1
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Wassenaar TM, Harville T, Chastain J, Wanchai V, Ussery DW. DNA structural features and variability of complete MHC locus sequences. FRONTIERS IN BIOINFORMATICS 2024; 4:1392613. [PMID: 39022183 PMCID: PMC11251971 DOI: 10.3389/fbinf.2024.1392613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/07/2024] [Indexed: 07/20/2024] Open
Abstract
The major histocompatibility (MHC) locus, also known as the Human Leukocyte Antigen (HLA) genes, is located on the short arm of chromosome 6, and contains three regions (Class I, Class II and Class III). This 5 Mbp locus is one of the most variable regions of the human genome, yet it also encodes a set of highly conserved and important proteins related to immunological response. Genetic variations in this region are responsible for more diseases than in the entire rest of the human genome. However, information on local structural features of the DNA is largely ignored. With recent advances in long-read sequencing technology, it is now becoming possible to sequence the entire 5 Mbp MHC locus, producing complete diploid haplotypes of the whole region. Here, we describe structural maps based on the complete sequences from six different homozygous HLA cell lines. We find long-range structural variability in the different sequences for DNA stacking energy, position preference and curvature, variation in repeats, as well as more local changes in regions forming open chromatin structures, likely to influence gene expression levels. These structural maps can be useful in visualizing large scale structural variation across HLA types, in particular when this can be complemented with epigenetic signals.
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Affiliation(s)
| | - Terry Harville
- Department of Pathology and Laboratory Services, and Department of Internal Medicine, Division of Hematology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Jonathan Chastain
- Department of Pediatrics, The University of Arkansas for Medical Sciences University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Visanu Wanchai
- Myeloma Center, Winthrop P. Rockefeller Institute, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - David W. Ussery
- Department of BioMedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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2
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Leonard WR. Pearl Memorial Lecture. Humans at the extremes: Exploring human adaptation to ecological and social stressors. Am J Hum Biol 2024; 36:e24010. [PMID: 37974340 DOI: 10.1002/ajhb.24010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023] Open
Abstract
The field of human biology has long explored how human populations have adapted to extreme environmental circumstances. Yet, it has become increasingly clear that conditions of social stress, poverty, and lifestyle change play equally important roles in shaping human biological variation and health. In this paper, I provide a brief background on the foundational human adaptability research of the International Biological Programme (IBP) from the 1960s, highlighting how its successes and critiques have shaped current research directions in the field. I then discuss and reflect on my own field research that has examined the influence of both environmental and social stresses on human populations living in different ecosystems: the Peruvian Andes, the Siberian arctic, and the Bolivian rainforest. Finally, I consider how the papers in this special issue advance our understanding of human adaptability to extreme conditions and offer directions for future research. Drawing on our field's distinctive evolutionary and biocultural perspectives, human biologists are uniquely positioned to examine how the interplay between social and ecological domains influences the human condition.
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Affiliation(s)
- William R Leonard
- Department of Anthropology & Program in Global Health Studies, Northwestern University, Evanston, Illinois, USA
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3
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Nayak SS, Panigrahi M, Kumar H, Rajawat D, Sharma A, Bhushan B, Dutt T. Evidence for selective sweeps in the MHC gene repertoire of various cattle breeds. Anim Biotechnol 2023; 34:4167-4173. [PMID: 37039747 DOI: 10.1080/10495398.2023.2196317] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Major Histocompatibility Complex (MHC) genes are among the immune genes that have been extensively studied in vertebrates and are necessary for adaptive immunity. In the immunological response to infectious diseases, they play several significant roles. This research paper provides the selection signatures in the MHC region of the bovine genome as well as how certain genes related to innate immunity are undergoing a positive selective sweep. Here, we investigated signatures of historical selection on MHC genes in 15 different cattle populations and a total of 427 individuals. To identify the selection signatures, we have used three separate summary statistics. The findings show potential selection signatures in cattle from whom we isolated genes involved in the MHC. The most significant regions related to the bovine MHC are BOLA, non-classical MHC class I antigen (BOLA-NC1), Microneme protein 1 (MIC1) , Cluster of Differentiation 244 (CD244), Gap Junction Alpha-5 Protein (GJA5). It will be possible to gain new insight into immune system evolution by understanding the distinctive characteristics of MHC in cattle.
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Affiliation(s)
- Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
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4
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Amin MR, Hasan M, Arnab SP, DeGiorgio M. Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data. Mol Biol Evol 2023; 40:msad216. [PMID: 37772983 PMCID: PMC10581699 DOI: 10.1093/molbev/msad216] [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: 03/02/2023] [Revised: 08/10/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023] Open
Abstract
Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under nonconvex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data although preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx, which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.
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Affiliation(s)
- Md Ruhul Amin
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Mahmudul Hasan
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Sandipan Paul Arnab
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
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5
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Oliveira MLG, Castelli EC, Veiga‐Castelli LC, Pereira ALE, Marcorin L, Carratto TMT, Souza AS, Andrade HS, Simões AL, Donadi EA, Courtin D, Sabbagh A, Giuliatti S, Mendes‐Junior CT. Genetic diversity of the
LILRB1
and
LILRB2
coding regions in an admixed Brazilian population sample. HLA 2022; 100:325-348. [DOI: 10.1111/tan.14725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/02/2022] [Accepted: 06/24/2022] [Indexed: 11/27/2022]
Affiliation(s)
| | - Erick C. Castelli
- Pathology Department, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Luciana C. Veiga‐Castelli
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Alison Luis E. Pereira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Thássia M. T. Carratto
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Andreia S. Souza
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Heloisa S. Andrade
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Aguinaldo L. Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Eduardo A. Donadi
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | | | | | - Silvana Giuliatti
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Celso Teixeira Mendes‐Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
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6
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Kumar H, Panigrahi M, Panwar A, Rajawat D, Nayak SS, Saravanan KA, Kaisa K, Parida S, Bhushan B, Dutt T. Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data. J Comput Biol 2022; 29:943-960. [PMID: 35639362 DOI: 10.1089/cmb.2021.0447] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Natural selection has been given a lot of attention because it relates to the adaptation of populations to their environments, both biotic and abiotic. An allele is selected when it is favored by natural selection. Consequently, the favored allele increases in frequency in the population and neighboring linked variation diminishes, causing so-called selective sweeps. A high-throughput genomic sequence allows one to disentangle the evolutionary forces at play in populations. With the development of high-throughput genome sequencing technologies, it has become easier to detect these selective sweeps/selection signatures. Various methods can be used to detect selective sweeps, from simple implementations using summary statistics to complex statistical approaches. One of the important problems of these statistical models is the potential to provide inaccurate results when their assumptions are violated. The use of machine learning (ML) in population genetics has been introduced as an alternative method of detecting selection by treating the problem of detecting selection signatures as a classification problem. Since the availability of population genomics data is increasing, researchers may incorporate ML into these statistical models to infer signatures of selection with higher predictive accuracy and better resolution. This article describes how ML can be used to aid in detecting and studying natural selection patterns using population genomic data.
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Affiliation(s)
- Harshit Kumar
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Manjit Panigrahi
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Anuradha Panwar
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Divya Rajawat
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Sonali Sonejita Nayak
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - K A Saravanan
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Kaiho Kaisa
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Subhashree Parida
- Divisions of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Bharat Bhushan
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, India
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7
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The Tumor Dynamism Is the Dark Matter of the NGS Galaxy: How to Understand It? Cancers (Basel) 2021; 13:cancers13215476. [PMID: 34771638 PMCID: PMC8582436 DOI: 10.3390/cancers13215476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 11/30/2022] Open
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8
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Nunes K, Maia MHT, Dos Santos EJM, Dos Santos SEB, Guerreiro JF, Petzl-Erler ML, Bedoya G, Gallo C, Poletti G, Llop E, Tsuneto L, Bortolini MC, Rothhammer F, Single R, Ruiz-Linares A, Rocha J, Meyer D. How natural selection shapes genetic differentiation in the MHC region: A case study with Native Americans. Hum Immunol 2021; 82:523-531. [PMID: 33812704 PMCID: PMC8217218 DOI: 10.1016/j.humimm.2021.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 02/15/2021] [Accepted: 03/09/2021] [Indexed: 12/19/2022]
Abstract
The Human Leukocyte Antigen (HLA) loci are extremely well documented targets of balancing selection, yet few studies have explored how selection affects population differentiation at these loci. In the present study we investigate genetic differentiation at HLA genes by comparing differentiation at microsatellites distributed genomewide to those in the MHC region. Our study uses a sample of 494 individuals from 30 human populations, 28 of which are Native Americans, all of whom were typed for genomewide and MHC region microsatellites. We find greater differentiation in the MHC than in the remainder of the genome (FST-MHC = 0.130 and FST-Genomic = 0.087), and use a permutation approach to show that this difference is statistically significant, and not accounted for by confounding factors. This finding lies in the opposite direction to the expectation that balancing selection reduces population differentiation. We interpret our findings as evidence that selection favors different sets of alleles in distinct localities, leading to increased differentiation. Thus, balancing selection at HLA genes simultaneously increases intra-population polymorphism and inter-population differentiation in Native Americans.
