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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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Lopes MQP, Teixeira RLF, Cabello PH, Nery JAC, Sales AM, Nahn J. R. EP, Moreira MV, Stahlke EVR, Possuelo LG, Rossetti MLR, Rabahi MF, Silva LFM, Leme PA, Woods WJ, Nobre ML, de Oliveira MLWDR, Narahashi K, Cavalcanti M, Suffys PN, Boukouvala S, Gallo MEN, Santos AR. Human N-acetyltransferase 2 ( NAT2) gene variability in Brazilian populations from different geographical areas. Front Pharmacol 2023; 14:1278720. [PMID: 38035025 PMCID: PMC10684696 DOI: 10.3389/fphar.2023.1278720] [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: 08/16/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction: Several polymorphisms altering the NAT2 activity have already been identified. The geographical distribution of NAT2 variants has been extensively studied and has been demonstrated to vary significantly among different ethnic population. Here, we describe the genetic variability of human N-acetyltransferase 2 (NAT2) gene and the predominant genotype-deduced acetylation profiles of Brazilians. Methods: A total of 964 individuals, from five geographical different regions, were genotyped for NAT2 by sequencing the entire coding exon. Results: Twenty-three previously described NAT2 single nucleotide polymorphisms (SNPs) were identified, including the seven most common ones globally (c.191G>A, c.282C>T, c.341T>C, c.481C>T, c.590G>A, c.803A>G and c.857G>A). The main allelic groups were NAT2*5 (36%) and NAT2*6 (18.2%), followed to the reference allele NAT2*4 (20.4%). Combined into genotypes, the most prevalent allelic groups were NAT2*5/*5 (14.6%), NAT2*5/*6 (11.9%) and NAT2*6/*6 (6.2%). The genotype deduced NAT2 slow acetylation phenotype was predominant but showed significant variability between geographical regions. The prevalence of slow acetylation phenotype was higher in the Northeast, North and Midwest (51.3%, 45.5% and 41.5%, respectively) of the country. In the Southeast, the intermediate acetylation phenotype was the most prevalent (40.3%) and, in the South, the prevalence of rapid acetylation phenotype was significantly higher (36.7%), when compared to other Brazilian states (p < 0.0001). Comparison of the predicted acetylation profile among regions showed homogeneity among the North and Northeast but was significantly different when compared to the Southeast (p = 0.0396). The Southern region was significantly different from all other regions (p < 0.0001). Discussion: This study contributes not only to current knowledge of the NAT2 population genetic diversity in different geographical regions of Brazil, but also to the reconstruction of a more accurate phenotypic picture of NAT2 acetylator profiles in those regions.
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Affiliation(s)
- Márcia Quinhones P. Lopes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Raquel Lima F. Teixeira
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Pedro Hernan Cabello
- Laboratory of Human Genetics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - José Augusto C. Nery
- Leprosy Laboratory, Souza Araújo Outpatient Clinic, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Anna Maria Sales
- Leprosy Laboratory, Souza Araújo Outpatient Clinic, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | | | | | | | - Lia Gonçalves Possuelo
- Department of Molecular Biology and Biotechnology, IB and Biotechnology Center, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Lucia R. Rossetti
- Department of Molecular Biology and Biotechnology, IB and Biotechnology Center, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marcelo F. Rabahi
- Anuar Auad Infectious Disease Reference Hospital, Goiania, GO, Brazil
| | | | | | | | | | | | | | | | - Philip Noel Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Sotiria Boukouvala
- Laboratory of Molecular Genetics and Pharmacogenomics - Toxicogenomics, Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Eugênia N. Gallo
- Leprosy Laboratory, Souza Araújo Outpatient Clinic, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Adalberto Rezende Santos
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
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Arencibia V, Muñoz M, Crespo CM, Russo MG, Vera P, Lia VV, García Guraieb S, Goñi RA, Avena S, Puebla A, Dejean CB. Novel B2 mitogenomes from Continental southern Patagonia's Late Holocene: New insights into the peopling of the Southern Cone. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 37548135 DOI: 10.1002/ajpa.24822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/23/2023] [Accepted: 07/09/2023] [Indexed: 08/08/2023]
Abstract
OBJECTIVES The main aim of this study is to discuss the migratory processes and peopling dynamics that shaped the genetic variability of populations during the settlement of the Southern Cone, through the analysis of complete mitogenomes of individuals from southern Patagonia. MATERIALS AND METHODS Complete mitogenomes were sequenced through massively parallel sequencing from two late Holocene individuals (SAC 1-1-3 and SAC 1-1-4) buried in the same chenque at Salitroso Lake Basin (Santa Cruz province, Argentina). To evaluate matrilineal phylogenetic affinities with other haplotypes, maximum likelihood and Bayesian phylogenetic reconstructions were performed, as well as a haplotype median-joining network. RESULTS The mitogenomes were assigned to haplogroups B2 and B2b, exhibiting an average depth of 54X and 89X (≥1X coverage of 98.6% and 100%), and a high number of nucleotide differences among them. The phylogenetic analyses showed a relatively close relationship between the haplotype found in SAC 1-1-4 and those retrieved from a Middle Holocene individual from Laguna Chica (Buenos Aires province), and from a group of individuals from the Peruvian coast. For the SAC 1-1-3, no clear affiliations to any other haplotype were established. DISCUSSION The large divergence between the haplotypes presented in this study suggests either a highly variable founder gene pool, or a later enrichment by frequent biological contact with other populations. Our results underline the persistence of genetic signals related to the first waves of peopling in South America, suggesting that the regional settlement of the southern end of the continent has been much more complex than initially thought.
