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Serradell JM, Lorenzo-Salazar JM, Flores C, Lao O, Comas D. Modelling the demographic history of human North African genomes points to a recent soft split divergence between populations. Genome Biol 2024; 25:201. [PMID: 39080715 PMCID: PMC11290046 DOI: 10.1186/s13059-024-03341-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND North African human populations present a complex demographic scenario due to the presence of an autochthonous genetic component and population substructure, plus extensive gene flow from the Middle East, Europe, and sub-Saharan Africa. RESULTS We conducted a comprehensive analysis of 364 genomes to construct detailed demographic models for the North African region, encompassing its two primary ethnic groups, the Arab and Amazigh populations. This was achieved through an Approximate Bayesian Computation with Deep Learning (ABC-DL) framework and a novel algorithm called Genetic Programming for Population Genetics (GP4PG). This innovative approach enabled us to effectively model intricate demographic scenarios, utilizing a subset of 16 whole genomes at > 30X coverage. The demographic model suggested by GP4PG exhibited a closer alignment with the observed data compared to the ABC-DL model. Both point to a back-to-Africa origin of North African individuals and a close relationship with Eurasian populations. Results support different origins for Amazigh and Arab populations, with Amazigh populations originating back in Epipaleolithic times, while GP4PG supports Arabization as the main source of Middle Eastern ancestry. The GP4PG model includes population substructure in surrounding populations (sub-Saharan Africa and Middle East) with continuous decaying gene flow after population split. Contrary to ABC-DL, the best GP4PG model does not require pulses of admixture from surrounding populations into North Africa pointing to soft splits as drivers of divergence in North Africa. CONCLUSIONS We have built a demographic model on North Africa that points to a back-to-Africa expansion and a differential origin between Arab and Amazigh populations.
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Affiliation(s)
- Jose M Serradell
- Departament de Medicina i Ciències de la Vida, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona s/n, Santa Cruz de Tenerife, 38600, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona s/n, Santa Cruz de Tenerife, 38600, Spain
- Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Santa Cruz de Tenerife, 38206, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario 145, Santa Cruz de Tenerife, 38010, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, Madrid, 28029, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, Calle de La Juventud S/N, Santa María de Guía, Las Palmas de Gran Canaria, 35450, Spain
| | - Oscar Lao
- Departament de Medicina i Ciències de la Vida, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain.
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain.
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Goli RC, Chishi KG, Ganguly I, Singh S, Dixit S, Rathi P, Diwakar V, Sree C C, Limbalkar OM, Sukhija N, Kanaka K. Global and Local Ancestry and its Importance: A Review. Curr Genomics 2024; 25:237-260. [PMID: 39156729 PMCID: PMC11327809 DOI: 10.2174/0113892029298909240426094055] [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: 01/13/2024] [Revised: 03/02/2024] [Accepted: 03/11/2024] [Indexed: 08/20/2024] Open
Abstract
The fastest way to significantly change the composition of a population is through admixture, an evolutionary mechanism. In animal breeding history, genetic admixture has provided both short-term and long-term advantages by utilizing the phenomenon of complementarity and heterosis in several traits and genetic diversity, respectively. The traditional method of admixture analysis by pedigree records has now been replaced greatly by genome-wide marker data that enables more precise estimations. Among these markers, SNPs have been the popular choice since they are cost-effective, not so laborious, and automation of genotyping is easy. Certain markers can suggest the possibility of a population's origin from a sample of DNA where the source individual is unknown or unwilling to disclose their lineage, which are called Ancestry-Informative Markers (AIMs). Revealing admixture level at the locus-specific level is termed as local ancestry and can be exploited to identify signs of recent selective response and can account for genetic drift. Considering the importance of genetic admixture and local ancestry, in this mini-review, both concepts are illustrated, encompassing basics, their estimation/identification methods, tools/software used and their applications.
