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Gopalakrishnan S, Ebenesersdóttir SS, Lundstrøm IKC, Turner-Walker G, Moore KHS, Luisi P, Margaryan A, Martin MD, Ellegaard MR, Magnússon ÓÞ, Sigurðsson Á, Snorradóttir S, Magnúsdóttir DN, Laffoon JE, van Dorp L, Liu X, Moltke I, Ávila-Arcos MC, Schraiber JG, Rasmussen S, Juan D, Gelabert P, de-Dios T, Fotakis AK, Iraeta-Orbegozo M, Vågene ÅJ, Denham SD, Christophersen A, Stenøien HK, Vieira FG, Liu S, Günther T, Kivisild T, Moseng OG, Skar B, Cheung C, Sandoval-Velasco M, Wales N, Schroeder H, Campos PF, Guðmundsdóttir VB, Sicheritz-Ponten T, Petersen B, Halgunset J, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Willerslev E, Balloux F, Marques-Bonet T, Lalueza-Fox C, Nielsen R, Stefánsson K, Helgason A, Gilbert MTP. The population genomic legacy of the second plague pandemic. Curr Biol 2022; 32:4743-4751.e6. [PMID: 36182700 DOI: 10.1016/j.cub.2022.09.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/15/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022]
Abstract
Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th-19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.
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Affiliation(s)
- Shyam Gopalakrishnan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark.
| | - S Sunna Ebenesersdóttir
- deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland
| | - Inge K C Lundstrøm
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Gordon Turner-Walker
- National Yunlin University of Science & Technology, 123 University Road, Section 3, 64002 Douliu, Yun-Lin County, Taiwan; Department of Archaeology and Anthropology, National Museum of Natural Science, 1 Guanqian Road, North District Taichung City 404023, Taiwan
| | | | - Pierre Luisi
- Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina; Microbial Paleogenomics Unit, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Ashot Margaryan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Michael D Martin
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Martin Rene Ellegaard
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | | | | | | | | | - Jason E Laffoon
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, Leiden, the Netherlands
| | - Lucy van Dorp
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano (LIIGH), Universidad Nacional Autónoma de México (UNAM), 3001 Boulevard Juriquilla, 76230 Querétaro, Mexico
| | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., San Diego, CA, USA
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Pere Gelabert
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Toni de-Dios
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Anna K Fotakis
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Miren Iraeta-Orbegozo
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Åshild J Vågene
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany; Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | | | - Axel Christophersen
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Hans K Stenøien
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Filipe G Vieira
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Shanlin Liu
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Torsten Günther
- Evolutionsbiologisk Centrum EBC, Norbyv. 18A, 752 36 Uppsala, Sweden
| | - Toomas Kivisild
- KU Leuven, Herestraat 49, 3000 Leuven, Belgium; Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Ole Georg Moseng
- Department of Business, History and Social Sciences, University of South-Eastern Norway, Notodden, Norway
| | - Birgitte Skar
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Christina Cheung
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; EA - Eco-anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
| | - Marcela Sandoval-Velasco
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Nathan Wales
- Department of Archaeology, Kings Manor and Principals House, University of York, Exhibition Square, York YO1 7EP, UK
| | - Hannes Schroeder
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Paula F Campos
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos, Portugal
| | - Valdís B Guðmundsdóttir
- deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland
| | - Thomas Sicheritz-Ponten
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology (AIMST), 08100 Bedong, Kedah, Malaysia
| | - Bent Petersen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology (AIMST), 08100 Bedong, Kedah, Malaysia
| | | | - Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, RCSI, Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, Dublin, Ireland
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, RCSI, Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, Dublin, Ireland
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark; The Globe Institute, Lundbeck Foundation Center for Geogenetics, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Eske Willerslev
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Francois Balloux
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Museu de Ciències Naturals de Barcelona, 08019 Barcelona, Spain
| | - Rasmus Nielsen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Department of Integrative Biology, University of California, Berkeley, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720-3140, USA
| | - Kári Stefánsson
- deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Agnar Helgason
- deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland
| | - M Thomas P Gilbert
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
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2
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Padró J, De Panis DN, Luisi P, Dopazo H, Szajnman S, Hasson E, Soto IM. Ortholog genes from cactophilic Drosophila provide insight into human adaptation to hallucinogenic cacti. Sci Rep 2022; 12:13180. [PMID: 35915153 PMCID: PMC9343604 DOI: 10.1038/s41598-022-17118-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
Cultural transformations of lifestyles and dietary practices have been key drivers of human evolution. However, while most of the evidence of genomic adaptations is related to the hunter-gatherer transition to agricultural societies, little is known on the influence of other major cultural manifestations. Shamanism is considered the oldest religion that predominated throughout most of human prehistory and still prevails in many indigenous populations. Several lines of evidence from ethno-archeological studies have demonstrated the continuity and importance of psychoactive plants in South American cultures. However, despite the well-known importance of secondary metabolites in human health, little is known about its role in the evolution of ethnic differences. Herein, we identified candidate genes of adaptation to hallucinogenic cactus in Native Andean populations with a long history of shamanic practices. We used genome-wide expression data from the cactophilic fly Drosophila buzzatii exposed to a hallucinogenic columnar cactus, also consumed by humans, to identify ortholog genes exhibiting adaptive footprints of alkaloid tolerance. Genomic analyses in human populations revealed a suite of ortholog genes evolving under recent positive selection in indigenous populations of the Central Andes. Our results provide evidence of selection in genetic variants related to alkaloids toxicity, xenobiotic metabolism, and neuronal plasticity in Aymara and Quechua populations, suggesting a possible process of gene-culture coevolution driven by religious practices.
