1
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Rey-Vargas L, Bejarano-Rivera LM, Serrano-Gómez SJ. Genetic ancestry is related to potential sources of breast cancer health disparities among Colombian women. PLoS One 2024; 19:e0306037. [PMID: 38935662 PMCID: PMC11210782 DOI: 10.1371/journal.pone.0306037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/09/2024] [Indexed: 06/29/2024] Open
Abstract
Breast cancer health disparities are linked to clinical-pathological determinants, socioeconomic inequities, and biological factors such as genetic ancestry. These factors collectively interact in complex ways, influencing disease behavior, especially among highly admixed populations like Colombians. In this study, we assessed contributing factors to breast cancer health disparities according to genetic ancestry in Colombian patients from a national cancer reference center. We collected non-tumoral paraffin embedded (FFPE) blocks from 361 women diagnosed with breast cancer at the National Cancer Institute (NCI) to estimate genetic ancestry using a 106-ancestry informative marker (AIM) panel. Differences in European, Indigenous American (IA) and African ancestry fractions were analyzed according to potential sources of breast cancer health disparities, like etiology, tumor-biology, treatment administration, and socioeconomic-related factors using a Kruskal-Wallis test. Our analysis revealed a significantly higher IA ancestry among overweight patients with larger tumors and those covered by a subsidized health insurance. Conversely, we found a significantly higher European ancestry among patients with smaller tumors, residing in middle-income households, and affiliated to the contributory health regime, whereas a higher median of African ancestry was observed among patients with either a clinical, pathological, or stable response to neoadjuvant treatment. Altogether, our results suggest that the genetic legacy among Colombian patients, measured as genetic ancestry fractions, may be reflected in many of the clinical-pathological variables and socioeconomic factors that end up contributing to health disparities for this disease.
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Affiliation(s)
- Laura Rey-Vargas
- National Cancer Institute, Cancer Biology Research Group, Bogotá, D.C, Colombia
- Doctoral Program in Biological Sciences, Pontificia Universidad Javeriana, Bogotá, D.C, Colombia
| | | | - Silvia J. Serrano-Gómez
- National Cancer Institute, Cancer Biology Research Group, Bogotá, D.C, Colombia
- National Cancer Institute, Research Support and Follow-Up Group, Bogotá, D.C, Colombia
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2
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Barquera R, Del Castillo-Chávez O, Nägele K, Pérez-Ramallo P, Hernández-Zaragoza DI, Szolek A, Rohrlach AB, Librado P, Childebayeva A, Bianco RA, Penman BS, Acuña-Alonzo V, Lucas M, Lara-Riegos JC, Moo-Mezeta ME, Torres-Romero JC, Roberts P, Kohlbacher O, Warinner C, Krause J. Ancient genomes reveal insights into ritual life at Chichén Itzá. Nature 2024; 630:912-919. [PMID: 38867041 PMCID: PMC11208145 DOI: 10.1038/s41586-024-07509-7] [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: 03/30/2023] [Accepted: 05/02/2024] [Indexed: 06/14/2024]
Abstract
The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (AD 600-1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica1-4. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population's genetic ties to other Mesoamerican groups, remain unanswered2. Here we present genome-wide data obtained from 64 subadult individuals dating to around AD 500-900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes5, but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.
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Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany.
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.
| | - Oana Del Castillo-Chávez
- Centro INAH Yucatán, Instituto Nacional de Antropología e Historia (INAH), Mérida, Yucatán, Mexico.
| | - Kathrin Nägele
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- University of the Basque Country (EHU), San Sebastián-Donostia, Spain
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology and Cultural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Diana Iraíz Hernández-Zaragoza
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - András Szolek
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Tübingen, Germany
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Adam Benjamin Rohrlach
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Pablo Librado
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Department of Anthropology, University of Texas at Austin, Austin, TX, USA
| | - Raffaela Angelina Bianco
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
| | - Bridget S Penman
- The Zeeman Institute and the School of Life Sciences, University of Warwick, Coventry, UK
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mary Lucas
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | | | | | | | - Patrick Roberts
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center, University of Tübingen, Tübingen, Germany
- Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany.
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3
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Roman S, Campos-Medina L, Leal-Mercado L. Personalized nutrition: the end of the one-diet-fits-all era. Front Nutr 2024; 11:1370595. [PMID: 38854164 PMCID: PMC11157041 DOI: 10.3389/fnut.2024.1370595] [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: 01/15/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024] Open
Abstract
Personalized Nutrition emerged as a new trend for providing nutritional and food advice based on the individual's genetic composition, a field driven by the advancements in the multi-omic sciences throughout the last century. It intends not only to tailor the recommended daily allowances of nutrients and functional foods that a person may need but also to maintain the principles of sustainability and eco-friendliness. This principle implies the implementation of strategies within the healthcare system to advocate for the ending of the one-diet-fits-all paradigm by considering a personalized diet as an ally to prevent diet-related chronic diseases. In this Perspective, we highlight the potential benefits of such a paradigm within the region of Latin America, particularly Mexico, where the genetic admixture of the population, food biodiversity, and food culture provide unique opportunities to establish personalized nutrigenetic strategies. These strategies could play a crucial role in preventing chronic diseases and addressing the challenges confronted in the region.
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Affiliation(s)
- Sonia Roman
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Liliana Campos-Medina
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
- Doctoral Program in Molecular Biology in Medicine, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Leonardo Leal-Mercado
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
- Doctoral Program in Molecular Biology in Medicine, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
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4
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Garro-Núñez D, Picado-Martínez MJ, Espinoza-Campos E, Ugalde-Araya D, Macaya G, Raventós H, Chavarría-Soley G. Systematic exploration of a decade of publications on psychiatric genetics in Latin America. Am J Med Genet B Neuropsychiatr Genet 2024; 195:e32960. [PMID: 37860990 DOI: 10.1002/ajmg.b.32960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 08/08/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023]
Abstract
Psychiatric disorders have a great impact in terms of mortality, morbidity, and disability across the lifespan. Considerable effort has been devoted to understanding their complex and heterogeneous genetic architecture, including diverse ancestry populations. Our aim was to review the psychiatric genetics research published with Latin American populations from 2010 to 2019, and classify it according to country of origin, type of analysis, source of funding, and other variables. We found that most publications came from Brazil, Mexico, and Colombia. Also, local funds are generally not large enough for genome-wide studies in Latin America, with the exception of Brazil and Mexico; larger studies are often done in collaboration with international partners, mostly funded by US agencies. In most of the larger studies, the participants are individuals of Latin American ancestry living in the United States, which limits the potential for exploring the complex gene-environment interaction. Family studies, traditionally strong in Latin America, represent about 30% of the total research publications. Scarce local resources for research in Latin America have probably been an important limitation for conducting bigger and more complex studies, contributing to the reduced representation of these populations in global psychiatric genetics studies. Increasing diversity must be a goal to improve generalizability and applicability in clinical settings.
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Affiliation(s)
| | | | | | - Daniela Ugalde-Araya
- Center for Research in Cellular and Molecular Biology, Universidad de Costa Rica, San José, Costa Rica
| | - Gabriel Macaya
- Center for Research in Cellular and Molecular Biology, Universidad de Costa Rica, San José, Costa Rica
| | - Henriette Raventós
- Biology School, Universidad de Costa Rica, San José, Costa Rica
- Center for Research in Cellular and Molecular Biology, Universidad de Costa Rica, San José, Costa Rica
| | - Gabriela Chavarría-Soley
- Biology School, Universidad de Costa Rica, San José, Costa Rica
- Center for Research in Cellular and Molecular Biology, Universidad de Costa Rica, San José, Costa Rica
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5
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Hünemeier T. Biogeographic Perspectives on Human Genetic Diversification. Mol Biol Evol 2024; 41:msae029. [PMID: 38349332 PMCID: PMC10917211 DOI: 10.1093/molbev/msae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 03/08/2024] Open
Abstract
Modern humans originated in Africa 300,000 yr ago, and before leaving their continent of origin, they underwent a process of intense diversification involving complex demographic dynamics. Upon exiting Africa, different populations emerged on the four other inhabited continents, shaped by the interplay of various evolutionary processes, such as migrations, founder effects, and natural selection. Within each region, continental populations, in turn, diversified and evolved almost independently for millennia. As a backdrop to this diversification, introgressions from archaic species contributed to establishing different patterns of genetic diversity in different geographic regions, reshaping our understanding of our species' variability. With the increasing availability of genomic data, it has become possible to delineate the subcontinental human population structure precisely. However, the bias toward the genomic research focused on populations from the global North has limited our understanding of the real diversity of our species and the processes and events that guided different human groups throughout their evolutionary history. This perspective is part of a series of articles celebrating 40 yr since our journal, Molecular Biology and Evolution, was founded (Russo et al. 2024). The perspective is accompanied by virtual issues, a selection of papers on human diversification published by Genome Biology and Evolution and Molecular Biology and Evolution.
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Affiliation(s)
- Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
- Population Genetics Department, Institute of Evolutionary Biology (IBE - CSIC/Universitat Pompeu Fabra), 08003 Barcelona, Spain
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6
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Espitia Fajardo M, Rivera Franco N, Braga Y, Barreto G. New Y-SNPs in QM3 indigenous populations of Colombia. PLoS One 2023; 18:e0294516. [PMID: 38055663 PMCID: PMC10699635 DOI: 10.1371/journal.pone.0294516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023] Open
Abstract
In evolutionary studies of human populations based on the Y chromosome, the majority of Native Americans belong to the QM3 lineage. Therefore, to study the history of groups inhabiting northern South America, it is necessary to have a higher resolution of the tree. The objective of this work was to identify new SNPs of the QM3 lineage that would allow the evaluation of the phylogenetic relationships between Andean and Amazonian populations of Colombia. Sequences previously obtained from two Y chromosomes of Amazonian populations were used, from which 13 potential SNPs were selected and typed in 171 Amazonian samples from the Vaupés region and in 60 samples from the Pasto, Nasa, Embera, Arhuaco and Kogüi ethnic groups of the Andean region. In addition, the main SNPs/markers (L56, L54, M346, M848, Z780, CTS11780) defining autochthonous Q lineages were typed, along with others defined by different SNPs/markers as reported in the literature (CTS11357, SA05, Z19319, Z5915, and Z19384). It was found that all the new SNPs are present in the Amazonian samples and only 2 of them are shared with the Embera, Nasa and Pasto, but none with the Kogüi and Arhuaco from the northern Andes, in the Colombian Caribbean. Combining the 13 variants of the present study with 14 previously reported and using TMRCA, a new QM3 tree proposal is generated. This method makes it possible to increase the number of sublineages of QM3 with a higher resolution and to detect differences between the different populations of Vaupés in the Amazon, as in the case of the Kubeos and Pisamiras, the latter of which is in grave danger of extinction. These new sublineages are useful for microevolutionary studies of the Amerindian populations of South America.
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Affiliation(s)
- Marisol Espitia Fajardo
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
| | - Nelson Rivera Franco
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
| | - Yamid Braga
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
- Research Group in Biology, Languages and History, IMGB, Corpodihva, Mitú, Colombia
| | - Guillermo Barreto
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
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7
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Mas-Sandoval A, Mathieson S, Fumagalli M. The genomic footprint of social stratification in admixing American populations. eLife 2023; 12:e84429. [PMID: 38038347 PMCID: PMC10776089 DOI: 10.7554/elife.84429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/22/2023] [Indexed: 12/02/2023] Open
Abstract
Cultural and socioeconomic differences stratify human societies and shape their genetic structure beyond the sole effect of geography. Despite mating being limited by sociocultural stratification, most demographic models in population genetics often assume random mating. Taking advantage of the correlation between sociocultural stratification and the proportion of genetic ancestry in admixed populations, we sought to infer the former process in the Americas. To this aim, we define a mating model where the individual proportions of the genome inherited from Native American, European, and sub-Saharan African ancestral populations constrain the mating probabilities through ancestry-related assortative mating and sex bias parameters. We simulate a wide range of admixture scenarios under this model. Then, we train a deep neural network and retrieve good performance in predicting mating parameters from genomic data. Our results show how population stratification, shaped by socially constructed racial and gender hierarchies, has constrained the admixture processes in the Americas since the European colonization and the subsequent Atlantic slave trade.
