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Agdzhoyan A, Iskandarov N, Ponomarev G, Pylev V, Koshel S, Salaev V, Pocheshkhova E, Kagazezheva Z, Balanovska E. Origins of East Caucasus Gene Pool: Contributions of Autochthonous Bronze Age Populations and Migrations from West Asia Estimated from Y-Chromosome Data. Genes (Basel) 2023; 14:1780. [PMID: 37761920 PMCID: PMC10530682 DOI: 10.3390/genes14091780] [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: 08/03/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The gene pool of the East Caucasus, encompassing modern-day Azerbaijan and Dagestan populations, was studied alongside adjacent populations using 83 Y-chromosome SNP markers. The analysis of genetic distances among 18 populations (N = 2216) representing Nakh-Dagestani, Altaic, and Indo-European language families revealed the presence of three components (Steppe, Iranian, and Dagestani) that emerged in different historical periods. The Steppe component occurs only in Karanogais, indicating a recent medieval migration of Turkic-speaking nomads from the Eurasian steppe. The Iranian component is observed in Azerbaijanis, Dagestani Tabasarans, and all Iranian-speaking peoples of the Caucasus. The Dagestani component predominates in Dagestani-speaking populations, except for Tabasarans, and in Turkic-speaking Kumyks. Each component is associated with distinct Y-chromosome haplogroup complexes: the Steppe includes C-M217, N-LLY22g, R1b-M73, and R1a-M198; the Iranian includes J2-M172(×M67, M12) and R1b-M269; the Dagestani includes J1-Y3495 lineages. We propose J1-Y3495 haplogroup's most common lineage originated in an autochthonous ancestral population in central Dagestan and splits up ~6 kya into J1-ZS3114 (Dargins, Laks, Lezgi-speaking populations) and J1-CTS1460 (Avar-Andi-Tsez linguistic group). Based on the archeological finds and DNA data, the analysis of J1-Y3495 phylogeography suggests the growth of the population in the territory of modern-day Dagestan that started in the Bronze Age, its further dispersal, and the microevolution of the diverged population.
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Affiliation(s)
| | - Nasib Iskandarov
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
| | - Georgy Ponomarev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
| | - Vladimir Pylev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
- Biobank of Northern Eurasia, 115201 Moscow, Russia
| | - Sergey Koshel
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
- Department of Cartography and Geoinformatics, Faculty of Geography, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vugar Salaev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
| | - Elvira Pocheshkhova
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
- Department of Biology with Course in Medical Genetics, Faculty of Pharmacy, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Zhaneta Kagazezheva
- Department of Biology with Course in Medical Genetics, Faculty of Pharmacy, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
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Genome-wide analyses disclose the distinctive HLA architecture and the pharmacogenetic landscape of the Somali population. Sci Rep 2020; 10:5652. [PMID: 32221414 PMCID: PMC7101338 DOI: 10.1038/s41598-020-62645-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/17/2020] [Indexed: 12/16/2022] Open
Abstract
African populations are underrepresented in medical genomics studies. For the Somali population, there is virtually no information on genomic markers with significance to precision medicine. Here, we analyzed nearly 900,000 genomic markers in samples collected from 95 unrelated individuals in the North Eastern Somalia. ADMIXTURE program for estimation of individual ancestries revealed a homogenous Somali population. Principal component analysis with PLINK software showed approximately 60% East African and 40% West Eurasian genes in the Somali population, with a close relation to the Cushitic and Semitic speaking Ethiopian populations. We report the unique features of human leukocyte antigens (HLA) in the Somali population, which seem to differentiate from all other neighboring regions compared. Current study identified high prevalence of the diabetes type 1 (T1D) predisposing HLA DR-DQ haplotypes in Somalia. This finding may explain the increased T1D risk observed among Somali children. In addition, ethnic Somalis were found to host the highest frequencies observed thus far for several pharmacogenetic variants, including UGT1A4*2. In conclusion, we report that the Somali population displays genetic traits of significance to health and disease. The Somali dataset is publicly available and will add more information to the few genomic datasets available for African populations.
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Frequency of PAR4 Ala120Thr variant associated with platelet reactivity significantly varies across sub-Saharan African populations. Blood 2018; 132:2103-2106. [PMID: 30143503 DOI: 10.1182/blood-2018-05-852335] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 08/15/2018] [Indexed: 12/22/2022] Open
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Abdi AA, Osman A. Prevalence of common hereditary risk factors for thrombophilia in Somalia and identification of a novel Gln544Arg mutation in coagulation factor V. J Thromb Thrombolysis 2018; 44:536-543. [PMID: 28889200 PMCID: PMC5658450 DOI: 10.1007/s11239-017-1543-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thrombophilia, commonly manifested as venous thromboembolism (VTE), is a worldwide concern but little is known on its genetic epidemiology in many parts of the globe particularly in the developing countries. Here we employed TaqMan genotyping and pyrosequencing to evaluate the prevalence of known common nucleotide polymorphisms associated with thrombophilia in a Somali population in the Puntland region of Somalia. We also employed next generation sequencing (NGS) to investigate other genetic variants in a Somali patient with deep venous thrombosis (DVT). As expected, we found no existence of factor V Leiden (rs6025) and prothrombin G20210A (rs1799963) in the Somali population. The G allele of ABO [261G/delG] polymorphism (rs8176719) was found at a frequency of 29%, similar to that observed in other African populations. We found the lowest so far reported frequency of MTHFR C677T (rs1801133) polymorphism in the Somali population (T allele frequency 1.5%). A novel and deleterious single nucleotide variation in exon 11 of coagulation factor V (c.1631A>G) causing Gln544Arg exchange in factor V was identified in a 29 years old Somali female with DVT. The same patient was heterozygous to VKORC1 Asp36Tyr polymorphism (rs61742245) that predisposes to warfarin resistance. In conclusion, this study shows that common hereditary factors for thromboembolism found in Caucasians are either less frequent or absent in the Somali population-similar to the situation in other Africans. NGS is possibly a better choice to detect genetic risk variants for thrombosis in this ethnic group.
