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Messaoudi M, Pakstis AJ, Ezzaher T, Boussetta S, Ben Ammar Elgaaied A, Kidd KK, Cherni L. Genetic diversity of North African populations in the 17q21 genomic region. Mamm Genome 2024; 35:445-460. [PMID: 38965090 DOI: 10.1007/s00335-024-10051-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
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.
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Affiliation(s)
- Mohsen Messaoudi
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Takwa Ezzaher
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Amel Ben Ammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Lotfi Cherni
- 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
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Serradell JM, Lorenzo-Salazar JM, Flores C, Lao O, Comas D. Modelling the demographic history of human North African genomes points to a recent soft split divergence between populations. Genome Biol 2024; 25:201. [PMID: 39080715 PMCID: PMC11290046 DOI: 10.1186/s13059-024-03341-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND North African human populations present a complex demographic scenario due to the presence of an autochthonous genetic component and population substructure, plus extensive gene flow from the Middle East, Europe, and sub-Saharan Africa. RESULTS We conducted a comprehensive analysis of 364 genomes to construct detailed demographic models for the North African region, encompassing its two primary ethnic groups, the Arab and Amazigh populations. This was achieved through an Approximate Bayesian Computation with Deep Learning (ABC-DL) framework and a novel algorithm called Genetic Programming for Population Genetics (GP4PG). This innovative approach enabled us to effectively model intricate demographic scenarios, utilizing a subset of 16 whole genomes at > 30X coverage. The demographic model suggested by GP4PG exhibited a closer alignment with the observed data compared to the ABC-DL model. Both point to a back-to-Africa origin of North African individuals and a close relationship with Eurasian populations. Results support different origins for Amazigh and Arab populations, with Amazigh populations originating back in Epipaleolithic times, while GP4PG supports Arabization as the main source of Middle Eastern ancestry. The GP4PG model includes population substructure in surrounding populations (sub-Saharan Africa and Middle East) with continuous decaying gene flow after population split. Contrary to ABC-DL, the best GP4PG model does not require pulses of admixture from surrounding populations into North Africa pointing to soft splits as drivers of divergence in North Africa. CONCLUSIONS We have built a demographic model on North Africa that points to a back-to-Africa expansion and a differential origin between Arab and Amazigh populations.
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Affiliation(s)
- Jose M Serradell
- Departament de Medicina i Ciències de la Vida, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona s/n, Santa Cruz de Tenerife, 38600, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona s/n, Santa Cruz de Tenerife, 38600, Spain
- Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Santa Cruz de Tenerife, 38206, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario 145, Santa Cruz de Tenerife, 38010, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, Madrid, 28029, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, Calle de La Juventud S/N, Santa María de Guía, Las Palmas de Gran Canaria, 35450, Spain
| | - Oscar Lao
- Departament de Medicina i Ciències de la Vida, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain.
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain.
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Puga M, Serrano JG, García EL, González Carracedo MA, Jiménez-Canino R, Pino-Yanes M, Karlsson R, Sullivan PF, Fregel R. El Hierro Genome Study: A Genomic and Health Study in an Isolated Canary Island Population. J Pers Med 2024; 14:626. [PMID: 38929847 PMCID: PMC11204744 DOI: 10.3390/jpm14060626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
El Hierro is the smallest and westernmost island of the Canary Islands, whose population derives from an admixture of different ancestral components and that has been subjected to genetic isolation. We established the "El Hierro Genome Study" to characterize the health status and the genetic composition of ~10% of the current population of the island, accounting for a total of 1054 participants. Detailed demographic and clinical data and a blood sample for DNA extraction were obtained from each participant. Genomic genotyping was performed with the Global Screening Array (Illumina). The genetic composition of El Hierro was analyzed in a subset of 416 unrelated individuals by characterizing the mitochondrial DNA (mtDNA) and Y-chromosome haplogroups and performing principal component analyses (PCAs). In order to explore signatures of isolation, runs of homozygosity (ROHs) were also estimated. Among the participants, high blood pressure, hypercholesterolemia, and diabetes were the most prevalent conditions. The most common mtDNA haplogroups observed were of North African indigenous origin, while the Y-chromosome ones were mainly European. The PCA showed that the El Hierro population clusters near 1000 Genomes' European population but with a shift toward African populations. Moreover, the ROH analysis revealed some individuals with an important portion of their genomes with ROHs exceeding 400 Mb. Overall, these results confirmed that the "El Hierro Genome" cohort offers an opportunity to study the genetic basis of several diseases in an unexplored isolated population.
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Affiliation(s)
- Marta Puga
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (M.P.); (E.L.G.); (M.A.G.C.); (M.P.-Y.)
| | - Javier G. Serrano
- Evolution, Paleogenomics and Population Genetics Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Spain;
| | - Elsa L. García
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (M.P.); (E.L.G.); (M.A.G.C.); (M.P.-Y.)
| | - Mario A. González Carracedo
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (M.P.); (E.L.G.); (M.A.G.C.); (M.P.-Y.)
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands (IUETSPC), Universidad de La Laguna (ULL), 38200 La Laguna, Spain
| | - Rubén Jiménez-Canino
- Genomics Service, Servicio General de Apoyo a la Investigación, Universidad de La Laguna (ULL), 38200 La Laguna, Spain;
| | - María Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (M.P.); (E.L.G.); (M.A.G.C.); (M.P.-Y.)
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), 38200 La Laguna, Spain
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden; (R.K.); (P.F.S.)
| | - Patrick F. Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden; (R.K.); (P.F.S.)
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rosa Fregel
- Evolution, Paleogenomics and Population Genetics Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Spain;
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Johnson MB, Ogishi M, Domingo-Vila C, De Franco E, Wakeling MN, Imane Z, Resnick B, Williams E, Galão RP, Caswell R, Russ-Silsby J, Seeleuthner Y, Rinchai D, Fagniez I, Benson B, Dufort MJ, Speake C, Smithmyer ME, Hudson M, Dobbs R, Quandt Z, Hattersley AT, Zhang P, Boisson-Dupuis S, Anderson MS, Casanova JL, Tree TI, Oram RA. Human inherited PD-L1 deficiency is clinically and immunologically less severe than PD-1 deficiency. J Exp Med 2024; 221:e20231704. [PMID: 38634869 PMCID: PMC11032109 DOI: 10.1084/jem.20231704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
We previously reported two siblings with inherited PD-1 deficiency who died from autoimmune pneumonitis at 3 and 11 years of age after developing other autoimmune manifestations, including type 1 diabetes (T1D). We report here two siblings, aged 10 and 11 years, with neonatal-onset T1D (diagnosed at the ages of 1 day and 7 wk), who are homozygous for a splice-site variant of CD274 (encoding PD-L1). This variant results in the exclusive expression of an alternative, loss-of-function PD-L1 protein isoform in overexpression experiments and in the patients' primary leukocytes. Surprisingly, cytometric immunophenotyping and single-cell RNA sequencing analysis on blood leukocytes showed largely normal development and transcriptional profiles across lymphoid and myeloid subsets in the PD-L1-deficient siblings, contrasting with the extensive dysregulation of both lymphoid and myeloid leukocyte compartments in PD-1 deficiency. Our findings suggest that PD-1 and PD-L1 are essential for preventing early-onset T1D but that, unlike PD-1 deficiency, PD-L1 deficiency does not lead to fatal autoimmunity with extensive leukocytic dysregulation.
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Affiliation(s)
- Matthew B. Johnson
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Clara Domingo-Vila
- Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Elisa De Franco
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Matthew N. Wakeling
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Zineb Imane
- Faculty of Medicine and Pharmacy, Mohammed 5 University of Rabat, Rabat, Morocco
| | - Brittany Resnick
- National Institute for Health and Care Research Exeter Clinical Research Facility, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Evangelia Williams
- Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Rui Pedro Galão
- Department of Infectious Diseases, School of Immunobiology and Microbial Sciences, Kings College London, London, UK
| | - Richard Caswell
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - James Russ-Silsby
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Imagine Institute, Paris Cité University, Paris, France
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Iris Fagniez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Basilin Benson
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Matthew J. Dufort
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Cate Speake
- Center for Interventional Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Megan E. Smithmyer
- Center for Interventional Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Michelle Hudson
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- National Institute for Health and Care Research Exeter Clinical Research Facility, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Rebecca Dobbs
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- National Institute for Health and Care Research Exeter Clinical Research Facility, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Zoe Quandt
- Endocrine Division, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Andrew T. Hattersley
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Stephanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Imagine Institute, Paris Cité University, Paris, France
| | - Mark S. Anderson
- Endocrine Division, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Imagine Institute, Paris Cité University, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Timothy I. Tree
- Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Richard A. Oram
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
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Jmel H, Boukhalfa W, Gouiza I, Seghaier RO, Dallali H, Kefi R. Pharmacogenetic landscape of pain management variants among Mediterranean populations. Front Pharmacol 2024; 15:1380613. [PMID: 38813106 PMCID: PMC11134176 DOI: 10.3389/fphar.2024.1380613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/05/2024] [Indexed: 05/31/2024] Open
Abstract
Background Chronic pain is a major socioeconomic burden in the Mediterranean region. However, we noticed an under-representation of these populations in the pharmacogenetics of pain management studies. In this context, we aimed 1) to decipher the pharmacogenetic variant landscape among Mediterranean populations compared to worldwide populations in order to identify therapeutic biomarkers for personalized pain management and 2) to better understand the biological process of pain management through in silico investigation of pharmacogenes pathways. Materials and Methods We collected genes and variants implicated in pain response using the Prisma guidelines from literature and PharmGK database. Next, we extracted these genes from genotyping data of 829 individuals. Then, we determined the variant distribution among the studied populations using multivariate (MDS) and admixture analysis with R and STRUCTURE software. We conducted a Chi2 test to compare the interethnic frequencies of the identified variants. We used SNPinfo web server, miRdSNP database to identify miRNA-binding sites. In addition, we investigated the functions of the identified genes and variants using pathway enrichment analysis and annotation tools. Finally, we performed docking analysis to assess the impact of variations on drug interactions. Results We identified 63 variants implicated in pain management. MDS analysis revealed that Mediterranean populations are genetically similar to Mexican populations and divergent from other populations. STRUCTURE analysis showed that Mediterranean populations are mainly composed of European ancestry. We highlighted differences in the minor allele frequencies of three variants (rs633, rs4680, and rs165728) located in the COMT gene. Moreover, variant annotation revealed ten variants with potential miRNA-binding sites. Finally, protein structure and docking analysis revealed that two missense variants (rs4680 and rs6267) induced a decrease in COMT protein activity and affinity for dopamine. Conclusion Our findings revealed that Mediterranean populations diverge from other ethnic groups. Furthermore, we emphasize the importance of pain-related pathways and miRNAs to better implement these markers as predictors of analgesic responses in the Mediterranean region.
