1
|
Tilahun M, Gebresilase TT, Aseffa A, Haile K, Wogayehu T, Murale MT, Yntiso H, Munung NS, Bobosha K, Kaba M. Public perceptions of genomic studies and hereditary diseases in Aari community, South Omo Zone, Ethiopia. Trans R Soc Trop Med Hyg 2024; 118:51-60. [PMID: 38165197 DOI: 10.1093/trstmh/trad051] [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: 04/18/2023] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Genetic and genomic research is revolutionizing precision medicine; however, addressing ethical and cultural aspects is crucial to ensure ethical conduct and respect for community values and beliefs. This study explored the beliefs, perceptions and concerns of the Aari community in South Ethiopia regarding genetic concepts, hereditary diseases and ethical research practices related to sample collection, storage and sharing. METHODS In-depth interviews and focus group discussions were conducted with community elders, health officials, tuberculosis patients and apparently healthy individuals. Data were thematically analysed using MAXQDA software. RESULTS Participants identified diseases such as podoconiosis, leprosy, goitre and epilepsy as hereditary and perceived some as 'curses' due to generational impact and social stigma. Disease susceptibility was attributed to divine intervention or factors such as malnutrition and sanitation. Although hereditary diseases were considered unavoidable, in some cases environmental factors were acknowledged. Participants shared personal examples to demonstrate inheritance concepts. Blood held cultural significance, and concerns about its potential misuse resulted in scepticism towards giving samples. CONCLUSIONS This study emphasizes the significance of comprehending local beliefs and perceptions and stresses the need to establish effective communication, build trust and address underlying causes of hesitancy to improve recruitment and ensure ethical conduct.
Collapse
Affiliation(s)
- Melaku Tilahun
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Department of Biology, College of Natural and Computational Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Tewodros Tariku Gebresilase
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Kassa Haile
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Teklu Wogayehu
- Department of Biology, College of Natural and Computational Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Moi Top Murale
- Department of Psychology, Jinka University, Jinka, Ethiopia
| | - Hailu Yntiso
- South Aari Woreda Administration, Gazer, South Omo, Ethiopia
| | - Nchangwi Syntia Munung
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kidist Bobosha
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Mirgissa Kaba
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Harris DN, Platt A, Hansen MEB, Fan S, McQuillan MA, Nyambo T, Mpoloka SW, Mokone GG, Belay G, Fokunang C, Njamnshi AK, Tishkoff SA. Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals. Curr Biol 2023; 33:4905-4916.e5. [PMID: 37837965 PMCID: PMC10841429 DOI: 10.1016/j.cub.2023.09.066] [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: 03/15/2023] [Revised: 07/18/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023]
Abstract
Comparisons of Neanderthal genomes to anatomically modern human (AMH) genomes show a history of Neanderthal-to-AMH introgression stemming from interbreeding after the migration of AMHs from Africa to Eurasia. All non-sub-Saharan African AMHs have genomic regions genetically similar to Neanderthals that descend from this introgression. Regions of the genome with Neanderthal similarities have also been identified in sub-Saharan African populations, but their origins have been unclear. To better understand how these regions are distributed across sub-Saharan Africa, the source of their origin, and what their distribution within the genome tells us about early AMH and Neanderthal evolution, we analyzed a dataset of high-coverage, whole-genome sequences from 180 individuals from 12 diverse sub-Saharan African populations. In sub-Saharan African populations with non-sub-Saharan African ancestry, as much as 1% of their genomes can be attributed to Neanderthal sequence introduced by recent migration, and subsequent admixture, of AMH populations originating from the Levant and North Africa. However, most Neanderthal homologous regions in sub-Saharan African populations originate from migration of AMH populations from Africa to Eurasia ∼250 kya, and subsequent admixture with Neanderthals, resulting in ∼6% AMH ancestry in Neanderthals. These results indicate that there have been multiple migration events of AMHs out of Africa and that Neanderthal and AMH gene flow has been bi-directional. Observing that genomic regions where AMHs show a depletion of Neanderthal introgression are also regions where Neanderthal genomes show a depletion of AMH introgression points to deleterious interactions between introgressed variants and background genomes in both groups-a hallmark of incipient speciation.
Collapse
Affiliation(s)
- Daniel N Harris
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexander Platt
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai 200438, China
| | - Michael A McQuillan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas Nyambo
- Department of Biochemistry and Molecular Biology, Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Alfred K Njamnshi
- Brain Research Africa Initiative (BRAIN), P.O. Box 25625, Yaoundé, Cameroon; Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
4
|
Belachew EB, Desta AF, Gebremariam TY, Deneke DB, Ashenafi S, Yeshi MM, Fenta BD, Alem AT, Alemu A, Abafogi AK, Desta T, Chanyalew M, Beshah D, Taylor L, Bauer M, Tsehay D, Girma S, Melka DS, Tessema TS, Kantelhardt EJ, Howe R. Immunohistochemistry-derived subtypes of breast cancer distribution in four regions of Ethiopia. Front Endocrinol (Lausanne) 2023; 14:1250189. [PMID: 38027092 PMCID: PMC10666628 DOI: 10.3389/fendo.2023.1250189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose Different biological characteristics, therapeutic responses, and disease-specific outcomes are associated with different molecular subtypes of breast cancer (BC). Although there have been different studies on BC in the Ethiopian capital city of Addis Ababa, there have been few studies in other parts of the nation, and none have evaluated biological characteristics in other locations in the context of the extensive ethnic and genetic diversity found in Ethiopia. This study was carried out to evaluate the distribution of immunohistochemistry (IHC) subtypes of BCs throughout four Ethiopian regions. Methods A total of 227 formalin-fixed paraffin-embedded (FFPE) tissue blocks were collected from tertiary hospitals in four Ethiopian regions between 2015 and 2021. The IHC staining was performed for subtyping, ER, PR, HER2, and Ki-67 proliferation markers. Results The mean age at diagnosis was 43.9 years. The percentage of ER and PR-negative tumors were 48.3% and 53.2%, respectively. The IHC subtypes showed the following distribution: 33.1% triple-negative breast cancer (TNBC), 27.6% luminal B, 25.2% luminal A, and 14.1% HER2 enriched. In multiple logistic regression analysis, grade III and HER2 positivity were associated with larger tumor size, and also originating from Jimma compared to Mekele. Conclusion Patients with ER-negative, PR-negative, and TNBC were found in 48.3%, 53.2%, and 33.1% of cases, respectively, showing that half the patients could potentially benefit from endocrine treatment. A considerably high prevalence of TNBC was reported in our study, demanding additional research that includes genetic predisposition factors. Additionally, aggressive tumors were found in a high percentage of younger age groups, which must be considered when planning personalized treatment strategies.
Collapse
Affiliation(s)
- Esmael Besufikad Belachew
- Biology Department, College of Natural and Computational Sciences, Mizan Tepi University, Mizan, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Non-Communicable Diseases (NCD) Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Adey Feleke Desta
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tewodros Yalew Gebremariam
- Department of Pathology, School of Medicine, College of Health Sciences, Tikur Anbessa Specialized Hospital and Addis Ababa University, Addis Ababa, Ethiopia
| | - Dinikisira Bekele Deneke
- Department of Pathology, School of Medicine, College of Health Sciences, Tikur Anbessa Specialized Hospital and Addis Ababa University, Addis Ababa, Ethiopia
| | - Senait Ashenafi
- Department of Pathology, School of Medicine, College of Health Sciences, Tikur Anbessa Specialized Hospital and Addis Ababa University, Addis Ababa, Ethiopia
| | - Melisachew Mulatu Yeshi
- Department of Pathology, School of Medicine, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | | | | | - Addisu Alemu
- College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia
| | - Abdo Kedir Abafogi
- Pathology Department, Jimma University Specialized Hospital, Jimma, Ethiopia
| | - Tigist Desta
- Non-Communicable Diseases (NCD) Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Menberework Chanyalew
- Non-Communicable Diseases (NCD) Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Daniel Beshah
- Department of Diagnostic Laboratory, Tikur Anbessa Specialized Hospital, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lesley Taylor
- City of Hope National Medical Center, Duarte, CA, United States
| | - Marcus Bauer
- Global Health Working Group, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Dareskedar Tsehay
- Non-Communicable Diseases (NCD) Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Selfu Girma
- Non-Communicable Diseases (NCD) Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Daniel Seifu Melka
- Department of Biochemistry, Division of Basic Sciences, University of Global Health Equity, Kigali, Rwanda
| | | | - Eva J. Kantelhardt
- Department of Gynecology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Institute of Medical Epidemiology, Biostatistics and Informatics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Rawleigh Howe
- Non-Communicable Diseases (NCD) Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Ayala NM, Genetti M, Corbett-Detig R. Inferring multi-locus selection in admixed populations. PLoS Genet 2023; 19:e1011062. [PMID: 38015992 PMCID: PMC10707604 DOI: 10.1371/journal.pgen.1011062] [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: 05/23/2023] [Revised: 12/08/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023] Open
Abstract
Admixture, the exchange of genetic information between distinct source populations, is thought to be a major source of adaptive genetic variation. Unlike mutation events, which periodically generate single alleles, admixture can introduce many selected alleles simultaneously. As such, the effects of linkage between selected alleles may be especially pronounced in admixed populations. However, existing tools for identifying selected mutations within admixed populations only account for selection at a single site, overlooking phenomena such as linkage among proximal selected alleles. Here, we develop and extensively validate a method for identifying and quantifying the individual effects of multiple linked selected sites on a chromosome in admixed populations. Our approach numerically calculates the expected local ancestry landscape in an admixed population for a given multi-locus selection model, and then maximizes the likelihood of the model. After applying this method to admixed populations of Drosophila melanogaster and Passer italiae, we found that the impacts between linked sites may be an important contributor to natural selection in admixed populations. Furthermore, for the situations we considered, the selection coefficients and number of selected sites are overestimated in analyses that do not consider the effects of linkage among selected sites. Our results imply that linkage among selected sites may be an important evolutionary force in admixed populations. This tool provides a powerful generalized method to investigate these crucial phenomena in diverse populations.
