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Sandoval-Velasco M, Jagadeesan A, Ramos-Madrigal J, Ávila-Arcos MC, Fortes-Lima CA, Watson J, Johannesdóttir E, Cruz-Dávalos DI, Gopalakrishnan S, Moreno-Mayar JV, Niemann J, Renaud G, Robson Brown KA, Bennett H, Pearson A, Helgason A, Gilbert MTP, Schroeder H. The ancestry and geographical origins of St Helena's liberated Africans. Am J Hum Genet 2023; 110:1590-1599. [PMID: 37683613 PMCID: PMC10502851 DOI: 10.1016/j.ajhg.2023.08.001] [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: 10/27/2022] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/10/2023] Open
Abstract
The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception point for enslaved Africans who had been "liberated" from slave ships intercepted by the British. In total, St Helena received approximately 27,000 liberated Africans between 1840 and 1867. Written sources suggest that the majority of these individuals came from West Central Africa, but their precise origins are unknown. Here, we report the results of ancient DNA analyses that we conducted as part of a wider effort to commemorate St Helena's liberated Africans and to restore knowledge of their lives and experiences. We generated partial genomes (0.1-0.5×) for 20 individuals whose remains had been recovered during archaeological excavations on the island. We compared their genomes with genotype data for over 3,000 present-day individuals from 90 populations across sub-Saharan Africa and conclude that the individuals most likely originated from different source populations within the general area between northern Angola and Gabon. We also find that the majority (17/20) of the individuals were male, supporting a well-documented sex bias in the latter phase of the transatlantic slave trade. The study expands our understanding of St Helena's liberated African community and illustrates how ancient DNA analyses can be used to investigate the origins and identities of individuals whose lives were bound up in the story of slavery and its abolition.
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Affiliation(s)
- Marcela Sandoval-Velasco
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
| | - Anuradha Jagadeesan
- deCODE Genetics/Amgen, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland
| | - Jazmín Ramos-Madrigal
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of Mexico, Juriquilla, 76230 Santiago de Querétaro, México
| | - Cesar A Fortes-Lima
- Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Judy Watson
- Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK
| | - Erna Johannesdóttir
- Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK
| | - Diana I Cruz-Dávalos
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Shyam Gopalakrishnan
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Jonas Niemann
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Gabriel Renaud
- Department of Health Technology Bioinformatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | | | - Helena Bennett
- St Helena National Trust, Broadway House, Mainstreet, Jamestown, St Helena
| | - Andrew Pearson
- Environmental Dimension Partnership, Atlantic Wharf, CF10 4HF Cardiff, UK
| | - Agnar Helgason
- deCODE Genetics/Amgen, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland
| | - M Thomas P Gilbert
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
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Soko ND, Dlamini S, Ntsekhe M, Dandara C. The COVID-19 Pandemic and Explaining Outcomes in Africa: Could Genomic Variation Add to the Debate? OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:594-607. [PMID: 36322905 PMCID: PMC9700373 DOI: 10.1089/omi.2022.0108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, emanated from the Wuhan Province in China and rapidly spread across the globe causing extensive morbidity and mortality rate, and affecting the global economy and livelihoods. Contrary to early predictions of "body bags" across Africa, the African COVID-19 pandemic was marked by apparent low case numbers and an overall mortality rate when compared with the other geographical regions. Factors used to describe this unexpected pattern included a younger population, a swifter and more effective national health policy, limited testing capacities, and the possibility of inadequate reporting of the cases, among others. However, despite genomics contributing to interindividual variations in many diseases across the world, there are inadequate genomic and multiomics data on COVID-19 in Africa that prevent richer transdisciplinary discussions on the contribution of genomics to the spread of COVID-19 pandemic. To invite future debates on comparative studies of COVID-19 genomics and the pandemic spread around the world regions, this expert review evaluates the reported frequency distribution of genetic variants in candidate genes that are likely to affect COVID-19 infection dynamics/disease outcomes. We propose here that genomic variation should be considered among the many factors determining the COVID-19 infection and its outcomes in African populations and across the world.
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Affiliation(s)
- Nyarai D. Soko
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- UCT/South African Medical Research Council (SAMRC) Platform for Pharmacogenomics Research and Translation, Cape Town, South Africa
- Address correspondence to: Nyarai D. Soko, PhD, Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Sipho Dlamini
- Division of Infectious Diseases, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Mpiko Ntsekhe
- Division of Cardiology, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Collet Dandara
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- UCT/South African Medical Research Council (SAMRC) Platform for Pharmacogenomics Research and Translation, Cape Town, South Africa
- Address correspondence to: Collet Dandara, PhD, Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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Wepeba PP, Abaidoo CS, Goodwin WH. Haplogroup prediction in the Ghanaian population using haplotype data of 27 Yfiler® Plus loci and TaqMan SNP genotyping. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Atkinson EG, Dalvie S, Pichkar Y, Kalungi A, Majara L, Stevenson A, Abebe T, Akena D, Alemayehu M, Ashaba FK, Atwoli L, Baker M, Chibnik LB, Creanza N, Daly MJ, Fekadu A, Gelaye B, Gichuru S, Injera WE, James R, Kariuki SM, Kigen G, Koen N, Koenen KC, Koenig Z, Kwobah E, Kyebuzibwa J, Musinguzi H, Mwema RM, Neale BM, Newman CP, Newton CRJC, Ongeri L, Ramachandran S, Ramesar R, Shiferaw W, Stein DJ, Stroud RE, Teferra S, Yohannes MT, Zingela Z, Martin AR. Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa. Am J Hum Genet 2022; 109:1667-1679. [PMID: 36055213 PMCID: PMC9502052 DOI: 10.1016/j.ajhg.2022.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/28/2022] [Indexed: 12/22/2022] Open
Abstract
African populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multi-generational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We find suggestive evidence for the rate of language transmission in matrilineal groups having been higher than that for patrilineal ones. We highlight both the diversity of variation within Africa as well as how within-Africa variation can be informative for broader variant interpretation; many variants that are rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity across Africa.
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Affiliation(s)
- Elizabeth G Atkinson
- Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Shareefa Dalvie
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Yakov Pichkar
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Allan Kalungi
- Department of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda; Mental Health Section of MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Lerato Majara
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anne Stevenson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tamrat Abebe
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dickens Akena
- Department of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Melkam Alemayehu
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Fred K Ashaba
- Department of Immunology & Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Lukoye Atwoli
- Department of Mental Health, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya; Brain and Mind Institute and Department of Internal Medicine, Medical College East Africa, the Aga Khan University, Nairobi, Kenya
| | - Mark Baker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lori B Chibnik
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Nicole Creanza
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abebaw Fekadu
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia; Centre for Innovative Drug Development & Therapeutic Trials for Africa, Addis Ababa University, Addis Ababa, Ethiopia
| | - Bizu Gelaye
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Stella Gichuru
- Department of Mental Health, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Wilfred E Injera
- Department of Immunology, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Roxanne James
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Symon M Kariuki
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Gabriel Kigen
- Department of Pharmacology and Toxicology, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Nastassja Koen
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Karestan C Koenen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Zan Koenig
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edith Kwobah
- Department of Mental Health, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Joseph Kyebuzibwa
- Department of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Henry Musinguzi
- Department of Immunology & Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Rehema M Mwema
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Carter P Newman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Charles R J C Newton
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Linnet Ongeri
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Raj Ramesar
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Welelta Shiferaw
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dan J Stein
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Rocky E Stroud
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Solomon Teferra
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mary T Yohannes
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zukiswa Zingela
- Executive Dean's Office, Faculty of Health Sciences, Nelson Mandela University, Port Elizabeth, South Africa
| | - Alicia R Martin
- Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Kasu M, Cloete K, Pitere R, Tsiana K, D’Amato M. The Genetic Landscape of South African males: A Y-STR Perspective. Forensic Sci Int Genet 2022; 58:102677. [DOI: 10.1016/j.fsigen.2022.102677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/04/2022]
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Rambaldi Migliore N, Colombo G, Capodiferro MR, Mazzocchi L, Chero Osorio AM, Raveane A, Tribaldos M, Perego UA, Mendizábal T, Montón AG, Lombardo G, Grugni V, Garofalo M, Ferretti L, Cereda C, Gagliardi S, Cooke R, Smith-Guzmán N, Olivieri A, Aram B, Torroni A, Motta J, Semino O, Achilli A. Weaving Mitochondrial DNA and Y-Chromosome Variation in the Panamanian Genetic Canvas. Genes (Basel) 2021; 12:genes12121921. [PMID: 34946870 PMCID: PMC8702192 DOI: 10.3390/genes12121921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 12/14/2022] Open
Abstract
The Isthmus of Panama was a crossroads between North and South America during the continent’s first peopling (and subsequent movements) also playing a pivotal role during European colonization and the African slave trade. Previous analyses of uniparental systems revealed significant sex biases in the genetic history of Panamanians, as testified by the high proportions of Indigenous and sub-Saharan mitochondrial DNAs (mtDNAs) and by the prevalence of Western European/northern African Y chromosomes. Those studies were conducted on the general population without considering any self-reported ethnic affiliations. Here, we compared the mtDNA and Y-chromosome lineages of a new sample collection from 431 individuals (301 males and 130 females) belonging to either the general population, mixed groups, or one of five Indigenous groups currently living in Panama. We found different proportions of paternal and maternal lineages in the Indigenous groups testifying to pre-contact demographic events and genetic inputs (some dated to Pleistocene times) that created genetic structure. Then, while the local mitochondrial gene pool was marginally involved in post-contact admixtures, the Indigenous Y chromosomes were differentially replaced, mostly by lineages of western Eurasian origin. Finally, our new estimates of the sub-Saharan contribution, on a more accurately defined general population, reduce an apparent divergence between genetic and historical data.