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Affiliation(s)
- Abshir Ali Abdi
- Faculty of Medicine, East Africa University, Bosaso, Puntland, Somalia
| | - Abdimajid Osman
- Division of Clinical Chemistry, Region Östergötland, Ingång 64, 581 85, Linköping, Sweden. .,Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
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Comparison of manual and automated AmpliSeq™ workflows in the typing of a Somali population with the Precision ID Identity Panel. Forensic Sci Int Genet 2017; 31:118-125. [DOI: 10.1016/j.fsigen.2017.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 01/15/2023]
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Pereira V, Mogensen HS, Børsting C, Morling N. Evaluation of the Precision ID Ancestry Panel for crime case work: A SNP typing assay developed for typing of 165 ancestral informative markers. Forensic Sci Int Genet 2017; 28:138-145. [DOI: 10.1016/j.fsigen.2017.02.013] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 11/24/2022]
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Genetic differentiation between upland and lowland populations shapes the Y-chromosomal landscape of West Asia. Hum Genet 2017; 136:437-450. [DOI: 10.1007/s00439-017-1770-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 02/20/2017] [Indexed: 12/22/2022]
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Sunni M, Noble JA, Yu L, Mahamed Z, Lane JA, Dhunkal AM, Bellin MD, Nathan B, Kyllo J, Abuzzahab MJ, Gottlieb PA, Babu S, Armstrong T, Moran A. Predominance of DR3 in Somali children with type 1 diabetes in the twin cities, Minnesota. Pediatr Diabetes 2017; 18:136-142. [PMID: 26854192 DOI: 10.1111/pedi.12369] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 01/08/2016] [Accepted: 01/08/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Minnesota is home to the largest Somali population in USA, and pediatric diabetes teams are seeing increasing numbers of Somali children with diabetes. OBJECTIVE To assess the immune basis of diabetes in Somali children in the Twin Cities, Minnesota. METHODS A total of 31 Somali children ≤19 yr were treated for type 1 diabetes (T1D) at the University of Minnesota Masonic Children's Hospital and Children's Hospitals and Clinics of Minnesota underwent analysis of human leukocyte antigen (HLA) alleles (n = 30) and diabetes autoantibodies [glutamic acid decarboxylase (GAD65), islet antigen 2 (IA-2), zinc transporter 8 (ZnT8); n = 31]. HLA alleles were analyzed in 49 Somalis without diabetes (controls). Anti-transglutaminase autoantibodies (TGA) for celiac disease were also measured. RESULTS In Somali children with T1D aged 13.5 ± 5 yr (35% female, disease duration 6.5 ± 3.6 yr), the most common HLA allele was DRB1*03:01 (93%, compared with 45% of Somali controls), followed by DRB1*13:02 (27%). There was a relatively low frequency of DR4 (13%). Controls showed a similar pattern. All 31 participants were positive for at least one diabetes autoantibody. Insulin antibodies were positive in 84% (all were on insulin). Excluding insulin antibodies, 23 (74%) subjects tested positive for at least one other diabetes autoantibody; 32% had 1 autoantibody, 32% had 2 autoantibodies, and 10% had 3 autoantibodies. GAD65 autoantibodies were found in 56% of subjects, IA-2 in 29%, and ZnT8 in 26%. Four (13%) were TGA positive. CONCLUSION The autoantibody and HLA profiles of Somali children with diabetes are consistent with autoimmune diabetes. Their HLA profile is unique with an exceptionally high prevalence of DRB1*03:01 allele and relative paucity of DR4 alleles compared with African Americans with T1D.
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Affiliation(s)
- Muna Sunni
- Department of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | - Janelle A Noble
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Liping Yu
- The Barbara Davis Center for Childhood Diabetes, University of Colorado, Denver, CO, USA
| | - Zahra Mahamed
- Department of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | - Julie A Lane
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Abdirahman M Dhunkal
- Department of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | - Melena D Bellin
- Department of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | - Brandon Nathan
- Department of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | - Jennifer Kyllo
- Pediatric Endocrinology and McNeely Diabetes Center, Children's Hospitals and Clinics of Minnesota, St. Paul, MN, USA
| | - M Jennifer Abuzzahab
- Pediatric Endocrinology and McNeely Diabetes Center, Children's Hospitals and Clinics of Minnesota, St. Paul, MN, USA
| | - Peter A Gottlieb
- The Barbara Davis Center for Childhood Diabetes, University of Colorado, Denver, CO, USA
| | - Sunanda Babu
- The Barbara Davis Center for Childhood Diabetes, University of Colorado, Denver, CO, USA
| | - Taylor Armstrong
- The Barbara Davis Center for Childhood Diabetes, University of Colorado, Denver, CO, USA
| | - Antoinette Moran
- Department of Pediatric Endocrinology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
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Gandini F, Achilli A, Pala M, Bodner M, Brandini S, Huber G, Egyed B, Ferretti L, Gómez-Carballa A, Salas A, Scozzari R, Cruciani F, Coppa A, Parson W, Semino O, Soares P, Torroni A, Richards MB, Olivieri A. Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes. Sci Rep 2016; 6:25472. [PMID: 27146119 PMCID: PMC4857117 DOI: 10.1038/srep25472] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/18/2016] [Indexed: 01/29/2023] Open
Abstract
Rare mitochondrial lineages with relict distributions can sometimes be disproportionately informative about deep events in human prehistory. We have studied one such lineage, haplogroup R0a, which uniquely is most frequent in Arabia and the Horn of Africa, but is distributed much more widely, from Europe to India. We conclude that: (1) the lineage ancestral to R0a is more ancient than previously thought, with a relict distribution across the Mediterranean/Southwest Asia; (2) R0a has a much deeper presence in Arabia than previously thought, highlighting the role of at least one Pleistocene glacial refugium, perhaps on the Red Sea plains; (3) the main episode of dispersal into Eastern Africa, at least concerning maternal lineages, was at the end of the Late Glacial, due to major expansions from one or more refugia in Arabia; (4) there was likely a minor Late Glacial/early postglacial dispersal from Arabia through the Levant and into Europe, possibly alongside other lineages from a Levantine refugium; and (5) the presence of R0a in Southwest Arabia in the Holocene at the nexus of a trading network that developed after ~3 ka between Africa and the Indian Ocean led to some gene flow even further afield, into Iran, Pakistan and India.
