasy littoral forest. Am J Phys Anthropol 2017; 163:542-552. [DOI: 10.1002/ajpa.23230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/30/2017] [Accepted: 04/04/2017] [Indexed: 11/10/2022]
Affiliation(s)
| | - Jacopo D'Ercole
- Department of Biology, University of PisaVia Ghini 13Pisa56126 Italy
- Department of Integrative Biology Centre for Biodiversity GenomicsUniversity of GuelphGuelph OntarioN1G 2W1 Canada
| | - Francesca Brisighelli
- Forensic Genetics LaboratoryInstitute of Legal Medicine, Università Cattolica del Sacro CuoreRoma Italia
- Department of ZoologyUniversity of OxfordSouth Parks RoadOxfordOX1 3PS United Kingdom
| | | | - Cristian Capelli
- Department of ZoologyUniversity of OxfordSouth Parks RoadOxfordOX1 3PS United Kingdom
| | - Sergio Tofanelli
- Department of Biology, University of PisaVia Ghini 13Pisa56126 Italy
| | - Giuseppe Donati
- Department of Social SciencesOxford Brookes UniversityOxford United Kingdom
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8
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Weiler N, Baca K, Ballard D, Balsa F, Bogus M, Børsting C, Brisighelli F, Červenáková J, Chaitanya L, Coble M, Decroyer V, Desmyter S, van der Gaag K, Gettings K, Haas C, Heinrich J, João Porto M, Kal A, Kayser M, Kúdelová A, Morling N, Mosquera-Miguel A, Noel F, Parson W, Pereira V, Phillips C, Schneider P, Syndercombe Court D, Turanska M, Vidaki A, Woliński P, Zatkalíková L, Sijen T. A collaborative EDNAP exercise on SNaPshot™-based mtDNA control region typing. Forensic Sci Int Genet 2017; 26:77-84. [DOI: 10.1016/j.fsigen.2016.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/04/2016] [Accepted: 10/23/2016] [Indexed: 01/27/2023]
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9
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Toscanini U, Brisighelli F, Llull C, Berardi G, Gómez A, Andreatta F, Pardo-Seco J, Gómez-Carballa A, Martinón-Torres F, Álvarez-Iglesias V, Salas A. Charting the Y-chromosome ancestry of present-day Argentinean Mennonites. J Hum Genet 2016; 61:507-13. [PMID: 26841831 DOI: 10.1038/jhg.2016.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/27/2015] [Accepted: 01/06/2016] [Indexed: 11/09/2022]
Abstract
Old Order Mennonite communities initially arose in Northern Europe (centered in the Netherlands) and derived from the Anabaptist movement of the 16th century. Mennonites migrated to the New World in the early 18th century, first to North America, and more recently to Mesoamerica and South America. We analyzed Y-chromosome short tandem repeats (STRs) and single nucleotide polymorphisms in males from a community of Mennonites, 'La Nueva Esperanza', which arrived to Argentina in 1985 from colonies in Bolivia and Mexico. Molecular diversity indices coupled with demographic simulations show that Mennonites have a reduced variability when compared with local Argentinean populations and 69 European population samples. Mennonite Y-STR haplotypes were mainly observed in Central Europe. In agreement, multidimensional scaling analyses based on RST genetic distances indicate that Mennonite Y-chromosomes are closely related to Central/Northern Europeans (the Netherlands, Switzerland and Denmark). In addition, statistical inferences made on the most likely geographic origin of Y-chromosome haplotypes point more specifically to the Netherlands as the populations that best represent the majority of the Mennonite Y-chromosomes. Overall, Y-chromosome variation of Mennonites shows the signatures of moderate reduction of variability when compared with source populations, which is in good agreement with their lifestyle in small endogamous demes. These genetic singularities could also help to understand disease conditions that are more prevalent among Mennonites.
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Affiliation(s)
- Ulises Toscanini
- PRICAI-Fundación Favaloro, Buenos Aires, Argentina.,Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Francesca Brisighelli
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Cintia Llull
- PRICAI-Fundación Favaloro, Buenos Aires, Argentina
| | | | - Andrea Gómez
- PRICAI-Fundación Favaloro, Buenos Aires, Argentina
| | | | - Jacobo Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Galicia, Spain
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
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10
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Coia V, Cipollini G, Anagnostou P, Maixner F, Battaggia C, Brisighelli F, Gómez-Carballa A, Destro Bisol G, Salas A, Zink A. Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman. Sci Rep 2016; 6:18932. [PMID: 26764605 PMCID: PMC4725900 DOI: 10.1038/srep18932] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/01/2015] [Indexed: 01/01/2023] Open
Abstract
The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps - putatively in genetic continuity with the Tyrolean Iceman-and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny, and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000 ybp. Based on the comparison of our results with published data, we propose a scenario that could explain the apparent contrast between the phylogeographic features of maternal and paternal lineages of the Tyrolean Iceman within the context of the demographic dynamics happening in Europe from 8,000 ybp.
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Affiliation(s)
- V Coia
- Accademia Europea di Bolzano (EURAC-Research), Istituto per le mummie e l´Iceman, Bolzano, Italy
| | - G Cipollini
- Accademia Europea di Bolzano (EURAC-Research), Istituto per le mummie e l´Iceman, Bolzano, Italy
| | - P Anagnostou
- Dipartimento Biologia Ambientale, Università La Sapienza, Roma, Italy
| | - F Maixner
- Accademia Europea di Bolzano (EURAC-Research), Istituto per le mummie e l´Iceman, Bolzano, Italy
| | - C Battaggia
- Dipartimento Biologia Ambientale, Università La Sapienza, Roma, Italy
| | - F Brisighelli
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - A Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - G Destro Bisol
- Dipartimento Biologia Ambientale, Università La Sapienza, Roma, Italy.,Istituto Italiano di Antropologia, Roma, Italy
| | - A Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - A Zink
- Accademia Europea di Bolzano (EURAC-Research), Istituto per le mummie e l´Iceman, Bolzano, Italy
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11
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Toscanini U, Brisighelli F, Moreno F, Pantoja-Astudillo JA, Morales EA, Bustos P, Pardo-Seco J, Salas A. Analysis of Y-chromosome STRs in Chile confirms an extensive introgression of European male lineages in urban populations. Forensic Sci Int Genet 2015; 21:76-80. [PMID: 26736138 DOI: 10.1016/j.fsigen.2015.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 12/05/2015] [Accepted: 12/09/2015] [Indexed: 12/09/2022]
Abstract
We analyzed the Y chromosome haplotypes (Yfiler) of 978 non-related Chilean males grouped in five sampling regions (Iquique, Santiago de Chile, Concepción, Temuco and Punta Arenas) covering main geo-political regions. Overall, 803 different haplotypes and 688 singletons were observed. Molecular diversity was moderately lower than in other neighboring countries (e.g. Argentina); and AMOVA analysis on Y-STR haplotypes showed that among variation within Chile accounted for only 0.25% of the total variation. Punta Arenas, in the southern cone, showed the lowest haplotype diversity, and discrimination capacity, and also the highest matching probability of the five Chilean samples, probably reflecting its more marked geographic isolation compared to the other regions. Multidimensional scaling (MDS) analysis based on RST genetic distances suggested a close proximity of Chilean Y-chromosome profiles to European ones. Consistently, haplogroups inferred from Y-STR profiles revealed that the Native American component constituted only 8% of all the haplotypes, and this component ranged from 5% in the Centre of the country to 9-10% in the South and 13% in the North, which is in good agreement with the distribution of Native American communities in these regions. AMOVA computed on inferred haplogroups confirmed the very low among variation observed in Chilean populations. The present project provides the first Chilean dataset to the international Y-chromosome STR Haplotype Reference Database (YHRD) and it is also the first reference database for Y-chromosome forensic casework of the country.
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Affiliation(s)
- Ulises Toscanini
- Pricai-Fundación Favaloro, Buenos Aires, Argentina; Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain; Infectious Diseases and Vaccines Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Francesca Brisighelli
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain; Sezione di Medicina Legale-Istituto di Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Fabián Moreno
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain; Servicio Medico Legal, Ministerio de Justicia, Santiago, Chile
| | | | - Eugenia Aguirre Morales
- Servicio Medico Legal, Ministerio de Justicia, Santiago, Chile; Infectious Diseases and Vaccines Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Patricio Bustos
- Servicio Medico Legal, Ministerio de Justicia, Santiago, Chile
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain; Infectious Diseases and Vaccines Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain; Infectious Diseases and Vaccines Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain.
