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Font-Porterias N, García-Fernández C, Aizpurua-Iraola J, Comas D, Torrents D, de Cid R, Calafell F. Sequence diversity of the uniparentally transmitted portions of the genome in the resident population of Catalonia. Forensic Sci Int Genet 2022; 61:102783. [DOI: 10.1016/j.fsigen.2022.102783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/30/2022]
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2
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Posth C, Zaro V, Spyrou MA, Vai S, Gnecchi-Ruscone GA, Modi A, Peltzer A, Mötsch A, Nägele K, Vågene ÅJ, Nelson EA, Radzevičiūtė R, Freund C, Bondioli LM, Cappuccini L, Frenzel H, Pacciani E, Boschin F, Capecchi G, Martini I, Moroni A, Ricci S, Sperduti A, Turchetti MA, Riga A, Zavattaro M, Zifferero A, Heyne HO, Fernández-Domínguez E, Kroonen GJ, McCormick M, Haak W, Lari M, Barbujani G, Bondioli L, Bos KI, Caramelli D, Krause J. The origin and legacy of the Etruscans through a 2000-year archeogenomic time transect. SCIENCE ADVANCES 2021; 7:eabi7673. [PMID: 34559560 PMCID: PMC8462907 DOI: 10.1126/sciadv.abi7673] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The origin, development, and legacy of the enigmatic Etruscan civilization from the central region of the Italian peninsula known as Etruria have been debated for centuries. Here we report a genomic time transect of 82 individuals spanning almost two millennia (800 BCE to 1000 CE) across Etruria and southern Italy. During the Iron Age, we detect a component of Indo-European–associated steppe ancestry and the lack of recent Anatolian-related admixture among the putative non–Indo-European–speaking Etruscans. Despite comprising diverse individuals of central European, northern African, and Near Eastern ancestry, the local gene pool is largely maintained across the first millennium BCE. This drastically changes during the Roman Imperial period where we report an abrupt population-wide shift to ~50% admixture with eastern Mediterranean ancestry. Last, we identify northern European components appearing in central Italy during the Early Middle Ages, which thus formed the genetic landscape of present-day Italian populations.
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Affiliation(s)
- Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72074, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen 72074, Germany
| | - Valentina Zaro
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Maria A. Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72074, Germany
| | - Stefania Vai
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Guido A. Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Alexander Peltzer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Angela Mötsch
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Åshild J. Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen 1350, Denmark
| | - Elizabeth A. Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA
| | - Rita Radzevičiūtė
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Cäcilia Freund
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | | | - Luca Cappuccini
- Department of History, Archeology, Geography, Art and Entertainment, University of Florence, Firenze 50121, Italy
| | - Hannah Frenzel
- Anatomy Institute, University of Leipzig, Leipzig 04103, Germany
| | - Elsa Pacciani
- Superintendence of Archaeology, Fine Arts and Landscape for Firenze, Pistoia and Prato, Italy
| | - Francesco Boschin
- Department of Physical Sciences, Earth and Environment, Research Unit Prehistory and Anthropology, University of Siena, Siena 53100, Italy
| | - Giulia Capecchi
- Department of Physical Sciences, Earth and Environment, Research Unit Prehistory and Anthropology, University of Siena, Siena 53100, Italy
| | - Ivan Martini
- Department of Physical Sciences, Earth and Environment, University of Siena, Siena 53100, Italy
| | - Adriana Moroni
- Department of Physical Sciences, Earth and Environment, Research Unit Prehistory and Anthropology, University of Siena, Siena 53100, Italy
| | - Stefano Ricci
- Department of Physical Sciences, Earth and Environment, Research Unit Prehistory and Anthropology, University of Siena, Siena 53100, Italy
| | - Alessandra Sperduti
- Bioarchaeology Service, Museum of Civilizations, Rome 00144, Italy
- Asia, Africa and Mediterranean Department, University of Naples, Naples 80134, Italy
| | | | - Alessandro Riga
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Monica Zavattaro
- Museum of Anthropology and Ethnology, Museum System of the University of Florence, Florence 50122, Italy
| | - Andrea Zifferero
- Department of History and Cultural Heritage, University of Siena, Siena 53100, Italy
| | - Henrike O. Heyne
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
- Program for Medical and Population Genetics/Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Guus J. Kroonen
- Department of Nordic Studies and Linguistics, University of Copenhagen, Copenhagen 2300, Denmark
- Leiden University Center for Linguistics, Leiden 2311 BE, Netherlands
| | - Michael McCormick
- Initiative for the Science of the Human Past, Department of History-Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Harvard University, Cambridge, MA 02138, USA
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Martina Lari
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy
| | - Luca Bondioli
- Bioarchaeology Service, Museum of Civilizations, Rome 00144, Italy
- Department of Cultural Heritage, University of Padua, Padua 35139, Italy
| | - Kirsten I. Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - David Caramelli
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