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Affiliation(s)
- Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil.
| | | | | | | | | | | | - Gabriel Bedoya
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Giovanni Poletti
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Elena Llop
- Instituto de Ciencias Biomédicas, Faculdad de Medicina, Universidade de Chile, Santiago, Chile
| | - Luiza Tsuneto
- Departamento de Ciências Básicas da Saúde, Universidade Estadual de Maringá, Maringá, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Richard Single
- Department of Mathematics and Statistics, University of Vermont, Burlington, VT, USA
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200433, China; D Aix-Marseille University, CNRS, EFS, ADES, Marseille 13007, France
| | - Jorge Rocha
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal; CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal.
| | - Diogo Meyer
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil.
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9
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Mao XF, Chen XP, Jin YB, Cui JH, Pan YM, Lai CY, Lin KR, Ling F, Luo W. The variations of TRBV genes usages in the peripheral blood of a healthy population are associated with their evolution and single nucleotide polymorphisms. Hum Immunol 2018; 80:195-203. [PMID: 30576702 DOI: 10.1016/j.humimm.2018.12.007] [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: 05/13/2018] [Revised: 12/10/2018] [Accepted: 12/17/2018] [Indexed: 11/16/2022]
Abstract
T cell receptors (TCRs) are a class of T cell surface molecules that recognize the antigen-derived peptides presented by the major histocompatibility complex (MHC) and are able to trigger a series of immune responses. TCRs are important members of the adaptive immune system that arose in the jawed fish 500 million years ago. T cell receptor beta variable (TRBV) genes have been widely used to characterize TCR repertoires. Studying the evolution of TRBV may help us to better understand the adaptive immune system. To investigate TRBV evolution and its impacts on the usages of TRBV genes in human populations, we compared the TRBV genes and their homologous sequences among humans, mouse, rhesus and chimpanzee, analyzed the single-nucleotide polymorphisms (SNPs) located at TRBV loci, and sequenced TCR repertoires in the peripheral blood of 97 healthy donors. We found that functional TRBVs are more evolutionarily conserved but possess more SNPs in human populations than do nonfunctional (pseudo) TRBVs. Based on the conservation levels in the four species, we classified the functional TRBVs into 2 groups: old (conserved between mouse and humans) and new (conserved only in primates). The new TRBVs evolve faster and possess more SNPs than the old TRBVs. The variations in TRBV genes frequencies in the peripheral blood of healthy donors are negatively correlated with SNP density. These observations suggest that TRBV usages may be influenced by TCR-MHC co-evolution.
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Affiliation(s)
- Xiao-Fan Mao
- Clinical Research Institute, Sun Yat-Sen University Foshan Hospital, Foshan, China; Department of Molecular Biology, School of Bioengineering and Biotechnology, South China University of Technology, Guangzhou, China
| | - Xiang-Ping Chen
- Clinical Research Institute, Sun Yat-Sen University Foshan Hospital, Foshan, China
| | - Ya-Bin Jin
- Clinical Research Institute, Sun Yat-Sen University Foshan Hospital, Foshan, China
| | - Jin-Huan Cui
- Clinical Research Institute, Sun Yat-Sen University Foshan Hospital, Foshan, China
| | - Ying-Ming Pan
- Clinical Research Institute, Sun Yat-Sen University Foshan Hospital, Foshan, China
| | - Chun-Yan Lai
- Center of Health Management, Sun Yat-Sen University Foshan Hospital, Foshan, China
| | - Kai-Rong Lin
- Clinical Research Institute, Sun Yat-Sen University Foshan Hospital, Foshan, China
| | - Fei Ling
- Department of Molecular Biology, School of Bioengineering and Biotechnology, South China University of Technology, Guangzhou, China.
| | - Wei Luo
- Clinical Research Institute, Sun Yat-Sen University Foshan Hospital, Foshan, China.
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10
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Goodswen SJ, Kennedy PJ, Ellis JT. A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen. Front Genet 2018; 9:332. [PMID: 30177953 PMCID: PMC6109633 DOI: 10.3389/fgene.2018.00332] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/02/2018] [Indexed: 11/22/2022] Open
Abstract
Over the last two decades, various in silico approaches have been developed and refined that attempt to identify protein and/or peptide vaccines candidates from informative signals encoded in protein sequences of a target pathogen. As to date, no signal has been identified that clearly indicates a protein will effectively contribute to a protective immune response in a host. The premise for this study is that proteins under positive selection from the immune system are more likely suitable vaccine candidates than proteins exposed to other selection pressures. Furthermore, our expectation is that protein sequence regions encoding major histocompatibility complexes (MHC) binding peptides will contain consecutive positive selection sites. Using freely available data and bioinformatic tools, we present a high-throughput approach through a pipeline that predicts positive selection sites, protein subcellular locations, and sequence locations of medium to high T-Cell MHC class I binding peptides. Positive selection sites are estimated from a sequence alignment by comparing rates of synonymous (dS) and non-synonymous (dN) substitutions among protein coding sequences of orthologous genes in a phylogeny. The main pipeline output is a list of protein vaccine candidates predicted to be naturally exposed to the immune system and containing sites under positive selection. Candidates are ranked with respect to the number of consecutive sites located on protein sequence regions encoding MHCI-binding peptides. Results are constrained by the reliability of prediction programs and quality of input data. Protein sequences from Toxoplasma gondii ME49 strain (TGME49) were used as a case study. Surface antigen (SAG), dense granules (GRA), microneme (MIC), and rhoptry (ROP) proteins are considered worthy T. gondii candidates. Given 8263 TGME49 protein sequences processed anonymously, the top 10 predicted candidates were all worthy candidates. In particular, the top ten included ROP5 and ROP18, which are T. gondii virulence determinants. The chance of randomly selecting a ROP protein was 0.2% given 8263 sequences. We conclude that the approach described is a valuable addition to other in silico approaches to identify vaccines candidates worthy of laboratory validation and could be adapted for other apicomplexan parasite species (with appropriate data).
