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Tallman S, Sungo MDD, Saranga S, Beleza S. Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations. Nat Commun 2023; 14:7967. [PMID: 38042927 PMCID: PMC10693643 DOI: 10.1038/s41467-023-43717-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
As the continent of origin for our species, Africa harbours the highest levels of diversity anywhere on Earth. However, many regions of Africa remain under-sampled genetically. Here we present 350 whole genomes from Angola and Mozambique belonging to ten Bantu ethnolinguistic groups, enabling the construction of a reference variation catalogue including 2.9 million novel SNPs. We investigate the emergence of Bantu speaker population structure, admixture involving migrations across sub-Saharan Africa and model the demographic histories of Angolan and Mozambican Bantu speakers. Our results bring together concordant views from genomics, archaeology, and linguistics to paint an updated view of the complexity of the Bantu Expansion. Moreover, we generate reference panels that better represents the diversity of African populations involved in the trans-Atlantic slave trade, improving imputation accuracy in African Americans and Brazilians. We anticipate that our collection of genomes will form the foundation for future African genomic healthcare initiatives.
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Affiliation(s)
- Sam Tallman
- University of Leicester, Department of Genetics & Genome Biology, University Road, Leicester, LE1 7RH, UK
- Genomics England, 1 Canada Square, London, E14 5AB, UK
| | | | - Sílvio Saranga
- Universidade Pedagógica, Avenida Eduardo Mondlane, CP 2107, Maputo, Mozambique
| | - Sandra Beleza
- University of Leicester, Department of Genetics & Genome Biology, University Road, Leicester, LE1 7RH, UK.
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2
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Hammarén R, Goldstein ST, Schlebusch CM. Eurasian back-migration into Northeast Africa was a complex and multifaceted process. PLoS One 2023; 18:e0290423. [PMID: 37939042 PMCID: PMC10631636 DOI: 10.1371/journal.pone.0290423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 08/08/2023] [Indexed: 11/10/2023] Open
Abstract
Recent studies have identified Northeast Africa as an important area for human movements during the Holocene. Eurasian populations have moved back into Northeastern Africa and contributed to the genetic composition of its people. By gathering the largest reference dataset to date of Northeast, North, and East African as well as Middle Eastern populations, we give new depth to our knowledge of Northeast African demographic history. By employing local ancestry methods, we isolated the Non-African parts of modern-day Northeast African genomes and identified the best putative source populations. Egyptians and Sudanese Copts bore most similarities to Levantine populations whilst other populations in the region generally had predominantly genetic contributions from the Arabian peninsula rather than Levantine populations for their Non-African genetic component. We also date admixture events and investigated which factors influenced the date of admixture and find that major linguistic families were associated with the date of Eurasian admixture. Taken as a whole we detect complex patterns of admixture and diverse origins of Eurasian admixture in Northeast African populations of today.
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Affiliation(s)
- Rickard Hammarén
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Steven T. Goldstein
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Carina M. Schlebusch
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa
- SciLifeLab, Uppsala, Sweden
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3
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Suarez-Trujillo F, El-Safi S, Juarez I, Palacio-Gruber J, Sanchez-Orta A, Martin-Villa JM, Arnaiz-Villena A. HLA alleles and haplotypes in Sudanese population and their relationship with Mediterraneans. Sci Rep 2023; 13:16203. [PMID: 37758772 PMCID: PMC10533553 DOI: 10.1038/s41598-023-40173-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/06/2023] [Indexed: 09/29/2023] Open
Abstract
The contribution of migrated people from once green Sahara (about 10,000-6000 years BC) towards Mediterranean area had probably a double effect: both genetic and cultural connections have been described between Western Europe and North Africa. Sudanese populations from different ethnicities have been studied for HLA-A, -B, -DRB1 and -DQB1 antigens by a standard microlymphotoxicity method. Results found show that Nubians are genetically related with African Sub-Saharan populations and distant from other Sudanese tribes, who are closer to Mediterranean populations than to Sub-Saharan ones. This is concordant with other authors and meta-analysis data. Our present work is, to our knowledge, the first and only one HLA research that studies Sudanese people according to different Sudan ethnic groups: samples were collected before Sudan partition between North and South. A prehistoric genetic and peoples exchange between Africa and the Mediterranean basin may be observed and is supported with the results obtained in this Sudanese HLA study. However, demic diffusion model of agriculture and other anthropological traits from Middle East to West Europe/Maghreb do not exist: a more detailed Sahel and North African countries ancient and recent admixture studies are also being carried out which may clearer explain pastoralists/agriculture innovations origins in Eurafrican Mediterranean and Atlantic façade.
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Affiliation(s)
- Fabio Suarez-Trujillo
- Department of Immunology, School of Medicine, University Complutense, Pabellón 5, Planta 4. Avda. Complutense S/N, 28040, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | - Ignacio Juarez
- Department of Immunology, School of Medicine, University Complutense, Pabellón 5, Planta 4. Avda. Complutense S/N, 28040, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - José Palacio-Gruber
- Department of Immunology, School of Medicine, University Complutense, Pabellón 5, Planta 4. Avda. Complutense S/N, 28040, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Alejandro Sanchez-Orta
- Department of Immunology, School of Medicine, University Complutense, Pabellón 5, Planta 4. Avda. Complutense S/N, 28040, Madrid, Spain
| | - José Manuel Martin-Villa
- Department of Immunology, School of Medicine, University Complutense, Pabellón 5, Planta 4. Avda. Complutense S/N, 28040, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Antonio Arnaiz-Villena
- Department of Immunology, School of Medicine, University Complutense, Pabellón 5, Planta 4. Avda. Complutense S/N, 28040, Madrid, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
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4
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Yahia A, Hamed AAA, Mohamed IN, Elseed MA, Salih MA, El-Sadig SM, Siddig HE, Nasreldien AEM, Abdullah MA, Elzubair M, Omer FY, Bakhiet AM, Abubaker R, Abozar F, Adil R, Emad S, Musallam MA, Eltazi IZM, Omer Z, Malik H, Mohamed MOE, Elhassan AA, Mohamed EOE, Ahmed AKMA, Ahmed EAA, Eltaraifee E, Hussein BK, Abd Allah ASI, Salah L, Nimir M, Tag Elseed OM, Elhassan TEA, Elbashier A, Alfadul ESA, Fadul M, Ali KF, Taha SOMA, Bushara EE, Amin M, Koko M, Ibrahim ME, Ahmed AE, Elsayed LEO, Stevanin G. Clinical phenotyping and genetic diagnosis of a large cohort of Sudanese families with hereditary spinocerebellar degenerations. Eur J Hum Genet 2023:10.1038/s41431-023-01344-6. [PMID: 37012327 DOI: 10.1038/s41431-023-01344-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/12/2023] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
Hereditary spinocerebellar degenerations (SCDs) is an umbrella term that covers a group of monogenic conditions that share common pathogenic mechanisms and include hereditary spastic paraplegia (HSP), cerebellar ataxia, and spinocerebellar ataxia. They are often complicated with axonal neuropathy and/or intellectual impairment and overlap with many neurological conditions, including neurodevelopmental disorders. More than 200 genes and loci inherited through all modes of Mendelian inheritance are known. Autosomal recessive inheritance predominates in consanguineous communities; however, autosomal dominant and X-linked inheritance can also occur. Sudan is inhabited by genetically diverse populations, yet it has high consanguinity rates. We used next-generation sequencing, genotyping, bioinformatics analysis, and candidate gene approaches to study 90 affected patients from 38 unrelated Sudanese families segregating multiple forms of SCDs. The age-at-onset in our cohort ranged from birth to 35 years; however, most patients manifested childhood-onset diseases (the mean and median ages at onset were 7.5 and 3 years, respectively). We reached the genetic diagnosis in 63% and possibly up to 73% of the studied families when considering variants of unknown significance. Combining the present data with our previous analysis of 25 Sudanese HSP families, the success rate reached 52-59% (31-35/59 families). In this article we report candidate variants in genes previously known to be associated with SCDs or other phenotypically related monogenic disorders. We also highlight the genetic and clinical heterogeneity of SCDs in Sudan, as we did not identify a major causative gene in our cohort, and the potential for discovering novel SCD genes in this population.