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De Angelis F, Scorrano G, Martínez-Labarga C, Scano G, Macciardi F, Rickards O. Mitochondrial variability in the Mediterranean area: a complex stage for human migrations. Ann Hum Biol 2018; 45:5-19. [PMID: 29382277 DOI: 10.1080/03014460.2017.1416172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CONTEXT The Mediterranean area has always played a significant role in human dispersal due to the large number of migratory events contributing to shape the cultural features and the genetic pool of its populations. OBJECTIVE This paper aims to review and diachronically describe the mitogenome variability in the Mediterranean population and the main demic diffusions that occurred in this area over time. METHODS Frequency distributions of the leading mitochondrial haplogroups have been geographically and chronologically evaluated. The variability of U5b and K lineages has been focussed to broaden the knowledge of their genetic histories. RESULTS The mitochondrial genetic makeup of Palaeolithic hunter-gatherers is poorly defined within the extant Mediterranean populations, since only a few traces of their genetic contribution are still detectable. The Neolithic lineages are more represented, suggesting that the Neolithic revolution had a marked effect on the peopling of the Mediterranean area. The largest effect, however, was provided by historical migrations. CONCLUSION Although the mitogenome variability has been widely used to try and clarify the evolution of the Mediterranean genetic makeup throughout almost 50 000 years, it is necessary to collect whole genome data on both extinct and extant populations from this area to fully reconstruct and interpret the impact of multiple migratory waves and their cultural and genetic consequences on the structure of the Mediterranean populations.
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Affiliation(s)
- Flavio De Angelis
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Gabriele Scorrano
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Cristina Martínez-Labarga
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Giuseppina Scano
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Fabio Macciardi
- b Laboratory of Molecular Psychiatry, Department of Psychiatry and Human Behavior , University of California , Irvine , CA , USA
| | - Olga Rickards
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
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Di Lorenzo P, Lancioni H, Ceccobelli S, Colli L, Cardinali I, Karsli T, Capodiferro MR, Sahin E, Ferretti L, Ajmone Marsan P, Sarti FM, Lasagna E, Panella F, Achilli A. Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin. PLoS One 2018; 13:e0192567. [PMID: 29462170 PMCID: PMC5819780 DOI: 10.1371/journal.pone.0192567] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/25/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Over the past 15 years, 300 out of 6000 breeds of all farm animal species identified by the Food and Agriculture Organization of the United Nations (FAO) have gone extinct. Among cattle, many Podolian breeds are seriously endangered in various European areas. Podolian cattle include a group of very ancient European breeds, phenotypically close to the aurochs ancestors (Bos primigenius). The aim of the present study was to assess the genetic diversity of Podolian breeds and to reconstruct their origin. METHODOLOGY The mitochondrial DNA (mtDNA) control-regions of 18 Podolian breeds have been phylogenetically assessed. Nine non-Podolian breeds have been also included for comparison. CONCLUSION The overall analysis clearly highlights some peculiarities in the mtDNA gene pool of some Podolian breeds. In particular, a principal component analysis point to a genetic proximity between five breeds (Chianina, Marchigiana, Maremmana, Podolica Italiana and Romagnola) reared in Central Italy and the Turkish Grey. We here propose the suggestive hypothesis of a dual ancestral contribution to the present gene pool of Podolian breeds, one deriving from Eastern European cattle; the other arising from the arrival of Middle Eastern cattle into Central Italy through a different route, perhaps by sea, ferried by Etruscan boats. The historical migration of Podolian cattle from North Eastern Europe towards Italy has not cancelled the mtDNA footprints of this previous ancient migration.
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Affiliation(s)
- Piera Di Lorenzo
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
- * E-mail: (HL); (AA)
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Licia Colli
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy
- Biodiversity and Ancient DNA Research Center–BioDNA, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, University of Akdeniz, Antalya, Turkey
| | | | - Emine Sahin
- Korkuteli Vocational School, University of Akdeniz, Antalya, Turkey
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
| | - Paolo Ajmone Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy
- Biodiversity and Ancient DNA Research Center–BioDNA, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Francesca Maria Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Francesco Panella
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
- * E-mail: (HL); (AA)
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5
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Origin and spread of human mitochondrial DNA haplogroup U7. Sci Rep 2017; 7:46044. [PMID: 28387361 PMCID: PMC5384202 DOI: 10.1038/srep46044] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/07/2017] [Indexed: 01/17/2023] Open
Abstract
Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16–19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that – analysed alongside 100 published ones – enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the Neolithic (~8 thousand years ago). These findings imply that the carriers of haplogroup U7 spread to South Asia and Europe before the suggested Bronze Age expansion of Indo-European languages from the Pontic-Caspian Steppe region.
