1
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Logan IS. Humanin P3S, haplogroup N1b and the risk of Alzheimer's disease. Aging Cell 2024:e14207. [PMID: 38757793 DOI: 10.1111/acel.14207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
A commentary of the paper 'Humanin variant P3S is associated with longevity in APOE4 carriers and resists APOE4-induced brain pathology' that appeared recently in Aging Cell. The possible association of a mitochondrial haplogroup with a disease is frequently discussed. The Humanin peptide encoded by the mtDNA has been shown to play an important regulatory role in cell metabolism. There are variants of Humanin caused by different mutations and it is known that the potent form of Humanin, termed S14G, is found naturally in the people of haplogroup U6a7a1a because they have the mutation m.A2672G; however it has not been shown that having this mutation is indeed beneficial. In their paper, the authors suggest that the mitochondrial DNA mutation, m.C2639T, may be beneficial in people who are in haplogroup N1b and also carry APOE4. The mutation changes the common form of Humanin to Humanin P3S. In the study, the researchers looked at a group of Ashkenazi women who were over the age of 95, and found that a higher proportion of them carried APOE4, suggesting that Humanin P3S protected them against the adverse effects of APOE4. A study in a mouse model supported this finding by showing treatment with Humanin P3S reduced APOE4-induced brain pathology. In the world population, there are about 500,000 Ashkenazi in haplogroup N1b, predominantly in the subgroup N1b1b1; and there are about 9.5 million non-Ashkenazi people with the mutation m.C2639T and are therefore also in haplogroup N1b and have Humanin P3S. However, the researchers have yet to show Humanin P3S is of benefit in non-Ashkenazi people. This paper raises the possibility of a therapeutic use of Humanin P3S in the treatment of Alzheimer's disease.
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Cabrera VM. New Canary Islands Roman mediated settlement hypothesis deduced from coalescence ages of curated maternal indigenous lineages. Sci Rep 2024; 14:11150. [PMID: 38750053 PMCID: PMC11096394 DOI: 10.1038/s41598-024-61731-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 05/09/2024] [Indexed: 05/18/2024] Open
Abstract
Numerous genetic studies have contributed to reconstructing the human history of the Canary Islands population. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples have greatly improved these molecular results. However, the bulk of the available data is still provided by the classic mitochondrial DNA phylogenetic and phylogeographic studies carried out on the indigenous, historical, and extant human populations of the Canary Islands. In the present study, making use of all the accumulated mitochondrial information, the existence of DNA contamination and archaeological sample misidentification in those samples is evidenced. Following a thorough review of these cases, the new phylogeographic analysis revealed the existence of a heterogeneous indigenous Canarian population, asymmetrically distributed across the various islands, which most likely descended from a unique mainland settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple dye manufacture in the Canary Islands.
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Affiliation(s)
- Vicente M Cabrera
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, 38200, San Cristobal de La Laguna, Spain.
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3
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Fewlass H, Zavala EI, Fagault Y, Tuna T, Bard E, Hublin JJ, Hajdinjak M, Wilczyński J. Chronological and genetic analysis of an Upper Palaeolithic female infant burial from Borsuka Cave, Poland. iScience 2023; 26:108283. [PMID: 38047066 PMCID: PMC10690573 DOI: 10.1016/j.isci.2023.108283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 12/05/2023] Open
Abstract
Six infant human teeth and 112 animal tooth pendants from Borsuka Cave were identified as the oldest burial in Poland. However, uncertainties around the dating and the association of the teeth to the pendants have precluded their association with an Upper Palaeolithic archaeological industry. Using <67 mg per tooth, we combined dating and genetic analyses of two human teeth and six herbivore tooth pendants to address these questions. Our interdisciplinary approach yielded informative results despite limited sampling material, and high levels of degradation and contamination. Our results confirm the Palaeolithic origin of the human remains and herbivore pendants, and permit us to identify the infant as female and discuss the association of the assemblage with different Palaeolithic industries. This study exemplifies the progress that has been made toward minimally destructive methods and the benefits of integrating methods to maximize data retrieval from precious but highly degraded and contaminated prehistoric material.
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Affiliation(s)
- Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Ancient Genomics Lab, Francis Crick Institute, London NW1 1AT, UK
| | - Elena I. Zavala
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Cell and Molecular Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | - Yoann Fagault
- CEREGE, Aix Marseille Université, CNRS, IRD, INRA, Collège de France, Technopôle de l’Arbois BP 80, 13545 Aix-en-Provence Cedex 4, France
| | - Thibaut Tuna
- CEREGE, Aix Marseille Université, CNRS, IRD, INRA, Collège de France, Technopôle de l’Arbois BP 80, 13545 Aix-en-Provence Cedex 4, France
| | - Edouard Bard
- CEREGE, Aix Marseille Université, CNRS, IRD, INRA, Collège de France, Technopôle de l’Arbois BP 80, 13545 Aix-en-Provence Cedex 4, France
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241 – U1050), Collège de France, 75231 Paris, France
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Krakow, Poland
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Aizpurua-Iraola J, Abdeli A, Benhassine T, Calafell F, Comas D. Whole mitogenomes reveal that NW Africa has acted both as a source and a destination for multiple human movements. Sci Rep 2023; 13:10395. [PMID: 37369751 DOI: 10.1038/s41598-023-37549-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023] Open
Abstract
Despite being enclosed between the Mediterranean Sea and the Sahara Desert, North Africa has been the scenario of multiple human migrations that have shaped the genetic structure of its present-day populations. Despite its richness, North Africa remains underrepresented in genomic studies. To overcome this, we have sequenced and analyzed 264 mitogenomes from the Algerian Chaoui-speaking Imazighen (a.k.a. Berbers) living in the Aurès region. The maternal genetic composition of the Aurès is similar to Arab populations in the region, dominated by West Eurasian lineages with a moderate presence of M1/U6 North African and L sub-Saharan lineages. When focusing on the time and geographic origin of the North African specific clades within the non-autochthonous haplogroups, different geographical neighboring regions contributed to the North African maternal gene pool during time periods that could be attributed to previously suggested admixture events in the region, since Paleolithic times to recent historical movements such as the Arabization. We have also observed the role of North Africa as a source of geneflow mainly in Southern European regions since Neolithic times. Finally, the present work constitutes an effort to increase the representation of North African populations in genetic databases, which is key to understand their history.
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Affiliation(s)
- Julen Aizpurua-Iraola
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Laboratorie de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Traki Benhassine
- Laboratorie de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.
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5
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García-Olivares V, Rubio-Rodríguez LA, Muñoz-Barrera A, Díaz-de Usera A, Jáspez D, Iñigo-Campos A, Rodríguez Pérez MDC, Cabrera de León A, Lorenzo-Salazar JM, González-Montelongo R, Cabrera VM, Flores C. Digging into the admixture strata of current-day Canary Islanders based on mitogenomes. iScience 2022; 26:105907. [PMID: 36647378 PMCID: PMC9840145 DOI: 10.1016/j.isci.2022.105907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/18/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
The conquest of the Canary Islands by Europeans began at the beginning of the 15th century and culminated in 1496 with the surrender of the aborigines. The collapse of the aboriginal population during the conquest and the arrival of settlers caused a drastic change in the demographic composition of the archipelago. To shed light on this historical process, we analyzed 896 mitogenomes of current inhabitants from the seven main islands. Our findings confirm the continuity of aboriginal maternal contributions and the persistence of their genetic footprints in the current population, even at higher levels (>60% on average) than previously evidenced. Moreover, the age estimates for most autochthonous founder lineages support a first aboriginal arrival to the islands at the beginning of the first millennium. We also revealed for the first time that the main recognizable genetic influences from Europe are from Portuguese and Galicians.