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Affiliation(s)
- Julian Padró
- INIBIOMA-CONICET, Universidad Nacional del Comahue, Quintral 1250, R8400FRF, San Carlos de Bariloche, Argentina.
| | - Diego N De Panis
- IEGEBA-CONICET, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes 2160, C1428EHA, Buenos Aires, Argentina
| | - Pierre Luisi
- Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba (FFyH-UNC), Córdoba, Argentina.,Microbial Paleogenomics Unit, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Hernan Dopazo
- IEGEBA-CONICET, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes 2160, C1428EHA, Buenos Aires, Argentina
| | - Sergio Szajnman
- Departamento de Química Orgánica and UMYMFOR (CONICET-FCEyN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes 2160, C1428EHA, Buenos Aires, Argentina
| | - Esteban Hasson
- IEGEBA-CONICET, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes 2160, C1428EHA, Buenos Aires, Argentina
| | - Ignacio M Soto
- IEGEBA-CONICET, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes 2160, C1428EHA, Buenos Aires, Argentina
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3
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García A, Nores R, Motti JMB, Pauro M, Luisi P, Bravi CM, Fabra M, Gosling AL, Kardailsky O, Boocock J, Solé-Morata N, Matisoo-Smith EA, Comas D, Demarchi DA. Ancient and modern mitogenomes from Central Argentina: new insights into population continuity, temporal depth and migration in South America. Hum Mol Genet 2021; 30:1200-1217. [PMID: 33856032 DOI: 10.1093/hmg/ddab105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/15/2021] [Accepted: 03/31/2021] [Indexed: 12/22/2022] Open
Abstract
The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.
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Affiliation(s)
- Angelina García
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Rodrigo Nores
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Josefina M B Motti
- FACSO (NEIPHPA), Universidad Nacional del Centro de la Provincia de Buenos Aires, CONICET, Quequén 7631, Argentina
| | - Maia Pauro
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Pierre Luisi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET, CICPBA, Universidad Nacional de La Plata, La Plata 1906, Argentina
| | - Mariana Fabra
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Anna L Gosling
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - James Boocock
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Neus Solé-Morata
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Darío A Demarchi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
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4
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Ávila-Arcos MC, McManus KF, Sandoval K, Rodríguez-Rodríguez JE, Villa-Islas V, Martin AR, Luisi P, Peñaloza-Espinosa RI, Eng C, Huntsman S, Burchard EG, Gignoux CR, Bustamante CD, Moreno-Estrada A. Population History and Gene Divergence in Native Mexicans Inferred from 76 Human Exomes. Mol Biol Evol 2021; 37:994-1006. [PMID: 31848607 PMCID: PMC7086176 DOI: 10.1093/molbev/msz282] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico’s Indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here we have targeted the coding fraction of the genome and characterized its full site frequency spectrum by sequencing 76 exomes from five Indigenous populations across Mexico. Using diffusion approximations, we modeled the demographic history of Indigenous populations from Mexico with northern and southern ethnic groups splitting 7.2 KYA and subsequently diverging locally 6.5 and 5.7 KYA, respectively. Selection scans for positive selection revealed BCL2L13 and KBTBD8 genes as potential candidates for adaptive evolution in Rarámuris and Triquis, respectively. BCL2L13 is highly expressed in skeletal muscle and could be related to physical endurance, a well-known phenotype of the northern Mexico Rarámuri. The KBTBD8 gene has been associated with idiopathic short stature and we found it to be highly differentiated in Triqui, a southern Indigenous group from Oaxaca whose height is extremely low compared to other Native populations.
