1
|
Uricoechea Patiño D, Collins A, García OJR, Santos Vecino G, Cuenca JVR, Bernal JE, Benavides Benítez E, Vergara Muñoz S, Briceño Balcázar I. High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia. Genes (Basel) 2023; 14:1853. [PMID: 37895202 PMCID: PMC10606881 DOI: 10.3390/genes14101853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/30/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia.
Collapse
Affiliation(s)
- Daniel Uricoechea Patiño
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
| | - Andrew Collins
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | | | - Gustavo Santos Vecino
- Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia;
| | | | - Jaime E. Bernal
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Escilda Benavides Benítez
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Saray Vergara Muñoz
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Ignacio Briceño Balcázar
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
| |
Collapse
|
2
|
Pereson MJ, Sanabria DJ, Torres C, Liotta DJ, Campos RH, Schurr TG, Di Lello FA, Badano I. Evolutionary analysis of JC polyomavirus in Misiones' population yields insight into the population dynamics of the early human dispersal in the Americas. Virology 2023; 585:100-108. [PMID: 37327595 DOI: 10.1016/j.virol.2023.05.009] [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: 03/14/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND JC polyomavirus (JCV) has an ethno-geographical distribution across human populations. OBJECTIVE Study the origins of the population of Misiones (Argentina) by using JCV as genetic marker. METHODS Viral detection and characterization was conducted by PCR amplification and evolutionary analysis of the intergenic region sequences. RESULTS 22 out of 121 samples were positive for JCV, including 5 viral lineages: MY (n = 8), Eu-a (n = 7), B1-c (n = 4), B1-b (n = 2) and Af2 (n = 1). MY sequences clustered within a branch of Native American origin that diverged from its Asian counterpart about 21,914 years ago (HPD 95% interval 15,383-30,177), followed by a sustained demographic expansion around 5000 years ago. CONCLUSIONS JCV in Misiones reflects the multiethnic origin of the current population, with an important Amerindian contribution. Analysis of the MY viral lineage shows a pattern consistent with the arrival of early human migrations to the Americas and a population expansion by the pre-Columbian native societies.
Collapse
Affiliation(s)
- Matias J Pereson
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Daiana J Sanabria
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina
| | - Carolina Torres
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Domingo J Liotta
- Instituto Nacional de Medicina Tropical-ANLIS ''Dr. Malbrán'', Neuquén y Jujuy S/n, N3370, Puerto Iguazú, Misiones, Argentina
| | - Rodolfo H Campos
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania. Philadelphia, PA 19104-6398, USA
| | - Federico A Di Lello
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Inés Badano
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina; Universidad Nacional de Misiones. Red de Laboratorios. Laboratorio de Antropología Biológica y Bioinformática Aplicada (LABBA). Misiones, Argentina.
| |
Collapse
|
3
|
Villa-Islas V, Izarraras-Gomez A, Larena M, Campos EMP, Sandoval-Velasco M, Rodríguez-Rodríguez JE, Bravo-Lopez M, Moguel B, Fregel R, Garfias-Morales E, Medina Tretmanis J, Velázquez-Ramírez DA, Herrera-Muñóz A, Sandoval K, Nieves-Colón MA, Zepeda García Moreno G, Villanea FA, Medina EFV, Aguayo-Haro R, Valdiosera C, Ioannidis AG, Moreno-Estrada A, Jay F, Huerta-Sanchez E, Moreno-Mayar JV, Sánchez-Quinto F, Ávila-Arcos MC. Demographic history and genetic structure in pre-Hispanic Central Mexico. Science 2023; 380:eadd6142. [PMID: 37167382 DOI: 10.1126/science.add6142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by Aridoamerican peoples. In this study, we present shotgun genome-wide data from 12 individuals and 27 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity that spans the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the past 2300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from two ancient unsampled "ghost" populations.
Collapse
Affiliation(s)
- Viridiana Villa-Islas
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Alan Izarraras-Gomez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Maximilian Larena
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Cuidad de México, Mexico
| | | | - Miriam Bravo-Lopez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Barbara Moguel
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
- Centro de Geociencias, UNAM Juriquilla, Juriquilla, Querétaro, México
| | - Rosa Fregel
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Ernesto Garfias-Morales
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | | | | | | | - Karla Sandoval
- Equity and Gender Office of the Centre for Research and Advanced Studies (CODIGO-C), CINVESTAV, Mexico City, Mexico
| | - Maria A Nieves-Colón
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | | | - Fernando A Villanea
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
| | | | | | - Cristina Valdiosera
- Departamento de Historia, Geografía y Comunicaciones, Universidad de Burgos, Burgos, Spain
- Department of History and Archaeology, La Trobe University, Melbourne, Australia
| | - Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Andrés Moreno-Estrada
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Flora Jay
- Laboratoire Interdisciplinaire des Sciences du Numérique, Université Paris-Saclay, CNRS, INRIA, 91400 Orsay, France
| | | | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| |
Collapse
|
4
|
Garcia OA, Arslanian K, Whorf D, Thariath S, Shriver M, Li JZ, Bigham AW. The Legacy of Infectious Disease Exposure on the Genomic Diversity of Indigenous Southern Mexicans. Genome Biol Evol 2023; 15:7023365. [PMID: 36726304 PMCID: PMC10016042 DOI: 10.1093/gbe/evad015] [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: 04/15/2022] [Revised: 12/19/2022] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
To characterize host risk factors for infectious disease in Mesoamerican populations, we interrogated 857,481 SNPs assayed using the Affymetrix 6.0 genotyping array for signatures of natural selection in immune response genes. We applied three statistical tests to identify signatures of natural selection: locus-specific branch length (LSBL), the cross-population extended haplotype homozygosity (XP-EHH), and the integrated haplotype score (iHS). Each of the haplotype tests (XP-EHH and iHS) were paired with LSBL and significance was determined at the 1% level. For the paired analyses, we identified 95 statistically significant windows for XP-EHH/LSBL and 63 statistically significant windows for iHS/LSBL. Among our top immune response loci, we found evidence of recent directional selection associated with the major histocompatibility complex (MHC) and the peroxisome proliferator-activated receptor gamma (PPAR-γ) signaling pathway. These findings illustrate that Mesoamerican populations' immunity has been shaped by exposure to infectious disease. As targets of selection, these variants are likely to encode phenotypes that manifest themselves physiologically and therefore may contribute to population-level variation in immune response. Our results shed light on past selective events influencing the host response to modern diseases, both pathogenic infection as well as autoimmune disorders.
Collapse
Affiliation(s)
- Obed A Garcia
- Department of Anthropology, University of Michigan, Ann Arbor, Michigan.,Department of Biomedical Data Science, Stanford University, Stanford, California
| | | | - Daniel Whorf
- College of Medicine, University of Illinois, Peoria, Illinois
| | - Serena Thariath
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee
| | - Mark Shriver
- Department of Anthropology, Penn State University, State College, Pennsylvania
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Abigail W Bigham
- Department of Anthropology, University of California, Los Angeles, California
| |
Collapse
|
5
|
De Oliveira TC, Secolin R, Lopes-Cendes I. A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations. Front Genet 2023; 14:1091269. [PMID: 36741309 PMCID: PMC9893294 DOI: 10.3389/fgene.2023.1091269] [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: 11/06/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.
Collapse
Affiliation(s)
- Thais C. De Oliveira
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Rodrigo Secolin
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil,*Correspondence: Iscia Lopes-Cendes,
| |
Collapse
|
6
|
García-Ortiz H, Barajas-Olmos F, Contreras-Cubas C, Reynolds AW, Flores-Huacuja M, Snow M, Ramos-Madrigal J, Mendoza-Caamal E, Baca P, López-Escobar TA, Bolnick DA, Flores-Martínez SE, Ortiz-Lopez R, Kostic AD, Villafan-Bernal JR, Galaviz-Hernández C, Centeno-Cruz F, García-Zapién AG, Monge-Cázares T, Lazalde-Ramos BP, Loeza-Becerra F, Abrahantes-Pérez MDC, Rangel-Villalobos H, Sosa-Macías M, Rojas-Martínez A, Martínez-Hernández A, Orozco L. Unraveling Signatures of Local Adaptation among Indigenous Groups from Mexico. Genes (Basel) 2022; 13:genes13122251. [PMID: 36553518 PMCID: PMC9778281 DOI: 10.3390/genes13122251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/05/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Few studies have addressed how selective pressures have shaped the genetic structure of the current Native American populations, and they have mostly limited their inferences to admixed Latin American populations. Here, we searched for local adaptation signals, based on integrated haplotype scores and population branch statistics, in 325 Mexican Indigenous individuals with at least 99% Native American ancestry from five previously defined geographical regions. Although each region exhibited its own local adaptation profile, only PPARG and AJAP1, both negative regulators of the Wnt/β catenin signaling pathway, showed significant adaptation signals in all the tested regions. Several signals were found, mainly in the genes related to the metabolic processes and immune response. A pathway enrichment analysis revealed the overrepresentation of selected genes related to several biological phenotypes/conditions, such as the immune response and metabolic pathways, in agreement with previous studies, suggesting that immunological and metabolic pressures are major drivers of human adaptation. Genes related to the gut microbiome measurements were overrepresented in all the regions, highlighting the importance of studying how humans have coevolved with the microbial communities that colonize them. Our results provide a further explanation of the human evolutionary history in response to environmental pressures in this region.
Collapse
Affiliation(s)
- Humberto García-Ortiz
- Instituto Nacional de Medicina Genómica, Tlalpan, Mexico City 14610, Mexico
- Correspondence:
| | | | | | | | | | - Meradeth Snow
- Department of Anthropology, University of Montana, Missoula, MT 59812, USA
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, The GLOBE Institute, The University of Copenhagen, Øster Farimagsgade 5A, 1352 Copenhagen, Denmark
| | | | - Paulina Baca
- Instituto Nacional de Medicina Genómica, Tlalpan, Mexico City 14610, Mexico
| | | | - Deborah A. Bolnick
- Department of Anthropology and Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269-3003, USA
| | - Silvia Esperanza Flores-Martínez
- División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara 44340, Mexico
| | - Rocio Ortiz-Lopez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Insitute for Obesity Research, Monterrey 64700, Mexico
- Centro de Investigacion y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey 64460, Mexico
| | | | | | | | | | - Alejandra Guadalupe García-Zapién
- Departamento de Farmacobiología, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara 44430, Mexico
| | | | | | | | | | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara Ocotlán, Ocotlán 44100, Mexico
| | | | - Augusto Rojas-Martínez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Insitute for Obesity Research, Monterrey 64700, Mexico
- Centro de Investigacion y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey 64460, Mexico
| | | | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Tlalpan, Mexico City 14610, Mexico
| |
Collapse
|
7
|
Collen EJ, Johar AS, Teixeira JC, Llamas B. The immunogenetic impact of European colonization in the Americas. Front Genet 2022; 13:918227. [PMID: 35991555 PMCID: PMC9388791 DOI: 10.3389/fgene.2022.918227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
The introduction of pathogens originating from Eurasia into the Americas during early European contact has been associated with high mortality rates among Indigenous peoples, likely contributing to their historical and precipitous population decline. However, the biological impacts of imported infectious diseases and resulting epidemics, especially in terms of pathogenic effects on the Indigenous immunity, remain poorly understood and highly contentious to this day. Here, we examine multidisciplinary evidence underpinning colonization-related immune genetic change, providing contextualization from anthropological studies, paleomicrobiological evidence of contrasting host-pathogen coevolutionary histories, and the timings of disease emergence. We further summarize current studies examining genetic signals reflecting post-contact Indigenous population bottlenecks, admixture with European and other populations, and the putative effects of natural selection, with a focus on ancient DNA studies and immunity-related findings. Considering current genetic evidence, together with a population genetics theoretical approach, we show that post-contact Indigenous immune adaptation, possibly influenced by selection exerted by introduced pathogens, is highly complex and likely to be affected by multifactorial causes. Disentangling putative adaptive signals from those of genetic drift thus remains a significant challenge, highlighting the need for the implementation of population genetic approaches that model the short time spans and complex demographic histories under consideration. This review adds to current understandings of post-contact immunity evolution in Indigenous peoples of America, with important implications for bettering our understanding of human adaptation in the face of emerging infectious diseases.