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Affiliation(s)
- Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Wided Boukhalfa
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Ismail Gouiza
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- MitoLab Team, Unité MitoVasc, Unité Mixte de Recherche Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale U1083, SFR ICAT, University of Angers, Angers, France
| | - Roua Ouled Seghaier
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
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Mezzi N, Abassi N, Fatnassi F, Abdelhak S, Romdhane L. Consanguinité et son impact sur la santé et la dynamique du génome : Un exemple de la Tunisie. LA TUNISIE MEDICALE 2024; 102:256-265. [PMID: 38801282 PMCID: PMC11358831 DOI: 10.62438/tunismed.v102i5.4787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 04/03/2024] [Indexed: 05/29/2024]
Abstract
The genetic disease spectrum in Tunisia arises from the founder effect, genetic drift, selection, and consanguinity. The latter represents a deviation from panmixia, characterized by a non-random matrimonial choice that may be subject to several rules, such as socio-cultural, economic, or other factors. This shifts the genetic structure away from the Hardy-Weinberg equilibrium, increasing homozygous genotypes and decreasing heterozygotes, thus raising the frequency of autosomal recessive diseases. Similar to other Arab populations, Tunisia displays high consanguinity rates that vary geographically. Approximately 60% of reported diseases in Tunisia are autosomal recessive, with consanguinity possibly occurring in 80% of families for a specific disease. In inbred populations, consanguinity amplifies autosomal recessive disease risk, yet it does not influence autosomal dominant disease likelihood but rather impacts its phenotype. Consanguinity is also suggested to be a major factor in the homozygosity of deleterious variants leading to comorbid expression. At the genome level, inbred individuals inherit homozygous mutations and adjacent genomic regions known as runs of homozygosity (ROHs). Short ROHs indicate distant inbreeding, while long ROHs refer to recent inbreeding. ROHs are distributed rather irregularly across the genome, with certain short regions featuring an excess of ROH, known as ROH islands. In this review, we discuss consanguinity's impact on population health and genome dynamics, using Tunisia as a model.
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Affiliation(s)
- Nessrine Mezzi
- Biomedical Genomics and Oncogenetics Laboratory. Institut Pasteur de Tunis, University of Tunis El Manar, Tunisia
- Department of Life Sciences, Faculty of Sciences of Bizerte, University of Carthage, Tunisia
| | - Najla Abassi
- Biomedical Genomics and Oncogenetics Laboratory. Institut Pasteur de Tunis, University of Tunis El Manar, Tunisia
| | - Faten Fatnassi
- Biomedical Genomics and Oncogenetics Laboratory. Institut Pasteur de Tunis, University of Tunis El Manar, Tunisia
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory. Institut Pasteur de Tunis, University of Tunis El Manar, Tunisia
| | - Lilia Romdhane
- Biomedical Genomics and Oncogenetics Laboratory. Institut Pasteur de Tunis, University of Tunis El Manar, Tunisia
- Department of Life Sciences, Faculty of Sciences of Bizerte, University of Carthage, Tunisia
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Vilà-Valls L, Abdeli A, Lucas-Sánchez M, Bekada A, Calafell F, Benhassine T, Comas D. Understanding the genomic heterogeneity of North African Imazighen: from broad to microgeographical perspectives. Sci Rep 2024; 14:9979. [PMID: 38693301 PMCID: PMC11063056 DOI: 10.1038/s41598-024-60568-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
The strategic location of North Africa has led to cultural and demographic shifts, shaping its genetic structure. Historical migrations brought different genetic components that are evident in present-day North African genomes, along with autochthonous components. The Imazighen (plural of Amazigh) are believed to be the descendants of autochthonous North Africans and speak various Amazigh languages, which belong to the Afro-Asiatic language family. However, the arrival of different human groups, especially during the Arab conquest, caused cultural and linguistic changes in local populations, increasing their heterogeneity. We aim to characterize the genetic structure of the region, using the largest Amazigh dataset to date and other reference samples. Our findings indicate microgeographical genetic heterogeneity among Amazigh populations, modeled by various admixture waves and different effective population sizes. A first admixture wave is detected group-wide around the twelfth century, whereas a second wave appears in some Amazigh groups around the nineteenth century. These events involved populations with higher genetic ancestry from south of the Sahara compared to the current North Africans. A plausible explanation would be the historical trans-Saharan slave trade, which lasted from the Roman times to the nineteenth century. Furthermore, our investigation shows that assortative mating in North Africa has been rare.
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Affiliation(s)
- Laura Vilà-Valls
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté Des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Marcel Lucas-Sánchez
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Traki Benhassine
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté Des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.
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Okoh AC, Onyeso OK, Ekemezie W, Oyinlola O, Akinrolie O, Kalu M. Building consensus on priority areas for Sub-Saharan Africa's ageing population research: An e-Delphi study protocol. PLoS One 2024; 19:e0298541. [PMID: 38603688 PMCID: PMC11008814 DOI: 10.1371/journal.pone.0298541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND Improvement in medico-social services has increased life expectancy and population ageing in Sub-Saharan Africa (SSA). It was estimated that about 163 million people aged 65 and older will be resident in SSA by 2050. There is inadequate ageing research capacity in SSA which necessitates this study to (a) identify a decade-long ageing research opportunities, challenges, and solutions, and (b) prioritize critical ageing research areas and methodologies relevant to the SSA. METHODS We designed an e-Delphi protocol following the Reporting Guideline for Priority Setting of Health Research with Stakeholder. The stakeholders will be researchers, practitioners, older adults, and caregivers purposively selected through snowballing quota sampling to complete three rounds of e-Delphi surveys. Round 1 will involve open-ended questions derived from the study objectives. Responses from round 1 will be prepared as a checklist for stakeholders to rate during rounds 2 & 3, using a 9-point scale: low priority (1-3), moderate priority (4-6), and high priority (7-9). The criterion for reaching a consensus will be ≥ 70% of stakeholders rating an item "high priority" and ≤ 15% as "low priority." Quantitative data will be analysed using descriptive statistics, Wilcoxon matched-pairs signed-rank test will be used to assess the stability of stakeholders' responses, and qualitative comments will be analysed using content analysis. DISCUSSION AND IMPLICATIONS Setting aging research/practice priorities will help maximize the benefits of research investment and provide valuable direction for allocating public and private research funds to areas of strategic importance.
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Affiliation(s)
- Augustine Chukwuebuka Okoh
- Emerging Researchers & Professionals in Ageing–African Network, Abuja, Nigeria
- Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Ogochukwu Kelechi Onyeso
- Emerging Researchers & Professionals in Ageing–African Network, Abuja, Nigeria
- Population Studies in Health, Faculty of Health Science, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Wendy Ekemezie
- Emerging Researchers & Professionals in Ageing–African Network, Abuja, Nigeria
| | - Oluwagbemiga Oyinlola
- Emerging Researchers & Professionals in Ageing–African Network, Abuja, Nigeria
- Medical Social Services Department, University College Hospital, Ibadan, Nigeria
- School of Social Work, McGill University, Montreal, Quebec, Canada
| | - Olayinka Akinrolie
- Emerging Researchers & Professionals in Ageing–African Network, Abuja, Nigeria
- Applied Health Science Program, Faculty of Graduate Studies, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael Kalu
- Emerging Researchers & Professionals in Ageing–African Network, Abuja, Nigeria
- School of Kinesiology and Health Science, Faculty of Health, York University, Toronto, Ontario, Canada
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9
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Ferreira RC, Rodrigues CR, Broach JR, Briones MRS. Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals. Int J Mol Sci 2024; 25:3785. [PMID: 38612593 PMCID: PMC11012180 DOI: 10.3390/ijms25073785] [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: 01/25/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024] Open
Abstract
The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.
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Affiliation(s)
- Renata C. Ferreira
- Center for Medical Bioinformatics, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
| | - Camila R. Rodrigues
- Graduate Program in Microbiology and Immunology, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
| | - James R. Broach
- Department of Biochemistry, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA;
| | - Marcelo R. S. Briones
- Center for Medical Bioinformatics, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
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10
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Jmel H, Sarno S, Giuliani C, Boukhalfa W, Abdelhak S, Luiselli D, Kefi R. Genetic diversity of variants involved in drug response among Tunisian and Italian populations toward personalized medicine. Sci Rep 2024; 14:5842. [PMID: 38462643 PMCID: PMC10925599 DOI: 10.1038/s41598-024-55239-7] [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: 03/01/2023] [Accepted: 02/21/2024] [Indexed: 03/12/2024] Open
Abstract
Adverse drug reactions (ADR) represent a significant contributor to morbidity and mortality, imposing a substantial financial burden. Genetic ancestry plays a crucial role in drug response. The aim of this study is to characterize the genetic variability of selected pharmacogenes involved with ADR in Tunisians and Italians, with a comparative analysis against global populations. A cohort of 135 healthy Tunisians and 737 Italians were genotyped using a SNP array. Variants located in 25 Very Important Pharmacogenes implicated in ADR were extracted from the genotyping data. Distribution analysis of common variants in Tunisian and Italian populations in comparison to 24 publicly available worldwide populations was performed using PLINK and R software. Results from Principle Component and ADMIXTURE analyses showed a high genetic similarity among Mediterranean populations, distinguishing them from Sub-Saharan African and Asian populations. The Fst comparative analysis identified 27 variants exhibiting significant differentiation between the studied populations. Among these variants, four SNPs rs622342, rs3846662, rs7294, rs5215 located in SLC22A1, HMGCR, VKORC1 and KCNJ11 genes respectively, are reported to be associated with ethnic variability in drug responses. In conclusion, correlating the frequencies of genotype risk variants with their associated ADRs would enhance drug outcomes and the implementation of personalized medicine in the studied populations.
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Affiliation(s)
- Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Genetic Typing DNA Service Pasteur Institute, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Stefania Sarno
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Wided Boukhalfa
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Donata Luiselli
- Laboratory of Ancient DNA (aDNALab), Department of Cultural Heritage (DBC), University of Bologna, Ravenna, Italy
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia.
- University of Tunis El Manar, Tunis, Tunisia.
- Genetic Typing DNA Service Pasteur Institute, Institut Pasteur de Tunis, Tunis, Tunisia.
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11
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Lucas-Sánchez M, Abdeli A, Bekada A, Calafell F, Benhassine T, Comas D. The Impact of Recent Demography on Functional Genetic Variation in North African Human Groups. Mol Biol Evol 2024; 41:msad283. [PMID: 38152862 PMCID: PMC10783648 DOI: 10.1093/molbev/msad283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/22/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023] Open
Abstract
The strategic location of North Africa has made the region the core of a wide range of human demographic events, including migrations, bottlenecks, and admixture processes. This has led to a complex and heterogeneous genetic and cultural landscape, which remains poorly studied compared to other world regions. Whole-exome sequencing is particularly relevant to determine the effects of these demographic events on current-day North Africans' genomes, since it allows to focus on those parts of the genome that are more likely to have direct biomedical consequences. Whole-exome sequencing can also be used to assess the effect of recent demography in functional genetic variation and the efficacy of natural selection, a long-lasting debate. In the present work, we use newly generated whole-exome sequencing and genome-wide array genotypes to investigate the effect of demography in functional variation in 7 North African populations, considering both cultural and demographic differences and with a special focus on Amazigh (plur. Imazighen) groups. We detect genetic differences among populations related to their degree of isolation and the presence of bottlenecks in their recent history. We find differences in the functional part of the genome that suggest a relaxation of purifying selection in the more isolated groups, allowing for an increase of putatively damaging variation. Our results also show a shift in mutational load coinciding with major demographic events in the region and reveal differences within and between cultural and geographic groups.
