1
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Levi R, Levi L, Louzoun Y. Bw4 ligand and direct T-cell receptor binding induced selection on HLA A and B alleles. Front Immunol 2023; 14:1236080. [PMID: 38077375 PMCID: PMC10703150 DOI: 10.3389/fimmu.2023.1236080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction The HLA region is the hallmark of balancing selection, argued to be driven by the pressure to present a wide variety of viral epitopes. As such selection on the peptide-binding positions has been proposed to drive HLA population genetics. MHC molecules also directly binds to the T-Cell Receptor and killer cell immunoglobulin-like receptors (KIR). Methods We here combine the HLA allele frequencies in over six-million Hematopoietic Stem Cells (HSC) donors with a novel machine-learning-based method to predict allele frequency. Results We show for the first time that allele frequency can be predicted from their sequences. This prediction yields a natural measure for selection. The strongest selection is affecting KIR binding regions, followed by the peptide-binding cleft. The selection from the direct interaction with the KIR and TCR is centered on positively charged residues (mainly Arginine), and some positions in the peptide-binding cleft are not associated with the allele frequency, especially Tyrosine residues. Discussion These results suggest that the balancing selection for peptide presentation is combined with a positive selection for KIR and TCR binding.
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Affiliation(s)
| | | | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
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2
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Nandakumar M, Lundberg M, Carlsson F, Råberg L. Balancing selection on the complement system of a wild rodent. BMC Ecol Evol 2023; 23:21. [PMID: 37231383 DOI: 10.1186/s12862-023-02122-0] [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: 10/03/2022] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Selection pressure exerted by pathogens can influence patterns of genetic diversity in the host. In the immune system especially, numerous genes encode proteins involved in antagonistic interactions with pathogens, paving the way for coevolution that results in increased genetic diversity as a consequence of balancing selection. The complement system is a key component of innate immunity. Many complement proteins interact directly with pathogens, either by recognising pathogen molecules for complement activation, or by serving as targets of pathogen immune evasion mechanisms. Complement genes can therefore be expected to be important targets of pathogen-mediated balancing selection, but analyses of such selection on this part of the immune system have been limited. RESULTS Using a population sample of whole-genome resequencing data from wild bank voles (n = 31), we estimated the extent of genetic diversity and tested for signatures of balancing selection in multiple complement genes (n = 44). Complement genes showed higher values of standardised β (a statistic expected to be high under balancing selection) than the genome-wide average of protein coding genes. One complement gene, FCNA, a pattern recognition molecule that interacts directly with pathogens, was found to have a signature of balancing selection, as indicated by the Hudson-Kreitman-Aguadé test (HKA) test. Scans for localised signatures of balancing selection in this gene indicated that the target of balancing selection was found in exonic regions involved in ligand binding. CONCLUSION The present study adds to the growing evidence that balancing selection may be an important evolutionary force on components of the innate immune system. The identified target in the complement system typifies the expectation that balancing selection acts on genes encoding proteins involved in direct interactions with pathogens.
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Affiliation(s)
| | - Max Lundberg
- Department of Biology, Lund University, Lund, Sweden
| | | | - Lars Råberg
- Department of Biology, Lund University, Lund, Sweden
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3
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Wang PY, Yang Y, Shi XQ, Chen Y, Liu SD, Wang HY, Peng T, Shi Q, Zhang W, Sun C. Distilling functional variations for human UGT2B4 upstream region based on selection signals and implications for phenotypes of Neanderthal and Denisovan. Sci Rep 2023; 13:3134. [PMID: 36823244 PMCID: PMC9950360 DOI: 10.1038/s41598-023-29682-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023] Open
Abstract
Our previous work identified one region upstream human UGT2B4 (UDP glucuronosyltransferase family 2 member B4) which is associated with breast cancer and under balancing selection. However, the distribution, functional variation and molecular mechanism underlying breast cancer and balancing selection remain unclear. In current study, the two haplotypes with deep divergence are described by analyzing 1000 genomes project data and observed to be with high frequencies in all human populations. Through population genetics analysis and genome annotation, the potential functional region is identified and verified by reporter gene assay. Further mutagenesis indicates that the functional mutations are rs66862535 and rs68096061. Both SNPs can alter the interaction efficiency of transcription factor POU2F1 (POU class 2 homeobox 1). Through chromosome conformation capture, it is identified that the enhancer containing these two SNPs can interact with UGT2B4 promoter. Expression quantitative trait loci analysis indicates that UGT2B4 expression is dependent on the genotype of this locus. The common haplotype in human is lost in four genomes of archaic hominins, which suggests that Neanderthal and Denisovan should present relatively lower UGT2B4 expression and further higher steroid hormone level. This study provides new insight into the contribution of ancient population structure to human phenotypes.
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Affiliation(s)
- Pin-Yi Wang
- grid.412498.20000 0004 1759 8395College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 Shaanxi People’s Republic of China ,grid.440773.30000 0000 9342 2456State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091 Yunnan People’s Republic of China
| | - Yuan Yang
- grid.412498.20000 0004 1759 8395College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 Shaanxi People’s Republic of China
| | - Xiao-Qian Shi
- grid.412498.20000 0004 1759 8395College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 Shaanxi People’s Republic of China
| | - Ying Chen
- grid.412498.20000 0004 1759 8395College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 Shaanxi People’s Republic of China
| | - Shao-Dong Liu
- grid.412498.20000 0004 1759 8395College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 Shaanxi People’s Republic of China
| | - Hong-Yan Wang
- grid.412498.20000 0004 1759 8395College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 Shaanxi People’s Republic of China
| | - Tao Peng
- grid.440773.30000 0000 9342 2456State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091 Yunnan People’s Republic of China
| | - Qiang Shi
- grid.412498.20000 0004 1759 8395College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 Shaanxi People’s Republic of China
| | - Wei Zhang
- grid.16753.360000 0001 2299 3507Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA ,grid.449428.70000 0004 1797 7280Institute of Precision Medicine, Jining Medical University, Jining, 272067 Shandong People’s Republic of China
| | - Chang Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China.
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4
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Myers AN, Lawhon SD, Diesel AB, Bradley CW, Rodrigues Hoffmann A, Murphy WJ. An ancient haplotype containing antimicrobial peptide gene variants is associated with severe fungal skin disease in Persian cats. PLoS Genet 2022; 18:e1010062. [PMID: 35157719 PMCID: PMC8880935 DOI: 10.1371/journal.pgen.1010062] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 02/25/2022] [Accepted: 01/28/2022] [Indexed: 11/19/2022] Open
Abstract
Dermatophytosis, also known as ringworm, is a contagious fungal skin disease affecting humans and animals worldwide. Persian cats exhibit severe forms of the disease more commonly than other breeds of cat, including other long-haired breeds. Certain types of severe dermatophytosis in humans are reportedly caused by monogenic inborn errors of immunity. The goal of this study was to identify genetic variants in Persian cats contributing to the phenotype of severe dermatophytosis. Whole-genome sequencing of case and control Persian cats followed by a genome-wide association study identified a highly divergent, disease-associated haplotype on chromosome F1 containing the S100 family of genes. S100 calcium binding protein A9 (S100A9), which encodes a subunit of the antimicrobial heterodimer known as calprotectin, contained 13 nonsynonymous variants between cases and controls. Evolutionary analysis of S100A9 haplotypes comparing cases, controls, and wild felids suggested the divergent disease-associated haplotype was likely introgressed into the domestic cat lineage and maintained via balancing selection. We demonstrated marked upregulation of calprotectin expression in the feline epidermis during dermatophytosis, suggesting involvement in disease pathogenesis. Given this divergent allele has been maintained in domestic cat and wildcat populations, this haplotype may have beneficial effects against other pathogens. The pathogen specificity of this altered protein should be investigated before attempting to reduce the allele frequency in the Persian cat breed. Further work is needed to clarify if severe Persian dermatophytosis is a monogenic disease or if hidden disease-susceptibility loci remain to be discovered. Consideration should be given to engineering antimicrobial peptides such as calprotectin for topical treatment of dermatophytosis in humans and animals. Fungal skin infections known as ringworm or dermatophytosis affect billions of humans and animals worldwide. Normally the disease is self-limiting in affected individuals. The Persian cat breed is a popular breed known for its long hair coat and short nose as well as its propensity to develop severe, chronic dermatophytosis. By examining the genomes of Persian cats, we discovered that a specific region of DNA is highly altered between cats with and without severe dermatophytosis. The DNA sequence in this region is particularly divergent within a cluster of genes involved in immune defense against pathogens. Notably, alterations to the DNA sequence cause several changes in the antimicrobial protein known as calprotectin, which defends against pathogens in the skin of cats. Persian cats with severe dermatophytosis have a version of calprotectin similar to a version maintained by certain desert-dwelling wild felids such as sand cats and Asiatic wildcats. Therefore, we think this version of the protein is beneficial in some environments or against certain pathogens but not against the fungus that causes ringworm in cats. Our findings suggest changes to calprotectin may affect pathogen specificity and engineered calprotectin could be considered as a novel therapy for dermatophytosis in humans and animals.
