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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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2
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Mazzarotto F, Argirò A, Zampieri M, Magri C, Giotti I, Boschi B, Frusconi S, Gennarelli M, Buxbaum J, Polimanti R, Olivotto I, Perfetto F, Cappelli F. Investigation on the high recurrence of the ATTRv-causing transthyretin variant Val142Ile in central Italy. Eur J Hum Genet 2023; 31:541-547. [PMID: 36380086 PMCID: PMC10172197 DOI: 10.1038/s41431-022-01235-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
The p.Val142Ile variant in transthyretin (encoded by the TTR gene) is the most common genetic cause of transthyretin-related amyloidosis. This allele is particularly prevalent in communities ofAfrican descent compared with populations of different ancestries, where its frequency is two orders of magnitude lower. For this reason, p.Val142Ile has always been considered an "African" variant, with limited studies performed on individuals of European descent. However, recent reports of higher-than-expected prevalence in European-ancestry populations question the African specificity of this allele. Here we show that the high recurrence of p.Val142Ile in central Italy is due to a founder effect and not to recent admixture from African populations, highlighting how this may be the case in other communities. This suggests a probable underestimate of the global prevalence of p.Val142Ile, and further emphasizes the importance of routine inclusion of TTR in gene panels used for clinical genetic testing in hypertrophic cardiomyopathy (independently of the patient's geographical origin), that transthyretin-related amyloidosis can mimic.
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Affiliation(s)
- Francesco Mazzarotto
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Alessia Argirò
- Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy
| | - Mattia Zampieri
- Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy
| | - Chiara Magri
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Irene Giotti
- Genetics Unit, Careggi University Hospital, Florence, Italy
| | | | | | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Joel Buxbaum
- The Scripps Research Institute, La Jolla, CA, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
- VA Connecticut Healthcare Center, West Haven, CT, USA
| | - Iacopo Olivotto
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Meyer Children's Hospital, Florence, Italy
| | - Federico Perfetto
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Tuscan Regional Amyloidosis Centre, Careggi University Hospital, Florence, Italy
| | - Francesco Cappelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Tuscan Regional Amyloidosis Centre, Careggi University Hospital, Florence, Italy
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3
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Souilmi Y, Tobler R, Johar A, Williams M, Grey ST, Schmidt J, Teixeira JC, Rohrlach A, Tuke J, Johnson O, Gower G, Turney C, Cox M, Cooper A, Huber CD. Admixture has obscured signals of historical hard sweeps in humans. Nat Ecol Evol 2022; 6:2003-2015. [PMID: 36316412 PMCID: PMC9715430 DOI: 10.1038/s41559-022-01914-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 09/16/2022] [Indexed: 11/06/2022]
Abstract
The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate.
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Affiliation(s)
- Yassine Souilmi
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
| | - Raymond Tobler
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Angad Johar
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA.
| | - Matthew Williams
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Shane T Grey
- Transplantation Immunology Group, Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, New South Wales, Australia
| | - Joshua Schmidt
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - João C Teixeira
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Adam Rohrlach
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, South Australia, Australia
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jonathan Tuke
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, South Australia, Australia
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Olivia Johnson
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Graham Gower
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Chris Turney
- Chronos 14Carbon-Cycle Facility and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Murray Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia.
- BlueSky Genetics, Ashton, South Australia, Australia.
| | - Christian D Huber
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Department of Biology, Penn State University, University Park, PA, USA.
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4
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Fedorova L, Khrunin A, Khvorykh G, Lim J, Thornton N, Mulyar OA, Limborska S, Fedorov A. Analysis of Common SNPs across Continents Reveals Major Genomic Differences between Human Populations. Genes (Basel) 2022; 13:genes13081472. [PMID: 36011383 PMCID: PMC9408407 DOI: 10.3390/genes13081472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/12/2022] [Accepted: 08/17/2022] [Indexed: 12/03/2022] Open
Abstract
Common alleles tend to be more ancient than rare alleles. These common SNPs appeared thousands of years ago and reflect intricate human evolution including various adaptations, admixtures, and migration events. Eighty-four thousand abundant region-specific alleles (ARSAs) that are common in one continent but absent in the rest of the world have been characterized by processing 3100 genomes from 230 populations. Also computed were 17,446 polymorphic sites with regional absence of common alleles (RACAs), which are widespread globally but absent in one region. A majority of these region-specific SNPs were found in Africa. America has the second greatest number of ARSAs (3348) and is even ahead of Europe (1911). Surprisingly, East Asia has the highest number of RACAs (10,524) and the lowest number of ARSAs (362). ARSAs and RACAs have distinct compositions of ancestral versus derived alleles in different geographical regions, reflecting their unique evolution. Genes associated with ARSA and RACA SNPs were identified and their functions were analyzed. The core 100 genes shared by multiple populations and associated with region-specific natural selection were examined. The largest part of them (42%) are related to the nervous system. ARSA and RACA SNPs are important for both association and human evolution studies.