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Chaitanya L, Ralf A, van Oven M, Kupiec T, Chang J, Lagacé R, Kayser M. Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine. Hum Mutat 2015; 36:1236-47. [PMID: 26387877 PMCID: PMC5057296 DOI: 10.1002/humu.22905] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/01/2015] [Indexed: 11/13/2022]
Abstract
Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long-range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications.
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Affiliation(s)
- Lakshmi Chaitanya
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Arwin Ralf
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Mannis van Oven
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Tomasz Kupiec
- Institute of Forensic ResearchSection of Forensic GeneticsKrakówPoland
| | - Joseph Chang
- Thermo Fisher ScientificSouth San FranciscoCalifornia, USA
| | - Robert Lagacé
- Thermo Fisher ScientificSouth San FranciscoCalifornia, USA
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
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7
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Gómez-Carballa A, Catelli L, Pardo-Seco J, Martinón-Torres F, Roewer L, Vullo C, Salas A. The complete mitogenome of a 500-year-old Inca child mummy. Sci Rep 2015; 5:16462. [PMID: 26561991 PMCID: PMC4642457 DOI: 10.1038/srep16462] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/16/2015] [Indexed: 01/27/2023] Open
Abstract
In 1985, a frozen mummy was found in Cerro Aconcagua (Argentina). Archaeological studies identified the mummy as a seven-year-old Inca sacrifice victim who lived >500 years ago, at the time of the expansion of the Inca Empire towards the southern cone. The sequence of its entire mitogenome was obtained. After querying a large worldwide database of mitogenomes (>28,000) we found that the Inca haplotype belonged to a branch of haplogroup C1b (C1bi) that has not yet been identified in modern Native Americans. The expansion of C1b into the Americas, as estimated using 203 C1b mitogenomes, dates to the initial Paleoindian settlements (~18.3 thousand years ago [kya]); however, its internal variation differs between Mesoamerica and South America. By querying large databases of control region haplotypes (>150,000), we found only a few C1bi members in Peru and Bolivia (e.g. Aymaras), including one haplotype retrieved from ancient DNA of an individual belonging to the Wari Empire (Peruvian Andes). Overall, the results suggest that the profile of the mummy represents a very rare sub-clade that arose 14.3 (5–23.6) kya and could have been more frequent in the past. A Peruvian Inca origin for present-day C1bi haplotypes would satisfy both the genetic and paleo-anthropological findings.
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Affiliation(s)
- 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, 15872, Galicia, Spain.,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
| | - Laura Catelli
- Equipo Argentino de Antropología Forense, Independencia 644-3A, Edif. EME1, Córdoba, 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, 15872, 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, Santiago de Compostela, Galicia, Spain
| | - Lutz Roewer
- Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Germany
| | - Carlos Vullo
- Equipo Argentino de Antropología Forense, Independencia 644-3A, Edif. EME1, Córdoba, Argentina
| | - 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.,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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Fiorito G, Di Gaetano C, Guarrera S, Rosa F, Feldman MW, Piazza A, Matullo G. The Italian genome reflects the history of Europe and the Mediterranean basin. Eur J Hum Genet 2015; 24:1056-62. [PMID: 26554880 DOI: 10.1038/ejhg.2015.233] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 11/09/2022] Open
Abstract
Recent scientific literature has highlighted the relevance of population genetic studies both for disease association mapping in admixed populations and for understanding the history of human migrations. Deeper insight into the history of the Italian population is critical for understanding the peopling of Europe. Because of its crucial position at the centre of the Mediterranean basin, the Italian peninsula has experienced a complex history of colonization and migration whose genetic signatures are still present in contemporary Italians. In this study, we investigated genomic variation in the Italian population using 2.5 million single-nucleotide polymorphisms in a sample of more than 300 unrelated Italian subjects with well-defined geographical origins. We combined several analytical approaches to interpret genome-wide data on 1272 individuals from European, Middle Eastern, and North African populations. We detected three major ancestral components contributing different proportions across the Italian peninsula, and signatures of continuous gene flow within Italy, which have produced remarkable genetic variability among contemporary Italians. In addition, we have extracted novel details about the Italian population's ancestry, identifying the genetic signatures of major historical events in Europe and the Mediterranean basin from the Neolithic (e.g., peopling of Sardinia) to recent times (e.g., 'barbarian invasion' of Northern and Central Italy). These results are valuable for further genetic, epidemiological and forensic studies in Italy and in Europe.
