1
|
Fähnrich A, Stephan I, Hirose M, Haarich F, Awadelkareem MA, Ibrahim S, Busch H, Wohlers I. North and East African mitochondrial genetic variation needs further characterization towards precision medicine. J Adv Res 2023; 54:59-76. [PMID: 36736695 DOI: 10.1016/j.jare.2023.01.021] [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: 10/04/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Mitochondria are maternally inherited cell organelles with their own genome, and perform various functions in eukaryotic cells such as energy production and cellular homeostasis. Due to their inheritance and manifold biological roles in health and disease, mitochondrial genetics serves a dual purpose of tracing the history as well as disease susceptibility of human populations across the globe. This work requires a comprehensive catalogue of commonly observed genetic variations in the mitochondrial DNAs for all regions throughout the world. So far, however, certain regions, such as North and East Africa have been understudied. OBJECTIVES To address this shortcoming, we have created the most comprehensive quality-controlled North and East African mitochondrial data set to date and use it for characterizing mitochondrial genetic variation in this region. METHODS We compiled 11 published cohorts with novel data for mitochondrial genomes from 159 Sudanese individuals. We combined these 641 mitochondrial sequences with sequences from the 1000 Genomes (n = 2504) and the Human Genome Diversity Project (n = 828) and used the tool haplocheck for extensive quality control and detection of in-sample contamination, as well as Nanopore long read sequencing for haplogroup validation of 18 samples. RESULTS Using a subset of high-coverage mitochondrial sequences, we predict 15 potentially novel haplogroups in North and East African subjects and observe likely phylogenetic deviations from the established PhyloTree reference for haplogroups L0a1 and L2a1. CONCLUSION Our findings demonstrate common hitherto unexplored variants in mitochondrial genomes of North and East Africa that lead to novel phylogenetic relationships between haplogroups present in these regions. These observations call for further in-depth population genetic studies in that region to enable the prospective use of mitochondrial genetic variation for precision medicine.
Collapse
Affiliation(s)
- Anke Fähnrich
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Isabel Stephan
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Misa Hirose
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Franziska Haarich
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, and University Heart Center, Lübeck, Lübeck, Germany
| | - Mosab Ali Awadelkareem
- Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Saleh Ibrahim
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Khalifa University, Abu Dhabi, United Arab Emirates
| | - Hauke Busch
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538 Lübeck, Germany
| | - Inken Wohlers
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Biomedical Data Science, Research Center Borstel, 23845 Borstel, Germany.
| |
Collapse
|
2
|
Frachetti M, Di Cosmo N, Esper J, Khalidi L, Mauelshagen F, Oppenheimer C, Rohland E, Büntgen U. The dahliagram: An interdisciplinary tool for investigation, visualization, and communication of past human-environmental interaction. SCIENCE ADVANCES 2023; 9:eadj3142. [PMID: 37992177 PMCID: PMC10664986 DOI: 10.1126/sciadv.adj3142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Investigation into the nexus of human-environmental behavior has seen increasing collaboration of archaeologists, historians, and paleo-scientists. However, many studies still lack interdisciplinarity and overlook incompatibilities in spatiotemporal scaling of environmental and societal data and their uncertainties. Here, we argue for a strengthened commitment to collaborative work and introduce the "dahliagram" as a tool to analyze and visualize quantitative and qualitative knowledge from diverse disciplinary sources and epistemological backgrounds. On the basis of regional cases of past human mobility in eastern Africa, Inner Eurasia, and the North Atlantic, we develop three dahliagrams that illustrate pull and push factors underlying key phases of population movement across different geographical scales and over contrasting periods of time since the end of the last Ice Age. Agnostic to analytical units, dahliagrams offer an effective tool for interdisciplinary investigation, visualization, and communication of complex human-environmental interactions at a diversity of spatiotemporal scales.
Collapse
Affiliation(s)
- Michael Frachetti
- Department of Anthropology, Washington University in St. Louis, 1 Brookings Drive, CB 1114, St. Louis, MO 63130, USA
- School of Cultural Heritage, Northwest University, Xi’an, China
| | - Nicola Di Cosmo
- Institute for Advanced Study, Princeton University, Princeton, NJ 08544, USA
| | - Jan Esper
- Department of Geography, Johannes Gutenberg University, Becherweg 21, 55099 Mainz, Germany
- Global Change Research Institute (CzechGlobe), Czech Academy of Sciences, 603 00 Brno, Czech Republic
| | - Lamya Khalidi
- Université Côte d’Azur, CNRS, CEPAM, 24 avenue des Diables Bleus, 06300 Nice, France
| | - Franz Mauelshagen
- Department of Social Anthropology, University of Bielefeld, 33615 Bielefeld, Germany
| | - Clive Oppenheimer
- Department of Geography, University of Cambridge, Cambridge CB2 3EN, UK
| | - Eleonora Rohland
- Department of History, University of Bielefeld, 33615 Bielefeld, Germany
| | - Ulf Büntgen
- Global Change Research Institute (CzechGlobe), Czech Academy of Sciences, 603 00 Brno, Czech Republic
- Department of Geography, University of Cambridge, Cambridge CB2 3EN, UK
- Swiss Federal Research Institute (WSL), 8903 Birmensdorf, Switzerland
- Department of Geography, Faculty of Science, Masaryk University, 613 00 Brno, Czech Republic
| |
Collapse
|
3
|
Roca-Umbert A, Garcia-Calleja J, Vogel-González M, Fierro-Villegas A, Ill-Raga G, Herrera-Fernández V, Bosnjak A, Muntané G, Gutiérrez E, Campelo F, Vicente R, Bosch E. Human genetic adaptation related to cellular zinc homeostasis. PLoS Genet 2023; 19:e1010950. [PMID: 37747921 PMCID: PMC10553801 DOI: 10.1371/journal.pgen.1010950] [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: 02/28/2023] [Revised: 10/05/2023] [Accepted: 08/31/2023] [Indexed: 09/27/2023] Open
Abstract
SLC30A9 encodes a ubiquitously zinc transporter (ZnT9) and has been consistently suggested as a candidate for positive selection in humans. However, no direct adaptive molecular phenotype has been demonstrated. Our results provide evidence for directional selection operating in two major complementary haplotypes in Africa and East Asia. These haplotypes are associated with differential gene expression but also differ in the Met50Val substitution (rs1047626) in ZnT9, which we show is found in homozygosis in the Denisovan genome and displays accompanying signatures suggestive of archaic introgression. Although we found no significant differences in systemic zinc content between individuals with different rs1047626 genotypes, we demonstrate that the expression of the derived isoform (ZnT9 50Val) in HEK293 cells shows a gain of function when compared with the ancestral (ZnT9 50Met) variant. Notably, the ZnT9 50Val variant was found associated with differences in zinc handling by the mitochondria and endoplasmic reticulum, with an impact on mitochondrial metabolism. Given the essential role of the mitochondria in skeletal muscle and since the derived allele at rs1047626 is known to be associated with greater susceptibility to several neuropsychiatric traits, we propose that adaptation to cold may have driven this selection event, while also impacting predisposition to neuropsychiatric disorders in modern humans.
Collapse
Affiliation(s)
- Ana Roca-Umbert
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Jorge Garcia-Calleja
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Marina Vogel-González
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Alejandro Fierro-Villegas
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Gerard Ill-Raga
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Víctor Herrera-Fernández
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Anja Bosnjak
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Gerard Muntané
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, Reus, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
| | - Esteban Gutiérrez
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rubén Vicente
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
4
|
Petersen BC. An economic model and evidence of the evolution of human intelligence in the Middle Pleistocene: Climate change and assortative mating. PLoS One 2023; 18:e0287964. [PMID: 37531351 PMCID: PMC10395973 DOI: 10.1371/journal.pone.0287964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
A main objective of this paper is to provide the first model of how climate change, working through sexual selection, could have led to dramatic increases in hominin brain size, and presumably intelligence, in the Middle Pleistocene. The model is built using core elements from the field of family economics, including assortative mating and specialization and complementarities between mates. The main assumptions are that family public goods (e.g., conversation, shelter, fire) were particularly cognitively intensive to produce and became increasingly important for child survival during glacial phases. Intermediate climates (e.g., not the depths of severe glacial phases) create the largest gains from specialization, encouraging negative assortative mating. In contrast, severe glacial phases encourage positive assortative mating because of the rising importance of family public goods. One testable hypothesis is that absence of severe glacial phases should have led to stasis in brain size. Two other testable hypotheses are that severe glacial phases should have led to speciation events, as well as increases in brain size. The evidence shows that there was a million-year stasis in cranial size prior to the start of the severe glacial phases. This stasis is broken by a speciation event (Homo heidelbergensis), with the oldest fossil evidence dated near the close of the first severe glacial phase. In the next 300 kyr, there are two additional severe glacial phases, accompanied by considerable increases in cranial capacity. The last speciation event is Homo sapiens, with the earliest fossils dated near the end of the last of these two glacial phases.
