دورية أكاديمية
Genetic diversity of North African populations in the 17q21 genomic region.
العنوان: | Genetic diversity of North African populations in the 17q21 genomic region. |
---|---|
المؤلفون: | Messaoudi M; Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia. messaoudi.prof@gmail.com., Pakstis AJ; Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA., Ezzaher T; Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia., Boussetta S; Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia., Ben Ammar Elgaaied A; Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia., Kidd KK; Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA., Cherni L; Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.; Higher Institute of Biotechnology of Monastir, Monastir University, 5000, Monastir, Tunisia. |
المصدر: | Mammalian genome : official journal of the International Mammalian Genome Society [Mamm Genome] 2024 Sep; Vol. 35 (3), pp. 445-460. Date of Electronic Publication: 2024 Jul 04. |
نوع المنشور: | Journal Article |
اللغة: | English |
بيانات الدورية: | Publisher: Springer-Verlag Country of Publication: United States NLM ID: 9100916 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1432-1777 (Electronic) Linking ISSN: 09388990 NLM ISO Abbreviation: Mamm Genome Subsets: MEDLINE |
أسماء مطبوعة: | Publication: New York, NY : Springer-Verlag Original Publication: New York, NY, USA : Springer International, c1991- |
مواضيع طبية MeSH: | Chromosomes, Human, Pair 17*/genetics , Polymorphism, Single Nucleotide* , Haplotypes* , Genetic Variation* , Genetics, Population*, Humans ; Africa, Northern ; Black People/genetics ; Tunisia ; Principal Component Analysis ; Libya ; Gene Frequency ; North African People |
مستخلص: | The demographic history of human populations in North Africa has been characterized by complex migration processes that have determined the current genetic structure of these populations. We examined the autosomal markers of eight sampled populations in northern Africa (Tunisia and Libya) to explore their genetic structure and to place them in a global context. We genotyped a set of 30 autosomal single-nucleotide polymorphisms (SNPs) extending 9.5 Mb and encompassing the 17q21 inversion region. Our data include 403 individuals from Tunisia and Libya. To put our populations in the global context, we analyzed our data in comparison with other populations, including those of the 1000 Genomes Project. To evaluate the data, we conducted genetic diversity, principal component, STRUCTURE, and haplotype analyses. The analysis of genetic composition revealed the genetic heterogeneity of North African populations. The principal component and STRUCTURE analyses converged and revealed the intermediate position of North Africans between Europeans and Asians. Haplotypic analysis demonstrated that the normal (H1) and inverted (H2) polymorphisms in the chromosome 17q21 region occur in North Africa at frequencies similar to those found in European and Southwest Asian populations. The results highlight the complex demographic history of North Africa, reflecting the influence of genetic flow from Europe and the Near East that dates to the prehistoric period. These gene flows added to demographic factors (inbreeding, endogamy), natural factors (topography, Sahara), and cultural factors that play a role in the emergence of the diverse and heterogeneous genetic structures of North African populations. This study contributes to a better understanding of the complex structure of North African populations. (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.) |
References: | Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR (2015) A global reference for human genetic variation. Nature 526(7571):68–74. https://doi.org/10.1038/nature15393. (PMID: 10.1038/nature1539326432245) Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21(2):263–265. https://doi.org/10.1093/bioinformatics/bth457. (PMID: 10.1093/bioinformatics/bth45715297300) Bekada A, Arauna LR, Deba T, Calafell F, Benhamamouch S, Comas D (2015) Genetic heterogeneity in Algerian human populations. PLoS ONE 10:e0138453. https://doi.org/10.1371/journal.pone.0138453. (PMID: 10.1371/journal.pone.0138453264024294581715) Ben Arab S, Masmoudi S, Beltaief N, Hachicha S, Ayadi H (2004) Consanguinity and endogamy in Northern Tunisia and its impact on non-syndromic deafness. Genet Epidemiol 27(1):74–79. https://doi.org/10.1002/gepi.10321. (PMID: 