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Affiliation(s)
- Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain,Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | | | - Antonio Cabrera de León
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain,Área de Medicina Preventiva y Salud Pública, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain,Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
| | | | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain,Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain,Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain,Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, Las Palmas de Gran Canaria, Spain,Corresponding author
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6
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Genetic ancestry in Afro-descendants from the Andes and Pacific Coast regions of Ecuador. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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The relevance of late MSA mandibles on the emergence of modern morphology in Northern Africa. Sci Rep 2022; 12:8841. [PMID: 35614148 PMCID: PMC9133045 DOI: 10.1038/s41598-022-12607-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/28/2022] [Indexed: 11/08/2022] Open
Abstract
North Africa is a key area for understanding hominin population movements and the expansion of our species. It is home to the earliest currently known Homo sapiens (Jebel Irhoud) and several late Middle Stone Age (MSA) fossils, notably Kébibat, Contrebandiers 1, Dar-es-Soltane II H5 and El Harhoura. Mostly referred to as “Aterian” they fill a gap in the North African fossil record between Jebel Irhoud and Iberomaurusians. We explore morphological continuity in this region by quantifying mandibular shape using 3D (semi)landmark geometric morphometric methods in a comparative framework of late Early and Middle Pleistocene hominins (n = 15), Neanderthals (n = 27) and H. sapiens (n = 145). We discovered a set of mixed features among late MSA fossils that is in line with an accretion of modern traits through time and an ongoing masticatory gracilization process. In Northern Africa, Aterians display similarities to Iberomaurusians and recent humans in the area as well as to the Tighenif and Thomas Quarry hominins, suggesting a greater time depth for regional continuity than previously assumed. The evidence we lay out for a long-term succession of hominins and humans emphasizes North Africa’s role as source area of the earliest H. sapiens.
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8
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McElhoe JA, Wilton PR, Parson W, Holland MM. Exploring statistical weight estimates for mitochondrial DNA matches involving heteroplasmy. Int J Legal Med 2022; 136:671-685. [PMID: 35243529 DOI: 10.1007/s00414-022-02774-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022]
Abstract
Massively parallel sequencing (MPS) of mitochondrial (mt) DNA allows forensic laboratories to report heteroplasmy on a routine basis. Statistical approaches will be needed to determine the relative frequency of observing an mtDNA haplotype when including the presence of a heteroplasmic site. Here, we examined 1301 control region (CR) sequences, collected from individuals in four major population groups (European, African, Asian, and Latino), and covering 24 geographically distributed haplogroups, to assess the rates of point heteroplasmy (PHP) on an individual and nucleotide position (np) basis. With a minor allele frequency (MAF) threshold of 2%, the data was similar across population groups, with an overall PHP rate of 37.7%, and the majority of heteroplasmic individuals (77.3%) having only one site of heteroplasmy. The majority (75.2%) of identified PHPs had an MAF of 2-10%, and were observed at 12.6% of the nps across the CR. Both the broad and phylogenetic testing suggested that in many cases the low number of observations of heteroplasmy at any one np results in a lack of statistical association. The posterior frequency estimates, which skew conservative to a degree depending on the sample size in a given haplogroup, had a mean of 0.152 (SD 0.134) and ranged from 0.031 to 0.83. As expected, posterior frequency estimates decreased in accordance with 1/n as the sample size (n) increased. This provides a proposed conservative statistical framework for assessing haplotype/heteroplasmy matches when applying an MPS technique in forensic cases and will allow for continual refinement as more data is generated, both within the CR and across the mitochondrial genome.
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Affiliation(s)
- Jennifer A McElhoe
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA.
| | - Peter R Wilton
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- 23andMe Inc, Sunnyvale, CA, 94086, USA
| | - Walther Parson
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria
| | - Mitchell M Holland
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
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9
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Silva M, Oteo-García G, Martiniano R, Guimarães J, von Tersch M, Madour A, Shoeib T, Fichera A, Justeau P, Foody MGB, McGrath K, Barrachina A, Palomar V, Dulias K, Yau B, Gandini F, Clarke DJ, Rosa A, Brehm A, Flaquer A, Rito T, Olivieri A, Achilli A, Torroni A, Gómez-Carballa A, Salas A, Bryk J, Ditchfield PW, Alexander M, Pala M, Soares PA, Edwards CJ, Richards MB. Biomolecular insights into North African-related ancestry, mobility and diet in eleventh-century Al-Andalus. Sci Rep 2021; 11:18121. [PMID: 34518562 PMCID: PMC8438022 DOI: 10.1038/s41598-021-95996-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/27/2021] [Indexed: 01/26/2023] Open
Abstract
Historical records document medieval immigration from North Africa to Iberia to create Islamic al-Andalus. Here, we present a low-coverage genome of an eleventh century CE man buried in an Islamic necropolis in Segorbe, near Valencia, Spain. Uniparental lineages indicate North African ancestry, but at the autosomal level he displays a mosaic of North African and European-like ancestries, distinct from any present-day population. Altogether, the genome-wide evidence, stable isotope results and the age of the burial indicate that his ancestry was ultimately a result of admixture between recently arrived Amazigh people (Berbers) and the population inhabiting the Peninsula prior to the Islamic conquest. We detect differences between our sample and a previously published group of contemporary individuals from Valencia, exemplifying how detailed, small-scale aDNA studies can illuminate fine-grained regional and temporal differences. His genome demonstrates how ancient DNA studies can capture portraits of past genetic variation that have been erased by later demographic shifts-in this case, most likely the seventeenth century CE expulsion of formerly Islamic communities as tolerance dissipated following the Reconquista by the Catholic kingdoms of the north.
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Affiliation(s)
- Marina Silva
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK.
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| | - Gonzalo Oteo-García
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK.
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - João Guimarães
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | | | - Ali Madour
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Tarek Shoeib
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
- Department of Forensic Science, Faculty of Biomedical Science, University of Benghazi, P.O. Box: 1308, Benghazi, Libya
| | - Alessandro Fichera
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Pierre Justeau
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - M George B Foody
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Krista McGrath
- BioArCh, Department of Archaeology, University of York, York, UK
- Department of Prehistory and Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Amparo Barrachina
- Servei d'Investigacions Arqueològiques i Prehistòriques - Museu Belles Arts de Castelló, Av. Germans Bou, 28, 12003, Castellón, Spain
| | - Vicente Palomar
- Museo Municipal de Arqueología y Etnología de Segorbe, Calle Colón, 98, 12400, Segorbe, Castellón, Spain
| | - Katharina Dulias
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
- BioArCh, Department of Archaeology, University of York, York, UK
- Institut für Geosysteme und Bioindikation, Technische Universität Braunschweig, Langer Kamp 19c, 38106, Braunschweig, Germany
| | - Bobby Yau
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Francesca Gandini
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Douglas J Clarke
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Alexandra Rosa
- Faculty of Life Sciences, University of Madeira, Campus of Penteada, 9000-390, Funchal, Portugal
- Human Genetics Laboratory, University of Madeira, Campus of Penteada, 9000-390, Funchal, Portugal
| | - António Brehm
- Human Genetics Laboratory, University of Madeira, Campus of Penteada, 9000-390, Funchal, Portugal
| | - Antònia Flaquer
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, LMU University, Munich, Germany
| | - Teresa Rito
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, 4710-057, Braga, Portugal
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani, Università di Pavia, 27100, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani, Università di Pavia, 27100, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani, Università di Pavia, 27100, Pavia, Italy
| | - Alberto Gómez-Carballa
- Grupo de Investigacion en Genetica, Vacunas, Infecciones y Pediatria (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Galicia, Spain
| | - Antonio Salas
- Grupo de Investigacion en Genetica, Vacunas, Infecciones y Pediatria (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Jaroslaw Bryk
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Peter W Ditchfield
- School of Archaeology, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK
| | | | - Maria Pala
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Pedro A Soares
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ceiridwen J Edwards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Martin B Richards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK.