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Affiliation(s)
- Nicola Rambaldi Migliore
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Giulia Colombo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Marco Rosario Capodiferro
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Lucia Mazzocchi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Ana Maria Chero Osorio
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Alessandro Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Maribel Tribaldos
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ugo Alessandro Perego
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Department of Math and Science, Southeastern Community College, West Burlington, IA 52655, USA
| | - Tomás Mendizábal
- Center for Historical, Anthropological and Cultural Research—AIP, Panama City 0816-07812, Panama;
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
| | - Alejandro García Montón
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Gianluca Lombardo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Viola Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Maria Garofalo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Luca Ferretti
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Stella Gagliardi
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Nicole Smith-Guzmán
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Bethany Aram
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ornella Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
| | - Alessandro Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
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Claerhout S, Verstraete P, Warnez L, Vanpaemel S, Larmuseau M, Decorte R. CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics. PLoS Genet 2021; 17:e1009758. [PMID: 34491993 PMCID: PMC8423258 DOI: 10.1371/journal.pgen.1009758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 08/05/2021] [Indexed: 11/26/2022] Open
Abstract
Male-specific Y-chromosome (chrY) polymorphisms are interesting components of the DNA for population genetics. While single nucleotide polymorphisms (Y-SNPs) indicate distant evolutionary ancestry, short tandem repeats (Y-STRs) are able to identify close familial kinships. Detailed chrY analysis provides thus both biogeographical background information as paternal lineage identification. The rapid advancement of high-throughput massive parallel sequencing (MPS) technology in the past decade has revolutionized genetic research. Using MPS, single-base information of both Y-SNPs as Y-STRs can be analyzed in a single assay typing multiple samples at once. In this study, we present the first extensive chrY-specific targeted resequencing panel, the ‘CSYseq’, which simultaneously identifies slow mutating Y-SNPs as evolution markers and rapid mutating Y-STRs as patrilineage markers. The panel was validated by paired-end sequencing of 130 males, distributed over 65 deep-rooted pedigrees covering 1,279 generations. The CSYseq successfully targets 15,611 Y-SNPs including 9,014 phylogenetic informative Y-SNPs to identify 1,443 human evolutionary Y-subhaplogroup lineages worldwide. In addition, the CSYseq properly targets 202 Y-STRs, including 81 slow, 68 moderate, 27 fast and 26 rapid mutating Y-STRs to individualize close paternal relatives. The targeted chrY markers cover a high average number of reads (Y-SNP = 717, Y-STR = 150), easy interpretation, powerful discrimination capacity and chrY specificity. The CSYseq is interesting for research on different time scales: to identify evolutionary ancestry, to find distant family and to discriminate closely related males. Therefore, this panel serves as a unique tool valuable for a wide range of genetic-genealogical applications in interdisciplinary research within evolutionary, population, molecular, medical and forensic genetics. Around 95% of the male-specific Y-chromosome (chrY) is non-recombining and therefore inherited in a conserved manner from father to son. It can therefore serve as a powerful marker for interdisciplinary genetic-genealogical research as it provides a strong link between genetic information and a family tree or pedigree. While Y-chromosomal short tandem repeats (Y-STRs) discriminate close paternal kinships, single nucleotide polymorphisms (Y-SNPs) enables the identification of far evolutionary ancestry. Unfortunately, an extensive chrY-specific sequencing panel combining a large number of familial Y-STRs and evolutionary Y-SNPs was not yet available. Therefore, chrY is rarely included in research projects and not often linked to a genealogical, history-demographical or life science database. In this way, the importance of chrY still remains not yet fully understood. Massive parallel sequencing (MPS) allows the simultaneous analysis at sequence level of Y-SNPs and Y-STRs with variable mutation rates in a large number of males. However, up until today, no commercial kit is exploiting the full potential that MPS offers on chrY. Therefore, we developed the ‘CSYseq’, which is the first extensive chrY-specific sequencing panel. The CSYseq simultaneously identifies 9,014 slow mutating Y-SNPs to identify evolutionary ancestry, and 202 rapid mutating Y-STRs to investigate paternal relationships. We validated and optimized the panel through the analysis of 130 males distributed over 65 families. This novel MPS panel is useful for biogeographical identity and ancestry analysis, together with Y-chromosome profiling for the identification of patrilineages and discrimination of closely related males. As the CSYseq includes a very diverse set of markers that can be easily interpreted, it is interesting for different interdisciplinary applications within evolutionary, population, molecular, medical and forensic genetics.
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Affiliation(s)
- Sofie Claerhout
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
- * E-mail:
| | - Paulien Verstraete
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Liesbeth Warnez
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Simon Vanpaemel
- KU Leuven, Department of Mechanical Engineering, Noise and Vibration Engineering, Leuven, Belgium
- DMMS Lab, Flanders Make, Heverlee, Belgium
| | - Maarten Larmuseau
- Histories vzw, Mechelen, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
- Laboratory of Forensic genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
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8
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Exchanging fluids The sociocultural implications of microbial, cultural, and ethnic admixture in Latin America. Politics Life Sci 2021; 39:56-86. [PMID: 32697057 DOI: 10.1017/pls.2020.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Knowledge of evolutionary influences on patterns of human mating, social interactions, and differential health is increasing, yet these insights have rarely been applied to historical analyses of human population dynamics. The genetic and evolutionary forces behind biases in interethnic mating and in the health of individuals of different ethnic groups in Latin America and the Caribbean since the European colonization of America are still largely ignored. We discuss how historical and contemporary sociocultural interactions and practices are strongly influenced by population-level evolutionary forces. Specifically, we discuss the historical implications of functional (de facto) polygyny, sex-biased admixture, and assortative mating in Latin America. We propose that these three evolutionary mechanisms influenced mating patterns, shaping the genetic and cultural landscape across Latin America and the Caribbean. Further, we discuss how genetic differences between the original populations that migrated at different times into Latin America contributed to their accommodation to and survival in the different local ecologies and interethnic interactions. Relevant medical and social implications follow from the genetic and cultural changes reviewed.
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9
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Khubrani YM, Jobling MA, Wetton JH. Massively parallel sequencing of sex-chromosomal STRs in Saudi Arabia reveals patrilineage-associated sequence variants. Forensic Sci Int Genet 2020; 49:102402. [PMID: 33035796 DOI: 10.1016/j.fsigen.2020.102402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/18/2020] [Accepted: 09/27/2020] [Indexed: 11/27/2022]
Abstract
Massively parallel sequencing (MPS) of forensic STRs has the potential to reveal additional allele diversity compared to conventional capillary electrophoresis (CE) typing strategies, but population studies are currently relatively few in number. The Verogen ForenSeq™ DNA Signature Prep Kit includes both Y-STRs and X-STRs among its targeted loci, and here we report the sequences of these loci, analysed using Verogen's ForenSeq™ Universal Analysis Software (UAS) v1.3 and STRait Razor v3.0, in a representative sample of 89 Saudi Arabian males. We identified 56 length variants (equivalent to CE alleles) and 75 repeat sequence sub-variants across the six X-STRs analysed; equivalent figures for the set of 24 Y-STRs were 147 and 192 respectively. We also observed two flanking sequence variants for the X-, and six for the Y-STRs. Recovery of sequence data and concordance with CE data (where available) across the tested loci was good, though rare flanking variation affected interpretation and allele calling at DYF387S1 and DXS7132. Examination of flanking sequences of the Y-STRs revealed five SNPs (L255, M4790, BY7692, Z16708 and S17543) previously shown to define specific haplogroups by Y-chromosome sequencing. These define Y-haplogroups in 62 % of our sample, a proportion that increases to 91 % when haplogroup-associated repeat-sequence motifs are also considered. A population-level comparison of the Saudi Arabian X-STRs with a global sample showed our dataset to be part of a large cluster of populations of West Eurasian and Middle Eastern origin.
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Affiliation(s)
- Yahya M Khubrani
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK; Forensic Genetics Laboratory, General Administration of Criminal Evidence, Public Security, Ministry of Interior, Saudi Arabia
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK.
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10
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D’Atanasio E, Trionfetti F, Bonito M, Sellitto D, Coppa A, Berti A, Trombetta B, Cruciani F. Y Haplogroup Diversity of the Dominican Republic: Reconstructing the Effect of the European Colonization and the Trans-Atlantic Slave Trades. Genome Biol Evol 2020; 12:1579-1590. [PMID: 32835369 PMCID: PMC7523727 DOI: 10.1093/gbe/evaa176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2020] [Indexed: 12/12/2022] Open
Abstract
The Dominican Republic is one of the two countries on the Hispaniola island, which is part of the Antilles. Hispaniola was affected by the European colonization and massive deportation of African slaves since the XVI century and these events heavily shaped the genetic composition of the present-day population. To shed light about the effect of the European rules, we analyzed 92 single nucleotide polymorphisms on the Y chromosome in 182 Dominican individuals from three different locations. The Dominican Y haplogroup composition was characterized by an excess of northern African/European lineages (59%), followed by the African clades (38%), whereas the Native-American lineages were rare (3%). The comparison with the mitochondrial DNA variability, dominated by African clades, revealed a sex-biased admixture pattern, in line with the colonial society dominated by European men. When other Caribbean and non-Caribbean former colonies were also considered, we noted a difference between territories under a Spanish rule (like the Dominican Republic) and British/French rule, with the former characterized by an excess of European Y lineages reflecting the more permissive Iberian legislation about mixed people and slavery. Finally, we analyzed the distribution in Africa of the Dominican lineages with a putative African origin, mainly focusing on central and western Africa, which were the main sources of African slaves. We found that most (83%) of the African lineages observed in Santo Domingo have a central African ancestry, suggesting that most of the slaves were deported from regions.