Collapse
Affiliation(s)
- Bruce C Petersen
- Department of Economics, Washington University, St. Louis, Missouri, United States of America
| |
Collapse
|
5
|
Majara L, Kalungi A, Koen N, Tsuo K, Wang Y, Gupta R, Nkambule LL, Zar H, Stein DJ, Kinyanda E, Atkinson EG, Martin AR. Low and differential polygenic score generalizability among African populations due largely to genetic diversity. HGG ADVANCES 2023; 4:100184. [PMID: 36873096 PMCID: PMC9982687 DOI: 10.1016/j.xhgg.2023.100184] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/04/2023] [Indexed: 02/15/2023] Open
Abstract
African populations are vastly underrepresented in genetic studies but have the most genetic variation and face wide-ranging environmental exposures globally. Because systematic evaluations of genetic prediction had not yet been conducted in ancestries that span African diversity, we calculated polygenic risk scores (PRSs) in simulations across Africa and in empirical data from South Africa, Uganda, and the United Kingdom to better understand the generalizability of genetic studies. PRS accuracy improves with ancestry-matched discovery cohorts more than from ancestry-mismatched studies. Within ancestrally and ethnically diverse South African individuals, we find that PRS accuracy is low for all traits but varies across groups. Differences in African ancestries contribute more to variability in PRS accuracy than other large cohort differences considered between individuals in the United Kingdom versus Uganda. We computed PRS in African ancestry populations using existing European-only versus ancestrally diverse genetic studies; the increased diversity produced the largest accuracy gains for hemoglobin concentration and white blood cell count, reflecting large-effect ancestry-enriched variants in genes known to influence sickle cell anemia and the allergic response, respectively. Differences in PRS accuracy across African ancestries originating from diverse regions are as large as across out-of-Africa continental ancestries, requiring commensurate nuance.
Collapse
Affiliation(s)
- Lerato Majara
- Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER), Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Allan Kalungi
- Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER), Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Department of Psychiatry, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Mental Health Project, Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) & London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Nastassja Koen
- Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER), Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Cape Town, South Africa
| | - Kristin Tsuo
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Ying Wang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rahul Gupta
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Lethukuthula L. Nkambule
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heather Zar
- Department of Paediatrics and Child Health, Red Cross Children’s Hospital and Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Dan J. Stein
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Cape Town, South Africa
| | - Eugene Kinyanda
- Mental Health Project, Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) & London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Elizabeth G. Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alicia R. Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
6
|
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
|
7
|
Alnaqbi H, Tay GK, Chehadeh SEH, Alsafar H. Characterizing the diversity of MHC conserved extended haplotypes using families from the United Arab Emirates. Sci Rep 2022; 12:7165. [PMID: 35504942 PMCID: PMC9065074 DOI: 10.1038/s41598-022-11256-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022] Open
Abstract
Aside from its anthropological relevance, the characterization of the allele frequencies of genes in the human Major Histocompatibility Complex (MHC) and the combination of these alleles that make up MHC conserved extended haplotypes (CEHs) is necessary for histocompatibility matching in transplantation as well as mapping disease association loci. The structure and content of the MHC region in Middle Eastern populations remain poorly characterized, posing challenges when establishing disease association studies in ethnic groups that inhabit the region and reducing the capacity to translate genetic research into clinical practice. This study was conceived to address a gap of knowledge, aiming to characterize CEHs in the United Arab Emirates (UAE) population through segregation analysis of high-resolution, pedigree-phased, MHC haplotypes derived from 41 families. Twenty per cent (20.5%) of the total haplotype pool derived from this study cohort were identified as putative CEHs in the UAE population. These consisted of CEHs that have been previously detected in other ethnic groups, including the South Asian CEH 8.2 [HLA- C*07:02-B*08:01-DRB1*03:01-DQA1*05:01-DQB1*02:01 (H.F. 0.094)] and the common East Asian CEH 58.1 [HLA- C*03:02-B*58:01-DRB1*03:01- DQA1*05:01-DQB1*02:01 (H.F. 0.024)]. Additionally, three novel CEHs were identified in the current cohort, including HLA- C*15:02-B*40:06-DRB1*16:02-DQB1*05:02 (H.F. 0.035), HLA- C*16:02-B*51:01-DRB1*16:01-DQA1*01:02-DQB1*05:02 (H.F. 0.029), and HLA- C*03:02-B*58:01-DRB1*16:01-DQA1*01:02-DQB1*05:02 (H.F. 0.024). Overall, the results indicate a substantial gene flow with neighbouring ethnic groups in the contemporary UAE population including South Asian, East Asian, African, and European populations. Importantly, alleles and haplotypes that have been previously associated with autoimmune diseases (e.g., Type 1 Diabetes) were also present. In this regard, this study emphasizes that an appreciation for ethnic differences can provide insights into subpopulation-specific disease-related polymorphisms, which has remained a difficult endeavour.
Collapse
Affiliation(s)
- Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science and Technology, P.O. BOX 127788, Abu Dhabi, UAE.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, P.O. BOX 127788, Abu Dhabi, UAE.,Division of Psychiatry, UWA Medical School, The University of Western Australia, Perth, WA, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Sarah El Hajj Chehadeh
- Center for Biotechnology, Khalifa University of Science and Technology, P.O. BOX 127788, Abu Dhabi, UAE.,Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, P.O. BOX 127788, Abu Dhabi, UAE. .,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. .,Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
8
|
Hellwig T, Abbo S, Ophir R. Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:419-439. [PMID: 35061306 PMCID: PMC9303476 DOI: 10.1111/tpj.15678] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/15/2022] [Indexed: 05/25/2023]
Abstract
Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well-diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so-called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.
Collapse
Affiliation(s)
- Timo Hellwig
- The Levi Eshkol School of AgricultureThe Hebrew University of JerusalemJerusalem, RehovotIsrael
- Volcani Center, Agricultural Research OrganizationRishon LeZionIsrael
- Institute of Plant Genetics, Heinrich‐Heine‐UniversityDüsseldorfGermany
| | - Shahal Abbo
- The Levi Eshkol School of AgricultureThe Hebrew University of JerusalemJerusalem, RehovotIsrael
| | - Ron Ophir
- Volcani Center, Agricultural Research OrganizationRishon LeZionIsrael
| |
Collapse
|
9
|
Verma RK, Kalyakulina A, Mishra A, Ivanchenko M, Jalan S. Role of mitochondrial genetic interactions in determining adaptation to high altitude human population. Sci Rep 2022; 12:2046. [PMID: 35132109 PMCID: PMC8821606 DOI: 10.1038/s41598-022-05719-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022] Open
Abstract
Physiological and haplogroup studies performed to understand high-altitude adaptation in humans are limited to individual genes and polymorphic sites. Due to stochastic evolutionary forces, the frequency of a polymorphism is affected by changes in the frequency of a near-by polymorphism on the same DNA sample making them connected in terms of evolution. Here, first, we provide a method to model these mitochondrial polymorphisms as "co-mutation networks" for three high-altitude populations, Tibetan, Ethiopian and Andean. Then, by transforming these co-mutation networks into weighted and undirected gene-gene interaction (GGI) networks, we were able to identify functionally enriched genetic interactions of CYB and CO3 genes in Tibetan and Andean populations, while NADH dehydrogenase genes in the Ethiopian population playing a significant role in high altitude adaptation. These co-mutation based genetic networks provide insights into the role of different set of genes in high-altitude adaptation in human sub-populations.
Collapse
Affiliation(s)
- Rahul K Verma
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Alena Kalyakulina
- Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Ankit Mishra
- Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Mikhail Ivanchenko
- Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Sarika Jalan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India. .,Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India.
| |
Collapse
|
10
|
Analysis of HLA gene polymorphisms in East Africans reveals evidence of gene flow in two Semitic populations from Sudan. Eur J Hum Genet 2021; 29:1259-1271. [PMID: 33753913 PMCID: PMC8384866 DOI: 10.1038/s41431-021-00845-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 11/28/2020] [Accepted: 02/25/2021] [Indexed: 02/02/2023] Open
Abstract
Sudan, a northeastern African country, is characterized by high levels of cultural, linguistic, and genetic diversity, which is believed to be affected by continuous migration from neighboring countries. Consistent with such demographic effect, genome-wide SNP data revealed a shared ancestral component among Sudanese Afro-Asiatic speaking groups and non-African populations, mainly from West Asia. Although this component is shared among all Afro-Asiatic speaking groups, the extent of this sharing in Semitic groups, such as Sudanese Arab, is still unknown. Using genotypes of six polymorphic human leukocyte antigen (HLA) genes (i.e., HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1), we examined the genetic structure of eight East African ethnic groups with origins in Sudan, South Sudan, and Ethiopia. We identified informative HLA alleles using principal component analysis, which revealed that the two Semitic groups (Gaalien and Shokrya) constituted a distinct cluster from the other Afro-Asiatic speaking groups in this study. The HLA alleles that distinguished Semitic Arabs co-exist in the same extended HLA haplotype, and those alleles are in strong linkage disequilibrium. Interestingly, we find the four-locus haplotype "C*12:02-B*52:01-DRB1*15:02-DQB1*06:01" exclusively in non-African populations and it is widely spread across Asia. The identification of this haplotype suggests a gene flow from Asia, and likely these haplotypes were brought to Africa through back migration from the Near East. These findings will be of interest to biomedical and anthropological studies that examine the demographic history of northeast Africa.