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Affiliation(s)
- Stephen J Goodswen
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Paul J Kennedy
- School of Software, Faculty of Engineering and Information Technology, Centre for Artificial Intelligence, University of Technology Sydney, Ultimo, NSW, Australia
| | - John T Ellis
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
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11
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Leonard WR. Centennial perspective on human adaptability. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:813-833. [DOI: 10.1002/ajpa.23401] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/19/2022]
Affiliation(s)
- William R. Leonard
- Department of Anthropology; Northwestern University; Evanston Illinois 60208
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12
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Liu H, Xue F, Gong J, Wan Q, Fang S. Limited polymorphism of the functional MHC class II B gene in the black-spotted frog ( Pelophylax nigromaculatus) identified by locus-specific genotyping. Ecol Evol 2017; 7:9860-9868. [PMID: 29238521 PMCID: PMC5723586 DOI: 10.1002/ece3.3408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 07/31/2017] [Accepted: 08/19/2017] [Indexed: 12/23/2022] Open
Abstract
Amphibians can be more vulnerable to environmental changes and diseases than other species because of their complex life cycle and physiological requirements. Therefore, understanding the adaptation of amphibians to environmental changes is crucial for their conservation. Major histocompatibility complex (MHC) presents an excellent tool for the investigation of adaptive variations and the assessment of adaptive potential because it can be under strong diversifying selection. Here, we isolated the MHC class II B (MHCIIB) gene from cDNA sequences of the black-spotted frog (Pelophylax nigromaculatus), a widespread amphibian species in China, and designed locus-specific primers to characterize adaptive variability of this amphibian. Ten alleles were identified from 67 individual frogs of three populations and no more than two alleles were present in each individual animal. Furthermore, none of the sequences had indels or/and stop codons, which is in good agreement with locus-specific amplification of a functional gene. However, we found low polymorphism at both nucleotide and amino acid levels, even in the antigen-binding region. Purifying selection acting at this locus was supported by the findings that the dN/dS ratio across all alleles was below 1 and that negatively selected sites were detected by different methods. Allele frequency distributions were significantly different among geographic populations, indicating that physiographic factors may have strong effect on the genetic structure of the black-spotted frog. This study revealed limited polymorphism of three adjacent black-spotted frog populations at the functional MHCIIB locus, which may be attributed to region-specific differences. The locus-specific genotyping technique developed in this study would provide a foundation for future studies on adaptive divergence among different frog populations.
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Affiliation(s)
- Hong‐Yi Liu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered WildlifeCollege of Life SciencesZhejiang UniversityHangzhouChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Fei Xue
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered WildlifeCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Jie Gong
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered WildlifeCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Qiu‐Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered WildlifeCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Sheng‐Guo Fang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered WildlifeCollege of Life SciencesZhejiang UniversityHangzhouChina
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13
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Sun H, Huang X, Lin K, Huang K, Chu J, Yang Z, Ma S. Molecular evolution of two asymptomatic echovirus 6 strains that constitute a novel branch of recently epidemic echovirus 6 in China. Virol J 2017; 14:140. [PMID: 28743260 PMCID: PMC5526271 DOI: 10.1186/s12985-017-0809-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/19/2017] [Indexed: 11/23/2022] Open
Abstract
Background Echovirus 6 (E6) infections are associated with aseptic meningitis and acute flaccid paralysis (AFP). But some infections, sometimes most of them, are asymptomatic. The mechanism of E6 virulence is unknown. Analyses of the molecular evolution of asymptomatic E6 may help understand why the infections show different manifestations. Methods Ninety-six stool samples of healthy children in Yunnan, China were collected and two E6 strains were isolated from them. The whole genomes of these two E6 strains were sequenced, and their molecular evolution was analyzed. Results The results showed that the two E6 strains may be derived from KJ7724XX strains, which were predominant in AFP patients in Shangdong in 2011. The evolution was accelerated when the two E6 strains formed, although no positive selection site was found. The 11 exclusive mutations on which selection force significantly changed were found in the 2C, 3AB and 3C genes. Conclusion There are some E6 strains which did not cause the disease in the children of Yunnan. These E6 strains maybe come from a recombinant E6 strain which was associated with the outbreak of AFP in Shangdong in 2011. However, some new mutations were found in the 2C, 3AB and 3C genes of these asymptomatic strains, and these mutations may be constraint by the natural selection and could be potentially responsible for clinical presentations. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0809-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Sun
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan Province, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Xiaoqin Huang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan Province, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Keqin Lin
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan Province, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Kai Huang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan Province, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Jiayou Chu
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan Province, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Zhaoqing Yang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan Province, People's Republic of China. .,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China.
| | - Shaohui Ma
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan Province, People's Republic of China. .,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China.
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14
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Beckett EL, Duesing K, Boyd L, Yates Z, Veysey M, Lucock M. A potential sex dimorphism in the relationship between bitter taste and alcohol consumption. Food Funct 2017; 8:1116-1123. [PMID: 28164195 DOI: 10.1039/c6fo01759b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Bitterness is an innate aversive taste important in detecting potentially toxic substances, including alcohol. However, bitter compounds exist in many foods and beverages, and can be desirable, such as in beer. TAS2R38 is a well-studied bitter taste receptor with common polymorphisms. Some have reported relationships between TAS2R38 genotypes, bitter taste phenotype and alcohol intake, however results have been mixed. These mixed results may be explained by the varying taste properties of different alcoholic beverages or a sex dimorphism in responses. METHODS Bitter taste phenotype was assessed using PROP taste test and TAS2R38-P49A genotype was assessed by RFLP-PCR. Alcohol intake was assessed by food frequency questionnaire and classified by beverage type (beer, wine, spirits or mixed drinks). The relationships between bitter taste phenotype and carriage of the P allele of the TAS2R38-A49P gene and alcohol intake were assessed adjusted for and stratified by sex, and the interaction between taste and sex was evaluated. RESULTS The relationship between alcohol intake and bitter taste phenotype varied by beverage type, with significant results for beer, spirits and mixed drinks, but not wine. When stratified, results varied by sex, and were only significant in males. Significant interactions were found for taster phenotype and sex (total alcohol intake and intake of beer and spirits). Results were similar for carriage of the TAS2R38-P49A P allele. CONCLUSIONS Sex-specific interactions between bitter taste phenotype, TAS2R38 genotype and alcohol intake may explain variance in previous studies and may have implications for sex-specific disease risk and public health interventions.
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Affiliation(s)
- Emma Louise Beckett
- School of Environmental and Life Sciences, The University of Newcastle, NSW 2258, Australia. and Food and Nutrition Flagship, CSIRO, NSW, Australia and School of Medicine & Public Health, University of Newcastle, NSW, Australia
| | | | - Lyndell Boyd
- School of Environmental and Life Sciences, The University of Newcastle, NSW 2258, Australia.
| | - Zoe Yates
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Ourimbah, NSW 2258, Australia
| | - Martin Veysey
- School of Medicine & Public Health, University of Newcastle, NSW, Australia and Teaching and Research Unit, Central Coast Local Health District, PO Box 361, Gosford, 2250, Australia
| | - Mark Lucock
- School of Environmental and Life Sciences, The University of Newcastle, NSW 2258, Australia.
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15
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Evolution of Brain Active Gene Promoters in Human Lineage Towards the Increased Plasticity of Gene Regulation. Mol Neurobiol 2017; 55:1871-1904. [PMID: 28233272 DOI: 10.1007/s12035-017-0427-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/26/2017] [Indexed: 01/31/2023]
Abstract
Adaptability to a variety of environmental conditions is a prominent feature of Homo sapiens. We hypothesize that this feature can be explained by evolutionary changes in gene promoters active in the brain prefrontal cortex leading to a more flexible gene regulation network. The genotype-dependent range of gene expression can be broader in humans than in other higher primates. Thus, we searched for specific signatures of evolutionary changes in promoter architectures of multiple hominid genes, including the genes active in human cortical neurons that may indicate an increase of variability of gene expression rather than just changes in the level of expression, such as downregulation or upregulation of the genes. We performed a whole-genome search for genetic-based alterations that may impact gene regulation "flexibility" in a process of hominids evolution, such as (i) CpG dinucleotide content, (ii) predicted nucleosome-DNA dissociation constant, and (iii) predicted affinities for TATA-binding protein (TBP) in gene promoters. We tested all putative promoter regions across the human genome and especially gene promoters in active chromatin state in neurons of prefrontal cortex, the brain region critical for abstract thinking and social and behavioral adaptation. Our data imply that the origin of modern man has been associated with an increase of flexibility of promoter-driven gene regulation in brain. In contrast, after splitting from the ancestral lineages of H. sapiens, the evolution of ape species is characterized by reduced flexibility of gene promoter functioning, underlying reduced variability of the gene expression.
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Abstract
The wealth of available genetic information is allowing the reconstruction of human demographic and adaptive history. Demography and purifying selection affect the purge of rare, deleterious mutations from the human population, whereas positive and balancing selection can increase the frequency of advantageous variants, improving survival and reproduction in specific environmental conditions. In this review, I discuss how theoretical and empirical population genetics studies, using both modern and ancient DNA data, are a powerful tool for obtaining new insight into the genetic basis of severe disorders and complex disease phenotypes, rare and common, focusing particularly on infectious disease risk.