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Affiliation(s)
- Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.,School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.,Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Maria Pala
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Balazs Egyed
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
| | - Rosaria Scozzari
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Martin B Richards
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
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Singh S, Singh A, Rajkumar R, Sampath Kumar K, Kadarkarai Samy S, Nizamuddin S, Singh A, Ahmed Sheikh S, Peddada V, Khanna V, Veeraiah P, Pandit A, Chaubey G, Singh L, Thangaraj K. Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup. Sci Rep 2016; 6:19157. [PMID: 26754573 PMCID: PMC4709632 DOI: 10.1038/srep19157] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 10/08/2015] [Indexed: 11/24/2022] Open
Abstract
The global distribution of J2-M172 sub-haplogroups has been associated with Neolithic demic diffusion. Two branches of J2-M172, J2a-M410 and J2b-M102 make a considerable part of Y chromosome gene pool of the Indian subcontinent. We investigated the Neolithic contribution of demic dispersal from West to Indian paternal lineages, which majorly consists of haplogroups of Late Pleistocene ancestry. To accomplish this, we have analysed 3023 Y-chromosomes from different ethnic populations, of which 355 belonged to J2-M172. Comparison of our data with worldwide data, including Y-STRs of 1157 individuals and haplogroup frequencies of 6966 individuals, suggested a complex scenario that cannot be explained by a single wave of agricultural expansion from Near East to South Asia. Contrary to the widely accepted elite dominance model, we found a substantial presence of J2a-M410 and J2b-M102 haplogroups in both caste and tribal populations of India. Unlike demic spread in Eurasia, our results advocate a unique, complex and ancient arrival of J2a-M410 and J2b-M102 haplogroups into Indian subcontinent.
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Affiliation(s)
- Sakshi Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Ashish Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Raja Rajkumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | | | - Sheikh Nizamuddin
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Amita Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Vidya Peddada
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Vinee Khanna
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Aridaman Pandit
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | | | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
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11
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Steele CD, Court DS, Balding DJ. Worldwide F(ST) estimates relative to five continental-scale populations. Ann Hum Genet 2015; 78:468-77. [PMID: 26460400 PMCID: PMC4223938 DOI: 10.1111/ahg.12081] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We estimate the population genetics parameter (also referred to as the fixation index) from short tandem repeat (STR) allele frequencies, comparing many worldwide human subpopulations at approximately the national level with continental-scale populations. is commonly used to measure population differentiation, and is important in forensic DNA analysis to account for remote shared ancestry between a suspect and an alternative source of the DNA. We estimate comparing subpopulations with a hypothetical ancestral population, which is the approach most widely used in population genetics, and also compare a subpopulation with a sampled reference population, which is more appropriate for forensic applications. Both estimation methods are likelihood-based, in which is related to the variance of the multinomial-Dirichlet distribution for allele counts. Overall, we find low values, with posterior 97.5 percentiles when comparing a subpopulation with the most appropriate population, and even for inter-population comparisons we find . These are much smaller than single nucleotide polymorphism-based inter-continental estimates, and are also about half the magnitude of STR-based estimates from population genetics surveys that focus on distinct ethnic groups rather than a general population. Our findings support the use of up to 3% in forensic calculations, which corresponds to some current practice.
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12
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Benton MC, Stuart S, Bellis C, Macartney-Coxson D, Eccles D, Curran JE, Chambers G, Blangero J, Lea RA, Grffiths LR. 'Mutiny on the Bounty': the genetic history of Norfolk Island reveals extreme gender-biased admixture. INVESTIGATIVE GENETICS 2015; 6:11. [PMID: 26339467 PMCID: PMC4558825 DOI: 10.1186/s13323-015-0028-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/28/2015] [Indexed: 11/17/2022]
Abstract
Background The Pacific Oceania region was one of the last regions of the world to be settled via human migration. Here we outline a settlement of this region that has given rise to a uniquely admixed population. The current Norfolk Island population has arisen from a small number of founders with mixed Caucasian and Polynesian ancestry, descendants of a famous historical event. The ‘Mutiny on the Bounty’ has been told in history books, songs and the big screen, but recently this story can be portrayed through comprehensive molecular genetics. Written history details betrayal and murder leading to the founding of Pitcairn Island by European mutineers and the Polynesian women who left Tahiti with them. Investigation of detailed genealogical records supports historical accounts. Findings Using genetics, we show distinct maternal Polynesian mitochondrial lineages in the present day population, as well as a European centric Y-chromosome phylogeny. These results comprehensively characterise the unique gender-biased admixture of this genetic isolate and further support the historical records relating to Norfolk Island. Conclusions Our results significantly refine previous population genetic studies investigating Polynesian versus Caucasian diversity in the Norfolk Island population and add information that is beneficial to future disease and gene mapping studies. Electronic supplementary material The online version of this article (doi:10.1186/s13323-015-0028-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miles C Benton