10.1002/gepi.1032115185405) Ben Halim N, Ben Alaya Bouafif N, Romdhane L, Kefi Ben Atig R, Chouchane I, Bouyacoub Y, Arfa I, Cherif W, Nouira S, Talmoudi F, Lasram K, Hsouna S, Ghazouani W, Azaiez H, El Matri L, Abid A, Tebib N, Ben Dridi M-F, Kachboura S, Amouri A, Mokni M, Ben Arab S, Dellagi K, Abdelhak S (2013) Consanguinity, endogamy, and genetic disorders in Tunisia. J Community Genet 4(2):273–284. https://doi.org/10.1007/s12687-012-0128-7. (PMID: 10.1007/s12687-012-0128-723208456) Cherni L, Loueslati BY, Pereira L, Ennafaa H, Amorim A, El Gaaied AB (2005a) Female gene pools of Berber and Arab neighboring communities in central Tunisia: microstructure of mtDNA variation in North Africa. Hum Biol 77(1):61–70. (PMID: 10.1353/hub.2005.002816114817) Cherni L, Pereira L, Goios A, Loueslati BY, Khodjet el Khil H, Gomes I, Gusmão L, Alves C, Slama A, Amorim A, Ben Ammar Elgaaied A (2005b) Y-Chromosomal STR haplotypes in three ethnic groups and one cosmopolitan population from Tunisia. Forensic Sci Int 152(1):95–99. https://doi.org/10.1016/j.forsciint.2005.02.007. (PMID: 10.1016/j.forsciint.2005.02.00715939181) Cherni L, Fernandes V, Pereira JB, Costa MD, Goios A, Frigi S, Yacoubi-Loueslati B, Ben Amor M, Slama A, Amorim A, Ben Ammar El Gaaied A, Pereira L (2009) Post-last glacial maximum expansion from Iberia to North Africa revealed by fine characterization of mtDNA H Haplogroup in Tunisia. Am J Phys Anthropol 139(2):253–260. https://doi.org/10.1002/ajpa.20979. (PMID: 10.1002/ajpa.2097919090581) Cherni L, Frigi S, Ennafaa H, Mtiraoui N, Mahjoub T, Benammar-Elgaaied A (2011) Human alu insertion polymorphisms in North African populations. Hum Biol 83:611–626. https://doi.org/10.3378/027.083.0503. (PMID: 10.3378/027.083.050322146064) Cherni L, Pakstis AJ, Boussetta S, Elkamel S, Frigi S, Khodjet-El-Khil H, Barton A, Haigh E, Speed WC, Ben Ammar Elgaaied A, Kidd JR, Kidd KK (2016) Genetic variation in Tunisia in the context of human diversity worldwide. Am J Phys Anthropol 161:62–71. https://doi.org/10.1002/ajpa.23008. (PMID: 10.1002/ajpa.23008271921815084816) Creekmore BC, Watanabe R, Lee EB (2024) Neurodegenerative disease tauopathies. Annu Rev Pathol Mech Dis 19(1):517522101. https://doi.org/10.1146/annurev-pathmechdis-051222-120750. (PMID: 10.1146/annurev-pathmechdis-051222-120750) Donnelly MP, Paschou P, Grigorenko E, Gurwitz D, Mehdi SQ, Kajuna SLB, Barta C, Kungulilo S, Karoma NJ, Lu R-B, Zhukova OV, Kim J-J, Comas D, Siniscalco M, New M, Li P, Li H, Manolopoulos VG, Speed WC, Rajeevan H, Pakstis AJ, Kidd JR, Kidd KK (2010) The distribution and most recent common ancestor of the 17q21 inversion in humans. Am J Hum Genet 86(2):161–171. https://doi.org/10.1016/j.ajhg.2010.01.007. (PMID: 10.1016/j.ajhg.2010.01.007201160452820164) Elkamel S, Boussetta S, Khodjet-El-Khil H, Benammar Elgaaied A, Cherni L (2018) Ancient and recent middle eastern maternal genetic contribution to North Africa as viewed by mtDNA diversity in Tunisian Arab populations. Am J Hum Biol 30(3):e23100. https://doi.org/10.1002/ajhb.23100. (PMID: 10.1002/ajhb.2310029359455) Ennafaa H, Cabrera VM, Abu-Amero KK, González AM, Amor MB, Bouhaha R, Dzimiri N, Elgaaïed AB, Larruga JM (2009) Mitochondrial DNA Haplogroup H structure in North Africa. BMC Genet 10:8. https://doi.org/10.1186/1471-2156-10-8. (PMID: 10.1186/1471-2156-10-8192435822657161) Espinosa I, Alfonso-Sanchez MA, Gomez-Perez L, Peña JA (2023) Neolithic expansion and the 17q21.31 inversion in Iberia: an evolutionary approach to H2 haplotype distribution in the Near East and Europe. Mol Genet Genom 298:153–160. https://doi.org/10.1007/s00438-022-01969-0. (PMID: 10.1007/s00438-022-01969-0) Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50. (PMID: 10.1177/117693430500100003) Fadhlaoui-Zid K, Plaza S, Calafell F, Ben Amor M, Comas D, Bennamar A, Gaaied E (2004) Mitochondrial DNA heterogeneity in Tunisian Berbers. Ann Hum Genet 68(3):222–233. https://doi.org/10.1046/j.1529-8817.2004.00096.x. (PMID: 10.1046/j.1529-8817.2004.00096.x15180702) Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7(4):574–578. https://doi.org/10.1111/j.14718286.2007.01758.x. (PMID: 10.1111/j.14718286.2007.01758.x187847911974779) Frigi S, Cherni L, Fadhlaoui-Zid K, Benammar-Elgaaied A (2010) Ancient local evolution of African mtDNA Haplogroups in Tunisian Berber populations. Hum Biol 82(4):367–384. https://doi.org/10.3378/027.082.0402. (PMID: 10.3378/027.082.040221082907) Frigi