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Affiliation(s)
- Alexandra N. Myers
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, Unites States of America
- * E-mail: (ANM); (WJM)
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, Unites States of America
| | - Alison B. Diesel
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, Unites States of America
| | - Charles W. Bradley
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, Unites States of America
| | - Aline Rodrigues Hoffmann
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, Unites States of America
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, Unites States of America
- * E-mail: (ANM); (WJM)
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5
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Forni D, Sironi M, Cagliani R. Evolutionary history of type II transmembrane serine proteases involved in viral priming. Hum Genet 2022; 141:1705-1722. [PMID: 35122525 PMCID: PMC8817155 DOI: 10.1007/s00439-022-02435-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/15/2022] [Indexed: 11/24/2022]
Abstract
Type II transmembrane serine proteases (TTSPs) are a family of trypsin-like membrane-anchored serine proteases that play key roles in the regulation of some crucial processes in physiological conditions, including cardiac function, digestion, cellular iron homeostasis, epidermal differentiation, and immune responses. However, some of them, in particular TTSPs expressed in the human airways, were identified as host factors that promote the proteolytic activation and spread of respiratory viruses such as influenza virus, human metapneumovirus, and coronaviruses, including SARS-CoV-2. Given their involvement in viral priming, we hypothesized that members of the TTSP family may represent targets of positive selection, possibly as the result of virus-driven pressure. Thus, we investigated the evolutionary history of sixteen TTSP genes in mammals. Evolutionary analyses indicate that most of the TTSP genes that have a verified role in viral proteolytic activation present signals of pervasive positive selection, suggesting that viral infections represent a selective pressure driving the evolution of these proteases. We also evaluated genetic diversity in human populations and we identified targets of balancing selection in TMPRSS2 and TMPRSS4. This scenario may be the result of an ancestral and still ongoing host–pathogen arms race. Overall, our results provide evolutionary information about candidate functional sites and polymorphic positions in TTSP genes.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842, Bosisio Parini, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842, Bosisio Parini, Italy.
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6
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Isildak U, Stella A, Fumagalli M. Distinguishing between recent balancing selection and incomplete sweep using deep neural networks. Mol Ecol Resour 2021; 21:2706-2718. [PMID: 33749134 DOI: 10.1111/1755-0998.13379] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 12/12/2022]
Abstract
Balancing selection is an important adaptive mechanism underpinning a wide range of phenotypes. Despite its relevance, the detection of recent balancing selection from genomic data is challenging as its signatures are qualitatively similar to those left by ongoing positive selection. In this study, we developed and implemented two deep neural networks and tested their performance to predict loci under recent selection, either due to balancing selection or incomplete sweep, from population genomic data. Specifically, we generated forward-in-time simulations to train and test an artificial neural network (ANN) and a convolutional neural network (CNN). ANN received as input multiple summary statistics calculated on the locus of interest, while CNN was applied directly on the matrix of haplotypes. We found that both architectures have high accuracy to identify loci under recent selection. CNN generally outperformed ANN to distinguish between signals of balancing selection and incomplete sweep and was less affected by incorrect training data. We deployed both trained networks on neutral genomic regions in European populations and demonstrated a lower false-positive rate for CNN than ANN. We finally deployed CNN within the MEFV gene region and identified several common variants predicted to be under incomplete sweep in a European population. Notably, two of these variants are functional changes and could modulate susceptibility to familial Mediterranean fever, possibly as a consequence of past adaptation to pathogens. In conclusion, deep neural networks were able to characterize signals of selection on intermediate frequency variants, an analysis currently inaccessible by commonly used strategies.
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Affiliation(s)
- Ulas Isildak
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Alessandro Stella
- Laboratory of Medical Genetics, Department of Biomedical Sciences and Human Oncology, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus, Imperial College London, London, UK
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7
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Ebert D, Fields PD. Host-parasite co-evolution and its genomic signature. Nat Rev Genet 2020; 21:754-768. [PMID: 32860017 DOI: 10.1038/s41576-020-0269-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 01/14/2023]
Abstract
Studies in diverse biological systems have indicated that host-parasite co-evolution is responsible for the extraordinary genetic diversity seen in some genomic regions, such as major histocompatibility (MHC) genes in jawed vertebrates and resistance genes in plants. This diversity is believed to evolve under balancing selection on hosts by parasites. However, the mechanisms that link the genomic signatures in these regions to the underlying co-evolutionary process are only slowly emerging. We still lack a clear picture of the co-evolutionary concepts and of the genetic basis of the co-evolving phenotypic traits in the interacting antagonists. Emerging genomic tools that provide new options for identifying underlying genes will contribute to a fuller understanding of the co-evolutionary process.
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Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland. .,Wissenschaftskolleg zu Berlin, Berlin, Germany.
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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8
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Lundberg M, Zhong X, Konrad A, Olsen RA, Råberg L. Balancing selection in Pattern Recognition Receptor signalling pathways is associated with gene function and pleiotropy in a wild rodent. Mol Ecol 2020; 29:1990-2003. [PMID: 32374503 DOI: 10.1111/mec.15459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 12/13/2022]
Abstract
Pathogen-mediated balancing selection is commonly considered to play an important role in the maintenance of genetic diversity, in particular in immune genes. However, the factors that may influence which immune genes are the targets of such selection are largely unknown. To address this, here we focus on Pattern Recognition Receptor (PRR) signalling pathways, which play a key role in innate immunity. We used whole-genome resequencing data from a population of bank voles (Myodes glareolus) to test for associations between balancing selection, pleiotropy and gene function in a set of 123 PRR signalling pathway genes. To investigate the effect of gene function, we compared genes encoding (a) receptors for microbial ligands versus downstream signalling proteins, and (b) receptors recognizing components of microbial cell walls, flagella and capsids versus receptors recognizing features of microbial nucleic acids. Analyses based on the nucleotide diversity of full coding sequences showed that balancing selection primarily targeted receptor genes with a low degree of pleiotropy. Moreover, genes encoding receptors recognizing components of microbial cell walls etc. were more important targets of balancing selection than receptors recognizing nucleic acids. Tests for localized signatures of balancing selection in coding and noncoding sequences showed that such signatures were mostly located in introns, and more evenly distributed among different functional categories of PRR pathway genes. The finding that signatures of balancing selection in full coding sequences primarily occur in receptor genes, in particular those encoding receptors for components of microbial cell walls etc., is consistent with the idea that coevolution between hosts and pathogens is an important cause of balancing selection on immune genes.
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Affiliation(s)
- Max Lundberg
- Department of Biology, Lund University, Lund, Sweden
| | - Xiuqin Zhong
- Department of Biology, Lund University, Lund, Sweden
| | - Anna Konrad
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Lars Råberg
- Department of Biology, Lund University, Lund, Sweden
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9
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Lazzaro BP, Zasloff M, Rolff J. Antimicrobial peptides: Application informed by evolution. Science 2020; 368:368/6490/eaau5480. [PMID: 32355003 DOI: 10.1126/science.aau5480] [Citation(s) in RCA: 461] [Impact Index Per Article: 115.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/25/2019] [Accepted: 03/09/2020] [Indexed: 12/13/2022]
Abstract
Antimicrobial peptides (AMPs) are essential components of immune defenses of multicellular organisms and are currently in development as anti-infective drugs. AMPs have been classically assumed to have broad-spectrum activity and simple kinetics, but recent evidence suggests an unexpected degree of specificity and a high capacity for synergies. Deeper evaluation of the molecular evolution and population genetics of AMP genes reveals more evidence for adaptive maintenance of polymorphism in AMP genes than has previously been appreciated, as well as adaptive loss of AMP activity. AMPs exhibit pharmacodynamic properties that reduce the evolution of resistance in target microbes, and AMPs may synergize with one another and with conventional antibiotics. Both of these properties make AMPs attractive for translational applications. However, if AMPs are to be used clinically, it is crucial to understand their natural biology in order to lessen the risk of collateral harm and avoid the crisis of resistance now facing conventional antibiotics.
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Affiliation(s)
- Brian P Lazzaro
- Department of Entomology, Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, USA
| | - Michael Zasloff
- MedStar Georgetown Transplant Institute, Georgetown University School of Medicine, Washington, DC, USA
| | - Jens Rolff
- Freie Universität Berlin, Evolutionary Biology, Institut für Biologie, Königin-Luise-Strasse 1-3, 14195 Berlin, Germany. .,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
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10
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Cortázar-Chinarro M, Meyer-Lucht Y, Van der Valk T, Richter-Boix A, Laurila A, Höglund J. Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans. BMC Genet 2020; 21:38. [PMID: 32228443 PMCID: PMC7106915 DOI: 10.1186/s12863-020-00839-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/06/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain (~ 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns. RESULTS We found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values. CONCLUSION Our results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.