Collapse
Affiliation(s)
- Nicolas M. Ayala
- Genomics Institute, University of California, Santa Cruz; Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California, Santa Cruz; Santa Cruz, California, United States of America
| | - Maximilian Genetti
- Genomics Institute, University of California, Santa Cruz; Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California, Santa Cruz; Santa Cruz, California, United States of America
| | - Russell Corbett-Detig
- Genomics Institute, University of California, Santa Cruz; Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California, Santa Cruz; Santa Cruz, California, United States of America
| |
Collapse
|
7
|
Faux P, Ding L, Ramirez-Aristeguieta LM, Chacón-Duque JC, Comini M, Mendoza-Revilla J, Fuentes-Guajardo M, Jaramillo C, Arias W, Hurtado M, Villegas V, Granja V, Barquera R, Everardo-Martínez P, Quinto-Sánchez M, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hünemeier T, Ramallo V, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Poletti G, Gallo C, Rothhammer F, Rojas W, Schmid AB, Adhikari K, Bennett DL, Ruiz-Linares A. Neanderthal introgression in SCN9A impacts mechanical pain sensitivity. Commun Biol 2023; 6:958. [PMID: 37816865 PMCID: PMC10564861 DOI: 10.1038/s42003-023-05286-z] [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: 02/24/2023] [Accepted: 08/25/2023] [Indexed: 10/12/2023] Open
Abstract
The Nav1.7 voltage-gated sodium channel plays a key role in nociception. Three functional variants in the SCN9A gene (encoding M932L, V991L, and D1908G in Nav1.7), have recently been identified as stemming from Neanderthal introgression and to associate with pain symptomatology in UK BioBank data. In 1000 genomes data, these variants are absent in Europeans but common in Latin Americans. Analysing high-density genotype data from 7594 Latin Americans, we characterized Neanderthal introgression in SCN9A. We find that tracts of introgression occur on a Native American genomic background, have an average length of ~123 kb and overlap the M932L, V991L, and D1908G coding positions. Furthermore, we measured experimentally six pain thresholds in 1623 healthy Colombians. We found that Neanderthal ancestry in SCN9A is significantly associated with a lower mechanical pain threshold after sensitization with mustard oil and evidence of additivity of effects across Nav1.7 variants. Our findings support the reported association of Neanderthal Nav1.7 variants with clinical pain, define a specific sensory modality affected by archaic introgression in SCN9A and are consistent with independent effects of the Neanderthal variants on Nav1.7 function.
Collapse
Affiliation(s)
- Pierre Faux
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, 200438, Shanghai, China
- UMR ADES, Aix-Marseille Université, CNRS, EFS, 13005, Marseille, France
- UMR GenPhySE, INRAE, INP, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Li Ding
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, 200438, Shanghai, China
| | | | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, SE-1069, Stockholm, Sweden
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Maddalena Comini
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, OX3 9DU, UK
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015, Paris, France
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, 1000000, Arica, Chile
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, 5001000, Medellín, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, 5001000, Medellín, Colombia
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, 6600, Mexico, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), 07745, Jena, Germany
| | - Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, 6600, Mexico, Mexico
| | - Mirsha Quinto-Sánchez
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), 06320, Mexico City, Mexico
| | - Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, 6600, Mexico, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, 4510, Mexico City, Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, 90040-060, Porto Alegre, Brasil
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, U9129ACD, Puerto Madryn, Argentina
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, U9129ACD, Puerto Madryn, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, 90040-060, Porto Alegre, Brasil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, 90040-060, Porto Alegre, Brasil
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, 6600, Mexico, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, 4510, Mexico City, Mexico
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, 1000000, Arica, Chile
| | - Winston Rojas
- GENMOL (Genética Molecular), Universidad de Antioquia, 5001000, Medellín, Colombia
| | - Annina B Schmid
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, OX3 9DU, UK
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, UK.
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
| | - David L Bennett
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, OX3 9DU, UK.
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, 200438, Shanghai, China.
- UMR ADES, Aix-Marseille Université, CNRS, EFS, 13005, Marseille, France.
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
| |
Collapse
|
8
|
Sandoval-Velasco M, Jagadeesan A, Ramos-Madrigal J, Ávila-Arcos MC, Fortes-Lima CA, Watson J, Johannesdóttir E, Cruz-Dávalos DI, Gopalakrishnan S, Moreno-Mayar JV, Niemann J, Renaud G, Robson Brown KA, Bennett H, Pearson A, Helgason A, Gilbert MTP, Schroeder H. The ancestry and geographical origins of St Helena's liberated Africans. Am J Hum Genet 2023; 110:1590-1599. [PMID: 37683613 PMCID: PMC10502851 DOI: 10.1016/j.ajhg.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/10/2023] Open
Abstract
The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception point for enslaved Africans who had been "liberated" from slave ships intercepted by the British. In total, St Helena received approximately 27,000 liberated Africans between 1840 and 1867. Written sources suggest that the majority of these individuals came from West Central Africa, but their precise origins are unknown. Here, we report the results of ancient DNA analyses that we conducted as part of a wider effort to commemorate St Helena's liberated Africans and to restore knowledge of their lives and experiences. We generated partial genomes (0.1-0.5×) for 20 individuals whose remains had been recovered during archaeological excavations on the island. We compared their genomes with genotype data for over 3,000 present-day individuals from 90 populations across sub-Saharan Africa and conclude that the individuals most likely originated from different source populations within the general area between northern Angola and Gabon. We also find that the majority (17/20) of the individuals were male, supporting a well-documented sex bias in the latter phase of the transatlantic slave trade. The study expands our understanding of St Helena's liberated African community and illustrates how ancient DNA analyses can be used to investigate the origins and identities of individuals whose lives were bound up in the story of slavery and its abolition.
Collapse
Affiliation(s)
- Marcela Sandoval-Velasco
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
| | - Anuradha Jagadeesan
- deCODE Genetics/Amgen, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland
| | - Jazmín Ramos-Madrigal
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of Mexico, Juriquilla, 76230 Santiago de Querétaro, México
| | - Cesar A Fortes-Lima
- Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Judy Watson
- Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK
| | - Erna Johannesdóttir
- Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK
| | - Diana I Cruz-Dávalos
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Shyam Gopalakrishnan
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Jonas Niemann
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Gabriel Renaud
- Department of Health Technology Bioinformatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | | | - Helena Bennett
- St Helena National Trust, Broadway House, Mainstreet, Jamestown, St Helena
| | - Andrew Pearson
- Environmental Dimension Partnership, Atlantic Wharf, CF10 4HF Cardiff, UK
| | - Agnar Helgason
- deCODE Genetics/Amgen, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland
| | - M Thomas P Gilbert
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
| |
Collapse
|
9
|
Zegeye T, Belay G, Vallejo-Trujillo A, Han J, Hanotte O. Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia. Front Genet 2023; 14:1050365. [PMID: 37600659 PMCID: PMC10432725 DOI: 10.3389/fgene.2023.1050365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 07/14/2023] [Indexed: 08/22/2023] Open
Abstract
The Tigray region, where we found around eight per cent of the indigenous cattle population of Ethiopia, is considered as the historic centre of the country, with the ancient pre-Aksumite and Aksumite civilisations in contact with the civilisations of the Fertile Crescent and the Indian subcontinent. Here, we used whole genome sequencing data to characterise the genomic diversity, relatedness, and admixture of five cattle populations (Abergelle, Arado, Begait, Erob, and Raya) indigenous to the Tigray region of Ethiopia. We detected 28 to 29 million SNPs and 2.7 to 2.9 million indels in each population, of which 7% of SNPs and 34% of indels were novel. Functional annotation of the variants showed around 0.01% SNPs and 0.22%-0.27% indels in coding regions. Enrichment analysis of genes overlapping missense private SNPs revealed 20 significant GO terms and KEGG pathways that were shared by or specific to breeds. They included important genes associated with morphology (SCN4A, TAS1R2 and KCNG4), milk yield (GABRG1), meat quality (MMRN2, VWC2), feed efficiency (PCDH8 and SLC26A3), immune response (LAMC1, PCDH18, CELSR1, TLR6 and ITGA5), heat resistance (NPFFR1 and HTR7) and genes belonging to the olfactory gene family, which may be related to adaptation to harsh environments. Tigray indigenous cattle are very diverse. Their genome-wide average nucleotide diversity ranged from 0.0035 to 0.0036. The number of heterozygous SNPs was about 0.6-0.7 times higher than homozygous ones. The within-breed average number of ROHs ranged from 777.82 to 1000.45, with the average sum of the length of ROHs ranging from 122.01 Mbp to 163.88 Mbp. The genomic inbreeding coefficients differed among animals and breeds, reaching up to 10% in some Begait and Raya animals. Tigray indigenous cattle shared a common ancestry with Asian indicine (85.6%-88.7%) and African taurine (11.3%-14.1%) cattle, with very small, if any, European taurine introgression. This study identified high within-breed genetic diversity representing an opportunity for breeding improvement programs and, also, significant novel variants that could increase the number of known cattle variants, an important contribution to the knowledge of domestic cattle genetic diversity.
Collapse
Affiliation(s)
- Tsadkan Zegeye
- Mekelle Agricultural Research Center, Tigray Agricultural Research Institute, Mekelle, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adriana Vallejo-Trujillo
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jianlin Han
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Olivier Hanotte
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
- Cells, Organism and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| |
Collapse
|
10
|
Tuncay IO, DeVries D, Gogate A, Kaur K, Kumar A, Xing C, Goodspeed K, Seyoum-Tesfa L, Chahrour MH. The genetics of autism spectrum disorder in an East African familial cohort. CELL GENOMICS 2023; 3:100322. [PMID: 37492102 PMCID: PMC10363748 DOI: 10.1016/j.xgen.2023.100322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/09/2023] [Accepted: 04/16/2023] [Indexed: 07/27/2023]
Abstract
Autism spectrum disorder (ASD) is a group of complex neurodevelopmental conditions affecting communication and social interaction in 2.3% of children. Studies that demonstrated its complex genetic architecture have been mainly performed in populations of European ancestry. We investigate the genetics of ASD in an East African cohort (129 individuals) from a population with higher prevalence (5%). Whole-genome sequencing identified 2.13 million private variants in the cohort and potentially pathogenic variants in known ASD genes (including CACNA1C, CHD7, FMR1, and TCF7L2). Admixture analysis demonstrated that the cohort comprises two ancestral populations, African and Eurasian. Admixture mapping discovered 10 regions that confer ASD risk on the African haplotypes, containing several known ASD genes. The increased ASD prevalence in this population suggests decreased heterogeneity in the underlying genetic etiology, enabling risk allele identification. Our approach emphasizes the power of African genetic variation and admixture analysis to inform the architecture of complex disorders.