Collapse
Affiliation(s)
- Evelyn Jane Collen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- *Correspondence: Evelyn Jane Collen, ; Bastien Llamas,
| | - Angad Singh Johar
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Culture History and Language, The Australian National University, Canberra, ACT, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
- Telethon Kids Institute, Indigenous Genomics Research Group, Adelaide, SA, Australia
- *Correspondence: Evelyn Jane Collen, ; Bastien Llamas,
| |
Collapse
|
8
|
Caro-Consuegra R, Nieves-Colón MA, Rawls E, Rubin-de-Celis V, Lizárraga B, Vidaurre T, Sandoval K, Fejerman L, Stone AC, Moreno-Estrada A, Bosch E. Uncovering signals of positive selection in Peruvian populations from three ecological regions. Mol Biol Evol 2022; 39:6647595. [PMID: 35860855 PMCID: PMC9356722 DOI: 10.1093/molbev/msac158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Perú hosts extremely diverse ecosystems which can be broadly classified into three major ecoregions: the Pacific desert coast, the Andean highlands, and the Amazon rainforest. Since its initial peopling approximately 12,000 years ago, the populations inhabiting such ecoregions might have differentially adapted to their contrasting environmental pressures. Previous studies have described several candidate genes underlying adaptation to hypobaric hypoxia among Andean highlanders. However, the adaptive genetic diversity of coastal and rainforest populations has been less studied. Here, we gathered genome-wide SNP-array data from 286 Peruvians living across the three ecoregions and analysed signals of recent positive selection through population differentiation and haplotype-based selection scans. Among highland populations, we identify candidate genes related to cardiovascular function (TLL1, DUSP27, TBX5, PLXNA4, SGCD), to the Hypoxia-Inducible Factor pathway (TGFA, APIP), to skin pigmentation (MITF), as well as to glucose (GLIS3) and glycogen metabolism (PPP1R3C, GANC). In contrast, most signatures of adaptation in coastal and rainforest populations comprise candidate genes related to the immune system (including SIGLEC8, TRIM21, CD44 and ICAM1 in the coast; CBLB and PRDM1 in rainforest and the BRD2- HLA-DOA- HLA-DPA1 region in both), possibly as a result of strong pathogen-driven selection. This study identifies candidate genes related to human adaptation to the diverse environments of South America.
Collapse
Affiliation(s)
- Rocio Caro-Consuegra
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Maria A Nieves-Colón
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Erin Rawls
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Verónica Rubin-de-Celis
- Laboratorio de Genómica Molecular Evolutiva, Instituto de Ciencia y Tecnología, Universidad Ricardo Palma, Lima, Perú
| | - Beatriz Lizárraga
- Emeritus Professor, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | | | - Karla Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Laura Fejerman
- Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Elena Bosch
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
| |
Collapse
|
9
|
Pastana LF, Silva TA, Gellen LPA, Vieira GM, de Assunção LA, Leitão LPC, da Silva NM, Coelho RDCC, de Alcântara AL, Vinagre LWMS, Rodrigues JCG, Borges Leal DFDV, Fernandes MR, de Souza SJ, Kroll JE, Ribeiro-dos-Santos AM, Burbano RMR, Guerreiro JF, de Assumpção PP, Ribeiro-dos-Santos ÂC, dos Santos SEB, dos Santos NPC. The Genomic Profile Associated with Risk of Severe Forms of COVID-19 in Amazonian Native American Populations. J Pers Med 2022; 12:jpm12040554. [PMID: 35455670 PMCID: PMC9027999 DOI: 10.3390/jpm12040554] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 12/12/2022] Open
Abstract
Genetic factors associated with COVID-19 disease outcomes are poorly understood. This study aimed to associate genetic variants in the SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, XCR1, and ABO genes with the risk of severe forms of COVID-19 in Amazonian Native Americans, and to compare the frequencies with continental populations. The study population was composed of 64 Amerindians from the Amazon region of northern Brazil. The difference in frequencies between the populations was analyzed using Fisher’s exact test, and the results were significant when p ≤ 0.05. We investigated 64 polymorphisms in 7 genes; we studied 47 genetic variants that were new or had impact predictions of high, moderate, or modifier. We identified 15 polymorphisms with moderate impact prediction in 4 genes (ABO, CXCR6, FYCO1, and SLC6A20). Among the variants analyzed, 18 showed significant differences in allele frequency in the NAM population when compared to others. We reported two new genetic variants with modifier impact in the Amazonian population that could be studied to validate the possible associations with COVID-19 outcomes. The genomic profile of Amazonian Native Americans may be associated with protection from severe forms of COVID-19. This work provides genomic data that may help forthcoming studies to improve COVID-19 outcomes.
Collapse
Affiliation(s)
- Lucas Favacho Pastana
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Thays Amâncio Silva
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Laura Patrícia Albarello Gellen
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Giovana Miranda Vieira
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Letícia Almeida de Assunção
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Luciana Pereira Colares Leitão
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Natasha Monte da Silva
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Rita de Cássia Calderaro Coelho
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Angélica Leite de Alcântara
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Lui Wallacy Morikawa Souza Vinagre
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Juliana Carla Gomes Rodrigues
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Diana Feio da Veiga Borges Leal
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Marianne Rodrigues Fernandes
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Sandro José de Souza
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal 59076-550, Brazil; (S.J.d.S.); (J.E.K.)
- BioME, Universidade Federal do Rio Grande do Norte, Natal 59078-400, Brazil
- Institute of Systems Genetics, West China Hospital, University of Sichuan, Chengdu 610041, China
| | - José Eduardo Kroll
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal 59076-550, Brazil; (S.J.d.S.); (J.E.K.)
| | - André Mauricio Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém 66075-110, Brazil; (A.M.R.-d.-S.); (J.F.G.); (Â.C.R.-d.-S.)
| | - Rommel Mario Rodríguez Burbano
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - João Farias Guerreiro
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém 66075-110, Brazil; (A.M.R.-d.-S.); (J.F.G.); (Â.C.R.-d.-S.)
| | - Paulo Pimentel de Assumpção
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Ândrea Campos Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém 66075-110, Brazil; (A.M.R.-d.-S.); (J.F.G.); (Â.C.R.-d.-S.)
| | - Sidney Emanuel Batista dos Santos
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
| | - Ney Pereira Carneiro dos Santos
- Laboratório do Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil; (L.F.P.); (T.A.S.); (L.P.A.G.); (G.M.V.); (L.A.d.A.); (L.P.C.L.); (N.M.d.S.); (R.d.C.C.C.); (A.L.d.A.); (L.W.M.S.V.); (J.C.G.R.); (D.F.d.V.B.L.); (M.R.F.); (R.M.R.B.); (P.P.d.A.); (S.E.B.d.S.)
- Correspondence: ; Tel.: +55-(91)-98107-0850
| |
Collapse
|
10
|
The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas. Nat Commun 2021; 12:5942. [PMID: 34642312 PMCID: PMC8511047 DOI: 10.1038/s41467-021-26188-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/22/2021] [Indexed: 12/30/2022] Open
Abstract
The genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history. Here, we perform a genome-wide analysis of 716 newly genotyped individuals from 60 of the 68 recognized ethnic groups in Mexico. We show that the genetic structure of these populations is strongly influenced by geography, and our demographic reconstructions suggest a decline in the population size of all tested populations in the last 15-30 generations. We find evidence that Aridoamerican and Mesoamerican populations diverged roughly 4-9.9 ka, around the time when sedentary farming started in Mesoamerica. Comparisons with ancient genomes indicate that the Upward Sun River 1 (USR1) individual is an outgroup to Mexican/South American Indigenous populations, whereas Anzick-1 was more closely related to Mesoamerican/South American populations than to those from Aridoamerica, showing an even more complex history of divergence than recognized so far.
Collapse
|
11
|
Vargas LDB, Beltrame MH, Ho B, Marin WM, Dandekar R, Montero-Martín G, Fernández-Viña MA, Hurtado AM, Hill KR, Tsuneto LT, Hutz MH, Salzano FM, Petzl-Erler ML, Hollenbach JA, Augusto DG. Remarkably low KIR and HLA diversity in Amerindians reveals signatures of strong purifying selection shaping the centromeric KIR region. Mol Biol Evol 2021; 39:6388041. [PMID: 34633459 PMCID: PMC8763117 DOI: 10.1093/molbev/msab298] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The killer-cell immunoglobulin-like receptors (KIR) recognize human leukocyte antigen (HLA) molecules to regulate the cytotoxic and inflammatory responses of natural killer cells. KIR genes are encoded by a rapidly evolving gene family on chromosome 19 and present an unusual variation of presence and absence of genes and high allelic diversity. Although many studies have associated KIR polymorphism with susceptibility to several diseases over the last decades, the high-resolution allele-level haplotypes have only recently started to be described in populations. Here, we use a highly innovative custom next-generation sequencing method that provides a state-of-art characterization of KIR and HLA diversity in 706 individuals from eight unique South American populations: five Amerindian populations from Brazil (three Guarani and two Kaingang); one Amerindian population from Paraguay (Aché); and two urban populations from Southern Brazil (European and Japanese descendants from Curitiba). For the first time, we describe complete high-resolution KIR haplotypes in South American populations, exploring copy number, linkage disequilibrium, and KIR-HLA interactions. We show that all Amerindians analyzed to date exhibit the lowest numbers of KIR-HLA interactions among all described worldwide populations, and that 83-97% of their KIR-HLA interactions rely on a few HLA-C molecules. Using multiple approaches, we found signatures of strong purifying selection on the KIR centromeric region, which codes for the strongest NK cell educator receptors, possibly driven by the limited HLA diversity in these populations. Our study expands the current knowledge of KIR genetic diversity in populations to understand KIR-HLA coevolution and its impact on human health and survival.