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12
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Busby GB, Hellenthal G, Montinaro F, Tofanelli S, Bulayeva K, Rudan I, Zemunik T, Hayward C, Toncheva D, Karachanak-Yankova S, Nesheva D, Anagnostou P, Cali F, Brisighelli F, Romano V, Lefranc G, Buresi C, Ben Chibani J, Haj-Khelil A, Denden S, Ploski R, Krajewski P, Hervig T, Moen T, Herrera RJ, Wilson JF, Myers S, Capelli C. The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape. Curr Biol 2015; 25:2878. [PMID: 28843288 PMCID: PMC5628165 DOI: 10.1016/j.cub.2015.10.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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13
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Busby GBJ, Hellenthal G, Montinaro F, Tofanelli S, Bulayeva K, Rudan I, Zemunik T, Hayward C, Toncheva D, Karachanak-Yankova S, Nesheva D, Anagnostou P, Cali F, Brisighelli F, Romano V, Lefranc G, Buresi C, Ben Chibani J, Haj-Khelil A, Denden S, Ploski R, Krajewski P, Hervig T, Moen T, Herrera RJ, Wilson JF, Myers S, Capelli C. The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape. Curr Biol 2015; 25:2518-26. [PMID: 26387712 PMCID: PMC4714572 DOI: 10.1016/j.cub.2015.08.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/29/2015] [Accepted: 08/05/2015] [Indexed: 11/19/2022]
Abstract
Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient humans across West Eurasia, demonstrating the presence of large-scale, dynamic population movements over the last 10,000 years, such that ancestry across present-day populations is likely to be a mixture of several ancient groups [1, 2, 3, 4, 5, 6, 7]. While these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled or have been either too regional or global in their outlook [8, 9, 10, 11]. Here, using recently described haplotype-based techniques [11], we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200 CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1,500 years are likely to have maintained differentiation among groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia. Recent admixture events involved outside groups at the edges of West Eurasia Admixture within Europe tended to fall within the European Migration Period West Eurasian genetic structure today is likely to have been maintained by admixture
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Affiliation(s)
- George B J Busby
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Garrett Hellenthal
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Francesco Montinaro
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Sergio Tofanelli
- Department of Biology, Università di Pisa, Via Ghini 13, 56126 Pisa, Italy
| | - Kazima Bulayeva
- N.I.Vavilov Institute of General Genetics, 3 Gubkin Street, Moscow 119991, Russia
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute of Population Heath Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Tatijana Zemunik
- Department of Medical Biology, School of Medicine Split, Soltanska 2, Split 21000, Croatia
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Draga Toncheva
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Sena Karachanak-Yankova
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Paolo Anagnostou
- Department of Environmental Biology, Università La Sapienza, Roma 00185, Italy; Istituto Italiano di Antropologia, Roma 00185, Italy
| | - Francesco Cali
- Laboratorio di Genetica Molecolare, IRCCS Associazione Oasi Maria SS, Troina 94018, Italy
| | - Francesca Brisighelli
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK; Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome 00168, Italy
| | - Valentino Romano
- Dipartimento di Fisica e Chimica, Università di Palermo, Palermo 90128, Italy
| | - Gerard Lefranc
- Institute of Human Genetics, CNRS UPR 1142, and Montpellier University, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
| | - Catherine Buresi
- Institute of Human Genetics, CNRS UPR 1142, and Montpellier University, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
| | - Jemni Ben Chibani
- Laboratory of Biochemistry and Molecular Biology, Faculty of Pharmacy, 1 Avenue Avicenne, 5019 Monastir, Tunisia
| | - Amel Haj-Khelil
- Laboratory of Biochemistry and Molecular Biology, Faculty of Pharmacy, 1 Avenue Avicenne, 5019 Monastir, Tunisia
| | - Sabri Denden
- Laboratory of Biochemistry and Molecular Biology, Faculty of Pharmacy, 1 Avenue Avicenne, 5019 Monastir, Tunisia
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, 3c Pawinskiego Street, Warsaw 02-106, Poland
| | - Pawel Krajewski
- Department of Forensic Medicine, Warsaw Medical University, 1 Oczki Street, Warsaw 02-007, Poland
| | - Tor Hervig
- Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | | | - Rene J Herrera
- Department of Human and Molecular Genetics, Florida International University, University Park, Miami, FL 33174, USA
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Heath Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Simon Myers
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; Department of Statistics, University of Oxford, South Parks Road, Oxford OX1 3TG, UK
| | - Cristian Capelli
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
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14
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Tofanelli S, Brisighelli F, Anagnostou P, Busby GBJ, Ferri G, Thomas MG, Taglioli L, Rudan I, Zemunik T, Hayward C, Bolnick D, Romano V, Cali F, Luiselli D, Shepherd GB, Tusa S, Facella A, Capelli C. The Greeks in the West: genetic signatures of the Hellenic colonisation in southern Italy and Sicily. Eur J Hum Genet 2015; 24:429-36. [PMID: 26173964 DOI: 10.1038/ejhg.2015.124] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/29/2015] [Accepted: 05/06/2015] [Indexed: 11/09/2022] Open
Abstract
Greek colonisation of South Italy and Sicily (Magna Graecia) was a defining event in European cultural history, although the demographic processes and genetic impacts involved have not been systematically investigated. Here, we combine high-resolution surveys of the variability at the uni-parentally inherited Y chromosome and mitochondrial DNA in selected samples of putative source and recipient populations with forward-in-time simulations of alternative demographic models to detect signatures of that impact. Using a subset of haplotypes chosen to represent historical sources, we recover a clear signature of Greek ancestry in East Sicily compatible with the settlement from Euboea during the Archaic Period (eighth to fifth century BCE). We inferred moderate sex-bias in the numbers of individuals involved in the colonisation: a few thousand breeding men and a few hundred breeding women were the estimated number of migrants. Last, we demonstrate that studies aimed at quantifying Hellenic genetic flow by the proportion of specific lineages surviving in present-day populations may be misleading.
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Affiliation(s)
| | - Francesca Brisighelli
- Department of Zoology, University of Oxford, Oxford, UK.,Sezione di Medicina Legale-Istituto di Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Università "La Sapienza", Roma, Italy.,Istituto Italiano di Antropologia, Roma, Italy
| | - George B J Busby
- Department of Zoology, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Gianmarco Ferri
- Dipartimento ad Attività Integrata di Laboratori, Anatomia Patologica, Medicina Legale, U.O. Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Modena, Italy
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Luca Taglioli
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Igor Rudan
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Scotland, UK
| | - Tatijana Zemunik
- Department of Medical Biology, University of Split, School of Medicine, Split, Croatia
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Deborah Bolnick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Valentino Romano
- Dipartimento di Fisica e Chimica, Università di Palermo, Palermo, Italy.,Laboratorio di Genetica Molecolare, I.R.C.C.S. Associazione Oasi Maria SS., Troina, Italy
| | - Francesco Cali
- Dipartimento di Fisica e Chimica, Università di Palermo, Palermo, Italy
| | - Donata Luiselli
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Gillian B Shepherd
- A.D. Trendall Research Centre for Ancient Mediterranean Studies, La Trobe University, Melbourne, Victoria, Australia
| | | | - Antonino Facella
- Soprintendenza per i Beni Archeologici della Calabria, Reggio Calabria, Italy
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15
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Sarno S, Tofanelli S, De Fanti S, Quagliariello A, Bortolini E, Ferri G, Anagnostou P, Brisighelli F, Capelli C, Tagarelli G, Sineo L, Luiselli D, Boattini A, Pettener D. Shared language, diverging genetic histories: high-resolution analysis of Y-chromosome variability in Calabrian and Sicilian Arbereshe. Eur J Hum Genet 2015; 24:600-6. [PMID: 26130483 PMCID: PMC4929864 DOI: 10.1038/ejhg.2015.138] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/02/2015] [Accepted: 04/14/2015] [Indexed: 11/25/2022] Open
Abstract
The relationship between genetic and linguistic diversification in human populations has been often explored to interpret some specific issues in human history. The Albanian-speaking minorities of Sicily and Southern Italy (Arbereshe) constitute an important portion of the ethnolinguistic variability of Italy. Their linguistic isolation from neighboring Italian populations and their documented migration history, make such minorities particularly effective for investigating the interplay between cultural, geographic and historical factors. Nevertheless, the extent of Arbereshe genetic relationships with the Balkan homeland and the Italian recipient populations has been only partially investigated. In the present study we address the genetic history of Arbereshe people by combining highly resolved analyses of Y-chromosome lineages and extensive computer simulations. A large set of slow- and fast-evolving molecular markers was typed in different Arbereshe communities from Sicily and Southern Italy (Calabria), as well as in both the putative Balkan source and Italian sink populations. Our results revealed that the considered Arbereshe groups, despite speaking closely related languages and sharing common cultural features, actually experienced diverging genetic histories. The estimated proportions of genetic admixture confirm the tight relationship of Calabrian Arbereshe with modern Albanian populations, in accordance with linguistic hypotheses. On the other hand, population stratification and/or an increased permeability of linguistic and geographic barriers may be hypothesized for Sicilian groups, to account for their partial similarity with Greek populations and their higher levels of local admixture. These processes ultimately resulted in the differential acquisition or preservation of specific paternal lineages by the present-day Arbereshe communities.