Collapse
Affiliation(s)
- Islam Oguz Tuncay
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Darlene DeVries
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashlesha Gogate
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kiran Kaur
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kimberly Goodspeed
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Maria H Chahrour
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
11
|
Fleskes RE, Owsley DW, Bruwelheide KS, Barca KG, Griffith DR, Cabana GS, Schurr TG. Historical genomes elucidate European settlement and the African diaspora in Delaware. Curr Biol 2023:S0960-9822(23)00551-1. [PMID: 37207647 DOI: 10.1016/j.cub.2023.04.069] [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: 09/16/2022] [Revised: 02/01/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
The 17th-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid-Atlantic region of the United States.1 The demographic features of these initial colonial migrations are not uniformly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.2 European colonizers also instituted a system of racialized slavery through which they forcibly transported thousands of Africans to the Chesapeake region. Historical information about African-descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.3,4 To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery's Rest archaeological site (circa 1675-1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individuals of European maternal descent, buried 15-20 feet from a northern group of three individuals of African maternal descent.5 Autosomal results further illuminate genomic similarities to Northwestern European reference populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17th and early 18th century North America.
Collapse
Affiliation(s)
- Raquel E Fleskes
- Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA; Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Douglas W Owsley
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
| | - Karin S Bruwelheide
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Kathryn G Barca
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | | | - Graciela S Cabana
- Department of Anthropology, University of Tennessee, Knoxville, TN 37996, USA; Molecular Anthropology Laboratories, University of Tennessee, Knoxville, TN 37996, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
12
|
Pless E, Eckburg AM, Henn BM. Predicting Environmental and Ecological Drivers of Human Population Structure. Mol Biol Evol 2023; 40:msad094. [PMID: 37146165 PMCID: PMC10172848 DOI: 10.1093/molbev/msad094] [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: 07/12/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 05/07/2023] Open
Abstract
Landscape, climate, and culture can all structure human populations, but few existing methods are designed to simultaneously disentangle among a large number of variables in explaining genetic patterns. We developed a machine learning method for identifying the variables which best explain migration rates, as measured by the coalescent-based program MAPS that uses shared identical by descent tracts to infer spatial migration across a region of interest. We applied our method to 30 human populations in eastern Africa with high-density single nucleotide polymorphism array data. The remarkable diversity of ethnicities, languages, and environments in this region offers a unique opportunity to explore the variables that shape migration and genetic structure. We explored more than 20 spatial variables relating to landscape, climate, and presence of tsetse flies. The full model explained ∼40% of the variance in migration rate over the past 56 generations. Precipitation, minimum temperature of the coldest month, and elevation were the variables with the highest impact. Among the three groups of tsetse flies, the most impactful was fusca which transmits livestock trypanosomiasis. We also tested for adaptation to high elevation among Ethiopian populations. We did not identify well-known genes related to high elevation, but we did find signatures of positive selection related to metabolism and disease. We conclude that the environment has influenced the migration and adaptation of human populations in eastern Africa; the remaining variance in structure is likely due in part to cultural or other factors not captured in our model.
Collapse
Affiliation(s)
- Evlyn Pless
- Department of Anthropology, Center for Population Biology, University of California, Davis, CA
| | - Anders M Eckburg
- Department of Anthropology, Center for Population Biology, University of California, Davis, CA
| | - Brenna M Henn
- Department of Anthropology, Center for Population Biology, University of California, Davis, CA
- UC Davis Genome Center, University of California, Davis, CA
| |
Collapse
|
13
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
14
|
Lucock MD. The evolution of human skin pigmentation: A changing medley of vitamins, genetic variability, and UV radiation during human expansion. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:252-271. [PMID: 36790744 PMCID: PMC10083917 DOI: 10.1002/ajpa.24564] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 04/12/2023]
Abstract
This review examines putative, yet likely critical evolutionary pressures contributing to human skin pigmentation and subsequently, depigmentation phenotypes. To achieve this, it provides a synthesis of ideas that frame contemporary thinking, without limiting the narrative to pigmentation genes alone. It examines how geography and hence the quality and quantity of UV exposure, pigmentation genes, diet-related genes, vitamins, anti-oxidant nutrients, and cultural practices intersect and interact to facilitate the evolution of human skin color. The article has a strong focus on the vitamin D-folate evolutionary model, with updates on the latest biophysical research findings to support this paradigm. This model is examined within a broad canvas that takes human expansion out of Africa and genetic architecture into account. A thorough discourse on the biology of melanization is provided (includes relationship to BH4 and DNA damage repair), with the relevance of this to the UV sensitivity of folate and UV photosynthesis of vitamin D explained in detail, including the relevance of these vitamins to reproductive success. It explores whether we might be able to predict vitamin-related gene polymorphisms that pivot metabolism to the prevailing UVR exposome within the vitamin D-folate evolutionary hypothesis context. This is discussed in terms of a primary adaptive phenotype (pigmentation/depigmentation), a secondary adaptive phenotype (flexible metabolic phenotype based on vitamin-related gene polymorphism profile), and a tertiary adaptive strategy (dietary anti-oxidants to support the secondary adaptive phenotype). Finally, alternative evolutionary models for pigmentation are discussed, as are challenges to future research in this area.
Collapse
Affiliation(s)
- Mark D. Lucock
- School of Environmental & Life SciencesUniversity of NewcastleOurimbahNew South WalesAustralia
| |
Collapse
|
15
|
Fleskes RE, Cabana GS, Gilmore JK, Juarez C, Karcher E, Oubré L, Mishoe G, Ofunniyin AA, Schurr TG. Community-engaged ancient DNA project reveals diverse origins of 18th-century African descendants in Charleston, South Carolina. Proc Natl Acad Sci U S A 2023; 120:e2201620120. [PMID: 36623185 PMCID: PMC9934026 DOI: 10.1073/pnas.2201620120] [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: 01/28/2022] [Accepted: 11/18/2022] [Indexed: 01/11/2023] Open
Abstract
In this study, we present the results of community-engaged ancient DNA research initiated after the remains of 36 African-descended individuals dating to the late 18th century were unearthed in the port city of Charleston, South Carolina. The Gullah Society of Charleston, along with other Charleston community members, initiated a collaborative genomic study of these ancestors of presumed enslaved status, in an effort to visibilize their histories. We generated 18 low-coverage genomes and 31 uniparental haplotypes to assess their genetic origins and interrelatedness. Our results indicate that they have predominantly West and West-Central African genomic ancestry, with one individual exhibiting some genomic affiliation with populations in the Americas. Most were assessed as genetic males, and no autosomal kin were identified among them. Overall, this study expands our understanding of the colonial histories of African descendant populations in the US South.
Collapse
Affiliation(s)
- Raquel E. Fleskes
- Department of Anthropology, University of Connecticut, Storrs, CT06269
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
| | | | - Joanna K. Gilmore
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
- Department of Sociology and Anthropology, The College of Charleston, Charleston, SC29424
| | - Chelsey Juarez
- Department of Anthropology, California State University, Fresno, CA93740
| | - Emilee Karcher
- Department of Anthropology, University of California, Davis, CA95616
| | - La’Sheia Oubré
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
| | - Grant Mishoe
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
| | - Ade A. Ofunniyin
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
- Department of Sociology and Anthropology, The College of Charleston, Charleston, SC29424
| | - Theodore G. Schurr
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA19104
| |
Collapse
|
16
|
Alva O, Leroy A, Heiske M, Pereda-Loth V, Tisseyre L, Boland A, Deleuze JF, Rocha J, Schlebusch C, Fortes-Lima C, Stoneking M, Radimilahy C, Rakotoarisoa JA, Letellier T, Pierron D. The loss of biodiversity in Madagascar is contemporaneous with major demographic events. Curr Biol 2022; 32:4997-5007.e5. [PMID: 36334586 DOI: 10.1016/j.cub.2022.09.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/13/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
Only 400 km off the coast of East Africa, the island of Madagascar is one of the last large land masses to have been colonized by humans. While many questions surround the human occupation of Madagascar, recent studies raise the question of human impact on endemic biodiversity and landscape transformation. Previous genetic and linguistic analyses have shown that the Malagasy population has emerged from an admixture that happened during the last millennium, between Bantu-speaking African populations and Austronesian-speaking Asian populations. By studying the sharing of chromosome segments between individuals (IBD determination), local ancestry information, and simulated genetic data, we inferred that the Malagasy ancestral Asian population was isolated for more than 1,000 years with an effective size of just a few hundred individuals. This isolation ended around 1,000 years before present (BP) by admixture with a small African population. Around the admixture time, there was a rapid demographic expansion due to intrinsic population growth of the newly admixed population, which coincides with extensive changes in Madagascar's landscape and the extinction of all endemic large-bodied vertebrates. Therefore, our approach can provide new insights into past human demography and associated impacts on ecosystems.
Collapse
Affiliation(s)
- Omar Alva
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Anaïs Leroy
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Margit Heiske
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Veronica Pereda-Loth
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Lenka Tisseyre
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Anne Boland
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000 Evry, France
| | - Jean-François Deleuze
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000 Evry, France
| | - Jorge Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Cesar Fortes-Lima
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany; Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Villeurbanne, France
| | - Chantal Radimilahy
- Musée d'Art et d'Archéologie, University of Antananarivo, Antananarivo, Madagascar
| | | | - Thierry Letellier
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Denis Pierron
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France.
| |
Collapse
|
17
|
Mouterde M, Daali Y, Rollason V, Čížková M, Mulugeta A, Al Balushi KA, Fakis G, Constantinidis TC, Al-Thihli K, Černá M, Makonnen E, Boukouvala S, Al-Yahyaee S, Yimer G, Černý V, Desmeules J, Poloni ES. Joint Analysis of Phenotypic and Genomic Diversity Sheds Light on the Evolution of Xenobiotic Metabolism in Humans. Genome Biol Evol 2022; 14:6852765. [PMID: 36445690 PMCID: PMC9750130 DOI: 10.1093/gbe/evac167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 11/03/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
Variation in genes involved in the absorption, distribution, metabolism, and excretion of drugs (ADME) can influence individual response to a therapeutic treatment. The study of ADME genetic diversity in human populations has led to evolutionary hypotheses of adaptation to distinct chemical environments. Population differentiation in measured drug metabolism phenotypes is, however, scarcely documented, often indirectly estimated via genotype-predicted phenotypes. We administered seven probe compounds devised to target six cytochrome P450 enzymes and the P-glycoprotein (P-gp) activity to assess phenotypic variation in four populations along a latitudinal transect spanning over Africa, the Middle East, and Europe (349 healthy Ethiopian, Omani, Greek, and Czech volunteers). We demonstrate significant population differentiation for all phenotypes except the one measuring CYP2D6 activity. Genome-wide association studies (GWAS) evidenced that the variability of phenotypes measuring CYP2B6, CYP2C9, CYP2C19, and CYP2D6 activity was associated with genetic variants linked to the corresponding encoding genes, and additional genes for the latter three. Instead, GWAS did not indicate any association between genetic diversity and the phenotypes measuring CYP1A2, CYP3A4, and P-gp activity. Genome scans of selection highlighted multiple candidate regions, a few of which included ADME genes, but none overlapped with the GWAS candidates. Our results suggest that different mechanisms have been shaping the evolution of these phenotypes, including phenotypic plasticity, and possibly some form of balancing selection. We discuss how these contrasting results highlight the diverse evolutionary trajectories of ADME genes and proteins, consistent with the wide spectrum of both endogenous and exogenous molecules that are their substrates.