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Affiliation(s)
- Alex Mas-Sandoval
- Department of Life Sciences, Silwood Park Campus, Imperial College LondonLondonUnited Kingdom
- Department of Statistical Sciences, University of BolognaBolognaItaly
| | - Sara Mathieson
- Department of Computer Science, Haverford CollegeHaverfordUnited States
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus, Imperial College LondonLondonUnited Kingdom
- School of Biological and Behavioural Sciences, Queen Mary University of LondonLondonUnited Kingdom
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8
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Herrick N, Walsh S. ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications. BMC Bioinformatics 2023; 24:424. [PMID: 37940870 PMCID: PMC10633908 DOI: 10.1186/s12859-023-05548-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Processing raw genomic data for downstream applications such as imputation, association studies, and modeling requires numerous third-party bioinformatics software tools. It is highly time-consuming and resource-intensive with computational demands and storage limitations that pose significant challenges that increase cost. The use of software tools independent of one another, in a disjointed stepwise fashion, increases the difficulty and sets forth higher error rates because of fragmented job executions in alignment, variant calling, and/or build conversion complications. As sequencing data availability grows, the ability for biologists to process it using stable, automated, and reproducible workflows is paramount as it significantly reduces the time to generate clean and reliable data. RESULTS The Iliad suite of genomic data workflows was developed to provide users with seamless file transitions from raw genomic data to a quality-controlled variant call format (VCF) file for downstream applications. Iliad benefits from the efficiency of the Snakemake best practices framework coupled with Singularity and Docker containers for repeatability, portability, and ease of installation. This feat is accomplished from the onset with download acquisitions of any raw data type (FASTQ, CRAM, IDAT) straight through to the generation of a clean merged data file that can combine any user-preferred datasets using robust programs such as BWA, Samtools, and BCFtools. Users can customize and direct their workflow with one straightforward configuration file. Iliad is compatible with Linux, MacOS, and Windows platforms and scalable from a local machine to a high-performance computing cluster. CONCLUSION Iliad offers automated workflows with optimized time and resource management that are comparable to other workflows available but generates analysis-ready VCF files from the most common datatypes using a single command. The storage footprint challenge of genomic data is overcome by utilizing temporary intermediate files before the final VCF is generated. This file is ready for use in imputation, genome-wide association study (GWAS) pipelines, high-throughput population genetics studies, select gene candidate studies, and more. Iliad was developed to be portable, compatible, scalable, robust, and repeatable with a simplistic setup, so biologists that are less familiar with programming can manage their own big data with this open-source suite of workflows.
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Affiliation(s)
- Noah Herrick
- Department of Biology, Indiana University Indianapolis, 723 W. Michigan Street, Indianapolis, IN, USA.
| | - Susan Walsh
- Department of Biology, Indiana University Indianapolis, 723 W. Michigan Street, Indianapolis, IN, USA
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9
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Ziyatdinov A, Torres J, Alegre-Díaz J, Backman J, Mbatchou J, Turner M, Gaynor SM, Joseph T, Zou Y, Liu D, Wade R, Staples J, Panea R, Popov A, Bai X, Balasubramanian S, Habegger L, Lanche R, Lopez A, Maxwell E, Jones M, García-Ortiz H, Ramirez-Reyes R, Santacruz-Benítez R, Nag A, Smith KR, Damask A, Lin N, Paulding C, Reppell M, Zöllner S, Jorgenson E, Salerno W, Petrovski S, Overton J, Reid J, Thornton TA, Abecasis G, Berumen J, Orozco-Orozco L, Collins R, Baras A, Hill MR, Emberson JR, Marchini J, Kuri-Morales P, Tapia-Conyer R. Genotyping, sequencing and analysis of 140,000 adults from Mexico City. Nature 2023; 622:784-793. [PMID: 37821707 PMCID: PMC10600010 DOI: 10.1038/s41586-023-06595-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/31/2023] [Indexed: 10/13/2023]
Abstract
The Mexico City Prospective Study is a prospective cohort of more than 150,000 adults recruited two decades ago from the urban districts of Coyoacán and Iztapalapa in Mexico City1. Here we generated genotype and exome-sequencing data for all individuals and whole-genome sequencing data for 9,950 selected individuals. We describe high levels of relatedness and substantial heterogeneity in ancestry composition across individuals. Most sequenced individuals had admixed Indigenous American, European and African ancestry, with extensive admixture from Indigenous populations in central, southern and southeastern Mexico. Indigenous Mexican segments of the genome had lower levels of coding variation but an excess of homozygous loss-of-function variants compared with segments of African and European origin. We estimated ancestry-specific allele frequencies at 142 million genomic variants, with an effective sample size of 91,856 for Indigenous Mexican ancestry at exome variants, all available through a public browser. Using whole-genome sequencing, we developed an imputation reference panel that outperforms existing panels at common variants in individuals with high proportions of central, southern and southeastern Indigenous Mexican ancestry. Our work illustrates the value of genetic studies in diverse populations and provides foundational imputation and allele frequency resources for future genetic studies in Mexico and in the United States, where the Hispanic/Latino population is predominantly of Mexican descent.
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Affiliation(s)
| | - Jason Torres
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
| | - Jesús Alegre-Díaz
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | | | | | - Michael Turner
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Oxford Kidney Unit, Churchill Hospital, Oxford, UK
| | | | | | - Yuxin Zou
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Daren Liu
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Rachel Wade
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | - Alex Popov
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | - Alex Lopez
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | - Raul Ramirez-Reyes
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Rogelio Santacruz-Benítez
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Abhishek Nag
- Centre for Genomics Research, Discovery Sciences, Research and Development Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | - Katherine R Smith
- Centre for Genomics Research, Discovery Sciences, Research and Development Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | - Amy Damask
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Nan Lin
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, Research and Development Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | | | | | | | | | - Jaime Berumen
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | | | - Rory Collins
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Michael R Hill
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan R Emberson
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Pablo Kuri-Morales
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
- Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| | - Roberto Tapia-Conyer
- Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico.
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10
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Caggiano C, Boudaie A, Shemirani R, Mefford J, Petter E, Chiu A, Ercelen D, He R, Tward D, Paul KC, Chang TS, Pasaniuc B, Kenny EE, Shortt JA, Gignoux CR, Balliu B, Arboleda VA, Belbin G, Zaitlen N. Disease risk and healthcare utilization among ancestrally diverse groups in the Los Angeles region. Nat Med 2023; 29:1845-1856. [PMID: 37464048 PMCID: PMC11121511 DOI: 10.1038/s41591-023-02425-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 05/30/2023] [Indexed: 07/20/2023]
Abstract
An individual's disease risk is affected by the populations that they belong to, due to shared genetics and environmental factors. The study of fine-scale populations in clinical care is important for identifying and reducing health disparities and for developing personalized interventions. To assess patterns of clinical diagnoses and healthcare utilization by fine-scale populations, we leveraged genetic data and electronic medical records from 35,968 patients as part of the UCLA ATLAS Community Health Initiative. We defined clusters of individuals using identity by descent, a form of genetic relatedness that utilizes shared genomic segments arising due to a common ancestor. In total, we identified 376 clusters, including clusters with patients of Afro-Caribbean, Puerto Rican, Lebanese Christian, Iranian Jewish and Gujarati ancestry. Our analysis uncovered 1,218 significant associations between disease diagnoses and clusters and 124 significant associations with specialty visits. We also examined the distribution of pathogenic alleles and found 189 significant alleles at elevated frequency in particular clusters, including many that are not regularly included in population screening efforts. Overall, this work progresses the understanding of health in understudied communities and can provide the foundation for further study into health inequities.
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Affiliation(s)
- Christa Caggiano
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Ruhollah Shemirani
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joel Mefford
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ella Petter
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alec Chiu
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Defne Ercelen
- Computational and Systems Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - Rosemary He
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel Tward
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kimberly C Paul
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Timothy S Chang
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bogdan Pasaniuc
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Institute of Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan A Shortt
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Bioinformatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Bioinformatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Brunilda Balliu
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Valerie A Arboleda
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gillian Belbin
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noah Zaitlen
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
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11
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Aizpurua-Iraola J, Rasal R, Prieto L, Comas D, Bonet N, Casals F, Calafell F, Vásquez P. Population analysis of complete mitogenomes for 334 samples from El Salvador. Forensic Sci Int Genet 2023; 66:102906. [PMID: 37364481 DOI: 10.1016/j.fsigen.2023.102906] [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: 03/22/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023]
Abstract
The use of mitochondrial DNA (mtDNA) in the field of forensic genetics is widely spread mainly due to its advantages when identifying highly degraded samples. In this sense, massive parallel sequencing has made the analysis of the whole mitogenome more accessible, noticeably increasing the informativeness of mtDNA haplotypes. The civil war (1980-1992) in El Salvador caused many deaths and disappearances (including children) all across the country and the economic and social instability after the war forced many people to emigration. For this reason, different organizations have collected DNA samples from relatives with the aim of identifying missing people. Thus, we present a dataset containing 334 complete mitogenomes from the Salvadoran general population. To the best of our knowledge, this is the first publication of a nationwide forensic-quality complete mitogenome database of any Latin American country. We found 293 different haplotypes, with a random match probability of 0.0041 and 26.6 mean pairwise differences, which is similar to other Latin American populations, and which represent a marked improvement from the values obtained with just control region sequences. These haplotypes belong to 54 different haplogroups, being 91% of them of Native American origin. Over a third (35.9%) of the individuals carried at least a heteroplasmic site (excluding length heteroplasmies). Ultimately, the present database aims to represent mtDNA haplotype diversity in the general Salvadoran populations as a basis for the identification of people that disappeared during or after the civil war.
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Affiliation(s)
- Julen Aizpurua-Iraola
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Lourdes Prieto
- Instituto de Ciencias Forenses, Universidad de Santiago de Compostela, Santiago de Compostela, Spain; Comisaría General de Policía Científica. DNA Laboratory, Madrid, Spain
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Patricia Vásquez
- Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos de El Salvador, San Salvador, El Salvador
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12
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Arango-Isaza E, Capodiferro MR, Aninao MJ, Babiker H, Aeschbacher S, Achilli A, Posth C, Campbell R, Martínez FI, Heggarty P, Sadowsky S, Shimizu KK, Barbieri C. The genetic history of the Southern Andes from present-day Mapuche ancestry. Curr Biol 2023:S0960-9822(23)00607-3. [PMID: 37279753 DOI: 10.1016/j.cub.2023.05.013] [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: 11/03/2022] [Revised: 03/01/2023] [Accepted: 05/05/2023] [Indexed: 06/08/2023]
Abstract
The southernmost regions of South America harbor some of the earliest evidence of human presence in the Americas. However, connections with the rest of the continent and the contextualization of present-day indigenous ancestries remain poorly resolved. In this study, we analyze the genetic ancestry of one of the largest indigenous groups in South America: the Mapuche. We generate genome-wide data from 64 participants from three Mapuche populations in Southern Chile: Pehuenche, Lafkenche, and Huilliche. Broadly, we describe three main ancestry blocks with a common origin, which characterize the Southern Cone, the Central Andes, and Amazonia. Within the Southern Cone, ancestors of the Mapuche lineages differentiated from those of the Far South during the Middle Holocene and did not experience further migration waves from the north. We find that the deep genetic split between the Central and Southern Andes is followed by instances of gene flow, which may have accompanied the southward spread of cultural traits from the Central Andes, including crops and loanwords from Quechua into Mapudungun (the language of the Mapuche). Finally, we report close genetic relatedness between the three populations analyzed, with the Huilliche characterized additionally by intense recent exchanges with the Far South. Our findings add new perspectives on the genetic (pre)history of South America, from the first settlement through to the present-day indigenous presence. Follow-up fieldwork took these results back to the indigenous communities to contextualize the genetic narrative alongside indigenous knowledge and perspectives.
