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Ali AA, Khalid KE, Mohammed SE, Akhtar MS, Saeed OK. Association of Human Leukocyte Antigen (HLA) class II ( DRB1 and DQB1) alleles and haplotypes with Rheumatoid Arthritis in Sudanese patients. Front Immunol 2023; 14:1178546. [PMID: 37426636 PMCID: PMC10324672 DOI: 10.3389/fimmu.2023.1178546] [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: 03/02/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023] Open
Abstract
The aim of this study was to determine the Human Leukocyte Antigen (HLA) class II (DRB1 and DQB1) alleles and haplotype frequency in Rheumatoid Arthritis (RA) in the Sudanese population. The frequency of HLA-DRB1 and -DQB1 alleles and DRB1-DQB1 haplotypes were determined in 122 RA patients and 100 controls. HLA alleles were genotyped by the polymerase chain reaction-sequence specific primers (PCR-SSP) method. In RA patients, HLA-DRB1*04 and *10 alleles were high in frequency (9.6% vs 14.2%, P = 0.038 and P = 0.042, respectively), and dependently on anti-citrullinated protein antibodies (ACPAs) seropositivity (P = 0.044 and P = 0.027, respectively). In contrast, the frequency of the HLA-DRB1*07 allele was significantly low in patients than in controls (11.7% vs 5.0%, P = 0.010). Moreover, the HLA-DQB1*03 allele was strongly associated with RA risk (42.2%, P = 2.2x10-8), whereas, HLA-DQB1*02 and *06 showed protective effects against RA (23.1% and 42.2%, P = 0.024 and P = 2.2x10-6, respectively). Five different HLA haplotypes, DRB1*03-DQB1*03 (P = 0.00003), DRB1*04-DQB1*03 (P = 0.00014), DRB1*08-DQB1*03 (P = 0.027), DRB1*13-DQB1*02 (P = 0.004), and DRB1*13-DQB1*03 (P = 3.79x10-8) were significantly associated with RA risk, while 3 protective haplotypes, DRB1*03-DQB1*02 (Pc = 0.008), DRB1*07-DQB1*02 (Pc = 0.004), and DRB1*13-DQB1*06 (Pc = 0.02) were identified. This is the first study determining the association between HLA class II alleles and haplotypes and RA risk in our population.
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Affiliation(s)
- Adil Ahmed Ali
- Department of Biochemistry and Nutrition, Faculty of Medicine, University of Gezira, Wad Medani, Sudan
| | - Khalid Eltahir Khalid
- Department of Biochemistry and Nutrition, Faculty of Medicine, University of Gezira, Wad Medani, Sudan
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Somaya Elhaj Mohammed
- Department of Pathology, Faculty of Medicine, University of Gezira, Wad Medani, Sudan
| | - Mohammed Salman Akhtar
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Osman Khalafalla Saeed
- Department of Internal Medicine, Faculty of Medicine, University of Gezira, Wad Medani, Sudan
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Ibrahim ME. Genetic diversity of the Sudanese: insights on origin and implications for health. Hum Mol Genet 2021; 30:R37-R41. [PMID: 33864377 PMCID: PMC8223596 DOI: 10.1093/hmg/ddab028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 11/21/2022] Open
Abstract
By virtue of their cultural, linguistic and genetic legacies, many populations from Sudan have deep histories in the region and retain high genetic diversities. Sudan’s location in north east Africa, a unique spot believed to act as a climatic refuge during periods of climate extremes, might have dictated that fate. Among the marked consequences of this diversity is the potential to provide information on the origin and structure of human populations within and outside the continent, as well as migration patterns towards various parts of the African continent, and out of Africa. The diverse Sudanese gene pool further has the potential to inform on genetic adaptations driven by culture and the environment resulting in unique and interesting traits, some of which are yet to be investigated. In addition, these genomes could offer clues to complex issues of causation amidst the challenge of new paradigms in biology underpinned by the genomic revolution.
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Ali Albsheer MM, Hussien A, Kwiatkowski D, Hamid MMA, Ibrahim ME. The Duffy T-33C is an insightful marker of human history and admixture. Meta Gene 2020; 26:100782. [PMID: 32837914 PMCID: PMC7418637 DOI: 10.1016/j.mgene.2020.100782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/13/2020] [Accepted: 08/08/2020] [Indexed: 01/07/2023] Open
Abstract
A contrasting genotype and allele frequency pattern between Africans and non-Africans in the Duffy (T-33C) locus is reported. Its near fixation in various populations suggest is no longer under natural selection, and that current distribution is possibly a relic of distant extreme selection combined with genetic drift during the out of Africa. We put this difference into the utility to infer the ancestral state of ambiguous loci in different populations.