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Affiliation(s)
- Ashraf Yahia
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan.
- Paris Brain Institute - ICM, CNRS UMR7225, INSERM 1127, Sorbonne University, F-75000, Paris, France.
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden.
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Solna, Sweden.
| | - Ahlam A A Hamed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Inaam N Mohamed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Maha A Elseed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- College of Medicine, AlMughtaribeen University, Khartoum, Sudan
| | | | | | - Ali Elsir Musa Nasreldien
- Pediatric Neurology Department, Red Cross Memorial Children Hospital (RCWMCH), University of Cape Town (UCT), Cape Town, South Africa
| | | | - Maha Elzubair
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | | | | | - Rayan Abubaker
- Sudanese Neurogenetics Research group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- National University Biomedical Research Institute, National University, Khartoum, Sudan
| | - Fatima Abozar
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rawaa Adil
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Sara Emad
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | | | - Isra Z M Eltazi
- Neurology Department, Hamad Medical Corporation, Doha, Qatar
| | - Zulfa Omer
- Department of Hematology and Medical Oncology, University of Cincinnati Medical Center, Ohio, USA
| | - Hiba Malik
- Department of Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Mayada O E Mohamed
- Division of Emergency Medicine, Sudan Medical Specialization Board, Khartoum, Sudan
| | - Ali A Elhassan
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | | | - Ahmed K M A Ahmed
- Department of Molecular Neuroscience, Graduate school of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, 3-1, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | | | | | - Bidour K Hussein
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | | | - Lina Salah
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mohamed Nimir
- Department of Pathology, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK
- Warwick Medical School, University of Warwick, Coventry, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | | | | | | | | | - Moneeb Fadul
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Khalil F Ali
- Department of Cardiology, Royal Derby Hospital, Derby, UK
| | | | | | - Mutaz Amin
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Al-Neelain University, Khartoum, Sudan
| | - Mahmoud Koko
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | | | - Ammar E Ahmed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Liena E O Elsayed
- Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, P.O.Box 84428, Riyadh, 11671, Saudi Arabia
| | - Giovanni Stevanin
- Paris Brain Institute - ICM, CNRS UMR7225, INSERM 1127, Sorbonne University, F-75000, Paris, France.
- Univ. Bordeaux, CNRS, INCIA, UMR 5287, F-33000, Bordeaux, France.
- EPHE, PSL Research university, CNRS, INCIA, UMR 5287, F-75000, Paris, France.
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5
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Bird N, Ormond L, Awah P, Caldwell EF, Connell B, Elamin M, Fadlelmola FM, Matthew Fomine FL, López S, MacEachern S, Moñino Y, Morris S, Näsänen-Gilmore P, Nketsia V NK, Veeramah K, Weale ME, Zeitlyn D, Thomas MG, Bradman N, Hellenthal G. Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture. SCIENCE ADVANCES 2023; 9:eabq2616. [PMID: 36989356 PMCID: PMC10058250 DOI: 10.1126/sciadv.abq2616] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Previous studies have highlighted how African genomes have been shaped by a complex series of historical events. Despite this, genome-wide data have only been obtained from a small proportion of present-day ethnolinguistic groups. By analyzing new autosomal genetic variation data of 1333 individuals from over 150 ethnic groups from Cameroon, Republic of the Congo, Ghana, Nigeria, and Sudan, we demonstrate a previously underappreciated fine-scale level of genetic structure within these countries, for example, correlating with historical polities in western Cameroon. By comparing genetic variation patterns among populations, we infer that many northern Cameroonian and Sudanese groups share genetic links with multiple geographically disparate populations, likely resulting from long-distance migrations. In Ghana and Nigeria, we infer signatures of intermixing dated to over 2000 years ago, corresponding to reports of environmental transformations possibly related to climate change. We also infer recent intermixing signals in multiple African populations, including Congolese, that likely relate to the expansions of Bantu language-speaking peoples.
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Affiliation(s)
- Nancy Bird
- Department of Genetics, Evolution and Environment, University College London Genetics Institute (UGI), University College London, London, UK
| | - Louise Ormond
- Department of Genetics, Evolution and Environment, University College London Genetics Institute (UGI), University College London, London, UK
| | - Paschal Awah
- Faculty of Arts, Letters and Social Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | | | - Bruce Connell
- Linguistics and Language Studies Program, York University, Toronto, Ontario, Canada
| | | | - Faisal M. Fadlelmola
- Kush Centre for Genomics and Biomedical Informatics, Biotechnology Perspectives Organisation, Khartoum, Sudan
| | | | | | - Scott MacEachern
- Division of Social Science, Duke Kunshan University, Kunshan, China
| | | | - Sam Morris
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Pieta Näsänen-Gilmore
- Tampere Centre for Child, Adolescent and Maternal Health Research: Global Health Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department for Health Promotion, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Krishna Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | | | - David Zeitlyn
- School of Anthropology and Museum Ethnography, University of Oxford, Oxford, UK
| | - Mark G. Thomas
- Department of Genetics, Evolution and Environment, University College London Genetics Institute (UGI), University College London, London, UK
| | | | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London Genetics Institute (UGI), University College London, London, UK
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6
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Černý V, Priehodová E, Fortes-Lima C. A Population Genetic Perspective on Subsistence Systems in the Sahel/Savannah Belt of Africa and the Historical Role of Pastoralism. Genes (Basel) 2023; 14:genes14030758. [PMID: 36981029 PMCID: PMC10048103 DOI: 10.3390/genes14030758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/26/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
This review focuses on the Sahel/Savannah belt, a large region of Africa where two alternative subsistence systems (pastoralism and agriculture), nowadays, interact. It is a long-standing question whether the pastoralists became isolated here from other populations after cattle began to spread into Africa (~8 thousand years ago, kya) or, rather, began to merge with other populations, such as agropastoralists, after the domestication of sorghum and pearl millet (~5 kya) and with the subsequent spread of agriculture. If we look at lactase persistence, a trait closely associated with pastoral lifestyle, we see that its variants in current pastoralists distinguish them from their farmer neighbours. Most other (mostly neutral) genetic polymorphisms do not, however, indicate such clear differentiation between these groups; they suggest a common origin and/or an extensive gene flow. Genetic affinity and ecological symbiosis between the two subsistence systems can help us better understand the population history of this African region. In this review, we show that genomic datasets of modern Sahel/Savannah belt populations properly collected in local populations can complement the still insufficient archaeological research of this region, especially when dealing with the prehistory of mobile populations with perishable material culture and therefore precarious archaeological visibility.
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Affiliation(s)
- Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Letenská 1, 118 01 Prague, Czech Republic
| | - Edita Priehodová
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Letenská 1, 118 01 Prague, Czech Republic
| | - Cesar Fortes-Lima
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
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7
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Fortes-Lima C, Tříska P, Čížková M, Podgorná E, Diallo MY, Schlebusch CM, Černý V. Demographic and Selection Histories of Populations Across the Sahel/Savannah Belt. Mol Biol Evol 2022; 39:6731090. [PMID: 36173804 PMCID: PMC9582163 DOI: 10.1093/molbev/msac209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Sahel/Savannah belt harbors diverse populations with different demographic histories and different subsistence patterns. However, populations from this large African region are notably under-represented in genomic research. To investigate the population structure and adaptation history of populations from the Sahel/Savannah space, we generated dense genome-wide genotype data of 327 individuals-comprising 14 ethnolinguistic groups, including 10 previously unsampled populations. Our results highlight fine-scale population structure and complex patterns of admixture, particularly in Fulani groups and Arabic-speaking populations. Among all studied Sahelian populations, only the Rashaayda Arabic-speaking population from eastern Sudan shows a lack of gene flow from African groups, which is consistent with the short history of this population in the African continent. They are recent migrants from Saudi Arabia with evidence of strong genetic isolation during the last few generations and a strong demographic bottleneck. This population also presents a strong selection signal in a genomic region around the CNR1 gene associated with substance dependence and chronic stress. In Western Sahelian populations, signatures of selection were detected in several other genetic regions, including pathways associated with lactase persistence, immune response, and malaria resistance. Taken together, these findings refine our current knowledge of genetic diversity, population structure, migration, admixture and adaptation of human populations in the Sahel/Savannah belt and contribute to our understanding of human history and health.