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Affiliation(s)
- Epifanía Arango-Isaza
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland.
| | - Marco Rosario Capodiferro
- Trinity College Dublin, Dublin 2, Ireland; Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | | | - Hiba Babiker
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Cosimo Posth
- Institute for Archaeological Sciences, Archaeo, and Palaeogenetics, University of Tübingen, Tübingen 72074, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen 72074, Germany
| | - Roberto Campbell
- Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago 6904411, Chile
| | - Felipe I Martínez
- Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago 6904411, Chile; Center for Intercultural and Indigenous Research, Santiago 7820436, Chile
| | - Paul Heggarty
- "Waves" ERC Group, Department of Human Behavior, Evolution and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Scott Sadowsky
- Department of Linguistics and Literature, Universidad de Cartagena, Cartagena 130001, Colombia
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland; Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
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13
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Witt KE, Funk A, Añorve-Garibay V, Fang LL, Huerta-Sánchez E. The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations. Genome Biol Evol 2023; 15:evad066. [PMID: 37103242 PMCID: PMC10194819 DOI: 10.1093/gbe/evad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 03/07/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, which have shaped genetic ancestry in modern humans. For example, populations in the Americas are often mosaics of different ancestries due to recent admixture events as part of European colonization. Admixed individuals also often have introgressed DNA from Neanderthals and Denisovans that may have come from multiple ancestral populations, which may affect how archaic ancestry is distributed across an admixed genome. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual's archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight increase of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.
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Affiliation(s)
- Kelsey E Witt
- Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
| | - Alyssa Funk
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
- Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, Rhode Island
| | - Valeria Añorve-Garibay
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
- Licenciatura en Ciencias Genómicas, Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, Querétaro, Mexico
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Lesly Lopez Fang
- Department of Life & Environmental Sciences, University of California, Merced, California, United States of America
| | - Emilia Huerta-Sánchez
- Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
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14
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Bellucci E, Benazzo A, Xu C, Bitocchi E, Rodriguez M, Alseekh S, Di Vittori V, Gioia T, Neumann K, Cortinovis G, Frascarelli G, Murube E, Trucchi E, Nanni L, Ariani A, Logozzo G, Shin JH, Liu C, Jiang L, Ferreira JJ, Campa A, Attene G, Morrell PL, Bertorelle G, Graner A, Gepts P, Fernie AR, Jackson SA, Papa R. Selection and adaptive introgression guided the complex evolutionary history of the European common bean. Nat Commun 2023; 14:1908. [PMID: 37019898 PMCID: PMC10076260 DOI: 10.1038/s41467-023-37332-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
Domesticated crops have been disseminated by humans over vast geographic areas. Common bean (Phaseolus vulgaris L.) was introduced in Europe after 1492. Here, by combining whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarro's expedition to northern Peru in 1529. We reveal that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.
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Affiliation(s)
- Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121, Ferrara, Italy
| | - Chunming Xu
- Center for Applied Genetic Technologies, University of Georgia, 30602, Athens, GA, USA
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, 07100, Sassari, Italy
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale-CBV, Università degli Studi di Sassari, 07041, Alghero, Italy
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), 14476, Potsdam-Golm, Germany
- Center for Plant Systems Biology and Plant Biotechnology, 4000, Plovdiv, Bulgaria
| | - Valerio Di Vittori
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), 14476, Potsdam-Golm, Germany
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland, Germany
| | - Gaia Cortinovis
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Giulia Frascarelli
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Ester Murube
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Emiliano Trucchi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121, Ferrara, Italy
- Department of Life and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Andrea Ariani
- Department of Plant Sciences, University of California, 95616-8780, Davis, CA, USA
| | - Giuseppina Logozzo
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Jin Hee Shin
- Center for Applied Genetic Technologies, University of Georgia, 30602, Athens, GA, USA
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108-6026, USA
| | - Liang Jiang
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), 14476, Potsdam-Golm, Germany
| | - Juan José Ferreira
- Regional Agrifood Research and Development Service (SERIDA), 33310, Villaviciosa, Asturias, Spain
| | - Ana Campa
- Regional Agrifood Research and Development Service (SERIDA), 33310, Villaviciosa, Asturias, Spain
| | - Giovanna Attene
- Department of Agriculture, University of Sassari, 07100, Sassari, Italy
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale-CBV, Università degli Studi di Sassari, 07041, Alghero, Italy
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108-6026, USA
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121, Ferrara, Italy
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland, Germany
| | - Paul Gepts
- Department of Plant Sciences, University of California, 95616-8780, Davis, CA, USA
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), 14476, Potsdam-Golm, Germany
- Center for Plant Systems Biology and Plant Biotechnology, 4000, Plovdiv, Bulgaria
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 30602, Athens, GA, USA
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.
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15
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Capodiferro MR, Chero Osorio AM, Rambaldi Migliore N, Tineo Tineo DH, Raveane A, Xavier C, Bodner M, Simão F, Ongaro L, Montinaro F, Lindo J, Huerta-Sanchez E, Politis G, Barbieri C, Parson W, Gusmão L, Achilli A. The multifaceted genomic history of Ashaninka from Amazonian Peru. Curr Biol 2023; 33:1573-1581.e5. [PMID: 36931272 DOI: 10.1016/j.cub.2023.02.046] [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: 09/20/2022] [Revised: 12/14/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Despite its crucial location, the western side of Amazonia between the Andes and the source(s) of the Amazon River is still understudied from a genomic and archaeogenomic point of view, albeit possibly harboring essential information to clarify the complex genetic history of local Indigenous groups and their interactions with nearby regions,1,2,3,4,5,6,7,8 including central America and the Caribbean.9,10,11,12 Focusing on this key region, we analyzed the genome-wide profiles of 51 Ashaninka individuals from Amazonian Peru, observing an unexpected extent of genomic variation. We identified at least two Ashaninka subgroups with distinctive genomic makeups, which were differentially shaped by the degree and timing of external admixtures, especially with the Indigenous groups from the Andes and the Pacific coast. On a continental scale, Ashaninka ancestors probably derived from a south-north migration of Indigenous groups moving into the Amazonian rainforest from a southeastern area with contributions from the Southern Cone and the Atlantic coast. These ancestral populations diversified in the variegated geographic regions of interior South America, on the eastern side of the Andes, differentially interacting with surrounding coastal groups. In this complex scenario, we also revealed strict connections between the ancestors of present-day Ashaninka, who belong to the Arawakan language family,13 and those Indigenous groups that moved further north into the Caribbean, contributing to the early Ceramic (Saladoid) tradition in the islands.14,15.
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Affiliation(s)
- Marco Rosario Capodiferro
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy; Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland.
| | - Ana María Chero Osorio
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Dean Herman Tineo Tineo
- Laboratorio de Biología Forense, Instituto de Medicina Legal y Ciencias Forenses, Ministerio Público, Lima 15033, Perú
| | | | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4099-002 Porto, Portugal
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Filipa Simão
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 23968-000, Brazil
| | - Linda Ongaro
- Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, 70125 Bari, Italy; Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Emilia Huerta-Sanchez
- Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland; Ecology and Evolutionary Biology and Center for Computational and Molecular Biology, Brown University, Providence, RI 02906, USA
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland; Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; Forensic Science Program, Pennsylvania State University, State College, PA 16801, USA
| | - Leonor Gusmão
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 23968-000, Brazil
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy.
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16
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Ancestry, diversity, and genetics of health-related traits in African-derived communities (quilombos) from Brazil. Funct Integr Genomics 2023; 23:74. [PMID: 36867305 PMCID: PMC9982798 DOI: 10.1007/s10142-023-00999-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
Brazilian quilombos are communities formed by enslaved Africans and their descendants all over the country during slavery and shortly after its abolition. Quilombos harbor a great fraction of the largely unknown genetic diversity of the African diaspora in Brazil. Thus, genetic studies in quilombos have the potential to provide important insights not only into the African roots of the Brazilian population but also into the genetic bases of complex traits and human adaptation to diverse environments. This review summarizes the main results of genetic studies performed on quilombos so far. Here, we analyzed the patterns of African, Amerindian, European, and subcontinental ancestry (within Africa) of quilombos from the five different geographic regions of Brazil. In addition, uniparental markers (from the mtDNA and the Y chromosome) studies are analyzed together to reveal demographic processes and sex-biased admixture that occurred during the formation of these unique populations. Lastly, the prevalence of known malaria-adaptive African mutations and other African-specific variants discovered in quilombos, as well as the genetic bases of health-related traits, are discussed here, together with their implication for the health of populations of African descent.
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17
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The impact of modern admixture on archaic human ancestry in human populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524232. [PMID: 36711776 PMCID: PMC9882123 DOI: 10.1101/2023.01.16.524232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, as well as introgression between humans and archaic humans, Neanderthals and Denisovans. One example are genomes from populations in the Americas, as these are often mosaics of different ancestries due to recent admixture events as part of European colonization. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual’s archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight enrichment of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.
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García-Ortiz H, Barajas-Olmos F, Flores-Huacuja M, Morales-Rivera MI, Martínez-Hernández A, Baca V, Contreras-Cubas C, Orozco L. Ancestry-dependent genetic structure of the Xq28 risk haplotype in the Mexican population and its association with childhood-onset systemic lupus erythematosus. Front Med (Lausanne) 2023; 9:1044856. [PMID: 36714151 PMCID: PMC9877425 DOI: 10.3389/fmed.2022.1044856] [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: 09/15/2022] [Accepted: 12/27/2022] [Indexed: 01/15/2023] Open
Abstract
Objective Here we aimed to investigate the association of the Xq28 risk haplotype (H1) with susceptibility to childhood-onset systemic lupus erythematosus (SLE), and to compare its frequency and genetic structure in the Mexican population with those in other continental populations. Methods We genotyped 15 single-nucleotide variants (SNVs) that form the H1 haplotype, using TaqMan real-time PCR. The association analysis [case-control and transmission disequilibrium test (TDT)] included 376 cases and 400 adult controls, all of whom were mestizos (MEZ). To identify risk alleles in Mexican Indigenous individuals, SNVs were imputed from whole-exome sequencing data of 1,074 individuals. The allelic frequencies determined in MEZ and Indigenous individuals were compared with those of the continental populations from the 1,000 Genomes database phase 3. Linkage disequilibrium (LD) analysis of risk alleles was performed on all populations. Interleukin-1 receptor associated kinase 1 (IRAK1) and methyl CpG binding protein 2 (MECP2) mRNA levels were determined using real-time PCR. Results Case-control analysis revealed genetic association with childhood-onset SLE for all 15 SNVs (OR = 1.49-1.75; p = 0.0095 to 1.81 × 10-4) and for the Xq28 risk haplotype (OR = 1.97, p = 4 × 10-6). Comparing with individuals of European ancestry (0.14-0.16), the frequencies of the risk alleles were significantly higher in the MEZ individuals (0.55-0.68) and even higher in Indigenous individuals (0.57-0.83). LD analysis indicated a differential haplotype structure within the Indigenous groups, which was inherited to the MEZ population as a result of genetic admixture. Individuals homozygous for the Xq28 risk haplotype exhibited decreased levels of both MECP2A and B transcripts. Conclusion We found that the H1 risk haplotype differs in its conformation in the Mexican population. This difference could be attributed to positive selection within the Indigenous population, with its inheritance now having an autoimmune health impact in both the Mexican Indigenous and MEZ populations.