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10
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Svensson E, Günther T, Hoischen A, Hervella M, Munters AR, Ioana M, Ridiche F, Edlund H, van Deuren RC, Soficaru A, de-la-Rua C, Netea MG, Jakobsson M. Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe. Curr Biol 2021; 31:2973-2983.e9. [PMID: 34010592 DOI: 10.1016/j.cub.2021.04.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 11/24/2022]
Abstract
Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from "Peştera Muierii," Romania who lived ∼34,000 years ago to 13.5× coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (∼3.1%) to most EUP humans but only half compared to the ∼40,000-year-old Peştera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.
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Affiliation(s)
- Emma Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6526 Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands
| | - Montserrat Hervella
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B° Sarriena s/n 48940 Leioa, Bizkaia, Spain
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Mihai Ioana
- Laboratory of Human Genetics, University of Medicine and Pharmacy, Craiova, Romania
| | | | - Hanna Edlund
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Rosanne C van Deuren
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands
| | - Andrei Soficaru
- "Francisc J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania
| | - Concepción de-la-Rua
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B° Sarriena s/n 48940 Leioa, Bizkaia, Spain
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands; Laboratory of Human Genetics, University of Medicine and Pharmacy, Craiova, Romania
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
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11
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Fregel R, Ordóñez AC, Serrano JG. The demography of the Canary Islands from a genetic perspective. Hum Mol Genet 2020; 30:R64-R71. [PMID: 33295602 DOI: 10.1093/hmg/ddaa262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/13/2022] Open
Abstract
The establishment of European colonies across the world had important demographic consequences because it brought together diverse and distant civilizations for the first time. One clear example of this phenomenon is observed in the Canary Islands. The modern Canarian population is mainly the result of the admixture of natives of North African origin and European colonizers. However, additional migratory flows reached the islands due to the importation of enslaved Africans to cultivate sugarcane and the intense commercial contact with the American continent. In this review, we evaluate how the genetic analysis of indigenous, historical and current populations has provided a glimpse into the Canary Islands' complex genetic composition. We show that each island subpopulation's characterization is needed to fully disentangle the demographic history of the Canarian archipelago. Finally, we discuss what research avenues remain to be explored to improve our knowledge of the impact that the European colonization had on its native population.
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Affiliation(s)
- Rosa Fregel
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Facultad de Ciencias, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Alejandra C Ordóñez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Facultad de Ciencias, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain.,Departamento Geografía e Historia, Facultad de Humanidades, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Javier G Serrano
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Facultad de Ciencias, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain
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12
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Lucas-Sánchez M, Serradell JM, Comas D. Population history of North Africa based on modern and ancient genomes. Hum Mol Genet 2020; 30:R17-R23. [PMID: 33284971 DOI: 10.1093/hmg/ddaa261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/09/2023] Open
Abstract
Compared with the rest of the African continent, North Africa has provided limited genomic data. Nonetheless, the genetic data available show a complex demographic scenario characterized by extensive admixture and drift. Despite the continuous gene flow from the Middle East, Europe and sub-Saharan Africa, an autochthonous genetic component that dates back to pre-Holocene times is still present in North African groups. The comparison of ancient and modern genomes has evidenced a genetic continuity in the region since Epipaleolithic times. Later population movements, especially the gene flow from the Middle East associated with the Neolithic, have diluted the genetic autochthonous component, creating an east to west gradient. Recent historical movements, such as the Arabization, have also contributed to the genetic landscape observed currently in North Africa and have culturally transformed the region. Genome analyses have not shown evidence of a clear correlation between cultural and genetic diversity in North Africa, as there is no genetic pattern of differentiation between Tamazight (i.e. Berber) and Arab speakers as a whole. Besides the gene flow received from neighboring areas, the analysis of North African genomes has shown that the region has also acted as a source of gene flow since ancient times. As a result of the genetic uniqueness of North African groups and the lack of available data, there is an urgent need for the study of genetic variation in the region and its implications in health and disease.
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Affiliation(s)
- Marcel Lucas-Sánchez
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Jose M Serradell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
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13
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Arauna LR, Hellenthal G, Comas D. Dissecting human North African gene-flow into its western coastal surroundings. Proc Biol Sci 2020; 286:20190471. [PMID: 31039721 DOI: 10.1098/rspb.2019.0471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
North African history and populations have exerted a pivotal influence on surrounding geographical regions, although scant genetic studies have addressed this issue. Our aim is to understand human historical migrations in the coastal surroundings of North Africa. We built a refined genome-wide dataset of North African populations to unearth the fine-scale genetic structure of the region, using haplotype information. The results suggest that the gene-flow from North Africa into the European Mediterranean coast (Tuscany and the Iberian Peninsula) arrived mainly from the Mediterranean coast of North Africa. In Tuscany, this North African admixture date estimate suggests the movement of peoples during the fall of the Roman Empire around the fourth century. In the Iberian Peninsula, the North African component probably reflects the impact of the Arab expansion since the seventh century and the subsequent expansion of the Christian Kingdoms. By contrast, the North African component in the Canary Islands has a source genetically related to present-day people from the Atlantic North African coast. We also find sub-Saharan gene-flow from the Senegambia region in the Canary Islands. Specifically, we detect a complex signal of admixture involving Atlantic, Senegambian and European sources intermixing around the fifteenth century, soon after the Castilian conquest. Our results highlight the differential genetic influence of North Africa into the surrounding coast and show that specific historical events have not only had a socio-cultural impact but additionally modified the gene pool of the populations.
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Affiliation(s)
- Lara R Arauna
- 1 Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra , Barcelona , Spain
| | - Garrett Hellenthal
- 2 UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London , London , UK
| | - David Comas
- 1 Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra , Barcelona , Spain
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14
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Environmental factors modulated ancient mitochondrial DNA variability and the prevalence of rheumatic diseases in the Basque Country. Sci Rep 2019; 9:20380. [PMID: 31892727 PMCID: PMC6938509 DOI: 10.1038/s41598-019-56921-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 12/17/2019] [Indexed: 11/09/2022] Open
Abstract
Among the factors that would explain the distribution of mitochondrial lineages in Europe, climate and diseases may have played an important role. A possible explanation lies in the nature of the mitochondrion, in which the energy generation process produces reactive oxygen species that may influence the development of different diseases. The present study is focused on the medieval necropolis of San Miguel de Ereñozar (13th-16th centuries, Basque Country), whose inhabitants presented a high prevalence of rheumatic diseases and lived during the Little Ice Age (LIA). Our results indicate a close relationship between rheumatic diseases and mitochondrial haplogroup H, and specifically between spondyloarthropathies and sub-haplogroup H2. One possible explanation may be the climate change that took place in the LIA that favoured those haplogroups that were more energy-efficient, such as haplogroup H, to endure lower temperatures and food shortage. However, it had a biological trade-off: the increased risk of developing rheumatic diseases.