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Affiliation(s)
- Giovanni Fiorito
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
| | - Cornelia Di Gaetano
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
| | - Simonetta Guarrera
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
| | - Fabio Rosa
- HuGeF Human Genetics Foundation, Turin, Italy
| | | | - Alberto Piazza
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
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9
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Mitogenomes from The 1000 Genome Project reveal new Near Eastern features in present-day Tuscans. PLoS One 2015; 10:e0119242. [PMID: 25786119 PMCID: PMC4365045 DOI: 10.1371/journal.pone.0119242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/13/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Genetic analyses have recently been carried out on present-day Tuscans (Central Italy) in order to investigate their presumable recent Near East ancestry in connection with the long-standing debate on the origins of the Etruscan civilization. We retrieved mitogenomes and genome-wide SNP data from 110 Tuscans analyzed within the context of The 1000 Genome Project. For phylogeographic and evolutionary analysis we made use of a large worldwide database of entire mitogenomes (>26,000) and partial control region sequences (>180,000). RESULTS Different analyses reveal the presence of typical Near East haplotypes in Tuscans representing isolated members of various mtDNA phylogenetic branches. As a whole, the Near East component in Tuscan mitogenomes can be estimated at about 8%; a proportion that is comparable to previous estimates but significantly lower than admixture estimates obtained from autosomal SNP data (21%). Phylogeographic and evolutionary inter-population comparisons indicate that the main signal of Near Eastern Tuscan mitogenomes comes from Iran. CONCLUSIONS Mitogenomes of recent Near East origin in present-day Tuscans do not show local or regional variation. This points to a demographic scenario that is compatible with a recent arrival of Near Easterners to this region in Italy with no founder events or bottlenecks.
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10
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Söchtig J, Álvarez-Iglesias V, Mosquera-Miguel A, Gelabert-Besada M, Gómez-Carballa A, Salas A. Genomic insights on the ethno-history of the Maya and the 'Ladinos' from Guatemala. BMC Genomics 2015; 16:131. [PMID: 25887241 PMCID: PMC4422311 DOI: 10.1186/s12864-015-1339-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 02/12/2015] [Indexed: 11/10/2022] Open
Abstract
Background Guatemala is a multiethnic and multilingual country located in Central America. The main population groups separate ‘Ladinos’ (mixed Native American-African-Spanish), and Native indigenous people of Maya descent. Among the present-day Guatemalan Maya, there are more than 20 different ethnic groups separated by different languages and cultures. Genetic variation of these communities still remains largely unexplored. The principal aim of this study is to explore the genetic variability of the Maya and ‘Ladinos’ from Guatemala by means of uniparental and ancestry informative markers (AIMs). Results Analyses of uniparental genetic markers indicate that Maya have a dominant Native American ancestry (mitochondrial DNA [mtDNA]: 100%; Y-chromosome: 94%). ‘Ladino’, however, show a clear gender-bias as indicated by the large European ancestry observed in the Y-chromosome (75%) compared to the mtDNA (0%). Autosomal polymorphisms (AIMs) also mirror this marked gender-bias: (i) Native American ancestry: 92% for the Maya vs. 55% for the ‘Ladino’, and (ii) European ancestry: 8% for the Maya vs. 41% for the ‘Ladino’. In addition, the impact of the Trans-Atlantic slave trade on the present-day Guatemalan population is very low (and only occurs in the ‘Ladino’; mtDNA: 9%; AIMs: 4%), in part mirroring the fact that Guatemala has a predominant orientation to the Pacific Ocean instead of a Caribbean one. Sequencing of entire Guatemalan mitogenomes has led to improved Native American phylogeny via the addition of new haplogroups that are mainly observed in Mesoamerica and/or the North of South America. Conclusions The data reveal the existence of a fluid gene flow in the Mesoamerican area and a predominant unidirectional flow towards South America, most likely occurring during the Pre-Classic (1800 BC-200 AD) and the Classic (200–1000 AD) Eras of the Mesoamerican chronology, coinciding with development of the most distinctive and advanced Mesoamerican civilization, the Maya. Phylogenetic features of mtDNA data also suggest a demographic scenario that is compatible with moderate local endogamy and isolation in the Maya combined with episodes of gene exchange between ethnic groups, suggesting an ethno-genesis in the Guatemalan Maya that is recent and supported on a cultural rather than a biological basis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1339-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jens Söchtig
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Ana Mosquera-Miguel
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Miguel Gelabert-Besada
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Alberto 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, CP 15872, Galicia, Spain.