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Affiliation(s)
- Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Marlen Flores-Huacuja
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Monserrat I. Morales-Rivera
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Vicente Baca
- Department of Rheumatology, Hospital de Pediatría, CMN Siglo XXI IMSS, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico,*Correspondence: Cecilia Contreras-Cubas,
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico,Lorena Orozco,
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Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, Kilinc GM, Kjellström A, Papmehl-Dufay L, Alfsdotter C, Berglund B, Alrawi L, Kashuba N, Sobrado V, Lagerholm VK, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Munters AR, Bernhardsson C, Skar B, Christophersen A, Turner-Walker G, Gopalakrishnan S, Daskalaki E, Omrak A, Pérez-Ramallo P, Skoglund P, Girdland-Flink L, Gunnarsson F, Hedenstierna-Jonson C, Gilbert MTP, Lidén K, Jakobsson M, Einarsson L, Victor H, Krzewińska M, Zachrisson T, Storå J, Stefánsson K, Helgason A, Götherström A. The genetic history of Scandinavia from the Roman Iron Age to the present. Cell 2023; 186:32-46.e19. [PMID: 36608656 DOI: 10.1016/j.cell.2022.11.024] [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: 06/27/2022] [Revised: 10/14/2022] [Accepted: 11/22/2022] [Indexed: 01/07/2023]
Abstract
We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
| | | | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland
| | - Gulsah Merve Kilinc
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Anna Kjellström
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Clara Alfsdotter
- Department of Archaeology, Bohusläns Museum, Museigatan 1, 451 19 Udevalla, Sweden
| | - Birgitta Berglund
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Loey Alrawi
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Natalija Kashuba
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Department of Archaeology and Ancient History, Archaeology, Uppsala University, 752 38 Uppsala, Sweden; Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Verónica Sobrado
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Centre for Bioinformatics, Department of Informatics, University of Oslo, 166 0450 Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
| | - Arielle R Munters
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Carolina Bernhardsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Axel Christophersen
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Gordon Turner-Walker
- Department of Archaeology and Anthropology National Museum of Natural Science, 404023 Taichung City, Taiwan
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Eva Daskalaki
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany; Department of Medical and Surgical Specialities, Faculty of Medicine and Nursing, University of the Basque Country (EHU), Donostia-San Sebastián 20014, Spain
| | | | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, AB24 3FX Aberdeen, UK; School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK
| | - Fredrik Gunnarsson
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Lars Einarsson
- Kronan, Marine Archaeological Department, Kalmar County Museum, Box 104, Kalmar S-39121, Sweden
| | - Helena Victor
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | - Maja Krzewińska
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Kári Stefánsson
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Agnar Helgason
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland.
| | - Anders Götherström
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
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20
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Silva MACE, Ferraz T, Hünemeier T. A genomic perspective on South American human history. Genet Mol Biol 2022; 45:e20220078. [PMID: 35925590 PMCID: PMC9351327 DOI: 10.1590/1678-4685-gmb-2022-0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/31/2022] [Indexed: 11/22/2022] Open
Abstract
It has generally been accepted that the current indigenous peoples of the Americas are derived from ancestors from northeastern Asia. The latter were believed to have spread into the American continent by the end of the Last Glacial Maximum. In this sense, a joint and in-depth study of the earliest settlement of East Asia and the Americas is required to elucidate these events accurately. The first Americans underwent an adaptation process to the Americas' vast environmental diversity, mediated by biological and cultural evolution and niche construction, resulting in enormous cultural diversity, a wealth of domesticated species, and extensive landscape modifications. Afterward, in the Late Holocene, the advent of intensive agricultural food production systems, sedentism, and climate change significantly reshaped genetic and cultural diversity across the continent, particularly in the Andes and Amazonia. Furthermore, starting around the end of the 15th century, European colonization resulted in massive extermination of indigenous peoples and extensive admixture. Thus, the present review aims to create a comprehensive picture of the main events involved in the formation of contemporary South American indigenous populations and the dynamics responsible for shaping their genetic diversity by integrating current genetic data with evidence from archeology, linguistics and other disciplines.
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Affiliation(s)
- Marcos Araújo Castro E Silva
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Tiago Ferraz
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Tábita Hünemeier
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
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21
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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.
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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,
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22
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Nieves-Colón MA. Anthropological genetic insights on Caribbean population history. Evol Anthropol 2022; 31:118-137. [PMID: 35060661 DOI: 10.1002/evan.21935] [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: 12/29/2020] [Revised: 06/18/2021] [Accepted: 12/15/2021] [Indexed: 11/09/2022]
Abstract
As the last American region settled by humans, yet the first to experience European colonization, the Caribbean islands have a complex history characterized by continuous migration, admixture, and demographic change. In the last 20 years, genetics research has transformed our understanding of Caribbean population history and revisited major debates in Caribbean anthropology, such as those surrounding the first peopling of the Antilles and the relationship between ancient Indigenous communities and present-day islanders. Genetics studies have also contributed novel perspectives for understanding pivotal events in Caribbean post-contact history such as European colonization, the Atlantic Slave Trade, and the Asian Indenture system. Here, I discuss the last 20 years of Caribbean genetics research and emphasize the importance of integrating genetics with interdisciplinary historic, archaeological, and anthropological approaches. Such interdisciplinary research is essential for investigating the dynamic history of the Caribbean and characterizing its impact on the biocultural diversity of present-day Caribbean peoples.
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Affiliation(s)
- Maria A Nieves-Colón
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
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23
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Gopalan S, Smith SP, Korunes K, Hamid I, Ramachandran S, Goldberg A. Human genetic admixture through the lens of population genomics. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200410. [PMID: 35430881 PMCID: PMC9014191 DOI: 10.1098/rstb.2020.0410] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Over the past 50 years, geneticists have made great strides in understanding how our species' evolutionary history gave rise to current patterns of human genetic diversity classically summarized by Lewontin in his 1972 paper, ‘The Apportionment of Human Diversity’. One evolutionary process that requires special attention in both population genetics and statistical genetics is admixture: gene flow between two or more previously separated source populations to form a new admixed population. The admixture process introduces ancestry-based structure into patterns of genetic variation within and between populations, which in turn influences the inference of demographic histories, identification of genetic targets of selection and prediction of complex traits. In this review, we outline some challenges for admixture population genetics, including limitations of applying methods designed for populations without recent admixture to the study of admixed populations. We highlight recent studies and methodological advances that aim to overcome such challenges, leveraging genomic signatures of admixture that occurred in the past tens of generations to gain insights into human history, natural selection and complex trait architecture. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Shyamalika Gopalan
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Samuel Pattillo Smith
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
| | - Katharine Korunes
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Iman Hamid
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Sohini Ramachandran
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
- Data Science Initiative, Brown University, Providence, RI 02912, USA
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
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24
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Nores R, Tavella MP, Fabra M, Demarchi DA. Ancient DNA analysis reveals temporal and geographical patterns of mitochondrial diversity in pre-Hispanic populations from Central Argentina. Am J Hum Biol 2022; 34:e23733. [PMID: 35238427 DOI: 10.1002/ajhb.23733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES The study of the ancient populations of Central Argentina has a crucial importance for our understanding of the evolutionary processes in the Southern Cone of South America, given its geographic position as a crossroads. Therefore, the aim of this study is to evaluate the temporal and geographical patterns of genetic variation among the groups that inhabited the current territory of Córdoba Province during the Middle and Late Holocene. METHODS We analyzed the mitochondrial haplogroups of 74 individuals and 46 Hypervariable Region I (HVR-I) sequences, both novel and previously reported, from archeological populations of the eastern Plains and western Sierras regions of the province of Córdoba. The HVR-I sequences were also compared with other ancient groups from Argentina and with present-day populations from Central Argentina by pairwise distance analysis and identification of shared haplotypes. RESULTS Significant differences in haplogroup and haplotype distributions between the two geographical regions were found. Sierras showed genetic affinities with certain ancient populations of Northwestern Argentina, while Plains resembled its neighbors from Santiago del Estero Province and the Pampas region. We did not observe genetic differences among the pre 1200 and post 1200 yBP temporal subsets of individuals defined by the emergence of horticulture, considering both geographical samples jointly. CONCLUSIONS The observed patterns of geographical heterogeneity could indicate the existence of biologically distinct populations inhabiting the mountainous region and the eastern plains of Córdoba Province in pre-Hispanic times. Maternal lineages analyses support a scenario of local evolution with great temporal depth in Central Argentina, with continuity until the present.
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Affiliation(s)
- Rodrigo Nores
- Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Departamento de Antropología, Córdoba, Argentina.,CONICET, Instituto de Antropología de Córdoba (IDACOR), Córdoba, Argentina
| | - María Pía Tavella
- Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Departamento de Antropología, Córdoba, Argentina.,CONICET, Instituto de Antropología de Córdoba (IDACOR), Córdoba, Argentina
| | - Mariana Fabra
- Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Departamento de Antropología, Córdoba, Argentina.,CONICET, Instituto de Antropología de Córdoba (IDACOR), Córdoba, Argentina
| | - Darío A Demarchi
- Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Departamento de Antropología, Córdoba, Argentina.,CONICET, Instituto de Antropología de Córdoba (IDACOR), Córdoba, Argentina
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25
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Gao Q, Yan D, Song S, Fan Y, Wang S, Liu Y, Huang Y, Rong C, Guo Y, Zhao S, Qin W, Xu J. Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes. J Fungi (Basel) 2022; 8:jof8020167. [PMID: 35205921 PMCID: PMC8877449 DOI: 10.3390/jof8020167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 01/02/2023] Open
Abstract
Lentinula edodes is a tetrapolar basidiomycete with two haploid nuclei in each cell during most of their life cycle. Understanding the two haploid nuclei genome structures and their interactions on growth and fruiting body development has significant practical implications, especially for commercial cultivars. In this study, we isolated and assembled the two haploid genomes from a commercial strain of L. edodes using Illumina, HiFi, and Hi-C technologies. The total genome lengths were 50.93 Mb and 49.80 Mb for the two monokaryons SP3 and SP30, respectively, with each assembled into 10 chromosomes with 99.63% and 98.91% anchoring rates, respectively, for contigs more than 100 Kb. Genome comparisons suggest that two haploid nuclei likely derived from distinct genetic ancestries, with ~30% of their genomes being unique or non-syntenic. Consistent with a tetrapolar mating system, the two mating-type loci A (matA) and B (matB) of L. edodes were found located on two different chromosomes. However, we identified a new but incomplete homeodomain (HD) sublocus at ~2.8 Mb from matA in both monokaryons. Our study provides a solid foundation for investigating the relationships among cultivars and between cultivars and wild strains and for studying how two genetically divergent nuclei coordinate to regulate fruiting body formation in L. edodes.
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Affiliation(s)
- Qi Gao
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Dong Yan
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- Correspondence: (D.Y.); (J.X.)
| | - Shuang Song
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yangyang Fan
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Shouxian Wang
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yu Liu
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yu Huang
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- College of Agriculture and Food Engineering, Baise University, 21 Zhongshan Second Street, Youjiang District, Baise 533000, China
| | - Chengbo Rong
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yuan Guo
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Shuang Zhao
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
| | - Wentao Qin
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
- Correspondence: (D.Y.); (J.X.)
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Overview of the Americas’ First Peopling from a Patrilineal Perspective: New Evidence from the Southern Continent. Genes (Basel) 2022; 13:genes13020220. [PMID: 35205264 PMCID: PMC8871784 DOI: 10.3390/genes13020220] [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] [Received: 12/21/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/24/2022] Open
Abstract
Uniparental genetic systems are unique sex indicators and complement the study of autosomal diversity by providing landmarks of human migrations that repeatedly shaped the structure of extant populations. Our knowledge of the variation of the male-specific region of the Y chromosome in Native Americans is still rather scarce and scattered, but by merging sequence information from modern and ancient individuals, we here provide a comprehensive and updated phylogeny of the distinctive Native American branches of haplogroups C and Q. Our analyses confirm C-MPB373, C-P39, Q-Z780, Q-M848, and Q-Y4276 as the main founding haplogroups and identify traces of unsuccessful (pre-Q-F1096) or extinct (C-L1373*, Q-YP4010*) Y-chromosome lineages, indicating that haplogroup diversity of the founder populations that first entered the Americas was greater than that observed in the Indigenous component of modern populations. In addition, through a diachronic and phylogeographic dissection of newly identified Q-M848 branches, we provide the first Y-chromosome insights into the early peopling of the South American hinterland (Q-BY104773 and Q-BY15730) and on overlying inland migrations (Q-BY139813).
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Joerin-Luque IA, Augusto DG, Calonga-Solís V, de Almeida RC, Lopes CVG, Petzl-Erler ML, Beltrame MH. Uniparental markers reveal new insights on subcontinental ancestry and sex-biased admixture in Brazil. Mol Genet Genomics 2022; 297:419-435. [DOI: 10.1007/s00438-022-01857-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
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Gómez R, Tapia-Guerrero YS, Cisneros B, Orozco L, Cerecedo-Zapata C, Mendoza-Caamal E, Leyva-Gómez G, Leyva-García N, Velázquez-Pérez L, Magaña JJ. Genetic Distribution of Five Spinocerebellar Ataxia Microsatellite Loci in Mexican Native American Populations and Its Impact on Contemporary Mestizo Populations. Genes (Basel) 2022; 13:genes13010157. [PMID: 35052497 PMCID: PMC8775409 DOI: 10.3390/genes13010157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/04/2022] [Accepted: 01/13/2022] [Indexed: 12/17/2022] Open
Abstract
Spinocerebellar ataxias (SCAs) conform a heterogeneous group of neurodegenerative disorders with autosomal dominant inheritance. Five of the most frequent SCAs are caused by a CAG repeat expansion in the exons of specific genes. The SCAs incidence and the distribution of polymorphic CAG alleles vary among populations and ethnicities. Thus, characterization of the genetic architecture of ethnically diverse populations, which have undergone recent admixture and demographic events, could facilitate the identification of genetic risk factors. Owing to the great ethnic diversity of the Mexican population, this study aimed to analyze the allele frequencies of five SCA microsatellite loci (SCA1, SCA2, SCA3, SCA6, and SCA7) in eleven Mexican Native American (MNA) populations. Data from the literature were used to compare the allelic distribution of SCA loci with worldwide populations. The SCA loci allelic frequencies evidenced a certain genetic homogeneity in the MNA populations, except for Mayans, who exhibited distinctive genetic profiles. Neither pathological nor large normal alleles were found in MNA populations, except for the SCA2 pre-mutated allele in the Zapotec population. Collectively, our findings demonstrated the contribution of the MNA ancestry in shaping the genetic structure of contemporary Mexican Mestizo populations. Our results also suggest that Native American ancestry has no impact on the origin of SCAs in the Mexican population. Instead, the acquisition of pathological SCA alleles could be associated with European migration.