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15
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Fregel R, Ordóñez AC, Santana-Cabrera J, Cabrera VM, Velasco-Vázquez J, Alberto V, Moreno-Benítez MA, Delgado-Darias T, Rodríguez-Rodríguez A, Hernández JC, Pais J, González-Montelongo R, Lorenzo-Salazar JM, Flores C, Cruz-de-Mercadal MC, Álvarez-Rodríguez N, Shapiro B, Arnay M, Bustamante CD. Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands. PLoS One 2019; 14:e0209125. [PMID: 30893316 PMCID: PMC6426200 DOI: 10.1371/journal.pone.0209125] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/15/2019] [Indexed: 12/30/2022] Open
Abstract
The Canary Islands’ indigenous people have been the subject of substantial archaeological, anthropological, linguistic and genetic research pointing to a most probable North African Berber source. However, neither agreement about the exact point of origin nor a model for the indigenous colonization of the islands has been established. To shed light on these questions, we analyzed 48 ancient mitogenomes from 25 archaeological sites from the seven main islands. Most lineages observed in the ancient samples have a Mediterranean distribution, and belong to lineages associated with the Neolithic expansion in the Near East and Europe (T2c, J2a, X3a…). This phylogeographic analysis of Canarian ancient mitogenomes, the first of its kind, shows that some lineages are restricted to Central North Africa (H1cf, J2a2d and T2c1d3), while others have a wider distribution, including both West and Central North Africa, and, in some cases, Europe and the Near East (U6a1a1, U6a7a1, U6b, X3a, U6c1). In addition, we identify four new Canarian-specific lineages (H1e1a9, H4a1e, J2a2d1a and L3b1a12) whose coalescence dates correlate with the estimated time for the colonization of the islands (1st millennia CE). Additionally, we observe an asymmetrical distribution of mtDNA haplogroups in the ancient population, with certain haplogroups appearing more frequently in the islands closer to the continent. This reinforces results based on modern mtDNA and Y-chromosome data, and archaeological evidence suggesting the existence of two distinct migrations. Comparisons between insular populations show that some populations had high genetic diversity, while others were probably affected by genetic drift and/or bottlenecks. In spite of observing interinsular differences in the survival of indigenous lineages, modern populations, with the sole exception of La Gomera, are homogenous across the islands, supporting the theory of extensive human mobility after the European conquest.
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Affiliation(s)
- Rosa Fregel
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- * E-mail:
| | - Alejandra C. Ordóñez
- Department of Prehistory, Anthropology and Ancient History, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | | | - Vicente M. Cabrera
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Javier Velasco-Vázquez
- Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Verónica Alberto
- Tibicena Arqueología y Patrimonio, Las Palmas de Gran Canaria, Spain
| | | | | | - Amelia Rodríguez-Rodríguez
- Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | | | - Jorge Pais
- Museo Arqueológico Benahoarita, Los Llanos de Aridane, Spain
| | | | | | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Granadilla, Spain
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Matilde Arnay
- Department of Prehistory, Anthropology and Ancient History, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
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16
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Mitochondrial DNA control region diversity in a population from Parana state-increasing the Brazilian forensic database. Int J Legal Med 2018; 133:347-351. [PMID: 29959556 DOI: 10.1007/s00414-018-1886-5] [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] [Received: 04/16/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
Abstract
The entire mitochondrial DNA (mtDNA) control region (nucleotide position 16024-576) sequences were obtained through Sanger sequencing method for 122 individuals from Parana state, South of Brazil. We observed a total of 108 different haplotypes of which 97 were unique and 11 were shared by more than one individual. The haplogroups were classified according to the updated mtDNA phylogeny, by EMMA (estimating mitochondrial haplogroups using a maximum likelihood approach). Our results revealed the predominance of Amerindian haplogroups with a frequency of 49.2% of the population sample, followed by European lineages with 38.5% and 12.3% of African lineages. Parana population sample set presented a high haplotype diversity (0.9976) and the random match probability was 0.0106. The phylogenetical findings and the diversity indices confirm the high genetic heterogeneity of this population and suggest a high informativeness of mtDNA analyses in forensic cases. The population data will contribute to increase the Brazilian mtDNA database for forensic purposes and it is available through EMPOP (European DNA Profiling Group mitochondrial DNA population database) under the accession number EMP00714.
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17
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Cabrera VM, Marrero P, Abu-Amero KK, Larruga JM. Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago. BMC Evol Biol 2018; 18:98. [PMID: 29921229 PMCID: PMC6009813 DOI: 10.1186/s12862-018-1211-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/05/2018] [Indexed: 11/15/2022] Open
Abstract
Background The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya. Results The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1211-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| | - Patricia Marrero
- Research Support General Service, E-38271, La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
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18
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Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. Proc Natl Acad Sci U S A 2018; 115:6774-6779. [PMID: 29895688 DOI: 10.1073/pnas.1800851115] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals' genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.
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19
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van de Loosdrecht M, Bouzouggar A, Humphrey L, Posth C, Barton N, Aximu-Petri A, Nickel B, Nagel S, Talbi EH, El Hajraoui MA, Amzazi S, Hublin JJ, Pääbo S, Schiffels S, Meyer M, Haak W, Jeong C, Krause J. Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Science 2018; 360:548-552. [PMID: 29545507 DOI: 10.1126/science.aar8380] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/28/2018] [Indexed: 12/22/2022]
Abstract
North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans, attributed to the Iberomaurusian culture, from Morocco. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans to Late Pleistocene North Africans. The Taforalt individuals derive one-third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.
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Affiliation(s)
- Marieke van de Loosdrecht
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Kahlaische Strasse 10, D-07745, Germany
| | - Abdeljalil Bouzouggar
- Origin and Evolution of Homo sapiens in Morocco Research Group, Institut National des Sciences de l'Archéologie et du Patrimoine, Hay Riad, Madinat Al Irfane, Angle rues 5 et 7, Rabat-Instituts, 10 000 Rabat, Morocco. .,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Louise Humphrey
- Department of Earth Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Kahlaische Strasse 10, D-07745, Germany
| | - Nick Barton
- Institute of Archaeology, University of Oxford, 36 Beaumont Street, Oxford OX1 2PG, UK
| | - Ayinuer Aximu-Petri
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Birgit Nickel
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - El Hassan Talbi
- Faculté des Sciences, Campus d'Al Qods, Université Mohammed Premier, B.P. 717 Oujda, Morocco
| | - Mohammed Abdeljalil El Hajraoui
- Origin and Evolution of Homo sapiens in Morocco Research Group, Institut National des Sciences de l'Archéologie et du Patrimoine, Hay Riad, Madinat Al Irfane, Angle rues 5 et 7, Rabat-Instituts, 10 000 Rabat, Morocco
| | - Saaïd Amzazi
- Mohammed V University, Avenue Ibn Batouta, Rabat, Morocco
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Kahlaische Strasse 10, D-07745, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Kahlaische Strasse 10, D-07745, Germany
| | - Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Kahlaische Strasse 10, D-07745, Germany.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Kahlaische Strasse 10, D-07745, Germany.