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Affiliation(s)
- Cesar Fortes-Lima
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Petr Tříska
- Archaeogenetics Laboratory, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Čížková
- Archaeogenetics Laboratory, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eliška Podgorná
- Archaeogenetics Laboratory, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Mame Yoro Diallo
- Archaeogenetics Laboratory, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic,Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
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8
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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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9
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Oill AMT, Handley C, Howell EK, Stone AC, Mathew S, Wilson MA. Genomic analysis reveals geography rather than culture as the predominant factor shaping genetic variation in northern Kenyan human populations. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 178:488-503. [PMID: 36790743 PMCID: PMC9949739 DOI: 10.1002/ajpa.24521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/04/2022] [Accepted: 02/21/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVES The aim of this study was to characterize the genetic relationships within and among four neighboring ethnolinguistic groups in northern Kenya in light of cultural relationships to understand the extent to which geography and culture shape patterns of genetic variation. MATERIALS AND METHODS We collected DNA and demographic information pertaining to aspects of social identity and heritage from 572 individuals across the Turkana, Samburu, Waso Borana, and Rendille of northern Kenya. We sampled individuals across a total of nine clans from these four groups and, additionally, three territorial sections within the Turkana and successfully genotyped 376 individuals. RESULTS Here we report that geography predominately shapes genetic variation within and among human groups in northern Kenya. We observed a clinal pattern of genetic variation that mirrors the overall geographic distribution of the individuals we sampled. We also found relatively higher rates of intermarriage between the Rendille and Samburu and evidence of gene flow between them that reflect these higher rates of intermarriage. Among the Turkana, we observed strong recent genetic substructuring based on territorial section affiliation. Within ethnolinguistic groups, we found that Y chromosome haplotypes do not consistently cluster by natal clan affiliation. Finally, we found that sampled populations that are geographically closer have lower genetic differentiation, and that cultural similarity does not predict genetic similarity as a whole across these northern Kenyan populations. DISCUSSION Overall, the results from this study highlight the importance of geography, even on a local geographic scale, in shaping observed patterns of genetic variation in human populations.
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Affiliation(s)
- Angela M. Taravella Oill
- School of Life Sciences, Arizona State University, Tempe, AZ 85287 USA,Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287 USA
| | - Carla Handley
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287 USA
| | - Emma K. Howell
- School of Life Sciences, Arizona State University, Tempe, AZ 85287 USA,Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287 USA
| | - Anne C. Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287 USA,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287 USA,Institute of Human Origins, Arizona State University, Tempe, AZ 85287, USA
| | - Sarah Mathew
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287 USA,Institute of Human Origins, Arizona State University, Tempe, AZ 85287, USA,Co-corresponding authors
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ 85287 USA,Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287 USA,Co-corresponding authors
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10
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Gopalan S, Berl REW, Myrick JW, Garfield ZH, Reynolds AW, Bafens BK, Belbin G, Mastoras M, Williams C, Daya M, Negash AN, Feldman MW, Hewlett BS, Henn BM. Hunter-gatherer genomes reveal diverse demographic trajectories during the rise of farming in Eastern Africa. Curr Biol 2022; 32:1852-1860.e5. [PMID: 35271793 PMCID: PMC9050894 DOI: 10.1016/j.cub.2022.02.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 05/12/2021] [Accepted: 02/16/2022] [Indexed: 12/31/2022]
Abstract
The fate of hunting and gathering populations following the rise of agriculture and pastoralism remains a topic of debate in the study of human prehistory. Studies of ancient and modern genomes have found that autochthonous groups were largely replaced by expanding farmer populations with varying levels of gene flow, a characterization that is influenced by the almost universal focus on the European Neolithic.1-5 We sought to understand the demographic impact of an ongoing cultural transition to farming in Southwest Ethiopia, one of the last regions in Africa to experience such shifts.6 Importantly, Southwest Ethiopia is home to several of the world's remaining hunter-gatherer groups, including the Chabu people, who are currently transitioning away from their traditional mode of subsistence.7 We generated genome-wide data from the Chabu and four neighboring populations, the Majang, Shekkacho, Bench, and Sheko, to characterize their genetic ancestry and estimate their effective population sizes over the last 60 generations. We show that the Chabu are a distinct population closely related to ancient people who occupied Southwest Ethiopia >4,500 years ago. Furthermore, the Chabu are undergoing a severe population bottleneck, which began approximately 1,400 years ago. By analyzing eleven Eastern African populations, we find evidence for divergent demographic trajectories among hunter-gatherer-descendant groups. Our results illustrate that although foragers respond to encroaching agriculture and pastoralism with multiple strategies, including cultural adoption of agropastoralism, gene flow, and economic specialization, they often face population decline.
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Affiliation(s)
- Shyamalika Gopalan
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA; Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Richard E W Berl
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA; Department of Human Dimensions of Natural Resources, Colorado State University, Fort Collins, CO 80523, USA
| | - Justin W Myrick
- Department of Anthropology, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Zachary H Garfield
- Department of Anthropology, Washington State University, Vancouver, WA 98686, USA; Institute for Advanced Study in Toulouse, Université Toulouse, Toulouse 31080, France
| | - Austin W Reynolds
- Department of Anthropology, University of California, Davis, Davis, CA 95616, USA; Department of Anthropology, Baylor University, Waco, TX 76798, USA
| | - Barnabas K Bafens
- Diaspora and Protocol Affairs Office, Bench Sheko Zone Administration, Mizan, Ethiopia
| | - Gillian Belbin
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mira Mastoras
- UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Cole Williams
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michelle Daya
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Akmel N Negash
- Department of Anthropology, Hawassa University, Hawassa, SNNPR, Ethiopia
| | - Marcus W Feldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Barry S Hewlett
- Department of Anthropology, Washington State University, Vancouver, WA 98686, USA.
| | - Brenna M Henn
- Department of Anthropology, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA.
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11
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Sirak KA, Fernandes DM, Lipson M, Mallick S, Mah M, Olalde I, Ringbauer H, Rohland N, Hadden CS, Harney É, Adamski N, Bernardos R, Broomandkhoshbacht N, Callan K, Ferry M, Lawson AM, Michel M, Oppenheimer J, Stewardson K, Zalzala F, Patterson N, Pinhasi R, Thompson JC, Van Gerven D, Reich D. Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia. Nat Commun 2021; 12:7283. [PMID: 34907168 PMCID: PMC8671435 DOI: 10.1038/s41467-021-27356-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 11/16/2021] [Indexed: 12/23/2022] Open
Abstract
Relatively little is known about Nubia's genetic landscape prior to the influence of the Islamic migrations that began in the late 1st millennium CE. Here, we increase the number of ancient individuals with genome-level data from the Nile Valley from three to 69, reporting data for 66 individuals from two cemeteries at the Christian Period (~650-1000 CE) site of Kulubnarti, where multiple lines of evidence suggest social stratification. The Kulubnarti Nubians had ~43% Nilotic-related ancestry (individual variation between ~36-54%) with the remaining ancestry consistent with being introduced through Egypt and ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The Kulubnarti gene pool - shaped over a millennium - harbors disproportionately female-associated West Eurasian-related ancestry. Genetic similarity among individuals from the two cemeteries supports a hypothesis of social division without genetic distinction. Seven pairs of inter-cemetery relatives suggest fluidity between cemetery groups. Present-day Nubians are not directly descended from the Kulubnarti Nubians, attesting to additional genetic input since the Christian Period.
