1
|
Aizpurua-Iraola J, Abdeli A, Benhassine T, Calafell F, Comas D. Whole mitogenomes reveal that NW Africa has acted both as a source and a destination for multiple human movements. Sci Rep 2023; 13:10395. [PMID: 37369751 DOI: 10.1038/s41598-023-37549-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023] Open
Abstract
Despite being enclosed between the Mediterranean Sea and the Sahara Desert, North Africa has been the scenario of multiple human migrations that have shaped the genetic structure of its present-day populations. Despite its richness, North Africa remains underrepresented in genomic studies. To overcome this, we have sequenced and analyzed 264 mitogenomes from the Algerian Chaoui-speaking Imazighen (a.k.a. Berbers) living in the Aurès region. The maternal genetic composition of the Aurès is similar to Arab populations in the region, dominated by West Eurasian lineages with a moderate presence of M1/U6 North African and L sub-Saharan lineages. When focusing on the time and geographic origin of the North African specific clades within the non-autochthonous haplogroups, different geographical neighboring regions contributed to the North African maternal gene pool during time periods that could be attributed to previously suggested admixture events in the region, since Paleolithic times to recent historical movements such as the Arabization. We have also observed the role of North Africa as a source of geneflow mainly in Southern European regions since Neolithic times. Finally, the present work constitutes an effort to increase the representation of North African populations in genetic databases, which is key to understand their history.
Collapse
Affiliation(s)
- Julen Aizpurua-Iraola
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Laboratorie de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Traki Benhassine
- Laboratorie de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.
| |
Collapse
|
2
|
Circum-Saharan Prehistory through the Lens of mtDNA Diversity. Genes (Basel) 2022; 13:genes13030533. [PMID: 35328086 PMCID: PMC8951852 DOI: 10.3390/genes13030533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
African history has been significantly influenced by the Sahara, which has represented a barrier for migrations of all living beings, including humans. Major exceptions were the gene flow events that took place between North African and sub-Saharan populations during the so-called African Humid Periods, especially in the Early Holocene (11.5 to 5.5 thousand years ago), and more recently in connection with trans-Saharan commercial routes. In this study, we describe mitochondrial DNA (mtDNA) diversity of human populations from both sides of the Sahara Desert, i.e., both from North Africa and the Sahel/Savannah belt. The final dataset of 7213 mtDNA sequences from 134 African populations encompasses 470 newly collected and 6743 previously published samples, which were analyzed using descriptive methods and Bayesian statistics. We completely sequenced 26 mtDNAs from sub-Saharan samples belonging to the Eurasian haplogroup N1. Analyses of these N1 mitogenomes revealed their possible routes to the Sahel, mostly via Bab el-Mandab. Our results indicate that maternal gene flow must have been important in this circum-Saharan space, not only within North Africa and the Sahel/Savannah belt but also between these two regions.
Collapse
|
3
|
Lucas-Sánchez M, Serradell JM, Comas D. Population history of North Africa based on modern and ancient genomes. Hum Mol Genet 2020; 30:R17-R23. [PMID: 33284971 DOI: 10.1093/hmg/ddaa261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/09/2023] Open
Abstract
Compared with the rest of the African continent, North Africa has provided limited genomic data. Nonetheless, the genetic data available show a complex demographic scenario characterized by extensive admixture and drift. Despite the continuous gene flow from the Middle East, Europe and sub-Saharan Africa, an autochthonous genetic component that dates back to pre-Holocene times is still present in North African groups. The comparison of ancient and modern genomes has evidenced a genetic continuity in the region since Epipaleolithic times. Later population movements, especially the gene flow from the Middle East associated with the Neolithic, have diluted the genetic autochthonous component, creating an east to west gradient. Recent historical movements, such as the Arabization, have also contributed to the genetic landscape observed currently in North Africa and have culturally transformed the region. Genome analyses have not shown evidence of a clear correlation between cultural and genetic diversity in North Africa, as there is no genetic pattern of differentiation between Tamazight (i.e. Berber) and Arab speakers as a whole. Besides the gene flow received from neighboring areas, the analysis of North African genomes has shown that the region has also acted as a source of gene flow since ancient times. As a result of the genetic uniqueness of North African groups and the lack of available data, there is an urgent need for the study of genetic variation in the region and its implications in health and disease.
