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Bateson ZW, Whittingham LA, Johnson JA, Dunn PO. Contrasting patterns of selection and drift between two categories of immune genes in prairie-chickens. Mol Ecol 2015; 24:6095-106. [PMID: 26547898 DOI: 10.1111/mec.13459] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 10/31/2015] [Accepted: 11/03/2015] [Indexed: 12/22/2022]
Abstract
Immune-receptor genes of the adaptive immune system, such as the major histocompatibility complex (MHC), are involved in recognizing specific pathogens and are known to have high rates of adaptive evolution, presumably as a consequence of rapid co-evolution between hosts and pathogens. In contrast, many 'mediating' genes of the immune system do not interact directly with specific pathogens and are involved in signalling (e.g. cytokines) or controlling immune cell growth. As a consequence, we might expect stronger selection at immune-receptor than mediating genes, but these two types of genes have not been compared directly in wild populations. Here, we tested the hypothesis that selection differs between MHC (class I and II) and mediating genes by comparing levels of population differentiation across the range of greater prairie-chickens (Tympanuchus cupido). As predicted, there was stronger population differentiation and isolation by distance at immune receptor (MHC) than at either mediating genes or neutral microsatellites, suggesting a stronger role of local adaptation at the MHC. In contrast, mediating genes displayed weaker differentiation between populations than neutral microsatellites, consistent with selection favouring similar alleles across populations for mediating genes. In addition to selection, drift also had a stronger effect on immune receptor (MHC) than mediating genes as indicated by the stronger decline of MHC variation in relation to population size. This is the first study in the wild to show that the effects of selection and drift on immune genes vary across populations depending on their functional role.
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Affiliation(s)
- Zachary W Bateson
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, TX, USA
| | - Peter O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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Gomez F, Tomas G, Ko WY, Ranciaro A, Froment A, Ibrahim M, Lema G, Nyambo TB, Omar SA, Wambebe C, Hirbo JB, Rocha J, Tishkoff SA. Patterns of nucleotide and haplotype diversity at ICAM-1 across global human populations with varying levels of malaria exposure. Hum Genet 2013; 132:987-99. [PMID: 23609612 DOI: 10.1007/s00439-013-1284-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 02/27/2013] [Indexed: 10/26/2022]
Abstract
Malaria is one of the strongest selective pressures in recent human evolution. African populations have been and continue to be at risk for malarial infections. However, few studies have re-sequenced malaria susceptibility loci across geographically and genetically diverse groups in Africa. We examined nucleotide diversity at Intercellular adhesion molecule-1 (ICAM-1), a malaria susceptibility candidate locus, in a number of human populations with a specific focus on diverse African ethnic groups. We used tests of neutrality to assess whether natural selection has impacted this locus and tested whether SNP variation at ICAM-1 is correlated with malaria endemicity. We observe differing patterns of nucleotide and haplotype variation in global populations and higher levels of diversity in Africa. Although we do not observe a deviation from neutrality based on the allele frequency distribution, we do observe several alleles at ICAM-1, including the ICAM-1 (Kilifi) allele, that are correlated with malaria endemicity. We show that the ICAM-1 (Kilifi) allele, which is common in Africa and Asia, exists on distinct haplotype backgrounds and is likely to have arisen more recently in Asia. Our results suggest that correlation analyses of allele frequencies and malaria endemicity may be useful for identifying candidate functional variants that play a role in malaria resistance and susceptibility.
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Affiliation(s)
- Felicia Gomez
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Maruki T, Kumar S, Kim Y. Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single-nucleotide polymorphisms. Mol Biol Evol 2012; 29:3617-23. [PMID: 22826460 PMCID: PMC3494274 DOI: 10.1093/molbev/mss187] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
An improved understanding of the biological and numerical properties of measures of population differentiation across loci is becoming increasingly more important because of their growing use in analyzing genome-wide polymorphism data for detecting population structures, inferring the rates of migration, and identifying local adaptations. In a genome-wide analysis, we discovered that the estimates of population differentiation (e.g., F(ST), θ, and Jost's D) calculated for human single-nucleotide polymorphisms (SNPs) are strongly and positively correlated to the position-specific evolutionary rates measured from multispecies alignments. That is, genomic positions (loci) experiencing higher purifying selection (lower evolutionary rates) produce lower values for the degree of population differentiation than those evolving with faster rates. We show that this pattern is completely mediated by the negative effects of purifying selection on the minor allele frequency (MAF) at individual loci. Our results suggest that inferences and methods relying on the comparison of population differentiation estimates (F(ST), θ, and Jost's D) based on SNPs across genomic positions should be restricted to loci with similar MAFs and/or the rates of evolution in genome scale surveys.