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Affiliation(s)
- Marcel Lucas-Sánchez
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Faculté des Sciences Biologiques, Laboratoire de Biologie Cellulaire et Moléculaire, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Traki Benhassine
- Faculté des Sciences Biologiques, Laboratoire de Biologie Cellulaire et Moléculaire, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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12
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Montero-Martin G, Kichula KM, Misra MK, Vargas LB, Marin WM, Hollenbach JA, Fernández-Viña MA, Elfishawi S, Norman PJ. Exceptional diversity of KIR and HLA class I in Egypt. HLA 2024; 103:e15177. [PMID: 37528739 PMCID: PMC11068459 DOI: 10.1111/tan.15177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/25/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023]
Abstract
Genetically determined variation of killer cell immunoglobulin like receptors (KIR) and their HLA class I ligands affects multiple aspects of human health. Their extreme diversity is generated through complex interplay of natural selection for pathogen resistance and reproductive health, combined with demographic structure and dispersal. Despite significant importance to multiple health conditions of differential effect across populations, the nature and extent of immunogenetic diversity is under-studied for many geographic regions. Here, we describe the first high-resolution analysis of KIR and HLA class I combinatorial diversity in Northern Africa. Analysis of 125 healthy unrelated individuals from Cairo in Egypt yielded 186 KIR alleles arranged in 146 distinct centromeric and 79 distinct telomeric haplotypes. The most frequent haplotypes observed were KIR-A, encoding two inhibitory receptors specific for HLA-C, two that are specific for HLA-A and -B, and no activating receptors. Together with 141 alleles of HLA class I, 75 of which encode a KIR ligand, we identified a mean of six distinct interacting pairs of inhibitory KIR and HLA allotypes per individual. We additionally characterize 16 KIR alleles newly identified in the study population. Our findings place Egyptians as one of the most highly diverse populations worldwide, with important implications for transplant matching and studies of immune-mediated diseases.
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Affiliation(s)
| | - Katherine M. Kichula
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Maneesh K. Misra
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of Chicago Medicine, Chicago, IL, USA
| | - Luciana B. Vargas
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Wesley M. Marin
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Jill A. Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | | | - Sally Elfishawi
- BMT lab unit, Clinical Pathology Dept., National Cancer Institute, Cairo University, Cairo, Egypt
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
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13
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Becher D, Jmel H, Kheriji N, Sarno S, Kefi R. Genetic landscape of forensic DNA phenotyping markers among Mediterranean populations. Forensic Sci Int 2024; 354:111906. [PMID: 38128201 DOI: 10.1016/j.forsciint.2023.111906] [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: 10/09/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023]
Abstract
Forensic DNA Phenotyping can reveal the appearance of an unknown individual by predicting the External Visible Characteristics (EVC) from DNA obtained at the crime scene. Our aim is to characterize the genetic landscape of Human identification markers responsible for EVC among Mediterranean populations compared to other worldwide groups. We conducted an exhaustive search for genes involved in EVC variation. Then, variants located on these genes were extracted from public genotypic data of Mediterranean, American, African and East Asiatic populations. The genetic landscape of these Human identification markers, their allelic distribution and admixture analyses, were determined using plink, R and ADMIXTURE softwares. Our results showed that the Mediterranean populations appear close to the Mexican populations and distinguished from sub Saharan African populations living in the USA and from East Asiatic populations. We highlighted a total of 103454 common variants shared between the studied populations and among them, 25 common variants associated with EVC. Interestingly, genotype frequencies results showed that the rs17646946, rs13016869, rs977588, rs1805008 and rs2240751 variants located respectively in the TCHH, PRKCE, OCA2, MC1R and MFSD12 genes are significantly different between the Mediterranean and Asiatic populations. The genotype frequencies of the variants rs977589 and rs7179994 located in the OCA2 gene, and of rs12913832 and rs2240751 located respectively in HERC2 and MFSD12 genes are significantly different between the Mediterranean and American populations. Our work generates a large number of EVC variants that could be a valuable resource for future studies in the forensic field.
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Affiliation(s)
- Dorra Becher
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; Directorate of Technical and Scientific Police, Sub-Directorate of Forensic and Scientific Laboratories, Tunis,Tunisia; University of Carthage, National Institute of Applied Science and Technology, Tunis, Tunisia
| | - Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; Genetic Typing Service, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; University of Tunis El Manar, 2092 El Manar I, Tunis, Tunisia
| | - Nadia Kheriji
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; University of Tunis El Manar, 2092 El Manar I, Tunis, Tunisia
| | - Stefania Sarno
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; Genetic Typing Service, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; University of Tunis El Manar, 2092 El Manar I, Tunis, Tunisia.
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14
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D'Atanasio E, Risi F, Ravasini F, Montinaro F, Hajiesmaeil M, Bonucci B, Pistacchia L, Amoako-Sakyi D, Bonito M, Onidi S, Colombo G, Semino O, Destro Bisol G, Anagnostou P, Metspalu M, Tambets K, Trombetta B, Cruciani F. The genomic echoes of the last Green Sahara on the Fulani and Sahelian people. Curr Biol 2023; 33:5495-5504.e4. [PMID: 37995693 DOI: 10.1016/j.cub.2023.10.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/28/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023]
Abstract
The population history of the Sahara/Sahelian belt is understudied, despite previous work highlighting complex dynamics.1,2,3,4,5,6,7 The Sahelian Fulani, i.e., the largest nomadic pastoral population in the world,8 represent an interesting case because they show a non-negligible proportion of an Eurasian genetic component, usually explained by recent admixture with northern Africans.1,2,5,6,7,9,10,11,12 Nevertheless, their origins are largely unknown, although several hypotheses have been proposed, including a possible link to ancient peoples settled in the Sahara during its last humid phase (Green Sahara, 12,000-5,000 years before present [BP]).13,14,15 To shed light about the Fulani ancient genetic roots, we produced 23 high-coverage (30×) whole genomes from Fulani individuals from 8 Sahelian countries, plus 17 samples from other African groups and 3 from Europeans as controls, for a total of 43 new whole genomes. These data have been compared with 814 published modern whole genomes2,16,17,18 and with relevant published ancient sequences (> 1,800 samples).19 These analyses showed some evidence that the non-sub-Saharan genetic ancestry component of the Fulani might have also been shaped by older events,1,5,6 possibly tracing the Fulani origins to unsampled ancient Green Saharan population(s). The joint analysis of modern and ancient samples allowed us to shed light on the genetic ancestry composition of such ancient Saharans, suggesting a similarity with Late Neolithic Moroccans and possibly pointing to a link with the spread of cattle herding. We also identified two different Fulani clusters whose admixture pattern may be informative about the historical Fulani movements and their later involvement in the western African empires.
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Affiliation(s)
- Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy.
| | - Flavia Risi
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Ravasini
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Montinaro
- Department of Biology, University of Bari, 70121 Bari, Italy; Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Mogge Hajiesmaeil
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Letizia Pistacchia
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy; Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Daniel Amoako-Sakyi
- Department of Microbiology and Immunology, University of Cape Coast, Cape Coast, Ghana
| | - Maria Bonito
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Sara Onidi
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Giulia Colombo
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Giovanni Destro Bisol
- Department of Enviromental Biology, Sapienza University of Rome, 00185 Rome, Italy; Istituto Italiano di Antropologia, 00185 Rome, Italy
| | - Paolo Anagnostou
- Department of Enviromental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Mait Metspalu
- Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | | | - Beniamino Trombetta
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Fulvio Cruciani
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy; Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy.
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15
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Ragsdale AP. Human evolution: Neanderthal footprints in African genomes. Curr Biol 2023; 33:R1197-R1200. [PMID: 37989099 DOI: 10.1016/j.cub.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Human and Neanderthal populations met and mixed on multiple occasions over evolutionary time, resulting in the exchange of genetic material. New genomic analyses of diverse African populations reveal a history of bidirectional gene flow and selection acting on introgressed alleles.
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Affiliation(s)
- Aaron P Ragsdale
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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16
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Harris DN, Platt A, Hansen MEB, Fan S, McQuillan MA, Nyambo T, Mpoloka SW, Mokone GG, Belay G, Fokunang C, Njamnshi AK, Tishkoff SA. Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals. Curr Biol 2023; 33:4905-4916.e5. [PMID: 37837965 PMCID: PMC10841429 DOI: 10.1016/j.cub.2023.09.066] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/18/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023]
Abstract
Comparisons of Neanderthal genomes to anatomically modern human (AMH) genomes show a history of Neanderthal-to-AMH introgression stemming from interbreeding after the migration of AMHs from Africa to Eurasia. All non-sub-Saharan African AMHs have genomic regions genetically similar to Neanderthals that descend from this introgression. Regions of the genome with Neanderthal similarities have also been identified in sub-Saharan African populations, but their origins have been unclear. To better understand how these regions are distributed across sub-Saharan Africa, the source of their origin, and what their distribution within the genome tells us about early AMH and Neanderthal evolution, we analyzed a dataset of high-coverage, whole-genome sequences from 180 individuals from 12 diverse sub-Saharan African populations. In sub-Saharan African populations with non-sub-Saharan African ancestry, as much as 1% of their genomes can be attributed to Neanderthal sequence introduced by recent migration, and subsequent admixture, of AMH populations originating from the Levant and North Africa. However, most Neanderthal homologous regions in sub-Saharan African populations originate from migration of AMH populations from Africa to Eurasia ∼250 kya, and subsequent admixture with Neanderthals, resulting in ∼6% AMH ancestry in Neanderthals. These results indicate that there have been multiple migration events of AMHs out of Africa and that Neanderthal and AMH gene flow has been bi-directional. Observing that genomic regions where AMHs show a depletion of Neanderthal introgression are also regions where Neanderthal genomes show a depletion of AMH introgression points to deleterious interactions between introgressed variants and background genomes in both groups-a hallmark of incipient speciation.
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Affiliation(s)
- Daniel N Harris
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexander Platt
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai 200438, China
| | - Michael A McQuillan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas Nyambo
- Department of Biochemistry and Molecular Biology, Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Alfred K Njamnshi
- Brain Research Africa Initiative (BRAIN), P.O. Box 25625, Yaoundé, Cameroon; Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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17
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Köksal Z, Meyer OL, Andersen JD, Gusmão L, Mogensen HS, Pereira V, Børsting C. Pitfalls and challenges with population assignments of individuals from admixed populations: Applying Genogeographer on Brazilian individuals. Forensic Sci Int Genet 2023; 67:102934. [PMID: 37713981 DOI: 10.1016/j.fsigen.2023.102934] [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: 01/09/2023] [Revised: 06/06/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
The assignment of individuals to a population can be of importance for the identification of mass disaster victims or criminal offenders in the field of forensic genetics. This assignment is based on biostatistical methods that process data of ancestry informative markers (AIMs), which are selected based on large allele frequency differences between the populations of interest. However, population assignments of individuals with an admixed genetic background are challenging. Admixed individuals are genetic mosaics of chromosomal segments from the parental populations, which may lead to ambiguous or no population assignment. This is problematic since admixture events are a substantial part of human history. In this study, we present challenges of interpreting the evidential weight of population assignments. We used Genogeographer for likelihood ratio (LR) calculations and Brazilians as examples of admixed individuals. Brazilians are a very heterogenous population representing a three-way admixture between Native Americans, Europeans, and Africans. Ancestry informative markers were typed in a total of 589 individuals from Brazil using the Precision ID Ancestry Panel. The Brazilians were assigned to six metapopulations (East Asia, Europe, Middle East, North Africa, South-Central Asia, Sub-Saharan Africa) defined in the Genogeographer software and LRs were calculated if the AIM profile was not an outlier in all metapopulations and simulated two-way (1:1) admixtures of the six metapopulations. Population assignments failed for 55% of the samples. These samples had significantly higher genetic contributions from East Asia, South-Central Asia and Sub-Saharan Africa, and significantly lower genetic contributions from Europe. Most of the individuals with population assignments were assigned to the metapopulations of Middle East (58%) or North Africa (36%), followed by Europe (4%), South-Central Asia (1%), and Sub-Saharan Africa (1%). For 8% of the samples, population assignments were only possible when assignments to simulated two-way (1:1) admixtures of the six metapopulations were considered. Most of these individuals were assigned to two-way admixtures of North Africa, South-Central Asia, or Sub-Saharan Africa. Relatively low median likelihood ratios (LRs<1000) were observed when comparing population likelihoods for Europe, Middle East, North Africa, South-Central Asia, or simulated 1:1 admixtures of these metapopulations. Comparisons including East Asian or Sub-Saharan African populations resulted in larger median LRs (LR>1010). The results suggested that the Precision ID Ancestry Panel provided too little information and that additional markers specifically selected for sub-continental differentiation may be required for accurate population assignment of admixed individuals. Furthermore, a Genogeographer database with additional populations including admixed populations would be advantageous for interpretation of admixed AIM profiles. It would likely increase the number of population assignments and illustrate alternatives to the most likely population, which would be valuable information for the case officer when writing the case report.