Collapse
Affiliation(s)
- Marcel Lucas-Sánchez
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Jose M Serradell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| |
Collapse
|
4
|
Černý V, Fortes-Lima C, Tříska P. Demographic history and admixture dynamics in African Sahelian populations. Hum Mol Genet 2020; 30:R29-R36. [PMID: 33105478 DOI: 10.1093/hmg/ddaa239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/18/2023] Open
Abstract
The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterized by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure and the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.
Collapse
Affiliation(s)
- Viktor Černý
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Cesar Fortes-Lima
- Subdepartment of Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Petr Tříska
- Archaeogenetics Laboratory, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| |
Collapse
|
5
|
Priehodová E, Austerlitz F, Čížková M, Nováčková J, Ricaut FX, Hofmanová Z, Schlebusch CM, Černý V. Sahelian pastoralism from the perspective of variants associated with lactase persistence. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:423-436. [PMID: 32812238 DOI: 10.1002/ajpa.24116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/17/2020] [Accepted: 06/02/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Archeological evidence shows that first nomadic pastoralists came to the African Sahel from northeastern Sahara, where milking is reported by ~7.5 ka. A second wave of pastoralists arrived with the expansion of Arabic tribes in 7th-14th century CE. All Sahelian pastoralists depend on milk production but genetic diversity underlying their lactase persistence (LP) is poorly understood. MATERIALS AND METHODS We investigated SNP variants associated with LP in 1,241 individuals from 29 mostly pastoralist populations in the Sahel. Then, we analyzed six SNPs in the neighboring fragment (419 kb) in the Fulani and Tuareg with the -13910*T mutation, reconstructed haplotypes, and calculated expansion age and growth rate of this variant. RESULTS Our results reveal a geographic localization of two different LP variants in the Sahel: -13910*T west of Lake Chad (Fulani and Tuareg pastoralists) and -13915*G east of there (mostly Arabic-speaking pastoralists). We show that -13910*T has a more diversified haplotype background among the Fulani than among the Tuareg and that the age estimate for expansion of this variant among the Fulani (~8.5 ka) corresponds to introduction of cattle to the area. CONCLUSIONS This is the first study showing that the "Eurasian" LP allele -13910*T is widespread both in northern Europe and in the Sahel; however, it is limited to pastoralists in the Sahel. Since the Fulani haplotype with -13910*T is shared with contemporary Eurasians, its origin could be in a region encompassing the Near East and northeastern Africa in a population ancestral to both Saharan pastoralists and European farmers.
Collapse
Affiliation(s)
- Edita Priehodová
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Frédéric Austerlitz
- UMR 7206 EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, Musée de l'Homme, Paris, France
| | - Martina Čížková
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jana Nováčková
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - François-Xavier Ricaut
- Department of Evolution and Biological Diversity (UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, Toulouse, France
| | - Zuzana Hofmanová
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Carina M Schlebusch
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.,SciLifeLab, Uppsala, Sweden
| | - Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| |
Collapse
|
6
|
Nováčková J, Čížková M, Mokhtar MG, Duda P, Stenzl V, Tříska P, Hofmanová Z, Černý V. Subsistence strategy was the main factor driving population differentiation in the bidirectional corridor of the African Sahel. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171:496-508. [DOI: 10.1002/ajpa.24001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/19/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Jana Nováčková
- Archaeogenetics LaboratoryInstitute of Archaeology of the Academy of Sciences of the Czech Republic Prague Czech Republic
| | - Martina Čížková
- Archaeogenetics LaboratoryInstitute of Archaeology of the Academy of Sciences of the Czech Republic Prague Czech Republic
| | | | - Pavel Duda
- Department of Zoology, Faculty of ScienceUniversity of South Bohemia České Budějovice Czech Republic
| | - Vlastimil Stenzl
- Department of Forensic GeneticsInstitute of Criminalistics Prague Czech Republic
| | - Petr Tříska