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Affiliation(s)
| | - Andrey Khrunin
- Institute of Molecular Genetics of National Research Centre, “Kurchatov Institute”, 123182 Moscow, Russia
| | - Gennady Khvorykh
- Institute of Molecular Genetics of National Research Centre, “Kurchatov Institute”, 123182 Moscow, Russia
| | - Jan Lim
- CRI Genetics LLC, Santa Monica, CA 90404, USA
| | | | | | - Svetlana Limborska
- Institute of Molecular Genetics of National Research Centre, “Kurchatov Institute”, 123182 Moscow, Russia
| | - Alexei Fedorov
- CRI Genetics LLC, Santa Monica, CA 90404, USA
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA
- Correspondence: ; Tel.: +1-419-383-5270
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5
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African Genomic Medicine Portal: A Web Portal for Biomedical Applications. J Pers Med 2022; 12:jpm12020265. [PMID: 35207753 PMCID: PMC8879570 DOI: 10.3390/jpm12020265] [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: 12/15/2021] [Revised: 01/22/2022] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available.
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6
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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] [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 Monastir Monastir Tunisia
- Higher Institute of Biotechnology of Monastir Monastir University Monastir Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis University of Tunis El Manar Tunis Tunisia
| | - Andrew J. Pakstis
- Department of Genetics Yale University School of Medicine New Haven Connecticut USA
| | - Sarra El Kamel
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis University of Tunis El Manar Tunis Tunisia
| | - Amel Ben Ammar El Gaaied
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis University of Tunis El Manar Tunis Tunisia
| | - Kenneth K. Kidd
- Department of Genetics Yale University School of Medicine New Haven Connecticut USA
| | - Lotfi Cherni
- Higher Institute of Biotechnology of Monastir Monastir University Monastir Tunisia
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis University of Tunis El Manar Tunis Tunisia
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7
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Versluys TMM, Flintham EO, Mas-Sandoval A, Savolainen V. Why do we pick similar mates, or do we? Biol Lett 2021; 17:20210463. [PMID: 34813721 DOI: 10.1098/rsbl.2021.0463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Humans often mate with those resembling themselves, a phenomenon described as positive assortative mating (PAM). The causes of this attract broad interest, but there is little agreement on the topic. This may be because empirical studies and reviews sometimes focus on just a few explanations, often based on disciplinary conventions. This review presents an interdisciplinary conceptual framework on the causes of PAM in humans, drawing on human and non-human biology, the social sciences, and the humanities. Viewing causality holistically, we first discuss the proximate causes (i.e. the 'how') of PAM, considering three mechanisms: stratification, convergence and mate choice. We also outline methods to control for confounders when studying mate choice. We then discuss ultimate explanations (i.e. 'the why') for PAM, including adaptive and non-adaptive processes. We conclude by suggesting a focus on interdisciplinarity in future research.
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Affiliation(s)
- Thomas M M Versluys
- Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, United Kingdom
| | - Ewan O Flintham
- Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, United Kingdom
| | - Alex Mas-Sandoval
- Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, United Kingdom
| | - Vincent Savolainen
- Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, United Kingdom
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8
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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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9
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Ferreira JC, Alshamali F, Montinaro F, Cavadas B, Torroni A, Pereira L, Raveane A, Fernandes V. Projecting Ancient Ancestry in Modern-Day Arabians and Iranians: A Key Role of the Past Exposed Arabo-Persian Gulf on Human Migrations. Genome Biol Evol 2021; 13:6364187. [PMID: 34480555 PMCID: PMC8435661 DOI: 10.1093/gbe/evab194] [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] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
The Arabian Peninsula is strategic for investigations centered on the early structuring of modern humans in the wake of the out-of-Africa migration. Despite its poor climatic conditions for the recovery of ancient human DNA evidence, the availability of both genomic data from neighboring ancient specimens and informative statistical tools allow modeling the ancestry of local modern populations. We applied this approach to a data set of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking western Arabia with the Levant, and eastern Arabia with Iran and the Caucasus. Eastern Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for a possible bias due to a recent sub-Saharan African input in their genomes. Not surprisingly, eastern Arabians were also the ones with highest similarity with Iberomaurusians, who were, so far, the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans who diverged from the common European-eastern Asian pool before 50,000 years ago, prior to the later interbred with Neanderthals. Our results appear to indicate that the exposed basin of the Arabo-Persian Gulf was the possible home of basal Eurasians, a scenario to be further investigated by searching ancient Arabian human specimens.