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Affiliation(s)
- Zehra Köksal
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Olivia Luxford Meyer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Helle Smidt Mogensen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Almohammed EK, Hadi A, Al-Asmakh M, Lazim H. The Qatari population's genetic structure and gene flow as revealed by the Y chromosome. PLoS One 2023; 18:e0290844. [PMID: 37656680 PMCID: PMC10473524 DOI: 10.1371/journal.pone.0290844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023] Open
Abstract
The Y-chromosome has been widely used in forensic genetic applications and human population genetic studies due to its uniparental origins. A large database on the Qatari population was created for comparison with other databases from the Arabian Peninsula, the Middle East, and Africa. We provide a study of 23 Y-STR loci included in PowerPlex Y23 (Promega, USA) that were genotyped to produce haplotypes in 379 unrelated males from Qatar, a country at the crossroads of migration patterns. Overall, the most polymorphic locus provided by the Promega kit was DYS458, with a genetic diversity value of 0.85 and a haplotype diversity of 0.998924. Athey's Haplogroup Predictor tool was used to predict haplogroups from Y-STR haplotypes in the Qatari population. In a median-joining network, the haplogroup J1 predominance (49%) in Qatar generated a star-like expansion cluster. The graph of population Q-matrix was developed using Y-STR data from 38 Middle Eastern and 97 African populations (11,305 individuals), and it demonstrated a stronger sub-grouping of countries within each ethnic group and showed the effect of Arabs on the indigenous Berbers of North Africa. The estimated migration rate between the Qatari and other Arabian populations was inferred using Bayesian coalescence theory in the Migrate-n program. According to the Gene Flow study, the main migration route was from Yemen to Kuwait through Qatar. Our research, using the PowerPlex Y23 database, shows the importance of gene diversity, as well as regional and social structuring, in determining the utility of demographic and forensic databases.
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Affiliation(s)
- Eida Khalaf Almohammed
- Ministry of Interior of Qatar, Doha, Qatar
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Abdullah Hadi
- University of Central Lancashire Medical School, Preston, United Kingdom
| | - Maha Al-Asmakh
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hayder Lazim
- School of Medicine, Faculty of Health, Social Care and Medicine (FHSCM), Edge Hill University, Ormskirk, United Kingdom
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19
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Serrano JG, Ordóñez AC, Santana J, Sánchez-Cañadillas E, Arnay M, Rodríguez-Rodríguez A, Morales J, Velasco-Vázquez J, Alberto-Barroso V, Delgado-Darias T, de Mercadal MCC, Hernández JC, Moreno-Benítez MA, Pais J, Ringbauer H, Sikora M, McColl H, Pino-Yanes M, Ferrer MH, Bustamante CD, Fregel R. The genomic history of the indigenous people of the Canary Islands. Nat Commun 2023; 14:4641. [PMID: 37582830 PMCID: PMC10427657 DOI: 10.1038/s41467-023-40198-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
The indigenous population of the Canary Islands, which colonized the archipelago around the 3rd century CE, provides both a window into the past of North Africa and a unique model to explore the effects of insularity. We generate genome-wide data from 40 individuals from the seven islands, dated between the 3rd-16rd centuries CE. Along with components already present in Moroccan Neolithic populations, the Canarian natives show signatures related to Bronze Age expansions in Eurasia and trans-Saharan migrations. The lack of gene flow between islands and constant or decreasing effective population sizes suggest that populations were isolated. While some island populations maintained relatively high genetic diversity, with the only detected bottleneck coinciding with the colonization time, other islands with fewer natural resources show the effects of insularity and isolation. Finally, consistent genetic differentiation between eastern and western islands points to a more complex colonization process than previously thought.
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Affiliation(s)
- Javier G Serrano
- Evolution, Paleogenomics and Population Genetics Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Alejandra C Ordóñez
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Jonathan Santana
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Elías Sánchez-Cañadillas
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Matilde Arnay
- Bioanthropology: Paleopathology, Diet and Nutrition in Ancient Populations Group, Department of Prehistory, Anthropology and Ancient History, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Amelia Rodríguez-Rodríguez
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Jacob Morales
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Javier Velasco-Vázquez
- Servicio de Patrimonio Histórico, Cabildo de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | | | | | | | - Juan Carlos Hernández
- Museo Arqueológico de La Gomera, San Sebastián de La Gomera, Santa Cruz de Tenerife, Spain
| | | | - Jorge Pais
- Museo Arqueológico Benahoarita, Los Llanos de Aridane, Santa Cruz de Tenerife, Spain
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Mariano Hernández Ferrer
- Molecular Genetics and Biodiversity Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | | | - Rosa Fregel
- Evolution, Paleogenomics and Population Genetics Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain.
- Department of Genetics, Stanford University, Stanford, CA, USA.
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20
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Rathmann H, Perretti S, Porcu V, Hanihara T, Scott GR, Irish JD, Reyes-Centeno H, Ghirotto S, Harvati K. Inferring human neutral genetic variation from craniodental phenotypes. PNAS NEXUS 2023; 2:pgad217. [PMID: 37457893 PMCID: PMC10338903 DOI: 10.1093/pnasnexus/pgad217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
There is a growing consensus that global patterns of modern human cranial and dental variation are shaped largely by neutral evolutionary processes, suggesting that craniodental features can be used as reliable proxies for inferring population structure and history in bioarchaeological, forensic, and paleoanthropological contexts. However, there is disagreement on whether certain types of data preserve a neutral signature to a greater degree than others. Here, we address this unresolved question and systematically test the relative neutrality of four standard metric and nonmetric craniodental data types employing an extensive computational genotype-phenotype comparison across modern populations from around the world. Our computation draws on the largest existing data sets currently available, while accounting for geographically structured environmental variation, population sampling uncertainty, disparate numbers of phenotypic variables, and stochastic variation inherent to a neutral model of evolution. Our results reveal that the four data types differentially capture neutral genomic variation, with highest signals preserved in dental nonmetric and cranial metric data, followed by cranial nonmetric and dental metric data. Importantly, we demonstrate that combining all four data types together maximizes the neutral genetic signal compared with using them separately, even with a limited number of phenotypic variables. We hypothesize that this reflects a lower level of genetic integration through pleiotropy between, compared to within, the four data types, effectively forming four different modules associated with relatively independent sets of loci. Therefore, we recommend that future craniodental investigations adopt holistic combined data approaches, allowing for more robust inferences about underlying neutral genetic variation.
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Affiliation(s)
| | - Silvia Perretti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy
| | - Valentina Porcu
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy
| | - Tsunehiko Hanihara
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara 252-0374, Japan
| | - G Richard Scott
- Department of Anthropology, University of Nevada, Reno, NV 89557, USA
| | - Joel D Irish
- Research Centre in Evolutionary Anthropology and Palaeoecology, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
- The Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Johannesburg WITS 2050, South Africa
| | - Hugo Reyes-Centeno
- Department of Anthropology, University of Kentucky, Lexington, KY 40506, USA
- William S. Webb Museum of Anthropology, University of Kentucky, Lexington, KY 40504, USA
- DFG Center for Advanced Studies ‘Words, Bones, Genes, Tools’, University of Tübingen, Tübingen 72070, Germany
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy
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21
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Aizpurua-Iraola J, Abdeli A, Benhassine T, Calafell F, Comas D. Whole mitogenomes reveal that NW Africa has acted both as a source and a destination for multiple human movements. Sci Rep 2023; 13:10395. [PMID: 37369751 DOI: 10.1038/s41598-023-37549-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023] Open
Abstract
Despite being enclosed between the Mediterranean Sea and the Sahara Desert, North Africa has been the scenario of multiple human migrations that have shaped the genetic structure of its present-day populations. Despite its richness, North Africa remains underrepresented in genomic studies. To overcome this, we have sequenced and analyzed 264 mitogenomes from the Algerian Chaoui-speaking Imazighen (a.k.a. Berbers) living in the Aurès region. The maternal genetic composition of the Aurès is similar to Arab populations in the region, dominated by West Eurasian lineages with a moderate presence of M1/U6 North African and L sub-Saharan lineages. When focusing on the time and geographic origin of the North African specific clades within the non-autochthonous haplogroups, different geographical neighboring regions contributed to the North African maternal gene pool during time periods that could be attributed to previously suggested admixture events in the region, since Paleolithic times to recent historical movements such as the Arabization. We have also observed the role of North Africa as a source of geneflow mainly in Southern European regions since Neolithic times. Finally, the present work constitutes an effort to increase the representation of North African populations in genetic databases, which is key to understand their history.
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Affiliation(s)
- Julen Aizpurua-Iraola
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Laboratorie de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Traki Benhassine
- Laboratorie de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.
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22
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Boukhalfa W, Jmel H, Kheriji N, Gouiza I, Dallali H, Hechmi M, Kefi R. Decoding the genetic relationship between Alzheimer's disease and type 2 diabetes: potential risk variants and future direction for North Africa. Front Aging Neurosci 2023; 15:1114810. [PMID: 37342358 PMCID: PMC10277480 DOI: 10.3389/fnagi.2023.1114810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/11/2023] [Indexed: 06/22/2023] Open
Abstract
Introduction Alzheimer's disease (AD) and Type 2 diabetes (T2D) are both age-associated diseases. Identification of shared genes could help develop early diagnosis and preventive strategies. Although genetic background plays a crucial role in these diseases, we noticed an underrepresentation tendency of North African populations in omics studies. Materials and methods First, we conducted a comprehensive review of genes and pathways shared between T2D and AD through PubMed. Then, the function of the identified genes and variants was investigated using annotation tools including PolyPhen2, RegulomeDB, and miRdSNP. Pathways enrichment analyses were performed with g:Profiler and EnrichmentMap. Next, we analyzed variant distributions in 16 worldwide populations using PLINK2, R, and STRUCTURE software. Finally, we performed an inter-ethnic comparison based on the minor allele frequency of T2D-AD common variants. Results A total of 59 eligible papers were included in our study. We found 231 variants and 363 genes shared between T2D and AD. Variant annotation revealed six single nucleotide polymorphisms (SNP) with a high pathogenic score, three SNPs with regulatory effects on the brain, and six SNPs with potential effects on miRNA-binding sites. The miRNAs affected were implicated in T2D, insulin signaling pathways, and AD. Moreover, replicated genes were significantly enriched in pathways related to plasma protein binding, positive regulation of amyloid fibril deposition, microglia activation, and cholesterol metabolism. Multidimensional screening performed based on the 363 shared genes showed that main North African populations are clustered together and are divergent from other worldwide populations. Interestingly, our results showed that 49 SNP associated with T2D and AD were present in North African populations. Among them, 11 variants located in DNM3, CFH, PPARG, ROHA, AGER, CLU, BDNF1, CST9, and PLCG1 genes display significant differences in risk allele frequencies between North African and other populations. Conclusion Our study highlighted the complexity and the unique molecular architecture of North African populations regarding T2D-AD shared genes. In conclusion, we emphasize the importance of T2D-AD shared genes and ethnicity-specific investigation studies for a better understanding of the link behind these diseases and to develop accurate diagnoses using personalized genetic biomarkers.