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20
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Abstract
In the human the peptide Humanin is produced from the small Humanin gene which is embedded as a gene-within-a-gene in the 16S ribosomal molecule of the mitochondrial DNA (mtDNA). The peptide itself appears to be significant in the prevention of cell death in many tissues and improve cognition in animal models. By using simple data mining techniques, it is possible to show that 99.4% of the human Humanin sequences in the GenBank database are unaffected by mutations. However, in other vertebrates, pseudogenization of the Humanin gene is a common feature; occurring apparently randomly in some species and not others. The persistence, or loss, of a functional Humanin gene may be an important factor in laboratory animals, especially if they are being used as animal models in studies of Alzheimer's disease (AD). The exact reason why Humanin underwent pseudogenization in some vertebrate species during their evolution remains to be determined. This study was originally planned to review the available information about Humanin and it was a surprise to be able to show that pseudogenization has occurred in a gene in the mtDNA and is not restricted solely to chromosomal genes.
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21
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Elkamel S, Boussetta S, Khodjet-El-Khil H, Benammar Elgaaied A, Cherni L. Ancient and recent Middle Eastern maternal genetic contribution to North Africa as viewed by mtDNA diversity in Tunisian Arab populations. Am J Hum Biol 2018; 30:e23100. [PMID: 29359455 DOI: 10.1002/ajhb.23100] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/06/2017] [Accepted: 12/29/2017] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES Through previous mitochondrial DNA studies, the Middle Eastern maternal genetic contribution to Tunisian populations appears limited. In fact, most of the studied communities were cosmopolitan, or of Berber or Andalusian origin. To provide genetic evidence for the actual contribution of Middle Eastern mtDNA lineages to Tunisia, we focused on two Arab speaking populations from Kairouan and Wesletia known to belong to an Arab genealogical lineage. MATERIALS AND METHODS A total of 114 samples were sequenced for the mtDNA HVS-I and HVS-II regions. Using these data, we evaluated the distribution of Middle Eastern haplogroups in the study populations, constructed interpolation maps, and established phylogenetic networks allowing estimation of the coalescence time for three specific Middle Eastern subclades (R0a, J1b, and T1). RESULTS Both studied populations displayed North African genetic structure and Middle Eastern lineages with a frequency of 12% and 28.12% in Kairouan and Wesletia, respectively. TMRCA estimates for haplogroups T1a, R0a, and J1b in Tunisian Arabian samples were around 15 000 YBP, 9000 to 5000 YBP, and 960 to 600 YBP, respectively. CONCLUSIONS The Middle Eastern maternal genetic contribution to Tunisian populations, as to other North African populations, occurred mostly in deep prehistory. They were brought in different migration waves during the Upper Paleolithic, probably with the expansion of Iberomaurusian culture, and during Epipaleolithic and Early Neolithic periods, which are concomitant with the Capsian civilization. Middle Eastern lineages also came to Tunisia during the recent Islamic expansion of the 7th CE and the subsequent massive Bedouin migration during the 11th CE.
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Affiliation(s)
- Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Houssein Khodjet-El-Khil
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Amel Benammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia.,High Institute of Biotechnology, University of Monastir, Monastir, 5000, Tunisia
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22
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Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol Biol 2017; 17:115. [PMID: 28535779 PMCID: PMC5442693 DOI: 10.1186/s12862-017-0964-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path. RESULTS Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines. CONCLUSIONS Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.
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Affiliation(s)
- Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Patricia Marrero
- Research Support General Service, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
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23
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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: 17] [Impact Index Per Article: 2.4] [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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24
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Rishishwar L, Jordan IK. Implications of human evolution and admixture for mitochondrial replacement therapy. BMC Genomics 2017; 18:140. [PMID: 28178941 PMCID: PMC5299762 DOI: 10.1186/s12864-017-3539-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/02/2017] [Indexed: 11/15/2022] Open
Abstract
Background Mitochondrial replacement (MR) therapy is a new assisted reproductive technology that allows women with mitochondrial disorders to give birth to healthy children by combining their nuclei with mitochondria from unaffected egg donors. Evolutionary biologists have raised concerns about the safety of MR therapy based on the extent to which nuclear and mitochondrial genomes are observed to co-evolve within natural populations, i.e. the nuclear-mitochondrial mismatch hypothesis. In support of this hypothesis, a number of previous studies on model organisms have provided evidence for incompatibility between nuclear and mitochondrial genomes from divergent populations of the same species. Results We tested the nuclear-mitochondrial mismatch hypothesis for humans by observing the extent of naturally occurring nuclear-mitochondrial mismatch seen for 2,504 individuals across 26 populations, from 5 continental populations groups, characterized as part of the 1000 Genomes Project (1KGP). We also performed a replication analysis on mitochondrial DNA (mtDNA) haplotypes for 1,043 individuals from 58 populations, characterized as part of the Human Genome Diversity Project (HGDP). Nuclear DNA (nDNA) and mtDNA sequences from the 1KGP were directly compared within and between populations, and the population distributions of mtDNA haplotypes derived from both sequence (1KGP) and genotype (HGDP) data were evaluated. Levels of nDNA and mtDNA pairwise sequence divergence are highly correlated, consistent with their co-evolution among human populations. However, there are numerous cases of co-occurrence of nuclear and mitochondrial genomes from divergent populations within individual humans. Furthermore, pairs of individuals with closely related nuclear genomes can have highly divergent mtDNA haplotypes. Supposedly mismatched nuclear-mitochondrial genome combinations are found not only within individuals from populations known to be admixed, where they may be expected, but also from populations with low overall levels of observed admixture. Conclusions These results show that mitochondrial and nuclear genomes from divergent human populations can co-exist within healthy individuals, indicating that mismatched nDNA-mtDNA combinations are not deleterious or subject to purifying selection. Accordingly, human nuclear-mitochondrial mismatches are not likely to jeopardize the safety of MR therapy. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3539-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lavanya Rishishwar
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Colombia.,Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - I King Jordan
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA. .,PanAmerican Bioinformatics Institute, Cali, Colombia. .,Applied Bioinformatics Laboratory, Atlanta, GA, USA.
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25
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Kefi R, Hechmi M, Naouali C, Jmel H, Hsouna S, Bouzaid E, Abdelhak S, Beraud-Colomb E, Stevanovitch A. On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:147-157. [PMID: 28034339 DOI: 10.1080/24701394.2016.1258406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Western North African population was characterized by the presence of Iberomaurusian civilization at the Epiplaeolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved in situ in North Africa. With the aim to contribute to a better knowledge of the settlement of North Africa we analysed the mitochondrial DNA extracted from Iberomaurusian skeletons exhumed from the archaeological site of Afalou (AFA) (15,000-11,000 YBP) in Algeria and from the archaeological site of Taforalt (TAF) (23,000-10,800 YBP) in Morocco. Then, we carried out a phylogenetic analysis relating these Iberomaurusians to 61 current Mediterranean populations. The genetic structure of TAF and AFA specimens contains only North African and Eurasian maternal lineages. These finding demonstrate the presence of these haplotypes in North Africa from at least 20,000 YBP. The very low contribution of a Sub-Saharan African haplotype in the Iberomaurusian samples is confirmed. We also highlighted the existence of genetic flows between Southern and Northern coast of the Mediterranean.