Collapse
|
11
|
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: 11] [Impact Index Per Article: 3.7] [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
|
12
|
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
|
13
|
Martin AR, Atkinson EG, Chapman SB, Stevenson A, Stroud RE, Abebe T, Akena D, Alemayehu M, Ashaba FK, Atwoli L, Bowers T, Chibnik LB, Daly MJ, DeSmet T, Dodge S, Fekadu A, Ferriera S, Gelaye B, Gichuru S, Injera WE, James R, Kariuki SM, Kigen G, Koenen KC, Kwobah E, Kyebuzibwa J, Majara L, Musinguzi H, Mwema RM, Neale BM, Newman CP, Newton CRJC, Pickrell JK, Ramesar R, Shiferaw W, Stein DJ, Teferra S, van der Merwe C, Zingela Z. Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations. Am J Hum Genet 2021; 108:656-668. [PMID: 33770507 PMCID: PMC8059370 DOI: 10.1016/j.ajhg.2021.03.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/05/2021] [Indexed: 12/21/2022] Open
Abstract
Genetic studies in underrepresented populations identify disproportionate numbers of novel associations. However, most genetic studies use genotyping arrays and sequenced reference panels that best capture variation most common in European ancestry populations. To compare data generation strategies best suited for underrepresented populations, we sequenced the whole genomes of 91 individuals to high coverage as part of the Neuropsychiatric Genetics of African Population-Psychosis (NeuroGAP-Psychosis) study with participants from Ethiopia, Kenya, South Africa, and Uganda. We used a downsampling approach to evaluate the quality of two cost-effective data generation strategies, GWAS arrays versus low-coverage sequencing, by calculating the concordance of imputed variants from these technologies with those from deep whole-genome sequencing data. We show that low-coverage sequencing at a depth of ≥4× captures variants of all frequencies more accurately than all commonly used GWAS arrays investigated and at a comparable cost. Lower depths of sequencing (0.5-1×) performed comparably to commonly used low-density GWAS arrays. Low-coverage sequencing is also sensitive to novel variation; 4× sequencing detects 45% of singletons and 95% of common variants identified in high-coverage African whole genomes. Low-coverage sequencing approaches surmount the problems induced by the ascertainment of common genotyping arrays, effectively identify novel variation particularly in underrepresented populations, and present opportunities to enhance variant discovery at a cost similar to traditional approaches.
Collapse
Affiliation(s)
- Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Elizabeth G Atkinson
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sinéad B Chapman
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Anne Stevenson
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Rocky E Stroud
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - 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
| | - Tera Bowers
- Broad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
| | - Lori B Chibnik
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Institute for Molecular Medicine Finland, Helsinki 00014, Finland
| | - Timothy DeSmet
- Broad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
| | - Sheila Dodge
- Broad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, 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
| | - Steven Ferriera
- Broad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
| | - Bizu Gelaye
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Stella Gichuru
- Department of Mental Health, Moi Teaching and Referral Hospital, 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 OX3 7JX, UK
| | - Gabriel Kigen
- Department of Pharmacology and Toxicology, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Karestan C Koenen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Edith Kwobah
- Department of Mental Health, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Joseph Kyebuzibwa
- Department of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Lerato Majara
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; SA MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
| | - 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, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Carter P Newman
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, 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 OX3 7JX, UK
| | | | - Raj Ramesar
- SA MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Welelta Shiferaw
- Department of Microbiology, Immunology, and Parasitology, 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; SA MRC Unit on Risk & Resilience in Mental Disorders, University of Cape Town and Neuroscience Institute, Cape Town, South Africa
| | - Solomon Teferra
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Celia van der Merwe
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Zukiswa Zingela
- Department of Psychiatry and Human Behavioral Sciences, Walter Sisulu University, Mthatha, South Africa
| |
Collapse
|
14
|
Wohlers I, Künstner A, Munz M, Olbrich M, Fähnrich A, Calonga-Solís V, Ma C, Hirose M, El-Mosallamy S, Salama M, Busch H, Ibrahim S. An integrated personal and population-based Egyptian genome reference. Nat Commun 2020; 11:4719. [PMID: 32948767 PMCID: PMC7501257 DOI: 10.1038/s41467-020-17964-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/24/2020] [Indexed: 02/05/2023] Open
Abstract
A small number of de novo assembled human genomes have been reported to date, and few have been complemented with population-based genetic variation, which is particularly important for North Africa, a region underrepresented in current genome-wide references. Here, we combine long- and short-read whole-genome sequencing data with recent assembly approaches into a de novo assembly of an Egyptian genome. The assembly demonstrates well-balanced quality metrics and is complemented with variant phasing via linked reads into haploblocks, which we associate with gene expression changes in blood. To construct an Egyptian genome reference, we identify genome-wide genetic variation within a cohort of 110 Egyptian individuals. We show that differences in allele frequencies and linkage disequilibrium between Egyptians and Europeans may compromise the transferability of European ancestry-based genetic disease risk and polygenic scores, substantiating the need for multi-ethnic genome references. Thus, the Egyptian genome reference will be a valuable resource for precision medicine.
Collapse
Affiliation(s)
- Inken Wohlers
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Axel Künstner
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Matthias Munz
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Michael Olbrich
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Anke Fähnrich
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Verónica Calonga-Solís
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990, Curitiba, Brazil
| | - Caixia Ma
- Novogene (UK) Company Limited, 25 Cambridge Science Park, Milton Road, CB4 0FW, Cambridge, UK
| | - Misa Hirose
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Shaaban El-Mosallamy
- Medical Experimental Research Center (MERC), Mansoura University, Elgomhouria St., Dakahlia Governorate, 35516, Mansoura, Egypt
| | - Mohamed Salama
- Medical Experimental Research Center (MERC), Mansoura University, Elgomhouria St., Dakahlia Governorate, 35516, Mansoura, Egypt
- Institute of Global Health and Human Ecology, The American University in Cairo, AUC avenue, 11835, Cairo, Egypt
| | - Hauke Busch
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
| | - Saleh Ibrahim
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
| |
Collapse
|
15
|
Tay GK, Henschel A, Daw Elbait G, Al Safar HS. Genetic Diversity and Low Stratification of the Population of the United Arab Emirates. Front Genet 2020; 11:608. [PMID: 32595703 PMCID: PMC7304494 DOI: 10.3389/fgene.2020.00608] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023] Open
Abstract
With high consanguinity rates on the Arabian Peninsula, it would not have been unexpected if the population of the United Arab Emirates (UAE) was shown to be relatively homogenous. However, this study of 1000 UAE nationals provided a contrasting perspective, one of a relatively heterogeneous population. Located at the apex of Europe, Asia, and Africa, the observed diversity could be explained by a plethora of migration patterns since the first Out-of-Africa movement. A strategy to explore the extent of genetic variation of the population of the UAE is presented. The first step involved a comprehensive population stratification study that was instructive for subsequent whole genome sequencing (WGS) of suitable representatives (which is described elsewhere). When these UAE data were compared to previous smaller studies from the region, the findings were consistent with a population that is a diverse and admixed group of people. However, rather than sharp and distinctive clusters, cluster analysis reveals low levels of stratification throughout the population. UAE emirates exhibit high within-Emirate-distance/among-Emirate distance ratios. Supervised admixture analysis showed a continuous gradient of ancestral populations, suggesting that admixture on the south eastern tip of the Arabian Peninsula occurred gradually. When visualized using a unique technique that combined admixture ratios and principal component analysis (PCA), unappreciated diversity was revealed while mitigating projection bias of conventional PCA. We observe low population stratification in the UAE in terms of homozygosity versus separation cluster coefficients. This holds for the UAE in a global context as well as for isolated cluster analysis of the Emirati birthplaces. However, the subtle clustering observed in the Emirates reflects geographic proximity and historic migration events. The analytical strategy used here highlights the complementary nature of data from genotype array and WGS for anthropological studies. Specifically, genotype array data were instructive to select representative subjects for WGS. Furthermore, from the 2.3 million allele frequencies obtained from genotype arrays, we identified 46,481 loci with allele frequencies that were significantly different with respect to other world populations. This comparison of allele frequencies facilitates variant prioritization in common diseases. In addition, these loci bear great potential as biomarkers in anthropological and forensic studies.
Collapse
Affiliation(s)
- Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, WA, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Andreas Henschel
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Gihan Daw Elbait
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba S Al Safar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| |
Collapse
|
16
|
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
|
17
|
Amambua-Ngwa A, Amenga-Etego L, Kamau E, Amato R, Ghansah A, Golassa L, Randrianarivelojosia M, Ishengoma D, Apinjoh T, Maïga-Ascofaré O, Andagalu B, Yavo W, Bouyou-Akotet M, Kolapo O, Mane K, Worwui A, Jeffries D, Simpson V, D'Alessandro U, Kwiatkowski D, Djimde AA. Major subpopulations of Plasmodium falciparum in sub-Saharan Africa. Science 2020; 365:813-816. [PMID: 31439796 DOI: 10.1126/science.aav5427] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 07/05/2019] [Indexed: 01/04/2023]
Abstract
Understanding genomic variation and population structure of Plasmodium falciparum across Africa is necessary to sustain progress toward malaria elimination. Genome clustering of 2263 P. falciparum isolates from 24 malaria-endemic settings in 15 African countries identified major western, central, and eastern ancestries, plus a highly divergent Ethiopian population. Ancestry aligned to these regional blocs, overlapping with both the parasite's origin and with historical human migration. The parasite populations are interbred and shared genomic haplotypes, especially across drug resistance loci, which showed the strongest recent identity-by-descent between populations. A recent signature of selection on chromosome 12 with candidate resistance loci against artemisinin derivatives was evident in Ghana and Malawi. Such selection and the emerging substructure may affect treatment-based intervention strategies against P. falciparum malaria.