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Q Block, 66 Musk Avenue, Kelvin Grove Campus, Brisbane, QLD 4001 Australia
| | - Shani Stuart
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Q Block, 66 Musk Avenue, Kelvin Grove Campus, Brisbane, QLD 4001 Australia
| | - Claire Bellis
- Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Donia Macartney-Coxson
- Kenepuru Science Centre, Institute of Environmental Science and Research, Wellington, 5240 New Zealand
| | - David Eccles
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Q Block, 66 Musk Avenue, Kelvin Grove Campus, Brisbane, QLD 4001 Australia
| | - Joanne E Curran
- Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Geoff Chambers
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140 New Zealand
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520 USA
| | - Rod A Lea
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Q Block, 66 Musk Avenue, Kelvin Grove Campus, Brisbane, QLD 4001 Australia
| | - Lyn R Grffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Q Block, 66 Musk Avenue, Kelvin Grove Campus, Brisbane, QLD 4001 Australia
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13
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Triki-Fendri S, Sánchez-Diz P, Rey-González D, Alfadhli S, Ayadi I, Ben Marzoug R, Carracedo Á, Rebai A. Genetic structure of the Kuwaiti population revealed by paternal lineages. Am J Hum Biol 2015; 28:203-12. [PMID: 26293354 DOI: 10.1002/ajhb.22773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/18/2015] [Accepted: 07/25/2015] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE We analyzed the Y-chromosome haplogroup diversity in the Kuwaiti population to gain a more complete overview of its genetic landscape. METHOD A sample of 117 males from the Kuwaiti population was studied through the analysis of 22 Y-SNPs. The results were then interpreted in conjunction with those of other populations from the Middle East, South Asia, North and East Africa, and East Europe. RESULTS The analyzed markers allowed the discrimination of 19 different haplogroups with a diversity of 0.7713. J-M304 was the most frequent haplogroup in the Kuwaiti population (55.5%) followed by E-M96 (18%). They revealed a genetic homogeneity between the Kuwaiti population and those of the Middle East (FST = 6.1%, P-value < 0.0001), although a significant correlation between genetic and geographic distances was found (r = 0.41, P-value = 0.009). Moreover, the nonsignificant pairwise FST genetic distances between the Kuwait population on the one hand and the Arabs of Iran and those of Sudan on the other, corroborate the hypothesis of bidirectional gene flow between Arabia and both Iran and Sudan. CONCLUSION Overall, we have revealed that the Kuwaiti population has experienced significant gene flow from neighboring populations like Saudi Arabia, Iran, and East Africa. Therefore, we have confirmed that the population of Kuwait is genetically coextensive with those of the Middle East.
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Affiliation(s)
- Soumaya Triki-Fendri
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Paula Sánchez-Diz
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain
| | - Danel Rey-González
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain
| | - Suad Alfadhli
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Kuwait
| | - Imen Ayadi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Riadh Ben Marzoug
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
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Olofsson JK, Mogensen HS, Buchard A, Børsting C, Morling N. Forensic and population genetic analyses of Danes, Greenlanders and Somalis typed with the Yfiler ® Plus PCR amplification kit. Forensic Sci Int Genet 2015; 16:232-236. [DOI: 10.1016/j.fsigen.2015.02.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/09/2015] [Accepted: 02/15/2015] [Indexed: 11/29/2022]
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Triki-Fendri S, Sánchez-Diz P, Rey-González D, Ayadi I, Carracedo Á, Rebai A. Paternal lineages in Libya inferred from Y-chromosome haplogroups. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 157:242-51. [DOI: 10.1002/ajpa.22705] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 01/09/2015] [Accepted: 01/13/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Soumaya Triki-Fendri
- Research Group on Molecular and Cellular Screening Processes, Laboratory of Microorganisms and Biomolecules, Centre of Biotechnology of Sfax; Tunisia
| | - Paula Sánchez-Diz
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago de Compostela; Galicia Spain
| | - Danel Rey-González
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago de Compostela; Galicia Spain
| | - Imen Ayadi
- Research Group on Molecular and Cellular Screening Processes, Laboratory of Microorganisms and Biomolecules, Centre of Biotechnology of Sfax; Tunisia
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago de Compostela; Galicia Spain
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University; Jeddah Saudi Arabia
| | - Ahmed Rebai
- Research Group on Molecular and Cellular Screening Processes, Laboratory of Microorganisms and Biomolecules, Centre of Biotechnology of Sfax; Tunisia
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Reguig A, Harich N, Barakat A, Rouba H. Phylogeography of E1b1b1b-M81 haplogroup and analysis of its subclades in Morocco. Hum Biol 2014; 86:105-12. [PMID: 25397701 DOI: 10.3378/027.086.0204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2014] [Indexed: 11/05/2022]
Abstract
In this study we analyzed 295 unrelated Berber-speaking men from northern, central, and southern Morocco to characterize frequency of the E1b1b1b-M81 haplogroup and to refine the phylogeny of its subclades: E1b1b1b1-M107, E1b1b1b2-M183, and E1b1b1b2a-M165. For this purpose, we typed four biallelic polymorphisms: M81, M107, M183, and M165. A large majority of the Berber-speaking male lineages belonged to the Y-chromosomal E1b1b1b-M81 haplogroup. The frequency ranged from 79.1% to 98.5% in all localities sampled. E1b1b1b2-M183 was the most dominant subclade in our samples, ranging from 65.1% to 83.1%. In contrast, the E1b1b1b1-M107 and E1b1b1b2a-M165 subclades were not found in our samples. Our results suggest a predominance of the E1b1b1b-M81 haplogroup among Moroccan Berber-speaking males with a decreasing gradient from south to north. The most prevalent subclade in this haplogroup was E1b1b1b2-M183, for which diffferences among these three groups were statistically significant between central and southern groups.