- Archaeogenetics LaboratoryInstitute of Archaeology of the Academy of Sciences of the Czech Republic Prague Czech Republic
| | - Zuzana Hofmanová
- Archaeogenetics LaboratoryInstitute of Archaeology of the Academy of Sciences of the Czech Republic Prague Czech Republic
| | - Viktor Černý
- Archaeogenetics LaboratoryInstitute of Archaeology of the Academy of Sciences of the Czech Republic Prague Czech Republic
| |
Collapse
|
7
|
Elkamel S, Boussetta S, Khodjet-El-Khil H, Benammar Elgaaied A, Cherni L. Ancient and recent Middle Eastern maternal genetic contribution to North Africa as viewed by mtDNA diversity in Tunisian Arab populations. Am J Hum Biol 2018; 30:e23100. [PMID: 29359455 DOI: 10.1002/ajhb.23100] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/06/2017] [Accepted: 12/29/2017] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES Through previous mitochondrial DNA studies, the Middle Eastern maternal genetic contribution to Tunisian populations appears limited. In fact, most of the studied communities were cosmopolitan, or of Berber or Andalusian origin. To provide genetic evidence for the actual contribution of Middle Eastern mtDNA lineages to Tunisia, we focused on two Arab speaking populations from Kairouan and Wesletia known to belong to an Arab genealogical lineage. MATERIALS AND METHODS A total of 114 samples were sequenced for the mtDNA HVS-I and HVS-II regions. Using these data, we evaluated the distribution of Middle Eastern haplogroups in the study populations, constructed interpolation maps, and established phylogenetic networks allowing estimation of the coalescence time for three specific Middle Eastern subclades (R0a, J1b, and T1). RESULTS Both studied populations displayed North African genetic structure and Middle Eastern lineages with a frequency of 12% and 28.12% in Kairouan and Wesletia, respectively. TMRCA estimates for haplogroups T1a, R0a, and J1b in Tunisian Arabian samples were around 15 000 YBP, 9000 to 5000 YBP, and 960 to 600 YBP, respectively. CONCLUSIONS The Middle Eastern maternal genetic contribution to Tunisian populations, as to other North African populations, occurred mostly in deep prehistory. They were brought in different migration waves during the Upper Paleolithic, probably with the expansion of Iberomaurusian culture, and during Epipaleolithic and Early Neolithic periods, which are concomitant with the Capsian civilization. Middle Eastern lineages also came to Tunisia during the recent Islamic expansion of the 7th CE and the subsequent massive Bedouin migration during the 11th CE.
Collapse
Affiliation(s)
- Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Houssein Khodjet-El-Khil
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Amel Benammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia.,High Institute of Biotechnology, University of Monastir, Monastir, 5000, Tunisia
| |
Collapse
|
8
|
Černý V, Kulichová I, Poloni ES, Nunes JM, Pereira L, Mayor A, Sanchez-Mazas A. Genetic history of the African Sahelian populations. HLA 2018; 91:153-166. [DOI: 10.1111/tan.13189] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/03/2017] [Indexed: 12/13/2022]
Affiliation(s)
- V. Černý
- Department of Anthropology, Faculty of Natural Sciences; Comenius University, Ilkovicova 6; 842 15 Bratislava Slovakia
| | - I. Kulichová
- Department of Anthropology and Human Genetics, Faculty of Science; Charles University in Prague; Prague Czech Republic
| | - E. S. Poloni
- Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution, Anthropology Unit; University of Geneva; Geneva Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3); Geneva Switzerland
| | - J. M. Nunes
- Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution, Anthropology Unit; University of Geneva; Geneva Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3); Geneva Switzerland
| | - L. Pereira
- Instituto de Investigação e Inovação em Saúde; Universidade do Porto (i3S); Porto Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto Portugal
| | - A. Mayor
- Laboratory of African Archaeology and Peopling History (APA), Department of Genetics and Evolution, Anthropology Unit; University of Geneva; Geneva Switzerland
| | - A. Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution, Anthropology Unit; University of Geneva; Geneva Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3); Geneva Switzerland
| |
Collapse
|
9
|
Kulichová I, Fernandes V, Deme A, Nováčková J, Stenzl V, Novelletto A, Pereira L, Černý V. Internal diversification of non-Sub-Saharan haplogroups in Sahelian populations and the spread of pastoralism beyond the Sahara. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:424-434. [DOI: 10.1002/ajpa.23285] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Iva Kulichová