Collapse
Affiliation(s)
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Edwin Kamau
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya.,Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK.,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research (NMIMR), Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Deus Ishengoma
- National Institute for Medical Research (NIMR), Tanga, Tanzania
| | - Tobias Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | | | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | - William Yavo
- Unite des Sciences Pharmaceutiques et Biologiques, University Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | | | - Oyebola Kolapo
- Medical Research Council Unit The Gambia at LSHTM, Banjul, The Gambia.,Department of Zoology, University of Lagos, Lagos, Nigeria
| | - Karim Mane
- Medical Research Council Unit The Gambia at LSHTM, Banjul, The Gambia
| | - Archibald Worwui
- Medical Research Council Unit The Gambia at LSHTM, Banjul, The Gambia
| | - David Jeffries
- Medical Research Council Unit The Gambia at LSHTM, Banjul, The Gambia
| | - Vikki Simpson
- Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA.,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | - Dominic Kwiatkowski
- Wellcome Sanger Institute, Hinxton, UK.,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Abdoulaye A Djimde
- Wellcome Sanger Institute, Hinxton, UK. .,Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| |
Collapse
|
18
|
Mogensen HS, Tvedebrink T, Børsting C, Pereira V, Morling N. Ancestry prediction efficiency of the software GenoGeographer using a z-score method and the ancestry informative markers in the Precision ID Ancestry Panel. Forensic Sci Int Genet 2020; 44:102154. [DOI: 10.1016/j.fsigen.2019.102154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/25/2019] [Accepted: 08/24/2019] [Indexed: 10/25/2022]
|
19
|
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
|
20
|
AlSafar HS, Al-Ali M, Elbait GD, Al-Maini MH, Ruta D, Peramo B, Henschel A, Tay GK. Introducing the first whole genomes of nationals from the United Arab Emirates. Sci Rep 2019; 9:14725. [PMID: 31604968 PMCID: PMC6789106 DOI: 10.1038/s41598-019-50876-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 09/20/2019] [Indexed: 12/30/2022] Open
Abstract
Whole Genome Sequencing (WGS) provides an in depth description of genome variation. In the era of large-scale population genome projects, the assembly of ethnic-specific genomes combined with mapping human reference genomes of underrepresented populations has improved the understanding of human diversity and disease associations. In this study, for the first time, whole genome sequences of two nationals of the United Arab Emirates (UAE) at >27X coverage are reported. The two Emirati individuals were predominantly of Central/South Asian ancestry. An in-house customized pipeline using BWA, Picard followed by the GATK tools to map the raw data from whole genome sequences of both individuals was used. A total of 3,994,521 variants (3,350,574 Single Nucleotide Polymorphisms (SNPs) and 643,947 indels) were identified for the first individual, the UAE S001 sample. A similar number of variants, 4,031,580 (3,373,501 SNPs and 658,079 indels), were identified for UAE S002. Variants that are associated with diabetes, hypertension, increased cholesterol levels, and obesity were also identified in these individuals. These Whole Genome Sequences has provided a starting point for constructing a UAE reference panel which will lead to improvements in the delivery of precision medicine, quality of life for affected individuals and a reduction in healthcare costs. The information compiled will likely lead to the identification of target genes that could potentially lead to the development of novel therapeutic modalities.
Collapse
Affiliation(s)
- Habiba S AlSafar
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mariam Al-Ali
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Gihan Daw Elbait
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | | | - Dymitr Ruta
- Etisalat-British Telecom Innovation Center, Abu Dhabi, United Arab Emirates
| | | | - Andreas Henschel
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. .,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. .,College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. .,School of Psychiatry and Clinical Neurosciences, University of Western Australia, Nedlands, Australia. .,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia.
| |
Collapse
|
21
|
Gene-dense autosomal chromosomes show evidence for increased selection. Heredity (Edinb) 2019; 123:774-783. [PMID: 31576017 DOI: 10.1038/s41437-019-0272-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022] Open
Abstract
Purifying selection tends to reduce nucleotide and haplotype diversity leading to increased linkage disequilibrium. However, detection of evidence for selection is difficult as the signature is confounded by wide variation in the recombination rate which has a complex relationship with selection. The effective bottleneck time (the ratio of the linkage disequilibrium map to the genetic map in Morgans) controls for variability in the recombination rate. Reduced effective bottleneck times indicate stronger residual linkage disequilibrium, consistent with increased selection. Using whole genome sequence data from one European and three Sub-Saharan African human populations we find, in the African samples, strong correlations between high gene densities and reduced effective bottleneck time for autosomal chromosomes. This suggests that gene-dense autosomes have been subject to increased purifying selection reducing effective bottleneck times compared to gene-poor autosomes. Although previous studies have shown unusually strong linkage disequilibrium for the sex chromosomes variation within the autosomes has not been recognised. The strongest relationship is between effective bottleneck time and the density of essential genes, which are likely targets of greater selective pressure (p = 0.006, for the 22 autosomes). The magnitude of the reduction in chromosome-specific effective bottleneck times from the least to the most gene-dense autosomes is ~17-21% for Sub-Saharan African populations. The effect size is greater in Sub-Saharan African populations, compared to a European sample, consistent with increased efficiency of selection in populations with larger effective population sizes which have not been subject to intense population bottlenecks as experienced by populations of European ancestry. The findings highlight the value of deeper analyses of selection within Sub-Saharan African populations.
Collapse
|
22
|
Fernandes V, Brucato N, Ferreira JC, Pedro N, Cavadas B, Ricaut FX, Alshamali F, Pereira L. Genome-Wide Characterization of Arabian Peninsula Populations: Shedding Light on the History of a Fundamental Bridge between Continents. Mol Biol Evol 2019; 36:575-586. [PMID: 30649405 DOI: 10.1093/molbev/msz005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Arabian Peninsula (AP) was an important crossroad between Africa, Asia, and Europe, being the cradle of the structure defining these main human population groups, and a continuing path for their admixture. The screening of 741,000 variants in 420 Arabians and 80 Iranians allowed us to quantify the dominant sub-Saharan African admixture in the west of the peninsula, whereas South Asian and Levantine/European influence was stronger in the east, leading to a rift between western and eastern sides of the Peninsula. Dating of the admixture events indicated that Indian Ocean slave trade and Islamization periods were important moments in the genetic makeup of the region. The western-eastern axis was also observable in terms of positive selection of diversity conferring lactose tolerance, with the West AP developing local adaptation and the East AP acquiring the derived allele selected in European populations and existing in South Asia. African selected malaria resistance through the DARC gene was enriched in all Arabian genomes, especially in the western part. Clear European influences associated with skin and eye color were equally frequent across the Peninsula.
Collapse
Affiliation(s)
- Veronica Fernandes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Nicolas Brucato
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Joana C Ferreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Nicole Pedro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Bruno Cavadas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - François-Xavier Ricaut
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Farida Alshamali
- Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Luisa Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| |
Collapse
|
23
|
Shultz DR, Montrey M, Shultz TR. Comparing fitness and drift explanations of Neanderthal replacement. Proc Biol Sci 2019; 286:20190907. [PMID: 31185865 DOI: 10.1098/rspb.2019.0907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
There is a general consensus among archaeologists that replacement of Neanderthals by anatomically modern humans in Europe occurred around 40-35 ka. However, the causal mechanism for this replacement continues to be debated. Proposed models have featured either fitness advantages in favour of anatomically modern humans or invoked neutral drift under various preconditions. Searching for specific fitness advantages in the archaeological record has proven difficult, as these may be obscured, absent or subject to interpretation. To bridge this gap, we rigorously compare the system-level properties of fitness- and drift-based explanations of Neanderthal replacement. Our stochastic simulations and analytical predictions show that, although both fitness and drift can produce replacement, they present important differences in (i) required initial conditions, (ii) reliability, (iii) time to replacement, and (iv) path to replacement (population histories). These results present useful opportunities for comparison with archaeological and genetic data. We find greater agreement between the available empirical evidence and the system-level properties of replacement by differential fitness, rather than by neutral drift.
Collapse
Affiliation(s)
- Daniel R Shultz
- 1 Department of Anthropology, McGill University , Montreal, Quebec , Canada.,2 Department of History, McGill University , Montreal, Quebec , Canada
| | - Marcel Montrey
- 3 Department of Psychology, McGill University , Montreal, Quebec , Canada
| | - Thomas R Shultz
- 3 Department of Psychology, McGill University , Montreal, Quebec , Canada.,4 School of Computer Science, McGill University , Montreal, Quebec , Canada
| |
Collapse
|
24
|
Vyas DN, Mulligan CJ. Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 169:227-239. [PMID: 30889271 DOI: 10.1002/ajpa.23818] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/11/2019] [Accepted: 02/21/2019] [Indexed: 01/31/2023]
Abstract
OBJECTIVES Modern humans are thought to have interbred with Neanderthals in the Near East soon after modern humans dispersed out of Africa. This introgression event likely took place in either the Levant or southern Arabia depending on the dispersal route out of Africa that was followed. In this study, we compare Neanderthal introgression in contemporary Levantine and southern Arabian populations to investigate Neanderthal introgression and to study Near Eastern population history. MATERIALS AND METHODS We analyzed genotyping data on >400,000 autosomal SNPs from seven Levantine and five southern Arabian populations and compared these data to those from populations from around the world including Neanderthal and Denisovan genomes. We used f4 and D statistics to estimate and compare levels of Neanderthal introgression between Levantine, southern Arabian, and comparative global populations. We also identified 1,581 putative Neanderthal-introgressed SNPs within our dataset and analyzed their allele frequencies as a means to compare introgression patterns in Levantine and southern Arabian genomes. RESULTS We find that Levantine and southern Arabian populations have similar levels of Neanderthal introgression to each other but lower levels than other non-Africans. Furthermore, we find that introgressed SNPs have very similar allele frequencies in the Levant and southern Arabia, which indicates that Neanderthal introgression is similarly distributed in Levantine and southern Arabian genomes. DISCUSSION We infer that the ancestors of contemporary Levantine and southern Arabian populations received Neanderthal introgression prior to separating from each other and that there has been extensive gene flow between these populations.