Collapse
Affiliation(s)
| | - Youssef Daali
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Victoria Rollason
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Martina Čížková
- Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Anwar Mulugeta
- Department of Pharmacology and Clinical Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Khalid A Al Balushi
- College of Pharmacy, National University of Science and Technology, Muscat, Sultanate of Oman
| | - Giannoulis Fakis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Khalid Al-Thihli
- Department of Genetics, Sultan Qaboos University Hospital, Muscat, Sultanate of Oman
| | - Marie Černá
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Eyasu Makonnen
- Department of Pharmacology and Clinical Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia,Center for Innovative Drug Development and Therapeutic Trials for Africa, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sotiria Boukouvala
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Said Al-Yahyaee
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Getnet Yimer
- Center for Global Genomics & Health Equity, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Viktor Černý
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jules Desmeules
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | | |
Collapse
|
18
|
Martini R, Delpe P, Chu TR, Arora K, Lord B, Verma A, Bedi D, Karanam B, Elhussin I, Chen Y, Gebregzabher E, Oppong JK, Adjei EK, Jibril Suleiman A, Awuah B, Muleta MB, Abebe E, Kyei I, Aitpillah FS, Adinku MO, Ankomah K, Osei-Bonsu EB, Chitale DA, Bensenhaver JM, Nathanson DS, Jackson L, Petersen LF, Proctor E, Stonaker B, Gyan KK, Gibbs LD, Monojlovic Z, Kittles RA, White J, Yates CC, Manne U, Gardner K, Mongan N, Cheng E, Ginter P, Hoda S, Elemento O, Robine N, Sboner A, Carpten JD, Newman L, Davis MB. African Ancestry-Associated Gene Expression Profiles in Triple-Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent. Cancer Discov 2022; 12:2530-2551. [PMID: 36121736 PMCID: PMC9627137 DOI: 10.1158/2159-8290.cd-22-0138] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/17/2022] [Accepted: 08/23/2022] [Indexed: 01/12/2023]
Abstract
Women of sub-Saharan African descent have disproportionately higher incidence of triple-negative breast cancer (TNBC) and TNBC-specific mortality across all populations. Population studies show racial differences in TNBC biology, including higher prevalence of basal-like and quadruple-negative subtypes in African Americans (AA). However, previous investigations relied on self-reported race (SRR) of primarily U.S. populations. Due to heterogeneous genetic admixture and biological consequences of social determinants, the true association of African ancestry with TNBC biology is unclear. To address this, we conducted RNA sequencing on an international cohort of AAs, as well as West and East Africans with TNBC. Using comprehensive genetic ancestry estimation in this African-enriched cohort, we found expression of 613 genes associated with African ancestry and 2,000+ associated with regional African ancestry. A subset of African-associated genes also showed differences in normal breast tissue. Pathway enrichment and deconvolution of tumor cellular composition revealed that tumor-associated immunologic profiles are distinct in patients of African descent. SIGNIFICANCE Our comprehensive ancestry quantification process revealed that ancestry-associated gene expression profiles in TNBC include population-level distinctions in immunologic landscapes. These differences may explain some differences in race-group clinical outcomes. This study shows the first definitive link between African ancestry and the TNBC immunologic landscape, from an African-enriched international multiethnic cohort. See related commentary by Hamilton et al., p. 2496. This article is highlighted in the In This Issue feature, p. 2483.
Collapse
Affiliation(s)
- Rachel Martini
- Department of Surgery, Weill Cornell Medical College, New York, New York.,Department of Genetics, University of Georgia, Athens, Georgia
| | - Princesca Delpe
- Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York
| | | | | | - Brittany Lord
- Department of Surgery, Weill Cornell Medical College, New York, New York.,Department of Genetics, University of Georgia, Athens, Georgia
| | - Akanksha Verma
- Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York
| | - Deepa Bedi
- Department of Biomedical Sciences, Tuskegee University, Tuskegee, Alabama
| | | | - Isra Elhussin
- Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
| | - Yalei Chen
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - Endale Gebregzabher
- Department of Biochemistry, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Joseph K Oppong
- Department of Surgery, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Ernest K Adjei
- Department of Pathology, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Aisha Jibril Suleiman
- Department of Pathology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Baffour Awuah
- Directorate of Oncology, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Mahteme Bekele Muleta
- Department of Surgery, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Engida Abebe
- Department of Surgery, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Ishmael Kyei
- Department of Surgery, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Frances S Aitpillah
- Department of Surgery, Komfo Anokye Teaching Hospital, Kumasi, Ghana.,Department of Surgery, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael O Adinku
- Department of Surgery, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Kwasi Ankomah
- Directorate of Radiology, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | | | | | | | | | - LaToya Jackson
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | | | - Erica Proctor
- Department of Surgery, Henry Ford Health System, Detroit, Michigan
| | - Brian Stonaker
- Department of Surgery, Weill Cornell Medical College, New York, New York
| | - Kofi K Gyan
- Department of Surgery, Weill Cornell Medical College, New York, New York
| | - Lee D Gibbs
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Zarko Monojlovic
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Rick A Kittles
- Department of Population Sciences, City of Hope, Duarte, California
| | - Jason White
- Department of Biology, Tuskegee University, Tuskegee, Alabama
| | - Clayton C Yates
- Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
| | - Upender Manne
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kevin Gardner
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Nigel Mongan
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom.,Department of Pharmacology, Weill Cornell Medical College, New York, New York
| | - Esther Cheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Paula Ginter
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Syed Hoda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York.,Institute of Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | | | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - John D Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Lisa Newman
- Department of Surgery, Weill Cornell Medical College, New York, New York
| | - Melissa B Davis
- Department of Surgery, Weill Cornell Medical College, New York, New York.,Department of Genetics, University of Georgia, Athens, Georgia.,Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York.,New York Genome Center, New York, New York.,Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| |
Collapse
|
19
|
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.
Collapse
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
| | | |
Collapse
|
20
|
Elhaik E. Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated. Sci Rep 2022; 12:14683. [PMID: 36038559 PMCID: PMC9424212 DOI: 10.1038/s41598-022-14395-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/06/2022] [Indexed: 12/29/2022] Open
Abstract
Principal Component Analysis (PCA) is a multivariate analysis that reduces the complexity of datasets while preserving data covariance. The outcome can be visualized on colorful scatterplots, ideally with only a minimal loss of information. PCA applications, implemented in well-cited packages like EIGENSOFT and PLINK, are extensively used as the foremost analyses in population genetics and related fields (e.g., animal and plant or medical genetics). PCA outcomes are used to shape study design, identify, and characterize individuals and populations, and draw historical and ethnobiological conclusions on origins, evolution, dispersion, and relatedness. The replicability crisis in science has prompted us to evaluate whether PCA results are reliable, robust, and replicable. We analyzed twelve common test cases using an intuitive color-based model alongside human population data. We demonstrate that PCA results can be artifacts of the data and can be easily manipulated to generate desired outcomes. PCA adjustment also yielded unfavorable outcomes in association studies. PCA results may not be reliable, robust, or replicable as the field assumes. Our findings raise concerns about the validity of results reported in the population genetics literature and related fields that place a disproportionate reliance upon PCA outcomes and the insights derived from them. We conclude that PCA may have a biasing role in genetic investigations and that 32,000-216,000 genetic studies should be reevaluated. An alternative mixed-admixture population genetic model is discussed.
Collapse
Affiliation(s)
- Eran Elhaik
- Department of Biology, Lund University, 22362, Lund, Sweden.
| |
Collapse
|
21
|
McQuillan MA, Ranciaro A, Hansen MEB, Fan S, Beggs W, Belay G, Woldemeskel D, Tishkoff SA. Signatures of Convergent Evolution and Natural Selection at the Alcohol Dehydrogenase Gene Region are Correlated with Agriculture in Ethnically Diverse Africans. Mol Biol Evol 2022; 39:6677382. [PMID: 36026493 PMCID: PMC9547508 DOI: 10.1093/molbev/msac183] [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: 01/19/2023] Open
Abstract
The alcohol dehydrogenase (ADH) family of genes encodes enzymes that catalyze the metabolism of ethanol into acetaldehyde. Nucleotide variation in ADH genes can affect the catalytic properties of these enzymes and is associated with a variety of traits, including alcoholism and cancer. Some ADH variants, including the ADH1B*48His (rs1229984) mutation in the ADH1B gene, reduce the risk of alcoholism and are under positive selection in multiple human populations. The advent of Neolithic agriculture and associated increase in fermented foods and beverages is hypothesized to have been a selective force acting on such variants. However, this hypothesis has not been tested in populations outside of Asia. Here, we use genome-wide selection scans to show that the ADH gene region is enriched for variants showing strong signals of positive selection in multiple Afroasiatic-speaking, agriculturalist populations from Ethiopia, and that this signal is unique among sub-Saharan Africans. We also observe strong selection signals at putatively functional variants in nearby lipid metabolism genes, which may influence evolutionary dynamics at the ADH region. Finally, we show that haplotypes carrying these selected variants were introduced into Northeast Africa from a West-Eurasian source within the last ∼2,000 years and experienced positive selection following admixture. These selection signals are not evident in nearby, genetically similar populations that practice hunting/gathering or pastoralist subsistence lifestyles, supporting the hypothesis that the emergence of agriculture shapes patterns of selection at ADH genes. Together, these results enhance our understanding of how adaptations to diverse environments and diets have influenced the African genomic landscape.
Collapse
Affiliation(s)
| | - Alessia Ranciaro
- Current address: Department of Biological Sciences, Human and Evolutionary Biology Section, University of Southern California, Los Angeles, CA
| | | | - Shaohua Fan
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dawit Woldemeskel
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy. Genomics 2022; 114:110405. [PMID: 35709925 DOI: 10.1016/j.ygeno.2022.110405] [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: 02/28/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022]
Abstract
Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithization and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidences point to a link between Southern Italians and the Balkans still present in modern times. To shed light on these dynamics, we analysed around 700 South Mediterranean genomes combined with informative ancient DNAs. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with a Bronze Age component ultimately originating from the Caucasus with high Iranian and Anatolian Neolithic ancestries. Furthermore, extremely differentiated allele frequencies among Northern and Southern Italy revealed putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits.