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Affiliation(s)
- Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Department of Genomes & Genetics, Institut Pasteur, Paris, 75015, France.
- Centre National de la Recherche Scientifique, URA3012, Paris, 75015, France.
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, 75015, France.
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17
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Dall'Ara I, Ghirotto S, Ingusci S, Bagarolo G, Bertolucci C, Barbujani G. Demographic history and adaptation account for clock gene diversity in humans. Heredity (Edinb) 2016; 117:165-72. [PMID: 27301334 DOI: 10.1038/hdy.2016.39] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/18/2016] [Accepted: 03/29/2016] [Indexed: 01/01/2023] Open
Abstract
Circadian clocks give rise to daily oscillations in behavior and physiological functions that often anticipate upcoming environmental changes generated by the Earth rotation. In model organisms a relationship exists between several genes affecting the circadian rhythms and latitude. We investigated the allele distributions at 116 000 single-nucleotide polymorphisms (SNPs) of 25 human clock and clock-related genes from the 1000Genomes Project, and at a reference data set of putatively neutral polymorphisms. The global genetic structure at the clock genes did not differ from that observed at the reference data set. We then tested for evidence of local adaptation searching for FST outliers under both an island and a hierarchical model, and for significant association between allele frequencies and environmental variables by a Bayesian approach. A total of 230 SNPs in 23 genes, or 84 SNPs in 19 genes, depending on the significance thresholds chosen, showed signs of local adaptation, whereas a maximum of 190 SNPs in 23 genes had significant covariance with one or more environmental variables. Only two SNPs from two genes (NPAS2 and AANAT) exhibit both elevated population differentiation and covariance with at least one environmental variable. We then checked whether the SNPs emerging from these analyses fall within a set of candidate SNPs associated with different chronotypes or sleep disorders. Correlation of five such SNPs with environmental variables supports a selective role of latitude or photoperiod, but certainly not a major one.
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Affiliation(s)
- I Dall'Ara
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - S Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - S Ingusci
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - G Bagarolo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - C Bertolucci
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - G Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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18
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Downey G. Being Human in Cities: Phenotypic Bias from Urban Niche Construction. CURRENT ANTHROPOLOGY 2016. [DOI: 10.1086/685710] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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19
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Podgorná E, Diallo I, Vangenot C, Sanchez-Mazas A, Sabbagh A, Černý V, Poloni ES. Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa. BMC Evol Biol 2015; 15:263. [PMID: 26620671 PMCID: PMC4665893 DOI: 10.1186/s12862-015-0543-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 11/13/2015] [Indexed: 12/21/2022] Open
Abstract
Background Dietary changes associated to shifts in subsistence strategies during human evolution may have induced new selective pressures on phenotypes, as currently held for lactase persistence. Similar hypotheses exist for arylamine N-acetyltransferase 2 (NAT2) mediated acetylation capacity, a well-known pharmacogenetic trait with wide inter-individual variation explained by polymorphisms in the NAT2 gene. The environmental causative factor (if any) driving its evolution is as yet unknown, but significant differences in prevalence of acetylation phenotypes are found between hunter-gatherer and food-producing populations, both in sub-Saharan Africa and worldwide, and between agriculturalists and pastoralists in Central Asia. These two subsistence strategies also prevail among sympatric populations of the African Sahel, but knowledge on NAT2 variation among African pastoral nomads was up to now very scarce. Here we addressed the hypothesis of different selective pressures associated to the agriculturalist or pastoralist lifestyles having acted on the evolution of NAT2 by sequencing the gene in 287 individuals from five pastoralist and one agriculturalist Sahelian populations. Results We show that the significant NAT2 genetic structure of African populations is mainly due to frequency differences of three major haplotypes, two of which are categorized as decreased function alleles (NAT2*5B and NAT2*6A), particularly common in populations living in arid environments, and one fast allele (NAT2*12A), more frequently detected in populations living in tropical humid environments. This genetic structure does associate more strongly with a classification of populations according to ecoregions than to subsistence strategies, mainly because most Sahelian and East African populations display little to no genetic differentiation between them, although both regions hold nomadic or semi-nomadic pastoralist and sedentary agriculturalist communities. Furthermore, we found significantly higher predicted proportions of slow acetylators in pastoralists than in agriculturalists, but also among food-producing populations living in the Sahelian and dry savanna zones than in those living in humid environments, irrespective of their mode of subsistence. Conclusion Our results suggest a possible independent influence of both the dietary habits associated with subsistence modes and the chemical environment associated with climatic zones and biomes on the evolution of NAT2 diversity in sub-Saharan African populations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0543-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eliška Podgorná
- Department of the Archaeology of Landscape and Archaeobiology, Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic. .,Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| | - Issa Diallo
- Département de Linguistique et Langues Nationales, Institut des Sciences des Sociétés, CNRST, Ouagadougou, Burkina Faso.
| | - Christelle Vangenot
- Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| | - Alicia Sanchez-Mazas
- Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| | - Audrey Sabbagh
- IRD, UMR216, Mère et enfant face aux infections tropicales, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France.
| | - Viktor Černý
- Department of the Archaeology of Landscape and Archaeobiology, Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic.
| | - Estella S Poloni
- Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
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Norton HL, Werren E, Friedlaender J. MC1R diversity in Northern Island Melanesia has not been constrained by strong purifying selection and cannot explain pigmentation phenotype variation in the region. BMC Genet 2015; 16:122. [PMID: 26482799 PMCID: PMC4615358 DOI: 10.1186/s12863-015-0277-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/06/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Variation in human skin pigmentation evolved in response to the selective pressure of ultra-violet radiation (UVR). Selection to maintain darker skin in high UVR environments is expected to constrain pigmentation phenotype and variation in pigmentation loci. Consistent with this hypothesis, the gene MC1R exhibits reduced diversity in African populations from high UVR regions compared to low-UVR non-African populations. However, MC1R diversity in non-African populations that have evolved under high-UVR conditions is not well characterized. METHODS In order to test the hypothesis that MC1R variation has been constrained in Melanesians the coding region of the MC1R gene was sequenced in 188 individuals from Northern Island Melanesia. The role of purifying selection was assessed using a modified McDonald Kreitman's test. Pairwise FST was calculated between Melanesian populations and populations from the 1000 Genomes Project. The SNP rs2228479 was genotyped in a larger sample (n = 635) of Melanesians and tested for associations with skin and hair pigmentation. RESULTS We observe three nonsynonymous and two synonymous mutations. A modified McDonald Kreitman's test failed to detect a significant signal of purifying selection. Pairwise FST values calculated between the four islands sampled here indicate little regional substructure in MC1R. When compared to African, European, East and South Asian populations, Melanesians do not exhibit reduced population divergence (measured as FST) or a high proportion of haplotype sharing with Africans, as one might expect if ancestral haplotypes were conserved across high UVR populations in and out of Africa. The only common nonsynonymous polymorphism observed, rs2228479, is not significantly associated with skin or hair pigmentation in a larger sample of Melanesians. CONCLUSIONS The pattern of sequence diversity here does not support a model of strong selective constraint on MC1R in Northern Island Melanesia This absence of strong constraint, as well as the recent population history of the region, may explain the observed frequencies of the derived rs2228479 allele. These results emphasize the complex genetic architecture of pigmentation phenotypes, which are controlled by multiple, possibly interacting loci. They also highlight the role that population history can play in influencing phenotypic diversity in the absence of strong natural selection.
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Affiliation(s)
- Heather L Norton
- Department of Anthropology, University of Cincinnati, 481 Braunstein Hall, PO Box 210380, Cincinnati, OH, 45221, USA.
| | - Elizabeth Werren
- Department of Anthropology, 101 West Hall, University of Michigan, 1085 South University Ave, Ann Arbor, MI, 48109, USA.
| | - Jonathan Friedlaender
- Department of Anthropology, Temple University, Gladfelter Hall, 1115 West Berks Street, Philadelphia, PA, 19122, USA.