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Affiliation(s)
- Wided Boukhalfa
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
| | - Nadia Kheriji
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Ismail Gouiza
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- University of Angers, MitoLab Team, Unité MitoVasc, UMR CNRS 6015, INSERM U1083, SFR ICAT, Angers, France
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
| | - Mariem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
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23
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Simões LG, Günther T, Martínez-Sánchez RM, Vera-Rodríguez JC, Iriarte E, Rodríguez-Varela R, Bokbot Y, Valdiosera C, Jakobsson M. Northwest African Neolithic initiated by migrants from Iberia and Levant. Nature 2023; 618:550-556. [PMID: 37286608 PMCID: PMC10266975 DOI: 10.1038/s41586-023-06166-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/03/2023] [Indexed: 06/09/2023]
Abstract
In northwestern Africa, lifestyle transitioned from foraging to food production around 7,400 years ago but what sparked that change remains unclear. Archaeological data support conflicting views: (1) that migrant European Neolithic farmers brought the new way of life to North Africa1-3 or (2) that local hunter-gatherers adopted technological innovations4,5. The latter view is also supported by archaeogenetic data6. Here we fill key chronological and archaeogenetic gaps for the Maghreb, from Epipalaeolithic to Middle Neolithic, by sequencing the genomes of nine individuals (to between 45.8- and 0.2-fold genome coverage). Notably, we trace 8,000 years of population continuity and isolation from the Upper Palaeolithic, via the Epipaleolithic, to some Maghrebi Neolithic farming groups. However, remains from the earliest Neolithic contexts showed mostly European Neolithic ancestry. We suggest that farming was introduced by European migrants and was then rapidly adopted by local groups. During the Middle Neolithic a new ancestry from the Levant appears in the Maghreb, coinciding with the arrival of pastoralism in the region, and all three ancestries blend together during the Late Neolithic. Our results show ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape, in a more multifaceted process than observed in other regions.
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Affiliation(s)
- Luciana G Simões
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | | | - Juan Carlos Vera-Rodríguez
- Área de Prehistoria, Departamento de Historia, Geografía y Antropología, Centro de Investigación en Patrimonio Histórico, Cultural y Natural, Facultad de Humanidades, Universidad de Huelva, Huelva, Spain
| | - Eneko Iriarte
- Universidad de Burgos, Departamento de Historia, Geografía y Comunicaciones, Burgos, Spain
| | - Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Youssef Bokbot
- Institut National des Sciences de l'Archéologie et du Patrimoine, Rabat, Morocco
| | - Cristina Valdiosera
- Universidad de Burgos, Departamento de Historia, Geografía y Comunicaciones, Burgos, Spain.
- Department of History and Archaeology, La Trobe University, Melbourne, Victoria, Australia.
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.
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24
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Caro-Consuegra R, Lucas-Sánchez M, Comas D, Bosch E. Identifying signatures of positive selection in human populations from North Africa. Sci Rep 2023; 13:8166. [PMID: 37210386 DOI: 10.1038/s41598-023-35312-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/16/2023] [Indexed: 05/22/2023] Open
Abstract
Because of its location, North Africa (NA) has witnessed continuous demographic movements with an impact on the genomes of present-day human populations. Genomic data describe a complex scenario with varying proportions of at least four main ancestry components: Maghrebi, Middle Eastern-, European-, and West-and-East-African-like. However, the footprint of positive selection in NA has not been studied. Here, we compile genome-wide genotyping data from 190 North Africans and individuals from surrounding populations, investigate for signatures of positive selection using allele frequencies and linkage disequilibrium-based methods and infer ancestry proportions to discern adaptive admixture from post-admixture selection events. Our results show private candidate genes for selection in NA involved in insulin processing (KIF5A), immune function (KIF5A, IL1RN, TLR3), and haemoglobin phenotypes (BCL11A). We also detect signatures of positive selection related to skin pigmentation (SLC24A5, KITLG), and immunity function (IL1R1, CD44, JAK1) shared with European populations and candidate genes associated with haemoglobin phenotypes (HPSE2, HBE1, HBG2), other immune-related (DOCK2) traits, and insulin processing (GLIS3) traits shared with West and East African populations. Finally, the SLC8A1 gene, which codifies for a sodium-calcium exchanger, was the only candidate identified under post-admixture selection in Western NA.
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Affiliation(s)
- Rocio Caro-Consuegra
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Marcel Lucas-Sánchez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - David Comas
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, 28029, Madrid, Spain.
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25
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Cheffi K, El Khair A, Dahbi N, Talbi J, Hilali A, El Ossmani H. Genetic analysis based on 15 autosomal short tandem repeats (STRs) in the Chaouia population, western center Morocco, and genetic relationships with worldwide populations. Mol Genet Genomics 2023; 298:931-941. [PMID: 37162566 DOI: 10.1007/s00438-023-02028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/29/2023] [Indexed: 05/11/2023]
Abstract
The complex demographic history of human populations in North Africa has resulted in a high degree of genetic heterogeneity across the region. However, little is known about the pattern of these genetic variations in its current populations. The present study provides new data on the genetic background of Chaouia, an Arabic-speaking North African population in the western center of Morocco. A random sample of 150 unrelated healthy individuals from Chaouia was assessed using the AmpFLSTR Identifiler kit. The most polymorphic markers were D21S11 and D18S51, with 23 and 22 alleles, respectively. After Bonferroni's correction, two loci (TH01 and D18S51) deviated from Hardy-Weinberg equilibrium. The phylogeny analysis separated North African populations into northeastern and northwestern groups. The Chaouia population was clustered with northwestern Africans. It was the closest to the Berbers of Azrou. The Chaouia shared close genetic affinities with populations from North Africa, the Middle East, and Europe, particularly Iberians, and to a lesser extent with sub-Saharan populations. The pattern of genetic admixture varied across North African populations without a clear correlation between their geographic (northeastern or northwestern) or linguistic identities (Arab or Berber), however, genetic heterogeneity among Berbers was observed. These findings suggest that the diversity observed in North African populations extends geographical and linguistic boundaries. It is further linked to each population's unique and complex demographic history. Human North African population genetics seems to present an intriguing landscape for future studies in the region and its surrounding populations to trace the origins of the genetic heterogeneity observed in these populations.
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Affiliation(s)
- Khadija Cheffi
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco.
| | - Abderrazak El Khair
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Noura Dahbi
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Jalal Talbi
- General Directorate of National Security, National Laboratory of the Scientific and Technical Police, Casablanca, Morocco
| | - Abderraouf Hilali
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Hicham El Ossmani
- Institut de Criminalistique de la Gendarmerie Royale, Rabat, Morocco
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26
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Majara L, Kalungi A, Koen N, Tsuo K, Wang Y, Gupta R, Nkambule LL, Zar H, Stein DJ, Kinyanda E, Atkinson EG, Martin AR. Low and differential polygenic score generalizability among African populations due largely to genetic diversity. HGG ADVANCES 2023; 4:100184. [PMID: 36873096 PMCID: PMC9982687 DOI: 10.1016/j.xhgg.2023.100184] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/04/2023] [Indexed: 02/15/2023] Open
Abstract
African populations are vastly underrepresented in genetic studies but have the most genetic variation and face wide-ranging environmental exposures globally. Because systematic evaluations of genetic prediction had not yet been conducted in ancestries that span African diversity, we calculated polygenic risk scores (PRSs) in simulations across Africa and in empirical data from South Africa, Uganda, and the United Kingdom to better understand the generalizability of genetic studies. PRS accuracy improves with ancestry-matched discovery cohorts more than from ancestry-mismatched studies. Within ancestrally and ethnically diverse South African individuals, we find that PRS accuracy is low for all traits but varies across groups. Differences in African ancestries contribute more to variability in PRS accuracy than other large cohort differences considered between individuals in the United Kingdom versus Uganda. We computed PRS in African ancestry populations using existing European-only versus ancestrally diverse genetic studies; the increased diversity produced the largest accuracy gains for hemoglobin concentration and white blood cell count, reflecting large-effect ancestry-enriched variants in genes known to influence sickle cell anemia and the allergic response, respectively. Differences in PRS accuracy across African ancestries originating from diverse regions are as large as across out-of-Africa continental ancestries, requiring commensurate nuance.
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Affiliation(s)
- Lerato Majara
- Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER), Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Allan Kalungi
- Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER), Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Department of Psychiatry, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Mental Health Project, Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) & London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Nastassja Koen
- Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER), Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Cape Town, South Africa
| | - Kristin Tsuo
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Ying Wang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rahul Gupta
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Lethukuthula L. Nkambule
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heather Zar
- Department of Paediatrics and Child Health, Red Cross Children’s Hospital and Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Dan J. Stein
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Cape Town, South Africa
| | - Eugene Kinyanda
- Mental Health Project, Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) & London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Elizabeth G. Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alicia R. Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Pfennig A, Petersen LN, Kachambwa P, Lachance J. Evolutionary Genetics and Admixture in African Populations. Genome Biol Evol 2023; 15:evad054. [PMID: 36987563 PMCID: PMC10118306 DOI: 10.1093/gbe/evad054] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
As the ancestral homeland of our species, Africa contains elevated levels of genetic diversity and substantial population structure. Importantly, African genomes are heterogeneous: They contain mixtures of multiple ancestries, each of which have experienced different evolutionary histories. In this review, we view population genetics through the lens of admixture, highlighting how multiple demographic events have shaped African genomes. Each of these historical vignettes paints a recurring picture of population divergence followed by secondary contact. First, we give a brief overview of genetic variation in Africa and examine deep population structure within Africa, including the evidence of ancient introgression from archaic "ghost" populations. Second, we describe the genetic legacies of admixture events that have occurred during the past 10,000 years. This includes gene flow between different click-speaking Khoe-San populations, the stepwise spread of pastoralism from eastern to southern Africa, multiple migrations of Bantu speakers across the continent, as well as admixture from the Middle East and Europe into the Sahel region and North Africa. Furthermore, the genomic signatures of more recent admixture can be found in the Cape Peninsula and throughout the African diaspora. Third, we highlight how natural selection has shaped patterns of genetic variation across the continent, noting that gene flow provides a potent source of adaptive variation and that selective pressures vary across Africa. Finally, we explore the biomedical implications of population structure in Africa on health and disease and call for more ethically conducted studies of genetic variation in Africa.
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Affiliation(s)
- Aaron Pfennig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | | | | | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
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28
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Bardan F, Higgins D, Austin JJ. A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage. Forensic Sci Int Genet 2023; 63:102822. [PMID: 36525814 DOI: 10.1016/j.fsigen.2022.102822] [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: 07/13/2022] [Revised: 11/02/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.
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Affiliation(s)
- Felicia Bardan
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Denice Higgins
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia; School of Dentistry, Health and Medical Sciences, The University of Adelaide, South Australia, Australia
| | - Jeremy J Austin
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia.