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Affiliation(s)
- Rocío Gómez
- Department of Toxicology, CINVESTAV-IPN, Mexico City 07360, Mexico;
| | - Yessica S. Tapia-Guerrero
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico; (Y.S.T.-G.); (C.C.-Z.); (N.L.-G.)
| | - Bulmaro Cisneros
- Department of Genetics and Molecular Biology, CINVESTAV-IPN, Mexico City 07360, Mexico;
| | - Lorena Orozco
- Laboratory of Immunogenomics and Metabolic Diseases, National Genomic Medicine Institute (INMEGEN), Mexico City 14610, Mexico; (L.O.); (E.M.-C.)
| | - César Cerecedo-Zapata
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico; (Y.S.T.-G.); (C.C.-Z.); (N.L.-G.)
- Rehabilitation and Social Inclusion Center of Veracruz (CRIS-DIF), Xalapa, Veracruz 91097, Mexico
| | - Elvia Mendoza-Caamal
- Laboratory of Immunogenomics and Metabolic Diseases, National Genomic Medicine Institute (INMEGEN), Mexico City 14610, Mexico; (L.O.); (E.M.-C.)
| | - Gerardo Leyva-Gómez
- Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México (UNAM); Mexico City 04510, Mexico;
| | - Norberto Leyva-García
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico; (Y.S.T.-G.); (C.C.-Z.); (N.L.-G.)
| | | | - Jonathan J. Magaña
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico; (Y.S.T.-G.); (C.C.-Z.); (N.L.-G.)
- Department of Bioengineering, School of Engineering and Sciences, Tecnologico de Monterrey, Campus Ciudad de México (ITESM-CCM), Mexico City 14380, Mexico
- Correspondence: ; Tel.: +52-(55)-5999-1000 (ext. 14708)
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Castro e Silva MA, Ferraz T, Couto-Silva CM, Lemes RB, Nunes K, Comas D, Hünemeier T. Population Histories and Genomic Diversity of South American Natives. Mol Biol Evol 2022; 39:msab339. [PMID: 34875092 PMCID: PMC8789086 DOI: 10.1093/molbev/msab339] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
South America is home to one of the most culturally diverse present-day native populations. However, the dispersion pattern, genetic substructure, and demographic complexity within South America are still poorly understood. Based on genome-wide data of 58 native populations, we provide a comprehensive scenario of South American indigenous groups considering the genomic, environmental, and linguistic data. Clear patterns of genetic structure were inferred among the South American natives, presenting at least four primary genetic clusters in the Amazonian and savanna regions and three clusters in the Andes and Pacific coast. We detected a cline of genetic variation along a west-east axis, contradicting a hard Andes-Amazon divide. This longitudinal genetic variation seemed to have been shaped by both serial population bottlenecks and isolation by distance. Results indicated that present-day South American substructures recapitulate ancient macroregional ancestries and western Amazonia groups show genetic evidence of cultural exchanges that led to language replacement in precontact times. Finally, demographic inferences pointed to a higher resilience of the western South American groups regarding population collapses caused by the European invasion and indicated precontact population reductions and demic expansions in South America.
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Affiliation(s)
- Marcos Araújo Castro e Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago Ferraz
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Cainã M Couto-Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Renan B Lemes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - David Comas
- Departament de Ciències, Institut de Biologia Evolutiva, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Casals F, Rasal R, Anglada R, Tormo M, Bonet N, Rivas N, Vásquez P, Calafell F. A forensic population database in El Salvador: 58 STRs and 94 SNPs. Forensic Sci Int Genet 2021; 57:102646. [PMID: 34875492 DOI: 10.1016/j.fsigen.2021.102646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 12/31/2022]
Abstract
We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in a sample of 248 men and 143 women from El Salvador, Central America. Regional division (Centro, Oriente, Occidente) showed in almost all cases FST values not significantly different from 0, and further analyses were applied only to the undivided, country-wide population. The overall random match probability (RMP) decreased from 6.79 × 10-31 in length-based genotypes in the 27 autosomal STRs to 1.47 × 10-34 in repeat-sequence based genotypes. Combining the autosomal loci in this set, RMP reaches 2.97 × 10-70. In a population genetic analysis, El Salvador showed the lowest FST values with US Hispanics both for autosomal and X-STRs; however, it was much closer to Native Americans for the latter than for the former, in accordance with the well-known gender-biased admixture that created most Latin American populations.
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Affiliation(s)
- Ferran Casals
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadísitca, Universitat de Barcelona, Barcelona, Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Roger Anglada
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Marc Tormo
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain; Scientific IT Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Nury Rivas
- Instituto de Medicina Legal Dr. Roberto Masferrer, San Salvador, El Salvador
| | - Patricia Vásquez
- Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos de El Salvador, 27 calle Pnte. No.1329 Colonia Layco, San Salvador, El Salvador
| | - Francesc Calafell
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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Rambaldi Migliore N, Colombo G, Capodiferro MR, Mazzocchi L, Chero Osorio AM, Raveane A, Tribaldos M, Perego UA, Mendizábal T, Montón AG, Lombardo G, Grugni V, Garofalo M, Ferretti L, Cereda C, Gagliardi S, Cooke R, Smith-Guzmán N, Olivieri A, Aram B, Torroni A, Motta J, Semino O, Achilli A. Weaving Mitochondrial DNA and Y-Chromosome Variation in the Panamanian Genetic Canvas. Genes (Basel) 2021; 12:genes12121921. [PMID: 34946870 PMCID: PMC8702192 DOI: 10.3390/genes12121921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 12/14/2022] Open
Abstract
The Isthmus of Panama was a crossroads between North and South America during the continent’s first peopling (and subsequent movements) also playing a pivotal role during European colonization and the African slave trade. Previous analyses of uniparental systems revealed significant sex biases in the genetic history of Panamanians, as testified by the high proportions of Indigenous and sub-Saharan mitochondrial DNAs (mtDNAs) and by the prevalence of Western European/northern African Y chromosomes. Those studies were conducted on the general population without considering any self-reported ethnic affiliations. Here, we compared the mtDNA and Y-chromosome lineages of a new sample collection from 431 individuals (301 males and 130 females) belonging to either the general population, mixed groups, or one of five Indigenous groups currently living in Panama. We found different proportions of paternal and maternal lineages in the Indigenous groups testifying to pre-contact demographic events and genetic inputs (some dated to Pleistocene times) that created genetic structure. Then, while the local mitochondrial gene pool was marginally involved in post-contact admixtures, the Indigenous Y chromosomes were differentially replaced, mostly by lineages of western Eurasian origin. Finally, our new estimates of the sub-Saharan contribution, on a more accurately defined general population, reduce an apparent divergence between genetic and historical data.
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Affiliation(s)
- Nicola Rambaldi Migliore
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Giulia Colombo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Marco Rosario Capodiferro
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Lucia Mazzocchi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Ana Maria Chero Osorio
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Alessandro Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Maribel Tribaldos
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ugo Alessandro Perego
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Department of Math and Science, Southeastern Community College, West Burlington, IA 52655, USA
| | - Tomás Mendizábal
- Center for Historical, Anthropological and Cultural Research—AIP, Panama City 0816-07812, Panama;
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
| | - Alejandro García Montón
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Gianluca Lombardo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Viola Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Maria Garofalo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Luca Ferretti
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Stella Gagliardi
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Nicole Smith-Guzmán
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Bethany Aram
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ornella Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
| | - Alessandro Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
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Nadachowska‐Brzyska K, Konczal M, Babik W. Navigating the temporal continuum of effective population size. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | - Wieslaw Babik
- Jagiellonian University in Kraków Faculty of Biology Institute of Environmental Sciences Kraków Poland
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Lezirovitz K, Mingroni-Netto RC. Genetic etiology of non-syndromic hearing loss in Latin America. Hum Genet 2021; 141:539-581. [PMID: 34652575 DOI: 10.1007/s00439-021-02354-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/23/2021] [Indexed: 12/16/2022]
Abstract
Latin America comprises all countries from South and Central America, in addition to Mexico. It is characterized by a complex mosaic of regions with heterogeneous genetic profiles regarding the geographical origin of the ancestors and proportions of admixture between the Native American, European and African components. In the first years following the findings of the role of the GJB2/GJB6 genes in the etiology of hearing loss, most scientific investigations about the genetics of hearing loss in Latin America focused on assessing the frequencies of pathogenic variants in these genes. More recently, modern techniques allowed researchers in Latin America to make exciting contributions to the finding of new candidate genes, novel mechanisms of inheritance in previously known genes, and characterize a wide diversity of variants, many of them unique to Latin America. This review aimed to provide a general landscape of the genetic studies about non-syndromic hearing loss in Latin America and their main scientific contributions. It allows the conclusion that, although there are similar contributions of some genes, such as GJB2/GJB6, when compared to European and North American countries, Latin American populations revealed some peculiarities that indicate the need for tailored strategies of screening and diagnosis to specific geographic regions.
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Affiliation(s)
- Karina Lezirovitz
- Laboratório de Otorrinolaringologia/LIM32, Faculdade de Medicina, Hospital das Clínicas, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Regina Célia Mingroni-Netto
- Departamento de Genética e Biologia Evolutiva, Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Spangenberg L, Fariello MI, Arce D, Illanes G, Greif G, Shin JY, Yoo SK, Seo JS, Robello C, Kim C, Novembre J, Sans M, Naya H. Indigenous Ancestry and Admixture in the Uruguayan Population. Front Genet 2021; 12:733195. [PMID: 34630523 PMCID: PMC8495321 DOI: 10.3389/fgene.2021.733195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/03/2021] [Indexed: 01/27/2023] Open
Abstract
The Amerindian group known as the Charrúas inhabited Uruguay at the timing of European colonial contact. Even though they were extinguished as an ethnic group as a result of a genocide, Charrúan heritage is part of the Uruguayan identity both culturally and genetically. While mitochondrial DNA studies have shown evidence of Amerindian ancestry in living Uruguayans, here we undertake whole-genome sequencing of 10 Uruguayan individuals with self-declared Charruan heritage. We detect chromosomal segments of Amerindian ancestry supporting the presence of indigenous genetic ancestry in living descendants. Specific haplotypes were found to be enriched in “Charrúas” and rare in the rest of the Amerindian groups studied. Some of these we interpret as the result of positive selection, as we identified selection signatures and they were located mostly within genes related to the infectivity of specific viruses. Historical records describe contacts of the Charrúas with other Amerindians, such as Guaraní, and patterns of genomic similarity observed here concur with genomic similarity between these groups. Less expected, we found a high genomic similarity of the Charrúas to Diaguita from Argentinian and Chile, which could be explained by geographically proximity. Finally, by fitting admixture models of Amerindian and European ancestry for the Uruguayan population, we were able to estimate the timing of the first pulse of admixture between European and Uruguayan indigenous peoples in approximately 1658 and the second migration pulse in 1683. Both dates roughly concurring with the Franciscan missions in 1662 and the foundation of the city of Colonia in 1680 by the Spanish.