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21
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Sun H, Yang Z, Lin K, Liu S, Huang K, Wang X, Chu J, Huang X. The Adaptive Change of HLA-DRB1 Allele Frequencies Caused by Natural Selection in a Mongolian Population That Migrated to the South of China. PLoS One 2015; 10:e0134334. [PMID: 26230582 PMCID: PMC4521750 DOI: 10.1371/journal.pone.0134334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 07/08/2015] [Indexed: 01/18/2023] Open
Abstract
Pathogen-driven balancing selection determines the richness of human leukocyte antigen (HLA) alleles. Changes in the pathogen spectrum may cause corresponding changes in HLA loci. Approximately 700 years ago, a Mongolian population moved from the north of China to the Yunnan region in the south of China. The pathogen spectrum in the south of China differs from that in the north. In this study, changes in the HLA genes in the Yunnan Mongolian population, as well as the underlying mechanism, were investigated. A sequence-based typing method (SBT) was used to genotype HLA-DRB1 in 470 individuals from two Mongolian populations and another five ethnic groups. Meanwhile, 10 autosomal short tandem repeats (STRs) were genotyped to assess the influence of genetic background on HLA-DRB1 frequencies. The frequencies of certain alleles changed significantly in the Mongolian population that migrated to Yunnan. For example, DRB1*12:02:01 increased from 6.1% to 35.4%. STR analysis excluded the possibility of a recent bottleneck and indicated that 50% of the genetic consistency between northern and southern Mongolians; Tajima's D value for HLA-DRB1 exon2 and dN/dS analysis showed that the HLA-DRB1 genes in both Mongolian populations were under balancing selection. However, the sites under natural selection changed. We proposed that the dramatically change of HLA frequencies in southern Mongolian was caused by a combination of inter-population gene flow and natural selection. Certain diseases specific to the south of China, such as malaria, may be the driving force behind the enhanced DRB1*12:02:01 frequency.
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Affiliation(s)
- Hao Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Zhaoqing Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Keqin Lin
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Shuyuan Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Kai Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Xiuyun Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Jiayou Chu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Xiaoqin Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
- * E-mail:
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22
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Meyer NJ, Ferguson JF, Feng R, Wang F, Patel PN, Li M, Xue C, Qu L, Liu Y, Boyd JH, Russell JA, Christie JD, Walley KR, Reilly MP. A functional synonymous coding variant in the IL1RN gene is associated with survival in septic shock. Am J Respir Crit Care Med 2014; 190:656-64. [PMID: 25089931 DOI: 10.1164/rccm.201403-0586oc] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
RATIONALE Death from infection is a highly heritable trait, yet there are few genetic variants with known mechanism influencing survival during septic shock. OBJECTIVES We hypothesized that a synonymous coding variant in the IL-1 receptor antagonist gene (IL1RN), rs315952, previously associated with reduced risk for acute respiratory distress syndrome, would be functional and associate with improved survival in septic shock. METHODS We used a human endotoxin (LPS) model of evoked inflammatory stress to measure plasma IL-1 receptor antagonist (IL1RA) following low-dose Food and Drug Administration-grade LPS injection (1 ng/kg) in 294 human volunteers. RNA sequencing of adipose tissue pre- and post-LPS was used to test for allelic imbalance at rs315952. In the Vasopressin and Septic Shock Trial cohort, we performed a genetic association study for survival, mortality, and organ failure-free days. MEASUREMENTS AND MAIN RESULTS Adipose tissue displayed significant allelic imbalance favoring the rs315952C allele in subjects of European ancestry. Consistent with this, carriers of rs315952C had slightly higher plasma IL1RA at baseline (0.039) and higher evoked IL1RA post-LPS (0.011). In the Vasopressin and Septic Shock Trial cohort, rs315952C associated with improved survival (P = 0.028), decreased adjusted 90-day mortality (P = 0.044), and faster resolution of shock (P = 0.029). CONCLUSIONS In European ancestry subjects, the IL1RN variant rs315952C is preferentially transcribed and associated with increased evoked plasma IL1RA and with improved survival from septic shock. It may be that genetically determined IL1RA levels influence survival from septic shock.
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Affiliation(s)
- Nuala J Meyer
- 1 Center for Translational Lung Biology, Pulmonary, Allergy, and Critical Care Division
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24
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de Simoni Gouveia JJ, da Silva MVGB, Paiva SR, de Oliveira SMP. Identification of selection signatures in livestock species. Genet Mol Biol 2014; 37:330-42. [PMID: 25071397 PMCID: PMC4094609 DOI: 10.1590/s1415-47572014000300004] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 02/27/2014] [Indexed: 11/22/2022] Open
Abstract
The identification of regions that have undergone selection is one of the principal goals of theoretical and applied evolutionary genetics. Such studies can also provide information about the evolutionary processes involved in shaping genomes, as well as physical and functional information about genes/genomic regions. Domestication followed by breed formation and selection schemes has allowed the formation of very diverse livestock breeds adapted to a wide variety of environments and with special characteristics. The advances in genomics in the last five years have enabled the development of several methods to detect selection signatures and have resulted in the publication of a considerable number of studies involving livestock species. The aims of this review are to describe the principal effects of natural/artificial selection on livestock genomes, to present the main methods used to detect selection signatures and to discuss some recent results in this area. This review should be useful also to research scientists working with wild animals/non-domesticated species and plant biologists working with breeding and evolutionary biology.
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Affiliation(s)
- João José de Simoni Gouveia
- Colegiado Acadêmico de Zootecnia , Universidade Federal do Vale do São Francisco , Petrolina, PE , Brazil . ; Programa de Doutorado Integrado em Zootecnia , Universidade Federal do Ceará , Fortaleza, CE , Brazil
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25
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Fumagalli M, Sironi M. Human genome variability, natural selection and infectious diseases. Curr Opin Immunol 2014; 30:9-16. [PMID: 24880709 DOI: 10.1016/j.coi.2014.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 04/29/2014] [Accepted: 05/02/2014] [Indexed: 01/04/2023]
Abstract
The recent availability of large-scale sequencing DNA data allowed researchers to investigate how genomic variation is distributed among populations. While demographic factors explain genome-wide population genetic diversity levels, scans for signatures of natural selection pinpointed several regions under non-neutral evolution. Recent studies found an enrichment of immune-related genes subjected to natural selection, suggesting that pathogens and infectious diseases have imposed a strong selective pressure throughout human history. Pathogen-mediated selection often targeted regulatory sites of genes belonging to the same biological pathway. Results from these studies have the potential to identify mutations that modulate infection susceptibility by integrating a population genomic approach with molecular immunology data and large-scale functional annotations.
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Affiliation(s)
- Matteo Fumagalli
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, United Kingdom.
| | - Manuela Sironi
- Bioinformatics - Scientific Institute IRCCS E.MEDEA, 23842 Bosisio Parini, Italy
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26
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Abstract
Adaptive evolution has provided us with a unique set of characteristics that define us as humans, including morphological, physiological and cellular changes. Yet, natural selection provides no assurances that adaptation is without human health consequences; advantageous mutations will increase in frequency so long as there is a net gain in fitness. As such, the current incidence of human disease can depend on previous adaptations. Here, I review genome-wide and gene-specific studies in which adaptive evolution has played a role in shaping human genetic disease. In addition to the disease consequences of adaptive phenotypes, such as bipedal locomotion and resistance to certain pathogens, I review evidence that adaptive mutations have influenced the frequency of linked disease alleles through genetic hitchhiking. Taken together, the links between human adaptation and disease highlight the importance of their combined influence on functional variation within the human genome and offer opportunities to discover and characterize such variation.
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Affiliation(s)
- Justin C. Fay
- 4444 Forest Park Ave. Rm 5526, St. Louis, MO 63108, United States. Tel.: + 1 314 747 1808; fax: + 1 314 362 2156.
