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Nguidi M, Gomes V, Vullo C, Rodrigues P, Rotondo M, Longaray M, Catelli L, Martínez B, Campos A, Carvalho E, Orovboni VO, Keshinro SO, Simão F, Gusmão L. Impact of patrilocality on contrasting patterns of paternal and maternal heritage in Central-West Africa. Sci Rep 2024; 14:15653. [PMID: 38977763 PMCID: PMC11231350 DOI: 10.1038/s41598-024-65428-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 06/20/2024] [Indexed: 07/10/2024] Open
Abstract
Despite their ancient past and high diversity, African populations are the least represented in human population genetic studies. In this study, uniparental markers (mtDNA and Y chromosome) were used to investigate the impact of sociocultural factors on the genetic diversity and inter-ethnolinguistic gene flow in the three major Nigerian groups: Hausa (n = 89), Yoruba (n = 135) and Igbo (n = 134). The results show a distinct history from the maternal and paternal perspectives. The three Nigerian groups present a similar substrate for mtDNA, but not for the Y chromosome. The two Niger-Congo groups, Yoruba and Igbo, are paternally genetically correlated with populations from the same ethnolinguistic affiliation. Meanwhile, the Hausa is paternally closer to other Afro-Asiatic populations and presented a high diversity of lineages from across Africa. When expanding the analyses to other African populations, it is observed that language did not act as a major barrier to female-mediated gene flow and that the differentiation of paternal lineages is better correlated with linguistic than geographic distances. The results obtained demonstrate the impact of patrilocality, a common and well-established practice in populations from Central-West Africa, in the preservation of the patrilineage gene pool and in the affirmation of identity between groups.
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Affiliation(s)
- Masinda Nguidi
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil.
| | - Verónica Gomes
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Institute of Pathology and Molecular Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Carlos Vullo
- DNA Forensic Laboratory, Equipo Argentino de Antropología Forense (EAAF), Córdoba, Argentina
| | - Pedro Rodrigues
- Institute of Pathology and Molecular Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Martina Rotondo
- DNA Forensic Laboratory, Equipo Argentino de Antropología Forense (EAAF), Córdoba, Argentina
| | - Micaela Longaray
- DNA Forensic Laboratory, Equipo Argentino de Antropología Forense (EAAF), Córdoba, Argentina
| | - Laura Catelli
- DNA Forensic Laboratory, Equipo Argentino de Antropología Forense (EAAF), Córdoba, Argentina
| | - Beatriz Martínez
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | - Afonso Campos
- Institute of Pathology and Molecular Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Elizeu Carvalho
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Victoria O Orovboni
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | | | - Filipa Simão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil.
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Fan H, Xu Y, Zhao Y, Feng K, Hong L, Zhao Q, Lu X, Shi M, Li H, Wang L, Wen S. Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis. Forensic Sci Int Genet 2024; 71:103029. [PMID: 38518712 DOI: 10.1016/j.fsigen.2024.103029] [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: 07/29/2023] [Revised: 02/12/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024]
Abstract
Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.
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Affiliation(s)
- Haoliang Fan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China.
| | - Yutao Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Kai Feng
- Duanzhou Branch of Zhaoqing Public Security Bureau, Zhaoqing 526060, China.
| | - Liuxi Hong
- Sihui Public Security Bureau of Guangdong Province, Zhaoqing 526299, China.
| | - Qiancheng Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Xiaoyu Lu
- Deepreads Biotech Company Limited, Guangzhou 510663, China.
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing 100088, China.
| | - Haiyan Li
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou 510050, China.