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Affiliation(s)
- Kendra A. Sirak
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA ,grid.189967.80000 0001 0941 6502Department of Anthropology, Emory University, Atlanta, GA 30322 USA ,grid.7886.10000 0001 0768 2743Earth Institute and School of Archaeology, University College Dublin, Dublin, 4 Ireland
| | - Daniel M. Fernandes
- grid.7886.10000 0001 0768 2743Earth Institute and School of Archaeology, University College Dublin, Dublin, 4 Ireland ,grid.10420.370000 0001 2286 1424Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090 Austria ,grid.8051.c0000 0000 9511 4342CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Mark Lipson
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA
| | - Swapan Mallick
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Matthew Mah
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Iñigo Olalde
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.5612.00000 0001 2172 2676Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Harald Ringbauer
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA
| | - Nadin Rohland
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Carla S. Hadden
- grid.213876.90000 0004 1936 738XCenter for Applied Isotope Studies, University of Georgia, Athens, GA 30602 USA
| | - Éadaoin Harney
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA ,grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA
| | - Nicole Adamski
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Rebecca Bernardos
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA
| | - Nasreen Broomandkhoshbacht
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA ,grid.205975.c0000 0001 0740 6917Present Address: Department of Anthropology, University of California, Santa Cruz, CA 95064 USA
| | - Kimberly Callan
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Matthew Ferry
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Ann Marie Lawson
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA ,grid.214458.e0000000086837370Present Address: Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Megan Michel
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XPresent Address: Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA
| | - Jonas Oppenheimer
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA ,grid.205975.c0000 0001 0740 6917Present Address: Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064 USA
| | - Kristin Stewardson
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Fatma Zalzala
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Nick Patterson
- grid.66859.34Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Ron Pinhasi
- grid.7886.10000 0001 0768 2743Earth Institute and School of Archaeology, University College Dublin, Dublin, 4 Ireland ,grid.10420.370000 0001 2286 1424Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090 Austria
| | - Jessica C. Thompson
- grid.189967.80000 0001 0941 6502Department of Anthropology, Emory University, Atlanta, GA 30322 USA ,grid.47100.320000000419368710Department of Anthropology, Yale University, New Haven, CT 06511 USA ,grid.47100.320000000419368710Yale Peabody Museum of Natural History, New Haven, CT 06511 USA ,grid.215654.10000 0001 2151 2636Institute of Human Origins, Arizona State University, Tempe, AZ 85287 USA
| | - Dennis Van Gerven
- grid.266190.a0000000096214564Department of Anthropology, University of Colorado at Boulder, Boulder, CO 80309 USA
| | - David Reich
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
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12
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Analysis of HLA gene polymorphisms in East Africans reveals evidence of gene flow in two Semitic populations from Sudan. Eur J Hum Genet 2021; 29:1259-1271. [PMID: 33753913 PMCID: PMC8384866 DOI: 10.1038/s41431-021-00845-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 11/28/2020] [Accepted: 02/25/2021] [Indexed: 02/02/2023] Open
Abstract
Sudan, a northeastern African country, is characterized by high levels of cultural, linguistic, and genetic diversity, which is believed to be affected by continuous migration from neighboring countries. Consistent with such demographic effect, genome-wide SNP data revealed a shared ancestral component among Sudanese Afro-Asiatic speaking groups and non-African populations, mainly from West Asia. Although this component is shared among all Afro-Asiatic speaking groups, the extent of this sharing in Semitic groups, such as Sudanese Arab, is still unknown. Using genotypes of six polymorphic human leukocyte antigen (HLA) genes (i.e., HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1), we examined the genetic structure of eight East African ethnic groups with origins in Sudan, South Sudan, and Ethiopia. We identified informative HLA alleles using principal component analysis, which revealed that the two Semitic groups (Gaalien and Shokrya) constituted a distinct cluster from the other Afro-Asiatic speaking groups in this study. The HLA alleles that distinguished Semitic Arabs co-exist in the same extended HLA haplotype, and those alleles are in strong linkage disequilibrium. Interestingly, we find the four-locus haplotype "C*12:02-B*52:01-DRB1*15:02-DQB1*06:01" exclusively in non-African populations and it is widely spread across Asia. The identification of this haplotype suggests a gene flow from Asia, and likely these haplotypes were brought to Africa through back migration from the Near East. These findings will be of interest to biomedical and anthropological studies that examine the demographic history of northeast Africa.
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13
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Lo E, Russo G, Pestana K, Kepple D, Abagero BR, Dongho GBD, Gunalan K, Miller LH, Hamid MMA, Yewhalaw D, Paganotti GM. Contrasting epidemiology and genetic variation of Plasmodium vivax infecting Duffy-negative individuals across Africa. Int J Infect Dis 2021; 108:63-71. [PMID: 33991680 DOI: 10.1016/j.ijid.2021.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Plasmodium vivax malaria was thought to be rare in Africans who lack the Duffy blood group antigen expression. However, recent studies indicate that P. vivax can infect Duffy-negative individuals and has spread into areas of high Duffy negativity across Africa. Our study compared epidemiological and genetic features of P. vivax between African regions. METHODS A standardized approach was used to identify and quantify P. vivax from Botswana, Ethiopia, and Sudan, where Duffy-positive and Duffy-negative individuals coexist. The study involved sequencing the Duffy binding protein (DBP) gene and inferring genetic relationships among P. vivax populations across Africa. RESULTS Among 1215 febrile patients, the proportions of Duffy negativity ranged from 20-36% in East Africa to 84% in southern Africa. Average P. vivax prevalence among Duffy-negative populations ranged from 9.2% in Sudan to 86% in Botswana. Parasite density in Duffy-negative infections was significantly lower than in Duffy-positive infections. P. vivax in Duffy-negative populations were not monophyletic, with P. vivax in Duffy-negative and Duffy-positive populations sharing similar DBP haplotypes and occurring in multiple, well-supported clades. CONCLUSIONS Duffy-negative Africans are not resistant to P. vivax, and the public health significance of this should not be neglected. Our study highlights the need for a standardized approach and more resources/training directed towards the diagnosis of vivax malaria in Africa.
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Affiliation(s)
- Eugenia Lo
- Biological Sciences, University of North Carolina at Charlotte, USA.
| | - Gianluca Russo
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy.
| | - Kareen Pestana
- Biological Sciences, University of North Carolina at Charlotte, USA
| | - Daniel Kepple
- Biological Sciences, University of North Carolina at Charlotte, USA
| | - Beka Raya Abagero
- Tropical Infectious Disease Research Center, Jimma University, Jimma, Ethiopia
| | - Ghyslaine Bruna Djeunang Dongho
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy; Evangelical University of Cameroon, Bandjoun, Cameroon
| | | | - Louis H Miller
- Laboratory of Malaria and Vector Research, NIAID/NIH, Bethesda, USA
| | - Muzamil Mahdi Abdel Hamid
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Delenasaw Yewhalaw
- Tropical Infectious Disease Research Center, Jimma University, Jimma, Ethiopia
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana; Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
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14
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Hollfelder N, Breton G, Sjödin P, Jakobsson M. The deep population history in Africa. Hum Mol Genet 2021; 30:R2-R10. [PMID: 33438014 PMCID: PMC8117439 DOI: 10.1093/hmg/ddab005] [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: 10/27/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 12/28/2022] Open
Abstract
Africa is the continent with the greatest genetic diversity among humans and the level of diversity is further enhanced by incorporating non-majority groups, which are often understudied. Many of today's minority populations historically practiced foraging lifestyles, which were the only subsistence strategies prior to the rise of agriculture and pastoralism, but only a few groups practicing these strategies remain today. Genomic investigations of Holocene human remains excavated across the African continent show that the genetic landscape was vastly different compared to today's genetic landscape and that many groups that today are population isolate inhabited larger regions in the past. It is becoming clear that there are periods of isolation among groups and geographic areas, but also genetic contact over large distances throughout human history in Africa. Genomic information from minority populations and from prehistoric remains provide an invaluable source of information on the human past, in particular deep human population history, as Holocene large-scale population movements obscure past patterns of population structure. Here we revisit questions on the nature and time of the radiation of early humans in Africa, the extent of gene-flow among human populations as well as introgression from archaic and extinct lineages on the continent.