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Affiliation(s)
- Stefania Sarno
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | | | - Sara De Fanti
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Andrea Quagliariello
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Eugenio Bortolini
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Gianmarco Ferri
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Università degli Studi di Modena e Reggio Emilia, Modena, Italia
| | - Paolo Anagnostou
- Dipartimento Biologia Ambientale, Sapienza Università di Roma, Roma, Italia.,Istituto Italiano di Antropologia, Roma, Italia
| | - Francesca Brisighelli
- Department of Zoology, University of Oxford, Oxford, UK.,Sezione di medicina Legale-Istituto di Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italia
| | | | | | - Luca Sineo
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italia
| | - Donata Luiselli
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Alessio Boattini
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Davide Pettener
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
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16
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Santos C, Fondevila M, Ballard D, Banemann R, Bento AM, Børsting C, Branicki W, Brisighelli F, Burrington M, Capal T, Chaitanya L, Daniel R, Decroyer V, England R, Gettings KB, Gross TE, Haas C, Harteveld J, Hoff-Olsen P, Hoffmann A, Kayser M, Kohler P, Linacre A, Mayr-Eduardoff M, McGovern C, Morling N, O'Donnell G, Parson W, Pascali VL, Porto MJ, Roseth A, Schneider PM, Sijen T, Stenzl V, Court DS, Templeton JE, Turanska M, Vallone PM, Oorschot RAHV, Zatkalikova L, Carracedo Á, Phillips C. Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise. Forensic Sci Int Genet 2015; 19:56-67. [PMID: 26122263 DOI: 10.1016/j.fsigen.2015.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/06/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain informative likelihood ratios for a third. Therefore, successful ancestry assignments were achieved by participants in 92 of 95 Snipper analyses. This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-generation sequencing analyses (each using different systems) and achieved high levels of genotyping concordance using the exercise PCR primer mixes unmodified.
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Affiliation(s)
- C Santos
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - M Fondevila
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - D Ballard
- Department of Forensic and Analytical Science, Faculty of Life Science, King's College London, UK
| | - R Banemann
- Federal Criminal Police Office, Wiesbaden, Germany
| | - A M Bento
- Forensic Genetic and Biology Service, Centre Branch, National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen, Denmark
| | - W Branicki
- Section of Forensic Genetics, Institute of Forensic Research, Kraków, Poland
| | - F Brisighelli
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - T Capal
- Department of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - L Chaitanya
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - R Daniel
- Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, Australia
| | - V Decroyer
- National Institute of Criminalistics and Criminology, Chaussée de Vilvoorde 100, Brussels, Belgium
| | - R England
- ESR, Private Bag 92021, Auckland, New Zealand
| | - K B Gettings
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - T E Gross
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - C Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - J Harteveld
- Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands
| | - P Hoff-Olsen
- Department of Forensic Biology, Norwegian Institute of Public Health, Oslo, Norway
| | - A Hoffmann
- Federal Criminal Police Office, Wiesbaden, Germany
| | - M Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - P Kohler
- Department of Forensic Biology, Norwegian Institute of Public Health, Oslo, Norway
| | - A Linacre
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5042, Australia
| | - M Mayr-Eduardoff
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - C McGovern
- ESR, Private Bag 92021, Auckland, New Zealand
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen, Denmark; National Institute of Criminalistics and Criminology, Chaussée de Vilvoorde 100, Brussels, Belgium
| | - G O'Donnell
- Forensic Science Laboratory, Dublin, Ireland
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - V L Pascali
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - M J Porto
- Forensic Genetic and Biology Service, Centre Branch, National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal
| | - A Roseth
- Department of Forensic Biology, Norwegian Institute of Public Health, Oslo, Norway
| | - P M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - T Sijen
- Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands
| | - V Stenzl
- Department of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - D Syndercombe Court
- Department of Forensic and Analytical Science, Faculty of Life Science, King's College London, UK
| | - J E Templeton
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5042, Australia
| | - M Turanska
- Institute of Forensic Science, Ministry of the Interior, Department of Biology and DNA Analysis, Slovenská Lupca, Slovakia
| | - P M Vallone
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - R A H van Oorschot
- Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, Australia
| | - L Zatkalikova
- Institute of Forensic Science, Ministry of the Interior, Department of Biology and DNA Analysis, Slovenská Lupca, Slovakia
| | - Á Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
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17
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Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, Nordenfelt S, Li H, de Filippo C, Prüfer K, Sawyer S, Posth C, Haak W, Hallgren F, Fornander E, Rohland N, Delsate D, Francken M, Guinet JM, Wahl J, Ayodo G, Babiker HA, Bailliet G, Balanovska E, Balanovsky O, Barrantes R, Bedoya G, Ben-Ami H, Bene J, Berrada F, Bravi CM, Brisighelli F, Busby GBJ, Cali F, Churnosov M, Cole DEC, Corach D, Damba L, van Driem G, Dryomov S, Dugoujon JM, Fedorova SA, Gallego Romero I, Gubina M, Hammer M, Henn BM, Hervig T, Hodoglugil U, Jha AR, Karachanak-Yankova S, Khusainova R, Khusnutdinova E, Kittles R, Kivisild T, Klitz W, Kučinskas V, Kushniarevich A, Laredj L, Litvinov S, Loukidis T, Mahley RW, Melegh B, Metspalu E, Molina J, Mountain J, Näkkäläjärvi K, Nesheva D, Nyambo T, Osipova L, Parik J, Platonov F, Posukh O, Romano V, Rothhammer F, Rudan I, Ruizbakiev R, Sahakyan H, Sajantila A, Salas A, Starikovskaya EB, Tarekegn A, Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Vasquez R, Villena M, Voevoda M, Winkler CA, Yepiskoposyan L, Zalloua P, Zemunik T, Cooper A, Capelli C, Thomas MG, Ruiz-Linares A, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Pääbo S, Kelso J, Reich D, Krause J. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 2014; 513:409-13. [PMID: 25230663 PMCID: PMC4170574 DOI: 10.1038/nature13673] [Citation(s) in RCA: 737] [Impact Index Per Article: 73.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 07/11/2014] [Indexed: 12/19/2022]
Abstract
We sequenced the genomes of a ~7,000 year old farmer from Germany and eight
~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other
ancient genomes1–4 with 2,345 contemporary humans to show that most
present Europeans derive from at least three highly differentiated populations: West
European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near
Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near
Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but
also harbored WHG-related ancestry. We model these populations’ deep relationships
and show that EEF had ~44% ancestry from a “Basal Eurasian”
population that split prior to the diversification of other non-African lineages.