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Affiliation(s)
- María C Ávila-Arcos
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico.,Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Kimberly F McManus
- Department of Biology, Stanford University, Stanford, CA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO), UGA, CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | | | - Viridiana Villa-Islas
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico
| | - Alicia R Martin
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Pierre Luisi
- Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas, Consejo Nacional de Investigaciones Científicas y Técnicas, Córdoba, Argentina.,Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Rosenda I Peñaloza-Espinosa
- Division of Biological and Health Sciences, Department of Biological Systems, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - Celeste Eng
- Department Bioengineering & Therapeutic Sciences and Medicine, University of California San Francisco, San Francisco, CA
| | - Scott Huntsman
- Department Bioengineering & Therapeutic Sciences and Medicine, University of California San Francisco, San Francisco, CA
| | - Esteban G Burchard
- Department Bioengineering & Therapeutic Sciences and Medicine, University of California San Francisco, San Francisco, CA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), UGA, CINVESTAV, Irapuato, Guanajuato 36821, Mexico
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5
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Nakatsuka N, Luisi P, Motti JMB, Salemme M, Santiago F, D'Angelo Del Campo MD, Vecchi RJ, Espinosa-Parrilla Y, Prieto A, Adamski N, Lawson AM, Harper TK, Culleton BJ, Kennett DJ, Lalueza-Fox C, Mallick S, Rohland N, Guichón RA, Cabana GS, Nores R, Reich D. Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography. Nat Commun 2020; 11:3868. [PMID: 32747648 PMCID: PMC7400565 DOI: 10.1038/s41467-020-17656-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/10/2020] [Indexed: 01/30/2023] Open
Abstract
Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700-2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200-1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast.
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Affiliation(s)
- Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA, 02115, USA.
| | - Pierre Luisi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, 5000, Córdoba, Argentina.
| | - Josefina M B Motti
- NEIPHPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, 7631, Quequén, Argentina
| | - Mónica Salemme
- Centro Austral de Investigaciones Científicas (CADIC-CONICET), 9410, Ushuaia, Tierra del Fuego, Argentina
- Instituto de Cultura, Sociedad y Estado (ICSE), Universidad Nacional de Tierra del Fuego, 9410, Ushuaia, Tierra del Fuego, Argentina
| | - Fernando Santiago
- Centro Austral de Investigaciones Científicas (CADIC-CONICET), 9410, Ushuaia, Tierra del Fuego, Argentina
| | - Manuel D D'Angelo Del Campo
- NEIPHPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, 7631, Quequén, Argentina
- Laboratorio de Poblaciones del Pasado (LAPP), Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid (UAM), E-28049, Madrid, Spain
| | - Rodrigo J Vecchi
- CONICET-Departamento de Humanidades, Universidad Nacional del Sur, 8000, Bahía Blanca, Argentina
| | - Yolanda Espinosa-Parrilla
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain
- School of Medicine and Laboratory of Molecular Medicine-LMM, Center for Education, Healthcare and Investigation-CADI, Universidad de Magallanes, Punta Arenas, Chile
| | - Alfredo Prieto
- Universidad de Magallanes, Avenida Bulnes 01855, Punta Arenas, Chile
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02446, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02446, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Brendan J Culleton
- Institutes for Energy and the Environment, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02446, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ricardo A Guichón
- NEIPHPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, 7631, Quequén, Argentina
| | - Graciela S Cabana
- Molecular Anthropology Laboratories, Department of Anthropology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Rodrigo Nores
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, 5000, Córdoba, Argentina.
- Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, 5000, Córdoba, Argentina.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02446, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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6
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Luisi P, García A, Berros JM, Motti JMB, Demarchi DA, Alfaro E, Aquilano E, Argüelles C, Avena S, Bailliet G, Beltramo J, Bravi CM, Cuello M, Dejean C, Dipierri JE, Jurado Medina LS, Lanata JL, Muzzio M, Parolin ML, Pauro M, Paz Sepúlveda PB, Rodríguez Golpe D, Santos MR, Schwab M, Silvero N, Zubrzycki J, Ramallo V, Dopazo H. Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina. PLoS One 2020; 15:e0233808. [PMID: 32673320 PMCID: PMC7365470 DOI: 10.1371/journal.pone.0233808] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/12/2020] [Indexed: 12/24/2022] Open
Abstract
Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries.