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
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11
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A genome-wide study of modern-day Tuscans: revisiting Herodotus's theory on the origin of the Etruscans. PLoS One 2014; 9:e105920. [PMID: 25230205 PMCID: PMC4167696 DOI: 10.1371/journal.pone.0105920] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/25/2014] [Indexed: 11/21/2022] Open
Abstract
Background The origin of the Etruscan civilization (Etruria, Central Italy) is a long-standing subject of debate among scholars from different disciplines. The bulk of the information has been reconstructed from ancient texts and archaeological findings and, in the last few years, through the analysis of uniparental genetic markers. Methods By meta-analyzing genome-wide data from The 1000 Genomes Project and the literature, we were able to compare the genomic patterns (>540,000 SNPs) of present day Tuscans (N = 98) with other population groups from the main hypothetical source populations, namely, Europe and the Middle East. Results Admixture analysis indicates the presence of 25–34% of Middle Eastern component in modern Tuscans. Different analyses have been carried out using identity-by-state (IBS) values and genetic distances point to Eastern Anatolia/Southern Caucasus as the most likely geographic origin of the main Middle Eastern genetic component observed in the genome of modern Tuscans. Conclusions The data indicate that the admixture event between local Tuscans and Middle Easterners could have occurred in Central Italy about 2,600–3,100 years ago (y.a.). On the whole, the results validate the theory of the ancient historian Herodotus on the origin of Etruscans.
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12
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Derenko M, Malyarchuk B, Bahmanimehr A, Denisova G, Perkova M, Farjadian S, Yepiskoposyan L. Complete mitochondrial DNA diversity in Iranians. PLoS One 2013; 8:e80673. [PMID: 24244704 PMCID: PMC3828245 DOI: 10.1371/journal.pone.0080673] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 10/07/2013] [Indexed: 11/19/2022] Open
Abstract
Due to its pivotal geographical location and proximity to transcontinental migratory routes, Iran has played a key role in subsequent migrations, both prehistoric and historic, between Africa, Asia and Europe. To shed light on the genetic structure of the Iranian population as well as on the expansion patterns and population movements which affected this region, the complete mitochondrial genomes of 352 Iranians were obtained. All Iranian populations studied here exhibit similarly high diversity values comparable to the other groups from the Caucasus, Anatolia and Europe. The results of AMOVA and MDS analyses did not associate any regional and/or linguistic group of populations in the Anatolia/Caucasus and Iran region pointing to close genetic positions of Persians and Qashqais to each other and to Armenians, and Azeris from Iran to Georgians. By reconstructing the complete mtDNA phylogeny of haplogroups R2, N3, U1, U3, U5a1g, U7, H13, HV2, HV12, M5a and C5c we have found a previously unexplored genetic connection between the studied Iranian populations and the Arabian Peninsula, India, Near East and Europe, likely the result of both ancient and recent gene flow. Our results for Persians and Qashqais point to a continuous increase of the population sizes from ∼24 kya to the present, although the phase between 14-24 kya is thought to be hyperarid according to the Gulf Oasis model. Since this would have affected hunter-gatherer ranges and mobility patterns and forced them to increasingly rely on coastal resources, this transition can explain the human expansion across the Persian Gulf region.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
- * E-mail:
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Ardeshir Bahmanimehr
- Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia
| | - Galina Denisova
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Maria Perkova
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Shirin Farjadian
- Immunology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Levon Yepiskoposyan
- Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia
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Tassi F, Ghirotto S, Caramelli D, Barbujani G. Genetic evidence does not support an Etruscan origin in Anatolia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 152:11-8. [PMID: 23900768 DOI: 10.1002/ajpa.22319] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 05/20/2013] [Indexed: 01/22/2023]
Abstract
The debate on the origins of Etruscans, documented in central Italy between the eighth century BC and the first century AD, dates back to antiquity. Herodotus described them as a group of immigrants from Lydia, in Western Anatolia, whereas for Dionysius of Halicarnassus they were an indigenous population. Dionysius' view is shared by most modern archeologists, but the observation of similarities between the (modern) mitochondrial DNAs (mtDNAs) of Turks and Tuscans was interpreted as supporting an Anatolian origin of the Etruscans. However, ancient DNA evidence shows that only some isolates, and not the bulk of the modern Tuscan population, are genetically related to the Etruscans. In this study, we tested alternative models of Etruscan origins by Approximate Bayesian Computation methods, comparing levels of genetic diversity in the mtDNAs of modern and ancient populations with those obtained by millions of computer simulations. The results show that the observed genetic similarities between modern Tuscans and Anatolians cannot be attributed to an immigration wave from the East leading to the onset of the Etruscan culture in Italy. Genetic links between Tuscany and Anatolia do exist, but date back to a remote stage of prehistory, possibly but not necessarily to the spread of farmers during the Neolithic period.