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Affiliation(s)
- Eugenia D’Atanasio
- Istituto di Biologia e Patologia Molecolari, CNR, Roma, Italy
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Flavia Trionfetti
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Maria Bonito
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | | | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Andrea Berti
- Reparto CC Investigazioni Scientifiche di Roma, Sezione di Biologia, Rome, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Istituto di Biologia e Patologia Molecolari, CNR, Roma, Italy
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
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11
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Aljasmi FA, Vijayan R, Sudalaimuthuasari N, Souid AK, Karuvantevida N, Almaskari R, Mohammed Abdul Kader H, Kundu B, Michel Hazzouri K, Amiri KMA. Genomic Landscape of the Mitochondrial Genome in the United Arab Emirates Native Population. Genes (Basel) 2020; 11:genes11080876. [PMID: 32752197 PMCID: PMC7464197 DOI: 10.3390/genes11080876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 11/19/2022] Open
Abstract
In order to assess the genomic landscape of the United Arab Emirates (UAE) mitogenome, we sequenced and analyzed the complete genomes of 232 Emirate females mitochondrial DNA (mtDNA) within and compared those to Africa. We investigated the prevalence of haplogroups, genetic variation, heteroplasmy, and demography among the UAE native population with diverse ethnicity and relatively high degree of consanguinity. We identified 968 mtDNA variants and high-resolution 15 haplogroups. Our results show that the UAE population received enough gene flow from Africa represented by the haplogroups L, U6, and M1, and that 16.8% of the population has an eastern provenance, depicted by the U haplogroup and the M Indian haplogroup (12%), whereas western Eurasian and Asian haplogroups (R, J, and K) represent 11 to 15%. Interestingly, we found an ancient migration present through the descendant of L (N1 and X) and other sub-haplogroups (L2a1d and L4) and (L3x1b), which is one of the oldest evolutionary histories outside of Africa. Our demographic analysis shows no population structure among populations, with low diversity and no population differentiation. In addition, we show that the transmission of mtDNA in the UAE population is under purifying selection with hints of diversifying selection on ATP8 gene. Last, our results show a population bottleneck, which coincides with the Western European contact (1400 ybp). Our study of the UAE mitogenomes suggest that several maternal lineage migratory episodes liking African–Asian corridors occurred since the first modern human emerges out of Africa.
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Affiliation(s)
- Fatma A Aljasmi
- Pediatric Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Ranjit Vijayan
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Abdul-Kader Souid
- Pediatric Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Raja Almaskari
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Biduth Kundu
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Khaled M A Amiri
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
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12
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Lipson M, Ribot I, Mallick S, Rohland N, Olalde I, Adamski N, Broomandkhoshbacht N, Lawson AM, López S, Oppenheimer J, Stewardson K, Asombang RN, Bocherens H, Bradman N, Culleton BJ, Cornelissen E, Crevecoeur I, de Maret P, Fomine FLM, Lavachery P, Mindzie CM, Orban R, Sawchuk E, Semal P, Thomas MG, Van Neer W, Veeramah KR, Kennett DJ, Patterson N, Hellenthal G, Lalueza-Fox C, MacEachern S, Prendergast ME, Reich D. Ancient West African foragers in the context of African population history. Nature 2020; 577:665-670. [PMID: 31969706 PMCID: PMC8386425 DOI: 10.1038/s41586-020-1929-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 11/29/2019] [Indexed: 12/31/2022]
Abstract
Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children-two of whom were buried approximately 8,000 years ago and two 3,000 years ago-from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group1-11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today-as well as speakers of Bantu languages from across the continent-are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.
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Affiliation(s)
- Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Isabelle Ribot
- Département d'Anthropologie, Université de Montréal, Montreal, Quebec, Canada
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Anthropology, University of California, Santa Cruz, CA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Saioa López
- UCL Genetics Institute, University College London, London, UK
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Hervé Bocherens
- Department of Geosciences, Biogeology, University of Tübingen, Tübingen, Germany
- Senckenberg Research Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Neil Bradman
- UCL Genetics Institute, University College London, London, UK
- The Henry Stewart Group, London, UK
| | - Brendan J Culleton
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA, USA
| | - Els Cornelissen
- Department of Cultural Anthropology and History, Royal Museum for Central Africa, Tervuren, Belgium
| | | | - Pierre de Maret
- Faculté de Philosophie et Sciences Sociales, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Philippe Lavachery
- Agence Wallonne du Patrimoine, Service Public de Wallonie, Namur, Belgium
| | | | - Rosine Orban
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Elizabeth Sawchuk
- Department of Anthropology, Stony Brook University, Stony Brook, NY, USA
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Mark G Thomas
- UCL Genetics Institute, University College London, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Wim Van Neer
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Department of Biology, University of Leuven, Leuven, Belgium
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Nick Patterson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Garrett Hellenthal
- UCL Genetics Institute, University College London, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Scott MacEachern
- Division of Social Science, Duke Kunshan University, Kunshan, China
| | - Mary E Prendergast
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Sociology and Anthropology, Saint Louis University, Madrid, Spain
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
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13
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Chung NN, Jacobs GS, Sudoyo H, Malik SG, Chew LY, Lansing JS, Cox MP. Sex-linked genetic diversity originates from persistent sociocultural processes at microgeographic scales. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190733. [PMID: 31598251 PMCID: PMC6731738 DOI: 10.1098/rsos.190733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/26/2019] [Indexed: 06/10/2023]
Abstract
Population genetics has been successful at identifying the relationships between human groups and their interconnected histories. However, the link between genetic demography inferred at large scales and the individual human behaviours that ultimately generate that demography is not always clear. While anthropological and historical context are routinely presented as adjuncts in population genetic studies to help describe the past, determining how underlying patterns of human sociocultural behaviour impact genetics still remains challenging. Here, we analyse patterns of genetic variation in village-scale samples from two islands in eastern Indonesia, patrilocal Sumba and a matrilocal region of Timor. Adopting a 'process modelling' approach, we iteratively explore combinations of structurally different models as a thinking tool. We find interconnected socio-genetic interactions involving sex-biased migration, lineage-focused founder effects, and on Sumba, heritable social dominance. Strikingly, founder ideology, a cultural model derived from anthropological and archaeological studies at larger regional scales, has both its origins and impact at the scale of villages. Process modelling lets us explore these complex interactions, first by circumventing the complexity of formal inference when studying large datasets with many interacting parts, and then by explicitly testing complex anthropological hypotheses about sociocultural behaviour from a more familiar population genetic standpoint.
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Affiliation(s)
- Ning Ning Chung
- Complexity Institute, Nanyang Technological University, Singapore
- Centre for University Core, Singapore University of Social Sciences, Singapore
| | - Guy S. Jacobs
- Complexity Institute, Nanyang Technological University, Singapore
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
- Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Safarina G. Malik
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Lock Yue Chew
- Complexity Institute, Nanyang Technological University, Singapore
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - J. Stephen Lansing
- Santa Fe Institute, Santa Fe, NM 87501, USA
- Stockholm Resilience Center, Kräftriket, 10405 Stockholm, Sweden
| | - Murray P. Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
- Te Pūnaha Matatini, Centre of Research Excellence for Complex Systems, Aukland, New Zealand
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14
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Zhang M, Zheng HX, Yan S, Jin L. Reconciling the father tongue and mother tongue hypotheses in Indo-European populations. Natl Sci Rev 2019; 6:293-300. [PMID: 34691868 PMCID: PMC8291526 DOI: 10.1093/nsr/nwy083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/01/2018] [Accepted: 08/06/2018] [Indexed: 12/04/2022] Open
Abstract
In opposition to the mother tongue hypothesis, the father tongue hypothesis states that humans tend to speak their fathers’ language, based on a stronger correlation of languages to paternal lineages (Y-chromosome) than to maternal lineages (mitochondria). To reassess these two competing hypotheses, we conducted a genetic–linguistic study of 34 modern Indo-European (IE) populations. In this study, genetic histories of paternal and maternal migrations in these IE populations were elucidated using phylogenetic networks of Y-chromosomal and mitochondrial DNA haplogroups, respectively. Unlike previous studies, we quantitatively characterized the languages based on lexical and phonemic systems separately. We showed that genetic and linguistic distances are significantly correlated with each other and that both are correlated with geographical distances among these populations. However, when controlling for geographical factors, only the correlation between the distances of paternal and lexical characteristics, and between those of maternal and phonemic characteristics, remained. These unbalanced correlations reconciled the two seemingly conflicting hypotheses.
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Affiliation(s)
- Menghan Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Hong-Xiang Zheng
- Human Phenome Institute, Fudan University, Shanghai 200438, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shi Yan
- Human Phenome Institute, Fudan University, Shanghai 200438, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Human Phenome Institute, Fudan University, Shanghai 200438, China
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai 200031, China
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15
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Oliveira S, Hübner A, Fehn AM, Aço T, Lages F, Pakendorf B, Stoneking M, Rocha J. The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola. Eur J Hum Genet 2018; 27:475-483. [PMID: 30467412 DOI: 10.1038/s41431-018-0304-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/25/2018] [Accepted: 11/01/2018] [Indexed: 11/09/2022] Open
Abstract
Southwestern Angola is a region characterized by contact between indigenous foragers and incoming food-producers, involving genetic and cultural exchanges between peoples speaking Kx'a, Khoe-Kwadi, and Bantu languages. Although present-day Bantu speakers share a patrilocal residence pattern and matrilineal principle of clan and group membership, a highly stratified social setting divides dominant pastoralists from marginalized groups that subsist on alternative strategies and have previously been thought to have pre-Bantu origins. Here, we compare new high-resolution sequence data from 2.3 Mb of the male-specific region of the Y chromosome (MSY) from 170 individuals with previously reported mitochondrial DNA (mtDNA) genomes, to investigate the population history of seven representative southwestern Angolan groups (Himba, Kuvale, Kwisi, Kwepe, Twa, Tjimba, !Xun), and to study the causes and consequences of sex-biased processes in their genetic variation. We found no clear link between the formerly Kwadi-speaking Kwepe and pre-Bantu eastern African migrants, and no pre-Bantu MSY lineages among Bantu-speaking groups, except for small amounts of "Khoisan" introgression. We therefore propose that irrespective of their subsistence strategies, all Bantu-speaking groups of the area share a male Bantu origin. Additionally, we show that in Bantu-speaking groups, the levels of among-group and between-group variation are higher for mtDNA than for MSY. These results, together with our previous demonstration that the matriclanic systems of southwestern Angolan Bantu groups are genealogically consistent, suggest that matrilineality strongly enhances both female population sizes and interpopulation mtDNA variation.