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Affiliation(s)
- Nina Hollfelder
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Gwenna Breton
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Per Sjödin
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Physical, Cnr Kingsway & University Roads, Auckland Park, Johannesburg 2092, South Africa
- SciLifeLab, Stockholm and Uppsala, Entrance C11, BMC, Husargatan 3, 752 37 Uppsala, Sweden
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15
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Ibrahim ME. Genetic diversity of the Sudanese: insights on origin and implications for health. Hum Mol Genet 2021; 30:R37-R41. [PMID: 33864377 PMCID: PMC8223596 DOI: 10.1093/hmg/ddab028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 11/21/2022] Open
Abstract
By virtue of their cultural, linguistic and genetic legacies, many populations from Sudan have deep histories in the region and retain high genetic diversities. Sudan’s location in north east Africa, a unique spot believed to act as a climatic refuge during periods of climate extremes, might have dictated that fate. Among the marked consequences of this diversity is the potential to provide information on the origin and structure of human populations within and outside the continent, as well as migration patterns towards various parts of the African continent, and out of Africa. The diverse Sudanese gene pool further has the potential to inform on genetic adaptations driven by culture and the environment resulting in unique and interesting traits, some of which are yet to be investigated. In addition, these genomes could offer clues to complex issues of causation amidst the challenge of new paradigms in biology underpinned by the genomic revolution.
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16
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Sjödin P, McKenna J, Jakobsson M. Estimating divergence times from DNA sequences. Genetics 2021; 217:iyab008. [PMID: 33769498 PMCID: PMC8049563 DOI: 10.1093/genetics/iyab008] [Citation(s) in RCA: 10] [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: 10/15/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
The patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the "Two-Two (TT)" and the "Two-Two-outgroup (TTo)" methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.
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Affiliation(s)
- Per Sjödin
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18 A, Uppsala 752 36, Sweden
| | - James McKenna
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18 A, Uppsala 752 36, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18 A, Uppsala 752 36, Sweden
- Science for Life Laboratory, Uppsala University, Norbyvägen 18 A, Uppsala 752 36, Sweden
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17
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Campbell MC, Ranciaro A. Human adaptation, demography and cattle domestication: an overview of the complexity of lactase persistence in Africa. Hum Mol Genet 2021; 30:R98-R109. [PMID: 33847744 DOI: 10.1093/hmg/ddab027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
Lactase persistence (LP) is a genetically-determined trait that is prevalent in African, European and Arab populations with a tradition of animal herding and milk consumption. To date, genetic analyses have identified several common variants that are associated with LP. Furthermore, data have indicated that these functional alleles likely have been maintained in pastoralist populations due to the action of recent selection, exemplifying the ongoing evolution of anatomically modern humans. Additionally, demographic history has also played a role in the geographic distribution of LP and associated alleles in Africa. In particular, the migration of ancestral herders and their subsequent admixture with local populations were integral to the spread of LP alleles and the culture of pastoralism across the continent. The timing of these demographic events was often correlated with known major environmental changes and/or the ability of domesticated cattle to resist/avoid infectious diseases. This review summarizes recent advances in our understanding of the genetic basis and evolutionary history of LP, as well as the factors that influenced the origin and spread of pastoralism in Africa.
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Affiliation(s)
- Michael C Campbell
- Department of Biology, Howard University, EE Just Hall Biology Building, 415 College Street NW, Washington, DC 20059, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA
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18
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Hollfelder N, Babiker H, Granehäll L, Schlebusch CM, Jakobsson M. The genetic variation of lactase persistence alleles in Sudan and South Sudan. Genome Biol Evol 2021; 13:6184864. [PMID: 33760047 PMCID: PMC8175049 DOI: 10.1093/gbe/evab065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2021] [Indexed: 12/27/2022] Open
Abstract
Lactase persistence (LP) is a well-studied example of a Mendelian trait under selection in some human groups due to gene-culture coevolution. We investigated the frequencies of genetic variants linked to LP in Sudanese and South Sudanese populations. These populations have diverse subsistence patterns, and some are dependent on milk to various extents, not only from cows but also from other livestock such as camels and goats. We sequenced a 316-bp region involved in regulating the expression of the LCT gene on chromosome 2, which encompasses five polymorphisms that have been associated with LP. Pastoralist populations showed a higher frequency of LP-associated alleles compared with nonpastoralist groups, hinting at positive selection also among northeast African pastoralists. Among the LP variants, the -14009:G variant occurs at the highest frequency among the investigated populations, followed by the -13915:G variant, which is likely of Middle Eastern origin, consistent with Middle Eastern gene flow to the Sudanese populations. There was no incidence of the “East African” LP allele (-14010:C) in the Sudanese and South Sudanese groups, and only one heterozygous individual for the “European” LP allele (-13910:T), suggesting limited recent admixture from these geographic regions. The Beja population of the Beni Amer show three different LP variants at substantial and similar levels, resulting in one of the greatest aggregation of LP variants among all populations across the world.
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Affiliation(s)
- Nina Hollfelder
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Hiba Babiker
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Lena Granehäll
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Institute for Mummy Studies, Eurac Research, Bolzano, Italy
| | - Carina M Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,SciLifeLab, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,SciLifeLab, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
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19
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Hernández CL, Pita G, Cavadas B, López S, Sánchez-Martínez LJ, Dugoujon JM, Novelletto A, Cuesta P, Pereira L, Calderón R. Human Genomic Diversity Where the Mediterranean Joins the Atlantic. Mol Biol Evol 2021; 37:1041-1055. [PMID: 31816048 PMCID: PMC7086172 DOI: 10.1093/molbev/msz288] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Throughout the past few years, a lively debate emerged about the timing and magnitude of the human migrations between the Iberian Peninsula and the Maghreb. Several pieces of evidence, including archaeological, anthropological, historical, and genetic data, have pointed to a complex and intermingled evolutionary history in the western Mediterranean area. To study to what extent connections across the Strait of Gibraltar and surrounding areas have shaped the present-day genomic diversity of its populations, we have performed a screening of 2.5 million single-nucleotide polymorphisms in 142 samples from southern Spain, southern Portugal, and Morocco. We built comprehensive data sets of the studied area and we implemented multistep bioinformatic approaches to assess population structure, demographic histories, and admixture dynamics. Both local and global ancestry inference showed an internal substructure in the Iberian Peninsula, mainly linked to a differential African ancestry. Western Iberia, from southern Portugal to Galicia, constituted an independent cluster within Iberia characterized by an enriched African genomic input. Migration time modeling showed recent historic dates for the admixture events occurring both in Iberia and in the North of Africa. However, an integrative vision of both paleogenomic and modern DNA data allowed us to detect chronological transitions and population turnovers that could be the result of transcontinental migrations dating back from Neolithic times. The present contribution aimed to fill the gaps in the modern human genomic record of a key geographic area, where the Mediterranean and the Atlantic come together.
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Affiliation(s)
- Candela L Hernández
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Bruno Cavadas
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Saioa López
- UCL Cancer Institute, London, United Kingdom
| | - Luis J Sánchez-Martínez
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Jean-Michel Dugoujon
- CNRS UMR 5288 Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse (AMIS), Université Paul Sabatier Toulouse III, Toulouse, France
| | | | - Pedro Cuesta
- Centro de Proceso de Datos, Universidad Complutense, Madrid, Spain
| | - Luisa Pereira
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Rosario Calderón
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología, Universidad Complutense, Madrid, Spain
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20
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Černý V, Fortes-Lima C, Tříska P. Demographic history and admixture dynamics in African Sahelian populations. Hum Mol Genet 2020; 30:R29-R36. [PMID: 33105478 DOI: 10.1093/hmg/ddaa239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/18/2023] Open
Abstract
The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterized by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure and the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.