- Department of Anthropology and Human Genetics, Faculty of Science; Charles University in Prague; Czech Republic
| | - Verónica Fernandes
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto; Porto Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto Portugal
| | - Alioune Deme
- Département d'Histoire, Faculté des Lettres et Sciences humaines; Université Cheikh Anta Diop de Dakar; Senegal
| | - Jana Nováčková
- Archaeogenetics Laboratory; Institute of Archaeology of the Academy of Sciences of the Czech Republic; Czech Republic
| | - Vlastimil Stenzl
- Department of Forensic Genetics; Institute of Criminalistics; Prague Czech Republic
| | | | - Luísa Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto; Porto Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto Portugal
- Faculdade de Medicina da Universidade do Porto; Porto Portugal
| | - Viktor Černý
- Archaeogenetics Laboratory; Institute of Archaeology of the Academy of Sciences of the Czech Republic; Czech Republic
| |
Collapse
|
10
|
Podgorná E, Diallo I, Vangenot C, Sanchez-Mazas A, Sabbagh A, Černý V, Poloni ES. Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa. BMC Evol Biol 2015; 15:263. [PMID: 26620671 PMCID: PMC4665893 DOI: 10.1186/s12862-015-0543-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 11/13/2015] [Indexed: 12/21/2022] Open
Abstract
Background Dietary changes associated to shifts in subsistence strategies during human evolution may have induced new selective pressures on phenotypes, as currently held for lactase persistence. Similar hypotheses exist for arylamine N-acetyltransferase 2 (NAT2) mediated acetylation capacity, a well-known pharmacogenetic trait with wide inter-individual variation explained by polymorphisms in the NAT2 gene. The environmental causative factor (if any) driving its evolution is as yet unknown, but significant differences in prevalence of acetylation phenotypes are found between hunter-gatherer and food-producing populations, both in sub-Saharan Africa and worldwide, and between agriculturalists and pastoralists in Central Asia. These two subsistence strategies also prevail among sympatric populations of the African Sahel, but knowledge on NAT2 variation among African pastoral nomads was up to now very scarce. Here we addressed the hypothesis of different selective pressures associated to the agriculturalist or pastoralist lifestyles having acted on the evolution of NAT2 by sequencing the gene in 287 individuals from five pastoralist and one agriculturalist Sahelian populations. Results We show that the significant NAT2 genetic structure of African populations is mainly due to frequency differences of three major haplotypes, two of which are categorized as decreased function alleles (NAT2*5B and NAT2*6A), particularly common in populations living in arid environments, and one fast allele (NAT2*12A), more frequently detected in populations living in tropical humid environments. This genetic structure does associate more strongly with a classification of populations according to ecoregions than to subsistence strategies, mainly because most Sahelian and East African populations display little to no genetic differentiation between them, although both regions hold nomadic or semi-nomadic pastoralist and sedentary agriculturalist communities. Furthermore, we found significantly higher predicted proportions of slow acetylators in pastoralists than in agriculturalists, but also among food-producing populations living in the Sahelian and dry savanna zones than in those living in humid environments, irrespective of their mode of subsistence. Conclusion Our results suggest a possible independent influence of both the dietary habits associated with subsistence modes and the chemical environment associated with climatic zones and biomes on the evolution of NAT2 diversity in sub-Saharan African populations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0543-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Eliška Podgorná
- 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. .,Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| | - Issa Diallo
- Département de Linguistique et Langues Nationales, Institut des Sciences des Sociétés, CNRST, Ouagadougou, Burkina Faso.
| | - Christelle Vangenot
- Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| | - Alicia Sanchez-Mazas
- Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| | - Audrey Sabbagh
- IRD, UMR216, Mère et enfant face aux infections tropicales, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France.
| | - Viktor Černý
- 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.