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Affiliation(s)
- Sandra Oliveira
- CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Anne-Maria Fehn
- CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, 4485-661, Vairão, Portugal.,Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, 00745, Jena, Germany.,Institute for African Studies, Goethe University, 60323, Frankfurt, Germany
| | - Teresa Aço
- Centro de Estudos do Deserto (CEDO), Namibe, Angola
| | - Fernanda Lages
- ISCED/Huíla-Instituto Superior de Ciências da Educação, Lubango, Angola
| | - Brigitte Pakendorf
- Laboratoire Dynamique du Langage, UMR5596, CNRS & Univ Lyon, 69007, Lyon, France
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Jorge Rocha
- CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,ISCED/Huíla-Instituto Superior de Ciências da Educação, Lubango, Angola
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16
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Bajić V, Barbieri C, Hübner A, Güldemann T, Naumann C, Gerlach L, Berthold F, Nakagawa H, Mpoloka SW, Roewer L, Purps J, Stoneking M, Pakendorf B. Genetic structure and sex-biased gene flow in the history of southern African populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:656-671. [PMID: 30192370 PMCID: PMC6667921 DOI: 10.1002/ajpa.23694] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 07/13/2018] [Accepted: 07/15/2018] [Indexed: 12/31/2022]
Abstract
Objectives We investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y‐chromosome haplogroup E1b1b (E‐M293) was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex‐biased gene flow in southern Africa. Materials and methods We analyzed previously published complete mtDNA genome sequences and ∼900 kb of NRY sequences from 23 populations from Namibia, Botswana, and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y‐linked STR loci for samples assigned to haplogroup E1b1b. Results Our results support an eastern African origin for Y‐chromosome haplogroup E1b1b (E‐M293); however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting more complex demographic events and/or changes in subsistence practices in this region. The Bantu expansion in southern Africa had a notable genetic impact and was probably a rapid, male‐dominated expansion. Our finding of a significant increase in the intensity of the sex‐biased gene flow from north to south may reflect changes in the social dynamics between Khoisan and Bantu groups over time. Conclusions Our study shows that the population history of southern Africa has been complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex‐biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.
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Affiliation(s)
- Vladimir Bajić
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Chiara Barbieri
- Department of Linguistic and Cultural Evolution, MPI for the Science of Human History, Jena, Germany.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Alexander Hübner
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Tom Güldemann
- Department of Linguistic and Cultural Evolution, MPI for the Science of Human History, Jena, Germany.,Institute of Asian and African Studies, Humboldt University, Berlin, Germany
| | - Christfried Naumann
- Institute of Asian and African Studies, Humboldt University, Berlin, Germany
| | - Linda Gerlach
- Department of Human Behavior, Ecology and Culture, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Falko Berthold
- Max Planck Research Group on Comparative Population Linguistics, MPI for Evolutionary Anthropology, Leipzig, Germary
| | - Hirosi Nakagawa
- Institute of Global Studies, Tokyo University of Foreign Studies, Tokyo, Japan
| | - Sununguko W Mpoloka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Lutz Roewer
- Charité - Universitätsmedizin Berlin, Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Berlin, Germany
| | - Josephine Purps
- Charité - Universitätsmedizin Berlin, Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Berlin, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Brigitte Pakendorf
- Laboratoire «Dynamique du Langage», CNRS & Université de Lyon, Lyon, France
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17
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Liu J, Wang Z, He G, Zhao X, Wang M, Luo T, Li C, Hou Y. Massively parallel sequencing of 124 SNPs included in the precision ID identity panel in three East Asian minority ethnicities. Forensic Sci Int Genet 2018; 35:141-148. [DOI: 10.1016/j.fsigen.2018.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/09/2018] [Accepted: 05/10/2018] [Indexed: 12/16/2022]
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18
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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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19
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D’Atanasio E, Trombetta B, Bonito M, Finocchio A, Di Vito G, Seghizzi M, Romano R, Russo G, Paganotti GM, Watson E, Coppa A, Anagnostou P, Dugoujon JM, Moral P, Sellitto D, Novelletto A, Cruciani F. The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages. Genome Biol 2018; 19:20. [PMID: 29433568 PMCID: PMC5809971 DOI: 10.1186/s13059-018-1393-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/19/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment. RESULTS In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. We identify 5,966 mutations, from which we extract 142 informative markers then genotyped in about 8,000 subjects from 145 African, Eurasian and African American populations. We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase. CONCLUSIONS Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.
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Affiliation(s)
- Eugenia D’Atanasio
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Maria Bonito
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Andrea Finocchio
- Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
| | - Genny Di Vito
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Mara Seghizzi
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Rita Romano
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Rome, Italy
| | - Gianluca Russo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Rome, Italy
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | | | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
- Istituto Italiano di Antropologia, Rome, Italy
| | - Jean-Michel Dugoujon
- Centre National de la Recherche Scientifique (CNRS), Université Toulouse-3–Paul-Sabatier, Toulouse, France
| | - Pedro Moral
- Department of Animal Biology-Anthropology, Biodiversity Research Institute, University of Barcelona, Barcelona, Spain
| | | | - Andrea Novelletto
- Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
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20
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Primativo G, Ottoni C, Biondi G, Serafino S, Martínez-Labarga C, Larmuseau MHD, Scardi M, Decorte R, Rickards O. Bight of Benin: a Maternal Perspective of Four Beninese Populations and their Genetic Implications on the American Populations of African Ancestry. Ann Hum Genet 2017; 81:78-90. [PMID: 28205221 DOI: 10.1111/ahg.12186] [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] [Received: 09/19/2016] [Accepted: 01/03/2017] [Indexed: 12/01/2022]
Abstract
The understanding of the first movements of the ancestral populations within the African continent is still unclear, particularly in West Africa, due to several factors that have shaped the African genetic pool across time. To improve the genetic representativeness of the Beninese population and to better understand the patterns of human settlement inside West Africa and the dynamics of peopling of the Democratic Republic of Benin, we analyzed the maternal genetic variation of 193 Beninese individuals belonging to Bariba, Berba, Dendi, and Fon populations. Results support the oral traditions indicating that the western neighbouring populations have been the ancestors of the first Beninese populations, and the extant genetic structure of the Beninese populations is most likely the result of admixture between populations from neighbouring countries and native people. The present findings highlight how the Beninese populations contributed to the gene pool of the extant populations of some American populations of African ancestry. This strengthens the hypothesis that the Bight of Benin was not only an assembly point for the slave trade during the Trans-Atlantic Slave Trade but also an important slave trapping area.
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Affiliation(s)
| | - Claudio Ottoni
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium
| | - Gianfranco Biondi
- Department of Clinical Medicine, Public Health, Life and Environment, University of L'Aquila, L'Aquila, Italy
| | - Sara Serafino
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.,Department of Public Health and Infectious Diseases, University of Rome Sapienza, Rome, Italy
| | | | - Maarten H D Larmuseau
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven - University of Leuven, Leuven, Belgium
| | - Michele Scardi
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Ronny Decorte
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium
| | - Olga Rickards
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
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21
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Forensic data and microvariant sequence characterization of 27 Y-STR loci analyzed in four Eastern African countries. Forensic Sci Int Genet 2017; 27:123-131. [DOI: 10.1016/j.fsigen.2016.12.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/19/2016] [Accepted: 12/29/2016] [Indexed: 11/17/2022]
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22
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Rowold DJ, Perez-Benedico D, Stojkovic O, Alfonso-Sanchez MA, Garcia-Bertrand R, Herrera RJ. On the Bantu expansion. Gene 2016; 593:48-57. [PMID: 27451076 DOI: 10.1016/j.gene.2016.07.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Abstract
Here we report the results of fine resolution Y chromosomal analyses (Y-SNP and Y-STR) of 267 Bantu-speaking males from three populations located in the southeast region of Africa. In an effort to determine the relative Y chromosomal affinities of these three genotyped populations, the findings are interpreted in the context of 74 geographically and ethnically targeted African reference populations representing four major ethno-linguistic groups (Afro-Asiatic, Niger Kordofanin, Khoisan and Pygmoid). In this investigation, we detected a general similarity in the Y chromosome lineages among the geographically dispersed Bantu-speaking populations suggesting a shared heritage and the shallow time depth of the Bantu Expansion. Also, micro-variations in the Bantu Y chromosomal composition across the continent highlight location-specific gene flow patterns with non-Bantu-speaking populations (Khoisan, Pygmy, Afro-Asiatic). Our Y chromosomal results also indicate that the three Bantu-speaking Southeast populations genotyped exhibit unique gene flow patterns involving Eurasian populations but fail to reveal a prevailing genetic affinity to East or Central African Bantu-speaking groups. In addition, the Y-SNP data underscores a longitudinal partitioning in sub-Sahara Africa of two R1b1 subgroups, R1b1-P25* (west) and R1b1a2-M269 (east). No evidence was observed linking the B2a haplogroup detected in the genotyped Southeast African Bantu-speaking populations to gene flow from contemporary Khoisan groups.
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Affiliation(s)
- Daine J Rowold
- Foundation for Applied Molecular Evolution, Gainesville, FL 32601, USA
| | | | - Oliver Stojkovic
- Institute of Forensic Medicine, School of Medicine, University of Belgrade, Belgrade, Serbia
| | | | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
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23
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Next generation sequencing of SNPs using the HID-Ion AmpliSeq™ Identity Panel on the Ion Torrent PGM™ platform. Forensic Sci Int Genet 2016; 25:73-84. [DOI: 10.1016/j.fsigen.2016.07.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 07/10/2016] [Accepted: 07/28/2016] [Indexed: 11/24/2022]
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24
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Creanza N, Feldman MW. Worldwide genetic and cultural change in human evolution. Curr Opin Genet Dev 2016; 41:85-92. [PMID: 27644074 DOI: 10.1016/j.gde.2016.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/04/2016] [Accepted: 08/19/2016] [Indexed: 01/04/2023]
Abstract
Both genetic variation and certain culturally transmitted phenotypes show geographic signatures of human demographic history. As a result of the human cultural predisposition to migrate to new areas, humans have adapted to a large number of different environments. Migration to new environments alters genetic selection pressures, and comparative genetic studies have pinpointed numerous likely targets of this selection. However, humans also exhibit many cultural adaptations to new environments, such as practices related to clothing, shelter, and food. Human culture interacts with genes and the environment in complex ways, and studying genes and culture together can deepen our understanding of human evolution.