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Affiliation(s)
- Maria Cortázar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.
| | - Yvonne Meyer-Lucht
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.,Centre for Paleogenetics Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
| | - Tom Van der Valk
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Alex Richter-Boix
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
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11
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Chapman JR, Hill T, Unckless RL. Balancing Selection Drives the Maintenance of Genetic Variation in Drosophila Antimicrobial Peptides. Genome Biol Evol 2019; 11:2691-2701. [PMID: 31504505 PMCID: PMC6764478 DOI: 10.1093/gbe/evz191] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2019] [Indexed: 12/19/2022] Open
Abstract
Genes involved in immune defense against pathogens provide some of the most well-known examples of both directional and balancing selection. Antimicrobial peptides (AMPs) are innate immune effector genes, playing a key role in pathogen clearance in many species, including Drosophila. Conflicting lines of evidence have suggested that AMPs may be under directional, balancing, or purifying selection. Here, we use both a linear model and control-gene-based approach to show that balancing selection is an important force shaping AMP diversity in Drosophila. In Drosophila melanogaster, this is most clearly observed in ancestral African populations. Furthermore, the signature of balancing selection is even more striking once background selection has been accounted for. Balancing selection also acts on AMPs in Drosophila mauritiana, an isolated island endemic separated from D. melanogaster by about 4 Myr of evolution. This suggests that balancing selection may be broadly acting to maintain adaptive diversity in Drosophila AMPs, as has been found in other taxa.
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Affiliation(s)
| | - Tom Hill
- Department of Molecular Biosciences, University of Kansas
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12
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Moir RD, Tanzi RE. Low Evolutionary Selection Pressure in Senescence Does Not Explain the Persistence of Aβ in the Vertebrate Genome. Front Aging Neurosci 2019; 11:70. [PMID: 30983989 PMCID: PMC6447958 DOI: 10.3389/fnagi.2019.00070] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/12/2019] [Indexed: 01/08/2023] Open
Abstract
The argument is frequently made that the amyloid-β protein (Aβ) persists in the human genome because Alzheimer's disease (AD) primarily afflicts individuals over reproductive age and, therefore, there is low selective pressure for the peptide's elimination or modification. This argument is an important premise for AD amyloidosis models and therapeutic strategies that characterize Aβ as a functionless and intrinsically pathological protein. Here, we review if evolutionary theory and data on the genetics and biology of Aβ are consistent with low selective pressure for the peptide's expression in senescence. Aβ is an ancient neuropeptide expressed across vertebrates. Consistent with unusually high evolutionary selection constraint, the human Aβ sequence is shared by a majority of vertebrate species and has been conserved across at least 400 million years. Unlike humans, the overwhelming majority of vertebrate species do not cease reproduction in senescence and selection pressure is maintained into old age. Hence, low selective pressure in senescence does not explain the persistence of Aβ across the vertebrate genome. The "Grandmother hypothesis" (GMH) is the prevailing model explaining the unusual extended postfertile period of humans. In the GMH, high risk associated with birthing in old age has lead to early cessation of reproduction and a shift to intergenerational care of descendants. The rechanneling of resources to grandchildren by postreproductive individuals increases reproductive success of descendants. In the GMH model, selection pressure does not end following menopause. Thus, evolutionary models and phylogenetic data are not consistent with the absence of reproductive selection pressure for Aβ among aged vertebrates, including humans. Our analysis suggests an alternative evolutionary model for the persistence of Aβ in the vertebrate genome. Aβ has recently been identified as an antimicrobial effector molecule of innate immunity. High conservation across the Chordata phylum is consistent with strong positive selection pressure driving human Aβ's remarkable evolutionary longevity. Ancient origins and widespread conservation suggest the human Aβ sequence is highly optimized for its immune role. We detail our analysis and discuss how the emerging "Antimicrobial Protection Hypothesis" of AD may provide insights into possible evolutionary roles for Aβ in infection, aging, and disease etiology.
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Affiliation(s)
- Robert D. Moir
- Genetics and Aging Research Unit, Department of Neurology, MassGeneral Institute for Neurodegenerative Disease, Harvard Medical School – Massachusetts General Hospital, Boston, MA, United States
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13
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Human Immunology through the Lens of Evolutionary Genetics. Cell 2019; 177:184-199. [DOI: 10.1016/j.cell.2019.02.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 01/04/2023]
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14
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Moir RD, Lathe R, Tanzi RE. The antimicrobial protection hypothesis of Alzheimer's disease. Alzheimers Dement 2018; 14:1602-1614. [DOI: 10.1016/j.jalz.2018.06.3040] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/22/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Robert D. Moir
- Genetics and Aging Research Unit; MassGeneral Institute for Neurodegenerative Disease; Department of Neurology; Massachusetts General Hospital and Harvard Medical School; Charlestown MA USA
| | - Richard Lathe
- Division of Infection and Pathway Medicine; University of Edinburgh; Little France Edinburgh UK
| | - Rudolph E. Tanzi
- Genetics and Aging Research Unit; MassGeneral Institute for Neurodegenerative Disease; Department of Neurology; Massachusetts General Hospital and Harvard Medical School; Charlestown MA USA
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15
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Viscardi LH, Paixão-Côrtes VR, Comas D, Salzano FM, Rovaris D, Bau CD, Amorim CEG, Bortolini MC. Searching for ancient balanced polymorphisms shared between Neanderthals and Modern Humans. Genet Mol Biol 2018; 41:67-81. [PMID: 29658973 PMCID: PMC5901502 DOI: 10.1590/1678-4685-gmb-2017-0308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/26/2017] [Indexed: 01/06/2023] Open
Abstract
Hominin evolution is characterized by adaptive solutions often rooted in behavioral and cognitive changes. If balancing selection had an important and long-lasting impact on the evolution of these traits, it can be hypothesized that genes associated with them should carry an excess of shared polymorphisms (trans- SNPs) across recent Homo species. In this study, we investigate the role of balancing selection in human evolution using available exomes from modern (Homo sapiens) and archaic humans (H. neanderthalensis and Denisovan) for an excess of trans-SNP in two gene sets: one associated with the immune system (IMMS) and another one with behavioral system (BEHS). We identified a significant excess of trans-SNPs in IMMS (N=547), of which six of these located within genes previously associated with schizophrenia. No excess of trans-SNPs was found in BEHS, but five genes in this system harbor potential signals for balancing selection and are associated with psychiatric or neurodevelopmental disorders. Our approach evidenced recent Homo trans-SNPs that have been previously implicated in psychiatric diseases such as schizophrenia, suggesting that a genetic repertoire common to the immune and behavioral systems could have been maintained by balancing selection starting before the split between archaic and modern humans.
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Affiliation(s)
- Lucas Henriques Viscardi
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de LaSalut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Diego Rovaris
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Claiton Dotto Bau
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Carlos Eduardo G. Amorim
- Department of Biological Sciences, Columbia University, New York, NY, U.S.A
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, U.S.A
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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16
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Simons ND, Eick GN, Ruiz-Lopez MJ, Omeja PA, Chapman CA, Goldberg TL, Ting N, Sterner KN. Cis-regulatory evolution in a wild primate: Infection-associated genetic variation drives differential expression of MHC-DQA1 in vitro. Mol Ecol 2017; 26:4523-4535. [PMID: 28665019 PMCID: PMC5570663 DOI: 10.1111/mec.14221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 06/10/2017] [Accepted: 06/13/2017] [Indexed: 12/14/2022]
Abstract
Few studies have combined genetic association analyses with functional characterization of infection-associated SNPs in natural populations of nonhuman primates. Here, we investigate the relationship between host genetic variation, parasitism and natural selection in a population of red colobus (Procolobus rufomitratus tephrosceles) in Kibale National Park, Uganda. We collected parasitological, cellular and genomic data to test the following hypotheses: (i) MHC-DQA1 regulatory genetic variation is associated with control of whipworm (Trichuris) infection in a natural population of red colobus; (ii) infection-associated SNPs are functional in driving differential gene expression in vitro; and (iii) balancing selection has shaped patterns of variation in the MHC-DQA1 promoter. We identified two SNPs in the MHC-DQA1 promoter, both in transcription factor binding sites, and both of which are associated with decreased control of Trichuris infection. We characterized the function of both SNPs by testing differences in gene expression between the two alleles of each SNP in two mammalian cell lines. Alleles of one of the SNPs drove differential gene expression in both cell lines, while the other SNP drove differences in expression in one of the cell lines. Additionally, we found evidence of balancing selection acting on the MHC-DQA1 promoter, including extensive trans-species polymorphisms between red colobus and other primates, and an excess of intermediate-frequency alleles relative to genome-wide, coding and noncoding RADseq data. Our data suggest that balancing selection provides adaptive regulatory flexibility that outweighs the consequences of increased parasite infection intensity in heterozygotes.