Collapse
Affiliation(s)
- Luciana de Brito Vargas
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Marcia H Beltrame
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Brenda Ho
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Wesley M Marin
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ravi Dandekar
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Gonzalo Montero-Martín
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | | | - A Magdalena Hurtado
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85287, USA
| | - Kim R Hill
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85287, USA
| | - Luiza T Tsuneto
- Departamento de Análises Clínicas, Universidade Estadual de Maringá, Maringá, PR, 87020-900, Brazil
| | - Mara H Hutz
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Maria Luiza Petzl-Erler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Jill A Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158, USA
| | - Danillo G Augusto
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil.,Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| |
Collapse
|
12
|
Feng Q, Nickels E, Muskens IS, de Smith AJ, Gauderman WJ, Yee AC, Ricker C, Mack T, Leavitt AD, Godley LA, Wiemels JL. Increased burden of familial-associated early-onset cancer risk among minority Americans compared to non-Latino Whites. eLife 2021; 10:e64793. [PMID: 34155975 PMCID: PMC8219377 DOI: 10.7554/elife.64793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/04/2021] [Indexed: 01/11/2023] Open
Abstract
Background The role of race/ethnicity in genetic predisposition of early-onset cancers can be estimated by comparing family-based cancer concordance rates among ethnic groups. Methods We used linked California health registries to evaluate the relative cancer risks for first-degree relatives of patients diagnosed between ages 0 and 26, and the relative risks of developing distinct second primary malignancies (SPMs). From 1989 to 2015, we identified 29,631 cancer patients and 62,863 healthy family members. We calculated the standardized incident ratios (SIRs) of early-onset primary cancers diagnosed in proband siblings and mothers, as well as SPMs detected among early-onset patients. Analyses were stratified by self-identified race/ethnicity. Results Given probands with cancer, there were increased relative risks of any cancer for siblings and mothers (SIR = 3.32; 95% confidence interval [CI]: 2.85-3.85) and of SPMs (SIR = 7.27; 95% CI: 6.56-8.03). Given a proband with solid cancer, both Latinos (SIR = 4.98; 95% CI: 3.82-6.39) and non-Latino Blacks (SIR = 7.35; 95% CI: 3.36-13.95) exhibited significantly higher relative risk of any cancer in siblings and mothers when compared to non-Latino White subjects (SIR = 3.02; 95% CI: 2.12-4.16). For hematologic cancers, higher familial risk was evident for Asian/Pacific Islanders (SIR = 7.56; 95% CI: 3.26-14.90) compared to non-Latino whites (SIR = 2.69; 95% CI: 1.62-4.20). Conclusions The data support a need for increased attention to the genetics of early-onset cancer predisposition and environmental factors in race/ethnic minority families in the United States. Funding This work was supported by the V Foundation for funding this work (Grant FP067172).
Collapse
Affiliation(s)
- Qianxi Feng
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| | - Eric Nickels
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
- Children's Hospital Los AngelesLos AngelesUnited States
| | - Ivo S Muskens
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| | - Adam J de Smith
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| | - W James Gauderman
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| | - Amy C Yee
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| | - Charite Ricker
- Norris Comprehensive Cancer Center, USC Keck School of MedicineLos AngelesUnited States
| | - Thomas Mack
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| | - Andrew D Leavitt
- Departments of Medicine and Laboratory Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Lucy A Godley
- Departments of Medicine and Human Genetics, The University of ChicagoChicagoUnited States
| | - Joseph L Wiemels
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| |
Collapse
|
13
|
Willerslev E, Meltzer DJ. Peopling of the Americas as inferred from ancient genomics. Nature 2021; 594:356-364. [PMID: 34135521 DOI: 10.1038/s41586-021-03499-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/26/2021] [Indexed: 02/05/2023]
Abstract
In less than a decade, analyses of ancient genomes have transformed our understanding of the Indigenous peopling and population history of the Americas. These studies have shown that this history, which began in the late Pleistocene epoch and continued episodically into the Holocene epoch, was far more complex than previously thought. It is now evident that the initial dispersal involved the movement from northeast Asia of distinct and previously unknown populations, including some for whom there are no currently known descendants. The first peoples, once south of the continental ice sheets, spread widely, expanded rapidly and branched into multiple populations. Their descendants-over the next fifteen millennia-experienced varying degrees of isolation, admixture, continuity and replacement, and their genomes help to illuminate the relationships among major subgroups of Native American populations. Notably, all ancient individuals in the Americas, save for later-arriving Arctic peoples, are more closely related to contemporary Indigenous American individuals than to any other population elsewhere, which challenges the claim-which is based on anatomical evidence-that there was an early, non-Native American population in the Americas. Here we review the patterns revealed by ancient genomics that help to shed light on the past peoples who created the archaeological landscape, and together lead to deeper insights into the population and cultural history of the Americas.
Collapse
Affiliation(s)
- Eske Willerslev
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK. .,Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Wellcome Trust Sanger Institute, Cambridge, UK.
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Anthropology, Southern Methodist University, Dallas, TX, USA.
| |
Collapse
|
14
|
da Silva Coelho FA, Gill S, Tomlin CM, Heaton TH, Lindqvist C. An early dog from southeast Alaska supports a coastal route for the first dog migration into the Americas. Proc Biol Sci 2021; 288:20203103. [PMID: 33622130 PMCID: PMC7934960 DOI: 10.1098/rspb.2020.3103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The oldest confirmed remains of domestic dogs in North America are from mid-continent archaeological sites dated approximately 9900 calibrated years before present (cal BP). Although this date suggests that dogs may not have arrived alongside the first Native Americans, the timing and routes for the entrance of New World dogs remain uncertain. Here, we present a complete mitochondrial genome of a dog from southeast Alaska, dated to 10 150 ± 260 cal BP. We compared this high-coverage genome with data from modern dog breeds, historical Arctic dogs and American precontact dogs (PCDs) from before European arrival. Our analyses demonstrate that the ancient dog belongs to the PCD lineage, which diverged from Siberian dogs around 16 700 years ago. This timing roughly coincides with the minimum suggested date for the opening of the North Pacific coastal (NPC) route along the Cordilleran Ice Sheet and genetic evidence for the initial peopling of the Americas. This ancient southeast Alaskan dog occupies an early branching position within the PCD clade, indicating it represents a close relative of the earliest PCDs that were brought alongside people migrating from eastern Beringia southward along the NPC to the rest of the Americas. The stable isotope δ13C value of this early dog indicates a marine diet, different from the younger mid-continent PCDs' terrestrial diet. Although PCDs were largely replaced by modern European dog breeds, our results indicate that their population decline started approximately 2000 years BP, coinciding with the expansion of Inuit peoples, who are associated with traditional sled-dog culture. Our findings suggest that dogs formed part of the initial human habitation of the New World, and provide insights into their replacement by both Arctic and European lineages.
Collapse
Affiliation(s)
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Timothy H Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, SD 57069, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| |
Collapse
|
15
|
Davidson R, Fehren-Schmitz L, Llamas B. A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations. Genes (Basel) 2021; 12:215. [PMID: 33540755 PMCID: PMC7913103 DOI: 10.3390/genes12020215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 01/10/2023] Open
Abstract
The rulers of the Inka empire conquered approximately 2 million km2 of the South American Andes in just under 100 years from 1438-1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.
Collapse
Affiliation(s)
- Roberta Davidson
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics (NCIG), Australian National University, Canberra, ACT 0200, Australia
| |
Collapse
|
16
|
|
17
|
Richalet JP. [Adaption to chronic hypoxaemia by populations living at high altitude]. Rev Mal Respir 2021; 38:395-403. [PMID: 33541755 DOI: 10.1016/j.rmr.2020.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/13/2020] [Indexed: 12/14/2022]
Abstract
Permanent life at high altitude induces important physiological stresses linked to the exposure to chronic hypoxia. Various strategies have been adopted by diverse populations living in the Andes, Tibet or East Africa. The main mechanism is an increase in red blood cell production, more marked in Andeans than in Tibetans or Ethiopians. Other changes are observed in the cardiovascular or respiratory systems, as well as in the utero-placental circulation. Sometimes, a de-adaptation process to hypoxia develops, when erythrocytosis becomes excessive and leads to haematological, vascular and cerebral complications (Monge's disease or chronic mountain sickness). Pulmonary hypertension may also appear. Therapeutic options are available but not sufficiently used. Genetic studies have recently been undertaken to try to better understand the evolution of the human genome in populations living in various high altitude regions of the world, as well as the genetic risk factors for chronic diseases. A new model has appeared, intermittent chronic hypoxia, due to the development of economic activities (mainly mining) in desert regions of the Altiplano.
Collapse
Affiliation(s)
- J-P Richalet
- Laboratoire « Hypoxie & Poumon », UMR Inserm U1272, Université Sorbonne Paris Nord 13, 74, rue Marcel-Cachin, 93017 Bobigny cedex, France.
| |
Collapse
|
18
|
Gutiérrez-Escobar AJ, Velapatiño B, Borda V, Rabkin CS, Tarazona-Santos E, Cabrera L, Cok J, Hooper CC, Jahuira-Arias H, Herrera P, Noureen M, Wang D, Romero-Gallo J, Tran B, Peek RM, Berg DE, Gilman RH, Camargo MC. Identification of New Helicobacter pylori Subpopulations in Native Americans and Mestizos From Peru. Front Microbiol 2020; 11:601839. [PMID: 33381095 PMCID: PMC7767971 DOI: 10.3389/fmicb.2020.601839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/16/2020] [Indexed: 01/01/2023] Open
Abstract
Region-specific Helicobacter pylori subpopulations have been identified. It is proposed that the hspAmerind subpopulation is being displaced from the Americans by an hpEurope population following the conquest. Our study aimed to describe the genomes and methylomes of H. pylori isolates from distinct Peruvian communities: 23 strains collected from three groups of Native Americans (Asháninkas [ASHA, n = 9], Shimaas [SHIM, n = 5] from Amazonas, and Punos from the Andean highlands [PUNO, n = 9]) and 9 modern mestizos from Lima (LIM). Closed genomes and DNA modification calls were obtained using SMRT/PacBio sequencing. We performed evolutionary analyses and evaluated genomic/epigenomic differences among strain groups. We also evaluated human genome-wide data from 74 individuals from the selected Native communities (including the 23 H. pylori strains donors) to compare host and bacterial backgrounds. There were varying degrees of hspAmerind ancestry in all strains, ranging from 7% in LIM to 99% in SHIM. We identified three H. pylori subpopulations corresponding to each of the Native groups and a novel hspEuropePeru which evolved in the modern mestizos. The divergence of the indigenous H. pylori strains recapitulated the genetic structure of Native Americans. Phylogenetic profiling showed that Orthogroups in the indigenous strains seem to have evolved differentially toward epigenomic regulation and chromosome maintenance, whereas OGs in the modern mestizo (LIM) seem to have evolved toward virulence and adherence. The prevalence of cagA+/vacA s1i1m1 genotype was similar across populations (p = 0.32): 89% in ASHA, 67% in PUNO, 56% in LIM and 40% in SHIM. Both cagA and vacA sequences showed that LIM strains were genetically differentiated (p < 0.001) as compared to indigenous strains. We identified 642 R-M systems with 39% of the associated genes located in the core genome. We found 692 methylation motifs, including 254 population-specific sequences not previously described. In Peru, hspAmerind is not extinct, with traces found even in a heavily admixed mestizo population. Notably, our study identified three new hspAmerind subpopulations, one per Native group; and a new subpopulation among mestizos that we named hspEuropePeru. This subpopulation seems to have more virulence-related elements than hspAmerind. Purifying selection driven by variable host immune response may have shaped the evolution of Peruvian subpopulations, potentially impacting disease outcomes.