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Affiliation(s)
- Nicole Creanza
- Department of Biology Stanford University, Gilbert Hall, 371 Serra Mall, Stanford, CA 94305, United States; Department of Biological Sciences, Vanderbilt University, 465 21st Ave. South, Nashville, TN 37212, United States.
| | - Marcus W Feldman
- Department of Biology Stanford University, Gilbert Hall, 371 Serra Mall, Stanford, CA 94305, United States
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25
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Shringarpure SS, Bustamante CD, Lange K, Alexander DH. Efficient analysis of large datasets and sex bias with ADMIXTURE. BMC Bioinformatics 2016; 17:218. [PMID: 27216439 PMCID: PMC4877806 DOI: 10.1186/s12859-016-1082-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A number of large genomic datasets are being generated for studies of human ancestry and diseases. The ADMIXTURE program is commonly used to infer individual ancestry from genomic data. RESULTS We describe two improvements to the ADMIXTURE software. The first enables ADMIXTURE to infer ancestry for a new set of individuals using cluster allele frequencies from a reference set of individuals. Using data from the 1000 Genomes Project, we show that this allows ADMIXTURE to infer ancestry for 10,920 individuals in a few hours (a 5 × speedup). This mode also allows ADMIXTURE to correctly estimate individual ancestry and allele frequencies from a set of related individuals. The second modification allows ADMIXTURE to correctly handle X-chromosome (and other haploid) data from both males and females. We demonstrate increased power to detect sex-biased admixture in African-American individuals from the 1000 Genomes project using this extension. CONCLUSIONS These modifications make ADMIXTURE more efficient and versatile, allowing users to extract more information from large genomic datasets.
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Affiliation(s)
| | | | - Kenneth Lange
- Department of Biomathematics, UCLA, Los Angeles, California, USA
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26
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Abstract
The serial founder model of modern human origins predicts that the phylogeny of ancestries exhibits bifurcating, tree-like behavior. Here, we tested this prediction using three methods designed to investigate gene flow in autosome-wide genotype data from 3,528 unrelated individuals from 163 global samples. Specifically, we investigated whether Cushitic ancestry has an East African or Middle Eastern origin. We found evidence for non-tree-like behavior in the form of four migration events. First, we found that Cushitic ancestry is a mixture of ancestries closely related to Arabian ancestry and Nilo-Saharan or Omotic ancestry. We found evidence for additional migration events in the histories of: 1) Indian and Arabian ancestries, 2) Kalash ancestry, and 3) Native American and Northern European ancestries. These findings, based on analysis of ancestry of present-day humans, reveal migration in the distant past and provide new insights into human history.
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27
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Barbieri C, Hübner A, Macholdt E, Ni S, Lippold S, Schröder R, Mpoloka SW, Purps J, Roewer L, Stoneking M, Pakendorf B. Refining the Y chromosome phylogeny with southern African sequences. Hum Genet 2016; 135:541-553. [PMID: 27043341 PMCID: PMC4835522 DOI: 10.1007/s00439-016-1651-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/18/2016] [Indexed: 12/04/2022]
Abstract
The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here, we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan- and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We identify new clades in the phylogeny, an older age for the root, and substantially older ages for some individual haplogroups. Furthermore, while haplogroup B2a is traditionally associated with the spread of Bantu speakers, we find that it probably also existed in Khoisan groups before the arrival of Bantu speakers. Finally, there is pronounced variation in branch length between major haplogroups; in particular, haplogroups associated with Bantu speakers have significantly longer branches. Technical artifacts cannot explain this branch length variation, which instead likely reflects aspects of the demographic history of Bantu speakers, such as recent population expansion and an older average paternal age. The influence of demographic factors on branch length variation has broader implications both for the human Y phylogeny and for similar analyses of other species.
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Affiliation(s)
- Chiara Barbieri
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Enrico Macholdt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Shengyu Ni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Sebastian Lippold
- 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
| | | | - Josephine Purps
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, 10559, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, 10559, Berlin, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Brigitte Pakendorf
- Dynamique du Langage, UMR5596, CNRS & Université Lyon 2, 69363, Lyon Cedex 07, France.
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28
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Messina F, Scano G, Contini I, Martínez-Labarga C, De Stefano GF, Rickards O. Linking between genetic structure and geographical distance: Study of the maternal gene pool in the Ethiopian population. Ann Hum Biol 2016; 44:53-69. [PMID: 26883569 DOI: 10.3109/03014460.2016.1155646] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background The correlation between genetics and geographical distance has already been examined through the study of the dispersion of human populations, especially in terms of uniparental genetic markers. Aim The present work characterises, at the level of the mitochondrial DNA (mtDNA), two new samples of Amhara and Oromo populations from Ethiopia to evaluate the possible pattern of distribution for mtDNA variation and to test the hypothesis of the Isolation-by-Distance (IBD) model among African, European and Middle-Eastern populations. Subjects and methods This study analysed 173 individuals belonging to two ethnic groups of Ethiopia, Amhara and Oromo, by assaying HVS-I and HVS-II of mtDNA D-loop and informative coding region SNPs of mtDNA. Results The analysis suggests a relationship between genetic and geographic distances, affirming that the mtDNA pool of Africa, Europe and the Middle East might be coherent with the IBD model. Moreover, the mtDNA gene pools of the Sub-Saharan African and Mediterranean populations were very different. Conclusion In this study the pattern of mtDNA distribution, beginning with the Ethiopian plateau, was tested in the IBD model. It could be affirmed that, on a continent scale, the mtDNA pool of Africa, Europe and the Middle East might fall under the IBD model.
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Affiliation(s)
- Francesco Messina
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Giuseppina Scano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Irene Contini
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Cristina Martínez-Labarga
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Gian Franco De Stefano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Olga Rickards
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
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Liebenberg L, L'Abbé EN, Stull KE. Population differences in the postcrania of modern South Africans and the implications for ancestry estimation. Forensic Sci Int 2015; 257:522-529. [PMID: 26584515 DOI: 10.1016/j.forsciint.2015.10.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/07/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
The cranium is widely recognized as the most important skeletal element to use when evaluating population differences and estimating ancestry. However, the cranium is not always intact or available for analysis, which emphasizes the need for postcranial alternatives. The purpose of this study was to quantify postcraniometric differences among South Africans that can be used to estimate ancestry. Thirty-nine standard measurements from 11 postcranial bones were collected from 360 modern black, white and coloured South Africans; the sex and ancestry distribution were equal. Group differences were explored with analysis of variance (ANOVA) and Tukey's honestly significant difference (HSD) test. Linear and flexible discriminant analysis (LDA and FDA, respectively) were conducted with bone models as well as numerous multivariate subsets to identify the model and method that yielded the highest correct classifications. Leave-one-out (LDA) and k-fold (k=10; FDA) cross-validation with equal priors were used for all models. ANOVA and Tukey's HSD results reveal statistically significant differences between at least two of the three groups for the majority of the variables, with varying degrees of group overlap. Bone models, which consisted of all measurements per bone, resulted in low accuracies that ranged from 46% to 63% (LDA) and 41% to 66% (FDA). In contrast, the multivariate subsets, which consisted of different variable combinations from all elements, achieved accuracies as high as 85% (LDA) and 87% (FDA). Thus, when using a multivariate approach, the postcranial skeleton can distinguish among three modern South African groups with high accuracy.
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Affiliation(s)
- Leandi Liebenberg
- Department of Anatomy, University of Pretoria, Arcadia, South Africa; Department of Basic Medical Sciences, University of the Free State, Bloemfontein, South Africa.
| | - Ericka N L'Abbé
- Department of Anatomy, University of Pretoria, Arcadia, South Africa
| | - Kyra E Stull
- Department of Anthropology, Idaho State University, Pocatello, ID, USA
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Gomes V, Pala M, Salas A, Álvarez-Iglesias V, Amorim A, Gómez-Carballa A, Carracedo Á, Clarke DJ, Hill C, Mormina M, Shaw MA, Dunne DW, Pereira R, Pereira V, Prata MJ, Sánchez-Diz P, Rito T, Soares P, Gusmão L, Richards MB. Mosaic maternal ancestry in the Great Lakes region of East Africa. Hum Genet 2015; 134:1013-27. [PMID: 26188410 DOI: 10.1007/s00439-015-1583-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 07/04/2015] [Indexed: 01/21/2023]
Abstract
The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.
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Affiliation(s)
- Verónica Gomes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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Pugach I, Stoneking M. Genome-wide insights into the genetic history of human populations. INVESTIGATIVE GENETICS 2015; 6:6. [PMID: 25834724 PMCID: PMC4381409 DOI: 10.1186/s13323-015-0024-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 03/05/2015] [Indexed: 12/21/2022]
Abstract
Although mtDNA and the non-recombining Y chromosome (NRY) studies continue to provide valuable insights into the genetic history of human populations, recent technical, methodological and computational advances and the increasing availability of large-scale, genome-wide data from contemporary human populations around the world promise to reveal new aspects, resolve finer points, and provide a more detailed look at our past demographic history. Genome-wide data are particularly useful for inferring migrations, admixture, and fine structure, as well as for estimating population divergence and admixture times and fluctuations in effective population sizes. In this review, we highlight some of the stories that have emerged from the analyses of genome-wide SNP genotyping data concerning the human history of Southern Africa, India, Oceania, Island South East Asia, Europe and the Americas and comment on possible future study directions. We also discuss advantages and drawbacks of using SNP-arrays, with a particular focus on the ascertainment bias, and ways to circumvent it.