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Affiliation(s)
- Noah D. Simons
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
| | - Geeta N. Eick
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
| | | | - Patrick A. Omeja
- Makerere University Biological Field Station, P.O Box 967, Fort Portal, Uganda
| | - Colin A. Chapman
- Makerere University Biological Field Station, P.O Box 967, Fort Portal, Uganda
- Department of Anthropology and McGill School of Environment, Montreal, Quebec, H3A 2T7, Canada
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53725, USA
- Global Health Institute, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Nelson Ting
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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17
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Fijarczyk A, Dudek K, Babik W. Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation. Genome Biol Evol 2016; 8:3417-3432. [PMID: 27702815 PMCID: PMC5203778 DOI: 10.1093/gbe/evw236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Host–pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases. Here, we present an analysis of polymorphism and divergence of 634 immune genes in two lineages of Lissotriton newts: L. montandoni and L. vulgaris graecus. Variation in newt immune genes has been shaped predominantly by widespread purifying selection and strong evolutionary constraint, implying long-term importance of these genes for functioning of the immune system. The two evolutionary lineages differ in the overall strength of purifying selection which can partially be explained by demographic history but may also signal differences in long-term pathogen pressure. The prevalent constraint notwithstanding, 23 putative targets of positive selection and 11 putative targets of balancing selection were identified. The latter were detected by composite tests involving the demographic model and further validated in independent population samples. Putative targets of balancing selection encode proteins which may interact closely with pathogens but include also regulators of immune response. The identified candidates will be useful for testing whether genes affected by balancing selection are more prone to interspecific introgression than other genes in the genome.
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Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Wieslaw Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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18
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McAssey EV, Corbi J, Burke JM. Range-wide phenotypic and genetic differentiation in wild sunflower. BMC PLANT BIOLOGY 2016; 16:249. [PMID: 27829377 PMCID: PMC5103407 DOI: 10.1186/s12870-016-0937-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/28/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Divergent phenotypes and genotypes are key signals for identifying the targets of natural selection in locally adapted populations. Here, we used a combination of common garden phenotyping for a variety of growth, plant architecture, and seed traits, along with single-nucleotide polymorphism (SNP) genotyping to characterize range-wide patterns of diversity in 15 populations of wild sunflower (Helianthus annuus L.) sampled along a latitudinal gradient in central North America. We analyzed geographic patterns of phenotypic diversity, quantified levels of within-population SNP diversity, and also determined the extent of population structure across the range of this species. We then used these data to identify significantly over-differentiated loci as indicators of genomic regions that likely contribute to local adaptation. RESULTS Traits including flowering time, plant height, and seed oil composition (i.e., percentage of saturated fatty acids) were significantly correlated with latitude, and thus differentiated northern vs. southern populations. Average pairwise FST was found to be 0.21, and a STRUCTURE analysis identified two significant clusters that largely separated northern and southern individuals. The significant FST outliers included a SNP in HaFT2, a flowering time gene that has been previously shown to co-localize with flowering time QTL, and which exhibits a known cline in gene expression. CONCLUSIONS Latitudinal differentiation in both phenotypic traits and SNP allele frequencies is observed across wild sunflower populations in central North America. Such differentiation may play an important adaptive role across the range of this species, and could facilitate adaptation to a changing climate.
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Affiliation(s)
- Edward V. McAssey
- Department of Plant Biology, University of Georgia, Miller Plant Sciences Building, Athens, GA 30602 USA
- University of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Road, Athens, GA 30602 USA
| | - Jonathan Corbi
- Department of Plant Biology, University of Georgia, Miller Plant Sciences Building, Athens, GA 30602 USA
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - John M. Burke
- Department of Plant Biology, University of Georgia, Miller Plant Sciences Building, Athens, GA 30602 USA
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19
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Sung MK, Jang J, Lee KS, Ghim CM, Choi JK. Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans. Genome Biol 2016; 17:164. [PMID: 27468897 PMCID: PMC4964047 DOI: 10.1186/s13059-016-1027-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/13/2016] [Indexed: 12/28/2022] Open
Abstract
Background Examples of heterozygote advantage in humans are scarce and limited to protein-coding sequences. Here, we attempt a genome-wide functional inference of advantageous heterozygosity at cis-regulatory regions. Results The single-nucleotide polymorphisms bearing the signatures of balancing selection are enriched in active cis-regulatory regions of immune cells and epithelial cells, the latter of which provide barrier function and innate immunity. Examples associated with ancient trans-specific balancing selection are also discovered. Allelic imbalance in chromatin accessibility and divergence in transcription factor motif sequences indicate that these balanced polymorphisms cause distinct regulatory variation. However, a majority of these variants show no association with the expression level of the target gene. Instead, single-cell experimental data for gene expression and chromatin accessibility demonstrate that heterozygous sequences can lower cell-to-cell variability in proportion to selection strengths. This negative correlation is more pronounced for highly expressed genes and consistently observed when using different data and methods. Based on mathematical modeling, we hypothesize that extrinsic noise from fluctuations in transcription factor activity may be amplified in homozygotes, whereas it is buffered in heterozygotes. While high expression levels are coupled with intrinsic noise reduction, regulatory heterozygosity can contribute to the suppression of extrinsic noise. Conclusions This mechanism may confer a selective advantage by increasing cell population homogeneity and thereby enhancing the collective action of the cells, especially of those involved in the defense systems in humans. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1027-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Kyung Sung
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Juneil Jang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Kang Seon Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Cheol-Min Ghim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.,Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.,Mathematical Bioscience Institute, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea.
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20
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Duforet-Frebourg N, Luu K, Laval G, Bazin E, Blum MGB. Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data. Mol Biol Evol 2016; 33:1082-93. [PMID: 26715629 PMCID: PMC4776707 DOI: 10.1093/molbev/msv334] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis (PCA). We show that the common FST index of genetic differentiation between populations can be viewed as the proportion of variance explained by the principal components. Considering the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local adaptation without any prior definition of populations. To validate the PCA-based approach, we consider the 1000 Genomes data (phase 1) considering 850 individuals coming from Africa, Asia, and Europe. The number of genetic variants is of the order of 36 millions obtained with a low-coverage sequencing depth (3×). The correlations between genetic variation and each principal component provide well-known targets for positive selection (EDAR, SLC24A5, SLC45A2, DARC), and also new candidate genes (APPBPP2, TP1A1, RTTN, KCNMA, MYO5C) and noncoding RNAs. In addition to identifying genes involved in biological adaptation, we identify two biological pathways involved in polygenic adaptation that are related to the innate immune system (beta defensins) and to lipid metabolism (fatty acid omega oxidation). An additional analysis of European data shows that a genome scan based on PCA retrieves classical examples of local adaptation even when there are no well-defined populations. PCA-based statistics, implemented in the PCAdapt R package and the PCAdapt fast open-source software, retrieve well-known signals of human adaptation, which is encouraging for future whole-genome sequencing project, especially when defining populations is difficult.
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Affiliation(s)
- Nicolas Duforet-Frebourg
- TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France CNRS, TIMC-IMAG, Grenoble, France Department of Integrative Biology, University of California, Berkeley
| | - Keurcien Luu
- TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France CNRS, TIMC-IMAG, Grenoble, France
| | - Guillaume Laval
- Department of Genomes and Genetics, Institut Pasteur, Human Evolutionary Genetics, Paris, France Centre National De La Recherche Scientifique, URA3012, Paris, France
| | - Eric Bazin
- CNRS, Laboratoire D'ecologie Alpine UMR 5553, Univ. Grenoble Alpes, Grenoble, France
| | - Michael G B Blum
- TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France CNRS, TIMC-IMAG, Grenoble, France
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21
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Azevedo L, Serrano C, Amorim A, Cooper DN. Trans-species polymorphism in humans and the great apes is generally maintained by balancing selection that modulates the host immune response. Hum Genomics 2015; 9:21. [PMID: 26337052 PMCID: PMC4559023 DOI: 10.1186/s40246-015-0043-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/20/2015] [Indexed: 12/20/2022] Open
Abstract
Known examples of ancient identical-by-descent genetic variants being shared between evolutionarily related species, known as trans-species polymorphisms (TSPs), result from counterbalancing selective forces acting on target genes to confer resistance against infectious agents. To date, putative TSPs between humans and other primate species have been identified for the highly polymorphic major histocompatibility complex (MHC), the histo-blood ABO group, two antiviral genes (ZC3HAV1 and TRIM5), an autoimmunity-related gene LAD1 and several non-coding genomic segments with a putative regulatory role. Although the number of well-characterized TSPs under long-term balancing selection is still very small, these examples are connected by a common thread, namely that they involve genes with key roles in the immune system and, in heterozygosity, appear to confer genetic resistance to pathogens. Here, we review known cases of shared polymorphism that appear to be under long-term balancing selection in humans and the great apes. Although the specific selective agent(s) responsible are still unknown, these TSPs may nevertheless be seen as constituting important adaptive events that have occurred during the evolution of the primate immune system.