Collapse
|
24
|
Cuadros-Espinoza S, Laval G, Quintana-Murci L, Patin E. The genomic signatures of natural selection in admixed human populations. Am J Hum Genet 2022; 109:710-726. [PMID: 35259336 DOI: 10.1016/j.ajhg.2022.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
Admixture has been a pervasive phenomenon in human history, extensively shaping the patterns of population genetic diversity. There is increasing evidence to suggest that admixture can also facilitate genetic adaptation to local environments, i.e., admixed populations acquire beneficial mutations from source populations, a process that we refer to as "adaptive admixture." However, the role of adaptive admixture in human evolution and the power to detect it remain poorly characterized. Here, we use extensive computer simulations to evaluate the power of several neutrality statistics to detect natural selection in the admixed population, assuming multiple admixture scenarios. We show that statistics based on admixture proportions, Fadm and LAD, show high power to detect mutations that are beneficial in the admixed population, whereas other statistics, including iHS and FST, falsely detect neutral mutations that have been selected in the source populations only. By combining Fadm and LAD into a single, powerful statistic, we scanned the genomes of 15 worldwide, admixed populations for signatures of adaptive admixture. We confirm that lactase persistence and resistance to malaria have been under adaptive admixture in West Africans and in Malagasy, North Africans, and South Asians, respectively. Our approach also uncovers other cases of adaptive admixture, including APOL1 in Fulani nomads and PKN2 in East Indonesians, involved in resistance to infection and metabolism, respectively. Collectively, our study provides evidence that adaptive admixture has occurred in human populations whose genetic history is characterized by periods of isolation and spatial expansions resulting in increased gene flow.
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
Elliott KS, Haber M, Daggag H, Busby GB, Sarwar R, Kennet D, Petraglia M, Petherbridge LJ, Yavari P, Heard-Bey FU, Shobi B, Ghulam T, Haj D, Al Tikriti A, Mohammad A, Antony S, Alyileili M, Alaydaroos S, Lau E, Butler M, Yavari A, Knight JC, Ashrafian H, Barakat MT. Fine-Scale Genetic Structure in the United Arab Emirates Reflects Endogamous and Consanguineous Culture, Population History, and Geography. Mol Biol Evol 2022; 39:msac039. [PMID: 35192718 PMCID: PMC8911814 DOI: 10.1093/molbev/msac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The indigenous population of the United Arab Emirates (UAE) has a unique demographic and cultural history. Its tradition of endogamy and consanguinity is expected to produce genetic homogeneity and partitioning of gene pools while population movements and intercontinental trade are likely to have contributed to genetic diversity. Emiratis and neighboring populations of the Middle East have been underrepresented in the population genetics literature with few studies covering the broader genetic history of the Arabian Peninsula. Here, we genotyped 1,198 individuals from the seven Emirates using 1.7 million markers and by employing haplotype-based algorithms and admixture analyses, we reveal the fine-scale genetic structure of the Emirati population. Shared ancestry and gene flow with neighboring populations display their unique geographic position while increased intra- versus inter-Emirati kinship and sharing of uniparental haplogroups, reflect the endogamous and consanguineous cultural traditions of the Emirates and their tribes.
Collapse
Affiliation(s)
- Katherine S Elliott
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Marc Haber
- Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | - Hinda Daggag
- Imperial College London Diabetes Centre, Abu Dhabi, UAE
| | - George B Busby
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Rizwan Sarwar
- Experimental Therapeutics, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Derek Kennet
- Department of Archaeology, Durham University, Durham, United Kingdom
| | - Michael Petraglia
- Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Parisa Yavari
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Bindu Shobi
- Imperial College London Diabetes Centre, Abu Dhabi, UAE
| | - Tariq Ghulam
- Imperial College London Diabetes Centre, Abu Dhabi, UAE
| | - Dalia Haj
- Imperial College London Diabetes Centre, Abu Dhabi, UAE
| | | | | | - Suma Antony
- Imperial College London Diabetes Centre, Abu Dhabi, UAE
| | | | | | - Evelyn Lau
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mark Butler
- Experimental Therapeutics, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Arash Yavari
- Experimental Therapeutics, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Houman Ashrafian
- Experimental Therapeutics, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
27
|
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: 10] [Impact Index Per Article: 3.3] [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.
Collapse
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
| |
Collapse
|
28
|
A reference database of forensic autosomal and gonosomal STR markers in the Tigray population of Ethiopia. Forensic Sci Int Genet 2021; 56:102618. [PMID: 34735940 DOI: 10.1016/j.fsigen.2021.102618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 11/20/2022]
Abstract
Allele frequencies of 21 autosomal STR markers (AmpF/STR GlobalFiler) and haplotype frequencies of 27 Y- and 12 X-STR markers (AmpF/STR YFiler Plus and Investigator Argus X-12, respectively) were investigated in the Tigray population of Ethiopia, representing the main population group in the Tigray regional state of Ethiopia and neighboring Eritrea. For autosomal STR allele frequencies, the average random match probability in the Tigray sample was 2.1 × 10-27. The average locus by locus FST distance calculated comparing autosomal STR allele frequencies from Tigray and from a broad regional reference dataset currently available for the Horn of Africa was 0.003. The Tigray male sample displayed high Y-STR diversity, with complete individualization of haplotypes using the AmpF/STR YFiler Plus panel. Analysis of molecular variance did not detect significant heterogeneity between Y-STR haplotypes observed in the present study and those previously reported in the literature for other Tigray population samples from Ethiopia and Eritrea. Study of the X-STR landscape in Tigray evidenced several distinctive features including: the molecular characterization of a novel null allele at locus DXS10146 with frequency > 1%; allele dependency between loci within linkage groups I and III; significant differences in haplotype distribution compared to other Horn of Africa populations, that should be taken into account in kinship analysis. The collected data can be used as a reference STR database by local forensic genetics services and in genetic identification procedures of victims of human trafficking in the Mediterranean Sea, which frequently involve individuals originating from the Horn of Africa.
Collapse
|
29
|
Kissel A, Gebreyohanns M, Chahrour MH. A Brief Survey of Medical Practitioner Knowledge and Attitudes Regarding Autism Spectrum Disorder in Bahir Dar, Ethiopia. AFRICAN JOURNAL OF HEALTH SCIENCES 2021; 34:364-373. [PMID: 37920188 PMCID: PMC10621471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
BACKGROUND Autism spectrum disorder (ASD) continues to climb in prevalence worldwide. Developed nations have focused on aligning their medical and research communities in order to investigate the mechanisms of pathogenesis, diagnosis, and societal impact of this disorder. A simultaneous rise of ASD has impacted developing nations, such as Ethiopia, without a commensurate ability to research the knowledge, beliefs, resources, and training regarding this condition in the country. MATERIALS AND METHODS We administered a brief survey during a medical conference in Bahir Dar, Ethiopia, to investigate some of the education, information, and experiences with ASD within a small sample of medical and mental health providers in Ethiopia. RESULTS The data provided insight into the following areas pertaining to ASD in Ethiopia: perceived causes, knowledge, training, and areas of need. CONCLUSIONS Understanding local beliefs for causes and cures, as well as gaining indigenous opinions regarding what is needed for ASD education and resources in their nation, is the first step towards understanding the impact of this disorder and the approach to its treatment in Ethiopia.
Collapse
Affiliation(s)
- Abigail Kissel
- Department of Pediatrics, Division of Developmental-Behavioral Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, US
| | - Mehari Gebreyohanns
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Maria H. Chahrour
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| |
Collapse
|
30
|
Ahlquist KD, Bañuelos MM, Funk A, Lai J, Rong S, Villanea FA, Witt KE. Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture. Genome Biol Evol 2021; 13:evab115. [PMID: 34028527 PMCID: PMC8480178 DOI: 10.1093/gbe/evab115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/07/2021] [Accepted: 05/22/2021] [Indexed: 11/30/2022] Open
Abstract
The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.
Collapse
Affiliation(s)
- K D Ahlquist
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Mayra M Bañuelos
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Alyssa Funk
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Jiaying Lai
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Brown Center for Biomedical Informatics, Brown University, Providence, Rhode Island, USA
| | - Stephen Rong
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Fernando A Villanea
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Anthropology, University of Colorado Boulder, Colorado, USA
| | - Kelsey E Witt
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
| |
Collapse
|
31
|
Tarekegn GM, Khayatzadeh N, Liu B, Osama S, Haile A, Rischkowsky B, Zhang W, Tesfaye K, Dessie T, Mwai OA, Djikeng A, Mwacharo JM. Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats. Evol Appl 2021; 14:1716-1731. [PMID: 34295359 PMCID: PMC8287980 DOI: 10.1111/eva.13118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/15/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.
Collapse
Affiliation(s)
- Getinet M. Tarekegn
- Department of Animal Production and TechnologySchool of Animal Sciences and Veterinary MedicineBahir Dar UniversityBahir DarEthiopia
- Department of Animal Breeding and GeneticsSwedish University of Agricultural Sciences (SLU)UppsalaSweden
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural SystemsDivision of Livestock SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Bin Liu
- Inner Mongolia Agricultural UniversityHohhotChina
| | - Sarah Osama
- The University of QueenslandSaint LuciaQLDAustralia
| | - Aynalem Haile
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | - Barbara Rischkowsky
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | | | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Okeyo A. Mwai
- International Livestock Research Institute (ILRI)NairobiKenya
| | - Appolinaire Djikeng
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
| | - Joram M. Mwacharo
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
| |
Collapse
|
32
|
López S, Tarekegn A, Band G, van Dorp L, Bird N, Morris S, Oljira T, Mekonnen E, Bekele E, Blench R, Thomas MG, Bradman N, Hellenthal G. Evidence of the interplay of genetics and culture in Ethiopia. Nat Commun 2021; 12:3581. [PMID: 34117245 PMCID: PMC8196081 DOI: 10.1038/s41467-021-23712-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/13/2021] [Indexed: 11/13/2022] Open
Abstract
The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with-and shape-genetic structure in human populations. Using primarily new genetic variation data covering 1,214 Ethiopians representing 68 different ethnic groups, together with information on individuals' birthplaces, linguistic/religious practices and 31 cultural practices, we disentangle the effects of geographic distance, elevation, and social factors on the genetic structure of Ethiopians today. We provide evidence of associations between social behaviours and genetic differences among present-day peoples. We show that genetic similarity is broadly associated with linguistic affiliation, but also identify pronounced genetic similarity among groups from disparate language classifications that may in part be attributable to recent intermixing. We also illustrate how groups reporting the same culture traits are more genetically similar on average and show evidence of recent intermixing, suggesting that shared cultural traits may promote admixture. In addition to providing insights into the genetic structure and history of Ethiopia, we identify the most important cultural and geographic predictors of genetic differentiation and provide a resource for designing sampling protocols for future genetic studies involving Ethiopians.