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Affiliation(s)
- Iosif Lazaridis
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Alissa Mittnik
- Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany
| | - Gabriel Renaud
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Swapan Mallick
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Karola Kirsanow
- Institute of Anthropology, Johannes Gutenberg University Mainz, Mainz D-55128, Germany
| | - Peter H Sudmant
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Joshua G Schraiber
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. [2] Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Sergi Castellano
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Mark Lipson
- Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Bonnie Berger
- 1] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. [2] Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Christos Economou
- Archaeological Research Laboratory, Stockholm University, 114 18, Sweden
| | - Ruth Bollongino
- Institute of Anthropology, Johannes Gutenberg University Mainz, Mainz D-55128, Germany
| | - Qiaomei Fu
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. [3] Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100049, China
| | - Kirsten I Bos
- Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany
| | - Susanne Nordenfelt
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Heng Li
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Susanna Sawyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Cosimo Posth
- Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany
| | - Wolfgang Haak
- Australian Centre for Ancient DNA and Environment Institute, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Elin Fornander
- The Cultural Heritage Foundation, Västerås 722 12, Sweden
| | - Nadin Rohland
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Dominique Delsate
- 1] National Museum of Natural History, L-2160, Luxembourg. [2] National Center of Archaeological Research, National Museum of History and Art, L-2345, Luxembourg
| | - Michael Francken
- Department of Paleoanthropology, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen D-72070, Germany
| | | | - Joachim Wahl
- State Office for Cultural Heritage Management Baden-Württemberg, Osteology, Konstanz D-78467, Germany
| | - George Ayodo
- Center for Global Health and Child Development, Kisumu 40100, Kenya
| | - Hamza A Babiker
- 1] Institutes of Evolution, Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK. [2] Biochemistry Department, Faculty of Medicine, Sultan Qaboos University, Alkhod, Muscat 123, Oman
| | - Graciela Bailliet
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET &CICPBA, La Plata, B1906APO, Argentina
| | | | - Oleg Balanovsky
- 1] Research Centre for Medical Genetics, Moscow 115478, Russia. [2] Vavilov Institute for General Genetics, Moscow 119991, Russia
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José 2060, Costa Rica
| | - Gabriel Bedoya
- Institute of Biology, Research group GENMOL, Universidad de Antioquia, Medellín, Colombia
| | | | - Judit Bene
- Department of Medical Genetics and Szentagothai Research Center, University of Pécs, Pécs H-7624, Hungary
| | - Fouad Berrada
- Al Akhawayn University in Ifrane (AUI), School of Science and Engineering, Ifrane 53000, Morocco
| | - Claudio M Bravi
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET &CICPBA, La Plata, B1906APO, Argentina
| | - Francesca Brisighelli
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome 00168, Italy
| | - George B J Busby
- 1] Department of Zoology, University of Oxford, Oxford OX1 3PS, UK. [2] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Francesco Cali
- Laboratorio di Genetica Molecolare, IRCCS Associazione Oasi Maria SS, Troina 94018, Italy
| | | | - David E C Cole
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1L5, Canada
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires, 1113 CABA, Argentina
| | - Larissa Damba
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - George van Driem
- Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland
| | - Stanislav Dryomov
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk 630090, Russia
| | - Jean-Michel Dugoujon
- Anthropologie Moléculaire et Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier Toulouse III, Toulouse 31000, France
| | - Sardana A Fedorova
- North-Eastern Federal University and Yakut Research Center of Complex Medical Problems, Yakutsk 677013, Russia
| | - Irene Gallego Romero
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Marina Gubina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Michael Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA
| | - Tor Hervig
- Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | | | - Aashish R Jha
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Sena Karachanak-Yankova
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Rita Khusainova
- 1] Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. [2] Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia
| | - Elza Khusnutdinova
- 1] Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. [2] Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia
| | - Rick Kittles
- College of Medicine, University of Arizona, Tucson, Arizona 85724, USA
| | - Toomas Kivisild
- Division of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - William Klitz
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Vilnius University, Vilnius LT-08661, Lithuania
| | | | - Leila Laredj
- Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France
| | - Sergey Litvinov
- 1] Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. [2] Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia. [3] Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia
| | - Theologos Loukidis
- 1] Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. [2] Amgen, 33 Kazantzaki Str, Ilioupolis 16342, Athens, Greece (T.L.); Banaras Hindu University, Varanasi 221 005, India (L.S.)
| | | | - Béla Melegh
- Department of Medical Genetics and Szentagothai Research Center, University of Pécs, Pécs H-7624, Hungary
| | - Ene Metspalu
- Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Julio Molina
- Centro de Investigaciones Biomédicas de Guatemala, Ciudad de Guatemala, Guatemala
| | - Joanna Mountain
- Research Department, 23andMe, Mountain View, California 94043, USA
| | | | - Desislava Nesheva
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Thomas Nyambo
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam 65001, Tanzania
| | - Ludmila Osipova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Jüri Parik
- Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Fedor Platonov
- Research Institute of Health, North-Eastern Federal University, Yakutsk 677000, Russia
| | - Olga Posukh
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Valentino Romano
- Dipartimento di Fisica e Chimica, Università di Palermo, Palermo 90128, Italy
| | - Francisco Rothhammer
- 1] Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile. [2] Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile, Santiago 8320000, Chile. [3] Centro de Investigaciones del Hombre en el Desierto, Arica 1000000, Chile
| | - Igor Rudan
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh EH8 9AG, UK
| | - Ruslan Ruizbakiev
- 1] Institute of Immunology, Academy of Science, Tashkent 70000, Uzbekistan. [2]
| | - Hovhannes Sahakyan
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia. [2] Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia
| | - Antti Sajantila
- 1] Department of Forensic Medicine, Hjelt Institute, University of Helsinki, Helsinki 00014, Finland. [2] Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galcia 15872, Spain
| | - Elena B Starikovskaya
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk 630090, Russia
| | - Ayele Tarekegn
- Research Fellow, Henry Stewart Group, Russell House, London WC1A 2HN, UK
| | - Draga Toncheva
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Shahlo Turdikulova
- Institute of Bioorganic Chemistry Academy of Sciences Republic of Uzbekistan, Tashkent 100125, Uzbekistan
| | - Ingrida Uktveryte
- Department of Human and Medical Genetics, Vilnius University, Vilnius LT-08661, Lithuania
| | - Olga Utevska
- Department of Genetics and Cytology, V. N. Karazin Kharkiv National University, Kharkiv 61077, Ukraine
| | - René Vasquez
- 1] Instituto Boliviano de Biología de la Altura, Universidad Mayor de San Andrés, 591 2 La Paz, Bolivia. [2] UniversidadAutonoma Tomás Frías, Potosí, Bolivia
| | - Mercedes Villena
- 1] Instituto Boliviano de Biología de la Altura, Universidad Mayor de San Andrés, 591 2 La Paz, Bolivia. [2] UniversidadAutonoma Tomás Frías, Potosí, Bolivia
| | - Mikhail Voevoda
- 1] Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. [2] Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk 630089, Russia. [3] Novosibirsk State University, Novosibirsk 630090, Russia
| | - Cheryl A Winkler
- Basic Research Laboratory, NCI, NIH, Frederick National Laboratory, Leidos Biomedical, Frederick, Maryland 21702, USA
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia
| | - Pierre Zalloua
- 1] Lebanese American University, School of Medicine, Beirut 13-5053, Lebanon. [2] Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Tatijana Zemunik
- Department of Medical Biology, University of Split, School of Medicine, Split 21000, Croatia
| | - Alan Cooper
- Australian Centre for Ancient DNA and Environment Institute, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Sarah A Tishkoff
- Department of Biology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Lalji Singh
- 1] CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India. [2] Amgen, 33 Kazantzaki Str, Ilioupolis 16342, Athens, Greece (T.L.); Banaras Hindu University, Varanasi 221 005, India (L.S.)
| | | | - Richard Villems
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia. [2] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia. [3] Estonian Academy of Sciences, Tallinn 10130, Estonia
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Rem Sukernik
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk 630090, Russia
| | - Mait Metspalu
- Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Evan E Eichler
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Joachim Burger
- Institute of Anthropology, Johannes Gutenberg University Mainz, Mainz D-55128, Germany
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - David Reich
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Johannes Krause
- 1] Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany. [2] Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72070 Tübingen, Germany. [3] Max Planck Institut für Geschichte und Naturwissenschaften, Jena 07745, Germany
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Marks SJ, Montinaro F, Levy H, Brisighelli F, Ferri G, Bertoncini S, Batini C, Busby GBJ, Arthur C, Mitchell P, Stewart BA, Oosthuizen O, Oosthuizen E, D'Amato ME, Davison S, Pascali V, Capelli C. Static and moving frontiers: the genetic landscape of Southern African Bantu-speaking populations. Mol Biol Evol 2014; 32:29-43. [PMID: 25223418 DOI: 10.1093/molbev/msu263] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A consensus on Bantu-speaking populations being genetically similar has emerged in the last few years, but the demographic scenarios associated with their dispersal are still a matter of debate. The frontier model proposed by archeologists postulates different degrees of interaction among incoming agropastoralist and resident foraging groups in the presence of "static" and "moving" frontiers. By combining mitochondrial DNA and Y chromosome data collected from several southern African populations, we show that Bantu-speaking populations from regions characterized by a moving frontier developing after a long-term static frontier have larger hunter-gatherer contributions than groups from areas where a static frontier was not followed by further spatial expansion. Differences in the female and male components suggest that the process of assimilation of the long-term resident groups into agropastoralist societies was gender biased. Our results show that the diffusion of Bantu languages and culture in Southern Africa was a process more complex than previously described and suggest that the admixture dynamics between farmers and foragers played an important role in shaping the current patterns of genetic diversity.