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Affiliation(s)
- Rym Kefi
- a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia.,b University Tunis El Manar , Tunis , Tunisia
| | - Meriem Hechmi
- a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia
| | - Chokri Naouali
- a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia.,b University Tunis El Manar , Tunis , Tunisia
| | - Haifa Jmel
- a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia
| | - Sana Hsouna
- a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia.,b University Tunis El Manar , Tunis , Tunisia
| | - Eric Bouzaid
- c Institut National de Police Scientifique Laboratoire de Marseille , Marseille , France
| | - Sonia Abdelhak
- a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia.,b University Tunis El Manar , Tunis , Tunisia
| | | | - Alain Stevanovitch
- c Institut National de Police Scientifique Laboratoire de Marseille , Marseille , France
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26
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Timing and causes of North African wet phases during the last glacial period and implications for modern human migration. Sci Rep 2016; 6:36367. [PMID: 27808237 PMCID: PMC5093410 DOI: 10.1038/srep36367] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/29/2016] [Indexed: 11/08/2022] Open
Abstract
We present the first speleothem-derived central North Africa rainfall record for the last glacial period. The record reveals three main wet periods at 65-61 ka, 52.5-50.5 ka and 37.5-33 ka that lead obliquity maxima and precession minima. We find additional minor wet episodes that are synchronous with Greenland interstadials. Our results demonstrate that sub-tropical hydrology is forced by both orbital cyclicity and North Atlantic moisture sources. The record shows that after the end of a Saharan wet phase around 70 ka ago, North Africa continued to intermittently receive substantially more rainfall than today, resulting in favourable environmental conditions for modern human expansion. The encounter and subsequent mixture of Neanderthals and modern humans – which, on genetic evidence, is considered to have occurred between 60 and 50 ka – occurred synchronously with the wet phase between 52.5 and 50.5 ka. Based on genetic evidence the dispersal of modern humans into Eurasia started less than 55 ka ago. This may have been initiated by dry conditions that prevailed in North Africa after 50.5 ka. The timing of a migration reversal of modern humans from Eurasia into North Africa is suggested to be coincident with the wet period between 37.5 and 33 ka.
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27
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Hervella M, Svensson EM, Alberdi A, Günther T, Izagirre N, Munters AR, Alonso S, Ioana M, Ridiche F, Soficaru A, Jakobsson M, Netea MG, de-la-Rua C. The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa. Sci Rep 2016; 6:25501. [PMID: 27195518 PMCID: PMC4872530 DOI: 10.1038/srep25501] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/19/2016] [Indexed: 01/23/2023] Open
Abstract
After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.
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Affiliation(s)
- M Hervella
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n. 48940 Leioa, Bizkaia, Spain
| | - E M Svensson
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - A Alberdi
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - T Günther
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - N Izagirre
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n. 48940 Leioa, Bizkaia, Spain
| | - A R Munters
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - S Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n. 48940 Leioa, Bizkaia, Spain
| | - M Ioana
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, Bvd. 1 Mai no 66, Romania.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - F Ridiche
- Museum of Oltenia, History and Archaeology Department, Madona Dudu str. no. 14, Craiova, Romania
| | - A Soficaru
- "Fr. J. Rainer" Institute of Anthropology, Romanian Academy, Eroii Sanitari 8, P. O. Box 35-13, Romania
| | - M Jakobsson
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden.,Science for Life laboratory, Uppsala University, 75123 Uppsala, Sweden
| | - M G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - C de-la-Rua
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n. 48940 Leioa, Bizkaia, Spain
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28
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Li M, Rothwell R, Vermaat M, Wachsmuth M, Schröder R, Laros JFJ, van Oven M, de Bakker PIW, Bovenberg JA, van Duijn CM, van Ommen GJB, Slagboom PE, Swertz MA, Wijmenga C, Kayser M, Boomsma DI, Zöllner S, de Knijff P, Stoneking M. Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck. Genome Res 2016; 26:417-26. [PMID: 26916109 PMCID: PMC4817766 DOI: 10.1101/gr.203216.115] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/21/2016] [Indexed: 12/17/2022]
Abstract
Although previous studies have documented a bottleneck in the transmission of mtDNA genomes from mothers to offspring, several aspects remain unclear, including the size and nature of the bottleneck. Here, we analyze the dynamics of mtDNA heteroplasmy transmission in the Genomes of the Netherlands (GoNL) data, which consists of complete mtDNA genome sequences from 228 trios, eight dizygotic (DZ) twin quartets, and 10 monozygotic (MZ) twin quartets. Using a minor allele frequency (MAF) threshold of 2%, we identified 189 heteroplasmies in the trio mothers, of which 59% were transmitted to offspring, and 159 heteroplasmies in the trio offspring, of which 70% were inherited from the mothers. MZ twin pairs exhibited greater similarity in MAF at heteroplasmic sites than DZ twin pairs, suggesting that the heteroplasmy MAF in the oocyte is the major determinant of the heteroplasmy MAF in the offspring. We used a likelihood method to estimate the effective number of mtDNA genomes transmitted to offspring under different bottleneck models; a variable bottleneck size model provided the best fit to the data, with an estimated mean of nine individual mtDNA genomes transmitted. We also found evidence for negative selection during transmission against novel heteroplasmies (in which the minor allele has never been observed in polymorphism data). These novel heteroplasmies are enhanced for tRNA and rRNA genes, and mutations associated with mtDNA diseases frequently occur in these genes. Our results thus suggest that the female germ line is able to recognize and select against deleterious heteroplasmies.
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Affiliation(s)
- Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; Fondation Mérieux, 69002 Lyon, France
| | - Rebecca Rothwell
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Martijn Vermaat
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Manja Wachsmuth
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Jeroen F J Laros
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Mannis van Oven
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Paul I W de Bakker
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, The Netherlands; Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3584 CG, The Netherlands
| | - Jasper A Bovenberg
- Department of Biological Psychology, VU University Amsterdam, Amsterdam 1081 BT, The Netherlands
| | - Cornelia M van Duijn
- Legal Pathways Institute for Health and Bio Law, Aerdenhout 2111, The Netherlands
| | - Gert-Jan B van Ommen
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - P Eline Slagboom
- Department of Human Genetics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Morris A Swertz
- Section of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700 RB, The Netherlands
| | - Cisca Wijmenga
- Section of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700 RB, The Netherlands
| | | | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Dorret I Boomsma
- Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen 9700 RB, The Netherlands
| | - Sebastian Zöllner
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA; Department of Psychiatry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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29
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Jaeger LH, Gijón-Botella H, Del Carmen Del Arco-Aguilar M, Martín-Oval M, Rodríguez-Maffiotte C, Del Arco-Aguilar M, Araújo A, Iñiguez AM. Evidence of Helminth Infection in Guanche Mummies: Integrating Paleoparasitological and Paleogenetic Investigations. J Parasitol 2015; 102:222-8. [PMID: 26641720 DOI: 10.1645/15-866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The Guanches, ancient inhabitants of the Canary Islands, Spain, practiced mummification of their dead. A paleoparasitological and paleogenetic analysis was conducted on mummified bodies (n = 6) (AD 1200, Cal BP 750) belonging to the Guanche culture from Gran Canaria Island. Coprolite and sediment samples (n = 19) were removed from below the abdominal region or sacral foramina. The samples were rehydrated in 0.5% trisodium phosphate solution for 72 hr at 4 C, and the paleoparasitological investigation was conducted by spontaneous sedimentation method and microscopic examination. The results revealed the presence of well-preserved eggs of Ascaris sp., Trichuris trichiura , Enterobius vermicularis , and hookworms. Ancient DNA was extracted from sediment samples to elucidate the ancestry of the mummies and for molecular detection of Ascaris sp. infection. Results of paleogenetic analysis demonstrated Ascaris sp. infection using 2 molecular targets, cytb and nad1. The mtDNA haplotypes U6b, U6b1, and HV were identified, which confirmed records of Guanche ancestry. The excellent preservation of Guanche mummies facilitated the paleoparasitological and paleogenetic study, the results of which contribute to our knowledge of Guanche culture and their health status.