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Affiliation(s)
- Ahmed Reguig
- Laboratoire de Génétique Moléculaire Humaine, Département de Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Nourdin Harich
- Equipe des sciences Anthropogénétiques et Biotechnologie, Département de Biologie, Faculté des Sciences El Jadida, Université Chouaib Eddoukkali, El Jadida, Morocco
| | - Abdelhamid Barakat
- Laboratoire de Génétique Moléculaire Humaine, Département de Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hassan Rouba
- Laboratoire de Génétique Moléculaire Humaine, Département de Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
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Børsting C, Fordyce SL, Olofsson J, Mogensen HS, Morling N. Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing. Forensic Sci Int Genet 2014; 12:144-54. [DOI: 10.1016/j.fsigen.2014.06.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 12/18/2022]
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18
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Kling D, Dell’Amico B, Haddeland PJT, Tillmar AO. Population genetic analysis of 12 X-STRs in a Somali population sample. Forensic Sci Int Genet 2014; 11:e7-8. [DOI: 10.1016/j.fsigen.2014.02.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/18/2014] [Accepted: 02/22/2014] [Indexed: 10/25/2022]
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Hodgson JA, Mulligan CJ, Al-Meeri A, Raaum RL. Early back-to-Africa migration into the Horn of Africa. PLoS Genet 2014; 10:e1004393. [PMID: 24921250 PMCID: PMC4055572 DOI: 10.1371/journal.pgen.1004393] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 04/07/2014] [Indexed: 11/19/2022] Open
Abstract
Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses on admixture and population structure in HOA populations. These analyses suggested that there might be distinct, differentiated African and non-African ancestries in the HOA. After partitioning the SNP data into African and non-African origin chromosome segments, we found support for a distinct African (Ethiopic) ancestry and a distinct non-African (Ethio-Somali) ancestry in HOA populations. The African Ethiopic ancestry is tightly restricted to HOA populations and likely represents an autochthonous HOA population. The non-African ancestry in the HOA, which is primarily attributed to a novel Ethio-Somali inferred ancestry component, is significantly differentiated from all neighboring non-African ancestries in North Africa, the Levant, and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic groups, shows little inter-individual variance within these ethnic groups, is estimated to have diverged from all other non-African ancestries by at least 23 ka, and does not carry the unique Arabian lactase persistence allele that arose about 4 ka. Taking into account published mitochondrial, Y chromosome, paleoclimate, and archaeological data, we find that the time of the Ethio-Somali back-to-Africa migration is most likely pre-agricultural.
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Affiliation(s)
- Jason A. Hodgson
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
| | - Connie J. Mulligan
- Department of Anthropology and the Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Ali Al-Meeri
- Department of Biochemistry and Molecular Biology, Sana'a University, Sana'a, Yemen
| | - Ryan L. Raaum
- Department of Anthropology, Lehman College and The Graduate Center, The City University of New York, Bronx, New York, New York, United States of America
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, United States of America
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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: 1.0] [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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Forensic and phylogeographic characterisation of mtDNA lineages from Somalia. Int J Legal Med 2012; 126:573-9. [DOI: 10.1007/s00414-012-0694-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 03/28/2012] [Indexed: 12/12/2022]
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Babiker HM, Schlebusch CM, Hassan HY, Jakobsson M. Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci. INVESTIGATIVE GENETICS 2011; 2:12. [PMID: 21542921 PMCID: PMC3118356 DOI: 10.1186/2041-2223-2-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 05/04/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region. RESULT We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia. CONCLUSION We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.
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Affiliation(s)
- Hiba Ma Babiker
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
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Terreros MC, Rowold DJ, Mirabal S, Herrera RJ. Mitochondrial DNA and Y-chromosomal stratification in Iran: relationship between Iran and the Arabian Peninsula. J Hum Genet 2011; 56:235-46. [PMID: 21326310 DOI: 10.1038/jhg.2010.174] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Modern day Iran is strategically located in the tri-continental corridor uniting Africa, Europe and Asia. Several ethnic groups belonging to distinct religions, speaking different languages and claiming divergent ancestries inhabit the region, generating a potentially diverse genetic reservoir. In addition, past pre-historical and historical events such as the out-of-Africa migrations, the Neolithic expansion from the Fertile Crescent, the Indo-Aryan treks from the Central Asian steppes, the westward Mongol expansions and the Muslim invasions may have chiseled their genetic fingerprints within the genealogical substrata of the Persians. On the other hand, the Iranian perimeter is bounded by the Zagros and Albrez mountain ranges, and the Dasht-e Kavir and Dash-e Lut deserts, which may have restricted gene flow from neighboring regions. By utilizing high-resolution mitochondrial DNA (mtDNA) markers and reanalyzing our previously published Y-chromosomal data, we have found a previously unexplored, genetic connection between Iranian populations and the Arabian Peninsula, likely the result of both ancient and recent gene flow. Furthermore, the regional distribution of mtDNA haplogroups J, I, U2 and U7 also provides evidence of barriers to gene flow posed by the two major Iranian deserts and the Zagros mountain range.
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Affiliation(s)
- Maria C Terreros
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL FL 33199, USA
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Mendez FL, Karafet TM, Krahn T, Ostrer H, Soodyall H, Hammer MF. Increased Resolution of Y Chromosome Haplogroup T Defines Relationships among Populations of the Near East, Europe, and Africa. Hum Biol 2011; 83:39-53. [DOI: 10.3378/027.083.0103] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages. Eur J Hum Genet 2010; 18:800-7. [PMID: 20051990 DOI: 10.1038/ejhg.2009.231] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Although human Y chromosomes belonging to haplogroup R1b are quite rare in Africa, being found mainly in Asia and Europe, a group of chromosomes within the paragroup R-P25(*) are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25(*) chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back migration in prehistoric times. Here, we describe six new mutations that define the relationships among the African R-P25(*) Y chromosomes and between these African chromosomes and earlier reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R1b haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25(*) and about half of the few European/west Asian R-P25(*) chromosomes. A worldwide phylogeographic analysis of the R1b haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in >1800 males from 69 African populations revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic-speaking groups from North Africa. The R-V88 coalescence time was estimated at 9.2-5.6 [corrected] kya, in the early mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin, and geomorphological evidence is consistent with this view.