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Affiliation(s)
- Viktor Černý
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Cesar Fortes-Lima
- Subdepartment of Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Petr Tříska
- Archaeogenetics Laboratory, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
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21
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Qu L, Wang L, He F, Han Y, Yang L, Wang MD, Zhu H. The Landscape of Micro-Inversions Provide Clues for Population Genetic Analysis of Humans. Interdiscip Sci 2020; 12:499-514. [PMID: 32929667 PMCID: PMC7658078 DOI: 10.1007/s12539-020-00392-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 11/04/2022]
Abstract
Background Variations in the human genome have been studied extensively. However, little is known about the role of micro-inversions (MIs), generally defined as small (< 100 bp) inversions, in human evolution, diversity, and health. Depicting the pattern of MIs among diverse populations is critical for interpreting human evolutionary history and obtaining insight into genetic diseases. Results In this paper, we explored the distribution of MIs in genomes from 26 human populations and 7 nonhuman primate genomes and analyzed the phylogenetic structure of the 26 human populations based on the MIs. We further investigated the functions of the MIs located within genes associated with human health. With hg19 as the reference genome, we detected 6968 MIs among the 1937 human samples and 24,476 MIs among the 7 nonhuman primate genomes. The analyses of MIs in human genomes showed that the MIs were rarely located in exonic regions. Nonhuman primates and human populations shared only 82 inverted alleles, and Africans had the most inverted alleles in common with nonhuman primates, which was consistent with the “Out of Africa” hypothesis. The clustering of MIs among the human populations also coincided with human migration history and ancestral lineages. Conclusions We propose that MIs are potential evolutionary markers for investigating population dynamics. Our results revealed the diversity of MIs in human populations and showed that they are essential to construct human population relationships and have a potential effect on human health. Electronic supplementary material The online version of this article (10.1007/s12539-020-00392-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li Qu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA, 30332, USA
| | - Luotong Wang
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Feifei He
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Yilun Han
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Longshu Yang
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - May D Wang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA, 30332, USA
| | - Huaiqiu Zhu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. .,Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA, 30332, USA. .,Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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22
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Mulindwa J, Noyes H, Ilboudo H, Pagani L, Nyangiri O, Kimuda MP, Ahouty B, Asina OF, Ofon E, Kamoto K, Kabore JW, Koffi M, Ngoyi DM, Simo G, Chisi J, Sidibe I, Enyaru J, Simuunza M, Alibu P, Jamonneau V, Camara M, Tait A, Hall N, Bucheton B, MacLeod A, Hertz-Fowler C, Matovu E, Matovu E, Sidibe I, Mumba D, Koffi M, Simo G, Chisi J, Alibu VP, Macleod A, Bucheton B, Hertzfowler C, Elliot A, Camara M, Bishop O, Mulindwa J, Nyangiri O, Kimuda MP, Ofon E, Ahouty B, Kabore J. High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation. Am J Hum Genet 2020; 107:473-486. [PMID: 32781046 PMCID: PMC7477016 DOI: 10.1016/j.ajhg.2020.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 12/23/2022] Open
Abstract
Africa contains more human genetic variation than any other continent, but the majority of the population-scale analyses of the African peoples have focused on just two of the four major linguistic groups, the Niger-Congo and Afro-Asiatic, leaving the Nilo-Saharan and Khoisan populations under-represented. In order to assess genetic variation and signatures of selection within a Nilo-Saharan population and between the Nilo-Saharan and Niger-Congo and Afro-Asiatic, we sequenced 50 genomes from the Nilo-Saharan Lugbara population of North-West Uganda and 250 genomes from 6 previously unsequenced Niger-Congo populations. We compared these data to data from a further 16 Eurasian and African populations including the Gumuz, another putative Nilo-Saharan population from Ethiopia. Of the 21 million variants identified in the Nilo-Saharan population, 3.57 million (17%) were not represented in dbSNP and included predicted non-synonymous mutations with possible phenotypic effects. We found greater genetic differentiation between the Nilo-Saharan Lugbara and Gumuz populations than between any two Afro-Asiatic or Niger-Congo populations. F3 tests showed that Gumuz contributed a genetic component to most Niger-Congo B populations whereas Lugabara did not. We scanned the genomes of the Lugbara for evidence of selective sweeps. We found selective sweeps at four loci (SLC24A5, SNX13, TYRP1, and UVRAG) associated with skin pigmentation, three of which already have been reported to be under selection. These selective sweeps point toward adaptations to the intense UV radiation of the Sahel.
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23
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Vicente M, Schlebusch CM. African population history: an ancient DNA perspective. Curr Opin Genet Dev 2020; 62:8-15. [DOI: 10.1016/j.gde.2020.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 11/30/2022]
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24
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Bruellman RJ, Watanabe Y, Ebrhim RS, Creech MK, Abdullah MA, Dumitrescu AM, Refetoff S, Weiss RE. Increased Prevalence of TG and TPO Mutations in Sudanese Children With Congenital Hypothyroidism. J Clin Endocrinol Metab 2020; 105:5684913. [PMID: 31867598 PMCID: PMC7093074 DOI: 10.1210/clinem/dgz297] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022]
Abstract
CONTEXT Congenital hypothyroidism (CH) is due to dyshormonogenesis in 10% to 15% of subjects worldwide but accounts for 60% of CH cases in the Sudan. OBJECTIVE To investigate the molecular basis of CH in Sudanese families. DESIGN Clinical phenotype reporting and serum thyroid hormone measurements. Deoxyribonucelic acid extraction for whole-exome sequencing and Sanger sequencing. SETTING University research center. PATIENTS Twenty-six Sudanese families with CH. INTERVENTION Clinical evaluation, thyroid function tests, genetic sequencing, and analysis. Our samples and information regarding samples from the literature were used to compare TG (thyroglobulin) and TPO (thyroid peroxidase) mutation rates in the Sudanese population with all populations. RESULTS Mutations were found in dual-oxidase 1 (DUOX1), dual-oxidase 2 (DUOX2), iodotyrosine deiodinase (IYD), solute-carrier (SLC) 26A4, SLC26A7, SLC5A5, TG, and TPO genes. The molecular basis of the CH in 7 families remains unknown. TG mutations were significantly higher on average in the Sudanese population compared with the average number of TG mutations in other populations (P < 0.05). CONCLUSIONS All described mutations occur in domains important for protein structure and function, predicting the CH phenotype. Genotype prediction based on phenotype includes low or undetectable thyroglobulin levels for TG gene mutations and markedly higher thyroglobulin levels for TPO mutations. The reasons for higher incidence of TG gene mutations include gene length and possible positive genetic selection due to endemic iodine deficiency.