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Affiliation(s)
- Sarah J Marks
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Francesco Montinaro
- Department of Zoology, University of Oxford, Oxford, United Kingdom Institute of Legal Medicine, Catholic University, Rome, Italy
| | - Hila Levy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Gianmarco Ferri
- Dipartimento ad Attività Integrata di Laboratori, Anatomia Patologica, Medicina Legale, U.O. Struttura Complessa di Medicina Legale, Azienda Ospedaliero, Universitaria di Modena, Modena, Italy
| | | | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - George B J Busby
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Charles Arthur
- School of Archaeology, University of Oxford, Oxford, United Kingdom
| | - Peter Mitchell
- School of Archaeology, University of Oxford, Oxford, United Kingdom School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | | | - Maria Eugenia D'Amato
- Biotechnology Department, Forensic DNA Laboratory, University of the Western Cape, Bellville, South Africa
| | - Sean Davison
- Biotechnology Department, Forensic DNA Laboratory, University of the Western Cape, Bellville, South Africa
| | | | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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19
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Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SMT, Santos LH, Anslinger K, Bayer B, Ayub Q, Wei W, Xue Y, Tyler-Smith C, Bafalluy MB, Martínez-Jarreta B, Egyed B, Balitzki B, Tschumi S, Ballard D, Court DS, Barrantes X, Bäßler G, Wiest T, Berger B, Niederstätter H, Parson W, Davis C, Budowle B, Burri H, Borer U, Koller C, Carvalho EF, Domingues PM, Chamoun WT, Coble MD, Hill CR, Corach D, Caputo M, D'Amato ME, Davison S, Decorte R, Larmuseau MHD, Ottoni C, Rickards O, Lu D, Jiang C, Dobosz T, Jonkisz A, Frank WE, Furac I, Gehrig C, Castella V, Grskovic B, Haas C, Wobst J, Hadzic G, Drobnic K, Honda K, Hou Y, Zhou D, Li Y, Hu S, Chen S, Immel UD, Lessig R, Jakovski Z, Ilievska T, Klann AE, García CC, de Knijff P, Kraaijenbrink T, Kondili A, Miniati P, Vouropoulou M, Kovacevic L, Marjanovic D, Lindner I, Mansour I, Al-Azem M, Andari AE, Marino M, Furfuro S, Locarno L, Martín P, Luque GM, Alonso A, Miranda LS, Moreira H, Mizuno N, Iwashima Y, Neto RSM, Nogueira TLS, Silva R, Nastainczyk-Wulf M, Edelmann J, Kohl M, Nie S, Wang X, Cheng B, Núñez C, Pancorbo MMD, Olofsson JK, Morling N, Onofri V, Tagliabracci A, Pamjav H, Volgyi A, Barany G, Pawlowski R, Maciejewska A, Pelotti S, Pepinski W, Abreu-Glowacka M, Phillips C, Cárdenas J, Rey-Gonzalez D, Salas A, Brisighelli F, Capelli C, Toscanini U, Piccinini A, Piglionica M, Baldassarra SL, Ploski R, Konarzewska M, Jastrzebska E, Robino C, Sajantila A, Palo JU, Guevara E, Salvador J, Ungria MCD, Rodriguez JJR, Schmidt U, Schlauderer N, Saukko P, Schneider PM, Sirker M, Shin KJ, Oh YN, Skitsa I, Ampati A, Smith TG, Calvit LSD, Stenzl V, Capal T, Tillmar A, Nilsson H, Turrina S, De Leo D, Verzeletti A, Cortellini V, Wetton JH, Gwynne GM, Jobling MA, Whittle MR, Sumita DR, Wolańska-Nowak P, Yong RYY, Krawczak M, Nothnagel M, Roewer L. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Sci Int Genet 2014; 12:12-23. [PMID: 24854874 PMCID: PMC4127773 DOI: 10.1016/j.fsigen.2014.04.008] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/19/2014] [Indexed: 02/05/2023]
Abstract
In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.
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Affiliation(s)
- Josephine Purps
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Sabine Siegert
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Germany
| | - Sascha Willuweit
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Marion Nagy
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Cíntia Alves
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Renato Salazar
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | | | - Lorna H Santos
- Philippine National Police Crime Laboratory, Quezon City, Philippines
| | - Katja Anslinger
- Institut für Rechtsmedizin, Ludwig-Maximilians-Universität, München, Germany
| | - Birgit Bayer
- Institut für Rechtsmedizin, Ludwig-Maximilians-Universität, München, Germany
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Wei Wei
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | | | - Balazs Egyed
- GenoID Forensic DNA Laboratory, Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Beate Balitzki
- Institut für Rechtsmedizin, Universität Basel, Switzerland
| | | | - David Ballard
- Department of Forensic and Analytical Science, King's College London, London, UK
| | | | - Xinia Barrantes
- Forensic Sciences Department, Poder Judicial, Heredia, Costa Rica
| | | | - Tina Wiest
- Landeskriminalamt Baden-Württemberg, Germany
| | - Burkhard Berger
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | | | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA
| | - Carey Davis
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA
| | - Bruce Budowle
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Helen Burri
- Forensische Genetik, Kantonsspital Aarau AG, Switzerland
| | - Urs Borer
- Forensische Genetik, Kantonsspital Aarau AG, Switzerland
| | | | - Elizeu F Carvalho
- Laboratorio de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Brazil
| | - Patricia M Domingues
- Laboratorio de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Brazil
| | | | - Michael D Coble
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Carolyn R Hill
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Daniel Corach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Servicio de Huellas Digitales Genetica and CONICET (National Scientific and Technical Research Council), Buenos Aires, Argentina
| | - Mariela Caputo
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Servicio de Huellas Digitales Genetica and CONICET (National Scientific and Technical Research Council), Buenos Aires, Argentina
| | - Maria E D'Amato
- University of the Western Cape, Biotechnology Department, Forensic DNA Laboratory, Cape Town, South Africa
| | - Sean Davison
- University of the Western Cape, Biotechnology Department, Forensic DNA Laboratory, Cape Town, South Africa
| | - Ronny Decorte
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Maarten H D Larmuseau
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Claudio Ottoni
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Olga Rickards
- Centre of Molecular Antropology For Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Italy
| | - Di Lu
- Collaborative Innovation Center of Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Chengtao Jiang
- Collaborative Innovation Center of Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Tadeusz Dobosz
- Institute of Forensic Medicine, Medical University, Wroclaw, Poland
| | - Anna Jonkisz
- Institute of Forensic Medicine, Medical University, Wroclaw, Poland
| | - William E Frank
- Illinois State Police, Research & Development Laboratory, Springfield, USA
| | - Ivana Furac
- Department of Forensic Medicine and Criminology, University of Zagreb, Croatia
| | - Christian Gehrig
- University Center of Legal Medicine, Lausanne-Geneva, Lausanne, Switzerland
| | - Vincent Castella
- University Center of Legal Medicine, Lausanne-Geneva, Lausanne, Switzerland
| | - Branka Grskovic
- Forensic Science Centre "Ivan Vucetic", General Police Directorate, Ministry of Interior, Zagreb, Croatia
| | - Cordula Haas
- Institut für Rechtsmedizin, Universität Zürich, Switzerland
| | - Jana Wobst
- Institut für Rechtsmedizin, Universität Zürich, Switzerland
| | | | | | - Katsuya Honda
- Department of Legal Medicine, Faculty of Medicine, University of Tsukuba, Japan
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Di Zhou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Yan Li
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Shengping Hu
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China
| | - Shenglan Chen
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China
| | | | | | - Zlatko Jakovski
- Institute for Forensic Medicine and Criminalistics, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Tanja Ilievska
- Institute for Forensic Medicine and Criminalistics, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Anja E Klann
- Institut für Rechtsmedizin, Universitätsmedizin Greifswald, Germany
| | | | - Peter de Knijff
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Thirsa Kraaijenbrink
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aikaterini Kondili
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Penelope Miniati
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Maria Vouropoulou
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Lejla Kovacevic
- Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
| | - Damir Marjanovic
- Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
| | - Iris Lindner
- Institut für Rechtsmedizin, Universität Rostock, Germany
| | - Issam Mansour
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Mouayyad Al-Azem
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Ansar El Andari
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Miguel Marino
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Sandra Furfuro
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Laura Locarno
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Pablo Martín
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | - Gracia M Luque
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | - Antonio Alonso
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | | | - Helena Moreira
- Departamento de Biologia, Universidade de Aveiro, Portugal
| | - Natsuko Mizuno
- National Research Institute of Police Science, Chiba, Japan
| | | | - Rodrigo S Moura Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro and DIMAV/INMETRO, Brazil
| | | | - Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
| | | | | | - Michael Kohl
- Institut für Rechtsmedizin, Universität Leipzig, Germany
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xianping Wang
- Department of Criminal Investigation, Xuanwei Public Security Bureau, Xuanwei, China
| | - Baowen Cheng
- Department of Criminal Investigation, Yunnan Provincial Public Security Bureau, Kunming, China
| | - Carolina Núñez
- BIOMICs Research Group, Universidad del País Vasco, Vitoria, Spain
| | | | - Jill K Olofsson