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Affiliation(s)
- Pierre Luisi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Angelina García
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Museo de Antropología, Córdoba, Argentina
| | - Juan Manuel Berros
- Consejo Nacional de Investigaciones Científicas y Técnicas - Laboratorio de Análisis de Datos, Biocódices S.A., Buenos Aires, Argentina
| | - Josefina M B Motti
- Núcleo de Estudios Interdisciplinarios de Poblaciones Humanas de Patagonia Austral (NEIPHA), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional del Centro de la Provincia de Buenos Aires, Quequén, Argentina
| | - Darío A Demarchi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Museo de Antropología, Córdoba, Argentina
| | - Emma Alfaro
- Instituto de Ecorregiones Andinas (INECOA), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Jujuy, Jujuy, Argentina.,Instituto de Biología de la Altura, Universidad Nacional de Jujuy, Jujuy, Argentina
| | - Eliana Aquilano
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Carina Argüelles
- Departamento de Genética, Grupo de Investigación en Genética Aplicada (GIGA), Facultad de Ciencias Exactas, Químicas y Naturales, Instituto de Biología Subtropical (IBS)-Nodo Posadas, Universidad Nacional de Misiones (UNaM)-Consejo Nacional de Investigaciones Científicas y Técnicas, Posadas, Argentina.,Cátedra de Biología Molecular, Carrera de Medicina, Facultad de Ciencias de la Salud, Universidad Católica de las Misiones (UCAMI), Posadas, Argentina
| | - Sergio Avena
- Instituto de Ciencias Antropológicas (ICA), Facultad de Filosofía y Letras, Universidad de Buenos Aires, Buenos Aires, Argentina.,Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | - Graciela Bailliet
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Julieta Beltramo
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina.,Laboratorio de Análisis Comparativo de ADN, Corte Suprema de Justicia de la Provincia de Buenos Aires, La Plata, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Mariela Cuello
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Cristina Dejean
- Instituto de Ciencias Antropológicas (ICA), Facultad de Filosofía y Letras, Universidad de Buenos Aires, Buenos Aires, Argentina.,Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | | | - Laura S Jurado Medina
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - José Luis Lanata
- Instituto de Investigaciones en Diversidad Cultural y Procesos de Cambio (IIDyPCa), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Río Negro, San Carlos de Bariloche, Argentina
| | - Marina Muzzio
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - María Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Consejo Nacional de Investigaciones Científicas y Técnicas - Centro Nacional Patagónico, Puerto Madryn, Argentina
| | - Maia Pauro
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Museo de Antropología, Córdoba, Argentina
| | - Paula B Paz Sepúlveda
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Daniela Rodríguez Golpe
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - María Rita Santos
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Marisol Schwab
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | - Natalia Silvero
- Instituto Multidisciplinario de Biología Celular (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas - Comisión de Investigaciones Científicas - Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH) - Consejo Nacional de Investigaciones Científicas y Técnicas-Centro Nacional Patagónico, Puerto Madryn, Argentina
| | - Hernán Dopazo
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas - Biocodices S.A., Buenos Aires, Argentina
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7
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de Valles-Ibáñez G, Hernandez-Rodriguez J, Prado-Martinez J, Luisi P, Marquès-Bonet T, Casals F. Genetic Load of Loss-of-Function Polymorphic Variants in Great Apes. Genome Biol Evol 2016; 8:871-7. [PMID: 26912403 PMCID: PMC4824148 DOI: 10.1093/gbe/evw040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Loss of function (LoF) genetic variants are predicted to disrupt gene function, and are therefore expected to substantially reduce individual's viability. Knowing the genetic burden of LoF variants in endangered species is of interest for a better understanding of the effects of declining population sizes on species viability. In this study, we have estimated the number of LoF polymorphic variants in six great ape populations, based on whole-genome sequencing data in 79 individuals. Our results show that although the number of functional variants per individual is conditioned by the effective population size, the number of variants with a drastic phenotypic effect is very similar across species. We hypothesize that for those variants with high selection coefficients, differences in effective population size are not important enough to affect the efficiency of natural selection to remove them. We also describe that mostly CpG LoF mutations are shared across species, and an accumulation of LoF variants at olfactory receptor genes in agreement with its pseudogenization in humans and other primate species.
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Affiliation(s)
- Guillem de Valles-Ibáñez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Javier Prado-Martinez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain Present address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Pierre Luisi
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain Centre Nacional d'Análisi Genómica (CNAG), Parc Científic de Barcelona, Barcelona, Catalonia, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
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8
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Patillon B, Luisi P, Poloni ES, Boukouvala S, Darlu P, Genin E, Sabbagh A. A homogenizing process of selection has maintained an "ultra-slow" acetylation NAT2 variant in humans. Hum Biol 2015; 86:185-214. [PMID: 25836746 DOI: 10.13110/humanbiology.86.3.0185] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
N-Acetyltransferase 2 (NAT2) is an important enzyme involved in the metabolism of a wide spectrum of naturally occurring xenobiotics, including therapeutic drugs and common environmental carcinogens. Extensive polymorphism in NAT2 gives rise to a wide interindividual variation in acetylation capacity, which influences individual susceptibility to various drug-induced adverse reactions and cancers. Striking patterns of geographic differentiation have been described for the main slow acetylation variants of the NAT2 gene, suggesting the action of natural selection at this locus. In the present study, we took advantage of whole-genome sequence data available from the 1000 Genomes project to investigate the global patterns of population genetic differentiation at NAT2 and determine whether they are atypical compared with the remaining variation of the genome. The nonsynonymous substitution c.590G>A (rs1799930) defining the slow NAT2*6 haplotype cluster exhibited an unusually low FST value compared with the genome average (FST = 0.006, P = 0.016). It was indicated as the most likely target of a homogenizing process of selection promoting the same allelic variant in globally distributed populations. The rs1799930 A allele has been associated with the slowest acetylation capacity in vivo, and its substantial correlation with the subsistence strategy adopted by past human populations suggests that it may have conferred a selective advantage in populations shifting from foraging to agricultural and pastoral activities in the Neolithic period. Results of neutrality tests further supported an adaptive evolution of the NAT2 gene through either balancing selection or directional selection acting on multiple standing slow acetylation variants.