S, Mota-Vieira L, Cherni L, van Oven M, Pires R, Boussetta S, Ben Ammar El-Gaaied A (2017) Mitochondrial DNA analysis of Tunisians reveals a mosaic genetic structure with recent population expansion. Homo 68(4):298–315. https://doi.org/10.1016/j.jchb.2017.05.003. (PMID: 10.1016/j.jchb.2017.05.00328838744) Gu S, Pakstis AJ, Kidd KK (2005) HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations. Bioinformatics 21:3938–3939. https://doi.org/10.1093/bioinformatics/bti649. (PMID: 10.1093/bioinformatics/bti64916131520) Henn BM, Botigue LR, Gravel S, Wang W, Brisbin A, Byrnes JK, Fadhlaoui-Zid K, Zalloua PA, Moreno-Estrada A, Bertranpetit J, Bustamante CD, Comas D (2012) Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet 8:e1002397. https://doi.org/10.1371/journal.pgen.1002397. (PMID: 10.1371/journal.pgen.1002397222536003257290) Kidd KK, Pakstis AJ, Speed WC, Grigorenko EL, Kajuna SLB, Karoma NJ, Kungulilo S, Kim J-J, Lu R-B, Odunsi A, Okonofua F, Parnas J, Schulz LO, Zhukova OV, Kidd JR (2006) Developing a SNP panel for forensic identification of individuals. Forensic Sci Int 164:20–32. https://doi.org/10.1016/j.forsciint.2005.11.017. (PMID: 10.1016/j.forsciint.2005.11.01716360294) Kidd JR, Friedlaender FR, Speed WC, Pakstis AJ, De La Vega FM, Kidd KK (2011) Analyses of a set of 128 ancestry informative single-nucleotide informative polymorphisms in a global set of 119 population samples. Investig Genet 2:1. https://doi.org/10.1186/2041-2223-2-1. (PMID: 10.1186/2041-2223-2-1212084343025953) Kidd KK, Speed WC, Pakstis AJ, Podini DS, Lagace R, Chang J, Wootton S, Haigh E, Soundararajan U (2017) Evaluating 130 microhaplotypes across a global set of 83 populations. Forensic Sci Int Genet 29:29–37. https://doi.org/10.1016/j.fsigen.2017.03.014. (PMID: 10.1016/j.fsigen.2017.03.01428359046) Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959. (PMID: 10.1093/genetics/155.2.945108354121461096) Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559–575. https://doi.org/10.1086/519795. (PMID: 10.1086/519795177019011950838) Rosenberg NA, Li LM, Ward R, Pritchard JK (2003) Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73(6):1402–1422. (PMID: 10.1086/380416146315571180403) Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78(4):629–644. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1424677/. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68(4):978–989. https://doi.org/10.1086/319501. (PMID: 10.1086/319501112544541275651) Stefansson H, Helgason A, Thorleifsson G, Steinthorsdottir V, Masson G, Barnard J, Baker A, Jonasdottir A, Ingason A, Gudnadottir VG, Desnica N, Hicks A, Gylfason A, Gudbjartsson DF, Jonsdottir GM, Sainz J, Agnarsson K, Birgisdottir B, Ghosh S, Olafsdottir A, Cazier J-B, Kristjansson K, Frigge ML, Thorgeirsson TE, Gulcher JR, Kong A, Stefansson K (2005) A common inversion under selection in Europeans. Nat Genet 37(2):129–137. https://doi.org/10.1038/ng1508. (PMID: 10.1038/ng150815654335) Steinberg KM, Antonacci F, Sudmant PH, Kidd JM, Campbell CD, Vives L, Malig M, Scheinfeldt L, Beggs W, Ibrahim M, Lema G, Nyambo TB, Omar SA, Bodo J-M, Froment A, Donnelly MP, Kidd KK, Tishkoff SA, Eichler EE (2012) Structural diversity and African origin of the 17q21.31 inversion polymorphism. Nat Genet 44(8):872–880. https://doi.org/10.1038/ng.2335. (PMID: 10.1038/ng.2335227511003408829) Wright S (1969) Evolution and the genetics of populations. The theory of gene frequencies Chicago and London vol 2. University of Chicago Press, Chicago. https://doi.org/10.1017/S0021932000008543. Yacoubi-Loueslati B, Cherni L, Khodjet-Elkhil H, Ennafaa H, Pereira L, Amorim A, Ben Ayed F, Ben Ammar Elgaaied A (2006) Islands inside an island: reproductive isolates on Jerba Island. Am J Hum Biol 18:149–153. https://doi.org/10.1002/ajhb.20473. (PMID: 10.1002/ajhb.20473) Zody MC, Jiang Z, Fung H-C, Antonacci F, Hillier LDW, Cardone MF, Graves TA, Kidd JM, Cheng Z, Abouelleil A, Chen L, Wallis J, Glasscock J, Wilson RK, Reily AD, Duckworth J, Ventura M, Hardy J, Warren WC, Eichler EE (2008) Evolutionary toggling of the MAPT 17q2131 inversion region. Nat Genet 40(9):1076–1083. (PMID: 10.1038/ng.193191659222684794) |
تواريخ الأحداث: | Date Created: 20240704 Date Completed: 20240816 Latest Revision: 20240816 |
رمز التحديث: | 20240816 |
DOI: | 10.1007/s00335-024-10051-6 |
PMID: | 38965090 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1432-1777 |
---|---|
DOI: | 10.1007/s00335-024-10051-6 |