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Affiliation(s)
- Lucía Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - María Inés Fariello
- Instituto de Matemática y Estadística Rafael Laguardia, Facultad de Ingeniería, Universidad de la República (UDELAR), Montevideo, Uruguay
| | - Darío Arce
- Agregado de Cooperación Lingüistica y Cultural de la Embajada de Francia en Uruguay, Montevideo, Uruguay
| | - Gabriel Illanes
- Centro de Matemáticas, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gonzalo Greif
- Molecular Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Jong-Yeon Shin
- Precision Medicine Institute, Macrogen Inc., Seoul, South Korea
| | - Seong-Keun Yoo
- Precision Medicine Institute, Macrogen Inc., Seoul, South Korea
| | - Jeong-Sun Seo
- Precision Medicine Institute, Macrogen Inc., Seoul, South Korea.,Asian Genome Institute, Seoul National University Bundang Hospital, Gyeonggi-do, South Korea
| | - Carlos Robello
- Molecular Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República (UDELAR), Montevideo, Uruguay
| | - Changhoon Kim
- Bioinfomatics Institute, Macrogen Inc., Seoul, South Korea
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, United States.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
| | - Mónica Sans
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República (UDELAR), Montevideo, Uruguay
| | - Hugo Naya
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República (UDELAR), Montevideo, Uruguay
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35
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Ongaro L, Molinaro L, Flores R, Marnetto D, Capodiferro MR, Alarcón-Riquelme ME, Moreno-Estrada A, Mabunda N, Ventura M, Tambets K, Achilli A, Capelli C, Metspalu M, Pagani L, Montinaro F. Evaluating the Impact of Sex-Biased Genetic Admixture in the Americas through the Analysis of Haplotype Data. Genes (Basel) 2021; 12:genes12101580. [PMID: 34680976 PMCID: PMC8535939 DOI: 10.3390/genes12101580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 01/30/2023] Open
Abstract
A general imbalance in the proportion of disembarked males and females in the Americas has been documented during the Trans-Atlantic Slave Trade and the Colonial Era and, although less prominent, more recently. This imbalance may have left a signature on the genomes of modern-day populations characterised by high levels of admixture. The analysis of the uniparental systems and the evaluation of continental proportion ratio of autosomal and X chromosomes revealed a general sex imbalance towards males for European and females for African and Indigenous American ancestries. However, the consistency and degree of this imbalance are variable, suggesting that other factors, such as cultural and social practices, may have played a role in shaping it. Moreover, very few investigations have evaluated the sex imbalance using haplotype data, containing more critical information than genotypes. Here, we analysed genome-wide data for more than 5000 admixed American individuals to assess the presence, direction and magnitude of sex-biased admixture in the Americas. For this purpose, we applied two haplotype-based approaches, ELAI and NNLS, and we compared them with a genotype-based method, ADMIXTURE. In doing so, besides a general agreement between methods, we unravelled that the post-colonial admixture dynamics show higher complexity than previously described.
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Affiliation(s)
- Linda Ongaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
- Correspondence:
| | - Ludovica Molinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
| | - Rodrigo Flores
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
| | - Davide Marnetto
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
| | - Marco R. Capodiferro
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (M.R.C.); (A.A.)
| | - Marta E. Alarcón-Riquelme
- Department of Medical Genomics, GENYO, Centro Pfizer—Universidad de Granada—Junta de Andalucía de Genómica e Investigación Oncológica, Av de la Ilustración 114, Parque Tecnológico de la Salud (PTS), 18016 Granada, Spain;
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico;
| | - Nedio Mabunda
- Instituto Nacional de Saúde, Distrito de Marracuene, Estrada Nacional N°1, Província de Maputo, Maputo 1120, Mozambique;
| | - Mario Ventura
- Department of Biology-Genetics, University of Bari, 70126 Bari, Italy;
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
| | - Alessandro Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (M.R.C.); (A.A.)
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK;
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
- Department of Biology, University of Padua, 35131 Padua, Italy
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; (L.M.); (R.F.); (D.M.); (K.T.); (M.M.); (L.P.); (F.M.)
- Department of Biology-Genetics, University of Bari, 70126 Bari, Italy;
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36
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Guimarães Alves AC, Sukow NM, Adelman Cipolla G, Mendes M, Leal TP, Petzl-Erler ML, Lehtonen Rodrigues Souza R, Rainha de Souza I, Sanchez C, Santolalla M, Loesch D, Dean M, Machado M, Moon JY, Kaplan R, North KE, Weiss S, Barreto ML, Lima-Costa MF, Guio H, Cáceres O, Padilla C, Tarazona-Santos E, Mata IF, Dieguez E, Raggio V, Lescano A, Tumas V, Borges V, Ferraz HB, Rieder CR, Schumacher-Schuh A, Santos-Lobato BL, Chana-Cuevas P, Fernandez W, Arboleda G, Arboleda H, Arboleda-Bustos CE, O’Connor TD, Beltrame MH, Borda V. Tracing the Distribution of European Lactase Persistence Genotypes Along the Americas. Front Genet 2021; 12:671079. [PMID: 34630506 PMCID: PMC8493957 DOI: 10.3389/fgene.2021.671079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/23/2021] [Indexed: 01/26/2023] Open
Abstract
In adulthood, the ability to digest lactose, the main sugar present in milk of mammals, is a phenotype (lactase persistence) observed in historically herder populations, mainly Northern Europeans, Eastern Africans, and Middle Eastern nomads. As the -13910∗T allele in the MCM6 gene is the most well-characterized allele responsible for the lactase persistence phenotype, the -13910C > T (rs4988235) polymorphism is commonly evaluated in lactase persistence studies. Lactase non-persistent adults may develop symptoms of lactose intolerance when consuming dairy products. In the Americas, there is no evidence of the consumption of these products until the arrival of Europeans. However, several American countries' dietary guidelines recommend consuming dairy for adequate human nutrition and health promotion. Considering the extensive use of dairy and the complex ancestry of Pan-American admixed populations, we studied the distribution of -13910C > T lactase persistence genotypes and its flanking haplotypes of European origin in 7,428 individuals from several Pan-American admixed populations. We found that the -13910∗T allele frequency in Pan-American admixed populations is directly correlated with allele frequency of the European sources. Moreover, we did not observe any overrepresentation of European haplotypes in the -13910C > T flanking region, suggesting no selective pressure after admixture in the Americas. Finally, considering the dominant effect of the -13910∗T allele, our results indicate that Pan-American admixed populations are likely to have higher frequency of lactose intolerance, suggesting that general dietary guidelines deserve further evaluation across the continent.
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Affiliation(s)
- Ana Cecília Guimarães Alves
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Natalie Mary Sukow
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Gabriel Adelman Cipolla
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Marla Mendes
- Laboratório de Diversidade Genética Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thiago P. Leal
- Laboratório de Diversidade Genética Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ricardo Lehtonen Rodrigues Souza
- Programa de Pós-Graduação em Genética, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Laboratório de Polimorfismos e Ligação, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ilíada Rainha de Souza
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Laboratório de Polimorfismos Genéticos, Departamento de Biologia Celular, Embriologia e Genética, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Cesar Sanchez
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
| | - Meddly Santolalla
- Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Douglas Loesch
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Moara Machado
- Laboratório de Diversidade Genética Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Scott Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Mauricio L. Barreto
- Universidade Federal da Bahia, Instituto de Saúde Coletiva, Salvador, Brazil
- Fundação Oswaldo Cruz, Centro de Integração de Dados e Conhecimentos para Saúde (Cidacs), Salvador, Brazil
| | - M. Fernanda Lima-Costa
- Fundação Oswaldo Cruz, Instituto René Rachou, Belo Horizonte, Brazil
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Saúde Pública, Belo Horizonte, Brazil
| | - Heinner Guio
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
- Facultad de Ciencias de la Salud, Universidad de Huánuco, Huánuco, Peru
| | - Omar Cáceres
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
- Carrera de Medicina Humana, Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima, Peru
| | - Carlos Padilla
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
| | - Eduardo Tarazona-Santos
- Laboratório de Diversidade Genética Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ignacio F. Mata
- Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
- Department of Neurology, University of Washington, Seattle, WA, United States
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, OH, United States
| | - Elena Dieguez
- Neurology Institute, Universidad de la República, Montevideo, Uruguay
| | - Víctor Raggio
- Department of Genetics, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Andres Lescano
- Neurology Institute, Universidad de la República, Montevideo, Uruguay
| | - Vitor Tumas
- Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vanderci Borges
- Movement Disorders Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Henrique B. Ferraz
- Movement Disorders Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Carlos R. Rieder
- Departamento de Neurologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Artur Schumacher-Schuh
- Serviço de Neurologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Departamento de Farmacologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Pedro Chana-Cuevas
- CETRAM, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
| | - William Fernandez
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Gonzalo Arboleda
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Humberto Arboleda
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Carlos E. Arboleda-Bustos
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
- Program for Personalized and Genomic Medicine, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
- Department of Medicine, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Marcia Holsbach Beltrame
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Victor Borda
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
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37
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Warshauer EM, Brown A, Fuentes I, Shortt J, Gignoux C, Montinaro F, Metspalu M, Youssefian L, Vahidnezhad H, Jacków J, Christiano AM, Uitto J, Fajardo-Ramírez ÓR, Salas-Alanis JC, McGrath JA, Consuegra L, Rivera C, Maier PA, Runfeldt G, Behar DM, Skorecki K, Sprecher E, Palisson F, Norris DA, Bruckner AL, Kogut I, Bilousova G, Roop DR. Ancestral patterns of recessive dystrophic epidermolysis bullosa mutations in Hispanic populations suggest sephardic ancestry. Am J Med Genet A 2021; 185:3390-3400. [PMID: 34435747 DOI: 10.1002/ajmg.a.62456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/11/2021] [Accepted: 07/14/2021] [Indexed: 11/11/2022]
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare genodermatosis caused by mutations in the gene coding for type VII collagen (COL7A1). More than 800 different pathogenic mutations in COL7A1 have been described to date; however, the ancestral origins of many of these mutations have not been precisely identified. In this study, 32 RDEB patient samples from the Southwestern United States, Mexico, Chile, and Colombia carrying common mutations in the COL7A1 gene were investigated to determine the origins of these mutations and the extent to which shared ancestry contributes to disease prevalence. The results demonstrate both shared European and American origins of RDEB mutations in distinct populations in the Americas and suggest the influence of Sephardic ancestry in at least some RDEB mutations of European origins. Knowledge of ancestry and relatedness among RDEB patient populations will be crucial for the development of future clinical trials and the advancement of novel therapeutics.
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Affiliation(s)
- Emily Mira Warshauer
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Adam Brown
- Avotaynu Research Partnership LLC, Englewood, New Jersey, USA
| | - Ignacia Fuentes
- Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile.,Fundación DEBRA Chile, Santiago, Chile
| | - Jonathan Shortt
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Chris Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Biology and Genetics, University of Bari, Bari, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Joanna Jacków
- Department of Dermatology, Columbia University, New York, New York, USA.,St. John's Institute of Dermatology, King's College London (Guy's Campus), London, UK
| | - Angela M Christiano
- Department of Dermatology, Columbia University, New York, New York, USA.,Department of Genetics and Development, Columbia University, New York, New York, USA
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Óscar R Fajardo-Ramírez
- DEBRA Mexico, Azteca Guadalupe, Mexico.,Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Julio C Salas-Alanis
- DEBRA Mexico, Azteca Guadalupe, Mexico.,Instituto Dermatologico de Jalisco, Zapopan, Mexico
| | - John A McGrath
- St. John's Institute of Dermatology, King's College London (Guy's Campus), London, UK
| | | | - Carolina Rivera
- Fundación DEBRA Colombia, Bogotá, Colombia.,Department of Medical Genetics, Pediatric Hospital, Fundacion Cardioinfantil-Universidad del Rosario, Bogotá, Colombia
| | - Paul A Maier
- Gene by Gene, Genomic Research Center, Houston, Texas, USA
| | - Goran Runfeldt
- Gene by Gene, Genomic Research Center, Houston, Texas, USA
| | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Gene by Gene, Genomic Research Center, Houston, Texas, USA
| | - Karl Skorecki
- Azrieli Faculty of Medicine of the Galilee, Bar-Ilan University, Safed, Israel
| | - Eli Sprecher
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel.,Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Francis Palisson
- Fundación DEBRA Chile, Santiago, Chile.,Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - David A Norris
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Anna L Bruckner
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Igor Kogut
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ganna Bilousova
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Dennis R Roop
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
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38
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Casares-Marfil D, Guillen-Guio B, Lorenzo-Salazar JM, Rodríguez-Pérez H, Kerick M, Jaimes-Campos MA, Díaz ML, Estupiñán E, Echeverría LE, González CI, Martin J, Flores C, Acosta-Herrera M. Admixture mapping analysis reveals differential genetic ancestry associated with Chagas disease susceptibility in the Colombian population. Hum Mol Genet 2021; 30:2503-2512. [PMID: 34302177 PMCID: PMC8643504 DOI: 10.1093/hmg/ddab213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 01/02/2023] Open
Abstract
Chagas disease is an infection caused by the parasite Trypanosoma cruzi, endemic in Latino America. Leveraging the three-way admixture between Native American (AMR), European (EUR) and African (AFR) populations in Latin Americans, we aimed to better understand the genetic basis of Chagas disease by performing an admixture mapping study in a Colombian population. A two-stage study was conducted, and subjects were classified as seropositive and seronegative for T. cruzi. In stage 1, global and local ancestries were estimated using reference data from the 1000 Genomes Project (1KGP) and local ancestry associations were performed by logistic regression models. The AMR ancestry showed a protective association with Chagas disease within the Major Histocompatibility Complex region (OR = 0.74, 95%CI = 0.66-0.83, lowest p-value = 4.53x10-8). The fine mapping assessment on imputed genotypes combining data from stage 1 and 2 from an independent Colombian cohort, revealed nominally associated variants in high linkage disequilibrium with the top signal (rs2032134, OR = 0.93, 95%CI = 0.90-0.97, p-value = 3.54x10-4) in the previously associated locus. To assess ancestry-specific adaptive signals, a selective sweep scan in an AMR reference population from 1KGP together with an in silico functional analysis highlighted the Tripartite Motif family and the Human Leukocyte Antigen (HLA) genes, with crucial role in the immune response against pathogens. Furthermore, these analyses emphasized the macrophages, neutrophils, and eosinophils, as key players in the defense against T. cruzi. This first admixture mapping study in Chagas disease provided novel insights underlying the host immune response in the pathogenesis of this neglected disease.