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Affiliation(s)
- B Patillon
- 1 IRD UMR216, Mère et enfant face aux infections tropicales, Paris, France
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9
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Pybus M, Luisi P, Dall'Olio GM, Uzkudun M, Laayouni H, Bertranpetit J, Engelken J. Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations. Bioinformatics 2015; 31:3946-52. [PMID: 26315912 DOI: 10.1093/bioinformatics/btv493] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/17/2015] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION Detecting positive selection in genomic regions is a recurrent topic in natural population genetic studies. However, there is little consistency among the regions detected in several genome-wide scans using different tests and/or populations. Furthermore, few methods address the challenge of classifying selective events according to specific features such as age, intensity or state (completeness). RESULTS We have developed a machine-learning classification framework that exploits the combined ability of some selection tests to uncover different polymorphism features expected under the hard sweep model, while controlling for population-specific demography. As a result, we achieve high sensitivity toward hard selective sweeps while adding insights about their completeness (whether a selected variant is fixed or not) and age of onset. Our method also determines the relevance of the individual methods implemented so far to detect positive selection under specific selective scenarios. We calibrated and applied the method to three reference human populations from The 1000 Genome Project to generate a genome-wide classification map of hard selective sweeps. This study improves detection of selective sweep by overcoming the classical selection versus no-selection classification strategy, and offers an explanation to the lack of consistency observed among selection tests when applied to real data. Very few signals were observed in the African population studied, while our method presents higher sensitivity in this population demography. AVAILABILITY AND IMPLEMENTATION The genome-wide results for three human populations from The 1000 Genomes Project and an R-package implementing the 'Hierarchical Boosting' framework are available at http://hsb.upf.edu/.
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Affiliation(s)
- Marc Pybus
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Pierre Luisi
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Giovanni Marco Dall'Olio
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain, Division of Cancer Studies, King's College of London, London SE1 1UL, UK and
| | - Manu Uzkudun
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain, Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra 8193, Spain
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Johannes Engelken
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain
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10
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Dobon B, Hassan HY, Laayouni H, Luisi P, Ricaño-Ponce I, Zhernakova A, Wijmenga C, Tahir H, Comas D, Netea MG, Bertranpetit J. The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape. Sci Rep 2015; 5:9996. [PMID: 26017457 PMCID: PMC4446898 DOI: 10.1038/srep09996] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/24/2015] [Indexed: 01/20/2023] Open
Abstract
East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic groups belonging to three African linguistic families: Niger-Kordofanian, Nilo-Saharan and Afro-Asiatic. A total of 500 individuals were genotyped for 200,000 single-nucleotide polymorphisms. Principal component analysis, clustering analysis using ADMIXTURE, FST statistics, and the three-population test were used to investigate the underlying genetic structure and ancestry of the different ethno-linguistic groups. Our analyses revealed a genetic component for Sudanese Nilo-Saharan speaking groups (Darfurians and part of Nuba populations) related to Nilotes of South Sudan, but not to other Sudanese populations or other sub-Saharan populations. Populations inhabiting the North of the region showed close genetic affinities with North Africa, with a component that could be remnant of North Africans before the migrations of Arabs from Arabia. In addition, we found very low genetic distances between populations in genes important for anti-malarial and anti-bacterial host defence, suggesting similar selective pressures on these genes and stressing the importance of considering functional pathways to understand the evolutionary history of populations.
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Affiliation(s)
- Begoña Dobon
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Hisham Y Hassan
- 1] College of Medical Laboratory Sciences, University of Science and Technology, Omdurman, Sudan [2] Banoon ART and Cytogenetics Centre, Bahrain Defence Force Hospital, Manama, Kingdom of Bahrain
| | - Hafid Laayouni
- 1] Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain [2] Departament de Genètica i de Microbiologia, Grup de Biologia Evolutiva (GBE), Universitat Autonòma de Barcelona, Bellaterra (Barcelona), Spain
| | - Pierre Luisi
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Isis Ricaño-Ponce
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Hanan Tahir
- Sudan Medical and Scientific Research Institute, University of Medical Sciences and Technology, Khartoum, Sudan
| | - David Comas
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Mihai G Netea
- 1] Department of Internal Medicine and [2] Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
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11
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Luisi P, Alvarez-Ponce D, Pybus M, Fares MA, Bertranpetit J, Laayouni H. Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome. Genome Biol Evol 2015; 7:1141-54. [PMID: 25840415 PMCID: PMC4419801 DOI: 10.1093/gbe/evv055] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genes vary in their likelihood to undergo adaptive evolution. The genomic factors that determine adaptability, however, remain poorly understood. Genes function in the context of molecular networks, with some occupying more important positions than others and thus being likely to be under stronger selective pressures. However, how positive selection distributes across the different parts of molecular networks is still not fully understood. Here, we inferred positive selection using comparative genomics and population genetics approaches through the comparison of 10 mammalian and 270 human genomes, respectively. In agreement with previous results, we found that genes with lower network centralities are more likely to evolve under positive selection (as inferred from divergence data). Surprisingly, polymorphism data yield results in the opposite direction than divergence data: Genes with higher centralities are more likely to have been targeted by recent positive selection during recent human evolution. Our results indicate that the relationship between centrality and the impact of adaptive evolution highly depends on the mode of positive selection and/or the evolutionary time-scale.