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Affiliation(s)
- Takahiro Maruki
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University
- School of Life Sciences, Arizona State University
| | - Sudhir Kumar
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University
- School of Life Sciences, Arizona State University
| | - Yuseob Kim
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University
- School of Life Sciences, Arizona State University
- Department of Life Science, Ewha Womans University, Seoul, Korea
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Abstract
In recent years, several functional polymorphisms, particularly, SNPs have been identified in cytokines and their receptor genes that regulate levels of cytokine expression. These have been implicated as immune prognostic markers in diseases, including differential response to therapy and as biomarkers of graft outcome following organ and stem cell transplantation. Population distribution of cytokine gene polymorphisms (CGPs) reveals significant variations in allele frequencies in different ethnic groups and this might explain, to some extent, the observed differences in SNP associations with various diseases and immune-pathologies. A number of molecular methods are available for defining CGPs. These include PCR-SSP, AFLP, Taqman probe assays as well as sequencing based typing. Of these, the PCR-based sequence-specific primer based test is the most widely accepted technique. This chapter describes steps involved in this procedure along with sources for procuring essential reagents. An important aspect of CGP analyses is the correct interpretation of results particularly determination of their multilocus haplotypes.
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Dall'Olio GM, Laayouni H, Luisi P, Sikora M, Montanucci L, Bertranpetit J. Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation. BMC Evol Biol 2012; 12:98. [PMID: 22731960 PMCID: PMC3426484 DOI: 10.1186/1471-2148-12-98] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Accepted: 06/25/2012] [Indexed: 01/11/2023] Open
Abstract
Background Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Results Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. Conclusions These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.
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Affiliation(s)
- Giovanni Marco Dall'Olio
- IBE, Institut de Biologia Evolutiva (UPF-CSIC), Parc de Recerca Biomèdica de Barcelona (PRBB), Dr, Aiguader, 88, 08003, Barcelona, Catalonia, Spain
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Szauter KM, Jansen MK, Okimoto G, Loomis M, Kimura JH, Heller M, Ku T, Tiirikainen M, Boyd CD, Csiszar K, Girton RA. Persistent Inflammatory Pathways Associated with Early Onset Myocardial Infarction in a Medicated Multiethnic Hawaiian Cohort. BIOCHEMISTRY INSIGHTS 2011. [DOI: 10.4137/bci.s6976] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In spite of current standard therapies to target the major pathomechanisms in myocardial infarction (MI), inflammatory gene expression patterns have been consistently revealed in MI patients. In a multiethnic cohort, we aimed to identify MI-associated pathomechanisms that may be unresponsive to medical treatment to improve diagnosis and therapy. Gene expression profiles in whole blood were analyzed in medicated Asian, African American and Caucasian patients living in Hawaii with a history of early MI and age, ethnicity, risk factor and medication-matched controls. PANTHER ontological and Ingenuity Pathway analysis and functional evaluation of the consistently differentially expressed genes identified coordinated up-regulation of genes for inflammation (LGALS3, PTX3, ZBTB32, BCL2L1), T-cell activation (IL12RB1, VAV3, JAG1, CAMP), immune imbalance (IL-8, IL2RA, CCR7, AHNAK), and active atherosclerosis (NR1H4, BIN1, GSTT1, MARCO) that persist in MI patients in spite of concerted treatment efforts to control vascular pathology. Furthermore, significant ethnic differences appear to exist within the active disease mechanisms that need to be further investigated to identify key targets for effective medical intervention.
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Affiliation(s)
| | | | - Gordon Okimoto
- Cancer Center, University of Hawaii, Honolulu, Hawaii, USA
| | - Michael Loomis
- Cancer Center, University of Hawaii, Honolulu, Hawaii, USA
| | | | | | - Tercia Ku
- John A. Burns School of Medicine, Honolulu, Hawaii, USA
| | | | | | | | - Richard A. Girton
- John A. Burns School of Medicine, Honolulu, Hawaii, USA
- Department of Veterans Affairs Medical Center, Honolulu, Hawaii, USA
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Juneja P, Lazzaro BP. Haplotype structure and expression divergence at the Drosophila cellular immune gene eater. Mol Biol Evol 2010; 27:2284-99. [PMID: 20444883 DOI: 10.1093/molbev/msq114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The protein Eater plays an important role in microbial recognition and defensive phagocytosis in Drosophila melanogaster. We sequenced multiple alleles of the eater gene from an African and a North American population of D. melanogaster and found signatures of a partial selective sweep in North America that is localized around the second intron. This pattern is consistent with local adaptation to novel selective pressures during range expansion out of Africa. The North American sample is divided into two predominant haplotype groups, and the putatively selected haplotype is associated with a significantly higher gene expression level, suggesting that gene regulation is a possible target of selection. The eater alleles contain from 22 to 40 repeat units that are characterized by the presence of a cysteine-rich NIM motif. NIM repeats in the structural stalk of the protein exhibit concerted evolution as a function of physical location in the repeat array. Several NIM repeats within eater have previously been implicated in binding to microbial ligands, a function which in principle might subject them to special evolutionary pressures. However, we find no evidence of elevated positive selection on these pathogen-interacting units. Our study presents an instance where gene expression rather than protein structure is thought to drive the adaptive evolution of a pathogen recognition molecule in the immune system.