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Affiliation(s)
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Martin Kerick
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Mayra A Jaimes-Campos
- Grupo de Inmunología y Epidemiología Molecular, Escuela de Microbiología, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Martha L Díaz
- Grupo de Inmunología y Epidemiología Molecular, Escuela de Microbiología, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Elkyn Estupiñán
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.,Grupo de Inmunología y Epidemiología Molecular, Escuela de Microbiología, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Luis E Echeverría
- Heart Failure and Heart Transplant Clinic, Fundación Cardiovascular de Colombia, Floridablanca, Colombia
| | - Clara I González
- Grupo de Inmunología y Epidemiología Molecular, Escuela de Microbiología, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Javier Martin
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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Yang XY, Rakha A, Chen W, Hou J, Qi XB, Shen QK, Dai SS, Sulaiman X, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Chen X, Yang WK, Adnan A, Zhao RH, Yao YG, Su B, Peng MS, Zhang YP. Tracing the Genetic Legacy of the Tibetan Empire in the Balti. Mol Biol Evol 2021; 38:1529-1536. [PMID: 33283852 PMCID: PMC8042757 DOI: 10.1093/molbev/msaa313] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The rise and expansion of Tibetan Empire in the 7th to 9th centuries AD affected the course of history across East Eurasia, but the genetic impact of Tibetans on surrounding populations remains undefined. We sequenced 60 genomes for four populations from Pakistan and Tajikistan to explore their demographic history. We showed that the genomes of Balti people from Baltistan comprised 22.6–26% Tibetan ancestry. We inferred a single admixture event and dated it to about 39–21 generations ago, a period that postdated the conquest of Baltistan by the ancient Tibetan Empire. The analyses of mitochondrial DNA, Y, and X chromosome data indicated that both ancient Tibetan males and females were involved in the male-biased dispersal. Given the fact that the Balti people adopted Tibetan language and culture in history, our study suggested the impact of Tibetan Empire on Baltistan involved dominant cultural and minor demic diffusion.
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Affiliation(s)
- Xing-Yan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wei Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Juzhi Hou
- Key Laboratory of Alpine Ecology (LAE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Xue-Bin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xierzhatijiang Sulaiman
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, Tajikistan
| | | | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei-Kang Yang
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, China
| | - Ruo-Han Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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40
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Shen D, Gao B, Miskey C, Chen C, Sang Y, Zong W, Wang S, Wang Y, Wang X, Ivics Z, Song C. Multiple Invasions of Visitor, a DD41D Family of Tc1/mariner Transposons, throughout the Evolution of Vertebrates. Genome Biol Evol 2021; 12:1060-1073. [PMID: 32602886 DOI: 10.1093/gbe/evaa135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 12/13/2022] Open
Abstract
Although the DD41D (named as Visitor, VS) family of Tc1/mariner transposons was discovered in Arthropods and Mollusca, the evolution profile of this family is still largely unknown. We found that VS is widespread in the animal kingdom, including 140 species of 18 orders in invertebrates and 30 species of 12 orders in vertebrates, and one land plant species. Our data revealed multiple horizontal transfer events in both invertebrates and vertebrates and invasion into multiple lineages of mammals, including Chiroptera (seven species), Dasyuromorphia/Marsupialia (one species), Didelphimorphia/Marsupialia (one species), Diprotodontia/Marsupialia (two species), and Primates (one species). Phylogenetic analysis revealed a close relationship of VSs to DD37D/maT and DD34D/mariner and confirmed that VSs with the DD40D signature identified previously are not a distinct family but originated from DD41D/VS. Age analysis revealed that the most recent invasion of VSs was found in ray-finned fishes and a toad, followed by relatively young invasions in bats and marsupials, whereas VSs in mammals, jawless fishes, and lizards were mainly represented by ancient copies, suggesting old age. Phylogenetic analyses and comparison of pairwise distances between VSs and recombination-activating gene 1 (RAG1) support horizontal transfer events of VSs in vertebrates. The intact VSs from bats were nonfunctional as determined by the transposition activity assay. Some vertebrate lineages and species were identified as the hot hosts of Tc1/mariner transposons. Overall, our study presents the evolution profile of VSs and suggests that VSs play roles in diversifying and shaping the genomes of diverse animal lineages.
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Affiliation(s)
- Dan Shen
- College of Animal Science & Technology, Yangzhou University, China.,Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, China
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, China
| | - Wencheng Zong
- College of Animal Science & Technology, Yangzhou University, China
| | - Saisai Wang
- College of Animal Science & Technology, Yangzhou University, China
| | - Yali Wang
- College of Animal Science & Technology, Yangzhou University, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, China
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, China
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41
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Phylogeographic review of Y chromosome haplogroups in Europe. Int J Legal Med 2021; 135:1675-1684. [PMID: 34216266 DOI: 10.1007/s00414-021-02644-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Europe, with numerous migrations and invasions, has turned this continent into a melting pot. For this reason, it is interesting to study the Y chromosome variability and how it has contributed to improving our knowledge of the distribution and development of European male genetic pool as it is today. The analysis of Y lineages in Europe shows the predominance of four haplogroups, R1b-M269, I1-M253, I2-M438 and R1a-M420. However, other haplogroups have been identified which, although less frequent, provide significant evidence about the paternal origin of the populations. In addition, the study of the Y chromosome in Europe is a valuable tool for revealing the genetic trace of the different European colonizations, mainly in several American countries, where the European ancestry is mostly detected by the presence of the R1b-M269 haplogroup. Therefore, the objective of this review is to compile the studies of the Y chromosome haplogroups in current European populations, in order to provide an outline of these haplogroups which facilitate their use in forensic studies.
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Ongaro L, Mondal M, Flores R, Marnetto D, Molinaro L, Alarcón-Riquelme ME, Moreno-Estrada A, Mabunda N, Ventura M, Tambets K, Hellenthal G, Capelli C, Kivisild T, Metspalu M, Pagani L, Montinaro F. Continental-scale genomic analysis suggests shared post-admixture adaptation in the Americas. Hum Mol Genet 2021; 30:2123-2134. [PMID: 34196708 PMCID: PMC8561420 DOI: 10.1093/hmg/ddab177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 01/05/2023] Open
Abstract
American populations are one of the most interesting examples of recently admixed groups, where ancestral components from three major continental human groups (Africans, Eurasians and Native Americans) have admixed within the last 15 generations. Recently, several genetic surveys focusing on thousands of individuals shed light on the geography, chronology and relevance of these events. However, even though gene flow could drive adaptive evolution, it is unclear whether and how natural selection acted on the resulting genetic variation in the Americas. In this study, we analysed the patterns of local ancestry of genomic fragments in genome-wide data for ~ 6000 admixed individuals from 10 American countries. In doing so, we identified regions characterized by a divergent ancestry profile (DAP), in which a significant over or under ancestral representation is evident. Our results highlighted a series of genomic regions with DAPs associated with immune system response and relevant medical traits, with the longest DAP region encompassing the human leukocyte antigen locus. Furthermore, we found that DAP regions are enriched in genes linked to cancer-related traits and autoimmune diseases. Then, analysing the biological impact of these regions, we showed that natural selection could have acted preferentially towards variants located in coding and non-coding transcripts and characterized by a high deleteriousness score. Taken together, our analyses suggest that shared patterns of post admixture adaptation occurred at a continental scale in the Americas, affecting more often functional and impactful genomic variants.
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Affiliation(s)
- Linda Ongaro
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Mayukh Mondal
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Rodrigo Flores
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Davide Marnetto
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Ludovica Molinaro
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Marta E Alarcón-Riquelme
- Department of Medical Genomics, GENYO. Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica, Av de la Ilustración 114, Parque Tecnológico de la Salud (PTS), 18016, Granada, Spain
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | - Nedio Mabunda
- Instituto Nacional de Saúde, Distrito de Marracuene, Estrada Nacional N°1, Província de Maputo, Maputo, 1120, Mozambique
| | - Mario Ventura
- Department of Biology-Genetics, University of Bari, Bari, 70126, Italy
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, UK.,Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Toomas Kivisild
- Department of Human Genetics, KU Leuven, Herestraat 49 - box 602, B-3000, Leuven, Belgium
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia.,Department of Biology, University of Padua, Padua, Italy
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia.,Department of Biology-Genetics, University of Bari, Bari, 70126, Italy
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Saupe T, Montinaro F, Scaggion C, Carrara N, Kivisild T, D'Atanasio E, Hui R, Solnik A, Lebrasseur O, Larson G, Alessandri L, Arienzo I, De Angelis F, Rolfo MF, Skeates R, Silvestri L, Beckett J, Talamo S, Dolfini A, Miari M, Metspalu M, Benazzi S, Capelli C, Pagani L, Scheib CL. Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula. Curr Biol 2021; 31:2576-2591.e12. [PMID: 33974848 DOI: 10.1016/j.cub.2021.04.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/28/2020] [Accepted: 04/09/2021] [Indexed: 12/30/2022]
Abstract
Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.
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Affiliation(s)
- Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia.
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology-Genetics, University of Bari, Via E. Orabona, 4, Bari 70124, Italy
| | - Cinzia Scaggion
- Department of Geosciences, University of Padova, Via Gradenigo 6, Padova 35131, Italy
| | - Nicola Carrara
- Museum of Anthropology, University of Padova, Palazzo Cavalli, via Giotto 1, Padova 35121, Italy
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, Leuven, Herestraat 49 3000, Belgium
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Ophélie Lebrasseur
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK; Palaeogenomics & Bio-Archaeology Research Network, School of Archaeology, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Greger Larson
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy
| | - Luca Alessandri
- Groningen Institute of Archaeology, University of Groningen, Poststraat 6, Groningen 9712, the Netherlands
| | - Ilenia Arienzo
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy
| | - Flavio De Angelis
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome "Tor Vergata," Via della Ricerca Scientifica 1, Rome 00133, Italy
| | - Mario Federico Rolfo
- Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy
| | - Robin Skeates
- Department of Archaeology, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Letizia Silvestri
- Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy
| | | | - Sahra Talamo
- Department of Chemistry "Giacomo Ciamician," University of Bologna, Via Selmi 2, Bologna 40126, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Andrea Dolfini
- School of History, Classics and Archaeology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Monica Miari
- Superintendency of Archeology, Fine Arts and Landscape for the metropolitan city of Bologna and the provinces of Modena, Reggio Emilia and Ferrara, Comune di Bologna, Sede Via Belle Arti n. 52, Bologna 40126, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1, Ravenna 40126, Italy
| | - Cristian Capelli
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, University of Parma, Parco Area delle Scienze 17/A, Parma 43124, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology, University of Padova, Via U. Bassi, 58/B, Padova 35122, Italy
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; St. John's College, University of Cambridge, St. John's Street, Cambridge CB2 1TP, UK.