Collapse
Affiliation(s)
- Deven N Vyas
- Department of Anthropology, University of Florida, Gainesville, Florida.,Genetics Institute, University of Florida, Gainesville, Florida
| | - Connie J Mulligan
- Department of Anthropology, University of Florida, Gainesville, Florida.,Genetics Institute, University of Florida, Gainesville, Florida
| |
Collapse
|
25
|
Traore K, Konate S, Thera MA, Niangaly A, Ba A, Niare A, Arama C, Di Cristofaro J, Baby M, Picot S, Chiaroni J, Boetsch G, Doumbo OK. Genetic polymorphisms with erythrocyte traits in malaria endemic areas of Mali. PLoS One 2019; 14:e0209966. [PMID: 30608964 PMCID: PMC6319707 DOI: 10.1371/journal.pone.0209966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 12/16/2018] [Indexed: 11/19/2022] Open
Abstract
African populations are characterized by high degree of genetic diversity. This high genetic diversity could result from the natural selection pressure. Several studies have described an association between some genetic diversities and difference of susceptibility to infectious diseases like malaria. It seems therefore important to consider genetic diversity impact when interpreting results of clinical trials in malaria endemic areas. This study aimed to determine the genetic polymorphism with erythrocyte traits in different populations of malaria endemic area in Mali. The cross-sectional surveys were carried out in different ethnic groups living in malaria endemic areas in Mali. Six milliliters of whole blood were collected in EDTA vials from each participant after informed consent has been obtained. The ABO, RH, Kell, MNSs, Kidd and Duffy systems phenotypes were assessed by the technique of gel filtration. A total of 231 subjects were included from six villages. The blood groups phenotypes O (40.7%) and A (31.2%) were more frequent with respective allele frequencies of 0.65 and 0.21. In the RH system the haplotypes R0 (0.55), r (0.20) and R1 (0.13) were the most frequent. Seven percent (7%) of Duffy positive and 4% of Glycophorin B deficiency (S-s-) were observed among participants. All participants were Kell negative. ABO and RH systems were polymorphic in these ethnic groups in Mali. Their implication in susceptibility to malaria should be taken into account in clinical trials interpretation, and for prevention of blood transfusion risks during anemia frequently caused by malaria in children.
Collapse
Affiliation(s)
- Karim Traore
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
- Univ Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaire et Supramoléculaire, UMR-5246 CNRS-INSA-CPE, Malaria Research Unit, Lyon, France
- Unité Mixte International UMI 3189 –Environnement—Santé—Sociétés, (CNRS/USTTB, CNRST/UGB/UCAD) Université Cheikh Anta Diop, Dakar, Sénégal
- * E-mail:
| | - Salimata Konate
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Mahamadou A. Thera
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
- Unité Mixte International UMI 3189 –Environnement—Santé—Sociétés, (CNRS/USTTB, CNRST/UGB/UCAD) Université Cheikh Anta Diop, Dakar, Sénégal
| | - Amadou Niangaly
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Alhassane Ba
- Centre National de Transfusion Sanguine (CNTS), Bamako, Mali
| | - Alassane Niare
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Charles Arama
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | | | - Mounirou Baby
- Centre National de Transfusion Sanguine (CNTS), Bamako, Mali
| | - Stephane Picot
- Univ Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaire et Supramoléculaire, UMR-5246 CNRS-INSA-CPE, Malaria Research Unit, Lyon, France
| | - Jacques Chiaroni
- Aix-Marseille Université,CNRS, EFS, ADES UMR 7268, Marseille, France
| | - Gilles Boetsch
- Unité Mixte International UMI 3189 –Environnement—Santé—Sociétés, (CNRS/USTTB, CNRST/UGB/UCAD) Université Cheikh Anta Diop, Dakar, Sénégal
| | - Ogobara K. Doumbo
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
- Unité Mixte International UMI 3189 –Environnement—Santé—Sociétés, (CNRS/USTTB, CNRST/UGB/UCAD) Université Cheikh Anta Diop, Dakar, Sénégal
| |
Collapse
|
26
|
Leplongeon A, Goder-Goldberger M, Pleurdeau D. International workshop on human occupations of the Nile Valley and neighboring regions between 75,000 and 15,000 years ago. Evol Anthropol 2018; 28:10-13. [PMID: 30576032 DOI: 10.1002/evan.21756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 10/30/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Alice Leplongeon
- UMR CNRS 7194, Département Homme et Environnement, Muséum national d'Histoire naturelle - Université de Perpignan Via Domitia - Alliance Sorbonne Université, Paris, France.,Istituto di Studi Avanzati e Dipartimento di Beni Culturali, University of Bologna, Bologna, Italy
| | | | - David Pleurdeau
- UMR CNRS 7194, Département Homme et Environnement, Muséum national d'Histoire naturelle - Université de Perpignan Via Domitia - Alliance Sorbonne Université, Paris, France
| |
Collapse
|
27
|
Rapid evolution of a skin-lightening allele in southern African KhoeSan. Proc Natl Acad Sci U S A 2018; 115:13324-13329. [PMID: 30530665 DOI: 10.1073/pnas.1801948115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Skin pigmentation is under strong directional selection in northern European and Asian populations. The indigenous KhoeSan populations of far southern Africa have lighter skin than other sub-Saharan African populations, potentially reflecting local adaptation to a region of Africa with reduced UV radiation. Here, we demonstrate that a canonical Eurasian skin pigmentation gene, SLC24A5, was introduced to southern Africa via recent migration and experienced strong adaptive evolution in the KhoeSan. To reconstruct the evolution of skin pigmentation, we collected phenotypes from over 400 ≠Khomani San and Nama individuals and high-throughput sequenced candidate pigmentation genes. The derived causal allele in SLC24A5, p.Ala111Thr, significantly lightens basal skin pigmentation in the KhoeSan and explains 8 to 15% of phenotypic variance in these populations. The frequency of this allele (33 to 53%) is far greater than expected from colonial period European gene flow; however, the most common derived haplotype is identical among European, eastern African, and KhoeSan individuals. Using four-population demographic simulations with selection, we show that the allele was introduced into the KhoeSan only 2,000 y ago via a back-to-Africa migration and then experienced a selective sweep (s = 0.04 to 0.05 in ≠Khomani and Nama). The SLC24A5 locus is both a rare example of intense, ongoing adaptation in very recent human history, as well as an adaptive gene flow at a pigmentation locus in humans.
Collapse
|
28
|
Molinaro L, Pagani L. Human evolutionary history of Eastern Africa. Curr Opin Genet Dev 2018; 53:134-139. [DOI: 10.1016/j.gde.2018.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/31/2018] [Accepted: 10/08/2018] [Indexed: 01/16/2023]
|
29
|
Frequency of PAR4 Ala120Thr variant associated with platelet reactivity significantly varies across sub-Saharan African populations. Blood 2018; 132:2103-2106. [PMID: 30143503 DOI: 10.1182/blood-2018-05-852335] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 08/15/2018] [Indexed: 12/22/2022] Open
|
30
|
Lawson DJ, van Dorp L, Falush D. A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. Nat Commun 2018; 9:3258. [PMID: 30108219 PMCID: PMC6092366 DOI: 10.1038/s41467-018-05257-7] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 06/21/2018] [Indexed: 01/05/2023] Open
Abstract
Genetic clustering algorithms, implemented in programs such as STRUCTURE and ADMIXTURE, have been used extensively in the characterisation of individuals and populations based on genetic data. A successful example is the reconstruction of the genetic history of African Americans as a product of recent admixture between highly differentiated populations. Histories can also be reconstructed using the same procedure for groups that do not have admixture in their recent history, where recent genetic drift is strong or that deviate in other ways from the underlying inference model. Unfortunately, such histories can be misleading. We have implemented an approach, badMIXTURE, to assess the goodness of fit of the model using the ancestry "palettes" estimated by CHROMOPAINTER and apply it to both simulated data and real case studies. Combining these complementary analyses with additional methods that are designed to test specific hypotheses allows a richer and more robust analysis of recent demographic history.
Collapse
Affiliation(s)
- Daniel J Lawson
- University of Bristol, Integrative Epidemiology Unit, Population Health Sciences, Bristol, BS8 1TH, UK
| | - Lucy van Dorp
- University College London Genetics Institute (UGI), University College London, London, WC1E 6BT, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, WC1E 6BT, UK
| | - Daniel Falush
- Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK.
| |
Collapse
|
31
|
The demographic and adaptive history of central African hunter-gatherers and farmers. Curr Opin Genet Dev 2018; 53:90-97. [PMID: 30103089 DOI: 10.1016/j.gde.2018.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/18/2018] [Indexed: 01/06/2023]
Abstract
Central Africa, a forested region that supports an exceptionally high biodiversity, hosts the world's largest group of hunter-gatherers, who live in close proximity with groups that have adopted agriculture over the past 5000 years. Our understanding of the prehistory of these populations has been dramatically hampered by the almost total absence of fossil remains in this region, a limitation that has recently been circumvented by population genomics approaches. Different studies have estimated that ancestors of rainforest hunter-gatherers and Bantu-speaking farmers separated more than 60 000 years ago, supporting the occurrence of ancient population structure in Africa since the Late Pleistocene. Conversely, the Holocene in central Africa was characterized by large-scale population migrations associated with the emergence of agriculture, and increased genetic interactions between autochthonous rainforest hunter-gatherers and expanding Bantu-speaking farmers. Genomic scans have detected numerous candidate loci for positive selection in these populations, including convergent adaptation for short stature in groups of rainforest hunter-gatherers and local adaptation to endemic malaria in western and central Africans. Furthermore, there is recent increasing evidence that adaptive variation has been acquired by various African populations through admixture, suggesting a previously unappreciated role of intraspecies gene flow in local adaptation. Ancient and modern DNA studies will greatly broaden, and probably challenge, our view on the past history of central Africa, where introgression from yet uncharacterized archaic hominins and long-term adaptation to distinct ecological niches are suspected.