| | - Estella S Poloni
- Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| |
Collapse
|
11
|
Triska P, Soares P, Patin E, Fernandes V, Cerny V, Pereira L. Extensive Admixture and Selective Pressure Across the Sahel Belt. Genome Biol Evol 2015; 7:3484-95. [PMID: 26614524 PMCID: PMC4700964 DOI: 10.1093/gbe/evv236] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genome-wide studies of African populations have the potential to reveal powerful insights into the evolution of our species, as these diverse populations have been exposed to intense selective pressures imposed by infectious diseases, diet, and environmental factors. Within Africa, the Sahel Belt extensively overlaps the geographical center of several endemic infections such as malaria, trypanosomiasis, meningitis, and hemorrhagic fevers. We screened 2.5 million single nucleotide polymorphisms in 161 individuals from 13 Sahelian populations, which together with published data cover Western, Central, and Eastern Sahel, and include both nomadic and sedentary groups. We confirmed the role of this Belt as a main corridor for human migrations across the continent. Strong admixture was observed in both Central and Eastern Sahelian populations, with North Africans and Near Eastern/Arabians, respectively, but it was inexistent in Western Sahelian populations. Genome-wide local ancestry inference in admixed Sahelian populations revealed several candidate regions that were significantly enriched for non-autochthonous haplotypes, and many showed to be under positive selection. The DARC gene region in Arabs and Nubians was enriched for African ancestry, whereas the RAB3GAP1/LCT/MCM6 region in Oromo, the TAS2R gene family in Fulani, and the ALMS1/NAT8 in Turkana and Samburu were enriched for non-African ancestry. Signals of positive selection varied in terms of geographic amplitude. Some genomic regions were selected across the Belt, the most striking example being the malaria-related DARC gene. Others were Western-specific (oxytocin, calcium, and heart pathways), Eastern-specific (lipid pathways), or even population-restricted (TAS2R genes in Fulani, which may reflect sexual selection).
Collapse
Affiliation(s)
- Petr Triska
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (ICBAS), Porto, Portugal
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Etienne Patin
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France Centre National de la Recherche Scientifique, Paris, France
| | - Veronica Fernandes
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Viktor Cerny
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Luisa Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| |
Collapse
|
12
|
Hernández CL, Soares P, Dugoujon JM, Novelletto A, Rodríguez JN, Rito T, Oliveira M, Melhaoui M, Baali A, Pereira L, Calderón R. Early Holocenic and Historic mtDNA African Signatures in the Iberian Peninsula: The Andalusian Region as a Paradigm. PLoS One 2015; 10:e0139784. [PMID: 26509580 PMCID: PMC4624789 DOI: 10.1371/journal.pone.0139784] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/17/2015] [Indexed: 11/18/2022] Open
Abstract
Determining the timing, identity and direction of migrations in the Mediterranean Basin, the role of "migratory routes" in and among regions of Africa, Europe and Asia, and the effects of sex-specific behaviors of population movements have important implications for our understanding of the present human genetic diversity. A crucial component of the Mediterranean world is its westernmost region. Clear features of transcontinental ancient contacts between North African and Iberian populations surrounding the maritime region of Gibraltar Strait have been identified from archeological data. The attempt to discern origin and dates of migration between close geographically related regions has been a challenge in the field of uniparental-based population genetics. Mitochondrial DNA (mtDNA) studies have been focused on surveying the H1, H3 and V lineages when trying to ascertain north-south migrations, and U6 and L in the opposite direction, assuming that those lineages are good proxies for the ancestry of each side of the Mediterranean. To this end, in the present work we have screened entire mtDNA sequences belonging to U6, M1 and L haplogroups in Andalusians--from Huelva and Granada provinces--and Moroccan Berbers. We present here pioneer data and interpretations on the role of NW Africa and the Iberian Peninsula regarding the time of origin, number of founders and expansion directions of these specific markers. The estimated entrance of the North African U6 lineages into Iberia at 10 ky correlates well with other L African clades, indicating that U6 and some L lineages moved together from Africa to Iberia in the Early Holocene. Still, founder analysis highlights that the high sharing of lineages between North Africa and Iberia results from a complex process continued through time, impairing simplistic interpretations. In particular, our work supports the existence of an ancient, frequently denied, bridge connecting the Maghreb and Andalusia.