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Affiliation(s)
- Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
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32
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Chimusa ER, Meintjies A, Tchanga M, Mulder N, Seoighe C, Soodyall H, Ramesar R. A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations. PLoS Genet 2015; 11:e1005052. [PMID: 25811879 PMCID: PMC4374865 DOI: 10.1371/journal.pgen.1005052] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 02/02/2015] [Indexed: 11/21/2022] Open
Abstract
We report a study of genome-wide, dense SNP (∼900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region. Genome-wide analysis of human populations is useful in shedding light on the evolutionary history of the human genome, with a wide range of applications from reconstructing past associations between different population histories to disease mapping. In this manuscript we report on the application of genome-wide data to southern African populations and the identification of genome-wide signatures of selection pre- and post-admixture. Several signals of selection, before and after admixture, were identified, some of which involved loci associated with human diseases, including malaria, influenza, tuberculosis and HIV/AIDS. These results may reflect adaptations of southern African populations to infectious diseases. Consistent with previous studies, this study highlights the significance of the San in the genetics of human populations, as they are distinct from the other populations in many respects i.e. haplotype structure, locations of recombination hotspots, copy number and population structure. Furthermore, our study demonstrates the admixture of the San, Bantu-speaking populations and populations of Eurasian ancestry in some of the southern and eastern African populations. It illustrates the value in correcting for this stratification in future genome-wide association studies, and suggests that a future admixture mapping in these populations would likely be warranted and successful.
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Affiliation(s)
- Emile R. Chimusa
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | - Ayton Meintjies
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Milaine Tchanga
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicola Mulder
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Rajkumar Ramesar
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- * E-mail:
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Kusuma P, Cox MP, Pierron D, Razafindrazaka H, Brucato N, Tonasso L, Suryadi HL, Letellier T, Sudoyo H, Ricaut FX. Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations. BMC Genomics 2015; 16:191. [PMID: 25880430 PMCID: PMC4373124 DOI: 10.1186/s12864-015-1394-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/24/2015] [Indexed: 11/18/2022] Open
Abstract
Background Linguistic, cultural and genetic characteristics of the Malagasy suggest that both Africans and Island Southeast Asians were involved in the colonization of Madagascar. Populations from the Indonesian archipelago played an especially important role because linguistic evidence suggests that the Malagasy language branches from the Southeast Barito language family of southern Borneo, Indonesia, with the closest language spoken today by the Ma’anyan. To test for a genetic link between Malagasy and these linguistically related Indonesian populations, we studied the Ma’anyan and other Indonesian ethnic groups (including the sea nomad Bajo) that, from their historical and linguistic contexts, may be modern descendants of the populations that helped enact the settlement of Madagascar. Result A combination of phylogeographic analysis of genetic distances, haplotype comparisons and inference of parental populations by linear optimization, using both maternal and paternal DNA lineages, suggests that Malagasy derive from multiple regional sources in Indonesia, with a focus on eastern Borneo, southern Sulawesi and the Lesser Sunda islands. Conclusion Settlement may have been mediated by ancient sea nomad movements because the linguistically closest population, Ma’anyan, has only subtle genetic connections to Malagasy, whereas genetic links with other sea nomads are more strongly supported. Our data hint at a more complex scenario for the Indonesian settlement of Madagascar than has previously been recognized. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1394-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pradiptajati Kusuma
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France. .,Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
| | - Denis Pierron
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
| | - Harilanto Razafindrazaka
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
| | - Nicolas Brucato
- Center for Linguistics, University of Leiden, Leiden, Netherlands.
| | - Laure Tonasso
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
| | - Helena Loa Suryadi
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
| | - Thierry Letellier
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia. .,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia.
| | - François-Xavier Ricaut
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
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Emery L, Magnaye K, Bigham A, Akey J, Bamshad M. Estimates of continental ancestry vary widely among individuals with the same mtDNA haplogroup. Am J Hum Genet 2015; 96:183-93. [PMID: 25620206 DOI: 10.1016/j.ajhg.2014.12.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 12/09/2014] [Indexed: 01/07/2023] Open
Abstract
The association between a geographical region and an mtDNA haplogroup(s) has provided the basis for using mtDNA haplogroups to infer an individual's place of origin and genetic ancestry. Although it is well known that ancestry inferences using mtDNA haplogroups and those using genome-wide markers are frequently discrepant, little empirical information exists on the magnitude and scope of such discrepancies between multiple mtDNA haplogroups and worldwide populations. We compared genetic-ancestry inferences made by mtDNA-haplogroup membership to those made by autosomal SNPs in ∼940 samples of the Human Genome Diversity Panel and recently admixed populations from the 1000 Genomes Project. Continental-ancestry proportions often varied widely among individuals sharing the same mtDNA haplogroup. For only half of mtDNA haplogroups did the highest average continental-ancestry proportion match the highest continental-ancestry proportion of a majority of individuals with that haplogroup. Prediction of an individual's mtDNA haplogroup from his or her continental-ancestry proportions was often incorrect. Collectively, these results indicate that for most individuals in the worldwide populations sampled, mtDNA-haplogroup membership provides limited information about either continental ancestry or continental region of origin.
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35
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Ralf A, van Oven M, Zhong K, Kayser M. Simultaneous analysis of hundreds of Y-chromosomal SNPs for high-resolution paternal lineage classification using targeted semiconductor sequencing. Hum Mutat 2014; 36:151-9. [PMID: 25338970 DOI: 10.1002/humu.22713] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/08/2014] [Indexed: 11/06/2022]
Abstract
SNPs from the non-recombining part of the human Y chromosome (Y-SNPs) are informative to classify paternal lineages in forensic, genealogical, anthropological, and evolutionary studies. Although thousands of Y-SNPs were identified thus far, previous Y-SNP multiplex tools target only dozens of markers simultaneously, thereby restricting the provided Y-haplogroup resolution and limiting their applications. Here, we overcome this shortcoming by introducing a high-resolution multiplex tool for parallel genotyping-by-sequencing of 530 Y-SNPs using the Ion Torrent PGM platform, which allows classification of 432 worldwide Y haplogroups. Contrary to previous Y-SNP multiplex tools, our approach covers branches of the entire Y tree, thereby maximizing the paternal lineage classification obtainable. We used a default DNA input amount of 10 ng per reaction but preliminary sensitivity testing revealed positive results from as little as 100 pg input DNA. Furthermore, we demonstrate that sample pooling using barcodes is feasible, allowing increased throughput for lower per-sample costs. In addition to the wetlab protocol, we provide a software tool for automated data quality control and haplogroup classification. The unique combination of ultra-high marker density and high sensitivity achievable from low amounts of potentially degraded DNA makes this new multiplex tool suitable for a wide range of Y-chromosome applications.
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Affiliation(s)
- Arwin Ralf
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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36
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Lippold S, Xu H, Ko A, Li M, Renaud G, Butthof A, Schröder R, Stoneking M. Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. INVESTIGATIVE GENETICS 2014; 5:13. [PMID: 25254093 PMCID: PMC4174254 DOI: 10.1186/2041-2223-5-13] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/22/2014] [Indexed: 02/07/2023]
Abstract
Background Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias. Results We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm. Conclusions The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.
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Affiliation(s)
- Sebastian Lippold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Hongyang Xu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany ; Department of Computational Genetics, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
| | - Albert Ko
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany ; Present address: Fondation Mérieux, 17 rue Bourgelat, Lyon 69002, France
| | - Gabriel Renaud
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Anne Butthof
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany ; Present address: Institute of Biochemistry, Faculty of Medicine, University of Leipzig, Leipzig D04103, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
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Marks SJ, Montinaro F, Levy H, Brisighelli F, Ferri G, Bertoncini S, Batini C, Busby GBJ, Arthur C, Mitchell P, Stewart BA, Oosthuizen O, Oosthuizen E, D'Amato ME, Davison S, Pascali V, Capelli C. Static and moving frontiers: the genetic landscape of Southern African Bantu-speaking populations. Mol Biol Evol 2014; 32:29-43. [PMID: 25223418 DOI: 10.1093/molbev/msu263] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A consensus on Bantu-speaking populations being genetically similar has emerged in the last few years, but the demographic scenarios associated with their dispersal are still a matter of debate. The frontier model proposed by archeologists postulates different degrees of interaction among incoming agropastoralist and resident foraging groups in the presence of "static" and "moving" frontiers. By combining mitochondrial DNA and Y chromosome data collected from several southern African populations, we show that Bantu-speaking populations from regions characterized by a moving frontier developing after a long-term static frontier have larger hunter-gatherer contributions than groups from areas where a static frontier was not followed by further spatial expansion. Differences in the female and male components suggest that the process of assimilation of the long-term resident groups into agropastoralist societies was gender biased. Our results show that the diffusion of Bantu languages and culture in Southern Africa was a process more complex than previously described and suggest that the admixture dynamics between farmers and foragers played an important role in shaping the current patterns of genetic diversity.
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Affiliation(s)
- Sarah J Marks
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Francesco Montinaro
- Department of Zoology, University of Oxford, Oxford, United Kingdom Institute of Legal Medicine, Catholic University, Rome, Italy
| | - Hila Levy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Gianmarco Ferri
- Dipartimento ad Attività Integrata di Laboratori, Anatomia Patologica, Medicina Legale, U.O. Struttura Complessa di Medicina Legale, Azienda Ospedaliero, Universitaria di Modena, Modena, Italy
| | | | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - George B J Busby
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Charles Arthur
- School of Archaeology, University of Oxford, Oxford, United Kingdom
| | - Peter Mitchell
- School of Archaeology, University of Oxford, Oxford, United Kingdom School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | | | - Maria Eugenia D'Amato
- Biotechnology Department, Forensic DNA Laboratory, University of the Western Cape, Bellville, South Africa
| | - Sean Davison
- Biotechnology Department, Forensic DNA Laboratory, University of the Western Cape, Bellville, South Africa
| | | | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Abstract
Sex-biased admixture has been observed in a wide variety of admixed populations. Genetic variation in sex chromosomes and functions of quantities computed from sex chromosomes and autosomes have often been examined to infer patterns of sex-biased admixture, typically using statistical approaches that do not mechanistically model the complexity of a sex-specific history of admixture. Here, expanding on a model of Verdu and Rosenberg (2011) that did not include sex specificity, we develop a model that mechanistically examines sex-specific admixture histories. Under the model, multiple source populations contribute to an admixed population, potentially with their male and female contributions varying over time. In an admixed population descended from two source groups, we derive the moments of the distribution of the autosomal admixture fraction from a specific source population as a function of sex-specific introgression parameters and time. Considering admixture processes that are constant in time, we demonstrate that surprisingly, although the mean autosomal admixture fraction from a specific source population does not reveal a sex bias in the admixture history, the variance of autosomal admixture is informative about sex bias. Specifically, the long-term variance decreases as the sex bias from a contributing source population increases. This result can be viewed as analogous to the reduction in effective population size for populations with an unequal number of breeding males and females. Our approach suggests that it may be possible to use the effect of sex-biased admixture on autosomal DNA to assist with methods for inference of the history of complex sex-biased admixture processes.