Collapse
Affiliation(s)
| | - Billie Velapatiño
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada.,Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Victor Borda
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC/MCTIC), Petrópolis, Brazil
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Eduardo Tarazona-Santos
- Universidad Peruana Cayetano Heredia, Lima, Peru.,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Jaime Cok
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | | | - Mehwish Noureen
- National Institute of Genetics, Mishima, Japan.,Department of Genetics, Graduate School of Life Sciences, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Judith Romero-Gallo
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Bao Tran
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Richard M Peek
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Douglas E Berg
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Robert H Gilman
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| |
Collapse
|
19
|
Mario-Vásquez JE, Naranjo-González CA, Montiel J, Zuluaga LM, Vásquez AM, Tobón-Castaño A, Bedoya G, Segura C. Association of variants in IL1B, TLR9, TREM1, IL10RA, and CD3G and Native American ancestry on malaria susceptibility in Colombian populations. INFECTION GENETICS AND EVOLUTION 2020; 87:104675. [PMID: 33316430 DOI: 10.1016/j.meegid.2020.104675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/19/2020] [Accepted: 12/09/2020] [Indexed: 12/24/2022]
Abstract
Host genetics is an influencing factor in the manifestation of infectious diseases. In this study, the association of mild malaria with 28 variants in 16 genes previously reported in other populations and/or close to ancestry-informative markers (AIMs) selected was evaluated in an admixed 736 Colombian population sample. Additionally, the effect of genetic ancestry on phenotype expression was explored. For this purpose, the ancestral genetic composition of Turbo and El Bagre was determined. A higher Native American ancestry trend was found in the population with lower malaria susceptibility [odds ratio (OR) = 0.416, 95% confidence interval (95% CI) = 0.234-0.740, P = 0.003]. Three AIMs presented significant associations with the disease phenotype (MID1752, MID921, and MID1586). The first two were associated with greater malaria susceptibility (D/D, OR = 2.23, 95% CI = 1.06-4.69, P = 0.032 and I/D-I/I, OR = 2.14, 95% CI = 1.18-3.87, P = 0.011, respectively), and the latter has a protective effect on the appearance of malaria (I/I, OR = 0.18, 95% CI = 0.08-0.40, P < 0.0001). After adjustment by age, sex, municipality, and genetic ancestry, genotype association analysis showed evidence of association with malaria susceptibility for variants in or near IL1B, TLR9, TREM1, IL10RA, and CD3G genes: rs1143629-IL1B (G/A-A/A, OR = 0.41, 95% CI = 0.21-0.78, P = 0.0051), rs352139-TLR9 (T/T, OR = 0.28, 95% CI = 0.11-0.72, P = 0.0053), rs352140-TLR9 (C/C, OR = 0.41, 95% CI = 0.20-0.87, P = 0.019), rs2234237-TREM1 (T/A-A/A, OR = 0.43, 95% CI = 0.23-0.79, P = 0.0056), rs4252246-IL10RA (C/A-A/A, OR = 2.11, 95% CI = 1.18-3.75, P = 0.01), and rs1561966-CD3G (A/A, OR = 0.20, 95% CI = 0.06-0.69, P = 0.0058). The results showed the participation of genes involved in immunological processes and suggested an effect of ancestral genetic composition over the traits analyzed. Compared to the paisa population (Antioquia), Turbo and El Bagre showed a strong decrease in European ancestry and an increase in African and Native American ancestries. Also, a novel association of two single nucleotide polymorphisms with malaria susceptibility was identified in this study.
Collapse
Affiliation(s)
- Jorge Eliécer Mario-Vásquez
- Grupo Genética Molecular (GENMOL), Universidad de Antioquia, Carrera 53 No. 61-30, Lab 430. Medellín, Colombia
| | | | - Jehidys Montiel
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Lina M Zuluaga
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Ana M Vásquez
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Alberto Tobón-Castaño
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Gabriel Bedoya
- Grupo Genética Molecular (GENMOL), Universidad de Antioquia, Carrera 53 No. 61-30, Lab 430. Medellín, Colombia
| | - Cesar Segura
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia.
| |
Collapse
|
20
|
Nieves-Colón MA, Pestle WJ, Reynolds AW, Llamas B, de la Fuente C, Fowler K, Skerry KM, Crespo-Torres E, Bustamante CD, Stone AC. Ancient DNA Reconstructs the Genetic Legacies of Precontact Puerto Rico Communities. Mol Biol Evol 2020; 37:611-626. [PMID: 31710665 DOI: 10.1093/molbev/msz267] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Indigenous peoples have occupied the island of Puerto Rico since at least 3000 BC. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of precontact Indigenous communities from Puerto Rico. Bone, tooth, and dental calculus samples were collected from 124 individuals from three precontact archaeological sites: Tibes, Punta Candelero, and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the precontact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, supports a primarily Amazonian South American origin for these populations and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from precontact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of precontact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between precontact individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of precontact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders.
Collapse
Affiliation(s)
- Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ.,National Laboratory of Genomics for Biodiversity (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - William J Pestle
- Department of Anthropology, University of Miami, Coral Gables, FL
| | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and Environment Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Kathleen Fowler
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ
| | - Katherine M Skerry
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ.,School of Life Sciences, Arizona State University, Tempe, AZ
| | - Edwin Crespo-Torres
- Forensic Anthropology and Bioarcheology Laboratory, University of Puerto Rico, Rio Piedras, Puerto Rico
| | | | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ
| |
Collapse
|
21
|
Chelico L, King A, Ticknor J, McDonald M, Rosenes R, Mercredi J, Saddleback J, Bailey G, King M. Perspectives of Saskatchewan researchers and community members on HIV-1 strains circulating in Saskatchewan. AIDS 2020; 34:1987-1989. [PMID: 32132362 PMCID: PMC7575011 DOI: 10.1097/qad.0000000000002515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 01/30/2020] [Accepted: 02/15/2020] [Indexed: 11/26/2022]
Affiliation(s)
| | - Alexandra King
- Department of Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan
| | | | - Michael McDonald
- W. Maurice Young Centre for Applied Ethics, School of Population and Public Health, University of British Columbia, Vancouver, British Columbia
| | - Ron Rosenes
- Community Health Advocate and Researcher, Toronto, Ontario
| | | | | | - Geri Bailey
- Saskatoon Tribal Council Health & Family Services Inc
| | - Malcolm King
- Department of Community Health and Epidemiology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| |
Collapse
|
22
|
Kim HI, Ye B, Gosalia N, Köroğlu Ç, Hanson RL, Hsueh WC, Knowler WC, Baier LJ, Bogardus C, Shuldiner AR, Van Hout CV, Van Hout CV. Characterization of Exome Variants and Their Metabolic Impact in 6,716 American Indians from the Southwest US. Am J Hum Genet 2020; 107:251-264. [PMID: 32640185 DOI: 10.1016/j.ajhg.2020.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/10/2020] [Indexed: 12/21/2022] Open
Abstract
Applying exome sequencing to populations with unique genetic architecture has the potential to reveal novel genes and variants associated with traits and diseases. We sequenced and analyzed the exomes of 6,716 individuals from a Southwestern American Indian (SWAI) population with well-characterized metabolic traits. We found that the SWAI population has distinct allelic architecture compared to populations of European and East Asian ancestry, and there were many predicted loss-of-function (pLOF) and nonsynonymous variants that were highly enriched or private in the SWAI population. We used pLOF and nonsynonymous variants in the SWAI population to evaluate gene-burden associations of candidate genes from European genome-wide association studies (GWASs) for type 2 diabetes, body mass index, and four major plasma lipids. We found 19 significant gene-burden associations for 11 genes, providing additional evidence for prioritizing candidate effector genes of GWAS signals. Interestingly, these associations were mainly driven by pLOF and nonsynonymous variants that are unique or highly enriched in the SWAI population. Particularly, we found four pLOF or nonsynonymous variants in APOB, APOE, PCSK9, and TM6SF2 that are private or enriched in the SWAI population and associated with low-density lipoprotein (LDL) cholesterol levels. Their large estimated effects on LDL cholesterol levels suggest strong impacts on protein function and potential clinical implications of these variants in cardiovascular health. In summary, our study illustrates the utility and potential of exome sequencing in genetically unique populations, such as the SWAI population, to prioritize candidate effector genes within GWAS loci and to find additional variants in known disease genes with potential clinical impact.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Cristopher V Van Hout
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA.
| |
Collapse
|
23
|
Between Foragers and Farmers: Climate Change and Human Strategies in Northwestern Patagonia. QUATERNARY 2020. [DOI: 10.3390/quat3020017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this paper we explore how changes in human strategies are differentially modulated by climate in a border area between hunter-gatherers and farmers. We analyze multiple proxies: radiocarbon summed probability distributions (SPDs), stable C and N isotopes, and zooarchaeological data from northwestern Patagonia. Based on these proxies, we discuss aspects of human population, subsistence, and dietary dynamics in relation to long-term climatic trends marked by variation in the Southern Annular Mode (SAM). Our results indicate that the farming frontier in northwestern Patagonia was dynamic in both time and space. We show how changes in temperature and precipitation over the last 1000 years cal BP have influenced the use of domestic plants and the hunting of highest-ranked wild animals, whereas no significant changes in human population size occurred. During the SAM positive phase between 900 and 550 years cal BP, warmer and drier summers are associated with an increase in C4 resource consumption (maize). After 550 years cal BP, when the SAM changes to the negative phase, wetter and cooler summer conditions are related to a change in diet focused on wild resources, especially meat. Over the past 1000 years, there was a non-significant change in the population based on the SPD.
Collapse
|
24
|
Southwick SV, Esch R, Gasser R, Cragun D, Redlinger-Grosse K, Marsalis S, Zierhut HA. Racial and ethnic differences in genetic counseling experiences and outcomes in the United States: A systematic review. J Genet Couns 2020; 29:147-165. [PMID: 32144851 DOI: 10.1002/jgc4.1230] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 12/12/2022]
Abstract
As genetic counseling services expand and reach a wider catchment of the population, there is a critical need to better understand the impact of services on a greater diversity of patients. We conducted a systematic review to evaluate genetic counseling experiences and outcomes among racial and ethnic minorities. Six databases extracted articles published from 2005 to 2019 that assessed genetic counseling participation, knowledge and awareness, motivators, barriers, perceptions, and outcomes for racial and ethnic minority populations in the United States. Genetic counseling outcomes were categorized using the Framework for Outcomes of Clinical commUnication Services. A total of 1,227 abstracts were identified, of which 23 papers met inclusion criteria. Results suggest the possibility of racial and ethnic differences in some genetic counseling experiences and outcomes but noted differences were not adequately replicated between studies. The few included studies differed greatly in aims, methods, and results, which made comparison across study designs challenging and effectively barred thematic analysis. Additional research is needed that includes more study populations and settings with patients of diverse racial and ethnic backgrounds, as well as more structured study designs that allow for elucidations of differences between White and non-White populations.