| | - Lingxiang Wang
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
| | - Shaoqing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Institute of Archaeological Science, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
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3
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Zeye MMJ, Li J, Ouedraogo SY, Zha L, Simpore J, Jifeng C. Population data and genetic structure analysis based on 29 Y-STR loci among the ethnolinguistic groups in Burkina Faso. Int J Legal Med 2021; 135:1767-1769. [PMID: 33677620 DOI: 10.1007/s00414-021-02544-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/15/2021] [Indexed: 10/22/2022]
Abstract
Burkina Faso (BF) is a landlocked Sahelian country located in the middle of West Africa. Sixty-three local languages are spoken in BF. Despite this high diversity, the BF population remains poorly investigated, and updated forensic parameters with a large number of Y chromosome short tandem repeats (Y-STRs) are still missing. Herein, 447 DNA samples were typed for a cocktail of 29 Y-STR loci. None of these 447 individuals in total shared a common haplotype. The overall Y-STR haplotypes were successfully uploaded online on the Y-STR Haplotype Reference Database (YHRD) with the accession numbers YA004690 and YA004691. The main haplotype diversity was 0.9999999965, which is much higher than that obtained with 12 Y-STRs in a previous study. Haploid Match Probability for the whole dataset was 0.002237. The phylogenetic analysis of 24 ethnic groups of BF shows that the ethnic group named BISSA is closer to Gur speakers than Mande speakers, where they belong. In addition, genetic structure analysis of 49 African subpopulations sheds light on the fact that geographic proximity turns out to be one of the best predictors of genetic affinity between populations.
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Affiliation(s)
- Moutanou Modeste Judes Zeye
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.,Laboratory of Molecular Biology and Genetics (LMBG), University Joseph KI - ZERBO, CERBA/LABIOGENE, Ouagadougou 01, 01 BP: 364, Burkina Faso.,Directorate General of the National Police of Burkina Faso, Directorate of Technical and Scientific Police, Ouagadougou 01, 01 BP: 22, Burkina Faso
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Serge Yannick Ouedraogo
- Laboratory of Molecular Biology and Genetics (LMBG), University Joseph KI - ZERBO, CERBA/LABIOGENE, Ouagadougou 01, 01 BP: 364, Burkina Faso.,Department of Biochemistry and molecular biology, School of Life sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.
| | - Jacques Simpore
- Laboratory of Molecular Biology and Genetics (LMBG), University Joseph KI - ZERBO, CERBA/LABIOGENE, Ouagadougou 01, 01 BP: 364, Burkina Faso.
| | - Cai Jifeng
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.
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Wu R, Peng D, Ren H, Li R, Li H, Wang N, Shen X, Huang E, Zhang Y, Sun H. Characterization of genetic polymorphisms in Nigerians residing in Guangzhou using massively parallel sequencing. Forensic Sci Int Genet 2020; 48:102323. [PMID: 32574994 DOI: 10.1016/j.fsigen.2020.102323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/21/2020] [Accepted: 06/03/2020] [Indexed: 01/13/2023]
Abstract
African populations exhibit extensive linguistic and cultural diversity but are less studied from a population genetic standpoint. Although much genetic data on admixed African individuals, such as African Americans, have been published, genetic polymorphism data, especially that based on sequence-based typing, are still insufficient in indigenous Africans. In this study, we examined the genetic diversity of 85 Nigerians residing in Guangzhou, China. Forensically relevant genetic markers, including autosomal short tandem repeats (A-STRs), X-chromosomal STRs (X-STRs), Y-chromosomal STRs (Y-STRs), and identity-informative single nucleotide polymorphisms (iiSNPs) were genotyped to uncover the genetic polymorphisms of this population. Sequence-based allelic variations were observed in 22 A-STRs, ten Y-STRs, and four X-STRs. Using massively parallel sequencing (MPS), the allele number increased from 475 length-based alleles to 683 sequence-based alleles. Compared to other populations, the overall observed heterozygosity of the 27 A-STRs was the highest in Nigerians, which reflected the higher genetic diversity of this population. The combined match probability of the 27 A-STRs was low at 9.06 × 10-38. When both A-STRs and iiSNPs were considered, the cumulative discrimination power, and combined power of exclusion for duo and trio paternity testing was 1-2.97 × 10-57, 1-2.20 × 10-10 and 1-4.61 × 10-17, respectively, which demonstrated that the STRs and SNPs analyzed here can be applied to forensic investigations. In summary, this study uncovers the genetic features of the Nigerian population and provides valuable frequency data for forensic applications.
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Affiliation(s)
- Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Han Ren
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Haixia Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Erwen Huang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China.
| | - Yinming Zhang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China.
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China.