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Gómez R, Vilar MG, Meraz-Ríos MA, Véliz D, Zúñiga G, Hernández-Tobías EA, Figueroa-Corona MDP, Owings AC, Gaieski JB, Schurr TG. Y chromosome diversity in Aztlan descendants and its implications for the history of Central Mexico. iScience 2021; 24:102487. [PMID: 34036249 PMCID: PMC8138773 DOI: 10.1016/j.isci.2021.102487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/08/2020] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
Native Mexican populations are crucial for understanding the genetic ancestry of Aztec descendants and coexisting ethnolinguistic groups in the Valley of Mexico and elucidating the population dynamics of the prehistoric colonization of the Americas. Mesoamerican societies were multicultural in nature and also experienced significant admixture during Spanish colonization of the region. Despite these facts, Native Mexican Y chromosome diversity has been greatly understudied. To further elucidate their genetic history, we conducted a high-resolution Y chromosome analysis with Chichimecas, Nahuas, Otomies, Popolocas, Tepehuas, and Totonacas using 19 Y-short tandem repeat and 21 single nucleotide polymorphism loci. We detected enormous paternal genetic diversity in these groups, with haplogroups Q-MEH2, Q-M3, Q-Z768, Q-L663, Q-Z780, and Q-PV3 being identified. These data affirmed the southward colonization of the Americas via Beringia and connected Native Mexicans with indigenous populations from South-Central Siberia and Canada. They also suggested that multiple population dispersals gave rise to Y chromosome diversity in these populations. Enormous Y chromosome diversity observed in Native Mexican populations. Haplogroups Q-MEH2, Q-M3, Q-Z768, Q-L663, Q-Z780, and Q-PV3 were identified. Patterns of Y chromosome diversity not shaped by ethnicity, geography, or language. Multiple population dispersals contributed to Y chromosome diversity in Mexico.
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Affiliation(s)
- Rocío Gómez
- Departamento de Toxicología, CINVESTAV-IPN, Mexico City 07360, Mexico
| | - Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA.,National Geographic Society, Washington, DC 20005, USA
| | | | - David Véliz
- Departamento de Ciencias Ecológicas, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile.,Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas, Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo 1781421, Chile
| | - Gerardo Zúñiga
- Departamento de Zoología, Laboratorio de Variación Biológica y Evolución, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | | | | | - Amanda C Owings
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
| | - Jill B Gaieski
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
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Update of the global distribution of human gammaherpesvirus 8 genotypes. Sci Rep 2021; 11:7640. [PMID: 33828146 PMCID: PMC8026617 DOI: 10.1038/s41598-021-87038-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/22/2021] [Indexed: 11/15/2022] Open
Abstract
Human gammaherpesvirus 8 (HHV-8) consists of six major clades (A–F) based on the genetic sequence of the open reading frame (ORF)-K1. There are a few conflicting reports regarding the global distribution of the different HHV-8 genotypes. This study aimed to determine the global distribution of the different HHV-8 genotypes based on phylogenetic analysis of the ORF-K1 coding region using sequences published in the GenBank during 1997–2020 and construct a phylogenetic tree using the maximum likelihood algorithm with the GTR + I + G nucleotide substitution model. A total of 550 sequences from 38 countries/origins were analysed in this study. Genotypes A and C had similar global distributions and were prevalent in Africa and Europe. Genotype B was prevalent in Africa. Of the rare genotypes, genotype D was reported in East Asia and Oceania and genotype E in South America, while genotype F was prevalent in Africa. The highest genotypic diversity was reported in the American continent, with Brazil housing five HHV-8 genotypes (A, B, C, E, and F). In this study, we present update of the global distribution of HHV-8 genotypes, providing a basis for future epidemiological and evolutionary studies of HHV-8.
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Capodiferro MR, Aram B, Raveane A, Rambaldi Migliore N, Colombo G, Ongaro L, Rivera J, Mendizábal T, Hernández-Mora I, Tribaldos M, Perego UA, Li H, Scheib CL, Modi A, Gòmez-Carballa A, Grugni V, Lombardo G, Hellenthal G, Pascale JM, Bertolini F, Grieco GS, Cereda C, Lari M, Caramelli D, Pagani L, Metspalu M, Friedrich R, Knipper C, Olivieri A, Salas A, Cooke R, Montinaro F, Motta J, Torroni A, Martín JG, Semino O, Malhi RS, Achilli A. Archaeogenomic distinctiveness of the Isthmo-Colombian area. Cell 2021; 184:1706-1723.e24. [PMID: 33761327 PMCID: PMC8024902 DOI: 10.1016/j.cell.2021.02.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/20/2020] [Accepted: 02/18/2021] [Indexed: 01/09/2023]
Abstract
The recently enriched genomic history of Indigenous groups in the Americas is still meager concerning continental Central America. Here, we report ten pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama. Our analyses reveal that pre-Hispanic demographic events contributed to the extensive genetic structure currently seen in the area, which is also characterized by a distinctive Isthmo-Colombian Indigenous component. This component drives these populations on a specific variability axis and derives from the local admixture of different ancestries of northern North American origin(s). Two of these ancestries were differentially associated to Pleistocene Indigenous groups that also moved into South America, leaving heterogenous genetic footprints. An additional Pleistocene ancestry was brought by a still unsampled population of the Isthmus (UPopI) that remained restricted to the Isthmian area, expanded locally during the early Holocene, and left genomic traces up to the present day.
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Affiliation(s)
| | - Bethany Aram
- Department of Geography, History and Philosophy, the Pablo de Olavide University of Seville, Seville 41013, Spain
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy; Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Giulia Colombo
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Linda Ongaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Javier Rivera
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia
| | - Tomás Mendizábal
- Patronato Panamá Viejo, Panama City 0823-05096, Panama; Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton 0843-03081, Panama
| | - Iosvany Hernández-Mora
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia
| | - Maribel Tribaldos
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Ugo Alessandro Perego
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Hongjie Li
- Department of Anthropology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
| | - Christiana Lyn Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Alberto Gòmez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; GenPoB Research Group, Instituto de Investigación Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706 Galicia, Spain
| | - Viola Grugni
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Gianluca Lombardo
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Garrett Hellenthal
- UCL Genetics Institute (UGI), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Juan Miguel Pascale
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
| | | | - Cristina Cereda
- Genomic and Post-Genomic Center, National Neurological Institute C. Mondino, Pavia 27100, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Florence 50122, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology, University of Padua, Padua 35121, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Ronny Friedrich
- Curt Engelhorn Center Archaeometry (CEZA), Mannheim 68159, Germany
| | - Corina Knipper
- Curt Engelhorn Center Archaeometry (CEZA), Mannheim 68159, Germany
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; GenPoB Research Group, Instituto de Investigación Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706 Galicia, Spain
| | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology-Genetics, University of Bari, Bari 70125, Italy
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Juan Guillermo Martín
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia; Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton 0843-03081, Panama
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Ripan Singh Malhi
- Department of Anthropology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy.
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Molinaro L, Marnetto D, Mondal M, Ongaro L, Yelmen B, Lawson DJ, Montinaro F, Pagani L. A Chromosome-Painting-Based Pipeline to Infer Local Ancestry under Limited Source Availability. Genome Biol Evol 2021; 13:6135079. [PMID: 33585906 PMCID: PMC8085126 DOI: 10.1093/gbe/evab025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2021] [Indexed: 01/09/2023] Open
Abstract
Contemporary individuals are the combination of genetic fragments inherited from ancestors belonging to multiple populations, as the result of migration and admixture. Isolating and characterizing these layers are crucial to the understanding of the genetic history of a given population. Ancestry deconvolution approaches make use of a large amount of source individuals, therefore constraining the performance of Local Ancestry Inferences when only few genomes are available from a given population. Here we present WINC, a local ancestry framework derived from the combination of ChromoPainter and NNLS approaches, as a method to retrieve local genetic assignments when only a few reference individuals are available. The framework is aided by a score assignment based on source differentiation to maximize the amount of sequences retrieved and is capable of retrieving accurate ancestry assignments when only two individuals for source populations are used.
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Affiliation(s)
- Ludovica Molinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Davide Marnetto
- Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia
| | - Mayukh Mondal
- Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia
| | - Linda Ongaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Burak Yelmen
- Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Daniel John Lawson
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School, University of Bristol, United Kingdom
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia.,Department of Biology-Genetics, University of Bari, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia.,Department of Biology, University of Padova, Italy
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48
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Response to Jackson. Am J Hum Genet 2021; 108:209-210. [PMID: 33321101 DOI: 10.1016/j.ajhg.2020.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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49
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Fortes-Lima C, Verdu P. Anthropological genetics perspectives on the transatlantic slave trade. Hum Mol Genet 2020; 30:R79-R87. [PMID: 33331897 DOI: 10.1093/hmg/ddaa271] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 01/07/2023] Open
Abstract
During the Trans-Atlantic Slave Trade (TAST), around twelve million Africans were enslaved and forcibly moved from Africa to the Americas and Europe, durably influencing the genetic and cultural landscape of a large part of humanity since the 15th century. Following historians, archaeologists, and anthropologists, population geneticists have, since the 1950's mainly, extensively investigated the genetic diversity of populations on both sides of the Atlantic. These studies shed new lights into the largely unknown genetic origins of numerous enslaved-African descendant communities in the Americas, by inferring their genetic relationships with extant African, European, and Native American populations. Furthermore, exploring genome-wide data with novel statistical and bioinformatics methods, population geneticists have been increasingly able to infer the last 500 years of admixture histories of these populations. These inferences have highlighted the diversity of histories experienced by enslaved-African descendants, and the complex influences of socioeconomic, political, and historical contexts on human genetic diversity patterns during and after the slave trade. Finally, the recent advances of paleogenomics unveiled crucial aspects of the life and health of the first generation of enslaved-Africans in the Americas. Altogether, human population genetics approaches in the genomic and paleogenomic era need to be coupled with history, archaeology, anthropology, and demography in interdisciplinary research, to reconstruct the multifaceted and largely unknown history of the TAST and its influence on human biological and cultural diversities today. Here, we review anthropological genomics studies published over the past 15 years and focusing on the history of enslaved-African descendant populations in the Americas.
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Affiliation(s)
- Cesar Fortes-Lima
- Sub-department of Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, 75236, Sweden
| | - Paul Verdu
- Unité Mixte de Recherche7206 Eco-Anthropology, CNRS-MNHN-Université de Paris, Musée de l'Homme, Paris, 75016, France
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50
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Pena SDJ, Santos FR, Tarazona-Santos E. Genetic admixture in Brazil. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:928-938. [PMID: 33205899 DOI: 10.1002/ajmg.c.31853] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 12/21/2022]
Abstract
We review studies from our laboratories using different molecular tools to characterize the Amerindian, European and African ancestry of Brazilians. Initially we used uniparental DNA markers to investigate the contribution of distinct Y chromosome and mitochondrial DNA lineages to present-day populations. High levels of genetic admixture and strong directional mating between European males and Amerindian and African females were unraveled. We next analyzed different types of biparental autosomal polymorphisms. Especially useful was a set of 40 insertion-deletion polymorphisms (indels) that when studied worldwide proved exquisitely sensitive in discriminating between Amerindians, Europeans and Sub-Saharan Africans. When applied to the study of Brazilians these markers confirmed extensive genomic admixture. We then studied ancestry differences in different regions by statistically controlling them to eliminate color considerations. The European ancestry was predominant in all regions studied, with proportions ranging from 60.6% in the Northeast to 77.7% in the South. We propose that the immigration of 6 million Europeans to Brazil in the 19th and 20th centuries is in large part responsible for dissipating previous ancestry dissimilarities that reflected region-specific population histories. Brazilians should be assessed individually, as 210 million human beings, and not as members of specific regions or color groups.
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Affiliation(s)
- Sergio D J Pena
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fabrício R Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Instituto de Estudos Avançados Transdisciplinares, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
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