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Affiliation(s)
- Ryan J Bruellman
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Yui Watanabe
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Reham S Ebrhim
- Department of Paediatrics and Child Health, Faculty of Medicine, University of Almughtaribeen, Khartoum, Sudan
| | - Matthew K Creech
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Mohamed A Abdullah
- Department of Paediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Alexandra M Dumitrescu
- Department of Medicine, The University of Chicago, Chicago, Illinois
- Committee on Molecular Medicine and Nutrition, The University of Chicago, Chicago, Illinois
| | - Samuel Refetoff
- Department of Medicine, The University of Chicago, Chicago, Illinois
- Department of Pediatrics, The University of Chicago, Chicago, Illinois
- Committee on Genetics, The University of Chicago, Chicago, Illinois
| | - Roy E Weiss
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
- Correspondence and Reprint Requests: Roy E. Weiss, MD, PhD, University of Miami Miller School of Medicine, 1120 NW 14th Street, Room 310F, Miami, Florida 33136. E-mail:
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25
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Inlamea OF, Soares P, Ikuta CY, Heinemann MB, Achá SJ, Machado A, Ferreira Neto JS, Correia-Neves M, Rito T. Evolutionary analysis of Mycobacterium bovis genotypes across Africa suggests co-evolution with livestock and humans. PLoS Negl Trop Dis 2020; 14:e0008081. [PMID: 32119671 PMCID: PMC7077849 DOI: 10.1371/journal.pntd.0008081] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/17/2020] [Accepted: 01/22/2020] [Indexed: 01/05/2023] Open
Abstract
Mycobacterium bovis is the pathogenic agent responsible for bovine tuberculosis (bTB), a zoonotic disease affecting mostly cattle, but also transmittable to humans and wildlife. Genetic studies on M. bovis allow to detect possible routes of bTB transmission and the identification of genetic reservoirs that may provide an essential framework for public health action. We used a database with 1235 M. bovis genotypes collected from different regions in Africa with 45 new Mozambican samples. Our analyses, based on phylogeographic and population genetics’ approaches, allowed to identify two clear trends. First, the genetic diversity of M. bovis is geographically clustered across the continent, with the only incidences of long-distance sharing of genotypes, between South Africa and Algeria, likely due to recent European introductions. Second, there is a broad gradient of diversity from Northern to Southern Africa with a diversity focus on the proximity to the Near East, where M. bovis likely emerged with animal domestication in the last 10,000 years. Diversity indices are higher in Eastern Africa, followed successively by Northern, Central, Southern and Western Africa, roughly correlating with the regional archaeological records of introduction of animal domesticates. Given this scenario M. bovis in Africa was probably established millennia ago following a concomitant spread with cattle, sheep and goat. Such scenario could translate into long-term locally adapted lineages across Africa. This work describes a novel scenario for the spread of M. bovis in Africa using the available genetic data, opening the field to further studies using higher resolution genomic data. We describe the genetic diversity distribution in Africa of the pathogen Mycobacterium bovis, the responsible for bovine tuberculosis, mostly present in cattle but also transmittable to other animals including humans. This diversity is geographically clustered within the African continent meaning that the genetic diversity was established through independent evolution within different areas. Higher diversity values of M. bovis are found in Eastern and Northern Africa, followed by Central Africa, with Western and Southern Africa displaying the lowest diversity. These levels of diversity correlate well with the introduction of domesticated livestock in the different regions of Africa, following their domestication in the Near East 10,000 ago. We hypothesize that M. bovis emerged in the Near East and it was carried across Africa together with domesticated animals and people that developed herding practices and biological tolerance for digesting milk in adulthood. Such scenario implies a strong evolution and co-evolution of M. bovis across Africa leading to locally adapted strains that could prove a challenge for public health actions.
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Affiliation(s)
- Osvaldo Frederico Inlamea
- Programa de pós-graduação Ciência Para o desenvolvimento (PGCD)–Instituto Gulbenkian de Ciência–Portugal
- Faculdade de Medicina Veterinária e Zootecnia (VPS-FMVZ), Universidade de São Paulo, USP–Brasil
- Instituto Nacional de Saúde, Ministério de Saúde, Moçambique
- Faculdade de Veterinária (FAVET), Universidade Eduardo Mondlane, Maputo, Moçambique
- * E-mail: (OFI); (TR)
| | - Pedro Soares
- Centre of Molecular and Environmental Biology (CBMA), School of Sciences, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Cassia Yumi Ikuta
- Faculdade de Medicina Veterinária e Zootecnia (VPS-FMVZ), Universidade de São Paulo, USP–Brasil
| | - Marcos Bryan Heinemann
- Faculdade de Medicina Veterinária e Zootecnia (VPS-FMVZ), Universidade de São Paulo, USP–Brasil
| | - Sara Juma Achá
- Direcção de Ciências Animais, Instituto de Investigação Agrária de Moçambique, Ministério de Agricultura e Segurança Alimentar, Maputo, Moçambique
| | - Adelina Machado
- Faculdade de Veterinária (FAVET), Universidade Eduardo Mondlane, Maputo, Moçambique
| | | | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Teresa Rito
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
- * E-mail: (OFI); (TR)
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26
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Wu Y, Guo T, Mu Q, Wang J, Li X, Wu Y, Tian B, Wang ML, Bai G, Perumal R, Trick HN, Bean SR, Dweikat IM, Tuinstra MR, Morris G, Tesso TT, Yu J, Li X. Allelochemicals targeted to balance competing selections in African agroecosystems. NATURE PLANTS 2019; 5:1229-1236. [PMID: 31792396 DOI: 10.1038/s41477-019-0563-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
Among major cereals domesticated as staple food, only sorghum has a high proportion of cultivars with condensed tannins in grain, which can trigger bitter taste perception in animals by binding to type 2 taste receptors (TAS2Rs). Here, we report the completion of uncovering of a pair of duplicate recessive genes (Tannin1 and Tannin2) underlying tannin presence. Three loss-of-function alleles from each gene were identified in non-tannin sorghum desired as palatable food. Condensed tannins effectively prevented sparrows from consuming sorghum grain. Parallel geographic distributions between tannin sorghum and Quelea quelea supported the role of tannins in fighting against this major herbivore threat. Association between geographic distributions of human TAS2R variants and tannin sorghum across Africa suggested that different causes had probably driven this bidirectional selection according to varied local herbivore threats and human taste sensitivity. Our investigation uncovered coevolution among humans, plants and environments linked by allelochemicals.
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Affiliation(s)
- Yuye Wu
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Tingting Guo
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Qi Mu
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Jinyu Wang
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Xin Li
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Yun Wu
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Bin Tian
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, KS, USA
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Scott R Bean
- USDA-ARS, Grain Quality and Structure Research Unit, Manhattan, KS, USA
| | - Ismail M Dweikat
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA
| | | | - Geoffrey Morris
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Tesfaye T Tesso
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA, USA.
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA, USA.
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27
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Runs of homozygosity in sub-Saharan African populations provide insights into complex demographic histories. Hum Genet 2019; 138:1123-1142. [DOI: 10.1007/s00439-019-02045-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/03/2019] [Indexed: 12/20/2022]
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28
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Prendergast ME, Lipson M, Sawchuk EA, Olalde I, Ogola CA, Rohland N, Sirak KA, Adamski N, Bernardos R, Broomandkhoshbacht N, Callan K, Culleton BJ, Eccles L, Harper TK, Lawson AM, Mah M, Oppenheimer J, Stewardson K, Zalzala F, Ambrose SH, Ayodo G, Gates HL, Gidna AO, Katongo M, Kwekason A, Mabulla AZP, Mudenda GS, Ndiema EK, Nelson C, Robertshaw P, Kennett DJ, Manthi FK, Reich D. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science 2019; 365:science.aaw6275. [PMID: 31147405 DOI: 10.1126/science.aaw6275] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/13/2019] [Indexed: 12/31/2022]
Abstract
How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.
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Affiliation(s)
- Mary E Prendergast
- Division of Humanities, Saint Louis University, 28003 Madrid, Spain. .,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Elizabeth A Sawchuk
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11790, USA.
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Christine A Ogola
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kendra A Sirak
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan J Culleton
- Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA
| | - Laurie Eccles
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Stanley H Ambrose
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - George Ayodo
- Department of Public and Community Health, School of Health Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | - Henry Louis Gates
- Hutchins Center for African and African American Research, Harvard University, Cambridge, MA 02138, USA
| | | | | | | | | | | | - Emmanuel K Ndiema
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Charles Nelson
- Academy for Lifelong Learning, Western Washington University, Bellingham, WA 98225, USA
| | - Peter Robertshaw
- Department of Anthropology, California State University, San Bernardino, CA 92407, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Fredrick K Manthi
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. .,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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He G, Gao B, Guo J, Su Y. Genetic diversity and forensic characteristics of 15 autosomal short tandem repeats in Tibet highland and Guangdong lowland Han Chinese populations. Ann Hum Biol 2019; 46:181-186. [PMID: 30994014 DOI: 10.1080/03014460.2019.1607553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Background: Much attention has been paid to the genetic variants of microsatellites in East Asian populations; however, genetic diversity of high-altitude adaptation in Tibet Han remains largely uncharacterised. Aim: To profile DNA samples from 338 high-altitude adaptation Han Chinese individuals and 933 low-altitude living Han Chinese individuals for 15 autosomal STRs which are used for human identification purposes and to estimate the forensic parameters as well as explore the genetic relationships among 38 Chinese populations. Subjects and methods: Fifteen autosomal STR loci and amelogenin genes were amplified in 1271 individuals using the AmpFℓSTR® Sinofiler™ PCR Amplification Kit. Allele frequencies and forensic parameters were calculated. Subsequently, population comparisons among 38 groups were analysed via principal components analysis, Reynolds genetic distance, neighbour-joining tree and multidimensional scaling plots. Results: In this study, no departures from Hardy-Weinberg equilibrium are identified in either Tibet or Guangdong Han populations after Bonferroni correction. The cumulative match probabilities are 3.1108 × 10-19 in Guangdong Han and 6.2102 × 10-19 in Tibet Han, and the combined probabilities of exclusion for trios are 0.99999948 and 0.99999936, respectively. Comprehensive population comparisons based on allele frequency distribution indicate that the Tibet Han population has a genetically close relationship with the surrounding population (Tibet Tibetan) and the Guangdong Han population has genetic affinity with southern Chinese populations. Conclusion: In general, genetic polymorphisms and forensic efficiency indicated that the 15 STRs studied are informative and polymorphic in both lowland and highland Han populations.