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27
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Genetic diversity of the HLA-G coding region in Amerindian populations from the Brazilian Amazon: a possible role of natural selection. Genes Immun 2013; 14:518-26. [PMID: 24089150 DOI: 10.1038/gene.2013.47] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 08/01/2013] [Accepted: 08/07/2013] [Indexed: 11/08/2022]
Abstract
HLA-G has an important role in the modulation of the maternal immune system during pregnancy, and evidence that balancing selection acts in the promoter and 3'UTR regions has been previously reported. To determine whether selection acts on the HLA-G coding region in the Amazon Rainforest, exons 2, 3 and 4 were analyzed in a sample of 142 Amerindians from nine villages of five isolated tribes that inhabit the Central Amazon. Six previously described single-nucleotide polymorphisms (SNPs) were identified and the Expectation-Maximization (EM) and PHASE algorithms were used to computationally reconstruct SNP haplotypes (HLA-G alleles). A new HLA-G allele, which originated in Amerindian populations by a crossing-over event between two widespread HLA-G alleles, was identified in 18 individuals. Neutrality tests evidenced that natural selection has a complex part in the HLA-G coding region. Although balancing selection is the type of selection that shapes variability at a local level (Native American populations), we have also shown that purifying selection may occur on a worldwide scale. Moreover, the balancing selection does not seem to act on the coding region as strongly as it acts on the flanking regulatory regions, and such coding signature may actually reflect a hitchhiking effect.
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Abstract
The molecular basis of adaptation--and, in particular, the relative roles of protein-coding versus gene expression changes--has long been the subject of speculation and debate. Recently, the genotyping of diverse human populations has led to the identification of many putative "local adaptations" that differ between populations. Here I show that these local adaptations are over 10-fold more likely to affect gene expression than amino acid sequence. In addition, a novel framework for identifying polygenic local adaptations detects recent positive selection on the expression levels of genes involved in UV radiation response, immune cell proliferation, and diabetes-related pathways. These results provide the first examples of polygenic gene expression adaptation in humans, as well as the first genome-scale support for the hypothesis that changes in gene expression have driven human adaptation.
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Affiliation(s)
- Hunter B Fraser
- Department of Biology, Stanford University, Stanford, California 94305, USA.
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Elhassan AAM, Hussein AA, Mohamed HS, Rockett K, Kwiatkowski D, Elhassan AM, Ibrahim ME. The 5q31 region in two African populations as a facet of natural selection by infectious diseases. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413020051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ekmekcioglu C, Blasche G, Dorner TE. Too Much Salt and How We Can Get Rid of It. ACTA ACUST UNITED AC 2013; 20:454-60. [DOI: 10.1159/000357413] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Stinson S, Bogin B, O'Rourke D, Huss-Ashmore R. Human Biology: An Evolutionary and Biocultural Perspective. Hum Biol 2012. [DOI: 10.1002/9781118108062.ch1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Molecular evolution of a malaria resistance gene (DARC) in primates. Immunogenetics 2012; 64:497-505. [PMID: 22395823 DOI: 10.1007/s00251-012-0608-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 02/08/2012] [Indexed: 01/06/2023]
Abstract
Genes involved in host-pathogen interactions are often strongly affected by positive natural selection. The Duffy antigen, coded by the Duffy antigen receptor for chemokines (DARC) gene, serves as a receptor for Plasmodium vivax in humans and for Plasmodium knowlesi in some nonhuman primates. In the majority of sub-Saharan Africans, a nucleic acid variant in GATA-1 of the gene promoter is responsible for the nonexpression of the Duffy antigen on red blood cells and consequently resistance to invasion by P. vivax. The Duffy antigen also acts as a receptor for chemokines and is expressed in red blood cells and many other tissues of the body. Because of this dual role, we sequenced a ~3,000-bp region encompassing the entire DARC gene as well as part of its 5' and 3' flanking regions in a phylogenetic sample of primates and used statistical methods to evaluate the nature of selection pressures acting on the gene during its evolution. We analyzed both coding and regulatory regions of the DARC gene. The regulatory analysis showed accelerated rates of substitution at several sites near known motifs. Our tests of positive selection in the coding region using maximum likelihood by branch sites and maximum likelihood by codon sites did not yield statistically significant evidence for the action of positive selection. However, the maximum likelihood test in which the gene was subdivided into different structural regions showed that the known binding region for P. vivax/P. knowlesi is under very different selective pressures than the remainder of the gene. In fact, most of the gene appears to be under strong purifying selection, but this is not evident in the binding region. We suggest that the binding region is under the influence of two opposing selective pressures, positive selection possibly exerted by the parasite and purifying selection exerted by chemokines.
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Rees JL, Harding RM. Understanding the Evolution of Human Pigmentation: Recent Contributions from Population Genetics. J Invest Dermatol 2012; 132:846-53. [DOI: 10.1038/jid.2011.358] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Lai CQ. Adaptive genetic variation and population differences. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 108:461-89. [PMID: 22656388 DOI: 10.1016/b978-0-12-398397-8.00018-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Since the expansion of modern humans (Homo sapiens) from Africa to the rest of the world between 50,000 and 100,000 years ago, the human genome has been shaped not only by demographic history but also by adaptation to local environments, including regional climate, landscape, food sources, culture, and pathogens. Genetic differences among populations interact with environmental factors, such as diet and lifestyle, leading to differences in nutrient metabolism, which translate into differences in susceptibility to a variety of diseases. Individuals from different populations sharing the same environments can exhibit differences in disease risk, as do individuals from the same population living in various regions of the globe. Therefore, it is important to understand how adaptive genetic variations interact with environments to influence health. This knowledge will provide a broad foundation for designing experiments and approaches in nutrigenomics research and strengthening the knowledge base for dietary recommendations for disease prevention. The objectives of this chapter are to (1) understand the methodology employed in examining adaptive genetic variation across populations, (2) establish the importance of adaptive genetic variation to human health, and (3) discuss the implications for nutrigenomics research and disease prevention.
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Affiliation(s)
- Chao-Qiang Lai
- Nutrition and Genomics Laboratory, Jean Meyer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
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De Angelis F, Garzoli A, Battistini A, Iorio A, De Stefano GF. Genetic response to an environmental pathogenic agent: HLA-DQ and onchocerciasis in northwestern Ecuador. ACTA ACUST UNITED AC 2011; 79:123-9. [PMID: 22117902 DOI: 10.1111/j.1399-0039.2011.01811.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The aim of this study is to explore human leukocyte antigen (HLA)-DQ variability in two populations (Cayapas Amerindians and Afro-Ecuadorians) who live near one another along the Cayapa River and who are exposed to the same environmental stresses, such as infection by Onchocerca volvulus. HLA-DQA1 and HLA-DQB1 of 149 unrelated individuals (74 Cayapas and 75 Afro-Ecuadorians) have been analyzed. HLA high-resolution molecular typing was performed by sequence-based typing, sequence-specific oligonucleotides hybridization and sequence-specific primer (SSP) amplification. The comparison between affected (cases) and unaffected people (controls) in both populations shows the key role of several HLA-DQA1 alleles in susceptibility and protection against onchocerciasis. In both populations, there is strong evidence related to the protective role of DQA1*0401 against onchocerciasis. Alleles HLA-DQA1*0102 and *0103 seem to represent risk factors in Afro-Ecuadorians, while HLA-DQA1*0301 is only a suggestive susceptibility allele in Cayapas. These findings represent new positive/negative associations with onchocerciasis in South America, whereas previous findings pertained only to African populations.
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Affiliation(s)
- F De Angelis
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.