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Affiliation(s)
- Joana C Ferreira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal.,ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Farida Alshamali
- Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia
| | - Bruno Cavadas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Italy
| | - Luisa Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Italy.,Laboratory of Haematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Veronica Fernandes
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
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10
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Lucas-Sánchez M, Serradell JM, Comas D. Population history of North Africa based on modern and ancient genomes. Hum Mol Genet 2020; 30:R17-R23. [PMID: 33284971 DOI: 10.1093/hmg/ddaa261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/09/2023] Open
Abstract
Compared with the rest of the African continent, North Africa has provided limited genomic data. Nonetheless, the genetic data available show a complex demographic scenario characterized by extensive admixture and drift. Despite the continuous gene flow from the Middle East, Europe and sub-Saharan Africa, an autochthonous genetic component that dates back to pre-Holocene times is still present in North African groups. The comparison of ancient and modern genomes has evidenced a genetic continuity in the region since Epipaleolithic times. Later population movements, especially the gene flow from the Middle East associated with the Neolithic, have diluted the genetic autochthonous component, creating an east to west gradient. Recent historical movements, such as the Arabization, have also contributed to the genetic landscape observed currently in North Africa and have culturally transformed the region. Genome analyses have not shown evidence of a clear correlation between cultural and genetic diversity in North Africa, as there is no genetic pattern of differentiation between Tamazight (i.e. Berber) and Arab speakers as a whole. Besides the gene flow received from neighboring areas, the analysis of North African genomes has shown that the region has also acted as a source of gene flow since ancient times. As a result of the genetic uniqueness of North African groups and the lack of available data, there is an urgent need for the study of genetic variation in the region and its implications in health and disease.
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Affiliation(s)
- Marcel Lucas-Sánchez
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Jose M Serradell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
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11
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Font-Porterias N, Arauna LR, Poveda A, Bianco E, Rebato E, Prata MJ, Calafell F, Comas D. European Roma groups show complex West Eurasian admixture footprints and a common South Asian genetic origin. PLoS Genet 2019; 15:e1008417. [PMID: 31545809 PMCID: PMC6779411 DOI: 10.1371/journal.pgen.1008417] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 10/07/2019] [Accepted: 09/12/2019] [Indexed: 02/07/2023] Open
Abstract
The Roma population is the largest transnational ethnic minority in Europe, characterized by a linguistic, cultural and historical heterogeneity. Comparative linguistics and genetic studies have placed the origin of European Roma in the Northwest of India. After their migration across Persia, they entered into the Balkan Peninsula, from where they spread into Europe, arriving in the Iberian Peninsula in the 15th century. Their particular demographic history has genetic implications linked to rare and common diseases. However, the South Asian source of the proto-Roma remains still untargeted and the West Eurasian Roma component has not been yet deeply characterized. Here, in order to describe both the South Asian and West Eurasian ancestries, we analyze previously published genome-wide data of 152 European Roma and 34 new Iberian Roma samples at a fine-scale and haplotype-based level, with special focus on the Iberian Roma genetic substructure. Our results suggest that the putative origin of the proto-Roma involves a Punjabi group with low levels of West Eurasian ancestry. In addition, we have identified a complex West Eurasian component (around 65%) in the Roma, as a result of the admixture events occurred with non-proto-Roma populations between 1270–1580. Particularly, we have detected the Balkan genetic footprint in all European Roma, and the Baltic and Iberian components in the Northern and Western Roma groups, respectively. Finally, our results show genetic substructure within the Iberian Roma, with different levels of West Eurasian admixture, as a result of the complex historical events occurred in the Peninsula. Human demographic processes and admixture events leave traceable footprints in the genomes of the populations and they can modulate the genetic architecture of complex diseases. Here, we aim to study the Roma people, an admixed population with a particular demographic history recognized as the largest ethnic minority in Europe. Previous studies suggest that they originated in South Asia 1,500 years ago and followed a diaspora towards Europe with extensive admixture with non-Roma West Eurasian groups. However, the genetic components of the Roma have not been deeply characterized. Our study reveals a common South Asian origin of all European Roma, closely related to a Punjabi group from Northwestern India. Through fine-scale haplotype-based methods, we describe a complex West Eurasian genetic component in the Roma groups, identifying a common Balkan ancestry and country-specific admixture footprints consistent with the dispersion through Europe. Our findings provide new insights into the demographic history and recent admixture events that have shaped the genetic composition of European Roma groups and could enable a better genetic characterization of complex disease in this population.
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Affiliation(s)
- Neus Font-Porterias
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Lara R. Arauna
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France
| | - Alaitz Poveda
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Erica Bianco
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Esther Rebato
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Maria Joao Prata
- Instituto de Investigacão e Inovacão em Saude/Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal; Faculty of Sciences, University of Porto, Porto, Portugal
| | - Francesc Calafell
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail:
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