Collapse
Affiliation(s)
- Saioa López
- Research Department of Genetics, Evolution & Environment, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
| | - Ayele Tarekegn
- Department of Archaeology and Heritage Management, College of Social Sciences, Addis Ababa University, New Classrooms (NCR) Building, Second Floor, Office No. 214, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lucy van Dorp
- Research Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Nancy Bird
- Research Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Sam Morris
- Research Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Tamiru Oljira
- Genomics & Bioinformatics Research Directorate (GBRD), Ethiopian Biotechnology Institute (EBTi), Addis Ababa, Ethiopia
| | - Ephrem Mekonnen
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Endashaw Bekele
- College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Roger Blench
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of History, University of Jos, Jos, Nigeria
| | - Mark G Thomas
- Research Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | | | - Garrett Hellenthal
- Research Department of Genetics, Evolution & Environment, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
| |
Collapse
|
33
|
Abstract
Behavioral genetics and cultural evolution have both revolutionized our understanding of human behavior-largely independent of each other. Here we reconcile these two fields under a dual inheritance framework, offering a more nuanced understanding of the interaction between genes and culture. Going beyond typical analyses of gene-environment interactions, we describe the cultural dynamics that shape these interactions by shaping the environment and population structure. A cultural evolutionary approach can explain, for example, how factors such as rates of innovation and diffusion, density of cultural sub-groups, and tolerance for behavioral diversity impact heritability estimates, thus yielding predictions for different social contexts. Moreover, when cumulative culture functionally overlaps with genes, genetic effects become masked, unmasked, or even reversed, and the causal effects of an identified gene become confounded with features of the cultural environment. The manner of confounding is specific to a particular society at a particular time, but a WEIRD (Western, educated, industrialized, rich, democratic) sampling problem obscures this boundedness. Cultural evolutionary dynamics are typically missing from models of gene-to-phenotype causality, hindering generalizability of genetic effects across societies and across time. We lay out a reconciled framework and use it to predict the ways in which heritability should differ between societies, between socioeconomic levels and other groupings within some societies but not others, and over the life course. An integrated cultural evolutionary behavioral genetic approach cuts through the nature-nurture debate and helps resolve controversies in topics such as IQ.
Collapse
|
34
|
New insights into human immunity from ancient genomics. Curr Opin Immunol 2021; 72:116-125. [PMID: 33992907 PMCID: PMC8452260 DOI: 10.1016/j.coi.2021.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/20/2022]
Abstract
Population genetic studies have clearly indicated that immunity and host defense are among the functions most frequently subject to natural selection, and increased our understanding of the biological relevance of the corresponding genes and their contribution to variable immune traits and diseases. Herein, we will focus on some recently studied forms of human adaptation to infectious agents, including hybridization with now-extinct hominins, such as Neanderthals and Denisovans, and admixture between modern human populations. These studies, which are partly enabled by the technological advances in the sequencing of DNA from ancient remains, provide new insight into the sources of immune response variation in contemporary humans, such as the recently reported link between Neanderthal heritage and susceptibility to severe COVID-19 disease. Furthermore, ancient DNA analyses, in both humans and pathogens, allow to measure the action of natural selection on immune genes across time and to reconstruct the impact of past epidemics on the evolution of human immunity.
Collapse
|
35
|
Hellenthal G, Bird N, Morris S. Structure and ancestry patterns of Ethiopians in genome-wide autosomal DNA. Hum Mol Genet 2021; 30:R42-R48. [PMID: 33547782 PMCID: PMC8242491 DOI: 10.1093/hmg/ddab019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/28/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
We review some of the current insights derived from the analyses of new large-scale, genome-wide autosomal variation data studies incorporating Ethiopians. Consistent with their substantial degree of cultural and linguistic diversity, genetic diversity among Ethiopians is higher than that seen across much larger geographic regions worldwide. This genetic variation is associated in part with ethnic identity, geography and linguistic classification. Numerous and varied admixture events have been inferred in Ethiopian groups, for example, involving sources related to present-day groups in West Eurasia and North Africa, with inferred dates spanning a few hundred to more than 4500 years ago. These disparate inferred ancestry patterns are correlated in part with groups' broad linguistic classifications, though with some notable exceptions. While deciphering these complex genetic signals remains challenging with available data, these studies and other projects focused on resolving competing hypotheses on the origins of specific ethnolinguistic groups demonstrate how genetic analyses can complement findings from anthropological and linguistic studies on Ethiopians.
Collapse
Affiliation(s)
- Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London Genetics Institute (UGI), University College London, London, WC1E 6BT, UK
| | - Nancy Bird
- Department of Genetics, Evolution and Environment, University College London Genetics Institute (UGI), University College London, London, WC1E 6BT, UK
| | - Sam Morris
- Department of Genetics, Evolution and Environment, University College London Genetics Institute (UGI), University College London, London, WC1E 6BT, UK
| |
Collapse
|
36
|
Huang X, Wang S, Jin L, He Y. Dissecting dynamics and differences of selective pressures in the evolution of human pigmentation. Biol Open 2021; 10:bio056523. [PMID: 33495209 PMCID: PMC7888712 DOI: 10.1242/bio.056523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023] Open
Abstract
Human pigmentation is a highly diverse and complex trait among populations and has drawn particular attention from both academic and non-academic investigators for thousands of years. Previous studies detected selection signals in several human pigmentation genes, but few studies have integrated contribution from multiple genes to the evolution of human pigmentation. Moreover, none has quantified selective pressures on human pigmentation over epochs and between populations. Here, we dissect dynamics and differences of selective pressures during different periods and between distinct populations with new approaches. We use genotype data of 19 genes associated with human pigmentation from 17 publicly available datasets and obtain data for 2346 individuals of six representative population groups from across the world. Our results quantify the strength of natural selection on light pigmentation not only in modern Europeans (0.0259/generation) but also in proto-Eurasians (0.00650/generation). Our results also suggest that several derived alleles associated with human dark pigmentation may be under positive directional selection in some African populations. Our study provides the first attempt to quantitatively investigate the dynamics of selective pressures during different time periods in the evolution of human pigmentation.This article has an associated First Person interview with the first author of the article.
Collapse
Affiliation(s)
- Xin Huang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Sijia Wang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Li Jin
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yungang He
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| |
Collapse
|
37
|
Coutinho A, Malmström H, Edlund H, Henshilwood CS, van Niekerk KL, Lombard M, Schlebusch CM, Jakobsson M. Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 174:701-713. [PMID: 33539553 DOI: 10.1002/ajpa.24236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 12/09/2020] [Accepted: 12/20/2020] [Indexed: 11/09/2022]
Abstract
Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter-gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry "Coloured" groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.
Collapse
Affiliation(s)
- Alexandra Coutinho
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa
| | - Hanna Edlund
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Christopher S Henshilwood
- SFF Centre for Early Sapiens Behaviour (SapienCE), University of Bergen, Bergen, Norway.,Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Karen L van Niekerk
- SFF Centre for Early Sapiens Behaviour (SapienCE), University of Bergen, Bergen, Norway
| | - Marlize Lombard
- Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa
| | - Carina M Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa.,Science for Life Laboratory, Uppsala, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa.,Science for Life Laboratory, Uppsala, Sweden
| |
Collapse
|
38
|
Kist NC, Lambert B, Campbell S, Katzourakis A, Lunn D, Lemey P, Iversen AKN. HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification. Virus Evol 2020; 6:veaa085. [PMID: 33343925 PMCID: PMC7733611 DOI: 10.1093/ve/veaa085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Pathogen-driven selection and past interbreeding with archaic human lineages have resulted in differences in human leukocyte antigen (HLA)-allele frequencies between modern human populations. Whether or not this variation affects pathogen subtype diversification is unknown. Here we show a strong positive correlation between ethnic diversity in African countries and both human immunodeficiency virus (HIV)-1 p24gag and subtype diversity. We demonstrate that ethnic HLA-allele differences between populations have influenced HIV-1 subtype diversification as the virus adapted to escape common antiviral immune responses. The evolution of HIV Subtype B (HIV-B), which does not appear to be indigenous to Africa, is strongly affected by immune responses associated with Eurasian HLA variants acquired through adaptive introgression from Neanderthals and Denisovans. Furthermore, we show that the increasing and disproportionate number of HIV-infections among African Americans in the USA drive HIV-B evolution towards an Africa-centric HIV-1 state. Similar adaptation of other pathogens to HLA variants common in affected populations is likely.
Collapse
Affiliation(s)
- Nicolaas C Kist
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Ben Lambert
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, Medical School Building St Mary’s Campus, Norfolk Place, London W2 1PG, UK
| | - Samuel Campbell
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Daniel Lunn
- Department of Statistics, University of Oxford, St Giles’, Oxford OX1 3LB, UK
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Leuven B-3000, Belgium
| | | |
Collapse
|
39
|
Walsh S, Izquierdo-Serra M, Acosta S, Edo A, Lloret M, Moret R, Bosch E, Oliva B, Bertranpetit J, Fernández-Fernández JM. Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population. Sci Rep 2020; 10:20999. [PMID: 33268808 PMCID: PMC7710729 DOI: 10.1038/s41598-020-78081-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/20/2020] [Indexed: 11/15/2022] Open
Abstract
TRPP3 (also called PKD2L1) is a nonselective, cation-permeable channel activated by multiple stimuli, including extracellular pH changes. TRPP3 had been considered a candidate for sour sensor in humans, due to its high expression in a subset of tongue receptor cells detecting sour, along with its membership to the TRP channel family known to function as sensory receptors. Here, we describe the functional consequences of two non-synonymous genetic variants (R278Q and R378W) found to be under strong positive selection in an Ethiopian population, the Gumuz. Electrophysiological studies and 3D modelling reveal TRPP3 loss-of-functions produced by both substitutions. R278Q impairs TRPP3 activation after alkalinisation by mislocation of H+ binding residues at the extracellular polycystin mucolipin domain. R378W dramatically reduces channel activity by altering conformation of the voltage sensor domain and hampering channel transition from closed to open state. Sour sensitivity tests in R278Q/R378W carriers argue against both any involvement of TRPP3 in sour detection and the role of such physiological process in the reported evolutionary positive selection past event.