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29
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Abstract
Admixture mapping is a powerful method of gene mapping for diseases or traits that show differential risk by ancestry. Admixture mapping has been applied most often to Americans who trace ancestry to various combinations of Native Americans, Europeans, and West Africans. Recent developments in admixture mapping include improvements in the methods and reference data needed to make inferences about ancestry as well as extensions of the mapping approach in the framework of linear mixed models. This overview outlines the key concepts of admixture mapping. It describes approaches for inferring local ancestry and provides strategies for performing admixture mapping depending on the study design. Finally, linkage analysis, association analysis, and admixture mapping are compared, with an emphasis on integrating admixture mapping and association testing. Published 2023. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland
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30
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Zhang X, Kim B, Singh A, Sankararaman S, Durvasula A, Lohmueller KE. MaLAdapt Reveals Novel Targets of Adaptive Introgression From Neanderthals and Denisovans in Worldwide Human Populations. Mol Biol Evol 2023; 40:msad001. [PMID: 36617238 PMCID: PMC9887621 DOI: 10.1093/molbev/msad001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 12/25/2022] [Accepted: 12/28/2022] [Indexed: 01/09/2023] Open
Abstract
Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, approaches intersecting outliers are vulnerable to a high false-negative rate as the power of different methods varies, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals to AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present a ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selective sweeps, heterosis from deleterious mutations, and demographic misspecification. Furthermore, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and the validation of empirical signals through visual inspection of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.
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Affiliation(s)
- Xinjun Zhang
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA
| | - Bernard Kim
- Department of Biology, Stanford University, Palo Alto, CA
| | - Armaan Singh
- Department of Computer Science, UCLA, Los Angeles, CA
| | - Sriram Sankararaman
- Department of Computer Science, UCLA, Los Angeles, CA
- Department of Computational Medicine, UCLA, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA
| | - Arun Durvasula
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA
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31
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Lucas-Sánchez M, Fadhlaoui-Zid K, Comas D. The genomic analysis of current-day North African populations reveals the existence of trans-Saharan migrations with different origins and dates. Hum Genet 2023; 142:305-320. [PMID: 36441222 PMCID: PMC9918576 DOI: 10.1007/s00439-022-02503-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/28/2022] [Indexed: 11/29/2022]
Abstract
The Sahara Desert has acted as a barrier to human gene-flow between the northern and central parts of Africa since its aridification. Nonetheless, some contacts between both sides of the desert have occurred throughout history, mainly driven by commercial activity. Part of this was the infamous trans-Saharan slave trade, which forcedly brought peoples from south of the Sahara to North Africa from Roman times until the nineteenth century. Although historical records exist, the genetic aspects of these trans-Saharan migrations have not been deeply studied. In the present study, we assess the genetic influence of trans-Saharan migrations in current-day North Africa and characterize its amount, geographical origin, and dates. We confirm the heterogeneous and generally low-frequency presence of genomic segments of sub-Saharan origin in present-day North Africans acquired in recent historical times, and we show evidence of at least two admixture events: one dated around the thirteenth-fourteenth centuries CE between North Africans and a Western-sub-Saharan-like source similar to current-day Senegambian populations, and another one dated around the seventeenth century CE involving Tunisians and an Eastern-sub-Saharan-like source related to current-day south-Sudan and Kenyan populations. Time and location coincide with the peak of trans-Saharan slave-trade activity between Western African empires and North African powers, and are also concordant with the possibility of continuous recent south-to-north gene-flow. These findings confirm the trans-Saharan human genetic contacts, providing new and precise evidence about its possible dates and geographical origins, which are pivotal to understanding the genomic composition of an underrepresented region such as North Africa.
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Affiliation(s)
- Marcel Lucas-Sánchez
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia ,College of Science, Department of Biology, Taibah University, Al Madinah Al Monawarah, Saudi Arabia
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain.
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32
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Developing CIRdb as a catalog of natural genetic variation in the Canary Islanders. Sci Rep 2022; 12:16132. [PMID: 36168029 PMCID: PMC9514705 DOI: 10.1038/s41598-022-20442-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
The current inhabitants of the Canary Islands have a unique genetic makeup in the European diversity landscape due to the existence of African footprints from recent admixture events, especially of North African components (> 20%). The underrepresentation of non-Europeans in genetic studies and the sizable North African ancestry, which is nearly absent from all existing catalogs of worldwide genetic diversity, justify the need to develop CIRdb, a population-specific reference catalog of natural genetic variation in the Canary Islanders. Based on array genotyping of the selected unrelated donors and comparisons against available datasets from European, sub-Saharan, and North African populations, we illustrate the intermediate genetic differentiation of Canary Islanders between Europeans and North Africans and the existence of within-population differences that are likely driven by genetic isolation. Here we describe the overall design and the methods that are being implemented to further develop CIRdb. This resource will help to strengthen the implementation of Precision Medicine in this population by contributing to increase the diversity in genetic studies. Among others, this will translate into improved ability to fine map disease genes and simplify the identification of causal variants and estimate the prevalence of unattended Mendelian diseases.
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33
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Atkinson EG, Dalvie S, Pichkar Y, Kalungi A, Majara L, Stevenson A, Abebe T, Akena D, Alemayehu M, Ashaba FK, Atwoli L, Baker M, Chibnik LB, Creanza N, Daly MJ, Fekadu A, Gelaye B, Gichuru S, Injera WE, James R, Kariuki SM, Kigen G, Koen N, Koenen KC, Koenig Z, Kwobah E, Kyebuzibwa J, Musinguzi H, Mwema RM, Neale BM, Newman CP, Newton CRJC, Ongeri L, Ramachandran S, Ramesar R, Shiferaw W, Stein DJ, Stroud RE, Teferra S, Yohannes MT, Zingela Z, Martin AR. Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa. Am J Hum Genet 2022; 109:1667-1679. [PMID: 36055213 PMCID: PMC9502052 DOI: 10.1016/j.ajhg.2022.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/28/2022] [Indexed: 12/22/2022] Open
Abstract
African populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multi-generational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We find suggestive evidence for the rate of language transmission in matrilineal groups having been higher than that for patrilineal ones. We highlight both the diversity of variation within Africa as well as how within-Africa variation can be informative for broader variant interpretation; many variants that are rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity across Africa.
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Affiliation(s)
- Elizabeth G Atkinson
- Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Shareefa Dalvie
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Yakov Pichkar
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Allan Kalungi
- Department of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda; Mental Health Section of MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Lerato Majara
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anne Stevenson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tamrat Abebe
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dickens Akena
- Department of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Melkam Alemayehu
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Fred K Ashaba
- Department of Immunology & Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Lukoye Atwoli
- Department of Mental Health, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya; Brain and Mind Institute and Department of Internal Medicine, Medical College East Africa, the Aga Khan University, Nairobi, Kenya
| | - Mark Baker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lori B Chibnik
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Nicole Creanza
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abebaw Fekadu
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia; Centre for Innovative Drug Development & Therapeutic Trials for Africa, Addis Ababa University, Addis Ababa, Ethiopia
| | - Bizu Gelaye
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Stella Gichuru
- Department of Mental Health, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Wilfred E Injera
- Department of Immunology, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Roxanne James
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Symon M Kariuki
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Gabriel Kigen
- Department of Pharmacology and Toxicology, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Nastassja Koen
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Karestan C Koenen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Zan Koenig
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edith Kwobah
- Department of Mental Health, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Joseph Kyebuzibwa
- Department of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Henry Musinguzi
- Department of Immunology & Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Rehema M Mwema
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Carter P Newman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Charles R J C Newton
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Linnet Ongeri
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Raj Ramesar
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Welelta Shiferaw
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dan J Stein
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Rocky E Stroud
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Solomon Teferra
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mary T Yohannes
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zukiswa Zingela
- Executive Dean's Office, Faculty of Health Sciences, Nelson Mandela University, Port Elizabeth, South Africa
| | - Alicia R Martin
- Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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34
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Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy. Genomics 2022; 114:110405. [PMID: 35709925 DOI: 10.1016/j.ygeno.2022.110405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022]
Abstract
Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithization and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidences point to a link between Southern Italians and the Balkans still present in modern times. To shed light on these dynamics, we analysed around 700 South Mediterranean genomes combined with informative ancient DNAs. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with a Bronze Age component ultimately originating from the Caucasus with high Iranian and Anatolian Neolithic ancestries. Furthermore, extremely differentiated allele frequencies among Northern and Southern Italy revealed putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits.
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35
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Chintalapati M, Patterson N, Moorjani P. The spatiotemporal patterns of major human admixture events during the European Holocene. eLife 2022; 11:77625. [PMID: 35635751 PMCID: PMC9293011 DOI: 10.7554/elife.77625] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/29/2022] [Indexed: 11/16/2022] Open
Abstract
Recent studies have shown that admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage ancient genomic data. Thus, we developed DATES (Distribution of Ancestry Tracts of Evolutionary Signals) that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. DATES provides reliable estimates under various demographic scenarios and outperforms available methods for ancient DNA applications. Using DATES on~1100 ancient genomes from sixteen regions in Europe and west Asia, we reconstruct the chronology of the formation of the ancestral populations and the fine-scale details of the spread of Neolithic farming and Steppe pastoralist-related ancestry across Europe. By studying the genetic formation of Anatolian farmers, we infer that gene flow related to Iranian Neolithic farmers occurred before 9600 BCE, predating the advent of agriculture in Anatolia. Contrary to the archaeological evidence, we estimate that early Steppe pastoralist groups (Yamnaya and Afanasievo) were genetically formed more than a millennium before the start of Steppe pastoralism. Our analyses provide new insights on the origins and spread of farming and Indo-European languages, highlighting the power of genomic dating methods to elucidate the legacy of human migrations.
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Affiliation(s)
- Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Nick Patterson
- Program in Medical and Population Genetics, Broad Institute, Cambridge, United States
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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Asiimwe IG, Pirmohamed M. Ethnic Diversity and Warfarin Pharmacogenomics. Front Pharmacol 2022; 13:866058. [PMID: 35444556 PMCID: PMC9014219 DOI: 10.3389/fphar.2022.866058] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/14/2022] [Indexed: 12/23/2022] Open
Abstract
Warfarin has remained the most commonly prescribed vitamin K oral anticoagulant worldwide since its approval in 1954. Dosing challenges including having a narrow therapeutic window and a wide interpatient variability in dosing requirements have contributed to making it the most studied drug in terms of genotype-phenotype relationships. However, most of these studies have been conducted in Whites or Asians which means the current pharmacogenomics evidence-base does not reflect ethnic diversity. Due to differences in minor allele frequencies of key genetic variants, studies conducted in Whites/Asians may not be applicable to underrepresented populations such as Blacks, Hispanics/Latinos, American Indians/Alaska Natives and Native Hawaiians/other Pacific Islanders. This may exacerbate health inequalities when Whites/Asians have better anticoagulation profiles due to the existence of validated pharmacogenomic dosing algorithms which fail to perform similarly in the underrepresented populations. To examine the extent to which individual races/ethnicities are represented in the existing body of pharmacogenomic evidence, we review evidence pertaining to published pharmacogenomic dosing algorithms, including clinical utility studies, cost-effectiveness studies and clinical implementation guidelines that have been published in the warfarin field.