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Affiliation(s)
- Luisa Azevedo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
| | - Catarina Serrano
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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22
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Fijarczyk A, Babik W. Detecting balancing selection in genomes: limits and prospects. Mol Ecol 2015; 24:3529-45. [DOI: 10.1111/mec.13226] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Wiesław Babik
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
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23
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Lin YL, Pavlidis P, Karakoc E, Ajay J, Gokcumen O. The evolution and functional impact of human deletion variants shared with archaic hominin genomes. Mol Biol Evol 2015; 32:1008-19. [PMID: 25556237 PMCID: PMC4379406 DOI: 10.1093/molbev/msu405] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Allele sharing between modern and archaic hominin genomes has been variously interpreted to have originated from ancestral genetic structure or through non-African introgression from archaic hominins. However, evolution of polymorphic human deletions that are shared with archaic hominin genomes has yet to be studied. We identified 427 polymorphic human deletions that are shared with archaic hominin genomes, approximately 87% of which originated before the Human–Neandertal divergence (ancient) and only approximately 9% of which have been introgressed from Neandertals (introgressed). Recurrence, incomplete lineage sorting between human and chimp lineages, and hominid-specific insertions constitute the remaining approximately 4% of allele sharing between humans and archaic hominins. We observed that ancient deletions correspond to more than 13% of all common (>5% allele frequency) deletion variation among modern humans. Our analyses indicate that the genomic landscapes of both ancient and introgressed deletion variants were primarily shaped by purifying selection, eliminating large and exonic variants. We found 17 exonic deletions that are shared with archaic hominin genomes, including those leading to three fusion transcripts. The affected genes are involved in metabolism of external and internal compounds, growth and sperm formation, as well as susceptibility to psoriasis and Crohn’s disease. Our analyses suggest that these “exonic” deletion variants have evolved through different adaptive forces, including balancing and population-specific positive selection. Our findings reveal that genomic structural variants that are shared between humans and archaic hominin genomes are common among modern humans and can influence biomedically and evolutionarily important phenotypes.
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Affiliation(s)
- Yen-Lung Lin
- Department of Biological Sciences, State University of New York at Buffalo, NY, US
| | - Pavlos Pavlidis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation of Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Emre Karakoc
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jerry Ajay
- Department of Computer Science and Engineering, State University of New York at Buffalo, NY, US
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, NY, US
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24
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Key FM, Teixeira JC, de Filippo C, Andrés AM. Advantageous diversity maintained by balancing selection in humans. Curr Opin Genet Dev 2014; 29:45-51. [PMID: 25173959 DOI: 10.1016/j.gde.2014.08.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 07/30/2014] [Accepted: 08/02/2014] [Indexed: 11/16/2022]
Abstract
Most human polymorphisms are neutral or slightly deleterious, but some genetic variation is advantageous and maintained in populations by balancing selection. Considered a rarity and overlooked for years, balanced polymorphisms have recently received renewed attention with several lines of evidence showing their relevance in human evolution. From theoretical work on its role in adaptation to empirical studies that identify its targets, recent developments have showed that balancing selection is more prevalent than previously thought. Here we review these developments and discuss their implications in our understanding of the influence of balancing selection in human evolution. We also review existing evidence on the biological functions that benefit most from advantageous diversity, and the functional consequences of these variants. Overall, we argue that balancing selection must be considered an important selective force in human evolution.
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Affiliation(s)
- Felix M Key
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - João C Teixeira
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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25
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Abstract
Because of their strong similarities to humans across physiologic, developmental, behavioral, immunologic, and genetic levels, nonhuman primates are essential models for a wide spectrum of biomedical research. But unlike other animal models, nonhuman primates possess substantial outbred genetic variation, reducing statistical power and potentially confounding interpretation of results in research studies. Although unknown genetic variation is a hindrance in studies that allocate animals randomly, taking genetic variation into account in study design affords an opportunity to transform the way that nonhuman primates are used in biomedical research. New understandings of how the function of individual genes in rhesus macaques mimics that seen in humans are greatly advancing the rhesus macaques utility as research models, but epistatic interaction, epigenetic regulatory mechanisms, and the intricacies of gene networks limit model development. We are now entering a new era of nonhuman primate research, brought on by the proliferation and rapid expansion of genomic data. Already the cost of a rhesus macaque genome is dwarfed by its purchase and husbandry costs, and complete genomic datasets will inevitably encompass each rhesus macaque used in biomedical research. Advancing this outcome is paramount. It represents an opportunity to transform the way animals are assigned and used in biomedical research and to develop new models of human disease. The genetic and genomic revolution brings with it a paradigm shift for nonhuman primates and new mandates on how nonhuman primates are used in biomedical research.
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26
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López Campos GN, Velarde Félix JS, Sandoval Ramírez L, Cázares Salazar S, Corona Nakamura AL, Amaya Tapia G, Prado Montes de Oca E. Polymorphism in cathelicidin gene (CAMP) that alters Hypoxia-inducible factor (HIF-1α::ARNT) binding is not associated with tuberculosis. Int J Immunogenet 2013; 41:54-62. [DOI: 10.1111/iji.12080] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/01/2013] [Accepted: 07/15/2013] [Indexed: 12/27/2022]
Affiliation(s)
- G. N. López Campos
- In silico Laboratory; Pharmaceutical and Medical Biotechnology Unit; Research Center in Technology and Design Assistance of Jalisco State (CIATEJ, AC); National Council of Science and Technology; Guadalajara Mexico
| | - J. S. Velarde Félix
- Biology Academic Unit; Sinaloa Autonomous University (UAS); Culiacán México
- Genomic Medicine Center; Dr. Bernardo J. Gastelum Culiacán Primary Care Hospital; Health Ministry (SS); Culiacán Mexico
| | - L. Sandoval Ramírez
- Genetics Division; Western Biomedical Research Center; National Institute of Social Security (CIBO-IMSS); Guadalajara Mexico
| | - S. Cázares Salazar
- Biology and Chemistry Sciences Faculty; Sinaloa Autonomous University (FCQB-UAS); Culiacán Mexico
| | - A. L. Corona Nakamura
- Infectology Service; External Attention Medical Unit (UMAE); Western National Medical Center (CMNO); Specialty Hospital; National Institute of Social Security (IMSS); Guadalajara Mexico
| | - G. Amaya Tapia
- Infectology Service; Primary Care Western Hospital; Health Ministry of Jalisco State (SSJ); Guadalajara Mexico
| | - E. Prado Montes de Oca
- In silico Laboratory; Pharmaceutical and Medical Biotechnology Unit; Research Center in Technology and Design Assistance of Jalisco State (CIATEJ, AC); National Council of Science and Technology; Guadalajara Mexico
- Molecular Biology Laboratory; Biosecurity Area, Pharmaceutical and Medical Biotechnology Unit; Research Center in Technology and Design Assistance of Jalisco State (CIATEJ, AC); National Council of Science and Technology (CONACYT); Guadalajara Mexico
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27
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Abal-Fabeiro JL, Maside X, Bello X, Llovo J, Bartolomé C. Multilocus patterns of genetic variation across Cryptosporidium species suggest balancing selection at the gp60 locus. Mol Ecol 2013; 22:4723-32. [PMID: 23915002 DOI: 10.1111/mec.12425] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/08/2013] [Accepted: 06/18/2013] [Indexed: 11/27/2022]
Abstract
Cryptosporidium is an apicomplexan protozoan that lives in most vertebrates, including humans. Its gp60 gene is functionally involved in its attachment to host cells, and its high level of genetic variation has made it the reference marker for sample typing in epidemiological studies. To understand the origin of such high diversity and to determine the extent to which this classification applies to the rest of the genome, we analysed the patterns of variation at gp60 and nine other nuclear loci in isolates of three Cryptosporidium species. Most loci showed low genetic polymorphism (πS <1%) and similar levels of between-species divergence. Contrastingly, gp60 exhibited very different characteristics: (i) it was nearly ten times more variable than the other loci; (ii) it displayed a significant excess of polymorphisms relative to between-species differences in a maximum-likelihood Hudson-Kreitman-Aguadé test; (iii) gp60 subtypes turned out to be much older than the species they were found in; and (iv) showed a significant excess of polymorphic variants shared across species from random expectations. These observations suggest that this locus evolves under balancing selection and specifically under negative frequency-dependent selection (FDS). Interestingly, genetic variation at the other loci clusters very well within the groups of isolates defined by gp60 subtypes, which may provide new tools to understand the genome-wide patterns of genetic variation of the parasite in the wild. These results suggest that gp60 plays an active and essential role in the life cycle of the parasite and that genetic variation at this locus might be essential for the parasite's long-term success.