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Affiliation(s)
- Pierre Luisi
- Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - David Alvarez-Ponce
- Integrative Systems Biology Group, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politécnica de Valencia (UPV), Spain Biology Department, University of Nevada, Reno Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Marc Pybus
- Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Mario A Fares
- Integrative Systems Biology Group, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politécnica de Valencia (UPV), Spain Smurfit Institute of Genetics, University of Dublin, Trinity College, Ireland
| | - Jaume Bertranpetit
- Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain Departament de Genètica i de Microbiologia, Grup de Biologia Evolutiva (GBE), Universitat Autonòma de Barcelona, Bellaterra, Spain
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12
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Gineau L, Luisi P, Castelli EC, Milet J, Courtin D, Cagnin N, Patillon B, Laayouni H, Moreau P, Donadi EA, Garcia A, Sabbagh A. Balancing immunity and tolerance: genetic footprint of natural selection in the transcriptional regulatory region of HLA-G. Genes Immun 2014; 16:57-70. [DOI: 10.1038/gene.2014.63] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 10/04/2014] [Accepted: 10/06/2014] [Indexed: 12/28/2022]
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Juyal G, Mondal M, Luisi P, Laayouni H, Sood A, Midha V, Heutink P, Bertranpetit J, Thelma BK, Casals F. Population and genomic lessons from genetic analysis of two Indian populations. Hum Genet 2014; 133:1273-87. [PMID: 24980708 DOI: 10.1007/s00439-014-1462-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/05/2014] [Indexed: 12/25/2022]
Abstract
Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.
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Affiliation(s)
- Garima Juyal
- Department of Genetics, University of Delhi South Campus, New Delhi, 110 021, India
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Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biol 2014; 15:R88. [PMID: 24980144 PMCID: PMC4197830 DOI: 10.1186/gb-2014-15-6-r88] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 06/30/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. RESULTS We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively. CONCLUSIONS We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.
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Pybus M, Dall'Olio GM, Luisi P, Uzkudun M, Carreño-Torres A, Pavlidis P, Laayouni H, Bertranpetit J, Engelken J. 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans. Nucleic Acids Res 2013; 42:D903-9. [PMID: 24275494 PMCID: PMC3965045 DOI: 10.1093/nar/gkt1188] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Searching for Darwinian selection in natural populations has been the focus of a multitude of studies over the last decades. Here we present the 1000 Genomes Selection Browser 1.0 (http://hsb.upf.edu) as a resource for signatures of recent natural selection in modern humans. We have implemented and applied a large number of neutrality tests as well as summary statistics informative for the action of selection such as Tajima’s D, CLR, Fay and Wu’s H, Fu and Li’s F* and D*, XPEHH, ΔiHH, iHS, FST, ΔDAF and XPCLR among others to low coverage sequencing data from the 1000 genomes project (Phase 1; release April 2012). We have implemented a publicly available genome-wide browser to communicate the results from three different populations of West African, Northern European and East Asian ancestry (YRI, CEU, CHB). Information is provided in UCSC-style format to facilitate the integration with the rich UCSC browser tracks and an access page is provided with instructions and for convenient visualization. We believe that this expandable resource will facilitate the interpretation of signals of selection on different temporal, geographical and genomic scales.
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Affiliation(s)
- Marc Pybus
- Program for Population Genetics, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain, Population Genomics Node, National Institute for Bioinformatics (INB), Universitat Pompeu Fabra, 08003 Barcelona, Spain, Institute of Molecular Biology and Biotechnology-FORTH, Heraklion, Crete GR 700 13, Greece and Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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Patillon B, Luisi P, Blanché H, Patin E, Cann HM, Génin E, Sabbagh A. Positive selection in the chromosome 16 VKORC1 genomic region has contributed to the variability of anticoagulant response in humans. PLoS One 2012; 7:e53049. [PMID: 23285254 PMCID: PMC3532425 DOI: 10.1371/journal.pone.0053049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 11/23/2012] [Indexed: 12/23/2022] Open
Abstract
VKORC1 (vitamin K epoxide reductase complex subunit 1, 16p11.2) is the main genetic determinant of human response to oral anticoagulants of antivitamin K type (AVK). This gene was recently suggested to be a putative target of positive selection in East Asian populations. In this study, we genotyped the HGDP-CEPH Panel for six VKORC1 SNPs and downloaded chromosome 16 genotypes from the HGDP-CEPH database in order to characterize the geographic distribution of footprints of positive selection within and around this locus. A unique VKORC1 haplotype carrying the promoter mutation associated with AVK sensitivity showed especially high frequencies in all the 17 HGDP-CEPH East Asian population samples. VKORC1 and 24 neighboring genes were found to lie in a 505 kb region of strong linkage disequilibrium in these populations. Patterns of allele frequency differentiation and haplotype structure suggest that this genomic region has been submitted to a near complete selective sweep in all East Asian populations and only in this geographic area. The most extreme scores of the different selection tests are found within a smaller 45 kb region that contains VKORC1 and three other genes (BCKDK, MYST1 (KAT8), and PRSS8) with different functions. Because of the strong linkage disequilibrium, it is not possible to determine if VKORC1 or one of the three other genes is the target of this strong positive selection that could explain present-day differences among human populations in AVK dose requirement. Our results show that the extended region surrounding a presumable single target of positive selection should be analyzed for genetic variation in a wide range of genetically diverse populations in order to account for other neighboring and confounding selective events and the hitchhiking effect.