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Tillmar AO, Bäckström G, Montelius K. Genetic variation of 15 autosomal STR loci in a Somali population. Forensic Sci Int Genet 2009; 4:e19-20. [DOI: 10.1016/j.fsigen.2009.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 11/25/2008] [Accepted: 01/02/2009] [Indexed: 11/16/2022]
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Abu-Amero KK, Hellani A, González AM, Larruga JM, Cabrera VM, Underhill PA. Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions. BMC Genet 2009; 10:59. [PMID: 19772609 PMCID: PMC2759955 DOI: 10.1186/1471-2156-10-59] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 09/22/2009] [Indexed: 11/15/2022] Open
Abstract
Background Human origins and migration models proposing the Horn of Africa as a prehistoric exit route to Asia have stimulated molecular genetic studies in the region using uniparental loci. However, from a Y-chromosome perspective, Saudi Arabia, the largest country of the region, has not yet been surveyed. To address this gap, a sample of 157 Saudi males was analyzed at high resolution using 67 Y-chromosome binary markers. In addition, haplotypic diversity for its most prominent J1-M267 lineage was estimated using a set of 17 Y-specific STR loci. Results Saudi Arabia differentiates from other Arabian Peninsula countries by a higher presence of J2-M172 lineages. It is significantly different from Yemen mainly due to a comparative reduction of sub-Saharan Africa E1-M123 and Levantine J1-M267 male lineages. Around 14% of the Saudi Arabia Y-chromosome pool is typical of African biogeographic ancestry, 17% arrived to the area from the East across Iran, while the remainder 69% could be considered of direct or indirect Levantine ascription. Interestingly, basal E-M96* (n = 2) and J-M304* (n = 3) lineages have been detected, for the first time, in the Arabian Peninsula. Coalescence time for the most prominent J1-M267 haplogroup in Saudi Arabia (11.6 ± 1.9 ky) is similar to that obtained previously for Yemen (11.3 ± 2) but significantly older that those estimated for Qatar (7.3 ± 1.8) and UAE (6.8 ± 1.5). Conclusion The Y-chromosome genetic structure of the Arabian Peninsula seems to be mainly modulated by geography. The data confirm that this area has mainly been a recipient of gene flow from its African and Asian surrounding areas, probably mainly since the last Glacial maximum onwards. Although rare deep rooting lineages for Y-chromosome haplogroups E and J have been detected, the presence of more basal clades supportive of the southern exit route of modern humans to Eurasian, were not found.
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Affiliation(s)
- Khaled K Abu-Amero
- Molecular Genetics Laboratory, College of Medicine, King Saud University, Riyadh 11411, Saudi Arabia.
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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: 4.3] [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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Tomas C, Sanchez JJ, Barbaro A, Brandt-Casadevall C, Hernandez A, Ben Dhiab M, Ramon M, Morling N. X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans). BMC Evol Biol 2008; 8:75. [PMID: 18312628 PMCID: PMC2315647 DOI: 10.1186/1471-2148-8-75] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Accepted: 02/29/2008] [Indexed: 11/20/2022] Open
Abstract
Background Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached on the genetic landscape of the Mediterranean populations. In order to further investigate the genetics of the human Mediterranean populations, we typed 894 individuals from 11 Mediterranean populations with 25 single-nucleotide polymorphisms (SNPs) located on the X-chromosome. Results A high overall homogeneity was found among the Mediterranean populations except for the population from Morocco, which seemed to differ genetically from the rest of the populations in the Mediterranean area. A very low genetic distance was found between populations in the Middle East and most of the western part of the Mediterranean Sea. A higher migration rate in females versus males was observed by comparing data from X-chromosome, mt-DNA and Y-chromosome SNPs both in the Mediterranean and a wider geographic area. Multilocus association was observed among the 25 SNPs on the X-chromosome in the populations from Ibiza and Cosenza. Conclusion Our results support both the hypothesis of (1) a reduced impact of the Neolithic Wave and more recent migration movements in NW-Africa, and (2) the importance of the Strait of Gibraltar as a geographic barrier. In contrast, the high genetic homogeneity observed in the Mediterranean area could be interpreted as the result of the Neolithic wave caused by a large demic diffusion and/or more recent migration events. A differentiated contribution of males and females to the genetic landscape of the Mediterranean area was observed with a higher migration rate in females than in males. A certain level of background linkage disequilibrium in populations in Ibiza and Cosenza could be attributed to their demographic background.
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Affiliation(s)
- Carmen Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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Sanchez JJ, Monaghan G, Børsting C, Norbury G, Morling N, Gaspar HB. Carrier frequency of a nonsense mutation in the adenosine deaminase (ADA) gene implies a high incidence of ADA-deficient severe combined immunodeficiency (SCID) in Somalia and a single, common haplotype indicates common ancestry. Ann Hum Genet 2007; 71:336-47. [PMID: 17181544 DOI: 10.1111/j.1469-1809.2006.00338.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inherited adenosine deaminase (ADA) deficiency is a rare metabolic disorder that causes immunodeficiency, varying from severe combined immunodeficiency (SCID) in the majority of cases to a less severe form in a small minority of patients. Five patients of Somali origin from four unrelated families, with severe ADA-SCID, were registered in the Greater London area. Patients and their parents were investigated for the nonsense mutation Q3X (ADA c7C>T), two missense mutations K80R (ADA c239A>G) and R142Q (ADA c425G>A), and a TAAA repeat located at the 3' end of an Alu element (AluVpA) positioned 1.1 kb upstream of the ADA transcription start site. All patients were homozygous for the haplotype ADA-7T/ADA-239G/ADA-425G/AluVpA7. Among 207 Somali immigrants to Denmark, the frequency of ADA c7C>T and the maximum likelihood estimate of the frequency of the haplotype ADA-7T/ADA-239G/ADA-425G/AluVpA7 were both 0.012 (carrier frequency 2.4%). Based on the analysis of AluVpA alleles, the ADA c7C/T mutation was estimated to be approximately 7,100 years old. Approximately 1 out of 5 - 10000 Somali children will be born with ADA deficiency due to an ADA c7C/T mutation, although within certain clans the frequency may be significantly higher. ADA-SCID may be a frequent immunodeficiency disorder in Somalia, but will be underdiagnosed due to the prevailing socioeconomic and nutritional deprivation.