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Affiliation(s)
| | - Kiyevi G. Chishi
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Indrajit Ganguly
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Sanjeev Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - S.P. Dixit
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Pallavi Rathi
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Vikas Diwakar
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Chandana Sree C
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | | | - Nidhi Sukhija
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
- Central Tasar Research and Training Institute, Ranchi, 835303, Jharkhand, India
| | - K.K Kanaka
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, 834010, Jharkhand, India
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Vilà-Valls L, Abdeli A, Lucas-Sánchez M, Bekada A, Calafell F, Benhassine T, Comas D. Understanding the genomic heterogeneity of North African Imazighen: from broad to microgeographical perspectives. Sci Rep 2024; 14:9979. [PMID: 38693301 PMCID: PMC11063056 DOI: 10.1038/s41598-024-60568-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
The strategic location of North Africa has led to cultural and demographic shifts, shaping its genetic structure. Historical migrations brought different genetic components that are evident in present-day North African genomes, along with autochthonous components. The Imazighen (plural of Amazigh) are believed to be the descendants of autochthonous North Africans and speak various Amazigh languages, which belong to the Afro-Asiatic language family. However, the arrival of different human groups, especially during the Arab conquest, caused cultural and linguistic changes in local populations, increasing their heterogeneity. We aim to characterize the genetic structure of the region, using the largest Amazigh dataset to date and other reference samples. Our findings indicate microgeographical genetic heterogeneity among Amazigh populations, modeled by various admixture waves and different effective population sizes. A first admixture wave is detected group-wide around the twelfth century, whereas a second wave appears in some Amazigh groups around the nineteenth century. These events involved populations with higher genetic ancestry from south of the Sahara compared to the current North Africans. A plausible explanation would be the historical trans-Saharan slave trade, which lasted from the Roman times to the nineteenth century. Furthermore, our investigation shows that assortative mating in North Africa has been rare.
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Affiliation(s)
- Laura Vilà-Valls
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté Des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Marcel Lucas-Sánchez
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Traki Benhassine
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté Des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.
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Lucas-Sánchez M, Abdeli A, Bekada A, Calafell F, Benhassine T, Comas D. The Impact of Recent Demography on Functional Genetic Variation in North African Human Groups. Mol Biol Evol 2024; 41:msad283. [PMID: 38152862 PMCID: PMC10783648 DOI: 10.1093/molbev/msad283] [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: 05/22/2023] [Revised: 11/22/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023] Open
Abstract
The strategic location of North Africa has made the region the core of a wide range of human demographic events, including migrations, bottlenecks, and admixture processes. This has led to a complex and heterogeneous genetic and cultural landscape, which remains poorly studied compared to other world regions. Whole-exome sequencing is particularly relevant to determine the effects of these demographic events on current-day North Africans' genomes, since it allows to focus on those parts of the genome that are more likely to have direct biomedical consequences. Whole-exome sequencing can also be used to assess the effect of recent demography in functional genetic variation and the efficacy of natural selection, a long-lasting debate. In the present work, we use newly generated whole-exome sequencing and genome-wide array genotypes to investigate the effect of demography in functional variation in 7 North African populations, considering both cultural and demographic differences and with a special focus on Amazigh (plur. Imazighen) groups. We detect genetic differences among populations related to their degree of isolation and the presence of bottlenecks in their recent history. We find differences in the functional part of the genome that suggest a relaxation of purifying selection in the more isolated groups, allowing for an increase of putatively damaging variation. Our results also show a shift in mutational load coinciding with major demographic events in the region and reveal differences within and between cultural and geographic groups.
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Affiliation(s)
- Marcel Lucas-Sánchez
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Faculté des Sciences Biologiques, Laboratoire de Biologie Cellulaire et Moléculaire, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Traki Benhassine
- Faculté des Sciences Biologiques, Laboratoire de Biologie Cellulaire et Moléculaire, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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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.
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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.