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Affiliation(s)
- Musab M Ali Albsheer
- Institute of Endemic Diseases, University of Khartoum, Sudan.,Faculty of Medical Laboratory Sciences, Sinnar University, Sudan
| | - Ayman Hussien
- Institute of Endemic Diseases, University of Khartoum, Sudan
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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: 4.5] [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.
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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:
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Daak AA, Elsamani E, Ali EH, Mohamed FA, Abdel-Rahman ME, Elderdery AY, Talbot O, Kraft P, Ghebremeskel K, Elbashir MI, Fawzi W. Sickle cell disease in western Sudan: genetic epidemiology and predictors of knowledge attitude and practices. Trop Med Int Health 2016; 21:642-53. [PMID: 27028397 PMCID: PMC10699227 DOI: 10.1111/tmi.12689] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To investigate the epidemiology of sickle cell disease (SCD) and determinants of knowledge, attitudes and practices (KAP) towards SCD in western Kordofan State, Sudan. METHODS A community-based, descriptive, cross-sectional study was conducted in three towns. Three hundred and seventy-two households were polled, and blood samples for haemoglobin phenotyping were collected from 1116 individuals. Sociodemographic, socio-economic and KAP data were collected using investigator-administered questionnaires. Descriptive, frequency distribution and multiple regression analyses were performed. RESULTS About 50.9% of the study population were Misseriya tribes. Consanguineous marriages were reported by 67.5% of the households. The highest percentage of homozygous SCD was 2.8% among children under 5 years of age. About 24.9% were carriers of HbS allele (HbAS). HbS allele frequency was highest in children aged 5-11 years (18.3%, CI: 13.7-22.9%) and lowest in males >15 years old (12.0%, CI: 6.1-17.9%). The average HbS frequency across all age groups was 14.5% (95% CI: 12.2-16.8%). The most frequent β-globin gene cluster haplotype was the Cameroon (30.8%), followed by the Benin (21.8%), the Senegal (12.8%) and the Bantu (2.2%) haplotypes. About 17.0% of all-cause child deaths were due to SCD. The estimated change in log odds of having the SS genotype per year increase in age was (-) 0.0058 (95% CI -0.0359, 0.0242). This represents a non-statistically significant 2.9% increase in 5-year mortality for individuals with the SS genotype relative to those with AS and AA genotypes. About 46.9% of the households had poor knowledge, 26.1% had satisfactory knowledge, and 26.9% had good knowledge about sickle cell disease. Mothers' and fathers' educational levels were significant predictors of good knowledge about SCD (P < 0.05). About 48.0% had a satisfactory attitude towards sickle cell disease while 30.7% had poor attitude and only 21.3 showed good attitudes. Poor knowledge about SCD and low socio-economic status were the strongest positive predictors of poor attitude and practices towards SCD (P < 0.01). CONCLUSIONS Sickle cell disease is a major health problem in West Kordofan, Sudan. Knowledge, attitude and practices towards the disease are not satisfactory. The development of public health programs is highly recommended to control and manage SCD in western parts of Sudan.
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Affiliation(s)
- Ahmed A. Daak
- Department of Global Health and Population, Harvard University, Boston, MA, USA
- Department of Medical Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Elfatih Elsamani
- Department of Community Medicine, School of Medicine, Ahfad University for Women, Khartoum, Sudan
| | - Eltigani H. Ali
- Lipidomics and Nutrition Research Centre, Faculty of Life Sciences and Computing, London Metropolitan University, London, UK
| | - Fatma A Mohamed
- School of Nursing Sciences, University of Khartoum, Khartoum, Sudan
| | - Manar E. Abdel-Rahman
- Department of Statistics, Faculty of Mathematical Sciences, University of Khartoum, Khartoum, Sudan
| | - Abozer Y. Elderdery
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Octavious Talbot
- Department of Biostatistics, Harvard University, Boston, MA, USA
| | - Peter Kraft
- Department of Biostatistics, Harvard University, Boston, MA, USA
| | - Kebreab Ghebremeskel
- Lipidomics and Nutrition Research Centre, Faculty of Life Sciences and Computing, London Metropolitan University, London, UK
| | - Mustafa I. Elbashir
- Department of Medical Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Wafaie Fawzi
- Department of Global Health and Population, Harvard University, Boston, MA, USA
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Sabahelzain MM, Hamamy H. The ethnic distribution of sickle cell disease in Sudan. Pan Afr Med J 2014; 18:13. [PMID: 25360197 PMCID: PMC4213521 DOI: 10.11604/pamj.2014.18.13.3280] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 01/08/2014] [Indexed: 11/11/2022] Open
Abstract
Sickle cell disease (SCD) is one of the most common inherited disorders of haemoglobin in Africa and it is expected that sickle cell trait varies in frequency in different areas in Sudan. An extensive literature search was carried out accessing the US National Library of Medicine, the WHO Eastern Mediterranean Region resources, the Catalogue for Transmission Genetics in Arabs and papers and documents published in Sudan that included data on the prevalence of sickle cell anaemia and trait. Rates of SCA and trait varied in different areas in Sudan with the highest rates reported from Western and Eastern Sudan where one in every 123 children born in Messeryia tribe in Western Sudan is at risk of having SCD. High consanguinity rates and malaria endemicity are strong related factors with sickle cell gene in Sudan. This review will present what is known about the rates of sickle cell gene in different ethnic groups in Sudan.