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Affiliation(s)
- Juan J Sanchez
- Department of Forensic Genetics, Institute of Forensic Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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Abstract
Arabia has served as a strategic crossroads for human disseminations, providing a natural connection between the distant populations of China and India in the east to the western civilizations along the Mediterranean. To explore this region's critical role in the migratory episodes leaving Africa to Eurasia and back, high-resolution Y-chromosome analysis of males from the United Arab Emirates (164), Qatar (72) and Yemen (62) was performed. The role of the Levant in the Neolithic dispersal of the E3b1-M35 sublineages is supported by the data, and the distribution and STR-based analyses of J1-M267 representatives points to their spread from the north, most likely during the Neolithic. With the exception of Yemen, southern Arabia, South Iran and South Pakistan display high diversity in their Y-haplogroup substructure possibly a result of gene flow along the coastal crescent-shaped corridor of the Gulf of Oman facilitating human dispersals. Elevated rates of consanguinity may have had an impact in Yemen and Qatar, which experience significant heterozygote deficiencies at various hypervariable autosomal STR loci.
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King TE, Bowden GR, Balaresque PL, Adams SM, Shanks ME, Jobling MA. Thomas Jefferson's Y chromosome belongs to a rare European lineage. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 132:584-9. [PMID: 17274013 DOI: 10.1002/ajpa.20557] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have characterized the Y chromosome carried by President Thomas Jefferson, the general rarity of which supported the idea that he, or a patrilineal relative, fathered the last son of his slave Sally Hemings. It belongs to haplogroup K2, a lineage representing only approximately 1% of chromosomes worldwide, and most common in East Africa and the Middle East. Phylogenetic network analysis of its Y-STR (short tandem repeat) haplotype shows that it is most closely related to an Egyptian K2 haplotype, but the presence of scattered and diverse European haplotypes within the network is nonetheless consistent with Jefferson's patrilineage belonging to an ancient and rare indigenous European type. This is supported by the observation that two of 85 unrelated British men sharing the surname Jefferson also share the President's Y-STR haplotype within haplogroup K2. Our findings represent a cautionary tale in showing the difficulty of assigning individual ancestry based on a Y-chromosome haplotype, particularly for rare lineages where population data are scarce.
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Affiliation(s)
- Turi E King
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
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King TE, Parkin EJ, Swinfield G, Cruciani F, Scozzari R, Rosa A, Lim SK, Xue Y, Tyler-Smith C, Jobling MA. Africans in Yorkshire? The deepest-rooting clade of the Y phylogeny within an English genealogy. Eur J Hum Genet 2007; 15:288-93. [PMID: 17245408 PMCID: PMC2590664 DOI: 10.1038/sj.ejhg.5201771] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The presence of Africans in Britain has been recorded since Roman times, but has left no apparent genetic trace among modern inhabitants. Y chromosomes belonging to the deepest-rooting clade of the Y phylogeny, haplogroup (hg) A, are regarded as African-specific, and no examples have been reported from Britain or elsewhere in Western Europe. We describe the presence of an hgA1 chromosome in an indigenous British male; comparison with African examples suggests a Western African origin. Seven out of 18 men carrying the same rare east-Yorkshire surname as the original male also carry hgA1 chromosomes, and documentary research resolves them into two genealogies with most-recent-common-ancestors living in Yorkshire in the late 18th century. Analysis using 77 Y-short tandem repeats (STRs) is consistent with coalescence a few generations earlier. Our findings represent the first genetic evidence of Africans among 'indigenous' British, and emphasize the complexity of human migration history as well as the pitfalls of assigning geographical origin from Y-chromosomal haplotypes.
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Affiliation(s)
- Turi E. King
- Department of Genetics, University of Leicester, UK
| | | | | | - Fulvio Cruciani
- Department of Genetics and Molecular Biology, Università degli Studi di Roma “La Sapienza”, Rome, Italy
| | - Rosaria Scozzari
- Department of Genetics and Molecular Biology, Università degli Studi di Roma “La Sapienza”, Rome, Italy
| | - Alexandra Rosa
- Human Genetics Laboratory, University of Madeira, Funchal, Portugal
| | - Si-Keun Lim
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Hinxton, UK
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Sanchez JJ, Phillips C, Børsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N. A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 2006; 27:1713-24. [PMID: 16586411 DOI: 10.1002/elps.200500671] [Citation(s) in RCA: 363] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A total of 52 SNPs reported to be polymorphic in European, Asian and African populations were selected. Of these, 42 were from the distal regions of each autosome (except chromosome 19). Nearly all selected SNPs were located at least 100 kb distant from known genes and commonly used STRs. We established a highly sensitive and reproducible SNP-typing method with amplification of all 52 DNA fragments in one PCR reaction followed by detection of the SNPs with two single base extension reactions analysed using CE. The amplicons ranged from 59 to 115 bp in length. Complete SNP profiles were obtained from 500 pg DNA. The 52 loci were efficiently amplified from degraded samples where previously only partial STR profiles had been obtained. A total of 700 individuals from Denmark, Greenland, Somalia, Turkey, China, Germany, Taiwan, Thailand and Japan were typed, and the allele frequencies estimated. All 52 SNPs were polymorphic in the three major population groups. The mean match probability was at least 5.0 x 10(-19) in the populations studied. Typical paternity indices ranged from 336 000 in Asians to 549 000 in Europeans. Details of the 52 SNP loci and population data generated in this work are freely available at http://www.snpforid.org.