Collapse
Affiliation(s)
- Sabrina V Southwick
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Riley Esch
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Rachel Gasser
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Deborah Cragun
- College of Public Health, University of South Florida, Tampa, FL, USA
| | - Krista Redlinger-Grosse
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | | | - Heather A Zierhut
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
25
|
Devaux CA, Mediannikov O, Medkour H, Raoult D. Infectious Disease Risk Across the Growing Human-Non Human Primate Interface: A Review of the Evidence. Front Public Health 2019; 7:305. [PMID: 31828053 PMCID: PMC6849485 DOI: 10.3389/fpubh.2019.00305] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/07/2019] [Indexed: 12/22/2022] Open
Abstract
Most of the human pandemics reported to date can be classified as zoonoses. Among these, there is a long history of infectious diseases that have spread from non-human primates (NHP) to humans. For millennia, indigenous groups that depend on wildlife for their survival were exposed to the risk of NHP pathogens' transmission through animal hunting and wild meat consumption. Usually, exposure is of no consequence or is limited to mild infections. In rare situations, it can be more severe or even become a real public health concern. Since the emergence of acquired immune deficiency syndrome (AIDS), nobody can ignore that an emerging infectious diseases (EID) might spread from NHP into the human population. In large parts of Central Africa and Asia, wildlife remains the primary source of meat and income for millions of people living in rural areas. However, in the past few decades the risk of exposure to an NHP pathogen has taken on a new dimension. Unprecedented breaking down of natural barriers between NHP and humans has increased exposure to health risks for a much larger population, including people living in urban areas. There are several reasons for this: (i) due to road development and massive destruction of ecosystems for agricultural needs, wildlife and humans come into contact more frequently; (ii) due to ecological awareness, many long distance travelers are in search of wildlife discovery, with a particular fascination for African great apes; (iii) due to the attraction for ancient temples and mystical practices, others travelers visit Asian places colonized by NHP. In each case, there is a risk of pathogen transmission through a bite or another route of infection. Beside the individual risk of contracting a pathogen, there is also the possibility of starting a new pandemic. This article reviews the known cases of NHP pathogens' transmission to humans whether they are hunters, travelers, ecotourists, veterinarians, or scientists working on NHP. Although pathogen transmission is supposed to be a rare outcome, Rabies virus, Herpes B virus, Monkeypox virus, Ebola virus, or Yellow fever virus infections are of greater concern and require quick countermeasures from public health professionals.
Collapse
Affiliation(s)
- Christian A. Devaux
- Aix-Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
- CNRS, Marseille, France
| | - Oleg Mediannikov
- Aix-Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Hacene Medkour
- Aix-Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| |
Collapse
|
26
|
Altan E, Dib JC, Gulloso AR, Escribano Juandigua D, Deng X, Bruhn R, Hildebrand K, Freiden P, Yamamoto J, Schultz-Cherry S, Delwart E. Effect of Geographic Isolation on the Nasal Virome of Indigenous Children. J Virol 2019; 93:e00681-19. [PMID: 31189707 PMCID: PMC6694818 DOI: 10.1128/jvi.00681-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/29/2019] [Indexed: 11/20/2022] Open
Abstract
The influence of living in small remote villages on the diversity of viruses in the nasal mucosa was investigated in three Colombian villages with very different levels of geographic isolation. Metagenomic analysis was used to characterize viral nucleic acids in nasal swabs from 63 apparently healthy young children. Sequences from human virus members of the families Anelloviridae, Papillomaviridae, Picornaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, and Paramyxoviridae were detected in decreasing proportions of children. The number of papillomavirus infections detected was greater among Hispanic children most exposed to outside contacts, while anellovirus infections were more common in the isolated indigenous villages. The diversity of the other human viruses detected did not differ among the villages. Closely related variants of rhinovirus A or B were identified in 2 to 4 children from each village, reflecting ongoing transmission clusters. Genomes of viruses not currently known to infect humans, including members of the families Parvoviridae, Partitiviridae, Dicistroviridae, and Iflaviridae and circular Rep-encoding single-stranded DNA (CRESS-DNA) virus, were also detected in nasal swabs, possibly reflecting environmental contamination from insect, fungal, or unknown sources. Despite the high levels of geographic and cultural isolation, the overall diversity of human viruses in the nasal passages of children was not reduced in highly isolated indigenous villages, indicating ongoing exposure to globally circulating viruses.IMPORTANCE Extreme geographic and cultural isolation can still be found in some indigenous South American villages. Such isolation may be expected to limit the introduction of otherwise common and widely distributed viruses. Very small population sizes may also result in rapid local viral extinction due to a lack of seronegative subjects to maintain transmission chains for rapidly cleared viruses. We compared the viruses in the nasal passages of young children in three villages with increasing levels of geographic isolation. We found that isolation did not reduce the overall diversity of viral infections. Multiple infections with nearly identical rhinoviruses could be detected within each village, likely reflecting recent viral introductions and transmission clusters among epidemiologically linked members of these very small communities. We conclude that, despite their geographic isolation, remote indigenous villages show evidence of ongoing exposure to globally circulating viruses.
Collapse
Affiliation(s)
- Eda Altan
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Juan Carlos Dib
- Universidad del Norte, Barranquilla, Atlantico, Colombia
- Fundación Salud Para el Trópico-Tropical Health Foundation, Santa Marta, Magdalena, Colombia
| | - Andres Rojas Gulloso
- Fundación Salud Para el Trópico-Tropical Health Foundation, Santa Marta, Magdalena, Colombia
| | | | - Xutao Deng
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Roberta Bruhn
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Kristen Hildebrand
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Pamela Freiden
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Janie Yamamoto
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| |
Collapse
|
27
|
Gazal S, Espinoza JR, Austerlitz F, Marchant D, Macarlupu JL, Rodriguez J, Ju-Preciado H, Rivera-Chira M, Hermine O, Leon-Velarde F, Villafuerte FC, Richalet JP, Gouya L. The Genetic Architecture of Chronic Mountain Sickness in Peru. Front Genet 2019; 10:690. [PMID: 31417607 PMCID: PMC6682665 DOI: 10.3389/fgene.2019.00690] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/02/2019] [Indexed: 12/23/2022] Open
Abstract
Chronic mountain sickness (CMS) is a pathological condition resulting from chronic exposure to high-altitude hypoxia. While its prevalence is high in native Andeans (>10%), little is known about the genetic architecture of this disease. Here, we performed the largest genome-wide association study (GWAS) of CMS (166 CMS patients and 146 controls living at 4,380 m in Peru) to detect genetic variants associated with CMS. We highlighted four new candidate loci, including the first CMS-associated variant reaching GWAS statistical significance (rs7304081; P = 4.58 × 10−9). By looking at differentially expressed genes between CMS patients and controls around these four loci, we suggested AEBP2, CAST, and MCTP2 as candidate CMS causal genes. None of the candidate loci were under strong natural selection, consistent with the observation that CMS affects fitness mainly after the reproductive years. Overall, our results reveal new insights on the genetic architecture of CMS and do not provide evidence that CMS-associated variants are linked to a strong ongoing adaptation to high altitude.
Collapse
Affiliation(s)
- Steven Gazal
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States.,INSERM, Infection, Antimicrobials, Modelling, Evolution (IAME), UMR 1137, Paris, France.,Plateforme de génomique constitutionnelle du GHU Nord, Assistance Publique des Hôpitaux de Paris (APHP), Hôpital Bichat, Paris, France
| | - Jose R Espinoza
- Laboratorio de Biotecnología Molecular-LID, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Frédéric Austerlitz
- UMR CNRS 7206 Eco-Anthropologie et Ethnobiologie, Musée de l'Homme, Paris, France
| | - Dominique Marchant
- Université Paris 13, Sorbonne Paris Cité, INSERM UMR 1272 Hypoxie et Poumon, Bobigny, France
| | - Jose Luis Macarlupu
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jorge Rodriguez
- Laboratorio de Biotecnología Molecular-LID, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Hugo Ju-Preciado
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Maria Rivera-Chira
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Olivier Hermine
- Université Paris Descartes, Institut National de la Santé et de la Recherche Médicale Unité 1163, Centre National de la Recherche Scientifique, Equipes de Recherche Labellisées 8254, Institut Imagine, Paris, France.,Laboratoire d'Excellence, Globule Rouge-Excellence, Paris, France
| | - Fabiola Leon-Velarde
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Francisco C Villafuerte
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jean-Paul Richalet
- Université Paris 13, Sorbonne Paris Cité, INSERM UMR 1272 Hypoxie et Poumon, Bobigny, France.,Laboratoire d'Excellence, Globule Rouge-Excellence, Paris, France
| | - Laurent Gouya
- Laboratoire d'Excellence, Globule Rouge-Excellence, Paris, France.,Université Paris Diderot, INSERM U1149, Hème, fer et pathologies inflammatoires, Assistance Publique des Hôpitaux de Paris (APHP), Hôpital Louis Mourier, Paris, France
| |
Collapse
|
28
|
Alfonso‐Sánchez MA, Gómez‐Pérez L, Dipierri JE, Peña JA. Paternal heritage in Jujuy province (Northwest Argentina): Evidence for sex‐biased gene flow and genetic drift effects. Am J Hum Biol 2019; 31:e23262. [DOI: 10.1002/ajhb.23262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/27/2019] [Accepted: 05/17/2019] [Indexed: 12/30/2022] Open
Affiliation(s)
- Miguel A. Alfonso‐Sánchez
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Bilbao Spain
| | - Luis Gómez‐Pérez
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Bilbao Spain
| | - José E. Dipierri
- Instituto de Biología de la AlturaUniversidad Nacional de Jujuy San Salvador de Jujuy Argentina
| | - José A. Peña
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Bilbao Spain
| |
Collapse
|
29
|
Measuring the impact of European colonization on Native American populations in Southern Brazil and Uruguay: Evidence from mtDNA. Am J Hum Biol 2019; 31:e23243. [DOI: 10.1002/ajhb.23243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 02/05/2019] [Accepted: 03/10/2019] [Indexed: 01/26/2023] Open
|
30
|
Caetano Andrade VL, Flores BM, Levis C, Clement CR, Roberts P, Schöngart J. Growth rings of Brazil nut trees (Bertholletia excelsa) as a living record of historical human disturbance in Central Amazonia. PLoS One 2019; 14:e0214128. [PMID: 30943230 PMCID: PMC6447161 DOI: 10.1371/journal.pone.0214128] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/07/2019] [Indexed: 11/19/2022] Open
Abstract
The Brazil nut tree (Bertholletia excelsa) is an iconic and economically valuable species that dominates vast swathes of the Amazon Basin. This species seems to have been an important part of human subsistence strategies in the region from at least the Early Holocene, and its current distribution may be a legacy of past human settlement. Because B. excelsa is a long-lived pioneer tree it requires natural or human disturbances to increase light availability in the understory for a successful establishment. However, it remains unclear how the long-term population dynamics of this species have been shaped by pre-colonial and post-colonial human practices. Here, we use tree-ring analyses to look at changes in growing conditions over the past 400 years in a Brazil nut tree population in Central Amazonia. We identify changes in tree recruitment and growth rates associated not only with regional climatic variability, but also major political and socio-economic activities recorded by historical documents in the vicinity of Manaus. We demonstrate that the expansion of a post-colonial political center (Manaus) from the middle of the 18th century onwards coincided with a reduction in recruitment of B. excelsa. We argue that this hiatus suggests the interruption of indigenous management practices, probably due to the collapse of pre-Columbian societies. A second recruitment pulse, and unprecedented cycles of growth release and suppression, aligns with a shift to modern exploitation of the forest into the 20th century. Our findings shed light on how past histories of human-forest interactions can be revealed by the growth rings of trees in Amazonia. Future interdisciplinary analysis of these trees should enable more detailed investigation of how human forest management has changed in this part of the world, through pre-colonial, colonial, and industrial periods of human activity, with potential implications for conservation.