Collapse
Affiliation(s)
- Sandra Walsh
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003, Barcelona, Catalonia, Spain
| | - Mercè Izquierdo-Serra
- Laboratory of Molecular Physiology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Sandra Acosta
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003, Barcelona, Catalonia, Spain
| | - Albert Edo
- Laboratory of Molecular Physiology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - María Lloret
- Laboratory of Molecular Physiology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Roser Moret
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003, Barcelona, Catalonia, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 43206, Reus, Spain
| | - Baldo Oliva
- Structural Bioinformatics Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003, Barcelona, Catalonia, Spain.
| | - José Manuel Fernández-Fernández
- Laboratory of Molecular Physiology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain.
| |
Collapse
|
40
|
Walsh S, Pagani L, Xue Y, Laayouni H, Tyler-Smith C, Bertranpetit J. Positive selection in admixed populations from Ethiopia. BMC Genet 2020; 21:108. [PMID: 33092534 PMCID: PMC7580818 DOI: 10.1186/s12863-020-00908-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/27/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In the process of adaptation of humans to their environment, positive or adaptive selection has played a main role. Positive selection has, however, been under-studied in African populations, despite their diversity and importance for understanding human history. RESULTS Here, we have used 119 available whole-genome sequences from five Ethiopian populations (Amhara, Oromo, Somali, Wolayta and Gumuz) to investigate the modes and targets of positive selection in this part of the world. The site frequency spectrum-based test SFselect was applied to idfentify a wide range of events of selection (old and recent), and the haplotype-based statistic integrated haplotype score to detect more recent events, in each case with evaluation of the significance of candidate signals by extensive simulations. Additional insights were provided by considering admixture proportions and functional categories of genes. We identified both individual loci that are likely targets of classic sweeps and groups of genes that may have experienced polygenic adaptation. We found population-specific as well as shared signals of selection, with folate metabolism and the related ultraviolet response and skin pigmentation standing out as a shared pathway, perhaps as a response to the high levels of ultraviolet irradiation, and in addition strong signals in genes such as IFNA, MRC1, immunoglobulins and T-cell receptors which contribute to defend against pathogens. CONCLUSIONS Signals of positive selection were detected in Ethiopian populations revealing novel adaptations in East Africa, and abundant targets for functional follow-up.
Collapse
Affiliation(s)
- Sandra Walsh
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88 08003, Barcelona, Catalonia, Spain
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
- Department of Biology, University of Padova, 35131, Padova, Italy
| | - Yali Xue
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88 08003, Barcelona, Catalonia, Spain
- Bioinformatics Studies, ESCI-UPF, Barcelona, Catalonia, Spain
| | - Chris Tyler-Smith
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88 08003, Barcelona, Catalonia, Spain.
| |
Collapse
|
41
|
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.
Collapse
|
42
|
Luisi P, García A, Berros JM, Motti JMB, Demarchi DA, Alfaro E, Aquilano E, Argüelles C, Avena S, Bailliet G, Beltramo J, Bravi CM, Cuello M, Dejean C, Dipierri JE, Jurado Medina LS, Lanata JL, Muzzio M, Parolin ML, Pauro M, Paz Sepúlveda PB, Rodríguez Golpe D, Santos MR, Schwab M, Silvero N, Zubrzycki J, Ramallo V, Dopazo H. Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina. PLoS One 2020; 15:e0233808. [PMID: 32673320 PMCID: PMC7365470 DOI: 10.1371/journal.pone.0233808] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/12/2020] [Indexed: 12/24/2022] Open
Abstract
Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries.
Collapse
Affiliation(s)
- Pierre Luisi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Angelina García
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Museo de Antropología, Córdoba, Argentina
| | - Juan Manuel Berros
- Consejo Nacional de Investigaciones Científicas y Técnicas - Laboratorio de Análisis de Datos, Biocódices S.A., Buenos Aires, Argentina
| | - Josefina M B Motti
- Núcleo de Estudios Interdisciplinarios de Poblaciones Humanas de Patagonia Austral (NEIPHA), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional del Centro de la Provincia de Buenos Aires, Quequén, Argentina
| | - Darío A Demarchi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Museo de Antropología, Córdoba, Argentina
| | - Emma Alfaro
- Instituto de Ecorregiones Andinas (INECOA), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Jujuy, Jujuy, Argentina.,Instituto de Biología de la Altura, Universidad Nacional de Jujuy, Jujuy, Argentina
| | - Eliana Aquilano
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Carina Argüelles
- Departamento de Genética, Grupo de Investigación en Genética Aplicada (GIGA), Facultad de Ciencias Exactas, Químicas y Naturales, Instituto de Biología Subtropical (IBS)-Nodo Posadas, Universidad Nacional de Misiones (UNaM)-Consejo Nacional de Investigaciones Científicas y Técnicas, Posadas, Argentina.,Cátedra de Biología Molecular, Carrera de Medicina, Facultad de Ciencias de la Salud, Universidad Católica de las Misiones (UCAMI), Posadas, Argentina
| | - Sergio Avena
- Instituto de Ciencias Antropológicas (ICA), Facultad de Filosofía y Letras, Universidad de Buenos Aires, Buenos Aires, Argentina.,Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | - Graciela Bailliet
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Julieta Beltramo
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina.,Laboratorio de Análisis Comparativo de ADN, Corte Suprema de Justicia de la Provincia de Buenos Aires, La Plata, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Mariela Cuello
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Cristina Dejean
- Instituto de Ciencias Antropológicas (ICA), Facultad de Filosofía y Letras, Universidad de Buenos Aires, Buenos Aires, Argentina.,Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | | | - Laura S Jurado Medina
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - José Luis Lanata
- Instituto de Investigaciones en Diversidad Cultural y Procesos de Cambio (IIDyPCa), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Río Negro, San Carlos de Bariloche, Argentina
| | - Marina Muzzio
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - María Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Consejo Nacional de Investigaciones Científicas y Técnicas - Centro Nacional Patagónico, Puerto Madryn, Argentina
| | - Maia Pauro
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Museo de Antropología, Córdoba, Argentina
| | - Paula B Paz Sepúlveda
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Daniela Rodríguez Golpe
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - María Rita Santos
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Marisol Schwab
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Natalia Silvero
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH) - Consejo Nacional de Investigaciones Científicas y Técnicas-Centro Nacional Patagónico, Puerto Madryn, Argentina
| | - Hernán Dopazo
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas - Biocodices S.A., Buenos Aires, Argentina
| |
Collapse
|
43
|
Kelemu T, Erlandsson L, Seifu D, Hansson E, Abebe M, Teklu S, Girma S, Traherne JA, Moffett A, Hansson SR. Polymorphism in killer cell immunoglobulin-like receptors and human leukocyte antigen-c and predisposition to preeclampsia in Ethiopian pregnant women population. J Reprod Immunol 2020; 141:103169. [PMID: 32603992 DOI: 10.1016/j.jri.2020.103169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/29/2020] [Accepted: 06/15/2020] [Indexed: 01/17/2023]
Abstract
INTRODUCTION Preeclampsia (PE) is a human specific pregnancy-related syndrome of unknown etiology that affects 2-8 % of pregnancies. Polymorphism in maternal Killer Cell Immunoglobulin-like Receptors (KIRs) and the ligand fetal Human Leukocyte Antigen-C (HLA-C) may predispose pregnant mothers for PE due to defective trophoblast invasion into the maternal decidua. Our study aimed to investigate the association between maternal KIR and fetal HLA-C polymorphism and PE in Ethiopian pregnant women. METHODS We included a total of 288 (157 controls and 131 PE cases) in a case-controls study at Adama Regional Referral Hospital, Ethiopia. The KIR and HLA-C genotyping was done using traditional polymerase chain reaction on genomic DNA extracted form maternal venous and cord blood followed by 2% agarose gel electrophoresis. RESULTS The statistical associations between variables were evaluated using Pearson's Chi-square test. P < 0.05, with 95 % confidence interval was considered statistically significant. A significant association was observed between the KIR2DS1 and PE, with a higher frequency (60.5 %) of the gene in the control group. Similarly, a significant association was observed between KIR AA genotype and PE, with a higher frequency (38.2 %) of this genotype in the PE group. Ethiopians share the same risk genotype for PE as seen in previous African and European studies, namely homozygosity of a maternal KIR AA genotype. However, Ethiopians differ from other East African populations by sharing the same protective KIR2DS1 gene as Europeans.
Collapse
Affiliation(s)
- Tsehayneh Kelemu
- Department of Biochemistry, College of Health Sciences, Addis Ababa University, Ethiopia.
| | - Lena Erlandsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences Lund, Lund University, Sweden.
| | - Daniel Seifu
- Department of Biochemistry, College of Health Sciences, Addis Ababa University, Ethiopia; Department of Biochemistry, Division of Biomedical Sciences, University of Global Health Equity, Rwanda.
| | - Eva Hansson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences Lund, Lund University, Sweden.
| | | | - Sisay Teklu
- Department of Obstetrics and Gynecology, College of Health Sciences, Addis Ababa University, Ethiopia.
| | - Selfu Girma
- Armauer Hanson Research Institute, Ethiopia.
| | - James A Traherne
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Ashley Moffett
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Stefan R Hansson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences Lund, Lund University, Sweden.
| |
Collapse
|
44
|
DNA Fingerprinting and Species Identification Uncovers the Genetic Diversity of Katsouni Pea in the Greek Islands Amorgos and Schinoussa. PLANTS 2020; 9:plants9040479. [PMID: 32283704 PMCID: PMC7238155 DOI: 10.3390/plants9040479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 11/17/2022]
Abstract
Pea (P. sativum L.), one of the most important legume crops worldwide, has been traditionally cultivated in Lesser Cyclades since ancient times. The commonly known traditional pea cultivar, ‘Katsouni’, is endemic to the islands of Amorgos and Schinoussa and is of great local economic importance. Despite the widespread cultivation of ‘Katsouni’ in both islands, it is still unknown whether the current Schinoussa and Amorgos pea populations are distinct landraces, and if they have common evolutionary origin. To assist conservation and breeding of the pea crop, the genetic diversity and phylogenetic relationships of 39 pea samples from Amorgos and 86 from Schinoussa were studied using DNA barcoding and ISSR marker analyses. The results indicate that both populations are different landraces with distinct geographical distribution and are more closely related to P. sativum subsp. elatius than the P. abyssinicum and P. fulvum species. Further characterization of the ‘Katsouni’ landraces for functional polymorphisms regarding pathogen resistance, revealed susceptibility to the powdery mildew (Erysiphe pisi DC.). This work represents the first investigation on the genetic diversity and population structure of the ‘Katsouni’ cultivar. Exploiting the local genetic diversity of traditional landraces is fundamental for conservation practices and crop improvement through breeding strategies.