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Affiliation(s)
- Valeria Arencibia
- Equipo de Antropología Biológica, CCNAA, Universidad Maimónides, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marianne Muñoz
- Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
- Instituto de Biotecnología-IABIMO (CONICET), Unidad de Genómica, Nodo CATG, Buenos Aires, Argentina
| | - Cristian M Crespo
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales (ICPA), Universidad Nacional de Tierra del Fuego, Ushuaia, Tierra del Fuego, Argentina
| | - M Gabriela Russo
- Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Grupo de Investigación en Biología Evolutiva (GIBE), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pablo Vera
- Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
- Instituto de Biotecnología-IABIMO (CONICET), Unidad de Genómica, Nodo CATG, Buenos Aires, Argentina
| | - Verónica V Lia
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Solana García Guraieb
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto Nacional de Antropología y Pensamiento Latinoamericano (INAPL), Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael A Goñi
- Instituto Nacional de Antropología y Pensamiento Latinoamericano (INAPL), Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sergio Avena
- Equipo de Antropología Biológica, CCNAA, Universidad Maimónides, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andrea Puebla
- Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
- Instituto de Biotecnología-IABIMO (CONICET), Unidad de Genómica, Nodo CATG, Buenos Aires, Argentina
| | - Cristina B Dejean
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Instituto de Ciencias Antropológicas, Sección Antropología Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina
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Resende GG, Saad CGS, de Oliveira DCM, de Sousa Bueno Filho JS, Sampaio-Barros PD, de Medeiros Pinheiro M. HLA-B27 positivity in a large miscegenated population of 5,389,143 healthy blood marrow donors in Brazil. Adv Rheumatol 2023; 63:16. [PMID: 37081582 DOI: 10.1186/s42358-023-00302-6] [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: 02/15/2023] [Accepted: 04/13/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND The prevalence of HLA-B27 gene positivity in healthy Caucasian communities varies between 8 and 14%. However, there is a lack of information in countries with a high rate of miscegenation, such as Brazil. AIM To estimate the frequency of HLA-B27 in the Brazilian general population using a large national registry database. METHODS This is a cross-sectional ecological study using the Brazilian Registry of Volunteer Bone Marrow Donors (REDOME) database on HLA-B27 allelic frequency and proportion of positives of healthy donors (18-60 years old). Data were analyzed according to sex, age, race (by self-reported skin color recommended by the Brazilian Institute of Geography and Statistics - IBGE), and geographic region of residence. RESULTS From 1994 to 2022, a total of 5,389,143 healthy bone marrow donors were included. The overall positivity for HLA-B27 was 4.35% (CI 95% 4.32-4.37%), regardless of sex and age (57.2% were women, mean age was 41.7yo). However, there was a difference between races: 4.85% in Whites; 2.92% in Blacks; 3.76% in Pardos (Browns i.e. mixed races); 3.95% in Amarelos (Yellows i.e. Asian Brazilians); and 3.18% in Indigenous. There was also a difference regarding geographic region of residence (North: 3.62%; Northeast: 3.63%; Southeast: 4.29%; Midwest: 4.5% and 5.25% in South). The homozygosity rate for the HLA-B27 was 1.32% of all the positives and only 0.06% in the general population. CONCLUSIONS Our findings provide the first Brazilian national prevalence for HLA-B27 in 4.35%. There is a gradient gene positivity from North to South, suggesting that the genetic background related to the miscegenation due to colonization, slavery, and some later waves of immigration together with internal migratory flows, could explain our findings.
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Affiliation(s)
- Gustavo Gomes Resende
- Hospital das Clínicas - Universidade Federal de Minas Gerais (HC-UFMG), Al. Álvaro Celso 175 / 2º floor, Belo Horizonte, MG, Brasil.
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dos Santos ALC, Sullasi HSL, Gokcumen O, Lindo J, DeGiorgio M. Spatiotemporal fluctuations of population structure in the Americas revealed by a meta-analysis of the first decade of archaeogenomes. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:703-714. [PMID: 39081397 PMCID: PMC11288623 DOI: 10.1002/ajpa.24673] [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] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/15/2022] [Indexed: 08/02/2024]
Abstract
Objectives Since 2010, genome-wide data from hundreds of ancient Native Americans have contributed to the understanding of Americas' prehistory. However, these samples have never been studied as a single dataset, and distinct relationships among themselves and with present-day populations may have never come to light. Here, we reassess genomic diversity and population structure of 223 ancient Native Americans published between 2010 and 2019. Materials and Methods The genomic data from ancient Americas was merged with a worldwide reference panel of 278 present-day genomes from the Simons Genome Diversity Project and then analyzed through ADMIXTURE, D-statistics, PCA, t-SNE, and UMAP. Results We find largely similar population structures in ancient and present-day Americas. However, the population structure of contemporary Native Americans, traced here to at least 10,000 years before present, is noticeably less diverse than their ancient counterparts, a possible outcome of the European contact. Additionally, in the past there were greater levels of population structure in North than in South America, except for ancient Brazil, which harbors comparatively high degrees of structure. Moreover, we find a component of genetic ancestry in the ancient dataset that is closely related to that of present-day Oceanic populations but does not correspond to the previously reported Australasian signal. Lastly, we report an expansion of the Ancient Beringian ancestry, previously reported for only one sample. Discussion Overall, our findings support a complex scenario for the settlement of the Americas, accommodating the occurrence of founder effects and the emergence of ancestral mixing events at the regional level.
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Affiliation(s)
- Andre Luiz Campelo dos Santos
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, USA
- Department of Archaeology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, Georgia, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, USA
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