Collapse
|
32
|
Abdi AA, Osman A. Prevalence of common hereditary risk factors for thrombophilia in Somalia and identification of a novel Gln544Arg mutation in coagulation factor V. J Thromb Thrombolysis 2018; 44:536-543. [PMID: 28889200 PMCID: PMC5658450 DOI: 10.1007/s11239-017-1543-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thrombophilia, commonly manifested as venous thromboembolism (VTE), is a worldwide concern but little is known on its genetic epidemiology in many parts of the globe particularly in the developing countries. Here we employed TaqMan genotyping and pyrosequencing to evaluate the prevalence of known common nucleotide polymorphisms associated with thrombophilia in a Somali population in the Puntland region of Somalia. We also employed next generation sequencing (NGS) to investigate other genetic variants in a Somali patient with deep venous thrombosis (DVT). As expected, we found no existence of factor V Leiden (rs6025) and prothrombin G20210A (rs1799963) in the Somali population. The G allele of ABO [261G/delG] polymorphism (rs8176719) was found at a frequency of 29%, similar to that observed in other African populations. We found the lowest so far reported frequency of MTHFR C677T (rs1801133) polymorphism in the Somali population (T allele frequency 1.5%). A novel and deleterious single nucleotide variation in exon 11 of coagulation factor V (c.1631A>G) causing Gln544Arg exchange in factor V was identified in a 29 years old Somali female with DVT. The same patient was heterozygous to VKORC1 Asp36Tyr polymorphism (rs61742245) that predisposes to warfarin resistance. In conclusion, this study shows that common hereditary factors for thromboembolism found in Caucasians are either less frequent or absent in the Somali population-similar to the situation in other Africans. NGS is possibly a better choice to detect genetic risk variants for thrombosis in this ethnic group.
Collapse
Affiliation(s)
- Abshir Ali Abdi
- Faculty of Medicine, East Africa University, Bosaso, Puntland, Somalia
| | - Abdimajid Osman
- Division of Clinical Chemistry, Region Östergötland, Ingång 64, 581 85, Linköping, Sweden. .,Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
| |
Collapse
|
33
|
|
34
|
Brucato N, Fernandes V, Mazières S, Kusuma P, Cox MP, Ng'ang'a JW, Omar M, Simeone-Senelle MC, Frassati C, Alshamali F, Fin B, Boland A, Deleuze JF, Stoneking M, Adelaar A, Crowther A, Boivin N, Pereira L, Bailly P, Chiaroni J, Ricaut FX. The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor. Am J Hum Genet 2018; 102:58-68. [PMID: 29304377 DOI: 10.1016/j.ajhg.2017.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/16/2017] [Indexed: 12/12/2022] Open
Abstract
At the dawn of the second millennium, the expansion of the Indian Ocean trading network aligned with the emergence of an outward-oriented community along the East African coast to create a cosmopolitan cultural and trading zone known as the Swahili Corridor. On the basis of analyses of new genome-wide genotyping data and uniparental data in 276 individuals from coastal Kenya and the Comoros islands, along with large-scale genetic datasets from the Indian Ocean rim, we reconstruct historical population dynamics to show that the Swahili Corridor is largely an eastern Bantu genetic continuum. Limited gene flows from the Middle East can be seen in Swahili and Comorian populations at dates corresponding to historically documented contacts. However, the main admixture event in southern insular populations, particularly Comorian and Malagasy groups, occurred with individuals from Island Southeast Asia as early as the 8th century, reflecting an earlier dispersal from this region. Remarkably, our results support recent archaeological and linguistic evidence-based suggestions that the Comoros archipelago was the earliest location of contact between Austronesian and African populations in the Swahili Corridor.
Collapse
Affiliation(s)
- Nicolas Brucato
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse 31073, France.
| | - Veronica Fernandes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal; Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto 4200-465, Portugal
| | - Stéphane Mazières
- Groupe Biologie des Groupes Sanguins, Aix Marseille Université, CNRS, Etablissement Francais du Sang, Anthropologie Bio-culturelle, Droit, Éthique et Santé, Marseille 13385, France
| | - Pradiptajati Kusuma
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse 31073, France; Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | | | | | - Marie-Claude Simeone-Senelle
- Langage, Langues et Cultures d'Afrique Noire, UMR 8135, CNRS, Institut National des Langues et Cultures Orientales, Université Sorbonne Paris Cité, BP 8, 94801 Villejuif-Cedex, France
| | - Coralie Frassati
- Groupe Biologie des Groupes Sanguins, Aix Marseille Université, CNRS, Etablissement Francais du Sang, Anthropologie Bio-culturelle, Droit, Éthique et Santé, Marseille 13385, France; Établissement Français du Sang Alpes Méditerranée, Marseille 13272, France
| | - Farida Alshamali
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, PO Box 1493, Dubai, United Arab Emirates
| | - Bertrand Fin
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Commissariat à L'Énergie Atomique et aux Énergies Alternatives, Evry 91000, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Commissariat à L'Énergie Atomique et aux Énergies Alternatives, Evry 91000, France
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Commissariat à L'Énergie Atomique et aux Énergies Alternatives, Evry 91000, France
| | | | - Alexander Adelaar
- Asia Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alison Crowther
- School of Social Science, University of Queensland, Brisbane 4072, Australia; Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Nicole Boivin
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Luisa Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal; Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto 4200-465, Portugal
| | - Pascal Bailly
- Groupe Biologie des Groupes Sanguins, Aix Marseille Université, CNRS, Etablissement Francais du Sang, Anthropologie Bio-culturelle, Droit, Éthique et Santé, Marseille 13385, France; Établissement Français du Sang Alpes Méditerranée, Marseille 13272, France
| | - Jacques Chiaroni
- Groupe Biologie des Groupes Sanguins, Aix Marseille Université, CNRS, Etablissement Francais du Sang, Anthropologie Bio-culturelle, Droit, Éthique et Santé, Marseille 13385, France; Établissement Français du Sang Alpes Méditerranée, Marseille 13272, France
| | - François-Xavier Ricaut
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse 31073, France.
| |
Collapse
|
35
|
Leplongeon A. Technological variability in the Late Palaeolithic lithic industries of the Egyptian Nile Valley: The case of the Silsilian and Afian industries. PLoS One 2017; 12:e0188824. [PMID: 29281660 PMCID: PMC5744920 DOI: 10.1371/journal.pone.0188824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 11/14/2017] [Indexed: 11/18/2022] Open
Abstract
During the Nubia Salvage Campaign and the subsequent expeditions from the 1960’s to the 1980’s, numerous sites attributed to the Late Palaeolithic (~25–15 ka) were found in the Nile Valley, particularly in Nubia and Upper Egypt. This region is one of the few to have allowed human occupations during the dry Marine Isotope Stage 2 and is therefore key to understanding how human populations adapted to environmental changes at this time. This paper focuses on two sites located in Upper Egypt, excavated by the Combined Prehistoric Expedition: E71K18, attributed to the Afian industry and E71K20, attributed to the Silsilian industry. It aims to review the geomorphological and chronological evidence of the sites, present a technological analysis of the lithic assemblages in order to provide data that can be used in detailed comparative studies, which will allow discussion of technological variability in the Late Palaeolithic of the Nile Valley and its place within the regional context. The lithic analysis relies on the chaîne opératoire concept combined with an attribute analysis to allow quantification. This study (1) casts doubts on the chronology of E71K18 and related Afian industry, which could be older or younger than previously suggested, highlights (2) distinct technological characteristics for the Afian and the Silsilian, as well as (3) similar technological characteristics which allow to group them under a same broad techno-cultural complex, distinct from those north or south of the area.
Collapse
Affiliation(s)
- Alice Leplongeon
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
- UMR CNRS 7194 HNHP, département Homme et Environnement, Muséum national d’Histoire naturelle–Université de Perpignan Via Domitia–Sorbonne Universités, Paris, France
- Institute of Archaeology, Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
| |
Collapse
|
36
|
Vyas DN, Al‐Meeri A, Mulligan CJ. Testing support for the northern and southern dispersal routes out of Africa: an analysis of Levantine and southern Arabian populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:736-749. [DOI: 10.1002/ajpa.23312] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Deven N. Vyas
- Department of AnthropologyUniversity of Florida, 1112 Turlington Hall, PO Box 117305Gainesville Florida 32611‐7305
- Genetics InstituteUniversity of Florida, Cancer & Genetics Research Complex, PO Box 103610Gainesville Florida 32610‐3610
| | - Ali Al‐Meeri
- Department of Clinical Biochemistry, Faculty of Medicine and Health SciencesUniversity of Sana'aSana'a Yemen
| | - Connie J. Mulligan
- Department of AnthropologyUniversity of Florida, 1112 Turlington Hall, PO Box 117305Gainesville Florida 32611‐7305
- Genetics InstituteUniversity of Florida, Cancer & Genetics Research Complex, PO Box 103610Gainesville Florida 32610‐3610
| |
Collapse
|
37
|
Hollfelder N, Schlebusch CM, Günther T, Babiker H, Hassan HY, Jakobsson M. Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations. PLoS Genet 2017; 13:e1006976. [PMID: 28837655 PMCID: PMC5587336 DOI: 10.1371/journal.pgen.1006976] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 09/06/2017] [Accepted: 08/13/2017] [Indexed: 12/26/2022] Open
Abstract
Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gate-way out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400–200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa. Northeast Africa has geographic and historical links to Eurasia via the Middle East and the Arabian Peninsula, but the demographic history of the region itself has been more elusive. We investigate genomic diversity of northeast African populations and found a clear bimodal distribution of variation, correlated with geography, and likely driven by Eurasian admixture in the wake of migrations along the Nile. This admixture process largely coincides with the time of the Arab conquest, spreading in a southbound direction along the Nile and the Blue Nile. Nilotic populations occupying the region around the White Nile show long-term continuity, genetic isolation and genetic links to ancestral East African people. Compared to current times, groups that are ancestral to the current-day Nilotes likely inhabited a larger area of northeast Africa prior to the migration from the Middle East as their ancestry component can still be found in a large area. Our findings reveal the genetic history of Sudanese and South Sudanese people, broaden our knowledge on demographic history of humans, and quantify the impact of large-scale historic migration events in northeast Africa.