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Affiliation(s)
- Lauren Hubert Jaeger
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Herminia Gijón-Botella
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - María Del Carmen Del Arco-Aguilar
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Mercedes Martín-Oval
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Conrado Rodríguez-Maffiotte
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Mercedes Del Arco-Aguilar
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Adauto Araújo
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Alena Mayo Iñiguez
- LABTRIP, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Pavilhão Rocha Lima, Sala 518, Av. Brasil 4365, Rio de Janeiro, 21045-900, RJ, Brazil
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30
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Hernández CL, Soares P, Dugoujon JM, Novelletto A, Rodríguez JN, Rito T, Oliveira M, Melhaoui M, Baali A, Pereira L, Calderón R. Early Holocenic and Historic mtDNA African Signatures in the Iberian Peninsula: The Andalusian Region as a Paradigm. PLoS One 2015; 10:e0139784. [PMID: 26509580 PMCID: PMC4624789 DOI: 10.1371/journal.pone.0139784] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/17/2015] [Indexed: 11/18/2022] Open
Abstract
Determining the timing, identity and direction of migrations in the Mediterranean Basin, the role of "migratory routes" in and among regions of Africa, Europe and Asia, and the effects of sex-specific behaviors of population movements have important implications for our understanding of the present human genetic diversity. A crucial component of the Mediterranean world is its westernmost region. Clear features of transcontinental ancient contacts between North African and Iberian populations surrounding the maritime region of Gibraltar Strait have been identified from archeological data. The attempt to discern origin and dates of migration between close geographically related regions has been a challenge in the field of uniparental-based population genetics. Mitochondrial DNA (mtDNA) studies have been focused on surveying the H1, H3 and V lineages when trying to ascertain north-south migrations, and U6 and L in the opposite direction, assuming that those lineages are good proxies for the ancestry of each side of the Mediterranean. To this end, in the present work we have screened entire mtDNA sequences belonging to U6, M1 and L haplogroups in Andalusians--from Huelva and Granada provinces--and Moroccan Berbers. We present here pioneer data and interpretations on the role of NW Africa and the Iberian Peninsula regarding the time of origin, number of founders and expansion directions of these specific markers. The estimated entrance of the North African U6 lineages into Iberia at 10 ky correlates well with other L African clades, indicating that U6 and some L lineages moved together from Africa to Iberia in the Early Holocene. Still, founder analysis highlights that the high sharing of lineages between North Africa and Iberia results from a complex process continued through time, impairing simplistic interpretations. In particular, our work supports the existence of an ancient, frequently denied, bridge connecting the Maghreb and Andalusia.
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Affiliation(s)
- Candela L. Hernández
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
| | - Jean M. Dugoujon
- CNRS UMR 5288 Laboratoire d’Anthropologie Moléculaire et d’Imagerie de Synthèse (AMIS), Université Paul Sabatier Toulouse III, 31073 Toulouse, France
| | - Andrea Novelletto
- Dipartimento di Biologia, Università Tor Vergata di Rome, Rome, Italy
| | | | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Marisa Oliveira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | | | - Abdellatif Baali
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - Luisa Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Rosario Calderón
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
- * E-mail:
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Bekada A, Arauna LR, Deba T, Calafell F, Benhamamouch S, Comas D. Genetic Heterogeneity in Algerian Human Populations. PLoS One 2015; 10:e0138453. [PMID: 26402429 PMCID: PMC4581715 DOI: 10.1371/journal.pone.0138453] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/31/2015] [Indexed: 11/18/2022] Open
Abstract
The demographic history of human populations in North Africa has been characterized by complex processes of admixture and isolation that have modeled its current gene pool. Diverse genetic ancestral components with different origins (autochthonous, European, Middle Eastern, and sub-Saharan) and genetic heterogeneity in the region have been described. In this complex genetic landscape, Algeria, the largest country in Africa, has been poorly covered, with most of the studies using a single Algerian sample. In order to evaluate the genetic heterogeneity of Algeria, Y-chromosome, mtDNA and autosomal genome-wide makers have been analyzed in several Berber- and Arab-speaking groups. Our results show that the genetic heterogeneity found in Algeria is not correlated with geography or linguistics, challenging the idea of Berber groups being genetically isolated and Arab groups open to gene flow. In addition, we have found that external sources of gene flow into North Africa have been carried more often by females than males, while the North African autochthonous component is more frequent in paternally transmitted genome regions. Our results highlight the different demographic history revealed by different markers and urge to be cautious when deriving general conclusions from partial genomic information or from single samples as representatives of the total population of a region.
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Affiliation(s)
- Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Lara R. Arauna
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Tahria Deba
- Centre de Transfusion Sanguine- Centre Hospitalo-Universitaire d’Oran (CTS-CHUO), Oran, Algeria
| | - Francesc Calafell
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Soraya Benhamamouch
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain
- * E-mail:
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Fregel R, Cabrera V, Larruga JM, Abu-Amero KK, González AM. Carriers of Mitochondrial DNA Macrohaplogroup N Lineages Reached Australia around 50,000 Years Ago following a Northern Asian Route. PLoS One 2015; 10:e0129839. [PMID: 26053380 PMCID: PMC4460043 DOI: 10.1371/journal.pone.0129839] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 05/13/2015] [Indexed: 01/17/2023] Open
Abstract
Background The modern human colonization of Eurasia and Australia is mostly explained by a single-out-of-Africa exit following a southern coastal route throughout Arabia and India. However, dispersal across the Levant would better explain the introgression with Neanderthals, and more than one exit would fit better with the different ancient genomic components discovered in indigenous Australians and in ancient Europeans. The existence of an additional Northern route used by modern humans to reach Australia was previously deduced from the phylogeography of mtDNA macrohaplogroup N. Here, we present new mtDNA data and new multidisciplinary information that add more support to this northern route. Methods MtDNA hypervariable segments and haplogroup diagnostic coding positions were analyzed in 2,278 Saudi Arabs, from which 1,725 are new samples. Besides, we used 623 published mtDNA genomes belonging to macrohaplogroup N, but not R, to build updated phylogenetic trees to calculate their coalescence ages, and more than 70,000 partial mtDNA sequences were screened to establish their respective geographic ranges. Results The Saudi mtDNA profile confirms the absence of autochthonous mtDNA lineages in Arabia with coalescence ages deep enough to support population continuity in the region since the out-of-Africa episode. In contrast to Australia, where N(xR) haplogroups are found in high frequency and with deep coalescence ages, there are not autochthonous N(xR) lineages in India nor N(xR) branches with coalescence ages as deep as those found in Australia. These patterns are at odds with the supposition that Australian colonizers harboring N(xR) lineages used a route involving India as a stage. The most ancient N(xR) lineages in Eurasia are found in China, and inconsistently with the coastal route, N(xR) haplogroups with the southernmost geographical range have all more recent radiations than the Australians. Conclusions Apart from a single migration event via a southern route, phylogeny and phylogeography of N(xR) lineages support that people carrying mtDNA N lineages could have reach Australia following a northern route through Asia. Data from other disciplines also support this scenario.