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Affiliation(s)
- Francesca Tassi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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14
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Taboada-Echalar P, Álvarez-Iglesias V, Heinz T, Vidal-Bralo L, Gómez-Carballa A, Catelli L, Pardo-Seco J, Pastoriza A, Carracedo Á, Torres-Balanza A, Rocabado O, Vullo C, Salas A. The genetic legacy of the pre-colonial period in contemporary Bolivians. PLoS One 2013; 8:e58980. [PMID: 23527064 PMCID: PMC3604014 DOI: 10.1371/journal.pone.0058980] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 02/12/2013] [Indexed: 01/27/2023] Open
Abstract
Only a few genetic studies have been carried out to date in Bolivia. However, some of the most important (pre)historical enclaves of South America were located in these territories. Thus, the (sub)-Andean region of Bolivia was part of the Inca Empire, the largest state in Pre-Columbian America. We have genotyped the first hypervariable region (HVS-I) of 720 samples representing the main regions in Bolivia, and these data have been analyzed in the context of other pan-American samples (>19,000 HVS-I mtDNAs). Entire mtDNA genome sequencing was also undertaken on selected Native American lineages. Additionally, a panel of 46 Ancestry Informative Markers (AIMs) was genotyped in a sub-set of samples. The vast majority of the Bolivian mtDNAs (98.4%) were found to belong to the main Native American haplogroups (A: 14.3%, B: 52.6%, C: 21.9%, D: 9.6%), with little indication of sub-Saharan and/or European lineages; however, marked patterns of haplogroup frequencies between main regions exist (e.g. haplogroup B: Andean [71%], Sub-Andean [61%], Llanos [32%]). Analysis of entire genomes unraveled the phylogenetic characteristics of three Native haplogroups: the pan-American haplogroup B2b (originated ∼21.4 thousand years ago [kya]), A2ah (∼5.2 kya), and B2o (∼2.6 kya). The data suggest that B2b could have arisen in North California (an origin even in the north most region of the American continent cannot be disregarded), moved southward following the Pacific coastline and crossed Meso-America. Then, it most likely spread into South America following two routes: the Pacific path towards Peru and Bolivia (arriving here at about ∼15.2 kya), and the Amazonian route of Venezuela and Brazil southwards. In contrast to the mtDNA, Ancestry Informative Markers (AIMs) reveal a higher (although geographically variable) European introgression in Bolivians (25%). Bolivia shows a decreasing autosomal molecular diversity pattern along the longitudinal axis, from the Altiplano to the lowlands. Both autosomes and mtDNA revealed a low impact (1-2%) of a sub-Saharan component in Bolivians.
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Affiliation(s)
- Patricia Taboada-Echalar
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Tanja Heinz
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Laura Vidal-Bralo
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Laura Catelli
- Equipo Argentino de Antropología Forense, Córdoba, Argentina
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Ana Pastoriza
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Antonio Torres-Balanza
- Instituto de Investigaciones Forenses, Fiscalía General del Estado Plurinacional de Bolivia, La Paz, Bolivia
| | - Omar Rocabado
- Instituto de Investigaciones Forenses, Fiscalía General del Estado Plurinacional de Bolivia, La Paz, Bolivia
| | - Carlos Vullo
- Equipo Argentino de Antropología Forense, Córdoba, Argentina
- Laboratorio de Inmunogenética y Diagnóstico Molecular, Córdoba, Argentina
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
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Ghirotto S, Tassi F, Fumagalli E, Colonna V, Sandionigi A, Lari M, Vai S, Petiti E, Corti G, Rizzi E, De Bellis G, Caramelli D, Barbujani G. Origins and evolution of the Etruscans' mtDNA. PLoS One 2013; 8:e55519. [PMID: 23405165 PMCID: PMC3566088 DOI: 10.1371/journal.pone.0055519] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 12/24/2012] [Indexed: 11/25/2022] Open
Abstract
The Etruscan culture is documented in Etruria, Central Italy, from the 8th to the 1st century BC. For more than 2,000 years there has been disagreement on the Etruscans’ biological origins, whether local or in Anatolia. Genetic affinities with both Tuscan and Anatolian populations have been reported, but so far all attempts have failed to fit the Etruscans’ and modern populations in the same genealogy. We extracted and typed the hypervariable region of mitochondrial DNA of 14 individuals buried in two Etruscan necropoleis, analyzing them along with other Etruscan and Medieval samples, and 4,910 contemporary individuals from the Mediterranean basin. Comparing ancient (30 Etruscans, 27 Medieval individuals) and modern DNA sequences (370 Tuscans), with the results of millions of computer simulations, we show that the Etruscans can be considered ancestral, with a high degree of confidence, to the current inhabitants of Casentino and Volterra, but not to the general contemporary population of the former Etruscan homeland. By further considering two Anatolian samples (35 and 123 individuals) we could estimate that the genetic links between Tuscany and Anatolia date back to at least 5,000 years ago, strongly suggesting that the Etruscan culture developed locally, and not as an immediate consequence of immigration from the Eastern Mediterranean shores.