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Affiliation(s)
- J L Abal-Fabeiro
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain; Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain; Xenómica Comparada de Parásitos Humanos, IDIS, 15782, Santiago de Compostela, Spain
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Prado Montes de Oca E, Li W. Human β-defensin 1 (DEFB1) allele and genotype frequencies probably impact on ethnic susceptibility to atopic dermatitis. Int J Dermatol 2013; 52:115-7. [PMID: 23278620 DOI: 10.1111/j.1365-4632.2010.04853.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Cagliani R, Guerini FR, Rubio-Acero R, Baglio F, Forni D, Agliardi C, Griffanti L, Fumagalli M, Pozzoli U, Riva S, Calabrese E, Sikora M, Casals F, Comi GP, Bresolin N, Cáceres M, Clerici M, Sironi M. Long-standing balancing selection in the THBS4 gene: influence on sex-specific brain expression and gray matter volumes in Alzheimer disease. Hum Mutat 2013; 34:743-53. [PMID: 23420636 DOI: 10.1002/humu.22301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/01/2013] [Indexed: 01/08/2023]
Abstract
The THBS4 gene encodes a glycoprotein involved in inflammatory responses and synaptogenesis. THBS4 is expressed at higher levels in the brain of humans compared with nonhuman primates, and the protein accumulates in β-amyloid plaques. We analyzed THBS4 genetic variability in humans and show that two haplotypes (hap1 and hap2) are maintained by balancing selection and modulate THBS4 expression in lymphocytes. Indeed, the balancing selection region covers a predicted transcriptional enhancer. In humans, but not in macaques and chimpanzees, THBS4 brain expression increases with age, and variants in the balancing selection region interact with sex in influencing THBS4 expression (pinteraction = 0.038), with hap1 homozygous females showing lowest expression. In Alzheimer disease (AD) patients, significant interactions between sex and THBS4 genotype were detected for peripheral gray matter (pinteraction = 0.014) and total gray matter (pinteraction = 0.012) volumes. Similarly to the gene expression results, the interaction is mainly mediated by hap1 homozygous AD females, who show reduced volumes. Thus, the balancing selection target in THBS4 is likely represented by one or more variants that regulate tissue-specific and sex-specific gene expression. The selection signature associated with THBS4 might not be related to AD pathogenesis, but rather to inflammatory responses.
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Abstract
Innate immunity involves direct interactions between the host and microorganisms, both pathogenic and symbiotic, so natural selection is expected to strongly influence genes involved in these processes. Population genetics investigates the impact of past natural selection events on the genome of present-day human populations, and it complements immunological as well as clinical and epidemiological genetic studies. Recent data show that the impact of selection on the different families of innate immune receptors and their downstream signalling molecules varies considerably. This Review discusses these findings and highlights how they help to delineate the relative functional importance of innate immune pathways, which can range from being essential to being redundant.
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Evolutionary Analysis of the Contact System Indicates that Kininogen Evolved Adaptively in Mammals and in Human Populations. Mol Biol Evol 2013; 30:1397-408. [DOI: 10.1093/molbev/mst054] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Signature of balancing selection at the MC1R gene in Kunming dog populations. PLoS One 2013; 8:e55469. [PMID: 23424634 PMCID: PMC3570536 DOI: 10.1371/journal.pone.0055469] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/23/2012] [Indexed: 12/21/2022] Open
Abstract
Coat color in dog breeds is an excellent character for revealing the power of artificial selection, as it is extremely diverse and likely the result of recent domestication. Coat color is generated by melanocytes, which synthesize pheomelanin (a red or yellow pigment) or eumelanin (a black or brown pigment) through the pigment type-switching pathway, and is regulated by three genes in dogs: MC1R (melanocortin receptor 1), CBD103 (β-defensin 103), and ASIP (agouti-signaling protein precursor). The genotypes of these three gene loci in dog breeds are associated with coat color pattern. Here, we resequenced these three gene loci in two Kunming dog populations and analyzed these sequences using population genetic approaches to identify evolutionary patterns that have occurred at these loci during the recent domestication and breeding of the Kunming dog. The analysis showed that MC1R undergoes balancing selection in both Kunming dog populations, and that the Fst value for MC1R indicates significant genetic differentiation across the two populations. In contrast, similar results were not observed for CBD103 or ASIP. These results suggest that high heterozygosity and allelic differences at the MC1R locus may explain both the mixed color coat, of yellow and black, and the difference in coat colors in both Kunming dog populations.
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Manry J, Quintana-Murci L. A genome-wide perspective of human diversity and its implications in infectious disease. Cold Spring Harb Perspect Med 2013; 3:a012450. [PMID: 23284079 DOI: 10.1101/cshperspect.a012450] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Progress in genomic technologies, such as DNA arrays and next-generation sequencing, is allowing systematic characterization of the degree of human genetic variation at the scale of individual genomes. Public efforts, such as the International HapMap Project and the 1000 Genomes Project, have provided a realistic picture of the levels of genetic diversity in individuals and populations. These genomic techniques are also making it possible to evaluate the contribution of host genetic diversity to differences in susceptibility to both rare and common infectious diseases. Recent studies have revealed the power of whole-exome sequencing for dissecting the immunological mechanisms underlying the pathogenesis of severe, rare infectious diseases. Likewise, genome-wide association studies on common viral, bacterial, and parasitic infections have shed light on the host genetic basis of susceptibility to infectious diseases and, in some cases, of disease progression and drug responses.
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Affiliation(s)
- Jérémy Manry
- Institut Pasteur, Unit of Human Evolutionary Genetics, Department of Genomes and Genetics, F-75015 Paris, France
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Mehlotra RK, Zimmerman PA, Weinberg A, Jurevic RJ. Variation in human β-defensin genes: new insights from a multi-population study. Int J Immunogenet 2012. [PMID: 23194186 DOI: 10.1111/iji.12021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Human β-defensin 2 (hBD-2) and hBD-3, encoded by DEFB4 and DEFB103A, respectively, have shown anti-HIV activity, and both genes exhibit copy number variation (CNV). Although the role of hBD-1, encoded by DEFB1, in HIV-1 infection is less clear, single nucleotide polymorphisms (SNPs) in DEFB1 may influence viral loads and disease progression. We examined the distribution of DEFB1 SNPs and DEFB4/103A CNV, and the relationship between DEFB1 SNPs and DEFB4/103A CNV using samples from two HIV/AIDS cohorts from the United States (n = 150) and five diverse populations from the Coriell Cell Repositories (n = 46). We determined the frequencies of 10 SNPs in DEFB1 using a post-PCR, oligonucleotide ligation detection reaction-fluorescent microsphere assay, and CNV in DEFB4/103A by real-time quantitative PCR. There were noticeable differences in the frequencies of DEFB1 SNP alleles and haplotypes among various racial/ethnic groups. The DEFB4/103A copy numbers varied from 2 to 8 (median, 4), and there was a significant difference between the copy numbers of self-identified whites and blacks in the US cohorts (Mann-Whitney U-test P = 0.04). A significant difference was observed in the distribution of DEFB4/103A CNV among DEFB1 -52G/A and -390T/A genotypes (Kruskal-Wallis P = 0.017 and 0.026, respectively), while not in the distribution of DEFB4/103A CNV among -52G/A_-44C/G_-20G/A diplotypes. These observations provide additional insights for further investigating the complex interplay between β-defensin genetic polymorphisms and susceptibility to, or the progression or severity of, HIV infection/disease.
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Affiliation(s)
- R K Mehlotra
- Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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Cagliani R, Guerini FR, Fumagalli M, Riva S, Agliardi C, Galimberti D, Pozzoli U, Goris A, Dubois B, Fenoglio C, Forni D, Sanna S, Zara I, Pitzalis M, Zoledziewska M, Cucca F, Marini F, Comi GP, Scarpini E, Bresolin N, Clerici M, Sironi M. A trans-specific polymorphism in ZC3HAV1 is maintained by long-standing balancing selection and may confer susceptibility to multiple sclerosis. Mol Biol Evol 2012; 29:1599-613. [PMID: 22319148 PMCID: PMC7187542 DOI: 10.1093/molbev/mss002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The human ZC3HAV1 gene encodes an antiviral protein. The longest splicing isoform of ZC3HAV1 contains a C-terminal PARP-like domain, which has evolved under positive selection in primates. We analyzed the evolutionary history of this same domain in humans and in Pan troglodytes. We identified two variants that segregate in both humans and chimpanzees; one of them (rs3735007) does not occur at a hypermutable site and accounts for a nonsynonymous substitution (Thr851Ile). The probability that the two trans-specific polymorphisms have occurred independently in the two lineages was estimated to be low (P = 0.0054), suggesting that at least one of them has arisen before speciation and has been maintained by selection. Population genetic analyses in humans indicated that the region surrounding the shared variants displays strong evidences of long-standing balancing selection. Selection signatures were also observed in a chimpanzee population sample. Inspection of 1000 Genomes data confirmed these findings but indicated that search for selection signatures using low-coverage whole-genome data may need masking of repetitive sequences. A case–control study of more than 1,000 individuals from mainland Italy indicated that the Thr851Ile SNP is significantly associated with susceptibility to multiple sclerosis (MS) (odds ratio [OR] = 1.47, 95% confidence intervals [CI]: 1.08–1.99, P = 0.011). This finding was confirmed in a larger sample of 4,416 Sardinians cases/controls (OR = 1.18, 95% CI: 1.037–1.344, P = 0.011), but not in a population from Belgium. We provide one of the first instances of human/chimpanzee trans-specific coding variant located outside the major histocompatibility complex region. The selective pressure is likely to be virus driven; in modern populations, this variant associates with susceptibility to MS, possibly via the interaction with environmental factors.
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Affiliation(s)
- R Cagliani
- Scientific Institute IRCCS E. Medea, Bosisio Parini, Lecco, Italy
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Human polymorphisms as clinical predictors in leprosy. J Trop Med 2011; 2011:923943. [PMID: 22220182 PMCID: PMC3246779 DOI: 10.1155/2011/923943] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/11/2011] [Accepted: 10/20/2011] [Indexed: 12/26/2022] Open
Abstract
Genetic and serum markers in human host can predict leprosy susceptibility per se as well as be useful in classification and/or prediction of clinical variants and immunological responses in leprosy. Adequate and timely assessment of potential risks associated with these 38 host leprosy genes could diminish epidemiological burden and improve life quality of patients with this still prevalent mycobacterial disease.