Collapse
Affiliation(s)
- Nina Hollfelder
- Dept. of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Torsten Günther
- Dept. of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Hiba Babiker
- Dept. of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hisham Y. Hassan
- Banoon ART and Cytogenetics Centre, Bahrain Defense Force Hospital, Manama, Kingdom of Bahrain
| | - Mattias Jakobsson
- Dept. of Organismal Biology, Uppsala University, Uppsala, Sweden
- SciLife Lab, Uppsala University, Uppsala, Sweden
- * E-mail:
| |
Collapse
|
38
|
Čížková M, Hofmanová Z, Mokhtar MG, Janoušek V, Diallo I, Munclinger P, Černý V. Alu insertion polymorphisms in the African Sahel and the origin of Fulani pastoralists. Ann Hum Biol 2017; 44:537-545. [PMID: 28502204 DOI: 10.1080/03014460.2017.1328073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND The origin of Western African pastoralism, represented today by the Fulani nomads, has been a highly debated issue for the past decades, and has not yet been conclusively resolved. AIM This study focused on Alu polymorphisms in sedentary and nomadic populations across the African Sahel to investigate patterns of diversity that can complement the existing results and contribute to resolving issues concerning the origin of West African pastoralism. SUBJECTS AND METHODS A new dataset of 21 Alu biallelic markers covering a substantial part of the African Sahel has been analysed jointly with several published North African populations. RESULTS Interestingly, with regard to Alu variation, the relationship of Fulani pastoralists to North Africans is not as evident as was earlier revealed by studies of uniparental loci such as mtDNA and NRY. Alu insertions point rather to an affinity of Fulani pastoralists to Eastern Africans also leading a pastoral lifestyle. CONCLUSIONS It is suggested that contemporary Fulani pastoralists might be descendants of an ancestral Eastern African population that, while crossing the Sahara in the Holocene, admixed slightly with a population of Eurasian (as evidenced by uniparental polymorphisms) ancestry. It seems that, in the Fulani pastoralists, Alu elements reflect more ancient genetic relationships than do uniparental genetic systems.
Collapse
Affiliation(s)
- Martina Čížková
- a Department of Anthropology and Human Genetics, Faculty of Science , Charles University , Prague , Czech Republic
| | - Zuzana Hofmanová
- a Department of Anthropology and Human Genetics, Faculty of Science , Charles University , Prague , Czech Republic.,b Palaeogenetics Group , Johannes Gutenberg University Mainz , Mainz , Germany
| | - Mohammed G Mokhtar
- c Arabic Department, Faculty of Arts , University of Kordofan , Al-Ubayyid , Sudan
| | - Václav Janoušek
- d Department of Zoology, Faculty of Science , Charles University , Prague , Czech Republic
| | - Issa Diallo
- e Département de Linguistique et Langues Nationales , Institut des Sciences des Sociétés, CNRST , Ouagadougou , Burkina Faso
| | - Pavel Munclinger
- d Department of Zoology, Faculty of Science , Charles University , Prague , Czech Republic
| | - Viktor Černý
- f Department of the Archaeology of Landscape and Archaeobiology, Archaeogenetics Laboratory , Institute of Archaeology of the Academy of Sciences of the Czech Republic , Prague , Czech Republic
| |
Collapse
|
39
|
Priehodová E, Austerlitz F, Čížková M, Mokhtar MG, Poloni ES, Černý V. The historical spread of
A
rabian
P
astoralists to the eastern
A
frican
S
ahel evidenced by the lactase persistence −13,915*G allele and mitochondrial DNA. Am J Hum Biol 2017; 29. [DOI: 10.1002/ajhb.22950] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 09/01/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022] Open
Affiliation(s)
- Edita Priehodová
- Department of Anthropology and Human GeneticsFaculty of Science Charles UniversityPrague Czech Republic
| | - Frédéric Austerlitz
- UMR 7206 EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, Musée de l'HommeParis
| | - Martina Čížková
- Department of Anthropology and Human GeneticsFaculty of Science Charles UniversityPrague Czech Republic
| | | | - Estella S. Poloni
- Department of Genetics and EvolutionAnthropology Unit, Faculty of Science, University of Geneva, Switzerland
| | - Viktor Černý
- Archaeogenetics LaboratoryInstitute of Archaeology of the Academy of Sciences of the Czech RepublicPrague
| |
Collapse
|
40
|
Across the Gap: Geochronological and Sedimentological Analyses from the Late Pleistocene-Holocene Sequence of Goda Buticha, Southeastern Ethiopia. PLoS One 2017; 12:e0169418. [PMID: 28125597 PMCID: PMC5268652 DOI: 10.1371/journal.pone.0169418] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/17/2016] [Indexed: 11/23/2022] Open
Abstract
Goda Buticha is a cave site near Dire Dawa in southeastern Ethiopia that contains an archaeological sequence sampling the late Pleistocene and Holocene of the region. The sedimentary sequence displays complex cultural, chronological and sedimentological histories that seem incongruent with one another. A first set of radiocarbon ages suggested a long sedimentological gap from the end of Marine Isotopic Stage (MIS) 3 to the mid-Holocene. Macroscopic observations suggest that the main sedimentological change does not coincide with the chronostratigraphic hiatus. The cultural sequence shows technological continuity with a late persistence of artifacts that are usually attributed to the Middle Stone Age into the younger parts of the stratigraphic sequence, yet become increasingly associated with lithic artifacts typically related to the Later Stone Age. While not a unique case, this combination of features is unusual in the Horn of Africa. In order to evaluate the possible implications of these observations, sedimentological analyses combined with optically stimulated luminescence (OSL) were conducted. The OSL data now extend the radiocarbon chronology up to 63 ± 7 ka; they also confirm the existence of the chronological gap between 24.8 ± 2.6 ka and 7.5 ± 0.3 ka. The sedimentological analyses suggest that the origin and mode of deposition were largely similar throughout the whole sequence, although the anthropic and faunal activities increased in the younger levels. Regional climatic records are used to support the sedimentological observations and interpretations. We discuss the implications of the sedimentological and dating analyses for understanding cultural processes in the region.
Collapse
|
41
|
Abstract
The Druze are an aggregate of communities in the Levant and Near East living almost exclusively in the mountains of Syria, Lebanon and Israel whose ~1000 year old religion formally opposes mixed marriages and conversions. Despite increasing interest in genetics of the population structure of the Druze, their population history remains unknown. We investigated the genetic relationships between Israeli Druze and both modern and ancient populations. We evaluated our findings in light of three hypotheses purporting to explain Druze history that posit Arabian, Persian or mixed Near Eastern-Levantine roots. The biogeographical analysis localised proto-Druze to the mountainous regions of southeastern Turkey, northern Iraq and southeast Syria and their descendants clustered along a trajectory between these two regions. The mixed Near Eastern–Middle Eastern localisation of the Druze, shown using both modern and ancient DNA data, is distinct from that of neighbouring Syrians, Palestinians and most of the Lebanese, who exhibit a high affinity to the Levant. Druze biogeographic affinity, migration patterns, time of emergence and genetic similarity to Near Eastern populations are highly suggestive of Armenian-Turkish ancestries for the proto-Druze.
Collapse
|
42
|
Busby GB, Band G, Si Le Q, Jallow M, Bougama E, Mangano VD, Amenga-Etego LN, Enimil A, Apinjoh T, Ndila CM, Manjurano A, Nyirongo V, Doumba O, Rockett KA, Kwiatkowski DP, Spencer CC. Admixture into and within sub-Saharan Africa. eLife 2016; 5. [PMID: 27324836 PMCID: PMC4915815 DOI: 10.7554/elife.15266] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/17/2016] [Indexed: 12/27/2022] Open
Abstract
Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology. DOI:http://dx.doi.org/10.7554/eLife.15266.001 Our genomes contain a record of historical events. This is because when groups of people are separated for generations, the DNA sequence in the two groups’ genomes will change in different ways. Looking at the differences in the genomes of people from the same population can help researchers to understand and reconstruct the historical interactions that brought their ancestors together. The mixing of two populations that were previously separate is known as admixture. Africa as a continent has few written records of its history. This means that it is somewhat unknown which important movements of people in the past generated the populations found in modern-day Africa. Busby et al. have now attempted to use DNA to look into this and reconstruct the last 4000 years of genetic history in African populations. As has been shown in other regions of the world, the new analysis showed that all African populations are the result of historical admixture events. However, Busby et al. could characterize these events to unprecedented level of detail. For example, multiple ethnic groups from The Gambia and Mali all show signs of sharing the same set of ancestors from West Africa, Europe and Asia who mixed around 2000 years ago. Evidence of a migration of people from Central West Africa, known as the Bantu expansion, could also be detected, and was shown to carry genes to the south and east. An important next step will be to now look at the consequences of the observed gene-flow, and ask if it has contributed to spreading beneficial, or detrimental, mutations around Africa. DOI:http://dx.doi.org/10.7554/eLife.15266.002
Collapse
Affiliation(s)
- George Bj Busby
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Quang Si Le
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Muminatou Jallow
- Medical Research Council Unit, Serrekunda, The Gambia.,Royal Victoria Teaching Hospital, Banjul, The Gambia
| | - Edith Bougama
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Valentina D Mangano
- Dipartimento di Sanita Publica e Malattie Infettive, University of Rome La Sapienza, Rome, Italy
| | | | | | - Tobias Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | | | - Alphaxard Manjurano
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Vysaul Nyirongo
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Ogobara Doumba
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Chris Ca Spencer
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | | |
Collapse
|
43
|
Abstract
The serial founder model of modern human origins predicts that the phylogeny of ancestries exhibits bifurcating, tree-like behavior. Here, we tested this prediction using three methods designed to investigate gene flow in autosome-wide genotype data from 3,528 unrelated individuals from 163 global samples. Specifically, we investigated whether Cushitic ancestry has an East African or Middle Eastern origin. We found evidence for non-tree-like behavior in the form of four migration events. First, we found that Cushitic ancestry is a mixture of ancestries closely related to Arabian ancestry and Nilo-Saharan or Omotic ancestry. We found evidence for additional migration events in the histories of: 1) Indian and Arabian ancestries, 2) Kalash ancestry, and 3) Native American and Northern European ancestries. These findings, based on analysis of ancestry of present-day humans, reveal migration in the distant past and provide new insights into human history.