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Valerio Onofri
- Section of Legal Medicine, Università Politecnica delle Marche, Ancona, Italy
| | | | - Horolma Pamjav
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Antonia Volgyi
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Gusztav Barany
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Ryszard Pawlowski
- Forensic Genetics Laboratory, Institute of Forensic Medicine, Medical University of Gdansk, Poland
| | - Agnieszka Maciejewska
- Forensic Genetics Laboratory, Institute of Forensic Medicine, Medical University of Gdansk, Poland
| | - Susi Pelotti
- Department of Medical and Surgical Sciences (DIMEC), Institute of Legal Medicine, School of Medicine, University of Bologna, Italy
| | - Witold Pepinski
- Department of Forensic Medicine, Medical University of Bialystok, Poland
| | | | - Christopher Phillips
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Jorge Cárdenas
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Danel Rey-Gonzalez
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Antonio Salas
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Francesca Brisighelli
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Cristian Capelli
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; Department of Zoology, University of Oxford, Oxford, UK
| | - Ulises Toscanini
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; PRICAI-Fundación Favaloro, Buenos Aires, Argentina
| | - Andrea Piccinini
- Forensic Genetics Laboratory, Department of Human Morphology and Biomedical Sciences, Università degli Studi di Milano, Italy
| | - Marilidia Piglionica
- Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy
| | - Stefania L Baldassarra
- Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, Poland
| | | | | | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, Italy
| | - Antti Sajantila
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA; Department of Forensic Medicine, University of Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, University of Helsinki, Finland
| | - Evelyn Guevara
- Department of Forensic Medicine, University of Helsinki, Finland
| | - Jazelyn Salvador
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines
| | - Maria Corazon De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines
| | - Jae Joseph Russell Rodriguez
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines; Institute of Biological Sciences, University of the Philippines Los Baños, Laguna, Philippines
| | - Ulrike Schmidt
- Institut für Rechtsmedizin, Universitätsklinikum Freiburg, Germany
| | | | - Pekka Saukko
- Department of Forensic Medicine, University of Turku, Finland
| | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Germany
| | - Miriam Sirker
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Germany
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Yu Na Oh
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Iulia Skitsa
- Athens Dept. of Legal Medicine, DNA Analysis Laboratory, Athens, Greece
| | - Alexandra Ampati
- Athens Dept. of Legal Medicine, DNA Analysis Laboratory, Athens, Greece
| | - Tobi-Gail Smith
- Department of Basic Medical Sciences, University of the West Indies, Kingston, Jamaica
| | | | - Vlastimil Stenzl
- Laboratory of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - Thomas Capal
- Laboratory of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Helena Nilsson
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Stefania Turrina
- Sezione di Medicina Legale, Dipartimento di Medicina e Sanità Pubblica, Università degli Studi di Verona, Italy
| | - Domenico De Leo
- Sezione di Medicina Legale, Dipartimento di Medicina e Sanità Pubblica, Università degli Studi di Verona, Italy
| | - Andrea Verzeletti
- Istituto di Medicina Legale, Universitá degli Studi di Brescia, Italy
| | | | - Jon H Wetton
- Department of Genetics, University of Leicester, UK
| | | | | | | | | | | | - Rita Y Y Yong
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Germany
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany.
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Anagnostou P, Battaggia C, Capocasa M, Boschi I, Brisighelli F, Batini C, Spedini G, Destro-Bisol G. Reevaluating a model of gender-biased gene flow among Sub-Saharan Hunter-gatherers and farmers. Hum Biol 2014; 85:597-606. [PMID: 25019191 DOI: 10.3378/027.085.0406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2013] [Indexed: 11/05/2022]
Abstract
In a previous study, we proposed a model for genetic admixture between African hunter-gatherers and food producers, in which we integrated demographic and genetic aspects together with ethnographic knowledge (Destro-Bisol et al. 2004b). In that study it was possible to test the model only using genetic information from widely dispersed and genetically heterogeneous populations. Here we reevaluate the congruence between the model and patterns of genetic variation using an anthropologically and geographically more homogeneous data set that includes Pygmies and farmers from Cameroon, Congo, and the Central African Republic. As implied by the model, the ratios of mtDNA to Y chromosome Nm estimates (effective population size, N, times the migration rate, m; 0.154 in Pygmies and 6.759 in farmers), support an asymmetric gene flow, with a higher Bantu-to-Pygmy gene flow for paternal than for maternal lineages, and vice versa for farmers. Analyses of intra- and interpopulation genetic variation further support the above observation, showing a prevailing effect of genetic drift on maternal lineages and gene flow on paternal lineages among Pygmies, and an opposite pattern among farmers. We also detected differences between patterns for classical and molecular measures of Y chromosome intrapopulation variation, which likely represent signatures of the introgression of Bantu lineages into the gene pool of Pygmy populations. On the whole, our results seem to reflect differences in the demographic history and the degree of patrilocality and polygyny between the two population groups, thus providing further support to our microevolutionary model in an anthropologically coherent framework.
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Affiliation(s)
- Paolo Anagnostou
- Università di Roma "La Sapienza," Dipartimento di Biologia Ambientale, Rome, Italy and Istituto Italiano di Antropologia, Rome, Italy
| | - Cinzia Battaggia
- Università di Roma "La Sapienza," Dipartimento di Biologia Ambientale, Rome, Italy
| | - Marco Capocasa
- Istituto Italiano di Antropologia, Rome, Italy and Università di Roma, "La Sapienza," Dipartimento Biologia e Biotecnologie "Charles Darwin," Rome, Italy
| | - Ilaria Boschi
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester, UK
| | - Gabriella Spedini
- Università di Roma "La Sapienza," Dipartimento di Biologia Ambientale, Rome, Italy and Istituti Italiano di Antropologia, Rome, Italy
| | - Giovanni Destro-Bisol
- Università di Roma "La Sapienza," Dipartimento di Biologia Ambientale, Rome, Italy and Istituti Italiano di Antropologia, Rome, Italy
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21
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Capocasa M, Anagnostou P, Bachis V, Battaggia C, Bertoncini S, Biondi G, Boattini A, Boschi I, Brisighelli F, Caló CM, Carta M, Coia V, Corrias L, Crivellaro F, De Fanti S, Dominici V, Ferri G, Francalacci P, Franceschi ZA, Luiselli D, Morelli L, Paoli G, Rickards O, Robledo R, Sanna D, Sanna E, Sarno S, Sineo L, Taglioli L, Tagarelli G, Tofanelli S, Vona G, Pettener D, Destro Bisol G. Linguistic, geographic and genetic isolation: a collaborative study of Italian populations. J Anthropol Sci 2014; 92:201-31. [PMID: 24607994 DOI: 10.4436/jass.92001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The animal and plant biodiversity of the Italian territory is known to be one of the richest in the Mediterranean basin and Europe as a whole, but does the genetic diversity of extant human populations show a comparable pattern? According to a number of studies, the genetic structure of Italian populations retains the signatures of complex peopling processes which took place from the Paleolithic to modern era. Although the observed patterns highlight a remarkable degree of genetic heterogeneity, they do not, however, take into account an important source of variation. In fact, Italy is home to numerous ethnolinguistic minorities which have yet to be studied systematically. Due to their difference in geographical origin and demographic history, such groups not only signal the cultural and social diversity of our country, but they are also potential contributors to its bio-anthropological heterogeneity. To fill this gap, research groups from four Italian Universities (Bologna, Cagliari, Pisa and Roma Sapienza) started a collaborative study in 2007, which was funded by the Italian Ministry of Education, University and Research and received partial support by the Istituto Italiano di Antropologia. In this paper, we present an account of the results obtained in the course of this initiative. Four case-studies relative to linguistic minorities from the Eastern Alps, Sardinia, Apennines and Southern Italy are first described and discussed, focusing on their micro-evolutionary and anthropological implications. Thereafter, we present the results of a systematic analysis of the relations between linguistic, geographic and genetic isolation. Integrating the data obtained in the course of the long-term study with literature and unpublished results on Italian populations, we show that a combination of linguistic and geographic factors is probably responsible for the presence of the most robust signatures of genetic isolation. Finally, we evaluate the magnitude of the diversity of Italian populations in the European context. The human genetic diversity of our country was found to be greater than observed throughout the continent at short (0-200 km) and intermediate (700-800km) distances, and accounted for most of the highest values of genetic distances observed at all geographic ranges. Interestingly, an important contribution to this pattern comes from the "linguistic islands"( e.g. German speaking groups of Sappada and Luserna from the Eastern Italian Alps), further proof of the importance of considering social and cultural factors when studying human genetic variation.