Collapse
Affiliation(s)
- Victor L. Caetano Andrade
- Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Thüringen, Germany
- * E-mail:
| | - Bernardo M. Flores
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Carolina Levis
- Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
- Forest Ecology and Forest Management Group, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Thüringen, Germany
| | | |
Collapse
|
31
|
Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients. Genes (Basel) 2018; 9:genes9100506. [PMID: 30340387 PMCID: PMC6210830 DOI: 10.3390/genes9100506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/11/2018] [Accepted: 10/16/2018] [Indexed: 11/16/2022] Open
Abstract
Selecting among alternative scenarios of human evolution is nowadays a common methodology to investigate the history of our species. This strategy is usually based on computer simulations of genetic data under different evolutionary scenarios, followed by a fitting of the simulated data with the real data. A recent trend in the investigation of ancestral evolutionary processes of modern humans is the application of genetic gradients as a measure of fitting, since evolutionary processes such as range expansions, range contractions, and population admixture (among others) can lead to different genetic gradients. In addition, this strategy allows the analysis of the genetic causes of the observed genetic gradients. Here, we review recent findings on the selection among alternative scenarios of human evolution based on simulated genetic gradients, including pros and cons. First, we describe common methodologies to simulate genetic gradients and apply them to select among alternative scenarios of human evolution. Next, we review previous studies on the influence of range expansions, population admixture, last glacial period, and migration with long-distance dispersal on genetic gradients for some regions of the world. Finally, we discuss this analytical approach, including technical limitations, required improvements, and advice. Although here we focus on human evolution, this approach could be extended to study other species.
Collapse
|
32
|
Siqueira JD, Dominguez-Bello MG, Contreras M, Lander O, Caballero-Arias H, Xutao D, Noya-Alarcon O, Delwart E. Complex virome in feces from Amerindian children in isolated Amazonian villages. Nat Commun 2018; 9:4270. [PMID: 30323210 PMCID: PMC6189175 DOI: 10.1038/s41467-018-06502-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/06/2018] [Indexed: 01/22/2023] Open
Abstract
The number of viruses circulating in small isolated human populations may be reduced by viral extinctions and rare introductions. Here we used viral metagenomics to characterize the eukaryotic virome in feces from healthy children from a large urban center and from three Amerindian villages with minimal outside contact. Numerous human enteric viruses, mainly from the Picornaviridae and Caliciviridae families, were sequenced from each of the sites. Multiple children from the same villages shed closely related viruses reflecting frequent transmission clusters. Feces of isolated villagers also contained multiple viral genomes of unknown cellular origin from the Picornavirales order and CRESS-DNA group and higher levels of nematode and protozoan DNA. Despite cultural and geographic isolation, the diversity of enteric human viruses was therefore not reduced in these Amazonian villages. Frequent viral introductions and/or increased susceptibility to enteric infections may account for the complex fecal virome of Amerindian children in isolated villages.
Collapse
Affiliation(s)
- Juliana D Siqueira
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, 20.231-050, Brazil
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology and of Anthropology, Rutgers University, New Brunswick, NJ, 08901-8554, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Orlana Lander
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela
| | - Hortensia Caballero-Arias
- Department of Anthropology, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Deng Xutao
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
| | - Oscar Noya-Alarcon
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela.,Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho, 7101, Venezuela
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, 94118, USA. .,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA.
| |
Collapse
|
33
|
Abstract
Supplemental Digital Content is available in the text Objective: HIV incidence in the Canadian province of Saskatchewan, where Indigenous persons make up 80% of those infected, are among the highest on the continent. Reports of accelerated HIV progression, associated with carriage of certain human leukocyte antigen (HLA) alleles (including the typically protective HLA-B∗51) have also emerged from the region. Given that acquisition of HIV preadapted to host HLA negatively impacts clinical outcome, we hypothesized that HIV-host adaptation may be elevated in Saskatchewan. Design: Comparative analysis of population-level HIV sequence datasets from Saskatchewan and elsewhere in Canada/USA. Methods: We analyzed 1144 HIV subtype B Pol sequences collected in Saskatchewan between 2000 and 2016, comprising ∼65% of cumulative provincial HIV cases, for the presence of 70 HLA-associated Pol mutations. Sequences from British Columbia (N = 6525) and elsewhere in Canada/USA (N = 6517) were used for comparison. HIV adaptation levels to 34 HLA alleles were also computed. Putative HIV transmission clusters were identified, and the prevalence of HLA-associated adaptations within and outside these clusters was investigated. Results: Analyses confirmed significantly elevated and temporally increasing levels of HIV adaptation to commonly expressed HLA alleles, in particular B∗51. Notably, HLA-adapted HIV strains were significantly enriched among phylogenetic clusters in Saskatchewan. Conclusion: Extensive circulating HIV adaptation to HLA in Saskatchewan provides a plausible explanation for accelerated progression, while enrichment of adapted variants in phylogenetic clusters suggests they are being widely transmitted. Results highlight the utility of Pol sequences, routinely collected for drug resistance monitoring, for surveillance of HIV-host adaptation, and underscore the urgent need to expand HIV prevention and treatment programmes in Saskatchewan.
Collapse
|
34
|
Fortes-Lima C, Bybjerg-Grauholm J, Marin-Padrón LC, Gomez-Cabezas EJ, Bækvad-Hansen M, Hansen CS, Le P, Hougaard DM, Verdu P, Mors O, Parra EJ, Marcheco-Teruel B. Exploring Cuba's population structure and demographic history using genome-wide data. Sci Rep 2018; 8:11422. [PMID: 30061702 PMCID: PMC6065444 DOI: 10.1038/s41598-018-29851-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/10/2018] [Indexed: 12/31/2022] Open
Abstract
Cuba is the most populated country in the Caribbean and has a rich and heterogeneous genetic heritage. Here, we take advantage of dense genomic data from 860 Cuban individuals to reconstruct the genetic structure and ancestral origins of this population. We found distinct admixture patterns between and within the Cuban provinces. Eastern provinces have higher African and Native American ancestry contributions (average 26% and 10%, respectively) than the rest of the Cuban provinces (average 17% and 5%, respectively). Furthermore, in the Eastern Cuban region, we identified more intense sex-specific admixture patterns, strongly biased towards European male and African/Native American female ancestries. Our subcontinental ancestry analyses in Cuba highlight the Iberian population as the best proxy European source population, South American and Mesoamerican populations as the closest Native American ancestral component, and populations from West Central and Central Africa as the best proxy sources of the African ancestral component. Finally, we found complex admixture processes involving two migration pulses from both Native American and African sources. Most of the inferred Native American admixture events happened early during the Cuban colonial period, whereas the African admixture took place during the slave trade and more recently as a probable result of large-scale migrations from Haiti.
Collapse
Affiliation(s)
- Cesar Fortes-Lima
- UMR7206 Eco-Anthropology and Ethno-Biology, CNRS-MNHN-University Paris Diderot, Musée de l'Homme, Paris, 75016, France
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, 2300, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, 8000, Denmark
| | | | | | - Marie Bækvad-Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, 2300, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, 8000, Denmark
| | - Christine Søholm Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, 2300, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, 8000, Denmark
| | - Phuong Le
- Department of Anthropology, University of Toronto, Mississauga, ON L5L 1C6, Canada
| | - David Michael Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, 2300, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, 8000, Denmark
| | - Paul Verdu
- UMR7206 Eco-Anthropology and Ethno-Biology, CNRS-MNHN-University Paris Diderot, Musée de l'Homme, Paris, 75016, France
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus University, Aarhus, 8000, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Aarhus, 8240, Denmark
| | - Esteban J Parra
- Department of Anthropology, University of Toronto, Mississauga, ON L5L 1C6, Canada.
| | | |
Collapse
|
35
|
Branco C, Velasco M, Benguigui M, Currat M, Ray N, Arenas M. Consequences of diverse evolutionary processes on american genetic gradients of modern humans. Heredity (Edinb) 2018; 121:548-556. [PMID: 30022169 DOI: 10.1038/s41437-018-0122-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 11/09/2022] Open
Abstract
European genetic gradients of modern humans were initially interpreted as a consequence of the demic diffusion of expanding Neolithic farmers. However, recent studies showed that these gradients may also be influenced by other evolutionary processes such as population admixture or range contractions. Genetic gradients were observed in the Americas, although their specific evolutionary causes were not investigated. Here we extended the approach used to study genetic gradients in Europe to analyze the influence of diverse evolutionary scenarios on American genetic gradients. Using extensive computer simulations, we evaluated the impact of (i) admixture between expansion waves of modern humans, (ii) the presence of ice-sheets during the last glacial maximum (LGM) and (iii) long-distance dispersal (LDD) events, on the genetic gradients (detected by principal component analysis) of the entire continent, North America and South America. The specific simulation of North and South America showed that genetic gradients are usually orthogonal to the direction of range expansions-either expansions from Bering or posterior re-expansions to recolonize northern regions after ice sheets melting-and we suggest that they result from allele surfing processes. Conversely, our results on the entire continent show a northwest-southeast gradient obtained with any scenario, which we interpreted as a consequence of isolation by distance along the long length of the continent. These findings suggest that distinct genetic gradients can be detected at different regions of the Americas and that subcontinent regions present gradients more sensible to evolutionary and environmental factors (such as LDD and the LGM) than the whole continent.
Collapse
Affiliation(s)
- Catarina Branco
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Miguel Velasco
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Macarena Benguigui
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mathias Currat
- Anthropology, Genetics and Peopling History Lab, Department of Genetics & Evolution -Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Nicolas Ray
- EnviroSPACE Lab, Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland.,Institute of Global Health, University of Geneva, Geneva, Switzerland
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain. .,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal. .,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal. .,Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
| |
Collapse
|
36
|
Lindo J, Rogers M, Mallott EK, Petzelt B, Mitchell J, Archer D, Cybulski JS, Malhi RS, DeGiorgio M. Patterns of Genetic Coding Variation in a Native American Population before and after European Contact. Am J Hum Genet 2018; 102:806-815. [PMID: 29706345 PMCID: PMC5986697 DOI: 10.1016/j.ajhg.2018.03.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
The effects of European colonization on the genomes of Native Americans may have produced excesses of potentially deleterious features, mainly due to the severe reductions in population size and corresponding losses of genetic diversity. This assumption, however, neither considers actual genomic patterns that existed before colonization nor does it adequately capture the effects of admixture. In this study, we analyze the whole-exome sequences of modern and ancient individuals from a Northwest Coast First Nation, with a demographic history similar to other indigenous populations from the Americas. We show that in approximately ten generations from initial European contact, the modern individuals exhibit reduced levels of novel and low-frequency variants, a lower proportion of potentially deleterious alleles, and decreased heterozygosity when compared to their ancestors. This pattern can be explained by a dramatic population decline, resulting in the loss of potentially damaging low-frequency variants, and subsequent admixture. We also find evidence that the indigenous population was on a steady decline in effective population size for several thousand years before contact, which emphasizes regional demography over the common conception of a uniform expansion after entry into the Americas. This study examines the genomic consequences of colonialism on an indigenous group and describes the continuing role of gene flow among modern populations.