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Affiliation(s)
- Innocent G Asiimwe
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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Hernandez-Beeftink T, Marcelino-Rodríguez I, Guillen-Guio B, Rodríguez-Pérez H, Lorenzo-Salazar JM, Corrales A, Díaz-de Usera A, González-Montelongo R, Domínguez D, Espinosa E, Villar J, Flores C. Admixture Mapping of Sepsis in European Individuals With African Ancestries. Front Med (Lausanne) 2022; 9:754440. [PMID: 35345767 PMCID: PMC8957104 DOI: 10.3389/fmed.2022.754440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/24/2022] [Indexed: 11/30/2022] Open
Abstract
Sepsis is a severe systemic inflammatory response to infections that is accompanied by organ dysfunction. Although the ancestral genetic background is a relevant factor for sepsis susceptibility, there is a lack of studies using the genetic singularities of a recently admixed population to identify loci involved in sepsis susceptibility. Here we aimed to discover new sepsis loci by completing the first admixture mapping study of sepsis in Canary Islanders, leveraging their distinctive genetic makeup as a mixture of Europeans and African ancestries. We used a case-control approach and inferred local ancestry blocks from genome-wide data from 113,414 polymorphisms genotyped in 343 patients with sepsis and 410 unrelated controls, all ascertained for grandparental origin in the Canary Islands (Spain). Deviations in local ancestries between cases and controls were tested using logistic regressions, followed by fine-mapping analyses based on imputed genotypes, in silico functional assessments, and gene expression analysis centered on the region of interest. The admixture mapping analysis detected that local European ancestry in a locus spanning 1.2 megabases of chromosome 8p23.1 was associated with sepsis (lowest p = 1.37 × 10−4; Odds Ratio [OR] = 0.51; 95%CI = 0.40–0.66). Fine-mapping studies prioritized the variant rs13249564 within intron 1 of MFHAS1 gene associated with sepsis (p = 9.94 × 10−4; OR = 0.65; 95%CI = 0.50–0.84). Functional and gene expression analyses focused on 8p23.1 allowed us to identify alternative genes with possible biological plausibility such as defensins, which are well-known effector molecules of innate immunity. By completing the first admixture mapping study of sepsis, our results revealed a new genetic locus (8p23.1) harboring a number of genes with plausible implications in sepsis susceptibility.
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Affiliation(s)
- Tamara Hernandez-Beeftink
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Research Unit, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Itahisa Marcelino-Rodríguez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | | | - David Domínguez
- Department of Anesthesiology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Elena Espinosa
- Department of Anesthesiology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jesús Villar
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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38
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Circum-Saharan Prehistory through the Lens of mtDNA Diversity. Genes (Basel) 2022; 13:genes13030533. [PMID: 35328086 PMCID: PMC8951852 DOI: 10.3390/genes13030533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
African history has been significantly influenced by the Sahara, which has represented a barrier for migrations of all living beings, including humans. Major exceptions were the gene flow events that took place between North African and sub-Saharan populations during the so-called African Humid Periods, especially in the Early Holocene (11.5 to 5.5 thousand years ago), and more recently in connection with trans-Saharan commercial routes. In this study, we describe mitochondrial DNA (mtDNA) diversity of human populations from both sides of the Sahara Desert, i.e., both from North Africa and the Sahel/Savannah belt. The final dataset of 7213 mtDNA sequences from 134 African populations encompasses 470 newly collected and 6743 previously published samples, which were analyzed using descriptive methods and Bayesian statistics. We completely sequenced 26 mtDNAs from sub-Saharan samples belonging to the Eurasian haplogroup N1. Analyses of these N1 mitogenomes revealed their possible routes to the Sahel, mostly via Bab el-Mandab. Our results indicate that maternal gene flow must have been important in this circum-Saharan space, not only within North Africa and the Sahel/Savannah belt but also between these two regions.
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Mestiri S, Boussetta S, Pakstis AJ, El Kamel S, Ben Ammar El Gaaied A, Kidd KK, Cherni L. New Insight into the human genetic diversity in North African populations by genotyping of SNPs in DRD3, CSMD1 and NRG1 genes. Mol Genet Genomic Med 2022; 10:e1871. [PMID: 35128830 PMCID: PMC8922960 DOI: 10.1002/mgg3.1871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/02/2021] [Accepted: 01/04/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The single nucleotide polymorphisms (SNPs) of the dopamine D3 receptor (DRD3), the CUB and sushi multiple domains 1 (CSMD1) and the neuregulin 1 (NRG1) genes were used to study the genetic diversity and affinity among North African populations and to examine their genetic relationships in worldwide populations. METHODS The rs3773678, rs3732783 and rs6280 SNPs of the DRD3 gene located on chromosome 3, the rs10108270 SNP of the CSMD1 gene and the rs383632, rs385396 and rs1462906 SNPs of the NRG1 gene located on chromosome 8 were analysed in 366 individuals from seven North African populations (Libya, Kairouan, Mehdia, Sousse, Kesra, Smar and Kerkennah). RESULTS The low values of FST indicated that only 0.27%-1.65% of the genetic variability was due to the differences between the populations. The Kairouan population has the lowest average heterozygosity among the North African populations. Haplotypes composed of the ancestral alleles ACC and ACAT were more frequent in the Kairouan population than in other North African populations. The PCA and the haplotypic analysis showed that the genetic structure of populations in North Africa was closer to that of Europeans, Admixed Americans, South Asians and East Asians. However, analysis of the rs3732783 and rs6280 SNPs revealed that the CT microhaplotype was specific to the North African population. CONCLUSIONS The Kairouan population exhibited a relatively low rate of genetic variability. The North African population has undergone significant gene flow but also evolutionary forces that have made it genetically distinct from other populations.
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Affiliation(s)
- Souhir Mestiri
- Laboratory of Genetics, Biodiversity and Bioresource Valorization (LR11ES41)University of MonastirMonastirTunisia
- Higher Institute of Biotechnology of MonastirMonastir UniversityMonastirTunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of TunisUniversity of Tunis El ManarTunisTunisia
| | - Andrew J. Pakstis
- Department of GeneticsYale University School of MedicineNew HavenConnecticutUSA
| | - Sarra El Kamel
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of TunisUniversity of Tunis El ManarTunisTunisia
| | - Amel Ben Ammar El Gaaied
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of TunisUniversity of Tunis El ManarTunisTunisia
| | - Kenneth K. Kidd
- Department of GeneticsYale University School of MedicineNew HavenConnecticutUSA
| | - Lotfi Cherni
- Higher Institute of Biotechnology of MonastirMonastir UniversityMonastirTunisia
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of TunisUniversity of Tunis El ManarTunisTunisia
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40
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Deng L, Pan Y, Wang Y, Chen H, Yuan K, Chen S, Lu D, Lu Y, Mokhtar SS, Rahman TA, Hoh BP, Xu S. Genetic Connections and Convergent Evolution of Tropical Indigenous Peoples in Asia. Mol Biol Evol 2022; 39:msab361. [PMID: 34940850 PMCID: PMC8826522 DOI: 10.1093/molbev/msab361] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large interarea genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g., LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g., NKAIN3), or different loci in an identical gene (e.g., TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g., DDB1/DAK) or genetic convergence driven by admixture (e.g., MTHFD1 and RAD18), new mutations (e.g., STK11), or notably purifying selection (e.g., MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples.
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Affiliation(s)
- Lian Deng
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yinan Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Sihan Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Dongsheng Lu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Siti Shuhada Mokhtar
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Sungai Buloh, Selangor, Malaysia
| | - Thuhairah Abdul Rahman
- Clinical Pathology Diagnostic Centre Research Laboratory, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Sungai Buloh, Selangor, Malaysia
| | - Boon-Peng Hoh
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Faculty of Medicine and Health Sciences, UCSI University, Cheras, Kuala Lumpur, Malaysia
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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41
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Nakanishi G, Bertagnolli LS, Pita-Oliveira M, Scudeler MM, Torres-Loureiro S, Almeida-Dantas T, Alves MLC, Cirino HS, Rodrigues-Soares F. GSTM1 and GSTT1 polymorphisms in healthy volunteers - a worldwide systematic review. Drug Metab Rev 2022; 54:37-45. [PMID: 35103568 DOI: 10.1080/03602532.2022.2036996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/29/2022] [Indexed: 02/06/2023]
Abstract
The GSTM1 and GSTT1 genes encode homonymous enzymes, which are responsible for the detoxification of several substances potentially harmful to the human body, such as air pollution, drugs, pesticides, and tobacco. However, some individuals may present a complete deletion of these genes and, consequently, an enzyme deficiency leading to an inadequate metabolism and, therefore, a higher susceptibility to some clinical conditions. Interethnic variations have also been described for both genes, making necessary the study of the deletion frequencies of GSTM1 and GSTT1 in different populations around the world. So, the aim of this study was to enable the synthesis and discussion of the main population differences of GSTM1 and GSTT1 polymorphisms in healthy volunteers. Searches were performed in the PubMed database, including 533 articles and 178,566 individuals in the analyses. We found an overrepresentation of European individuals and studies, and an underrepresentation of non-European ethnicities. Moreover, there are significant frequency differences among distinct ethnic groups: East Asians present the highest frequencies worldwide for GSTM1 and GSTT1 deletions, which could suggest higher disorders risk for this population; in contrast, Sub-Saharan Africans presented the lowest frequency of GSTM1 worldwide, corroborating evolution inferences performed previously for other genes codifying metabolism enzymes. Also, admixture is a relevant component when analyzing frequency values for both genes, but further studies focusing on this subject are warranted.
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Affiliation(s)
- Giovana Nakanishi
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Laísa S Bertagnolli
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Murilo Pita-Oliveira
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Mariana M Scudeler
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Sabrina Torres-Loureiro
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Thaís Almeida-Dantas
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Maria Laura C Alves
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Heithor S Cirino
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Fernanda Rodrigues-Soares
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
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Ferwerda B, Abdellaoui A, Nieuwdorp M, Zwinderman K. A Genetic Map of the Modern Urban Society of Amsterdam. Front Genet 2021; 12:727269. [PMID: 34917125 PMCID: PMC8670378 DOI: 10.3389/fgene.2021.727269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic differences between individuals underlie susceptibility to many diseases. Genome-wide association studies (GWAS) have discovered many susceptibility genes but were often limited to cohorts of predominantly European ancestry. Genetic diversity between individuals due to different ancestries and evolutionary histories shows that this approach has limitations. In order to gain a better understanding of the associated genetic variation, we need a more global genomics approach including a greater diversity. Here, we introduce the Healthy Life in an Urban Setting (HELIUS) cohort. The HELIUS cohort consists of participants living in Amsterdam, with a level of diversity that reflects the Dutch colonial and recent migration past. The current study includes 10,283 participants with genetic data available from seven groups of inhabitants, namely, Dutch, African Surinamese, South-Asian Surinamese, Turkish, Moroccan, Ghanaian, and Javanese Surinamese. First, we describe the genetic variation and admixture within the HELIUS cohort. Second, we show the challenges during imputation when having a genetically diverse cohort. Third, we conduct a body mass index (BMI) and height GWAS where we investigate the effects of a joint analysis of the entire cohort and a meta-analysis approach for the different subgroups. Finally, we construct polygenic scores for BMI and height and compare their predictive power across the different ethnic groups. Overall, we give a comprehensive overview of a genetically diverse cohort from Amsterdam. Our study emphasizes the importance of a less biased and more realistic representation of urban populations for mapping genetic associations with complex traits and disease risk for all.
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Affiliation(s)
- Bart Ferwerda
- Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Abdel Abdellaoui
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Max Nieuwdorp
- Department of Vascular Medicine, Amsterdam University Medical Center, Amsterdam, Netherlands.,Internal Medicine, Amsterdam University Medical Center, Amsterdam, Netherlands.,Institute for Cardiovascular Research, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Koos Zwinderman
- Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, Amsterdam, Netherlands
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Whole-exome analysis in Tunisian Imazighen and Arabs shows the impact of demography in functional variation. Sci Rep 2021; 11:21125. [PMID: 34702931 PMCID: PMC8548440 DOI: 10.1038/s41598-021-00576-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/14/2021] [Indexed: 11/08/2022] Open
Abstract
Human populations are genetically affected by their demographic history, which shapes the distribution of their functional genomic variation. However, the genetic impact of recent demography is debated. This issue has been studied in different populations, but never in North Africans, despite their relevant cultural and demographic diversity. In this study we address the question by analyzing new whole-exome sequences from two culturally different Tunisian populations, an isolated Amazigh population and a close non-isolated Arab-speaking population, focusing on the distribution of functional variation. Both populations present clear differences in their variant frequency distribution, in general and for putatively damaging variation. This suggests a relevant effect in the Amazigh population of genetic isolation, drift, and inbreeding, pointing to relaxed purifying selection. We also discover the enrichment in Imazighen of variation associated to specific diseases or phenotypic traits, but the scarce genetic and biomedical data in the region limits further interpretation. Our results show the genomic impact of recent demography and reveal a clear genetic differentiation probably related to culture. These findings highlight the importance of considering cultural and demographic heterogeneity within North Africa when defining population groups, and the need for more data to improve knowledge on the region's health and disease landscape.