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Fumagalli M, Sironi M, Pozzoli U, Ferrer-Admetlla A, Pattini L, Nielsen R. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS Genet 2011; 7:e1002355. [PMID: 22072984 PMCID: PMC3207877 DOI: 10.1371/journal.pgen.1002355] [Citation(s) in RCA: 336] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 09/08/2011] [Indexed: 12/27/2022] Open
Abstract
Previous genome-wide scans of positive natural selection in humans have identified a number of non-neutrally evolving genes that play important roles in skin pigmentation, metabolism, or immune function. Recent studies have also shown that a genome-wide pattern of local adaptation can be detected by identifying correlations between patterns of allele frequencies and environmental variables. Despite these observations, the degree to which natural selection is primarily driven by adaptation to local environments, and the role of pathogens or other ecological factors as selective agents, is still under debate. To address this issue, we correlated the spatial allele frequency distribution of a large sample of SNPs from 55 distinct human populations to a set of environmental factors that describe local geographical features such as climate, diet regimes, and pathogen loads. In concordance with previous studies, we detected a significant enrichment of genic SNPs, and particularly non-synonymous SNPs associated with local adaptation. Furthermore, we show that the diversity of the local pathogenic environment is the predominant driver of local adaptation, and that climate, at least as measured here, only plays a relatively minor role. While background demography by far makes the strongest contribution in explaining the genetic variance among populations, we detected about 100 genes which show an unexpectedly strong correlation between allele frequencies and pathogenic environment, after correcting for demography. Conversely, for diet regimes and climatic conditions, no genes show a similar correlation between the environmental factor and allele frequencies. This result is validated using low-coverage sequencing data for multiple populations. Among the loci targeted by pathogen-driven selection, we found an enrichment of genes associated to autoimmune diseases, such as celiac disease, type 1 diabetes, and multiples sclerosis, which lends credence to the hypothesis that some susceptibility alleles for autoimmune diseases may be maintained in human population due to past selective processes. Adaptation to local environments is one of the most important factors shaping human genetic variation among different geographically distributed populations. Here we develop a statistical framework aimed at identifying signals of genetic adaptation. We correlate the spatial distribution of allele frequencies of a large sample of SNPs, genotyped in more than 50 populations distributed worldwide, to a set of environmental factors, describing local geographical features such as climate conditions, diet regimes, and pathogens load. Our results show an excess of putative functional variants for high levels of population differentiation, measured by the degree to which genetic variation correlates with a set of environmental variables. We demonstrate that selection on pathogens is the primary driver of local adaptation and affects the distribution of genetic variation at a large number of genes. Among the selected genes, we also identify an excess of genes associated with autoimmune diseases, such as celiac disease, type 1 diabetes, and multiples sclerosis.
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Affiliation(s)
- Matteo Fumagalli
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Bosisio Parini, Italy.
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Anno S, Ohshima K, Abe T. Approaches to understanding adaptations of skin color variation by detecting gene-environment interactions. Expert Rev Mol Diagn 2011; 10:987-91. [PMID: 21080816 DOI: 10.1586/erm.10.90] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genetic and environmental factors are both part of an elaborate feedback mechanism whereby the human adaptive form reacts to environmental stimuli via internal adjustments. Human survival may ultimately depend on understanding two important components of future environmental adaptation. First, we must elucidate the dynamics of the human genome underpinning the complex human phenotype. Second, we must understand how the environment pressures and affects the genome, helping to determine human traits. This article reviews current approaches to detecting the natural selection of skin color variation in human populations. We include statistical methods for clarifying gene-environment interactions applicable to the interactions with UV radiation levels. We recommend spatial data mining as an efficient approach that applies environmental association rules, extending our knowledge of adaptation to the environment.
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Affiliation(s)
- Sumiko Anno
- Shibaura Institute of Technology, 3-7-5 Toyosu, Koto-ku, Tokyo 135-8548, Japan.
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38
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Abstract
In this review, I describe how evolutionary genomics is uniquely suited to spearhead advances in understanding human disease risk, owing to the privileged position of genes as fundamental causes of phenotypic variation, and the ability of population genetic and phylogenetic methods to robustly infer processes of natural selection, drift, and mutation from genetic variation at the levels of family, population, species, and clade. I first provide an overview of models for the origins and maintenance of genetically based disease risk in humans. I then discuss how analyses of genetic disease risk can be dovetailed with studies of positive and balancing selection, to evaluate the degree to which the 'genes that make us human' also represent the genes that mediate risk of polygenic disease. Finally, I present four basic principles for the nascent field of human evolutionary medical genomics, each of which represents a process that is nonintuitive from a proximate perspective. Joint consideration of these principles compels novel forms of interdisciplinary analyses, most notably studies that (i) analyze tradeoffs at the level of molecular genetics, and (ii) identify genetic variants that are derived in the human lineage or in specific populations, and then compare individuals with derived versus ancestral alleles.
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Affiliation(s)
- Bernard J Crespi
- Department of Biosciences, Simon Fraser University Burnaby, BC, Canada
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Quintana-Murci L, Barreiro LB. The role played by natural selection on Mendelian traits in humans. Ann N Y Acad Sci 2011; 1214:1-17. [PMID: 21175682 DOI: 10.1111/j.1749-6632.2010.05856.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Detecting whether and how natural selection has targeted regions of the human genome represents a complementary strategy for identifying functionally important loci and variants involved in disease resistance and adaptation to the environment. In contrast with most complex diseases or traits, the genetic architecture of most Mendelian traits is relatively well established. Most mutations associated with Mendelian disease-related traits are highly penetrant and kept at low population frequencies because of the effects of purifying selection. However, this is not always the case. Here, we review several examples of Mendelian mutations-associated with various disease conditions or other traits of anthropological interest-that have increased in frequency in the human population as a result of past positive selection. These examples clearly illustrate the value of a population genetics approach to unravel the biological mechanisms that have been central to our past and present survival against the selective pressures imposed by diseases and other environmental factors.
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Affiliation(s)
- Lluis Quintana-Murci
- Institut Pasteur, Human Evolutionary Genetics, Department of Genomes and Genetics, Paris, France.
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Harris EE. Nonadaptive processes in primate and human evolution. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 143 Suppl 51:13-45. [PMID: 21086525 DOI: 10.1002/ajpa.21439] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Evolutionary biology has tended to focus on adaptive evolution by positive selection as the primum mobile of evolutionary trajectories in species while underestimating the importance of nonadaptive evolutionary processes. In this review, I describe evidence that suggests that primate and human evolution has been strongly influenced by nonadaptive processes, particularly random genetic drift and mutation. This is evidenced by three fundamental effects: a relative relaxation of selective constraints (i.e., purifying selection), a relative increase in the fixation of slightly deleterious mutations, and a general reduction in the efficacy of positive selection. These effects are observed in protein-coding, regulatory regions, and in gene expression data, as well as in an augmentation of fixation of large-scale mutations, including duplicated genes, mobile genetic elements, and nuclear mitochondrial DNA. The evidence suggests a general population-level explanation such as a reduction in effective population size (N(e)). This would have tipped the balance between the evolutionary forces of natural selection and random genetic drift toward genetic drift for variants having small selective effects. After describing these proximate effects, I describe the potential consequences of these effects for primate and human evolution. For example, an increase in the fixation of slightly deleterious mutations could potentially have led to an increase in the fixation rate of compensatory mutations that act to suppress the effects of slightly deleterious substitutions. The potential consequences of compensatory evolution for the evolution of novel gene functions and in potentially confounding the detection of positively selected genes are explored. The consequences of the passive accumulation of large-scale genomic mutations by genetic drift are unclear, though evidence suggests that new gene copies as well as insertions of transposable elements into genes can potentially lead to adaptive phenotypes. Finally, because a decrease in selective constraint at the genetic level is expected to have effects at the morphological level, I review studies that compare rates of morphological change in various mammalian and island populations where N(e) is reduced. Furthermore, I discuss evidence that suggests that craniofacial morphology in the Homo lineage has shifted from an evolutionary rate constrained by purifying selection toward a neutral evolutionary rate.
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Affiliation(s)
- Eugene E Harris
- Department of Biological Sciences and Geology, Queensborough Community College, City University of New York, Bayside, NY 10364, USA.
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Paixão-Côrtes VR, Meyer D, Pereira TV, Mazières S, Elion J, Krishnamoorthy R, Zago MA, Silva WA, Salzano FM, Bortolini MC. Genetic variation among major human geographic groups supports a peculiar evolutionary trend in PAX9. PLoS One 2011; 6:e15656. [PMID: 21298044 PMCID: PMC3029280 DOI: 10.1371/journal.pone.0015656] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 11/19/2010] [Indexed: 11/18/2022] Open
Abstract
A total of 172 persons from nine South Amerindian, three African and one Eskimo populations were studied in relation to the Paired box gene 9 (PAX9) exon 3 (138 base pairs) as well as its 5'and 3'flanking intronic segments (232 bp and 220 bp, respectively) and integrated with the information available for the same genetic region from individuals of different geographical origins. Nine mutations were scored in exon 3 and six in its flanking regions; four of them are new South American tribe-specific singletons. Exon3 nucleotide diversity is several orders of magnitude higher than its intronic regions. Additionally, a set of variants in the PAX9 and 101 other genes related with dentition can define at least some dental morphological differences between Sub-Saharan Africans and non-Africans, probably associated with adaptations after the modern human exodus from Africa. Exon 3 of PAX9 could be a good molecular example of how evolvability works.