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Sun C, Huo D, Southard C, Nemesure B, Hennis A, Cristina Leske M, Wu SY, Witonsky DB, Olopade OI, Di Rienzo A. A signature of balancing selection in the region upstream to the human UGT2B4 gene and implications for breast cancer risk. Hum Genet 2011; 130:767-75. [PMID: 21660508 PMCID: PMC4478588 DOI: 10.1007/s00439-011-1025-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 05/28/2011] [Indexed: 10/18/2022]
Abstract
UDP-glucuronosyltransferase 2 family, polypeptide B4 (UGT2B4) is an important metabolizing enzyme involved in the clearance of many xenobiotics and endogenous substrates, especially steroid hormones and bile acids. The HapMap data show that numerous SNPs upstream of UGT2B4 are in near-perfect linkage disequilibrium with each other and occur at intermediate frequency, indicating that this region might contain a target of natural selection. To investigate this possibility, we chose three regions (4.8 kb in total) for resequencing and observed a striking excess of intermediate-frequency alleles that define two major haplotypes separated by many mutation events and with little differentiation across populations, thus suggesting that the variation pattern upstream UGT2B4 is highly unusual and may be the result of balancing selection. We propose that this pattern is due to the maintenance of a regulatory polymorphism involved in the fine tuning of UGT2B4 expression so that heterozygous genotypes result in optimal enzyme levels. Considering the important role of steroid hormones in breast cancer susceptibility, we hypothesized that variation in this region could predispose to breast cancer. To test this hypothesis, we genotyped tag SNP rs13129471 in 1,261 patients and 825 normal women of African ancestry from three populations. The frequency comparison indicated that rs13129471 was significantly associated with breast cancer after adjusting for ethnicity [P = 0.003; heterozygous odds ratio (OR) 1.02, 95% confidence interval (CI) 0.81-1.28; homozygous OR 1.50, 95% CI 1.15-1.95]. Our results provide new insights into UGT2B4 sequence variation and indicate that a signal of natural selection may lead to the identification of disease susceptibility variants.
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Affiliation(s)
- Chang Sun
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA
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Thomas JC, Godfrey PA, Feldgarden M, Robinson DA. Candidate targets of balancing selection in the genome of Staphylococcus aureus. Mol Biol Evol 2011; 29:1175-86. [PMID: 22114360 DOI: 10.1093/molbev/msr286] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Signatures of balancing selection can highlight polymorphisms and functions that are important to the long-term fitness of a species. We performed a first genome-wide scan for balancing selection in a bacterial species, Staphylococcus aureus, which is a common cause of serious antimicrobial-resistant infections of humans. Using a sliding window approach, the genomes of 16 strains of S. aureus, including 5 new genome sequences presented here, and 1 outgroup strain of S. epidermidis were scanned for signatures of balancing selection. A total of 195 short windows were investigated based on their extreme values of both Tajima's D (>2.03) and π/K ratios (>0.12) relative to the rest of the genome. To test the unusualness of these windows, an Approximate Bayesian Computation framework was used to select a null demographic model that better accounted for the observed data than did the standard neutral model. A total of 186 windows were demonstrated to be unusual under the null model and, thus, represented candidate loci under balancing selection. These 186 candidate windows were located within 99 candidate genes that were spread across 62 different loci. Nearly all the signal (97.2%) was located within coding sequences; balancing selection on gene regulation apparently occurs through the targeting of global regulators such as agr and gra/aps. The agr locus had some of the strongest signatures of balancing selection, which provides new insight into the causes of diversity at this locus. The list of candidate genes included multiple virulence-associated genes and was significantly enriched for functions in amino acid and inorganic ion transport and metabolism and in defense mechanisms against innate immunity and antimicrobials, highlighting these particular functions as important to the fitness of this pathogen.
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Affiliation(s)
- Jonathan C Thomas
- Department of Microbiology, University of Mississippi Medical Center, USA
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Ferguson W, Dvora S, Fikes RW, Stone AC, Boissinot S. Long-term balancing selection at the antiviral gene OAS1 in Central African chimpanzees. Mol Biol Evol 2011; 29:1093-103. [PMID: 22104212 DOI: 10.1093/molbev/msr247] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Oligoadenylate synthetases (OAS) are interferon-induced enzymes that participate in the first line of defense against a wide range of viral infection in animals. Upon activation by viral double-stranded RNA, OAS synthesizes (2-5) oligoadenylates, which activate RNase L, leading to the nonspecific degradation of cellular and viral RNA. Some association studies in humans suggest that variation at one of the OAS genes, OAS1, could be influencing host susceptibility to viral infection. We assessed the diversity of OAS1 in hominoid primates with a focus on chimpanzees. We found that the OAS1 gene is extremely polymorphic in Central African chimpanzee and exhibits levels of silent and replacement diversity much higher than neutral regions of the chimpanzee genome. This level of variation strongly suggests that balancing selection is acting on OAS1, and indeed, this conclusion was validated by several tests of neutrality. We further demonstrated that balancing selection has been acting at this locus since the split between chimpanzees, humans, and gorillas (~8.6 Ma) and caused the persistence of two deeply divergent allelic lineages in Central African chimpanzees. These two groups of OAS1 alleles differ by a large number of amino acids (a.a.), including several a.a. putatively involved in RNA binding. It is therefore very likely that variation at the OAS1 locus affects the innate immune response of individuals to specific viral infection. Our data strongly suggest that interactions between viral RNA and OAS1 are responsible for the maintenance of ancestral polymorphisms at this locus for at least 13.2 My.
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Affiliation(s)
- William Ferguson
- Department of Biology, Queens College, the City University of New York, NY, USA
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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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Casals F, Sikora M, Laayouni H, Montanucci L, Muntasell A, Lazarus R, Calafell F, Awadalla P, Netea MG, Bertranpetit J. Genetic adaptation of the antibacterial human innate immunity network. BMC Evol Biol 2011; 11:202. [PMID: 21745391 PMCID: PMC3155920 DOI: 10.1186/1471-2148-11-202] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 07/11/2011] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Pathogens have represented an important selective force during the adaptation of modern human populations to changing social and other environmental conditions. The evolution of the immune system has therefore been influenced by these pressures. Genomic scans have revealed that immune system is one of the functions enriched with genes under adaptive selection. RESULTS Here, we describe how the innate immune system has responded to these challenges, through the analysis of resequencing data for 132 innate immunity genes in two human populations. Results are interpreted in the context of the functional and interaction networks defined by these genes. Nucleotide diversity is lower in the adaptors and modulators functional classes, and is negatively correlated with the centrality of the proteins within the interaction network. We also produced a list of candidate genes under positive or balancing selection in each population detected by neutrality tests and showed that some functional classes are preferential targets for selection. CONCLUSIONS We found evidence that the role of each gene in the network conditions the capacity to evolve or their evolvability: genes at the core of the network are more constrained, while adaptation mostly occurred at particular positions at the network edges. Interestingly, the functional classes containing most of the genes with signatures of balancing selection are involved in autoinflammatory and autoimmune diseases, suggesting a counterbalance between the beneficial and deleterious effects of the immune response.
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Affiliation(s)
- Ferran Casals
- Institute of Evolutionary Biology (UPF-CSIC), CEXS - UPF - PRBB, Barcelona, Catalonia, Spain.
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Cagliani R, Fumagalli M, Biasin M, Piacentini L, Riva S, Pozzoli U, Bonaglia MC, Bresolin N, Clerici M, Sironi M. Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 gene. Hum Genet 2010; 128:577-88. [PMID: 20811909 DOI: 10.1007/s00439-010-0884-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 08/25/2010] [Indexed: 01/09/2023]
Abstract
The human TRIM5 genes encodes a retroviral restriction factor (TRIM5α). Evolutionary analyses of this gene in mammals have revealed a complex and multifaceted scenario, suggesting that TRIM5 has been the target of exceptionally strong selective pressures, possibly exerted by recurrent waves of retroviral infections. TRIM5 displays inter-individual expression variability in humans and high levels of TRIM5 mRNA have been associated with a reduced risk of HIV-1 infection. We resequenced TRIM5 in chimpanzees and identified two polymorphisms in intron 1 that are shared with humans. Analysis of the gene region encompassing the two trans-specific variants in human populations identified exceptional nucleotide diversity levels and an excess of polymorphism compared to fixed divergence. Most tests rejected the null hypothesis of neutral evolution for this region and haplotype analysis revealed the presence of two deeply separated clades. Calculation of the time to the most recent common ancestor (TMRCA) for TRIM5 haplotypes yielded estimates ranging between 4 and 7 million years. Overall, these data indicate that long-term balancing selection, an extremely rare process outside MHC genes, has maintained trans-specific polymorphisms in the first intron of TRIM5. Bioinformatic analyses indicated that variants in intron 1 may affect transcription factor-binding sites and, therefore, TRIM5 transcriptional activity. Data herein confirm an extremely complex evolutionary history of TRIM5 genes in primates and open the possibility that regulatory variants in the gene modulate the susceptibility to HIV-1.