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44
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The genetic structure of the Turkish population reveals high levels of variation and admixture. Proc Natl Acad Sci U S A 2021; 118:2026076118. [PMID: 34426522 DOI: 10.1073/pnas.2026076118] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The construction of population-based variomes has contributed substantially to our understanding of the genetic basis of human inherited disease. Here, we investigated the genetic structure of Turkey from 3,362 unrelated subjects whose whole exomes (n = 2,589) or whole genomes (n = 773) were sequenced to generate a Turkish (TR) Variome that should serve to facilitate disease gene discovery in Turkey. Consistent with the history of present-day Turkey as a crossroads between Europe and Asia, we found extensive admixture between Balkan, Caucasus, Middle Eastern, and European populations with a closer genetic relationship of the TR population to Europeans than hitherto appreciated. We determined that 50% of TR individuals had high inbreeding coefficients (≥0.0156) with runs of homozygosity longer than 4 Mb being found exclusively in the TR population when compared to 1000 Genomes Project populations. We also found that 28% of exome and 49% of genome variants in the very rare range (allele frequency < 0.005) are unique to the modern TR population. We annotated these variants based on their functional consequences to establish a TR Variome containing alleles of potential medical relevance, a repository of homozygous loss-of-function variants and a TR reference panel for genotype imputation using high-quality haplotypes, to facilitate genome-wide association studies. In addition to providing information on the genetic structure of the modern TR population, these data provide an invaluable resource for future studies to identify variants that are associated with specific phenotypes as well as establishing the phenotypic consequences of mutations in specific genes.
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45
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Frayer ME, Payseur BA. Demographic history shapes genomic ancestry in hybrid zones. Ecol Evol 2021; 11:10290-10302. [PMID: 34367575 PMCID: PMC8328415 DOI: 10.1002/ece3.7833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 12/26/2022] Open
Abstract
Demographic factors such as migration rate and population size can impede or facilitate speciation. In hybrid zones, reproductive boundaries between species are tested and demography mediates the opportunity for admixture between lineages that are partially isolated. Genomic ancestry is a powerful tool for revealing the history of admixed populations, but models and methods based on local ancestry are rarely applied to structured hybrid zones. To understand the effects of demography on ancestry in hybrids zones, we performed individual-based simulations under a stepping-stone model, treating migration rate, deme size, and hybrid zone age as parameters. We find that the number of ancestry junctions (the transition points between genomic regions with different ancestries) and heterogenicity (the genomic proportion heterozygous for ancestry) are often closely connected to demographic history. Reducing deme size reduces junction number and heterogenicity. Elevating migration rate increases heterogenicity, but migration affects junction number in more complex ways. We highlight the junction frequency spectrum as a novel and informative summary of ancestry that responds to demographic history. A substantial proportion of junctions are expected to fix when migration is limited or deme size is small, changing the shape of the spectrum. Our findings suggest that genomic patterns of ancestry could be used to infer demographic history in hybrid zones.
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Affiliation(s)
- Megan E. Frayer
- Laboratory of GeneticsUniversity of Wisconsin MadisonMadisonWIUSA
| | - Bret A. Payseur
- Laboratory of GeneticsUniversity of Wisconsin MadisonMadisonWIUSA
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Zimmerman KD, Schurr TG, Chen W, Nayak U, Mychaleckyj JC, Quet Q, Moultrie LH, Divers J, Keene KL, Kamen DL, Gilkeson GS, Hunt KJ, Spruill IJ, Fernandes JK, Aldrich MC, Reich D, Garvey WT, Langefeld CD, Sale MM, Ramos PS. Genetic landscape of Gullah African Americans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175:905-919. [PMID: 34008864 PMCID: PMC8286328 DOI: 10.1002/ajpa.24333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/30/2021] [Accepted: 04/17/2021] [Indexed: 01/20/2023]
Abstract
OBJECTIVES Gullah African Americans are descendants of formerly enslaved Africans living in the Sea Islands along the coast of the southeastern U.S., from North Carolina to Florida. Their relatively high numbers and geographic isolation were conducive to the development and preservation of a unique culture that retains deep African features. Although historical evidence supports a West-Central African ancestry for the Gullah, linguistic and cultural evidence of a connection to Sierra Leone has led to the suggestion of this country/region as their ancestral home. This study sought to elucidate the genetic structure and ancestry of the Gullah. MATERIALS AND METHODS We leveraged whole-genome genotype data from Gullah, African Americans from Jackson, Mississippi, African populations from Sierra Leone, and population reference panels from Africa and Europe to infer population structure, ancestry proportions, and global estimates of admixture. RESULTS Relative to non-Gullah African Americans from the Southeast US, the Gullah exhibited higher mean African ancestry, lower European admixture, a similarly small Native American contribution, and increased male-biased European admixture. A slightly tighter bottleneck in the Gullah 13 generations ago suggests a largely shared demographic history with non-Gullah African Americans. Despite a slightly higher relatedness to populations from Sierra Leone, our data demonstrate that the Gullah are genetically related to many West African populations. DISCUSSION This study confirms that subtle differences in African American population structure exist at finer regional levels. Such observations can help to inform medical genetics research in African Americans, and guide the interpretation of genetic data used by African Americans seeking to explore ancestral identities.
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Affiliation(s)
- Kip D. Zimmerman
- Center for Precision MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Theodore G. Schurr
- Department of AnthropologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Wei‐Min Chen
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Public Health SciencesUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Uma Nayak
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Josyf C. Mychaleckyj
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Public Health SciencesUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Queen Quet
- Gullah/Geechee NationSt. Helena IslandSouth CarolinaUSA
| | - Lee H. Moultrie
- Lee H. Moultrie & AssociatesNorth CharlestonSouth CarolinaUSA
| | - Jasmin Divers
- Department of Health Services ResearchNew York University Winthrop HospitalMineolaNew YorkUSA
| | - Keith L. Keene
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
- Center for Health DisparitiesEast Carolina University Brody School of MedicineGreenvilleNorth CarolinaUSA
| | - Diane L. Kamen
- Department of MedicineMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Gary S. Gilkeson
- Department of MedicineMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Kelly J. Hunt
- Department of Public Health SciencesMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Ida J. Spruill
- College of NursingMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Jyotika K. Fernandes
- Department of MedicineMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Melinda C. Aldrich
- Department of Thoracic SurgeryVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Genetics InstituteVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - David Reich
- Department of GeneticsHarvard Medical SchoolBostonMassachusettsUSA
- Howard Hughes Medical InstituteHarvard Medical SchoolBostonMassachusettsUSA
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Department of Human Evolutionary BiologyHarvard UniversityCambridgeMassachusettsUSA
| | - W. Timothy Garvey
- Department of Nutrition ScienceUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Carl D. Langefeld
- Center for Precision MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Michèle M. Sale
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Public Health SciencesUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Paula S. Ramos
- Department of MedicineMedical University of South CarolinaCharlestonSouth CarolinaUSA
- Department of Public Health SciencesMedical University of South CarolinaCharlestonSouth CarolinaUSA
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Souissi A, Gibriel AA, Masmoudi S. Genetics and meta-analysis of recessive non-syndromic hearing impairment and Usher syndrome in Maghreb population: lessons from the past, contemporary actualities and future challenges. Hum Genet 2021; 141:583-593. [PMID: 34268600 DOI: 10.1007/s00439-021-02314-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022]
Abstract
Hereditary hearing impairment (HI) is a heterogeneous condition with over 130 genes associated with genetic non-syndromic HI (NSHI) and Usher syndrome (USH). Approximately 80% of hereditary NSHI cases have autosomal recessive (AR) mode of inheritance. The high rate of consanguinity and endogamy in the Maghreb countries, including Tunisia, Algeria and Morocco, represents a major contributing factor to the development of ARHI. Since the 90s, those populations, with their particular large familiar structure, represented an effective key towards the discovery of the first HI loci and genes. In this study, we performed a deep literature database search to analyze the mutational spectrum and the distribution of pathogenic variants responsible of USH and the NSHI among those populations. To date, 124 pathogenic variants were identified in 32 genes of which over 70% represent population-specific variants. The particular variants' distribution is related to the high rate of consanguinity as well as the multiple shared features such as demographic history of migrations and social behavior that promoted the spreading of several founder mutations within those countries. This is the first study to report lessons from the past and current actualities of HI within the three Maghreb countries. However, despite the great impact placed by such population for the HI genetic studies, only a few next-generation sequencing platforms have so far been implemented with those countries. We, therefore, believe that those countries should be supported to implement this technology that would definitely be of great value in the discovery of additional novel HI genes/variants.
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Affiliation(s)
- Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour road Km 6, BP "1177", 3018, Sfax, Tunisia
| | - Abdullah A Gibriel
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour road Km 6, BP "1177", 3018, Sfax, Tunisia.
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48
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Ahlquist KD, Bañuelos MM, Funk A, Lai J, Rong S, Villanea FA, Witt KE. Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture. Genome Biol Evol 2021; 13:evab115. [PMID: 34028527 PMCID: PMC8480178 DOI: 10.1093/gbe/evab115] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/07/2021] [Accepted: 05/22/2021] [Indexed: 11/30/2022] Open
Abstract
The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.
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Affiliation(s)
- K D Ahlquist
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Mayra M Bañuelos
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Alyssa Funk
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Jiaying Lai
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Brown Center for Biomedical Informatics, Brown University, Providence, Rhode Island, USA
| | - Stephen Rong
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Fernando A Villanea
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Anthropology, University of Colorado Boulder, Colorado, USA
| | - Kelsey E Witt
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
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49
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Abstract
Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova Cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here, we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 48,700 (16,000-59,500) y ago, and selection started around 9,000 (2,500-42,000) y ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.
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50
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Svensson E, Günther T, Hoischen A, Hervella M, Munters AR, Ioana M, Ridiche F, Edlund H, van Deuren RC, Soficaru A, de-la-Rua C, Netea MG, Jakobsson M. Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe. Curr Biol 2021; 31:2973-2983.e9. [PMID: 34010592 DOI: 10.1016/j.cub.2021.04.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 11/24/2022]
Abstract
Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from "Peştera Muierii," Romania who lived ∼34,000 years ago to 13.5× coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (∼3.1%) to most EUP humans but only half compared to the ∼40,000-year-old Peştera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.
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Affiliation(s)
- Emma Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6526 Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands
| | - Montserrat Hervella
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B° Sarriena s/n 48940 Leioa, Bizkaia, Spain
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Mihai Ioana
- Laboratory of Human Genetics, University of Medicine and Pharmacy, Craiova, Romania
| | | | - Hanna Edlund
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Rosanne C van Deuren
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands
| | - Andrei Soficaru
- "Francisc J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania
| | - Concepción de-la-Rua
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B° Sarriena s/n 48940 Leioa, Bizkaia, Spain
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands; Laboratory of Human Genetics, University of Medicine and Pharmacy, Craiova, Romania
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
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