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Affiliation(s)
- Vanessa R. Paixão-Côrtes
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Diogo Meyer
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Tiago V. Pereira
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Stéphane Mazières
- Laboratoire d'Anthropobiologie, FRE2960, CNRS, Toulouse, France
- Anthropologie Bioculturelle, Faculté de Médecine, CS80011, Marseille, France
| | - Jacques Elion
- Insern, UMR 763, Université Paris Diderot, Hôpital Robert Debré, Paris, France
| | | | - Marco A. Zago
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Wilson A. Silva
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Francisco M. Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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Alam MT, de Souza DK, Vinayak S, Griffing SM, Poe AC, Duah NO, Ghansah A, Asamoa K, Slutsker L, Wilson MD, Barnwell JW, Udhayakumar V, Koram KA. Selective sweeps and genetic lineages of Plasmodium falciparum drug -resistant alleles in Ghana. J Infect Dis 2011; 203:220-7. [PMID: 21288822 PMCID: PMC3071065 DOI: 10.1093/infdis/jiq038] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND In 2005, Ghana adopted artemisinin-based combination therapy (ACT) for primary treatment of falciparum malaria. A comprehensive study of the drug-resistance-associated mutations and their genetic lineages will lead to a better understanding of the evolution of antimalarial drug resistance in this region. METHODS The pfcrt, pfmdr1, dhps, and dhfr mutations associated with chloroquine (CQ) and sulfadoxine-pyrimethamine (SP) resistance and the microsatellite loci flanking these genes were genotyped in Plasmodium falciparum isolates from Ghana. RESULTS The prevalence of mutations associated with both CQ and SP resistance was high in Ghana. However, we observed a decrease in prevalence of the pfcrt K76T mutation in northern Ghana after the change in drug policy from CQ to ACT. Analysis of genetic diversity and differentiation at microsatellite loci flanking all 4 genes indicated that they have been under strong selection, because of CQ and SP use. The triple-mutant pfcrt and dhfr alleles in Ghana were derived from Southeast Asia, whereas the double-mutant dhfr, dhps, and pfmdr1 alleles were of African lineage. CONCLUSION Because of the possible role of pfmdr1 in amodiaquine and mefloquine resistance, demonstrating selection on pfmdr1 and defining lineages of resistant alleles in an African population holds great importance.
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Affiliation(s)
- Md Tauqeer Alam
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
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Shi H, Su B. Molecular adaptation of modern human populations. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2010; 2011:484769. [PMID: 21350631 PMCID: PMC3039432 DOI: 10.4061/2011/484769] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 12/14/2010] [Indexed: 12/19/2022]
Abstract
Modern humans have gone through varied processes of genetic adaptations when their ancestors left Africa about 100,000 years ago. The environmental stresses and the social transitions (e.g., emergence of the Neolithic culture) have been acting as the major selective forces reshaping the genetic make-up of human populations. Genetic adaptations have occurred in many aspects of human life, including the adaptation to cold climate and high-altitude hypoxia, the improved ability of defending infectious diseases, and the polished strategy of utilizing new diet with the advent of agriculture. At the same time, the adaptations once developed during evolution may sometimes generate deleterious effects (e.g., susceptibility to diseases) when facing new environmental and social changes. The molecular (especially the genome-wide screening of genetic variations) studies in recent years have detected many genetic variants that show signals of Darwinian positive selection in modern human populations, which will not only provide a better understanding of human evolutionary history, but also help dissecting the genetic basis of human complex diseases.
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Affiliation(s)
- Hong Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology and Kunming Primate Research Centre, Chinese Academy of Sciences, Kunming 650223, China
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Ramalho RF, Santos EJ, Guerreiro JF, Meyer D. Balanced polymorphism in bottlenecked populations: The case of the CCR5 5′ cis-regulatory region in Amazonian Amerindians. Hum Immunol 2010; 71:922-8. [DOI: 10.1016/j.humimm.2010.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 05/20/2010] [Accepted: 05/26/2010] [Indexed: 11/28/2022]
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Lambert CA, Tishkoff SA. Genetic structure in African populations: implications for human demographic history. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2010; 74:395-402. [PMID: 20453204 DOI: 10.1101/sqb.2009.74.053] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The continent of Africa is the source of all anatomically modern humans that dispersed across the planet during the past 100,000 years. As such, African populations are characterized by high genetic diversity and low levels of linkage disequilibrium (LD) among loci, as compared to populations from other continents. African populations also possess a number of genetic adaptations that have evolved in response to the diverse climates, diets, geographic environments, and infectious agents that characterize the African continent. Recently, Tishkoff et al. (2009) performed a genome-wide analysis of substructure based on DNA from 2432 Africans from 121 geographically diverse populations. The authors analyzed patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers and identified 14 ancestral population clusters that correlate well with self-described ethnicity and shared cultural or linguistic properties. The results suggest that African populations may have maintained a large and subdivided population structure throughout much of their evolutionary history. In this chapter, we synthesize recent work documenting evidence of African population structure and discuss the implications for inferences about evolutionary history in both African populations and anatomically modern humans as a whole.
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Affiliation(s)
- C A Lambert
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
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Mendes-Junior CT, Castelli EC, Moreau P, Simões AL, Donadi EA. Absence of the HLA-G*0113N allele in Amerindian populations from the Brazilian Amazon region. Hum Immunol 2010; 71:428-31. [DOI: 10.1016/j.humimm.2010.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 01/04/2010] [Accepted: 01/13/2010] [Indexed: 10/19/2022]
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47
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Chemical ecology in coupled human and natural systems: people, manioc, multitrophic interactions and global change. CHEMOECOLOGY 2010. [DOI: 10.1007/s00049-010-0047-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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48
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CUTRERA ANAPAULA, LACEY EILEENA, MORA MATÍASS, LESSA ENRIQUEP. Effects of contrasting demographic histories on selection at major histocompatibility complex loci in two sympatric species of tuco-tucos (Rodentia: Ctenomyidae). Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2009.01358.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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49
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Bamshad M, Stephens JC. Assessing human variation data for signatures of natural selection. Cold Spring Harb Protoc 2009; 2009:pdb.top61. [PMID: 20150073 DOI: 10.1101/pdb.top61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In this article, we highlight some of the different types of natural selection, their effects on patterns of DNA variation, and some of the statistical tests that are commonly used to detect such effects. We also explain some of the relative strengths and weaknesses of different strategies that can be used to detect signatures of natural selection at individual loci. These strategies are illustrated by their application to empirical data from gene variants that are often associated with differences in disease susceptibility. We briefly outline some of the methods proposed to scan the genome for evidence of selection. Finally, we discuss some of the problems associated with identifying signatures of selection and with making inferences about the nature of the selective process.
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Akey JM. Constructing genomic maps of positive selection in humans: where do we go from here? Genome Res 2009; 19:711-22. [PMID: 19411596 DOI: 10.1101/gr.086652.108] [Citation(s) in RCA: 348] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Identifying targets of positive selection in humans has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of natural selection. To date, 21 genome-wide scans for recent or ongoing positive selection have been performed in humans. A key challenge is to begin synthesizing these newly constructed maps of positive selection into a coherent narrative of human evolutionary history and derive a deeper mechanistic understanding of how natural populations evolve. Here, I chronicle the recent history of the burgeoning field of human population genomics, critically assess genome-wide scans for positive selection in humans, identify important gaps in knowledge, and discuss both short- and long-term strategies for traversing the path from the low-resolution, incomplete, and error-prone maps of selection today to the ultimate goal of a detailed molecular, mechanistic, phenotypic, and population genetics characterization of adaptive alleles.
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Affiliation(s)
- Joshua M Akey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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