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Affiliation(s)
- Majdi Mohammed Sabahelzain
- Reproductive and Child Health Research Unit, University of Medical Sciences and Technology, Khartoum, Sudan
| | - Hanan Hamamy
- Department of Genetic Medicine and Development Geneva University, Geneva, Switzerland
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Gebremeskel EI, Ibrahim ME. Y-chromosome E haplogroups: their distribution and implication to the origin of Afro-Asiatic languages and pastoralism. Eur J Hum Genet 2014; 22:1387-92. [PMID: 24667790 PMCID: PMC4231410 DOI: 10.1038/ejhg.2014.41] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 02/11/2014] [Accepted: 02/13/2014] [Indexed: 11/09/2022] Open
Abstract
Archeological and paleontological evidences point to East Africa as the likely area of early evolution of modern humans. Genetic studies also indicate that populations from the region often contain, but not exclusively, representatives of the more basal clades of mitochondrial and Y-chromosome phylogenies. Most Y-chromosome haplogroup diversity in Africa, however, is present within macrohaplogroup E that seem to have appeared 21 000-32 000 YBP somewhere between the Red Sea and Lake Chad. The combined analysis of 17 bi-allelic markers in 1214 Y chromosomes together with cultural background of 49 populations displayed in various metrics: network, multidimensional scaling, principal component analysis and neighbor-joining plots, indicate a major contribution of East African populations to the foundation of the macrohaplogroup, suggesting a diversification that predates the appearance of some cultural traits and the subsequent expansion that is more associated with the cultural and linguistic diversity witnessed today. The proto-Afro-Asiatic group carrying the E-P2 mutation may have appeared at this point in time and subsequently gave rise to the different major population groups including current speakers of the Afro-Asiatic languages and pastoralist populations.
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Affiliation(s)
- Eyoab I Gebremeskel
- 1] Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan [2] Department of Biology, Eritrea Institute of Technology, Mai-Nefhi, Eritrea
| | - Muntaser E Ibrahim
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
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Cerezo M, Černý V, Carracedo Á, Salas A. New insights into the Lake Chad Basin population structure revealed by high-throughput genotyping of mitochondrial DNA coding SNPs. PLoS One 2011; 6:e18682. [PMID: 21533064 PMCID: PMC3080428 DOI: 10.1371/journal.pone.0018682] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Accepted: 03/13/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Located in the Sudan belt, the Chad Basin forms a remarkable ecosystem, where several unique agricultural and pastoral techniques have been developed. Both from an archaeological and a genetic point of view, this region has been interpreted to be the center of a bidirectional corridor connecting West and East Africa, as well as a meeting point for populations coming from North Africa through the Saharan desert. METHODOLOGY/PRINCIPAL FINDINGS Samples from twelve ethnic groups from the Chad Basin (n = 542) have been high-throughput genotyped for 230 coding region mitochondrial DNA (mtDNA) Single Nucleotide Polymorphisms (mtSNPs) using Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-TOF) mass spectrometry. This set of mtSNPs allowed for much better phylogenetic resolution than previous studies of this geographic region, enabling new insights into its population history. Notable haplogroup (hg) heterogeneity has been observed in the Chad Basin mirroring the different demographic histories of these ethnic groups. As estimated using a Bayesian framework, nomadic populations showed negative growth which was not always correlated to their estimated effective population sizes. Nomads also showed lower diversity values than sedentary groups. CONCLUSIONS/SIGNIFICANCE Compared to sedentary population, nomads showed signals of stronger genetic drift occurring in their ancestral populations. These populations, however, retained more haplotype diversity in their hypervariable segments I (HVS-I), but not their mtSNPs, suggesting a more ancestral ethnogenesis. Whereas the nomadic population showed a higher Mediterranean influence signaled mainly by sub-lineages of M1, R0, U6, and U5, the other populations showed a more consistent sub-Saharan pattern. Although lifestyle may have an influence on diversity patterns and hg composition, analysis of molecular variance has not identified these differences. The present study indicates that analysis of mtSNPs at high resolution could be a fast and extensive approach for screening variation in population studies where labor-intensive techniques such as entire genome sequencing remain unfeasible.