Collapse
|
45
|
Genome-wide analyses disclose the distinctive HLA architecture and the pharmacogenetic landscape of the Somali population. Sci Rep 2020; 10:5652. [PMID: 32221414 PMCID: PMC7101338 DOI: 10.1038/s41598-020-62645-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/17/2020] [Indexed: 12/16/2022] Open
Abstract
African populations are underrepresented in medical genomics studies. For the Somali population, there is virtually no information on genomic markers with significance to precision medicine. Here, we analyzed nearly 900,000 genomic markers in samples collected from 95 unrelated individuals in the North Eastern Somalia. ADMIXTURE program for estimation of individual ancestries revealed a homogenous Somali population. Principal component analysis with PLINK software showed approximately 60% East African and 40% West Eurasian genes in the Somali population, with a close relation to the Cushitic and Semitic speaking Ethiopian populations. We report the unique features of human leukocyte antigens (HLA) in the Somali population, which seem to differentiate from all other neighboring regions compared. Current study identified high prevalence of the diabetes type 1 (T1D) predisposing HLA DR-DQ haplotypes in Somalia. This finding may explain the increased T1D risk observed among Somali children. In addition, ethnic Somalis were found to host the highest frequencies observed thus far for several pharmacogenetic variants, including UGT1A4*2. In conclusion, we report that the Somali population displays genetic traits of significance to health and disease. The Somali dataset is publicly available and will add more information to the few genomic datasets available for African populations.
Collapse
|
46
|
d'Errico F, Pitarch Martí A, Shipton C, Le Vraux E, Ndiema E, Goldstein S, Petraglia MD, Boivin N. Trajectories of cultural innovation from the Middle to Later Stone Age in Eastern Africa: Personal ornaments, bone artifacts, and ocher from Panga ya Saidi, Kenya. J Hum Evol 2020; 141:102737. [PMID: 32163764 DOI: 10.1016/j.jhevol.2019.102737] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 01/16/2023]
Abstract
African Middle Stone Age (MSA) populations used pigments, manufactured and wore personal ornaments, made abstract engravings, and produced fully shaped bone tools. However, ongoing research across Africa reveals variability in the emergence of cultural innovations in the MSA and their subsequent development through the Later Stone Age (LSA). When present, it appears that cultural innovations manifest regional variability, suggestive of distinct cultural traditions. In eastern Africa, several Late Pleistocene sites have produced evidence for novel activities, but the chronologies of key behavioral innovations remain unclear. The 3 m deep, well-dated, Panga ya Saidi sequence in eastern Kenya, encompassing 19 layers covering a time span of 78 kyr beginning in late Marine Isotope Stage 5, is the only known African site recording the interplay between cultural and ecological diversity in a coastal forested environment. Excavations have yielded worked and incised bones, ostrich eggshell beads (OES), beads made from seashells, worked and engraved ocher pieces, fragments of coral, and a belemnite fossil. Here, we provide, for the first time, a detailed analysis of this material. This includes a taphonomic, archeozoological, technological, and functional study of bone artifacts; a technological and morphometric analysis of personal ornaments; and a technological and geochemical analysis of ocher pieces. The interpretation of the results stemming from the analysis of OES beads is guided by an ethnoarcheological perspective and field observations. We demonstrate that key cultural innovations on the eastern African coast are evident by 67 ka and exhibit remarkable diversity through the LSA and Iron Age. We suggest the cultural trajectories evident at Panga ya Saidi were shaped by both regional traditions and cultural/demic diffusion.
Collapse
Affiliation(s)
- Francesco d'Errico
- UMR 5199 CNRS De La Préhistoire à L'Actuel: Culture, Environnement, et Anthropologie (PACEA), Université Bordeaux, Allée Geoffroy Saint Hilaire, CS 50023 F - 33615 Pessac CEDEX, Talence, France; Centre for Early Sapiens Behaviour, Øysteinsgate 3, Postboks 7805, 5020 University of Bergen, Norway.
| | - Africa Pitarch Martí
- UMR 5199 CNRS De La Préhistoire à L'Actuel: Culture, Environnement, et Anthropologie (PACEA), Université Bordeaux, Allée Geoffroy Saint Hilaire, CS 50023 F - 33615 Pessac CEDEX, Talence, France; Seminari d'Estudis i Recerques Prehistòriques (SERP), Facultat de Geografia i Història, Departament d'Història i Arqueologia, Universitat de Barcelona, Montalegre 6, 08001, Barcelona, Spain
| | - Ceri Shipton
- Centre of Excellence for Australian Biodiversity and Heritage, College of Asia and the Pacific, The Australian National University, ACT 0200, Australia
| | - Emma Le Vraux
- UMR 5199 CNRS De La Préhistoire à L'Actuel: Culture, Environnement, et Anthropologie (PACEA), Université Bordeaux, Allée Geoffroy Saint Hilaire, CS 50023 F - 33615 Pessac CEDEX, Talence, France
| | - Emmanuel Ndiema
- National Museums of Kenya, Department of Earth Sciences, Box 40658 - 00100, Nairobi, Kenya
| | - Steven Goldstein
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07745 Jena, Germany
| | - Michael D Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07745 Jena, Germany; Human Origins Program, Smithsonian Institution, Washington, D.C., 20560, USA; School of Social Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07745 Jena, Germany; School of Social Science, The University of Queensland, Brisbane, QLD 4072, Australia; Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr. N.W., Calgary, AB, T2N 1N4, Canada; Department of Anthropology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW Washington, D.C. 20560, USA
| |
Collapse
|
47
|
Characterization of ancestry informative markers in the Tigray population of Ethiopia: A contribution to the identification process of dead migrants in the Mediterranean Sea. Forensic Sci Int Genet 2020; 45:102207. [DOI: 10.1016/j.fsigen.2019.102207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 11/16/2019] [Accepted: 11/19/2019] [Indexed: 01/16/2023]
|
48
|
Yelmen B, Mondal M, Marnetto D, Pathak AK, Montinaro F, Gallego Romero I, Kivisild T, Metspalu M, Pagani L. Ancestry-Specific Analyses Reveal Differential Demographic Histories and Opposite Selective Pressures in Modern South Asian Populations. Mol Biol Evol 2020; 36:1628-1642. [PMID: 30952160 PMCID: PMC6657728 DOI: 10.1093/molbev/msz037] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high-quality modern genomes, these models can be tested for gene and genome level deviations. Using local ancestry deconvolution and masking, we reconstructed population-specific surrogates of the two main ancestral components for more than 500 samples from 25 South Asian populations and showed our approach to be robust via coalescent simulations. Our f3 and f4 statistics–based estimates reveal that the reconstructed haplotypes are good proxies for the source populations that admixed in the area and point to complex interpopulation relationships within the West Eurasian component, compatible with multiple waves of arrival, as opposed to a simpler one wave scenario. Our approach also provides reliable local haplotypes for future downstream analyses. As one such example, the local ancestry deconvolution in South Asians reveals opposite selective pressures on two pigmentation genes (SLC45A2 and SLC24A5) that are common or fixed in West Eurasians, suggesting post-admixture purifying and positive selection signals, respectively.
Collapse
Affiliation(s)
- Burak Yelmen
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mayukh Mondal
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Ajai K Pathak
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Francesco Montinaro
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Irene Gallego Romero
- Melbourne Integrative Genomics and School of BioSciences, University of Melbourne, Parkville, Australia
| | - Toomas Kivisild
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Luca Pagani
- Institute of Genomics, University of Tartu, Tartu, Estonia.,APE Lab, Department of Biology, University of Padova, Padova, Italy
| |
Collapse
|
49
|
Vicente M, Jakobsson M, Ebbesen P, Schlebusch CM. Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations. Mol Biol Evol 2020; 36:1849-1861. [PMID: 31288264 PMCID: PMC6735883 DOI: 10.1093/molbev/msz089] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Southern African indigenous groups, traditionally hunter-gatherers (San) and herders (Khoekhoe), are commonly referred to as “Khoe-San” populations and have a long history in southern Africa. Their ancestors were largely isolated up until ∼2,000 years ago before the arrival of pastoralists and farmers in southern Africa. Assessing relationships among regional Khoe-San groups has been challenging due to admixture with immigrant populations that obscure past population affinities and gene flow among these autochthonous communities. We re-evaluate a combined genome-wide data set of previously published southern Africa Khoe-San populations in conjunction with novel data from Khoe-San individuals collected in Xade (Central Kalahari Game Reserve, Botswana) prior to their resettlement outside the reserve. After excluding regions in the genome that trace their ancestry to recent migrant groups, the genetic diversity of 20 Khoe-San groups fitted an isolation-by-distance model. Even though isolation-by-distance explained most genetic affinities between the different autochthonous groups, additional signals of contact between Khoe-San groups could be detected. For instance, we found stronger genetic affinities, than what would be explained by isolation-by-distance gene flow, between the two geographically separated Khoe-San groups, who speak branches of the Kx’a-language family (ǂHoan and Ju). We also scanned the genome-wide data for signals of adaptive gene flow from farmers/herders into Khoe-San groups and identified a number of genomic regions potentially introduced by the arrival of the new groups. This study provides a comprehensive picture of affinities among Khoe-San groups, prior to the arrival of recent migrants, and found that these affinities are primarily determined by the geographic landscape.
Collapse
Affiliation(s)
- Mário Vicente
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.,SciLifeLab, Uppsala, Sweden
| | - Peter Ebbesen
- Department of Health Science and Technology, University of Aalborg, Aalborg, Denmark
| | - Carina M Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.,SciLifeLab, Uppsala, Sweden
| |
Collapse
|
50
|
West Asian sources of the Eurasian component in Ethiopians: a reassessment. Sci Rep 2019; 9:18811. [PMID: 31827175 PMCID: PMC6906521 DOI: 10.1038/s41598-019-55344-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/25/2019] [Indexed: 01/17/2023] Open
Abstract
The presence of genomic signatures of Eurasian origin in contemporary Ethiopians has been reported by several authors and estimated to have arrived in the area from 3000 years ago. Several studies reported plausible source populations for such a signature, using haplotype based methods on modern data or single-site methods on modern or ancient data. These studies did not reach a consensus and suggested an Anatolian or Sardinia-like proxy, broadly Levantine or Neolithic Levantine as possible sources. We demonstrate, however, that the deeply divergent, autochthonous African component which accounts for ~50% of most contemporary Ethiopian genomes, affects the overall allele frequency spectrum to an extent that makes it hard to control for it and, at once, to discern between subtly different, yet important, Eurasian sources (such as Anatolian or Levant Neolithic ones). Here we re-assess pattern of allele sharing between the Eurasian component of Ethiopians (here called “NAF” for Non African) and ancient and modern proxies. Our results unveil a genomic legacy that may connect the Eurasian genetic component of contemporary Ethiopians with Sea People and with population movements that affected the Mediterranean area and the Levant after the fall of the Minoan civilization.
Collapse
|