Collapse
Affiliation(s)
- John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Mary Rogers
- Department of Anthropology, University of Illinois, Urbana, IL 61821, USA
| | - Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA
| | | | | | - David Archer
- Department of Anthropology, Northwestern Community College, Prince Rupert, BC V8J 3P6, Canada
| | - Jerome S Cybulski
- Research, Canadian Museum of History, Gatineau, QC K1A 0M8, Canada; Department of Anthropology, University of Western Ontario, London, ON N6A 3K7, Canada; Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois, Urbana, IL 61821, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61820, USA.
| | - Michael DeGiorgio
- Departments of Biology and Statistics, Pennsylvania State University, University Park, PA 16801, USA; Institute for CyberScience, Pennsylvania State University, University Park, PA 16801, USA.
| |
Collapse
|
37
|
Russo MG, Mendisco F, Avena SA, Crespo CM, Arencibia V, Dejean CB, Seldes V. Ancient DNA reveals temporal population structure within the South‐Central Andes area. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 166:851-860. [DOI: 10.1002/ajpa.23475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 03/15/2018] [Accepted: 03/18/2018] [Indexed: 11/05/2022]
Affiliation(s)
- M. Gabriela Russo
- Universidad Maimónides, CONICET, Equipo de Antropología BiológicaDepartamento de Cs. Naturales y Antropológicas, CEBBADBuenos Aires C1405BCK Argentina
| | - Fanny Mendisco
- Laboratory of Molecular Anthropology and Image Synthesis (AMIS)University Paul Sabatier (Toulouse III), Faculté de Médecine, CNRSToulouse UMR 5288 France
| | - Sergio A. Avena
- Universidad Maimónides, CONICET, Equipo de Antropología BiológicaDepartamento de Cs. Naturales y Antropológicas, CEBBADBuenos Aires C1405BCK Argentina
- UBA, Sección de Antropología Biológica, ICAFFyLBuenos Aires C1406CQJ Argentina
| | - Cristian M. Crespo
- Universidad Maimónides, CONICET, Equipo de Antropología BiológicaDepartamento de Cs. Naturales y Antropológicas, CEBBADBuenos Aires C1405BCK Argentina
| | - Valeria Arencibia
- Universidad Maimónides, Equipo de Antropología BiológicaDepartamento de Cs. Naturales y Antropológicas, CEBBADBuenos Aires C1405BCK Argentina
| | - Cristina B. Dejean
- UBA, Sección de Antropología Biológica, ICAFFyLBuenos Aires C1406CQJ Argentina
- Universidad Maimónides, Equipo de Antropología BiológicaDepartamento de Cs. Naturales y Antropológicas, CEBBADBuenos Aires C1405BCK Argentina
| | - Verónica Seldes
- UBA, CONICET, Instituto Interdisciplinario Tilcara, Centro Universitario TilcaraFFyLTilcara Jujuy Y4624AFI Argentina
| |
Collapse
|
38
|
Tallavaara M, Eronen JT, Luoto M. Productivity, biodiversity, and pathogens influence the global hunter-gatherer population density. Proc Natl Acad Sci U S A 2018; 115:1232-1237. [PMID: 29282314 PMCID: PMC5819417 DOI: 10.1073/pnas.1715638115] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The environmental drivers of species distributions and abundances are at the core of ecological research. However, the effects of these drivers on human abundance are not well-known. Here, we report how net primary productivity, biodiversity, and pathogen stress affect human population density using global ethnographic hunter-gatherer data. Our results show that productivity has significant effects on population density globally. The most important direct drivers, however, depend on environmental conditions: biodiversity influences population density exclusively in low-productivity regions, whereas pathogen stress does so in high-productivity regions. Our results also indicate that subtropical and temperate forest biomes provide the highest carrying capacity for hunter-gatherer populations. These findings document that environmental factors play a key role in shaping global population density patterns of preagricultural humans.
Collapse
Affiliation(s)
- Miikka Tallavaara
- Department of Geosciences and Geography, University of Helsinki, FI-00014 Helsinki, Finland;
| | - Jussi T Eronen
- Department of Geosciences and Geography, University of Helsinki, FI-00014 Helsinki, Finland
- BIOS Research Unit, FI-00170 Helsinki, Finland
| | - Miska Luoto
- Department of Geosciences and Geography, University of Helsinki, FI-00014 Helsinki, Finland
| |
Collapse
|
39
|
Brandini S, Bergamaschi P, Cerna MF, Gandini F, Bastaroli F, Bertolini E, Cereda C, Ferretti L, Gómez-Carballa A, Battaglia V, Salas A, Semino O, Achilli A, Olivieri A, Torroni A. The Paleo-Indian Entry into South America According to Mitogenomes. Mol Biol Evol 2018; 35:299-311. [PMID: 29099937 PMCID: PMC5850732 DOI: 10.1093/molbev/msx267] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recent and compelling archaeological evidence attests to human presence ∼14.5 ka at multiple sites in South America and a very early exploitation of extreme high-altitude Andean environments. Considering that, according to genetic evidence, human entry into North America from Beringia most likely occurred ∼16 ka, these archeological findings would imply an extremely rapid spread along the double continent. To shed light on this issue from a genetic perspective, we first completely sequenced 217 novel modern mitogenomes of Native American ancestry from the northwestern area of South America (Ecuador and Peru); we then evaluated them phylogenetically together with other available mitogenomes (430 samples, both modern and ancient) from the same geographic area and, finally, with all closely related mitogenomes from the entire double continent. We detected a large number (N = 48) of novel subhaplogroups, often branching into further subclades, belonging to two classes: those that arose in South America early after its peopling and those that instead originated in North or Central America and reached South America with the first settlers. Coalescence age estimates for these subhaplogroups provide time boundaries indicating that early Paleo-Indians probably moved from North America to the area corresponding to modern Ecuador and Peru over the short time frame of ∼1.5 ka comprised between 16.0 and 14.6 ka.
Collapse
Affiliation(s)
- Stefania Brandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Paola Bergamaschi
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Servizio di Immunoematologia e Medicina Trasfusionale, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marco Fernando Cerna
- Biotechnology Laboratory, Salesian Polytechnic University of Ecuador, Quito, Ecuador
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | | | - Emilie Bertolini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, National Neurological Institute C. Mondino, Pavia, Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alberto Gómez-Carballa
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Unidade de Xenética, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Galicia, Spain
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, Galicia, Spain
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Antonio Salas
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Unidade de Xenética, Galicia, Spain
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Galicia, Spain
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| |
Collapse
|
40
|
Morales-Arce AY, Hofman CA, Duggan AT, Benfer AK, Katzenberg MA, McCafferty G, Warinner C. Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico. Sci Rep 2017; 7:18100. [PMID: 29273718 PMCID: PMC5741722 DOI: 10.1038/s41598-017-18356-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022] Open
Abstract
The northern and southern peripheries of ancient Mesoamerica are poorly understood. There has been speculation over whether borderland cultures such as Greater Nicoya and Casas Grandes represent Mesoamerican outposts in the Isthmo-Colombian area and the Greater Southwest, respectively. Poor ancient DNA preservation in these regions challenged previous attempts to resolve these questions using conventional genetic techniques. We apply advanced in-solution mitogenome capture and high-throughput sequencing to fourteen dental samples obtained from the Greater Nicoya sites of Jícaro and La Cascabel in northwest Costa Rica (n = 9; A.D. 800–1250) and the Casas Grandes sites of Paquimé and Convento in northwest Mexico (n = 5; A.D. 1200–1450). Full mitogenome reconstruction was successful for three individuals from Jícaro and five individuals from Paquimé and Convento. The three Jícaro individuals belong to haplogroup B2d, a haplogroup found today only among Central American Chibchan-speakers. The five Paquimé and Convento individuals belong to haplogroups C1c1a, C1c5, B2f and B2a which, are found in contemporary populations in North America and Mesoamerica. We report the first successfully reconstructed ancient mitogenomes from Central America, and the first genetic evidence of ancestry affinity of the ancient inhabitants of Greater Nicoya and Casas Grandes with contemporary Isthmo-Columbian and Greater Southwest populations, respectively.
Collapse
Affiliation(s)
- Ana Y Morales-Arce
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
| | - Courtney A Hofman
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Adam K Benfer
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - M Anne Katzenberg
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Geoffrey McCafferty
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, 73019, USA. .,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07743, Germany.
| |
Collapse
|
41
|
Llamas B, Willerslev E, Orlando L. Human evolution: a tale from ancient genomes. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0484. [PMID: 27994125 DOI: 10.1098/rstb.2015.0484] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 12/21/2022] Open
Abstract
The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
Collapse
Affiliation(s)
- Bastien Llamas
- Australian Centre for ADNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Wellcome Genome Campus Hinxton, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark .,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, CNRS UMR 5288, 31000 Toulouse, France
| |
Collapse
|
42
|
Koehl AJ, Long JC. The contributions of admixture and genetic drift to diversity among post-contact populations in the Americas. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 165:256-268. [DOI: 10.1002/ajpa.23347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Anthony J. Koehl
- Department of Anthropology; University of New Mexico, MSC01-1040, Anthropology 1; Albuquerque New Mexico 87131
| | - Jeffrey C. Long
- Department of Anthropology; University of New Mexico, MSC01-1040, Anthropology 1; Albuquerque New Mexico 87131
| |
Collapse
|
43
|
Pischedda S, Barral-Arca R, Gómez-Carballa A, Pardo-Seco J, Catelli ML, Álvarez-Iglesias V, Cárdenas JM, Nguyen ND, Ha HH, Le AT, Martinón-Torres F, Vullo C, Salas A. Phylogeographic and genome-wide investigations of Vietnam ethnic groups reveal signatures of complex historical demographic movements. Sci Rep 2017; 7:12630. [PMID: 28974757 PMCID: PMC5626762 DOI: 10.1038/s41598-017-12813-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/14/2017] [Indexed: 01/21/2023] Open
Abstract
The territory of present-day Vietnam was the cradle of one of the world’s earliest civilizations, and one of the first world regions to develop agriculture. We analyzed the mitochondrial DNA (mtDNA) complete control region of six ethnic groups and the mitogenomes from Vietnamese in The 1000 Genomes Project (1000G). Genome-wide data from 1000G (~55k SNPs) were also investigated to explore different demographic scenarios. All Vietnamese carry South East Asian (SEA) haplotypes, which show a moderate geographic and ethnic stratification, with the Mong constituting the most distinctive group. Two new mtDNA clades (M7b1a1f1 and F1f1) point to historical gene flow between the Vietnamese and other neighboring countries. Bayesian-based inferences indicate a time-deep and continuous population growth of Vietnamese, although with some exceptions. The dramatic population decrease experienced by the Cham 700 years ago (ya) fits well with the Nam tiến (“southern expansion”) southwards from their original heartland in the Red River Delta. Autosomal SNPs consistently point to important historical gene flow within mainland SEA, and add support to a main admixture event occurring between Chinese and a southern Asian ancestral composite (mainly represented by the Malay). This admixture event occurred ~800 ya, again coinciding with the Nam tiến.