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Gomez F, Hirbo J, Tishkoff SA. Genetic variation and adaptation in Africa: implications for human evolution and disease. Cold Spring Harb Perspect Biol 2014; 6:a008524. [PMID: 24984772 DOI: 10.1101/cshperspect.a008524] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Because modern humans originated in Africa and have adapted to diverse environments, African populations have high levels of genetic and phenotypic diversity. Thus, genomic studies of diverse African ethnic groups are essential for understanding human evolutionary history and how this leads to differential disease risk in all humans. Comparative studies of genetic diversity within and between African ethnic groups creates an opportunity to reconstruct some of the earliest events in human population history and are useful for identifying patterns of genetic variation that have been influenced by recent natural selection. Here we describe what is currently known about genetic variation and evolutionary history of diverse African ethnic groups. We also describe examples of recent natural selection in African genomes and how these data are informative for understanding the frequency of many genetic traits, including those that cause disease susceptibility in African populations and populations of recent African descent.
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Affiliation(s)
- Felicia Gomez
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104 Hominid Paleobiology Doctoral Program and The Center for the Advanced Study of Hominid Paleobiology, Department of Anthropology, The George Washington University, Washington, D.C. 20052
| | - Jibril Hirbo
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Sarah A Tishkoff
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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40
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Barbieri C, Vicente M, Oliveira S, Bostoen K, Rocha J, Stoneking M, Pakendorf B. Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa. PLoS One 2014; 9:e99117. [PMID: 24901532 PMCID: PMC4047067 DOI: 10.1371/journal.pone.0099117] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/11/2014] [Indexed: 01/10/2023] Open
Abstract
Bantu speech communities expanded over large parts of sub-Saharan Africa within the last 4000–5000 years, reaching different parts of southern Africa 1200–2000 years ago. The Bantu languages subdivide in several major branches, with languages belonging to the Eastern and Western Bantu branches spreading over large parts of Central, Eastern, and Southern Africa. There is still debate whether this linguistic divide is correlated with a genetic distinction between Eastern and Western Bantu speakers. During their expansion, Bantu speakers would have come into contact with diverse local populations, such as the Khoisan hunter-gatherers and pastoralists of southern Africa, with whom they may have intermarried. In this study, we analyze complete mtDNA genome sequences from over 900 Bantu-speaking individuals from Angola, Zambia, Namibia, and Botswana to investigate the demographic processes at play during the last stages of the Bantu expansion. Our results show that most of these Bantu-speaking populations are genetically very homogenous, with no genetic division between speakers of Eastern and Western Bantu languages. Most of the mtDNA diversity in our dataset is due to different degrees of admixture with autochthonous populations. Only the pastoralist Himba and Herero stand out due to high frequencies of particular L3f and L3d lineages; the latter are also found in the neighboring Damara, who speak a Khoisan language and were foragers and small-stock herders. In contrast, the close cultural and linguistic relatives of the Herero and Himba, the Kuvale, are genetically similar to other Bantu-speakers. Nevertheless, as demonstrated by resampling tests, the genetic divergence of Herero, Himba, and Kuvale is compatible with a common shared ancestry with high levels of drift, while the similarity of the Herero, Himba, and Damara probably reflects admixture, as also suggested by linguistic analyses.
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Affiliation(s)
- Chiara Barbieri
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology, University of Bologna, Bologna, Italy
- * E-mail: (CB); (BP)
| | - Mário Vicente
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
- STAB VIDA, Investigação e Serviços em Ciências Biológicas, Lda, Oeiras, Portugal
| | - Sandra Oliveira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Koen Bostoen
- Department of African Languages and Cultures, Ghent University, KongoKing Research Group, Ghent, Belgium
- Université libre de Bruxelles, Faculté de Philosophie et Lettres, Brussels, Belgium
| | - Jorge Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Mark Stoneking
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Brigitte Pakendorf
- Laboratoire Dynamique du Langage, UMR5596, CNRS and Université Lyon Lumière 2, Lyon, France
- * E-mail: (CB); (BP)
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Veeramah KR, Hammer MF. The impact of whole-genome sequencing on the reconstruction of human population history. Nat Rev Genet 2014; 15:149-62. [PMID: 24492235 DOI: 10.1038/nrg3625] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Examining patterns of molecular genetic variation in both modern-day and ancient humans has proved to be a powerful approach to learn about our origins. Rapid advances in DNA sequencing technology have allowed us to characterize increasing amounts of genomic information. Although this clearly provides unprecedented power for inference, it also introduces more complexity into the way we use and interpret such data. Here, we review ongoing debates that have been influenced by improvements in our ability to sequence DNA and discuss some of the analytical challenges that need to be overcome in order to fully exploit the rich historical information that is contained in the entirety of the human genome.
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Affiliation(s)
- Krishna R Veeramah
- 1] Arizona Research Laboratories Division of Biotechnology, Room 231, Life Sciences South, 1007 East Lowell Street, University of Arizona, Tucson, Arizona 85721, USA. [2] Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Michael F Hammer
- Arizona Research Laboratories Division of Biotechnology, Room 231, Life Sciences South, 1007 East Lowell Street, University of Arizona, Tucson, Arizona 85721, USA
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42
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Natural Selection on Human Y Chromosomes. J Genet Genomics 2014; 41:47-52. [DOI: 10.1016/j.jgg.2014.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 01/23/2014] [Accepted: 01/23/2014] [Indexed: 12/24/2022]
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Affiliation(s)
- Tom Güldemann
- Humboldt University Berlin / Max Planck Institute for Evolutionary Anthropology Leipzig
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Capredon M, Brucato N, Tonasso L, Choesmel-Cadamuro V, Ricaut FX, Razafindrazaka H, Rakotondrabe AB, Ratolojanahary MA, Randriamarolaza LP, Champion B, Dugoujon JM. Tracing Arab-Islamic inheritance in Madagascar: study of the Y-chromosome and mitochondrial DNA in the Antemoro. PLoS One 2013; 8:e80932. [PMID: 24278350 PMCID: PMC3838347 DOI: 10.1371/journal.pone.0080932] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/08/2013] [Indexed: 11/19/2022] Open
Abstract
Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human genetic diversity in Madagascar.
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Affiliation(s)
- Mélanie Capredon
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
- Centre de recherche littéraire et historique de l’Océan Indien (CRLHOI), Département d’ethnologie, Université de La Réunion, Saint-Denis, France
- Department of Pediatrics, CHU Sainte Justine, Faculty of Medecine, University of Montreal, Quebec, Canada
- *
| | - Nicolas Brucato
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Laure Tonasso
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - Valérie Choesmel-Cadamuro
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - François-Xavier Ricaut
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - Harilanto Razafindrazaka
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | | | - Mamisoa Adelta Ratolojanahary
- Laboratoire d'Anthropologie Patrimoine -Transformations sociales- Transculturalité (LAP2T), Université Antananarivo, Antananarivo, Madagascar
| | - Louis-Paul Randriamarolaza
- Laboratoire d'Anthropologie Patrimoine -Transformations sociales- Transculturalité (LAP2T), Université Antananarivo, Antananarivo, Madagascar
| | - Bernard Champion
- Centre de recherche littéraire et historique de l’Océan Indien (CRLHOI), Département d’ethnologie, Université de La Réunion, Saint-Denis, France
| | - Jean-Michel Dugoujon
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
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Mona S, Mordret E, Veuille M, Tommaseo-Ponzetta M. Investigating sex-specific dynamics using uniparental markers: West New Guinea as a case study. Ecol Evol 2013; 3:2647-60. [PMID: 24567829 PMCID: PMC3930047 DOI: 10.1002/ece3.660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/27/2013] [Accepted: 05/31/2013] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial DNA (mtDNA) and Y chromosome (NRY) genetic markers have been often contrasted to investigate sex-specific dynamics. Traditionally, isolation by distance, intrapopulation genetic diversity and population differentiation are estimated from both markers and compared. Two possible sources of bias are often neglected. First, kilometric distances are frequently used as predictor of the connectivity between groups, hiding the role played by environmental features at a microgeographic scale. Second, the comparison of intrapopulation diversity and population differentiation between mtDNA and NRY is hampered by their different mutational mechanisms and rates. Here, we show how to account for these biases by analyzing from a different perspective a published dataset of eight West New Guinea (WNG) populations for which mtDNA control region sequences and seven linked NRY microsatellites had been typed. First, we modeled the connectivity among sampled populations by computing the number of days required to travel between groups. Then, we investigated the differences between the two sexes accounting for the molecular characteristics of the markers examined to obtain estimates on the product of the effective population size and the migration rate among demes (Nm). We achieved this goal by studying the shape of the gene genealogy at several sampling levels and using spatial explicit simulations. Both the direction and the rate of migration differ between male and females, with an Nm estimated to be >6 times higher in the latter under many evolutionary scenarios. We finally highlight the importance of applying metapopulation models when analyzing the genetic diversity of a species. We have applied the prediction of the sampling theory in a meta-population and we have corroborated our finding using spatial explicit simulations. Both approaches are fundamentally meant to deal with structured populations: we strongly believe in the importance of tacking structure into account when inferring the demographic history of a species.