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Affiliation(s)
- R Cagliani
- Scientific Institute IRCCS E. Medea, Via don L. Monza 20, 23842, Bosisio Parini, LC, Italy
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Li MH, Merilä J. Sex-specific population structure, natural selection, and linkage disequilibrium in a wild bird population as revealed by genome-wide microsatellite analyses. BMC Evol Biol 2010; 10:66. [PMID: 20211004 PMCID: PMC2846931 DOI: 10.1186/1471-2148-10-66] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 03/08/2010] [Indexed: 11/26/2022] Open
Abstract
Background Sexual dimorphism in ecologically important traits is widespread, yet the differences in the genomic architecture between the two sexes are largely unexplored. We employed a genome-wide multilocus approach to examine the sexual differences in population subdivision, natural selection and linkage disequilibrium (LD) in a wild Siberian jay (Perisoreus infaustus) population, using genotypes at a total of 107 autosomal and Z-chromosomal microsatellites. Results Mean observed heterozygosity was significantly higher in females (HO = 0.567) than in males (HO = 0.532), and autosomal markers (HO = 0.561) were more variable than Z-chromosomal markers (HO = 0.512). Genetic differentiation (FST = 0.002, P < 0.05) between the two sexes was low but significant and males were on average significantly more genetically related to each other than females. Genomescan analyses revealed that 3 out of 101 (3%) autosomal loci were under directional selection, while 4 out of 6 (67%) Z-chromosomal markers were indicated to be under balancing selection. This suggests a significantly greater but contrasting selection force on the Z-chromosome in comparison to autosomes, which is consistent with an overall significantly (P < 0.05) lower FSTvalue for Z-chromosomal (-0.014, 95% CI: -0.025 - -0.011) than for the autosomal loci (0.003, 95% CI: 0.001 - 0.004). Analysis of syntenic marker pairs revealed high levels of LD in both sexes but significantly (P < 0.05) lower levels of LD in the females both on autosomes and Z-chromosome, probably due to the higher rate of dispersal and the higher recombination rates on autosomes, as well as the pseudoautosomal markers. In both sexes LD decayed rapidly with genetic distance in a similar fashion on autosomes, while a more rapid decay of LD in Z-chromosome was detected in females than in males. Conclusion We conclude that there are many clear differences in genomic architecture between the sexes studied here which can be at least partly understood in the light of higher dispersal rate of females as compared to males and the unusual structure of the Z-chromosome of the species.
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Affiliation(s)
- Meng-Hua Li
- Ecological Genetics Research Unit, Department of Biosciences, PO Box 65, FI-00014 University of Helsinki, Finland.
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The sound of silence: human beta-defensin-1 gene untranslated SNPs change the predicted mRNA secondary structure in a length-dependent manner. Immunol Lett 2010; 129:53-5. [PMID: 20060856 DOI: 10.1016/j.imlet.2009.12.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 12/17/2009] [Accepted: 12/23/2009] [Indexed: 10/20/2022]
Abstract
This study investigated how 5'-UTR of DEFB1 gene (encoding for the human beta-defensin-1) affects mRNA secondary structure and its correlation with translation efficiency in the susceptibility of diseases. It was possible to determine DEFB1 mRNA folding under the influence of 5'-UTR SNPs haplotypes and putative alternative transcript lengths. Different DEFB1 mRNAs that fold in a pattern that is haplotype and length-dependent are potentially able to drive changes in peptide expression dynamics.
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Ferrer-Admetlla A, Sikora M, Laayouni H, Esteve A, Roubinet F, Blancher A, Calafell F, Bertranpetit J, Casals F. A natural history of FUT2 polymorphism in humans. Mol Biol Evol 2009; 26:1993-2003. [PMID: 19487333 DOI: 10.1093/molbev/msp108] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Because pathogens are powerful selective agents, host-cell surface molecules used by pathogens as identification signals can reveal the signature of selection. Most of them are oligosaccharides, synthesized by glycosyltransferases. One known example is balancing selection shaping ABO evolution as a consequence of both, A and B antigens being recognized as receptors by some pathogens, and anti-A and/or anti-B natural antibodies produced by hosts conferring protection against the numerous infectious agents expressing A and B motifs. These antigens can also be found in tissues other than blood if there is activity of another enzyme, FUT2, a fucosyltransferase responsible for ABO biosynthesis in body fluids. Homozygotes for null variants at this locus present the nonsecretor phenotype (se), because they cannot express ABO antigens in secretions. Multiple independent mutations have been shown to be responsible for the nonsecretor phenotype, which is coexisting with the secretor phenotype in most populations. In this study, we have resequenced the coding region of FUT2 in 732 individuals from 39 worldwide human populations. We report a complex pattern of natural selection acting on the gene. Although frequencies of secretor and nonsecretor phenotypes are similar in different populations, the point mutations at the base of the phenotypes are different, with some variants showing a long history of balancing selection among Eurasian and African populations, and one recent variant showing a fast spread in East Asia, likely due to positive selection. Thus, a convergent phenotype composition has been achieved through different mutations with different evolutionary histories.
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Affiliation(s)
- Anna Ferrer-Admetlla
- Institut de Biologia Evolutiva (CSIC-UPF), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
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Predicting alternative candidates as binding sites to DEFB1 668 (-44) SNP: a long way from statistical association with multifactorial diseases. INFECTION GENETICS AND EVOLUTION 2009; 9:1129-31. [PMID: 19712755 DOI: 10.1016/j.meegid.2009.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 08/02/2009] [Accepted: 08/18/2009] [Indexed: 11/22/2022]
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Fumagalli M, Cagliani R, Pozzoli U, Riva S, Comi GP, Menozzi G, Bresolin N, Sironi M. A population genetics study of the Familial Mediterranean Fever gene: evidence of balancing selection under an overdominance regime. Genes Immun 2009; 10:678-86. [DOI: 10.1038/gene.2009.59] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Role of beta-defensin-1 polymorphisms in mother-to-child transmission of HIV-1. J Acquir Immune Defic Syndr 2009; 51:13-9. [PMID: 19390326 DOI: 10.1097/qai.0b013e31819df249] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND AND OBJECTIVES Mother-to-child transmission (MTCT) of HIV-1, the main source of pediatric AIDS, is multifactorial. Defensins provide microbial barriers and function as effectors of innate immunity. This study investigated the relationship between genetic variants of beta-defensin-1 gene and MTCT of HIV-1. PATIENTS AND METHODS Three hundred children, 118 HIV-1 infected and 182 HIV-1 uninfected, born to HIV-1-infected mothers who had not undergone antiretroviral therapy during pregnancy, and 84 HIV-1-infected mothers were analyzed. The single nucleotide polymorphisms -44C/G (rs1800972) and -52G/A (rs1799946) were genotyped by TaqMan allelic discrimination assay and sequencing. Statistical analyses were performed using SNPStats and Bonferroni correction for multiple tests. RESULTS In children, the -52GG genotype and the -44G/-52G haplotype had a protective role against HIV-1 infection [odds ratio (OR) = 0.52, 95% confidence interval (CI) 0.31 to 0.86, P = 0.03 and OR = 0.50, 95% CI 0.31 to 0.83, P = 0.014, respectively]. In mothers, the -52GG genotype and the -44G/-52G haplotype were associated with low levels of HIV-1 plasma viremia (<1000 copies/mL) and a lower risk of maternal HIV-1 transmission (OR = 0.14, 95% CI 0.03 to 0.67, P = 0.009 and OR = 0.23, 95% CI 0.08 to 0.66, P = 0.012, respectively). CONCLUSIONS These results demonstrate a significant relationship between genetic variants of beta-defensin-1 gene, viral load, and MTCT of HIV-1, thus supporting a critical role of innate immunity in pediatric HIV-1 infection.
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Are defensin beta 1 gene polymorphisms associated with HIV infection and virus replication? AIDS 2009; 23:647-9; author reply 649-50. [PMID: 19516112 DOI: 10.1097/qad.0b013e3283277247] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hurst LD. Fundamental concepts in genetics: genetics and the understanding of selection. Nat Rev Genet 2009; 10:83-93. [PMID: 19119264 DOI: 10.1038/nrg2506] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
At first sight selection is a simple notion, and some consider it the most important evolutionary force. But how important is selection, is it really so trivial to understand and what are the alternatives? Here I discuss how genetics is crucial for addressing all of these questions: genetics allowed the concept of natural selection to become viable, it contributed to our understanding of the complexities of selection and it spurred the development of competing models of evolution. Understanding how and why selection acts has important potential applications, from understanding the mechanisms of disease and microbial resistance, to improving the design of transgenes and drugs.
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Affiliation(s)
- Laurence D Hurst
- Department of Biology and Biochemistry, University of Bath, Somerset, BA2 7AY, UK.
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