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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, CIBERER, Galicia, Spain
| | - Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, The Czech Republic
| | - Ángel Carracedo
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, CIBERER, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, CIBERER, Galicia, Spain
- * E-mail:
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Černý V, Pereira L, Musilová E, Kujanová M, Vašíková A, Blasi P, Garofalo L, Soares P, Diallo I, Brdička R, Novelletto A. Genetic Structure of Pastoral and Farmer Populations in the African Sahel. Mol Biol Evol 2011; 28:2491-500. [DOI: 10.1093/molbev/msr067] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Haber M, Platt DE, Khoury S, Badro DA, Abboud M, Tyler-Smith C, Zalloua PA. Y-chromosome R-M343 African lineages and sickle cell disease reveal structured assimilation in Lebanon. J Hum Genet 2010; 56:29-33. [PMID: 20981037 DOI: 10.1038/jhg.2010.131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have sought to identify signals of assimilation of African male lines in Lebanon by exploring the association of sickle cell disease (SCD) in Lebanon with Y-chromosome haplogroups that are informative of the disease origin and its exclusivity to the Muslim community. A total of 732 samples were analyzed, including 33 SCD patients from Lebanon genotyped for 28 binary markers and 19 short tandem repeats on the non-recombinant segment of the Y chromosome. Genetic organization was identified using populations known to have influenced the genetic structure of the Lebanese population, in addition to African populations with high incidence of SCD. Y-chromosome haplogroup R-M343 sub-lineages distinguish between sub-Saharan African and Lebanese Y chromosomes. We detected a limited penetration of SCD into Lebanese R-M343 carriers, restricted to Lebanese Muslims. We suggest that this penetration brought the sickle cell gene along with the African R-M343, probably with the Saharan caravan slave trade.
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Affiliation(s)
- Marc Haber
- Medical School, The Lebanese American University, Beirut, Lebanon
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A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. Eur J Hum Genet 2010; 19:95-101. [PMID: 20736979 DOI: 10.1038/ejhg.2010.146] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The phylogenetic relationships of numerous branches within the core Y-chromosome haplogroup R-M207 support a West Asian origin of haplogroup R1b, its initial differentiation there followed by a rapid spread of one of its sub-clades carrying the M269 mutation to Europe. Here, we present phylogeographically resolved data for 2043 M269-derived Y-chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largely separates the majority of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomy, the major S116 sub-clade shows a frequency peak in the upper Danube basin and Paris area with declining frequency toward Italy, Iberia, Southern France and British Isles. Although this frequency pattern closely approximates the spread of the Linearbandkeramik (LBK), Neolithic culture, an advent leading to a number of pre-historic cultural developments during the past ≤10 thousand years, more complex pre-Neolithic scenarios remain possible for the L23(xM412) components in Southeast Europe and elsewhere.
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Scheinfeldt LB, Soi S, Tishkoff SA. Colloquium paper: working toward a synthesis of archaeological, linguistic, and genetic data for inferring African population history. Proc Natl Acad Sci U S A 2010; 107 Suppl 2:8931-8. [PMID: 20445100 PMCID: PMC3024023 DOI: 10.1073/pnas.1002563107] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although Africa is the origin of modern humans, the pattern and distribution of genetic variation and correlations with cultural and linguistic diversity in Africa have been understudied. Recent advances in genomic technology, however, have led to genomewide studies of African samples. In this article, we discuss genetic variation in African populations contextualized with what is known about archaeological and linguistic variation. What emerges from this review is the importance of using independent lines of evidence in the interpretation of genetic and genomic data in the reconstruction of past population histories.