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Affiliation(s)
- Stefano Mona
- Laboratoire Biologie intégrative des populations, Ecole Pratique des Hautes Etudes 46 rue de Lille, 75007, Paris, France ; CNRS UMR 7205, Muséum National d'Histoire Naturelle Rue Buffon, 75005, Paris, France
| | - Ernest Mordret
- Laboratoire Biologie intégrative des populations, Ecole Pratique des Hautes Etudes 46 rue de Lille, 75007, Paris, France ; CNRS UMR 7205, Muséum National d'Histoire Naturelle Rue Buffon, 75005, Paris, France
| | - Michel Veuille
- Laboratoire Biologie intégrative des populations, Ecole Pratique des Hautes Etudes 46 rue de Lille, 75007, Paris, France ; CNRS UMR 7205, Muséum National d'Histoire Naturelle Rue Buffon, 75005, Paris, France
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Roewer L, Nothnagel M, Gusmão L, Gomes V, González M, Corach D, Sala A, Alechine E, Palha T, Santos N, Ribeiro-Dos-Santos A, Geppert M, Willuweit S, Nagy M, Zweynert S, Baeta M, Núñez C, Martínez-Jarreta B, González-Andrade F, Fagundes de Carvalho E, da Silva DA, Builes JJ, Turbón D, Lopez Parra AM, Arroyo-Pardo E, Toscanini U, Borjas L, Barletta C, Ewart E, Santos S, Krawczak M. Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans. PLoS Genet 2013; 9:e1003460. [PMID: 23593040 PMCID: PMC3623769 DOI: 10.1371/journal.pgen.1003460] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 03/04/2013] [Indexed: 01/07/2023] Open
Abstract
Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans. In the largest population genetic study of South Americans to date, we analyzed the Y-chromosomal makeup of more than 1,000 male natives. We found that the male-specific genetic variation of Native Americans lacks any clear structure that could sensibly be related to their geographic and/or linguistic relationships. This finding is consistent with a rapid initial peopling of South America, followed by long periods of isolation in small tribal groups. The observed continent-wide decoupling of geography, spoken language, and genetics contrasts strikingly with previous reports of such correlation from many parts of Europe and Asia. Moreover, we identified a cluster of Native American founding lineages of Y chromosomes, called C-M217 (C3*), within a restricted area of Ecuador in North-Western South America. The same haplogroup occurs at high frequency in Central, East, and North East Asia, but is virtually absent from North (except Alaska) and Central America. Possible scenarios for the introduction of C-M217 (C3*) into Ecuador may thus include a coastal or trans-Pacific route, an idea also supported by occasional archeological evidence and the recent coalescence of the C3* haplotypes, estimated from our data to have occurred some 6,000 years ago.
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Affiliation(s)
- Lutz Roewer
- Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Pijpe J, de Voogt A, van Oven M, Henneman P, van der Gaag KJ, Kayser M, de Knijff P. Indian Ocean crossroads: human genetic origin and population structure in the Maldives. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 151:58-67. [PMID: 23526367 PMCID: PMC3652038 DOI: 10.1002/ajpa.22256] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 02/05/2013] [Indexed: 11/07/2022]
Abstract
The Maldives are an 850 km-long string of atolls located centrally in the northern Indian Ocean basin. Because of this geographic situation, the present-day Maldivian population has potential for uncovering genetic signatures of historic migration events in the region. We therefore studied autosomal DNA-, mitochondrial DNA-, and Y-chromosomal DNA markers in a representative sample of 141 unrelated Maldivians, with 119 from six major settlements. We found a total of 63 different mtDNA haplotypes that could be allocated to 29 mtDNA haplogroups, mostly within the M, R, and U clades. We found 66 different Y-STR haplotypes in 10 Y-chromosome haplogroups, predominantly H1, J2, L, R1a1a, and R2. Parental admixture analysis for mtDNA- and Y-haplogroup data indicates a strong genetic link between the Maldive Islands and mainland South Asia, and excludes significant gene flow from Southeast Asia. Paternal admixture from West Asia is detected, but cannot be distinguished from admixture from South Asia. Maternal admixture from West Asia is excluded. Within the Maldives, we find a subtle genetic substructure in all marker systems that is not directly related to geographic distance or linguistic dialect. We found reduced Y-STR diversity and reduced male-mediated gene flow between atolls, suggesting independent male founder effects for each atoll. Detected reduced female-mediated gene flow between atolls confirms a Maldives-specific history of matrilocality. In conclusion, our new genetic data agree with the commonly reported Maldivian ancestry in South Asia, but furthermore suggest multiple, independent immigration events and asymmetrical migration of females and males across the archipelago.
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Affiliation(s)
- Jeroen Pijpe
- Department of Human Genetics, Leiden University Medical Center, Postzone S5, 2300 RC Leiden, The Netherlands.
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Sanchez-Faddeev H, Pijpe J, van der Hulle T, Meij HJ, van der Gaag KJ, Slagboom PE, Westendorp RGJ, de Knijff P. The influence of clan structure on the genetic variation in a single Ghanaian village. Eur J Hum Genet 2013; 21:1134-9. [PMID: 23443025 PMCID: PMC3778349 DOI: 10.1038/ejhg.2013.12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 12/18/2012] [Accepted: 01/10/2013] [Indexed: 11/09/2022] Open
Abstract
Socioeconomic and cultural factors are thought to have an important role in influencing human population genetic structure. To explain such population structure differences, most studies analyse genetic differences among widely dispersed human populations. In contrast, we have studied the genetic structure of an ethnic group occupying a single village in north-eastern Ghana. We found a markedly skewed male population substructure because of an almost complete lack of male gene flow among Bimoba clans in this village. We also observed a deep male substructure within one of the clans in this village. Among all males, we observed only three Y-single-nucleotide polymorphism (SNP) haplogroups: E1b1a*-M2, E1b1a7a*-U174 and E1b1a8a*-U209, P277, P278. In contrast to the marked Y-chromosomal substructure, mitochondrial DNA HVS-1 sequence variation and autosomal short-tandem repeats variation patterns indicate high genetic diversities and a virtually random female-mediated gene flow among clans. On the extreme micro-geographical scale of this single Bimoba village, correspondence between the Y-chromosome lineages and clan membership could be due to the combined effects of the strict patrilocal and patrilineal structure. If translated to larger geographic scales, our results would imply that the extent of variation in uniparentally inherited genetic markers, which are typically associated with historical migration on a continental scale, could equally likely be the result of many small and different cumulative effects of social factors such as clan membership that act at a local scale. Such local scale effects should therefore be considered in genetic studies, especially those that use uniparental markers, before making inferences about human history at large.
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Affiliation(s)
- Hernando Sanchez-Faddeev
- 1] Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands [2] Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
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Batai K, Babrowski KB, Arroyo JP, Kusimba CM, Williams SR. Mitochondrial DNA diversity in two ethnic groups in southeastern Kenya: perspectives from the northeastern periphery of the Bantu expansion. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 150:482-91. [PMID: 23382080 DOI: 10.1002/ajpa.22227] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 12/14/2012] [Indexed: 12/18/2022]
Abstract
The Bantu languages are widely distributed throughout sub-Saharan Africa. Genetic research supports linguists and historians who argue that migration played an important role in the spread of this language family, but the genetic data also indicates a more complex process involving substantial gene flow with resident populations. In order to understand the Bantu expansion process in east Africa, mtDNA hypervariable region I variation in 352 individuals from the Taita and Mijikenda ethnic groups was analyzed, and we evaluated the interactions that took place between the Bantu- and non-Bantu-speaking populations in east Africa. The Taita and Mijikenda are Bantu-speaking agropastoralists from southeastern Kenya, at least some of whose ancestors probably migrated into the area as part of Bantu migrations that began around 3,000 BCE. Our analyses indicate that they show some distinctive differences that reflect their unique cultural histories. The Taita are genetically more diverse than the Mijikenda with larger estimates of genetic diversity. The Taita cluster with other east African groups, having high frequencies of haplogroups from that region, while the Mijikenda have high frequencies of central African haplogroups and cluster more closely with central African Bantu-speaking groups. The non-Bantu speakers who lived in southeastern Kenya before Bantu speaking groups arrived were at least partially incorporated into what are now Bantu-speaking Taita groups. In contrast, gene flow from non-Bantu speakers into the Mijikenda was more limited. These results suggest a more complex demographic history where the nature of Bantu and non-Bantu interactions varied throughout the area.
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Affiliation(s)
- Ken Batai
- Cancer Education and Career Development Program, Institute for Health Research and Policy, University of Illinois at Chicago, Chicago, IL 60607, USA.
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Badro DA, Douaihy B, Haber M, Youhanna SC, Salloum A, Ghassibe-Sabbagh M, Johnsrud B, Khazen G, Matisoo-Smith E, Soria-Hernanz DF, Wells RS, Tyler-Smith C, Platt DE, Zalloua PA. Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern Middle Eastern populations with European and African populations. PLoS One 2013; 8:e54616. [PMID: 23382925 PMCID: PMC3559847 DOI: 10.1371/journal.pone.0054616] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 12/13/2012] [Indexed: 11/21/2022] Open
Abstract
The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.
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Affiliation(s)
| | | | - Marc Haber
- The Lebanese American University, Chouran, Beirut, Lebanon
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | | | - Brian Johnsrud
- Modern Thought and Literature, Stanford University, Stanford, California, United States of America
| | - Georges Khazen
- The Lebanese American University, Chouran, Beirut, Lebanon
| | - Elizabeth Matisoo-Smith
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand
| | - David F. Soria-Hernanz
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
| | - R. Spencer Wells
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Daniel E. Platt
- Computational Biology Centre, IBM TJ Watson Research Centre, Yorktown Heights, New York, United States of America
| | - Pierre A. Zalloua
- The Lebanese American University, Chouran, Beirut, Lebanon
- Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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