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Caro-Consuegra R, Lucas-Sánchez M, Comas D, Bosch E. Identifying signatures of positive selection in human populations from North Africa. Sci Rep 2023; 13:8166. [PMID: 37210386 DOI: 10.1038/s41598-023-35312-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/16/2023] [Indexed: 05/22/2023] Open
Abstract
Because of its location, North Africa (NA) has witnessed continuous demographic movements with an impact on the genomes of present-day human populations. Genomic data describe a complex scenario with varying proportions of at least four main ancestry components: Maghrebi, Middle Eastern-, European-, and West-and-East-African-like. However, the footprint of positive selection in NA has not been studied. Here, we compile genome-wide genotyping data from 190 North Africans and individuals from surrounding populations, investigate for signatures of positive selection using allele frequencies and linkage disequilibrium-based methods and infer ancestry proportions to discern adaptive admixture from post-admixture selection events. Our results show private candidate genes for selection in NA involved in insulin processing (KIF5A), immune function (KIF5A, IL1RN, TLR3), and haemoglobin phenotypes (BCL11A). We also detect signatures of positive selection related to skin pigmentation (SLC24A5, KITLG), and immunity function (IL1R1, CD44, JAK1) shared with European populations and candidate genes associated with haemoglobin phenotypes (HPSE2, HBE1, HBG2), other immune-related (DOCK2) traits, and insulin processing (GLIS3) traits shared with West and East African populations. Finally, the SLC8A1 gene, which codifies for a sodium-calcium exchanger, was the only candidate identified under post-admixture selection in Western NA.
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Affiliation(s)
- Rocio Caro-Consuegra
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Marcel Lucas-Sánchez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - David Comas
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, 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, 08003, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, 28029, Madrid, Spain.
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Cheffi K, El Khair A, Dahbi N, Talbi J, Hilali A, El Ossmani H. Genetic analysis based on 15 autosomal short tandem repeats (STRs) in the Chaouia population, western center Morocco, and genetic relationships with worldwide populations. Mol Genet Genomics 2023; 298:931-941. [PMID: 37162566 DOI: 10.1007/s00438-023-02028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/29/2023] [Indexed: 05/11/2023]
Abstract
The complex demographic history of human populations in North Africa has resulted in a high degree of genetic heterogeneity across the region. However, little is known about the pattern of these genetic variations in its current populations. The present study provides new data on the genetic background of Chaouia, an Arabic-speaking North African population in the western center of Morocco. A random sample of 150 unrelated healthy individuals from Chaouia was assessed using the AmpFLSTR Identifiler kit. The most polymorphic markers were D21S11 and D18S51, with 23 and 22 alleles, respectively. After Bonferroni's correction, two loci (TH01 and D18S51) deviated from Hardy-Weinberg equilibrium. The phylogeny analysis separated North African populations into northeastern and northwestern groups. The Chaouia population was clustered with northwestern Africans. It was the closest to the Berbers of Azrou. The Chaouia shared close genetic affinities with populations from North Africa, the Middle East, and Europe, particularly Iberians, and to a lesser extent with sub-Saharan populations. The pattern of genetic admixture varied across North African populations without a clear correlation between their geographic (northeastern or northwestern) or linguistic identities (Arab or Berber), however, genetic heterogeneity among Berbers was observed. These findings suggest that the diversity observed in North African populations extends geographical and linguistic boundaries. It is further linked to each population's unique and complex demographic history. Human North African population genetics seems to present an intriguing landscape for future studies in the region and its surrounding populations to trace the origins of the genetic heterogeneity observed in these populations.
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Affiliation(s)
- Khadija Cheffi
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco.
| | - Abderrazak El Khair
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Noura Dahbi
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Jalal Talbi
- General Directorate of National Security, National Laboratory of the Scientific and Technical Police, Casablanca, Morocco
| | - Abderraouf Hilali
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Hicham El Ossmani
- Institut de Criminalistique de la Gendarmerie Royale, Rabat, Morocco
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