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Affiliation(s)
- Juan J Sanchez
- Department of Forensic Genetics, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark.
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Regueiro M, Cadenas AM, Gayden T, Underhill PA, Herrera RJ. Iran: tricontinental nexus for Y-chromosome driven migration. Hum Hered 2006; 61:132-43. [PMID: 16770078 DOI: 10.1159/000093774] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Accepted: 03/23/2006] [Indexed: 11/19/2022] Open
Abstract
Due to its pivotal geographic position, present day Iran likely served as a gateway of reciprocal human movements. However, the extent to which the deserts within the Iranian plateau and the mountain ranges surrounding Persia inhibited gene flow via this corridor remains uncertain. In order to assess the magnitude of this region's role as a nexus for Africa, Asia and Europe in human migrations, high-resolution Y-chromosome analyses were performed on 150 Iranian males. Haplogroup data were subsequently compared to regional populations characterized at similar phylogenetic levels. The Iranians display considerable haplogroup diversity consistent with patterns observed in populations of the Middle East overall, reinforcing the notion of Persia as a venue for human disseminations. Admixture analyses of geographically targeted, regional populations along the latitudinal corridor spanning from Anatolia to the Indus Valley demonstrated contributions to Persia from both the east and west. However, significant differences were uncovered upon stratification of the gene donors, including higher proportions from central east and southeast Turkey as compared to Pakistan. In addition to the modulating effects of geographic obstacles, culturally mediated amalgamations consistent with the diverse spectrum of a variety of historical empires may account for the distribution of haplogroups and lineages observed. Our study of high-resolution Y-chromosome genotyping allowed for an in-depth analysis unattained in previous studies of the area, revealing important migratory and demographic events that shaped the contemporary genetic landscape.
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Affiliation(s)
- M Regueiro
- Department of Biological Sciences, Florida International University, University Park, OE 304, Miami, FL 33199, USA
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Brión M, Sanchez JJ, Balogh K, Thacker C, Blanco-Verea A, Børsting C, Stradmann-Bellinghausen B, Bogus M, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N. Introduction of an single nucleodite polymorphism-based "Major Y-chromosome haplogroup typing kit" suitable for predicting the geographical origin of male lineages. Electrophoresis 2006; 26:4411-20. [PMID: 16273584 DOI: 10.1002/elps.200500293] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The European Consortium "High-throughput analysis of single nucleotide polymorphisms for the forensic identification of persons--SNPforID", has performed a selection of candidate Y-chromosome single nucleotide polymorphisms (SNPs) for making inferences on the geographic origin of an unknown sample. From more than 200 SNPs compiled in the phylogenetic tree published by the Y-Chromosome Consortium, and looking at the population studies previously published, a package of 29 SNPs has been selected for the identification of major population haplogroups. A "Major Y-chromosome haplogroup typing kit" has been developed, which allows the multiplex amplification of all 29 SNPs in a single reaction. Allele genotyping was performed with a single base extension reaction (minisequencing) detected by CE. The validation of the multiplex was performed in a total of 1126 unrelated males distributed among 12 worldwide populations. The approach takes advantage of the specific geographic distribution of the Y-chromosome haplogroups and demonstrates the utility of binary polymorphisms to infer the origin of a male lineage.
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Affiliation(s)
- María Brión
- Institute of Legal Medicine, National Genotyping Center (CEGEN), University of Santiago de Compostela, Spain.
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Flores C, Maca-Meyer N, Larruga JM, Cabrera VM, Karadsheh N, Gonzalez AM. Isolates in a corridor of migrations: a high-resolution analysis of Y-chromosome variation in Jordan. J Hum Genet 2005; 50:435-441. [PMID: 16142507 DOI: 10.1007/s10038-005-0274-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Accepted: 06/20/2005] [Indexed: 11/26/2022]
Abstract
A high-resolution, Y-chromosome analysis using 46 binary markers has been carried out in two Jordan populations, one from the metropolitan area of Amman and the other from the Dead Sea, an area geographically isolated. Comparisons with neighboring populations showed that whereas the sample from Amman did not significantly differ from their Levantine neighbors, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its high R1*-M173 frequency (40%) has until now only been found in northern Cameroonian samples. This contrasts with the comparatively low presence of J representatives (9%), which is the modal clade in Middle Eastern populations, including Amman. The Dead Sea sample also showed a high presence of E3b3a-M34 lineages (31%), which is only comparable to that found in Ethiopians. Although ancient and recent ties with sub-Saharan and eastern Africans cannot be discarded, it seems that isolation, strong drift, and/or founder effects are responsible for the anomalous Y-chromosome pool of this population. These results demonstrate that, at a fine scale, the smooth, continental clines detected for several Y-chromosome markers are often disrupted by genetically divergent populations.
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Affiliation(s)
- Carlos Flores
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, 38271, Tenerife, Spain
- Unidad de Investigación, Hospital Universitario N.S. de Candelaria, 38010, Tenerife, Spain
| | - Nicole Maca-Meyer
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, 38271, Tenerife, Spain
- Unidad de Investigación, Hospital Universitario N.S. de Candelaria, 38010, Tenerife, Spain
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, 38271, Tenerife, Spain
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, 38271, Tenerife, Spain
| | - Naif Karadsheh
- Department of Biochemistry and Physiology, Faculty of Medicine, University of Jordan, Amman, Jordan
| | - Ana M Gonzalez
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, 38271, Tenerife, Spain.
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