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Affiliation(s)
- Punita Juneja
- Department of Entomology, Cornell University, Ithaca, New York, USA.
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Garte S. Human population genetic diversity as a function of SNP type from HapMap data. Am J Hum Biol 2009; 22:297-300. [DOI: 10.1002/ajhb.20984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Kullo IJ, Ding K. Patterns of population differentiation of candidate genes for cardiovascular disease. BMC Genet 2007; 8:48. [PMID: 17626638 PMCID: PMC1937006 DOI: 10.1186/1471-2156-8-48] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Accepted: 07/12/2007] [Indexed: 12/19/2022] Open
Abstract
Background The basis for ethnic differences in cardiovascular disease (CVD) susceptibility is not fully understood. We investigated patterns of population differentiation (FST) of a set of genes in etiologic pathways of CVD among 3 ethnic groups: Yoruba in Nigeria (YRI), Utah residents with European ancestry (CEU), and Han Chinese (CHB) + Japanese (JPT). We identified 37 pathways implicated in CVD based on the PANTHER classification and 416 genes in these pathways were further studied; these genes belonged to 6 biological processes (apoptosis, blood circulation and gas exchange, blood clotting, homeostasis, immune response, and lipoprotein metabolism). Genotype data were obtained from the HapMap database. Results We calculated FST for 15,559 common SNPs (minor allele frequency ≥ 0.10 in at least one population) in genes that co-segregated among the populations, as well as an average-weighted FST for each gene. SNPs were classified as putatively functional (non-synonymous and untranslated regions) or non-functional (intronic and synonymous sites). Mean FST values for common putatively functional variants were significantly higher than FST values for nonfunctional variants. A significant variation in FST was also seen based on biological processes; the processes of 'apoptosis' and 'lipoprotein metabolism' showed an excess of genes with high FST. Thus, putative functional SNPs in genes in etiologic pathways for CVD show greater population differentiation than non-functional SNPs and a significant variance of FST values was noted among pairwise population comparisons for different biological processes. Conclusion These results suggest a possible basis for varying susceptibility to CVD among ethnic groups.
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Affiliation(s)
- Iftikhar J Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester MN, USA
| | - Keyue Ding
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester MN, USA
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Kaur G, Rapthap CC, Kumar N, Kumar S, Neolia S, Mehra NK. Frequency distribution of cytokine gene polymorphisms in the healthy North Indian population. ACTA ACUST UNITED AC 2007; 69:113-20. [PMID: 17257312 DOI: 10.1111/j.1399-0039.2006.00740.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The allelic and genotype frequencies corresponding to 22 single nucleotide polymorphisms (SNPs) in 13 cytokine genes interleukin (IL) 1-alpha (T/C -889), IL1-beta (C/T -511, T/C +3962), IL12 (C/A -1188), interferon-gamma (A/T UTR 5644), transforming growth factor-beta (C/T codon 10, G/C codon 25), tumour necrosis factor-alpha (G/A -308, G/A -238), IL2 (T/G -330, G/T +160), IL4 (T/G -1098, T/C -590, T/C -33), IL6 (G/C -174, G/A nt 565), IL10 (G/A -1082, C/T -819, C/A -592), IL1R (C/T pst11970), IL1RA (T/C mspa111100) and IL4RA (G/A +1902) were determined in 130 healthy North Indian subjects. All genomic typings were performed with polymerase chain reaction with sequence-specific assays. An analysis of the allelic and haplotype frequencies in the North Indian population showed a good fit with the Hardy-Weinberg equilibrium for most of the SNPs. The data can be used for anthropological comparisons, as well as for association studies with different diseases and for use in transplant situations involving acute and chronic rejection.
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Affiliation(s)
- G Kaur
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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