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Affiliation(s)
- Silvia Ghirotto
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Francesca Tassi
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Erica Fumagalli
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Vincenza Colonna
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
- Institute of Genetics e Biophysics “Adriano Buzzati-Traverso”, National Research Council, Naples, Italy
| | - Anna Sandionigi
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Martina Lari
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Stefania Vai
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Emmanuele Petiti
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Giorgio Corti
- Institute for Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Gianluca De Bellis
- Institute for Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - David Caramelli
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Guido Barbujani
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
- * E-mail:
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16
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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] [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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Fu Q, Rudan P, Pääbo S, Krause J. Complete mitochondrial genomes reveal neolithic expansion into Europe. PLoS One 2012; 7:e32473. [PMID: 22427842 PMCID: PMC3302788 DOI: 10.1371/journal.pone.0032473] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/31/2012] [Indexed: 11/18/2022] Open
Abstract
The Neolithic transition from hunting and gathering to farming and cattle breeding marks one of the most drastic cultural changes in European prehistory. Short stretches of ancient mitochondrial DNA (mtDNA) from skeletons of pre-Neolithic hunter-gatherers as well as early Neolithic farmers support the demic diffusion model where a migration of early farmers from the Near East and a replacement of pre-Neolithic hunter-gatherers are largely responsible for cultural innovation and changes in subsistence strategies during the Neolithic revolution in Europe. In order to test if a signal of population expansion is still present in modern European mitochondrial DNA, we analyzed a comprehensive dataset of 1,151 complete mtDNAs from present-day Europeans. Relying upon ancient DNA data from previous investigations, we identified mtDNA haplogroups that are typical for early farmers and hunter-gatherers, namely H and U respectively. Bayesian skyline coalescence estimates were then used on subsets of complete mtDNAs from modern populations to look for signals of past population expansions. Our analyses revealed a population expansion between 15,000 and 10,000 years before present (YBP) in mtDNAs typical for hunters and gatherers, with a decline between 10,000 and 5,000 YBP. These corresponded to an analogous population increase approximately 9,000 YBP for mtDNAs typical of early farmers. The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers. Our data show that contemporary mtDNA datasets can be used to study ancient population history if only limited ancient genetic data is available.
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Affiliation(s)
- Qiaomei Fu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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Gómez-Carballa A, Ignacio-Veiga A, Alvarez-Iglesias V, Pastoriza-Mourelle A, Ruíz Y, Pineda L, Carracedo A, Salas A. A melting pot of multicontinental mtDNA lineages in admixed Venezuelans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 147:78-87. [PMID: 22120584 DOI: 10.1002/ajpa.21629] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 09/09/2011] [Indexed: 11/08/2022]
Abstract
The arrival of Europeans in Colonial and post-Colonial times coupled with the forced introduction of sub-Saharan Africans have dramatically changed the genetic background of Venezuela. The main aim of the present study was to evaluate, through the study of mitochondrial DNA (mtDNA) variation, the extent of admixture and the characterization of the most likely continental ancestral sources of present-day urban Venezuelans. We analyzed two admixed populations that have experienced different demographic histories, namely, Caracas (n = 131) and Pueblo Llano (n = 219). The native American component of admixed Venezuelans accounted for 80% (46% haplogroup [hg] A2, 7% hg B2, 21% hg C1, and 6% hg D1) of all mtDNAs; while the sub-Saharan and European contributions made up ∼10% each, indicating that Trans-Atlantic immigrants have only partially erased the native American nature of Venezuelans. A Bayesian-based model allowed the different contributions of European countries to admixed Venezuelans to be disentangled (Spain: ∼38.4%, Portugal: ∼35.5%, Italy: ∼27.0%), in good agreement with the documented history. Seventeen entire mtDNA genomes were sequenced, which allowed five new native American branches to be discovered. B2j and B2k, are supported by two different haplotypes and control region data, and their coalescence ages are 3.9 k.y. (95% C.I. 0-7.8) and 2.6 k.y. (95% C.I. 0.1-5.2), respectively. The other clades were exclusively observed in Pueblo Llano and they show the fingerprint of strong recent genetic drift coupled with severe historical consanguinity episodes that might explain the high prevalence of certain Mendelian and complex multi-factorial diseases in this region.