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Affiliation(s)
| | - Sameer Soi
- Genomics and Computational Biology Graduate Group, and
| | - Sarah A. Tishkoff
- Department of Genetics
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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Salih NA, Hussain AA, Almugtaba IA, Elzein AM, Elhassan IM, Khalil EAG, Ishag HB, Mohammed HS, Kwiatkowski D, Ibrahim ME. Loss of balancing selection in the betaS globin locus. BMC MEDICAL GENETICS 2010; 11:21. [PMID: 20128890 PMCID: PMC2829010 DOI: 10.1186/1471-2350-11-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 02/03/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND Probably the best example of the rise and maintenance of balancing selection as an evolutionary trend is the role of S-haemoglobin (HbS - rs334) in protecting from malaria. Yet, the dynamics of such a process remains poorly understood, particularly in relation to different malaria transmission rates and the genetic background of the affected populations. METHODS We investigated the association of haemoglobin HbS in protection from clinical episodes of malaria in two populations/villages where malaria is endemic, but mostly presenting in mild clinical forms. Five-hundred and forty-six individuals comprising 65 and 82 families from the Hausa and Massalit villages respectively were genotyped for HbS. Allele and genotype frequencies as well as departure from Hardy-Weinberg Equilibrium were estimated from four-hundred and seventy independent genotypes across different age groups. Age-group frequencies were used to calculate the coefficient-of-fitness and to simulate the expected frequencies in future generations. RESULTS Genotype frequencies were within Hardy-Weinberg expectations in Hausa and Massalit in the total sample set but not within the different age groups. There was a trend for a decrease of the HbS allele frequency in Hausa and an increase of frequency in Massalit. Although the HbS allele was able to confer significant protection from the clinical episodes of malaria in the two populations, as suggested by the odds ratios, the overall relative fitness of the HbS allele seems to have declined in Hausa. CONCLUSIONS Such loss of balancing selection could be due to a combined effect of preponderance of non-clinical malaria in Hausa, and the deleterious effect of the homozygous HbS under circumstances of endogamy.
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Affiliation(s)
- Niven A Salih
- Department of Molecular Biology, Institute of Endemic Diseases, Medical Campus, Qasser Street, University of Khartoum, Khartoum, Sudan
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Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A, Froment A, Hirbo JB, Awomoyi AA, Bodo JM, Doumbo O, Ibrahim M, Juma AT, Kotze MJ, Lema G, Moore JH, Mortensen H, Nyambo TB, Omar SA, Powell K, Pretorius GS, Smith MW, Thera MA, Wambebe C, Weber JL, Williams SM. The genetic structure and history of Africans and African Americans. Science 2009; 324:1035-44. [PMID: 19407144 PMCID: PMC2947357 DOI: 10.1126/science.1172257] [Citation(s) in RCA: 975] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations across the continent has been enigmatic. We studied 121 African populations, four African American populations, and 60 non-African populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral population clusters in Africa that correlate with self-described ethnicity and shared cultural and/or linguistic properties. We observed high levels of mixed ancestry in most populations, reflecting historical migration events across the continent. Our data also provide evidence for shared ancestry among geographically diverse hunter-gatherer populations (Khoesan speakers and Pygmies). The ancestry of African Americans is predominantly from Niger-Kordofanian (approximately 71%), European (approximately 13%), and other African (approximately 8%) populations, although admixture levels varied considerably among individuals. This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies.
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Affiliation(s)
- Sarah A Tishkoff
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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Hassan HY, Underhill PA, Cavalli-Sforza LL, Ibrahim ME. Y-chromosome variation among Sudanese: restricted gene flow, concordance with language, geography, and history. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 137:316-23. [PMID: 18618658 DOI: 10.1002/ajpa.20876] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We study the major levels of Y-chromosome haplogroup variation in 15 Sudanese populations by typing major Y-haplogroups in 445 unrelated males representing the three linguistic families in Sudan. Our analysis shows Sudanese populations fall into haplogroups A, B, E, F, I, J, K, and R in frequencies of 16.9, 7.9, 34.4, 3.1, 1.3, 22.5, 0.9, and 13% respectively. Haplogroups A, B, and E occur mainly in Nilo-Saharan speaking groups including Nilotics, Fur, Borgu, and Masalit; whereas haplogroups F, I, J, K, and R are more frequent among Afro-Asiatic speaking groups including Arabs, Beja, Copts, and Hausa, and Niger-Congo speakers from the Fulani ethnic group. Mantel tests reveal a strong correlation between genetic and linguistic structures (r = 0.31, P = 0.007), and a similar correlation between genetic and geographic distances (r = 0.29, P = 0.025) that appears after removing nomadic pastoralists of no known geographic locality from the analysis. The bulk of genetic diversity appears to be a consequence of recent migrations and demographic events mainly from Asia and Europe, evident in a higher migration rate for speakers of Afro-Asiatic as compared with the Nilo-Saharan family of languages, and a generally higher effective population size for the former. The data provide insights not only into the history of the Nile Valley, but also in part to the history of Africa and the area of the Sahel.
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Affiliation(s)
- Hisham Y Hassan
- Institute of Endemic Diseases, University of Khartoum, Sudan
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