Collapse
|
44
|
Gandini F, Achilli A, Pala M, Bodner M, Brandini S, Huber G, Egyed B, Ferretti L, Gómez-Carballa A, Salas A, Scozzari R, Cruciani F, Coppa A, Parson W, Semino O, Soares P, Torroni A, Richards MB, Olivieri A. Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes. Sci Rep 2016; 6:25472. [PMID: 27146119 PMCID: PMC4857117 DOI: 10.1038/srep25472] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/18/2016] [Indexed: 01/29/2023] Open
Abstract
Rare mitochondrial lineages with relict distributions can sometimes be disproportionately informative about deep events in human prehistory. We have studied one such lineage, haplogroup R0a, which uniquely is most frequent in Arabia and the Horn of Africa, but is distributed much more widely, from Europe to India. We conclude that: (1) the lineage ancestral to R0a is more ancient than previously thought, with a relict distribution across the Mediterranean/Southwest Asia; (2) R0a has a much deeper presence in Arabia than previously thought, highlighting the role of at least one Pleistocene glacial refugium, perhaps on the Red Sea plains; (3) the main episode of dispersal into Eastern Africa, at least concerning maternal lineages, was at the end of the Late Glacial, due to major expansions from one or more refugia in Arabia; (4) there was likely a minor Late Glacial/early postglacial dispersal from Arabia through the Levant and into Europe, possibly alongside other lineages from a Levantine refugium; and (5) the presence of R0a in Southwest Arabia in the Holocene at the nexus of a trading network that developed after ~3 ka between Africa and the Indian Ocean led to some gene flow even further afield, into Iran, Pakistan and India.
Collapse
Affiliation(s)
- Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.,School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.,Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Maria Pala
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Balazs Egyed
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
| | - Rosaria Scozzari
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Martin B Richards
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| |
Collapse
|
45
|
López S, van Dorp L, Hellenthal G. Human Dispersal Out of Africa: A Lasting Debate. Evol Bioinform Online 2016; 11:57-68. [PMID: 27127403 PMCID: PMC4844272 DOI: 10.4137/ebo.s33489] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/21/2016] [Accepted: 02/21/2016] [Indexed: 01/01/2023] Open
Abstract
Unraveling the first migrations of anatomically modern humans out of Africa has invoked great interest among researchers from a wide range of disciplines. Available fossil, archeological, and climatic data offer many hypotheses, and as such genetics, with the advent of genome-wide genotyping and sequencing techniques and an increase in the availability of ancient samples, offers another important tool for testing theories relating to our own history. In this review, we report the ongoing debates regarding how and when our ancestors left Africa, how many waves of dispersal there were and what geographical routes were taken. We explore the validity of each, using current genetic literature coupled with some of the key archeological findings.
Collapse
Affiliation(s)
- Saioa López
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London, UK
| |
Collapse
|
46
|
Lasisi T, Ito S, Wakamatsu K, Shaw CN. Quantifying variation in human scalp hair fiber shape and pigmentation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:341-52. [DOI: 10.1002/ajpa.22971] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Tina Lasisi
- Department of Archaeology and Anthropology, PAVE Research Group; University of Cambridge; UK
- Department of Anthropology; Pennsylvania State University, University Park; PA 16802
| | - Shosuke Ito
- Department of Chemistry; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | - Kazumasa Wakamatsu
- Department of Chemistry; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | - Colin N. Shaw
- Department of Archaeology and Anthropology, PAVE Research Group; University of Cambridge; UK
- Department of Archaeology and Anthropology; McDonald Institute for Archaeological Research, University of Cambridge; UK
- Department of Zoology, Cambridge BioTomography Centre; University of Cambridge; UK
| |
Collapse
|
47
|
Rodriguez-Flores JL, Fakhro K, Agosto-Perez F, Ramstetter MD, Arbiza L, Vincent TL, Robay A, Malek JA, Suhre K, Chouchane L, Badii R, Al-Nabet Al-Marri A, Abi Khalil C, Zirie M, Jayyousi A, Salit J, Keinan A, Clark AG, Crystal RG, Mezey JG. Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations. Genome Res 2016; 26:151-62. [PMID: 26728717 PMCID: PMC4728368 DOI: 10.1101/gr.191478.115] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 12/15/2015] [Indexed: 12/26/2022]
Abstract
An open question in the history of human migration is the identity of the earliest Eurasian populations that have left contemporary descendants. The Arabian Peninsula was the initial site of the out-of-Africa migrations that occurred between 125,000 and 60,000 yr ago, leading to the hypothesis that the first Eurasian populations were established on the Peninsula and that contemporary indigenous Arabs are direct descendants of these ancient peoples. To assess this hypothesis, we sequenced the entire genomes of 104 unrelated natives of the Arabian Peninsula at high coverage, including 56 of indigenous Arab ancestry. The indigenous Arab genomes defined a cluster distinct from other ancestral groups, and these genomes showed clear hallmarks of an ancient out-of-Africa bottleneck. Similar to other Middle Eastern populations, the indigenous Arabs had higher levels of Neanderthal admixture compared to Africans but had lower levels than Europeans and Asians. These levels of Neanderthal admixture are consistent with an early divergence of Arab ancestors after the out-of-Africa bottleneck but before the major Neanderthal admixture events in Europe and other regions of Eurasia. When compared to worldwide populations sampled in the 1000 Genomes Project, although the indigenous Arabs had a signal of admixture with Europeans, they clustered in a basal, outgroup position to all 1000 Genomes non-Africans when considering pairwise similarity across the entire genome. These results place indigenous Arabs as the most distant relatives of all other contemporary non-Africans and identify these people as direct descendants of the first Eurasian populations established by the out-of-Africa migrations.
Collapse
Affiliation(s)
- Juan L Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Khalid Fakhro
- Sidra Medical and Research Center, Doha, Qatar; Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Francisco Agosto-Perez
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Monica D Ramstetter
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Leonardo Arbiza
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Thomas L Vincent
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Amal Robay
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Joel A Malek
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Ramin Badii
- Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | | | - Charbel Abi Khalil
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Mahmoud Zirie
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Amin Jayyousi
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Andrew G Clark
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Jason G Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| |
Collapse
|
48
|
Bradburd GS, Ralph PL, Coop GM. A Spatial Framework for Understanding Population Structure and Admixture. PLoS Genet 2016; 12:e1005703. [PMID: 26771578 PMCID: PMC4714911 DOI: 10.1371/journal.pgen.1005703] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 11/05/2015] [Indexed: 01/26/2023] Open
Abstract
Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build "geogenetic maps," which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.
Collapse
Affiliation(s)
- Gideon S. Bradburd
- Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Peter L. Ralph
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Graham M. Coop
- Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, California, United States of America
| |
Collapse
|
49
|
Černý V, Čížková M, Poloni ES, Al‐Meeri A, Mulligan CJ. Comprehensive view of the population history of
A
rabia as inferred by mt
DNA
variation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:607-16. [DOI: 10.1002/ajpa.22920] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/06/2015] [Accepted: 11/23/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Viktor Černý
- Archaeogenetics LaboratoryInstitute of Archaeology of the Academy of Sciences of the Czech Republic Czech Republic
| | - Martina Čížková
- Department of Anthropology and Human GeneticsFaculty of Science, Charles University in Prague Czech Republic
| | - Estella S. Poloni
- Department of Genetics and EvolutionAnthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of GenevaGeneva Switzerland
| | - Ali Al‐Meeri
- Department of Clinical BiochemistryFaculty of Medicine and Health Sciences, University of Sana'aSana'a Yemen
| | | |
Collapse
|
50
|
Vyas DN, Kitchen A, Miró‐Herrans AT, Pearson LN, Al‐Meeri A, Mulligan CJ. Bayesian analyses of Yemeni mitochondrial genomes suggest multiple migration events with Africa and Western Eurasia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:382-93. [DOI: 10.1002/ajpa.22890] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/21/2015] [Accepted: 10/23/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Deven N. Vyas
- Department of AnthropologyUniversity of FloridaGainesville FL32611‐7305
- Genetics Institute, University of FloridaGainesville FL32610‐3610
| | - Andrew Kitchen
- Department of AnthropologyUniversity of IowaIowa City IA52242
| | - Aida T. Miró‐Herrans
- Department of AnthropologyUniversity of FloridaGainesville FL32611‐7305
- Genetics Institute, University of FloridaGainesville FL32610‐3610
| | - Laurel N. Pearson
- Department of AnthropologyUniversity of FloridaGainesville FL32611‐7305
- Genetics Institute, University of FloridaGainesville FL32610‐3610
| | - Ali Al‐Meeri
- Department of Clinical Biochemistry, Faculty of Medicine and Health SciencesUniversity of Sana'aSana'a Yemen
| | - Connie J. Mulligan
- Department of AnthropologyUniversity of FloridaGainesville FL32611‐7305
- Genetics Institute, University of FloridaGainesville FL32610‐3610
| |
Collapse
|