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Affiliation(s)
- Marco Capocasa
- Istituto Italiano di Antropologia, Roma, Italy; Sapienza Universitá di Roma, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Roma, Italy,
| | - Paolo Anagnostou
- Sapienza Universitá di Roma, Dipartimento di Biologia Ambientale, Roma, Italy; Istituto Italiano di Antropologia, Roma, Italy
| | - Valeria Bachis
- Universitá di Cagliari, Dipartimento di Scienze della Vita e dell'Ambiente, Cagliari, Italy
| | - Cinzia Battaggia
- Universitá di Roma, Dipartimento di Biologia Ambientale, Roma, Italy
| | | | - Gianfranco Biondi
- Universitá dell'Aquila, Dipartimento di Scienze Ambientali, L'Aquila, Italy
| | - Alessio Boattini
- Universitá di Bologna, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Bologna, Italy
| | - Ilaria Boschi
- Universitá Cattolica del Sacro Cuore, Istituto di Medicina Legale, Roma, Italy
| | - Francesca Brisighelli
- Sapienza Universitá di Roma, Dipartimento di Biologia Ambientale, Roma, Italy; Universidade de Santiago de Compostela, Instituto de Ciencias Forenses, Santiago de Compostela, Spain
| | - Carla Maria Caló
- Universitá di Cagliari, Dipartimento di Scienze della Vita e dell'Ambiente, Cagliari, Italy
| | - Marilisa Carta
- Universitá di Bologna, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Bologna, Italy
| | - Valentina Coia
- Universitá di Trento, Dipartimento di Filosofia, Storia e Beni Culturali, Trento, Italy; Accademia Europea di Bolzano, Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Laura Corrias
- Universitá di Cagliari, Dipartimento di Scienze della Vita e dell'Ambiente, Cagliari, Italy
| | - Federica Crivellaro
- Sezione di Antropologia, Museo Nazionale Preistorico Etnografico "Luigi Pigorini", Roma, Italy
| | - Sara De Fanti
- Universitá di Bologna, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Bologna, Italy
| | - Valentina Dominici
- Sapienza Universitá di Roma, Dipartimento di Biologia Ambientale, Roma, Italy; Istituto Italiano di Antropologia, Roma, Italy
| | - Gianmarco Ferri
- Universitá di Modena e Reggio Emilia, Dipartimento di Medicina Diagnostica, Clinica e di Sanitá Pubblica, Modena, Italy
| | - Paolo Francalacci
- Universitá di Sassari, Dipartimento di Scienze della Natura e del Territorio, Sassari, Italy
| | - Zelda Alice Franceschi
- Universitá di Bologna, Dipartimento di Discipline Storiche, Antropologiche e Geografiche, Bologna, Italy
| | - Donata Luiselli
- Universitá di Bologna, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Bologna, Italy
| | - Laura Morelli
- Universitá di Sassari, Dipartimento di Scienze della Natura e del Territorio, Sassari, Italy
| | - Giorgio Paoli
- Universitá di Pisa, Dipartimento di Biologia, Pisa, Italy
| | - Olga Rickards
- Universitá degli Studi di Roma "Tor Vergata", Centro di Antropologia Molecolare per lo studio del DNA Antico, Dipartimento di Biologia, Roma, Italy
| | - Renato Robledo
- Universitá di Cagliari, Dipartimento di Scienze Biomediche, Cagliari, Italy
| | - Daria Sanna
- Universitá di Sassari, Dipartimento di Scienze della Natura e del Territorio, Sassari, Italy
| | - Emanuele Sanna
- Universitá di Cagliari, Dipartimento di Scienze della Vita e dell'Ambiente, Cagliari, Italy
| | - Stefania Sarno
- Universitá di Bologna, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Bologna, Italy
| | - Luca Sineo
- Universitá di Palermo, Dipartimento di Biologia Ambientale e Biodiversitá , Palermo, Italy
| | - Luca Taglioli
- Universitá di Pisa, Dipartimento di Biologia, Pisa, Italy
| | | | | | - Giuseppe Vona
- Universitá di Cagliari, Dipartimento di Scienze della Vita e dell'Ambiente, Cagliari, Italy
| | - Davide Pettener
- Universitá di Bologna, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Bologna, Italy,
| | - Giovanni Destro Bisol
- Sapienza Universitá di Roma, Dipartimento di Biologia Ambientale, Roma, Italy; Istituto Italiano di Antropologia, Roma, Italy,
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22
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Coia V, Capocasa M, Anagnostou P, Pascali V, Scarnicci F, Boschi I, Battaggia C, Crivellaro F, Ferri G, Alù M, Brisighelli F, Busby GBJ, Capelli C, Maixner F, Cipollini G, Viazzo PP, Zink A, Destro Bisol G. Demographic histories, isolation and social factors as determinants of the genetic structure of Alpine linguistic groups. PLoS One 2013; 8:e81704. [PMID: 24312576 PMCID: PMC3847036 DOI: 10.1371/journal.pone.0081704] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 10/15/2013] [Indexed: 11/25/2022] Open
Abstract
Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of “local ethnicity” on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood aspects of the genetic structure of European populations.
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MESH Headings
- Chromosomes, Human, Y/genetics
- Demography/history
- Ethnicity/genetics
- Ethnicity/history
- Evolution, Molecular
- Female
- Gene Flow
- Genetic Variation
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- Humans
- Linguistics
- Male
- Mitochondria/genetics
- Polymorphism, Single Nucleotide
- White People/ethnology
- White People/genetics
- White People/history
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Affiliation(s)
- Valentina Coia
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
- * E-mail: (VC); (GDB)
| | - Marco Capocasa
- Dipartimento Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto Italiano di Antropologia, Rome, Italy
| | - Paolo Anagnostou
- Istituto Italiano di Antropologia, Rome, Italy
- Dipartimento Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Vincenzo Pascali
- Istituto di Medicina Legale e delle Assicurazioni, Università Cattolica di Roma, Rome, Italy
| | - Francesca Scarnicci
- Istituto di Medicina Legale e delle Assicurazioni, Università Cattolica di Roma, Rome, Italy
| | - Ilaria Boschi
- Istituto di Medicina Legale e delle Assicurazioni, Università Cattolica di Roma, Rome, Italy
| | - Cinzia Battaggia
- Dipartimento Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Federica Crivellaro
- Sezione di Antropologia, Museo Nazionale Preistorico Etnografico “Luigi Pigorini”, Rome, Italy
| | - Gianmarco Ferri
- Dipartimento Integrato di Servizi Diagnostici e di Laboratorio e di Medicina Legale, Università di Modena e Reggio Emilia, Modena, Italy
| | - Milena Alù
- Dipartimento Integrato di Servizi Diagnostici e di Laboratorio e di Medicina Legale, Università di Modena e Reggio Emilia, Modena, Italy
| | - Francesca Brisighelli
- Istituto di Medicina Legale e delle Assicurazioni, Università Cattolica di Roma, Rome, Italy
| | | | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Frank Maixner
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Giovanna Cipollini
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Pier Paolo Viazzo
- Dipartimento Culture, Politica e Società-Sezione Scienze Antropologiche, Università degli Studi di Torino, Turin, Italy
| | - Albert Zink
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Giovanni Destro Bisol
- Istituto Italiano di Antropologia, Rome, Italy
- Dipartimento Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
- * E-mail: (VC); (GDB)
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23
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Brisighelli F, Álvarez-Iglesias V, Fondevila M, Blanco-Verea A, Carracedo Á, Pascali VL, Capelli C, Salas A. Uniparental markers of contemporary Italian population reveals details on its pre-Roman heritage. PLoS One 2012; 7:e50794. [PMID: 23251386 PMCID: PMC3519480 DOI: 10.1371/journal.pone.0050794] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 10/24/2012] [Indexed: 11/18/2022] Open
Abstract
Background According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country. Methods/Principal Findings A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy – probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers. Conclusions/Significance Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.