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Affiliation(s)
- Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Universidade de Santiago de Compostela, Galicia, Spain
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A reduced number of mtSNPs saturates mitochondrial DNA haplotype diversity of worldwide population groups. PLoS One 2010; 5:e10218. [PMID: 20454657 PMCID: PMC2862705 DOI: 10.1371/journal.pone.0010218] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 03/22/2010] [Indexed: 12/31/2022] Open
Abstract
Background The high levels of variation characterising the mitochondrial DNA (mtDNA) molecule are due ultimately to its high average mutation rate; moreover, mtDNA variation is deeply structured in different populations and ethnic groups. There is growing interest in selecting a reduced number of mtDNA single nucleotide polymorphisms (mtSNPs) that account for the maximum level of discrimination power in a given population. Applications of the selected mtSNP panel range from anthropologic and medical studies to forensic genetic casework. Methodology/Principal Findings This study proposes a new simulation-based method that explores the ability of different mtSNP panels to yield the maximum levels of discrimination power. The method explores subsets of mtSNPs of different sizes randomly chosen from a preselected panel of mtSNPs based on frequency. More than 2,000 complete genomes representing three main continental human population groups (Africa, Europe, and Asia) and two admixed populations (“African-Americans” and “Hispanics”) were collected from GenBank and the literature, and were used as training sets. Haplotype diversity was measured for each combination of mtSNP and compared with existing mtSNP panels available in the literature. The data indicates that only a reduced number of mtSNPs ranging from six to 22 are needed to account for 95% of the maximum haplotype diversity of a given population sample. However, only a small proportion of the best mtSNPs are shared between populations, indicating that there is not a perfect set of “universal” mtSNPs suitable for all population contexts. The discrimination power provided by these mtSNPs is much higher than the power of the mtSNP panels proposed in the literature to date. Some mtSNP combinations also yield high diversity values in admixed populations. Conclusions/Significance The proposed computational approach for exploring combinations of mtSNPs that optimise the discrimination power of a given set of mtSNPs is more efficient than previous empirical approaches. In contrast to precedent findings, the results seem to indicate that only few mtSNPs are needed to reach high levels of discrimination power in a population, independently of its ancestral background.
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Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel. Eur J Hum Genet 2010; 18:915-23. [PMID: 20234393 DOI: 10.1038/ejhg.2010.21] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The Tuareg presently live in the Sahara and the Sahel. Their ancestors are commonly believed to be the Garamantes of the Libyan Fezzan, ever since it was suggested by authors of antiquity. Biological evidence, based on classical genetic markers, however, indicates kinship with the Beja of Eastern Sudan. Our study of mitochondrial DNA (mtDNA) sequences and Y chromosome SNPs of three different southern Tuareg groups from Mali, Burkina Faso and the Republic of Niger reveals a West Eurasian-North African composition of their gene pool. The data show that certain genetic lineages could not have been introduced into this population earlier than approximately 9000 years ago whereas local expansions establish a minimal date at around 3000 years ago. Some of the mtDNA haplogroups observed in the Tuareg population were involved in the post-Last Glacial Maximum human expansion from Iberian refugia towards both Europe and North Africa. Interestingly, no Near Eastern mtDNA lineages connected with the Neolithic expansion have been observed in our population sample. On the other hand, the Y chromosome SNPs data show that the paternal lineages can very probably be traced to the Near Eastern Neolithic demic expansion towards North Africa, a period that is otherwise concordant with the above-mentioned mtDNA expansion. The time frame for the migration of the Tuareg towards the African Sahel belt overlaps that of early Holocene climatic changes across the Sahara (from the optimal greening approximately 10 000 YBP to the extant aridity beginning at approximately 6000 YBP) and the migrations of other African nomadic peoples in the area.
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Cerezo M, Černý V, Carracedo Á, Salas A. Applications of MALDI-TOF MS to large-scale human mtDNA population-based studies. Electrophoresis 2009; 30:3665-73. [DOI: 10.1002/elps.200900294] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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