Collapse
Affiliation(s)
- S Pischedda
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - R Barral-Arca
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - A Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - J Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - M L Catelli
- Equipo Argentino de Antropología Forense, Independencia, 644, Córdoba, Argentina
| | - V Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - J M Cárdenas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Grupo de Investigación en Genética Forense - Instituto Nacional de Medicina Legal y Ciencias Forenses, Bogotá, Colombia
| | - N D Nguyen
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - H H Ha
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - A T Le
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - F Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - C Vullo
- Equipo Argentino de Antropología Forense, Independencia, 644, Córdoba, Argentina
| | - A Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain. .,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.
| |
Collapse
|
44
|
Rothhammer F, Fehren-Schmitz L, Puddu G, Capriles J. Mitochondrial DNA haplogroup variation of contemporary mixed South Americans reveals prehistoric displacements linked to archaeologically-derived culture history. Am J Hum Biol 2017; 29. [DOI: 10.1002/ajhb.23029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 05/12/2017] [Accepted: 06/07/2017] [Indexed: 12/11/2022] Open
Affiliation(s)
| | - Lars Fehren-Schmitz
- Department of Anthropology; University of California Santa Cruz; Santa Cruz California
| | - Giannina Puddu
- Instituto de Alta Investigación; Universidad de Tarapacá; Arica Chile
| | - José Capriles
- Department of Anthropology; Pennsylvania State University; Pennsylvania
| |
Collapse
|
45
|
Levis C, Costa FRC, Bongers F, Peña-Claros M, Clement CR, Junqueira AB, Neves EG, Tamanaha EK, Figueiredo FOG, Salomão RP, Castilho CV, Magnusson WE, Phillips OL, Guevara JE, Sabatier D, Molino JF, López DC, Mendoza AM, Pitman NCA, Duque A, Vargas PN, Zartman CE, Vasquez R, Andrade A, Camargo JL, Feldpausch TR, Laurance SGW, Laurance WF, Killeen TJ, Nascimento HEM, Montero JC, Mostacedo B, Amaral IL, Guimarães Vieira IC, Brienen R, Castellanos H, Terborgh J, Carim MDJV, Guimarães JRDS, Coelho LDS, Matos FDDA, Wittmann F, Mogollón HF, Damasco G, Dávila N, García-Villacorta R, Coronado ENH, Emilio T, Filho DDAL, Schietti J, Souza P, Targhetta N, Comiskey JA, Marimon BS, Marimon BH, Neill D, Alonso A, Arroyo L, Carvalho FA, de Souza FC, Dallmeier F, Pansonato MP, Duivenvoorden JF, Fine PVA, Stevenson PR, Araujo-Murakami A, Aymard C. GA, Baraloto C, do Amaral DD, Engel J, Henkel TW, Maas P, Petronelli P, Revilla JDC, Stropp J, Daly D, Gribel R, Paredes MR, Silveira M, Thomas-Caesar R, Baker TR, da Silva NF, Ferreira LV, Peres CA, Silman MR, Cerón C, Valverde FC, Di Fiore A, Jimenez EM, Mora MCP, Toledo M, Barbosa EM, Bonates LCDM, Arboleda NC, Farias EDS, Fuentes A, Guillaumet JL, Jørgensen PM, Malhi Y, de Andrade Miranda IP, Phillips JF, Prieto A, Rudas A, Ruschel AR, Silva N, von Hildebrand P, Vos VA, Zent EL, Zent S, Cintra BBL, Nascimento MT, Oliveira AA, Ramirez-Angulo H, Ramos JF, Rivas G, Schöngart J, Sierra R, Tirado M, van der Heijden G, Torre EV, Wang O, Young KR, Baider C, Cano A, Farfan-Rios W, Ferreira C, Hoffman B, Mendoza C, Mesones I, Torres-Lezama A, Medina MNU, van Andel TR, Villarroel D, Zagt R, Alexiades MN, Balslev H, Garcia-Cabrera K, Gonzales T, Hernandez L, Huamantupa-Chuquimaco I, Manzatto AG, Milliken W, Cuenca WP, Pansini S, Pauletto D, Arevalo FR, Reis NFC, Sampaio AF, Giraldo LEU, Sandoval EHV, Gamarra LV, Vela CIA, ter Steege H. Persistent effects of pre-Columbian plant domestication on Amazonian forest composition. Science 2017; 355:925-931. [DOI: 10.1126/science.aal0157] [Citation(s) in RCA: 306] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/20/2017] [Indexed: 11/02/2022]
|
46
|
Perez SI, Postillone MB, Rindel D. Domestication and human demographic history in South America. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 163:44-52. [PMID: 28109124 DOI: 10.1002/ajpa.23176] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 01/02/2017] [Accepted: 01/04/2017] [Indexed: 11/12/2022]
Abstract
OBJECTIVES The early groups of hunter-gatherers who peopled South America faced significant ecological changes in their trophic niche for a relatively short period after the initial peopling. In particular, the incorporation of cultigens during the Holocene led to a wider trophic niche and probably to an increased carrying capacity of the environment. Here, we study the relationship between the incorporation of domestic resources during the Holocene and the demographic dynamics of human populations at a regional scale in South America. MATERIAL AND METHODS We employ mitochondrial DNA (mtDNA), radiocarbon data and Bayesian methods to estimate differences in population size, human occupation and explore the demographic changes of human populations in three regions (i.e., South-Central Andes, Northwest, and South Patagonia). We also use archaeological evidence to infer the main diet changes in these regions. RESULTS The absolute population size during the later Late Holocene was fifteen times larger in the South-Central Andes than in Northwest Patagonia, and two times larger in the latter region than in South Patagonia. The South-Central Andes display the earlier and more abrupt population growth, beginning about 9000 years BP, whereas Northwest Patagonia exhibits a more slow growth, beginning about 7000-7500 years BP. South Patagonia represents a later and slower population increase. DISCUSSION In this work we uncovered a well-supported pattern of the demographic change in the populations from South-Central Andes and Patagonia, obtained on the basis of different data and quantitative approaches, which suggests that the incorporation of domestic resources was paramount for the demographic expansion of these populations during the Holocene.
Collapse
Affiliation(s)
- S Ivan Perez
- División Antropología, (FCNyM, UNLP), CONICET, La Plata, Argentina
| | - María Bárbara Postillone
- Departamento de Ciencias Naturales y Antropológicas, (CEBBAD, UM), CONICET, Buenos Aires, Argentina
| | - Diego Rindel
- Instituto Nacional de Antropología y Pensamiento Latinoamericano, CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
47
|
A time transect of exomes from a Native American population before and after European contact. Nat Commun 2016; 7:13175. [PMID: 27845766 PMCID: PMC5116069 DOI: 10.1038/ncomms13175] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/07/2016] [Indexed: 12/20/2022] Open
Abstract
A major factor for the population decline of Native Americans after European contact has been attributed to infectious disease susceptibility. To investigate whether a pre-existing genetic component contributed to this phenomenon, here we analyse 50 exomes of a continuous population from the Northwest Coast of North America, dating from before and after European contact. We model the population collapse after European contact, inferring a 57% reduction in effective population size. We also identify signatures of positive selection on immune-related genes in the ancient but not the modern group, with the strongest signal deriving from the human leucocyte antigen (HLA) gene HLA-DQA1. The modern individuals show a marked frequency decrease in the same alleles, likely due to the environmental change associated with European colonization, whereby negative selection may have acted on the same gene after contact. The evident shift in selection pressures correlates to the regional European-borne epidemics of the 1800s. A First Nation population declined after European contact, likely as a result of infectious disease. Here, researchers partner with indigenous communities to analyse ancient and modern Native American exomes, and find a shift in selection pressure on immune genes, correlated to European-borne epidemics.
Collapse
|
48
|
Bolnick DA, Raff JA, Springs LC, Reynolds AW, Miró-Herrans AT. Native American Genomics and Population Histories. ANNUAL REVIEW OF ANTHROPOLOGY 2016. [DOI: 10.1146/annurev-anthro-102215-100036] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Studies of Native American genetic diversity and population history have been transformed over the last decade by important developments in anthropological genetics. During this time, researchers have adopted new DNA technologies and computational approaches for analyzing genomic data, and they have become increasingly sensitive to the views of research participants and communities. As new methods are applied to long-standing questions, and as more research is conducted in collaboration with indigenous communities, we are gaining new insights into the history and diversity of indigenous populations. This review discusses the recent methodological advances and genetic studies that have improved our understanding of Native American genomics and population histories. We synthesize current knowledge about Native American genomic variation and build a model of population history in the Americas. We also discuss the broader implications of this research for anthropology and related disciplines, and we highlight challenges and other considerations for future research.
Collapse
Affiliation(s)
- Deborah A. Bolnick
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Population Research Center, University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A. Raff
- Department of Anthropology, University of Kansas, Lawrence, Kansas 66045-7556
| | - Lauren C. Springs
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
| | - Austin W. Reynolds
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Aida T. Miró-Herrans
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
| |
Collapse
|
49
|
Contreras-Cubas C, Sánchez-Hernández BE, García-Ortiz H, Martínez-Hernández A, Barajas-Olmos F, Cid M, Mendoza-Caamal EC, Centeno-Cruz F, Ortiz-Cruz G, Jiménez-López JC, Córdova EJ, Salas-Bautista EG, Saldaña-Alvarez Y, Fernández-López JC, Mutchinick OM, Orozco L. Heterogenous Distribution of MTHFR Gene Variants among Mestizos and Diverse Amerindian Groups from Mexico. PLoS One 2016; 11:e0163248. [PMID: 27649570 PMCID: PMC5029802 DOI: 10.1371/journal.pone.0163248] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 09/05/2016] [Indexed: 11/18/2022] Open
Abstract
Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme in folate metabolism. Folate deficiency has been related to several conditions, including neural tube defects (NTDs) and cardiovascular diseases. Hence, MTHFR genetic variants have been studied worldwide, particularly the C677T and A1298C. We genotyped the C677T and A1298C MTHFR polymorphisms in Mexican Amerindians (MAs), from the largest sample included in a genetic study (n = 2026, from 62 ethnic groups), and in a geographically-matched Mexican Mestizo population (MEZ, n = 638). The 677T allele was most frequent in Mexican individuals, particularly in MAs. The frequency of this allele in both MAs and MEZs was clearly enriched in the South region of the country, followed by the Central East and South East regions. In contrast, the frequency of the 1298C risk allele in Mexicans was one of the lowest in the world. Both in MAs and MEZs the variants 677T and 1298C displayed opposite allele frequency gradients from southern to northern Mexico. Our findings suggest that in Mestizos the 677T allele was derived from Amerindians while the 1298C allele was a European contribution. Some subgroups showed an allele frequency distribution that highlighted their genetic diversity. Notably, the distribution of the frequency of the 677T allele was consistent with that of the high incidence of NTDs reported in MEZ.
Collapse
Affiliation(s)
- Cecilia Contreras-Cubas
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Beatríz E. Sánchez-Hernández
- Genetic Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, SS, Mexico City, Mexico
| | - Humberto García-Ortiz
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Miguel Cid
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Elvia C. Mendoza-Caamal
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Federico Centeno-Cruz
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Gabriela Ortiz-Cruz
- Genetic Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, SS, Mexico City, Mexico
| | - José Concepción Jiménez-López
- Physic Anthropology Direction, Instituto Nacional de Antropología e Historia, Museo Nacional de Antropología, Mexico City, Mexico
| | - Emilio J. Córdova
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | - Eva Gabriela Salas-Bautista
- Physic Anthropology Direction, Instituto Nacional de Antropología e Historia, Museo Nacional de Antropología, Mexico City, Mexico
| | - Yolanda Saldaña-Alvarez
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
| | | | - Osvaldo M. Mutchinick
- Genetic Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, SS, Mexico City, Mexico
| | - Lorena Orozco
- Inmunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genómica, SS, Mexico City, Mexico
- * E-mail:
| |
Collapse
|
50
|
Valverde G, Barreto Romero MI, Flores Espinoza I, Cooper A, Fehren-Schmitz L, Llamas B, Haak W. Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru's Central Coast during the Middle Horizon. PLoS One 2016; 11:e0155508. [PMID: 27248693 PMCID: PMC4889149 DOI: 10.1371/journal.pone.0155508] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 04/30/2016] [Indexed: 11/19/2022] Open
Abstract
The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650–1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region’s demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500–700 AD), Wari (Middle Horizon, 800–1000 AD) and Ychsma (Late Intermediate Period, 1000–1450 AD). We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast.
Collapse
Affiliation(s)
- Guido Valverde
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
| | | | | | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Lars Fehren-Schmitz
- Department of Anthropology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Max Planck Institute for the Science of Human History, Jena, Germany
| |
Collapse
|