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Affiliation(s)
- Guanglin He
- a Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Bo Gao
- b Institute of Forensic Science , Yili Public Security Bureau of Xinjiang , Kuitun , PR China
| | - Jianxin Guo
- c Department of History , Xiamen University , Xiamen , PR China
| | - Yongdong Su
- d Forensic Identification Center , Public Security Bureau of Tibet Autonomous Region , Lhasa , PR China
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30
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Molinaro L, Pagani L. Human evolutionary history of Eastern Africa. Curr Opin Genet Dev 2018; 53:134-139. [DOI: 10.1016/j.gde.2018.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/31/2018] [Accepted: 10/08/2018] [Indexed: 01/16/2023]
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31
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Genetic structure and polymorphisms of Gelao ethnicity residing in southwest china revealed by X-chromosomal genetic markers. Sci Rep 2018; 8:14585. [PMID: 30275508 PMCID: PMC6167355 DOI: 10.1038/s41598-018-32945-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/19/2018] [Indexed: 01/10/2023] Open
Abstract
X-chromosome short tandem repeat markers (X-STRs), due to their special inheritance models, physical location on a single chromosome and the absence of recombination in male meiosis, play an important role in forensic and population genetics. While a series of genetic analyses focusing on the genetic diversity and forensic characteristics of X-STRs are well studied for ethnically/linguistically diverse and demographically large Chinese populations, genetic evidence from Gelao ethnicity is still sparse. Here, we genotyped the first batch of 19 X-STRs in 513 Chinese Gelao individuals (265 females and 248 males), and reported genetic polymorphisms, forensic characteristics based on the single locus and seven linkage groups. DXS10135 with the highest PIC (0.9106) and LG1 (DXS10148-DXS10135-DXS8378) with the largest HD (0.9970) are polymorphic and informative. The CPDs in Gelao males and females are respectively larger than 0.999999999997095 and 0.99999999999999999999918, and the combined MECs are larger than 0.999999975715109. Subsequently, we investigated the population relationships among 14 Chinese populations based on 19 X-STRs and among 23 populations based on 11 overlapped X-STRs. Our results revealed genetic differentiations among Tibeto-Burman, Altaic and other Chinese homogenous populations, and demonstrated that Guizhou Gelao has the genetically closer relationships with Han Chinese and geographically close Guizhou Miao.
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32
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Shriner D, Rotimi CN. Genetic history of Chad. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:804-812. [PMID: 30259956 DOI: 10.1002/ajpa.23711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/17/2018] [Accepted: 08/29/2018] [Indexed: 11/11/2022]
Abstract
OBJECTIVES The Sahel is a semi-arid zone stretching from the Atlantic Ocean in the west to the Red Sea in the east and from the Sahara in the north to the Sudanian Savanna in the south. Here, we investigated the genetic history of the spread of Northern African ancestry common among Berbers, the Y DNA haplogroup R1b-V88, and Chadic languages throughout the Sahel, with a focus on Chad. MATERIALS AND METHODS We integrated and analyzed genotype data from 751 individuals from Chad, Burkina Faso, Mali, South Sudan, and Sudan in the context of a global reference panel of 5,966 individuals. RESULTS We found that genetic diversity in Chad was broadly divided by a north-south axis. The core ancestry of Southern Chadians was Central African, most closely related to Pygmies. Southern Chadians then experienced four waves of gene flow over the last 3,000 years from West-Central Africans, Eastern Africans, West-Central Africans again, and then Arabians. In contrast, Northern Chadians did not share Central African ancestry and were not influenced by the first wave of West-Central Africans but were influenced by Northern African ancestry. DISCUSSION We found that Y DNA haplogroup R1b entered the Chadian gene pool during Baggarization. Baggara Arabs spoke Arabic, not Chadic, implying that people carrying R1b-V88 were not responsible for the spread of Chadic languages, which may have spread approximately 3,700 years ago. We found no evidence for migration of Near Eastern farmers or any ancient episodes involving Eurasian backflow.
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Affiliation(s)
- Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland
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Schlebusch CM, Jakobsson M. Tales of Human Migration, Admixture, and Selection in Africa. Annu Rev Genomics Hum Genet 2018; 19:405-428. [DOI: 10.1146/annurev-genom-083117-021759] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the last three decades, genetic studies have played an increasingly important role in exploring human history. They have helped to conclusively establish that anatomically modern humans first appeared in Africa roughly 250,000–350,000 years before present and subsequently migrated to other parts of the world. The history of humans in Africa is complex and includes demographic events that influenced patterns of genetic variation across the continent. Through genetic studies, it has become evident that deep African population history is captured by relationships among African hunter–gatherers, as the world's deepest population divergences occur among these groups, and that the deepest population divergence dates to 300,000 years before present. However, the spread of pastoralism and agriculture in the last few thousand years has shaped the geographic distribution of present-day Africans and their genetic diversity. With today's sequencing technologies, we can obtain full genome sequences from diverse sets of extant and prehistoric Africans. The coming years will contribute exciting new insights toward deciphering human evolutionary history in Africa.
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Affiliation(s)
- Carina M. Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden;,
- Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, 2006 Johannesburg, South Africa
- SciLifeLab, SE-751 23 Uppsala, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden;,
- Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, 2006 Johannesburg, South Africa
- SciLifeLab, SE-751 23 Uppsala, Sweden
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Choudhury A, Aron S, Sengupta D, Hazelhurst S, Ramsay M. African genetic diversity provides novel insights into evolutionary history and local adaptations. Hum Mol Genet 2018; 27:R209-R218. [PMID: 29741686 PMCID: PMC6061870 DOI: 10.1093/hmg/ddy161] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 12/22/2022] Open
Abstract
Genetic variation and susceptibility to disease are shaped by human demographic history and adaptation. We can now study the genomes of extant Africans and uncover traces of population migration, admixture, assimilation and selection by applying sophisticated computational algorithms. There are four major ethnolinguistic divisions among present day Africans: Hunter-gatherer populations in southern and central Africa; Nilo-Saharan speakers from north and northeast Africa; Afro-Asiatic speakers from north and east Africa; and Niger-Congo speakers who are the predominant ethnolinguistic group spread across most of sub-Saharan Africa. The enormous ethnolinguistic diversity in sub-Saharan African populations is largely paralleled by extensive genetic diversity and until a decade ago, little was known about detailed origins and divergence of these groups. Results from large-scale population genetic studies, and more recently whole genome sequence data, are unravelling the critical role of events like migration and admixture and environmental factors including diet, infectious diseases and climatic conditions in shaping current population diversity. It is now possible to start providing quantitative estimates of divergence times, population size and dynamic processes that have affected populations and their genetic risk for disease. Finally, the availability of ancient genomes from Africa provides historical insights of unprecedented depth. In this review, we highlight some key interpretations that have emerged from recent African genome studies.
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Affiliation(s)
- Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shaun Aron
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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35
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Abstract
Two administrations of the Coloured Progressive Matrices in Egypt were compared. The first was administered to a large, representative national sample between 2011 and 2013. The second was administered to primary school pupils in villages in Menoufia in northern Egypt in 2017. Adjusting for the Flynn Effect, the IQ of the rural northern Egyptians was shown to be statistically significantly higher than the national average. It is demonstrated that this is consistent with regional socioeconomic differences in Egypt, which strongly imply that northern Egypt has a higher average IQ than southern Egypt.
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