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Affiliation(s)
- Blandine Patillon
- Inserm UMRS-946, Genetic Variability and Human Diseases, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France.
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Dall'Olio GM, Laayouni H, Luisi P, Sikora M, Montanucci L, Bertranpetit J. Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation. BMC Evol Biol 2012; 12:98. [PMID: 22731960 PMCID: PMC3426484 DOI: 10.1186/1471-2148-12-98] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Accepted: 06/25/2012] [Indexed: 01/11/2023] Open
Abstract
Background Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Results Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. Conclusions These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.
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Affiliation(s)
- Giovanni Marco Dall'Olio
- IBE, Institut de Biologia Evolutiva (UPF-CSIC), Parc de Recerca Biomèdica de Barcelona (PRBB), Dr, Aiguader, 88, 08003, Barcelona, Catalonia, Spain
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Luisi P, Alvarez-Ponce D, Dall'Olio GM, Sikora M, Bertranpetit J, Laayouni H. Network-Level and Population Genetics Analysis of the Insulin/TOR Signal Transduction Pathway Across Human Populations. Mol Biol Evol 2011; 29:1379-92. [DOI: 10.1093/molbev/msr298] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Littger R, Alke A, Tewes B, Gropp F, Asai T, Watanabe K, Kuromi K, Kurohane K, Ogino K, Taki T, Tsukada H, Nakayama J, Oku N, Babai I, Matyas G, Baranji L, Milosevits J, Alving CR, Bendas G, Rothe U, Scherphof GL, Kamps JAAM, Kessner S, Rothe U, Bendas G, Carafa M, Di Stefano A, Sozio P, Cacciatore I, Mosciatti B, Santucci E, Choice E, Harvie P, Galbraith T, Zunder E, Dutzar B, Anklesaria P, Paul R, Cocquyt J, De Cuyper M, Van der Meeren P, Cruz MEM, Gaspar MM, Silva MT, Dathe M, Nikolenko H, Wessolowski A, Schmieder P, Beyermann M, Bienert M, Santos ND, Cox KA, Allen C, Gallagher RC, Ickenstein L, Mayer LD, Bally MB, Fischer S, Margalit R, Freisleben HJ, Garidel P, Chen HC, Moore D, Mendelsohn R, Garidel P, Keller M, Hildebrand A, Blume A, Girão da Cruz MT, Simões S, Pedroso de Lima MC, Graser A, Nahde T, Fahr A, Müller R, Müller-Brüsselbach S, Harvie P, Dutzar B, Choice E, Cudmore S, O'Mahony D, Anklesaria P, Paul R, Hoving S, van Tiel ST, Seynhaeve ALB, Ambagtsheer G, Eggermont AMM, ten Hagen TLM, Høyrup P, Jensen SS, Jørgensen K, Iden D, Kuang H, Mullen P, Jacobs C, Roben P, Stevens T, Lollo C, Ishida T, Maeda R, Masuda K, Ichihara M, Kiwada H, Jung K, Reszka R, Kaiser N, Ohloff I, Linser-Haar S, Massing U, Schubert R, Kan P, Tsao CW, Chen WK, Wang AJ, Kimpfler A, Gerber C, Wieschollek A, Bruchelt G, Schubert R, Kobayashi T, Okada Y, Ishida T, Sone S, Harashima H, Maruyama K, Kiwada H, Kondo M, Lee CM, Tanaka T, Su W, Kitagawa T, Ito T, Matsuda H, Murai T, Miyasaka M, Junji K, Kondo M, Asai T, Ogino K, Taki T, Tsukada H, Baba K, Oku N, Koning GA, Wauben MHM, ten Hagen TLM, Vestweber D, Everts M, Kok RJ, Schraa AJ, Molema G, Schiffelers RM, Storm G, Kristl J, Šentjurc M, Abramović Z, Landry S, Perron S, Bestman-Smith J, Désormeaux A, Tremblay MJ, Bergeron MG, Madeira C, Loura LMS, Fedorov A, Prieto M, Aires-Barros MR, Marques CM, Simões SI, Cruz ME, Cevc G, Martins MB, Moreira JN, Gaspar R, Allen TM, Esposito C, Ortaggi G, Bianco A, Bonadies F, Malizia D, Napolitano R, Cametti C, Mossa G, Endert G, Essler F, Lutz S, Panzner S, Pastorino F, Brignole C, Pagnan G, Moase EH, Allen TM, Ponzoni M, Pavelic Z, Škalko-Basnet N, Jalšenjak I, Penacho N, Simões S, Pedroso de Lima MC, Pisano C, Bucci F, Serafini S, Martinelli R, Cupelli A, Marconi A, Ferrara FF, Santaniello M, Critelli L, Tinti O, Luisi P, Carminati P, Santaniello M, Bucci F, Tinti O, Pisano C, Critelli L, Galletti B, Luisi P, Carminati P, Sauer