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Affiliation(s)
- Rosa Fregel
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
- * E-mail:
| | - Vicente Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Jose M. Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Khaled K. Abu-Amero
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ana M. González
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
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Komiyama T, Hirokawa T, Sato K, Oka A, Kamiguchi H, Nagata E, Sakura H, Otsuka K, Kobayashi H. Relationship between human evolution and neurally mediated syncope disclosed by the polymorphic sites of the adrenergic receptor gene α2B-AR. PLoS One 2015; 10:e0120788. [PMID: 25860977 PMCID: PMC4393242 DOI: 10.1371/journal.pone.0120788] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/06/2015] [Indexed: 11/18/2022] Open
Abstract
The objective of this study was to clarify the effects of disease on neurally mediated syncope (NMS) during an acute stress reaction. We analyzed the mechanism of the molecular interaction and the polymorphisms of the alpha-2 adrenoreceptor (α2B-AR) gene as the potential psychiatric cause of incentive stress. We focused on the following three genotypes of the repeat polymorphism site at Glu 301-303 in the α2B-AR gene: Glu12/12, Glu12/9, and Glu9/9. On the basis of our clinical research, NMS is likely to occur in people with the Glu12/9 heterotype. To verify this, we assessed this relationship with the interaction of Gi protein and adenylate cyclase by in silico analysis of the Glu12/9 heterotype. By measuring the difference in the dissociation time of the Gi-α subunit twice, we found that the Glu12/9 heterotype suppressed the action of adenylate cyclase longer than the Glu homotypes. As this difference in the Glu repeat number effect is thought to be one of the causes of NMS, we investigated the evolutionary significance of the Glu repeat number. Glu8 was originally repeated in simians, while the Glu12 repeats occurred over time during the evolution of bipedalism in humans. Taken with the Glu12 numbers, NMS would likely become a defensive measure to prevent significant blood flow to the human brain.
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MESH Headings
- Alleles
- Animals
- Base Sequence
- DNA/analysis
- DNA/isolation & purification
- DNA, Mitochondrial/analysis
- DNA, Mitochondrial/classification
- Epinephrine/blood
- Evolution, Molecular
- Female
- GTP-Binding Protein alpha Subunits, Gi-Go/metabolism
- Gene Frequency
- Genotype
- Humans
- Male
- Norepinephrine/blood
- Phylogeny
- Polymorphism, Single Nucleotide
- Primates/genetics
- Protein Binding
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Receptors, Adrenergic, alpha-2/chemistry
- Receptors, Adrenergic, alpha-2/genetics
- Receptors, Adrenergic, alpha-2/metabolism
- Syncope, Vasovagal/metabolism
- Syncope, Vasovagal/pathology
- Thermodynamics
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Affiliation(s)
- Tomoyoshi Komiyama
- Department of Clinical Pharmacology, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259–1193, Japan
| | - Takatsugu Hirokawa
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building 2-4-7 Aomi, Koto-ku, Tokyo, 135–0064, Japan
| | - Kyoko Sato
- Tokyo Women’s Medical University Medical Center East, 2-1-10 Higashiogu, Arakawa-ku, Tokyo, 116–8567, Japan
| | - Akira Oka
- The Institute of Medical Science, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259–1193, Japan
| | - Hiroshi Kamiguchi
- Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259–1193, Japan
| | - Eiichiro Nagata
- Department of Neurology, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259–1193, Japan
| | - Hiroshi Sakura
- Tokyo Women’s Medical University Medical Center East, 2-1-10 Higashiogu, Arakawa-ku, Tokyo, 116–8567, Japan
| | - Kuniaki Otsuka
- Tokyo Women’s Medical University Medical Center East, 2-1-10 Higashiogu, Arakawa-ku, Tokyo, 116–8567, Japan
| | - Hiroyuki Kobayashi
- Department of Clinical Pharmacology, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259–1193, Japan
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Yang H, Liu R, Wang CC. Searching the co-occurrence of pathogenic mutations for Leber's hereditary optic neuropathy and hearing loss in more than 26,000 whole mitochondrial genomes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3399-402. [PMID: 25714144 DOI: 10.3109/19401736.2015.1018239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The co-occurrence of pathogenic or candidate mutations for Leber's hereditary optic neuropathy (LHON) and hearing loss has long been suggested to be a rare incident. The "rare" is probably caused by inadequate database searches. In this study, we created and released a comprehensive database with detailed information of haplogroup, variants, coding sites, and potential pathogenic mutations for more than 26,000 whole mitochondrial genomes. We found the co-occurrence in more than 200 individuals including not only LHON or hearing loss patients but also individuals sampled from general populations with various haplogroup backgrounds. The results highlighted the significant importance of adequate database searching in the genetic analysis of mitochondrial disorders.
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Affiliation(s)
- Haixin Yang
- a Department of Neurology , Liaocheng People's Hospital , Liaocheng , Shandong , P.R. China and
| | - Rui Liu
- b State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology , Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai , P.R. China
| | - Chuan-Chao Wang
- b State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology , Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai , P.R. China
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Fregel R, Cabrera VM, Larruga JM, Hernández JC, Gámez A, Pestano JJ, Arnay M, González AM. Isolation and prominent aboriginal maternal legacy in the present-day population of La Gomera (Canary Islands). Eur J Hum Genet 2014; 23:1236-43. [PMID: 25407001 PMCID: PMC4538205 DOI: 10.1038/ejhg.2014.251] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/08/2014] [Accepted: 10/10/2014] [Indexed: 11/09/2022] Open
Abstract
The present-day population structure of La Gomera is outstanding in its high aboriginal heritage, the greatest in the Canary Islands. This was earlier confirmed by both mitochondrial DNA and autosomal analyses, although genetic drift due to the fifteenth century European colonization could not be excluded as the main factor responsible. The present mtDNA study of aboriginal remains and extant samples from the six municipal districts of the island indeed demonstrates that the pre-Hispanic colonization of La Gomera by North African people involved a strong founder event, shown by the high frequency of the indigenous Canarian U6b1a lineage in the aboriginal samples (65%). This value is even greater than that observed in the extant population (44%), which in turn is the highest of all the seven Canary Islands. In contrast to previous results obtained for the aboriginal populations of Tenerife and La Palma, haplogroups related to secondary waves of migration were not detected in La Gomera aborigines, indicating that isolation also had an important role in shaping the current population. The rugged relief of La Gomera divided into several distinct valleys probably promoted subsequent aboriginal intra-insular differentiation that has continued after the European colonization, as seen in the present-day population structure observed on the island.
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Affiliation(s)
- Rosa Fregel
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - José M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Juan C Hernández
- Museo Arqueológico de La Gomera, Unidad de Patrimonio Histórico, Cabildo de La Gomera, San Sebastián de la Gomera, La Gomera, Spain
| | - Alejandro Gámez
- Departamento de Geografía e Historia, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Jose J Pestano
- Laboratorio de Genética, Facultad de Medicina, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Gran Canaria, Spain
| | - Matilde Arnay
- Departamento de Geografía e Historia, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Ana M González
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
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