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Abdeli A, Benhassine T. Paternal lineage of the Berbers from Aurès in Algeria: estimate of their genetic variation. Ann Hum Biol 2019; 46:160-168. [PMID: 30939942 DOI: 10.1080/03014460.2019.1602166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Background: Aurès is a vast territory in the east of Algeria, characterised by its traditional Berber settlement which has preserved its language and its rich history; its name goes back to antiquity and before the Roman conquest it was part of the territory of ancient Numidia. The Chaoui people in this region are one of Algeria's largest Berber groups. Aim: The aims were to investigate the level of genetic diversity of the Berbers of Aurès through the analysis of the paternal gene pool and to estimate the percentage of genetic variation among different geographical regions and linguistic groups from Algeria. Subjects and methods: Twenty-three Y-STRs were genotyped in a sample of 218 unrelated males of the Berbers of Aurès. Algorithms were used to estimate the Y-chromosome haplogroups. Genetic distance, non-metric MDS and AMOVA were used to analyse the genetic relationships between sample groups. Results: The paternal lineage of this sample of the Aurès region did not exhibit strong signals of differentiation with other samples from North-central, Northwest, and South Algeria. However, significant differences were found within this sample, demonstrating a high degree of heterogeneity. Conclusion: The results demonstrate that Aurès people are isolated and closed, but nevertheless have quite different genetic profiles.
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Affiliation(s)
- Amine Abdeli
- a Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques , Université des Sciences et de la Technologie Houari Boumediene , Algiers , Algeria.,b Institut National de Criminalistique et de Criminologie de la Gendarmerie Nationale , Algiers , Algeria
| | - Traki Benhassine
- a Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques , Université des Sciences et de la Technologie Houari Boumediene , Algiers , Algeria
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Liu C, Yang X, Chen L, Liu H, Liu C. Haplotype analysis of the polymorphic 24 Y-STR markers in six ethnic populations from China. AUST J FORENSIC SCI 2018. [DOI: 10.1080/00450618.2017.1281347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Changhui Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University , Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute , Guangzhou, People’s Republic of China
| | - Xingyi Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University , Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute , Guangzhou, People’s Republic of China
| | - Ling Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University , Guangzhou, People’s Republic of China
| | - Hong Liu
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute , Guangzhou, People’s Republic of China
| | - Chao Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University , Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute , Guangzhou, People’s Republic of China
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Primativo G, Ottoni C, Biondi G, Serafino S, Martínez-Labarga C, Larmuseau MHD, Scardi M, Decorte R, Rickards O. Bight of Benin: a Maternal Perspective of Four Beninese Populations and their Genetic Implications on the American Populations of African Ancestry. Ann Hum Genet 2017; 81:78-90. [PMID: 28205221 DOI: 10.1111/ahg.12186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/03/2017] [Indexed: 12/01/2022]
Abstract
The understanding of the first movements of the ancestral populations within the African continent is still unclear, particularly in West Africa, due to several factors that have shaped the African genetic pool across time. To improve the genetic representativeness of the Beninese population and to better understand the patterns of human settlement inside West Africa and the dynamics of peopling of the Democratic Republic of Benin, we analyzed the maternal genetic variation of 193 Beninese individuals belonging to Bariba, Berba, Dendi, and Fon populations. Results support the oral traditions indicating that the western neighbouring populations have been the ancestors of the first Beninese populations, and the extant genetic structure of the Beninese populations is most likely the result of admixture between populations from neighbouring countries and native people. The present findings highlight how the Beninese populations contributed to the gene pool of the extant populations of some American populations of African ancestry. This strengthens the hypothesis that the Bight of Benin was not only an assembly point for the slave trade during the Trans-Atlantic Slave Trade but also an important slave trapping area.
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Affiliation(s)
| | - Claudio Ottoni
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium
| | - Gianfranco Biondi
- Department of Clinical Medicine, Public Health, Life and Environment, University of L'Aquila, L'Aquila, Italy
| | - Sara Serafino
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.,Department of Public Health and Infectious Diseases, University of Rome Sapienza, Rome, Italy
| | | | - Maarten H D Larmuseau
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven - University of Leuven, Leuven, Belgium
| | - Michele Scardi
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Ronny Decorte
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium
| | - Olga Rickards
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
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