I, Nikolenko H, Dathe M, Schleef M, Voß C, Schmidt T, Flaschel E, König S, Wenger T, Dumond J, Bogetto N, Reboud-Ravaux M, Schramm HJ, Schramm W, Sheynis T, Rozner S, Kolusheva S, Satchell D, Jelnik R, Shigeta Y, Imanaka H, Ando H, Makino T, Kurohane K, Oku N, Baba N, Shimizu K, Asai T, Takada M, Baba K, Namba Y, Oku N, Simberg D, Danino D, Talmon Y, Minsky A, Ferrari ME, Wheeler CJ, Barenholz Y, Takada M, Shimizu K, Kuromi K, Asai T, Baba K, Oku N, Takeuchi Y, Kurohane K, North JR, Namba Y, Nango M, Oku N, Tewes B, Köchling T, Deissler M, Kühl C, Marx U, Strote G, Gropp F, Qualls MM, Kim JM, Thompson DH, Zhang ZY, Shum P, Collier JH, Hu BH, Ruberti JW, Messersmith PB, Thompson DH, Tsuruda T, Nakade A, Sadzuka Y, Hirota S, Sonobe T, Vorauer-Uhl K, Wagner A, Katinger H, Wagner A, Vorauer-Uhl K, Katinger H, Weeke-Klimp AH, Bartsch M, Meijer DKF, Scherphof GL, Kamps JAAM, Zeisig R, Walther W, Reß A, Fichtner I, Zschörnig O, Schiller J, Süß M, Bergmeier C, Arnold K, Nchinda G, Überla K, Zschörnig O. Poster Abstracts. J Liposome Res 2003. [DOI: 10.1081/lpr-120017490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
The entrapment efficiency of three main methods used in the literature for the encapsulation of nucleic acids in liposomes were studied using 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) liposomes. In particular the reverse phase method, the dehydration/rehydration method, and the freeze/thawing method were compared to each other under standardised conditions, i.e. using in every case the same concentration of guest molecules (DNA, tRNA and ATP as low molecular weight analogue) and equally extruded liposomes. The percentage of entrapment strictly referred to the material localized inside the liposomes, i.e. particular care was devoted to ruling out the contribution of the nucleic acid material bound to the outer surface of the liposomes: this was eliminated by extensive enzymatic digestion prior to column chromatography. Depending on the conditions used, the percentage of the entrapped material varied between 10 and 54% of the initial amount. Further, the encapsulation efficiency was markedly affected by the salt concentration, by the size of liposomes, but to a lower degree by the molecular weight of the guest molecules. In general, we observed that the freeze/thawing encapsulation procedure was the most efficient one. In a second part of the work the freeze/thawing method was applied to encapsulate DNA (369 bp and 3368 bp, respectively) using liposomes obtained from POPC mixed with 1-10% charged cosurfactant, i.e. phosphatidylserine (PS) or didodecyldimethylammonium bromide (DDAB), respectively. Whereas PS had no significant effect, the entrapment efficiency went up to 60% in POPC/DDAB (97.5:2.5) liposomes. The large entrapment efficiency of DNA permits spectroscopic investigations of the DNA encapsulated in the water pool of the liposomes. UV absorption and circular dichroism spectra were practically the same as in water, indicating no appreciable perturbation of the electronic transitions or of the conformation of the entrapped biopolymer. This was in contrast to the DNA bound externally to the POPC/DDAB liposomes which showed significant spectral changes with respect to DNA dissolved in water.
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Affiliation(s)
- P A Monnard
- ETH-Zentrum, Institut für Polymere, Zürich, Switzerland
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Rizzo V, Luisi P, Straub B, Guarnaccia R. Co-oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. VI. Circular dichroism studies of Co-oligopeptides of l-phenylalanine, L-tryptophan, and glycine. Biopolymers 1977; 16:449-60. [PMID: 12843 DOI: 10.1002/bip.1977.360160217] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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