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Affiliation(s)
- Francesca Brisighelli
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
| | - Manuel Fondevila
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
| | - Alejandro Blanco-Verea
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
- Fundación Pública Galega de Medicina Xenómica (FPGMX-SERGAS), CIBER enfermedades raras, Santiago de Compostela, Galicia, Spain
| | - Vincenzo L. Pascali
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Antonio Salas
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
- * E-mail:
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24
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Cerezo M, Achilli A, Olivieri A, Perego UA, Gómez-Carballa A, Brisighelli F, Lancioni H, Woodward SR, López-Soto M, Carracedo Á, Capelli C, Torroni A, Salas A. Reconstructing ancient mitochondrial DNA links between Africa and Europe. Genome Res 2012; 22:821-6. [PMID: 22454235 PMCID: PMC3337428 DOI: 10.1101/gr.134452.111] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 02/29/2012] [Indexed: 11/25/2022]
Abstract
Mitochondrial DNA (mtDNA) lineages of macro-haplogroup L (excluding the derived L3 branches M and N) represent the majority of the typical sub-Saharan mtDNA variability. In Europe, these mtDNAs account for <1% of the total but, when analyzed at the level of control region, they show no signals of having evolved within the European continent, an observation that is compatible with a recent arrival from the African continent. To further evaluate this issue, we analyzed 69 mitochondrial genomes belonging to various L sublineages from a wide range of European populations. Phylogeographic analyses showed that ~65% of the European L lineages most likely arrived in rather recent historical times, including the Romanization period, the Arab conquest of the Iberian Peninsula and Sicily, and during the period of the Atlantic slave trade. However, the remaining 35% of L mtDNAs form European-specific subclades, revealing that there was gene flow from sub-Saharan Africa toward Europe as early as 11,000 yr ago.
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Affiliation(s)
- María Cerezo
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela, 15782 Galicia, Spain
| | - Alessandro Achilli
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, 06123 Perugia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27100 Pavia, Italy
| | - Ugo A. Perego
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27100 Pavia, Italy
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah 84115, USA
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela, 15782 Galicia, Spain
| | - Francesca Brisighelli
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela, 15782 Galicia, Spain
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Hovirag Lancioni
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, 06123 Perugia, Italy
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah 84115, USA
| | - Manuel López-Soto
- Instituto Nacional de Toxicología y Ciencias Forenses, 41018 Sevilla, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela, 15782 Galicia, Spain
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27100 Pavia, Italy
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela, 15782 Galicia, Spain
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Batini C, Ferri G, Destro-Bisol G, Brisighelli F, Luiselli D, Sanchez-Diz P, Rocha J, Simonson T, Brehm A, Montano V, Elwali NE, Spedini G, D'Amato ME, Myres N, Ebbesen P, Comas D, Capelli C. Signatures of the Preagricultural Peopling Processes in Sub-Saharan Africa as Revealed by the Phylogeography of Early Y Chromosome Lineages. Mol Biol Evol 2011; 28:2603-13. [DOI: 10.1093/molbev/msr089] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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27
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Pala M, Achilli A, Olivieri A, Kashani BH, Perego UA, Sanna D, Metspalu E, Tambets K, Tamm E, Accetturo M, Carossa V, Lancioni H, Panara F, Zimmermann B, Huber G, Al-Zahery N, Brisighelli F, Woodward SR, Francalacci P, Parson W, Salas A, Behar DM, Villems R, Semino O, Bandelt HJ, Torroni A. Mitochondrial haplogroup U5b3: a distant echo of the epipaleolithic in Italy and the legacy of the early Sardinians. Am J Hum Genet 2009; 84:814-21. [PMID: 19500771 PMCID: PMC2694970 DOI: 10.1016/j.ajhg.2009.05.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 05/15/2009] [Accepted: 05/15/2009] [Indexed: 11/16/2022] Open
Abstract
There are extensive data indicating that some glacial refuge zones of southern Europe (Franco-Cantabria, Balkans, and Ukraine) were major genetic sources for the human recolonization of the continent at the beginning of the Holocene. Intriguingly, there is no genetic evidence that the refuge area located in the Italian Peninsula contributed to this process. Here we show, through phylogeographic analyses of mitochondrial DNA (mtDNA) variation performed at the highest level of molecular resolution (52 entire mitochondrial genomes), that the most likely homeland for U5b3-a haplogroup present at a very low frequency across Europe-was the Italian Peninsula. In contrast to mtDNA haplogroups that expanded from other refugia, the Holocene expansion of haplogroup U5b3 toward the North was restricted by the Alps and occurred only along the Mediterranean coasts, mainly toward nearby Provence (southern France). From there, approximately 7,000-9,000 years ago, a subclade of this haplogroup moved to Sardinia, possibly as a result of the obsidian trade that linked the two regions, leaving a distinctive signature in the modern people of the island. This scenario strikingly matches the age, distribution, and postulated geographic source of a Sardinian Y chromosome haplogroup (I2a2-M26), a paradigmatic case in the European context of a founder event marking both female and male lineages.
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Affiliation(s)
- Maria Pala
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | - Alessandro Achilli
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia 06123, Italy
| | - Anna Olivieri
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | | | - Ugo A. Perego
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA
| | - Daria Sanna
- Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari 07100, Italy
| | - Ene Metspalu
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Kristiina Tambets
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Erika Tamm
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Matteo Accetturo
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | - Valeria Carossa
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | - Hovirag Lancioni
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia 06123, Italy
| | - Fausto Panara
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia 06123, Italy
| | - Bettina Zimmermann
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck A-6020, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck A-6020, Austria
| | - Nadia Al-Zahery
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
- Department of Biotechnology, College of Science, University of Baghdad, Iraq
| | - Francesca Brisighelli
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses; and Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia 15782, Spain
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA
| | - Paolo Francalacci
- Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari 07100, Italy
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck A-6020, Austria
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses; and Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia 15782, Spain
| | - Doron M. Behar
- Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel
| | - Richard Villems
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Ornella Semino
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | | | - Antonio Torroni
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
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Onofri V, Tagliabracci A, Boschi I, Brisighelli F, Scarnicci F, Pascali VL, Ferri G, Pelotti S, Capelli C. Y chromosome J2 subtyping in an Italian sample: Population and forensic implications. Forensic Science International: Genetics Supplement Series 2008. [DOI: 10.1016/j.fsigss.2007.10.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Capelli C, Brisighelli F, Scarnicci F, Blanco-Verea A, Brion M, Pascali VL. Phylogenetic evidence for multiple independent duplication events at the DYS19 locus. Forensic Sci Int Genet 2007; 1:287-90. [PMID: 19083776 DOI: 10.1016/j.fsigen.2007.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 05/10/2007] [Accepted: 06/01/2007] [Indexed: 11/19/2022]
Abstract
Duplication events at Y chromosome STR loci have been repeatedly described in human populations. DYS19 is probably the best known example and it exhibits duplicate state in individuals from all continents. Despite the large amount of available data, evolutionary relationship between DYS19 duplication-bearing chromosomes has not been so far investigated. We address the genealogical correlation among such chromosomes by analysing newly identified DYS19 duplicated Y chromosomes by SNP genotyping and microsatellite-based network analysis. SNP and network analysis show that DYS19 duplicated Y chromosomes associate with different Y chromosome lineages. These results indicate that DYS19 duplication occurred more than once during human evolution.
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Affiliation(s)
- Cristian Capelli
- Department of Zoology, University of Oxford, Tinbergen Building, South Parks Road, OX1 3PS Oxford, UK.
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Capelli C, MacPhee RDE, Roca AL, Brisighelli F, Georgiadis N, O'Brien SJ, Greenwood AD. A nuclear DNA phylogeny of the woolly mammoth (Mammuthus primigenius). Mol Phylogenet Evol 2006; 40:620-7. [PMID: 16631387 DOI: 10.1016/j.ympev.2006.03.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Revised: 02/28/2006] [Accepted: 03/07/2006] [Indexed: 11/19/2022]
Affiliation(s)
- Cristian Capelli
- Istituto di Medicina Legale, Universitá Cattolica del Sacro Cuore, Rome, Italy
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31
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Capelli C, Arredi B, Baldassari L, Boschi I, Brisighelli F, Caglià A, Dobosz M, Scarnicci F, Vetrugno G, Pascali VL. A 9-loci Y chromosome haplotype in three Italian populations. Forensic Sci Int 2006; 159:64-70. [PMID: 15998574 DOI: 10.1016/j.forsciint.2005.05.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Revised: 05/03/2005] [Accepted: 05/10/2005] [Indexed: 10/25/2022]
Abstract
Three geographic areas of Italy have been sampled and genotyped for 9 Y chromosome STRs: DYS19, DYS385, DYS388, DYS389 I and II, DYS390, DYS391, DYS392, DYS393. Sampling was focused on residents of small areas, well distant from major urban centres. Only individuals whose grandfather would live in the same area were included. A total of 210 unrelated individuals were collected. Distribution of genetic variation across the three samples and comparison with previously published Italian database indicated that so far Y chromosome diversity has been only partially explored in the Italian Peninsula.
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Affiliation(s)
- Cristian Capelli
- Laboratorio di Genetica Forense, Istituto di Medicina Legale, Università Cattolica del S. Cuore, Lgo F. Vito 1, Rome, Italy.
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