Collapse
Affiliation(s)
- Candela L. Hernández
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
| | - Jean M. Dugoujon
- CNRS UMR 5288 Laboratoire d’Anthropologie Moléculaire et d’Imagerie de Synthèse (AMIS), Université Paul Sabatier Toulouse III, 31073 Toulouse, France
| | - Andrea Novelletto
- Dipartimento di Biologia, Università Tor Vergata di Rome, Rome, Italy
| | | | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Marisa Oliveira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | | | - Abdellatif Baali
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - Luisa Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Rosario Calderón
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
- * E-mail:
| |
Collapse
|
13
|
Cerezo M, Gusmão L, Černý V, Uddin N, Syndercombe-Court D, Gómez-Carballa A, Göbel T, Schneider PM, Salas A. Comprehensive Analysis of Pan-African Mitochondrial DNA Variation Provides New Insights into Continental Variation and Demography. J Genet Genomics 2015; 43:133-43. [PMID: 27020033 DOI: 10.1016/j.jgg.2015.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/30/2015] [Accepted: 09/15/2015] [Indexed: 01/15/2023]
Abstract
Africa is the cradle of all human beings, and although it has been the focus of a number of genetic studies, there are many questions that remain unresolved. We have performed one of the largest and most comprehensive meta-analyses of mitochondrial DNA (mtDNA) lineages carried out in the African continent to date. We generated high-throughput mtDNA single nucleotide polymorphism (SNP) data (230 SNPs) from 2024 Africans, where more than 500 of them were additionally genotyped for the control region. These data were analyzed together with over 12,700 control region profiles collected from the literature, representing more than 300 population samples from Africa. Insights into the African homeland of humans are discussed. Phylogeographic patterns for the African continent are shown at a high phylogeographic resolution as well as at the population and regional levels. The deepest branch of the mtDNA tree, haplogroup L0, shows the highest sub-haplogroup diversity in Southeast and East Africa, suggesting this region as the homeland for modern humans. Several demographic estimates point to the coast as a facilitator of human migration in Africa, but the data indicate complex patterns, perhaps mirroring the effect of recent continental-scaled demographic events in re-shaping African mtDNA variability.
Collapse
Affiliation(s)
- María Cerezo
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia 15782, Spain; The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, Institute of Biology, State University of Rio de Janeiro, Rio de Janeiro 20550-900, Brazil; IPATIMUP Institute of Molecular Pathology and Immunology of the University of Porto, Porto 4200-465, Portugal
| | - Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague 118-01, Czech Republic
| | - Nabeel Uddin
- Faculty of Life Sciences and Medicine, King's College London, London SE1 9NH, UK
| | | | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia 15782, Spain
| | - Tanja Göbel
- Institute of Legal Medicine, Medical Faculty, University of Cologne, Cologne D-50823, Germany
| | - Peter M Schneider
- Institute of Legal Medicine, Medical Faculty, University of Cologne, Cologne D-50823, Germany
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia 15782, Spain.
| |
Collapse
|
14
|
60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2. Sci Rep 2015. [PMID: 26211407 PMCID: PMC4515592 DOI: 10.1038/srep12526] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial DNA (mtDNA) haplogroup L2 originated in Western Africa but is nowadays spread across the entire continent. L2 movements were previously postulated to be related to the Bantu expansion, but L2 expansions eastwards probably occurred much earlier. By reconstructing the phylogeny of L2 (44 new complete sequences) we provide insights on the complex net of within-African migrations in the last 60 thousand years (ka). Results show that lineages in Southern Africa cluster with Western/Central African lineages at a recent time scale, whereas, eastern lineages seem to be substantially more ancient. Three moments of expansion from a Central African source are associated to L2: (1) one migration at 70–50 ka into Eastern or Southern Africa, (2) postglacial movements (15–10 ka) into Eastern Africa; and (3) the southward Bantu Expansion in the last 5 ka. The complementary population and L0a phylogeography analyses indicate no strong evidence of mtDNA gene flow between eastern and southern populations during the later movement, suggesting low admixture between Eastern African populations and the Bantu migrants. This implies that, at least in the early stages, the Bantu expansion was mainly a demic diffusion with little incorporation of local populations.
Collapse
|