Balancing Selection Drives the Maintenance of Genetic Variation in Drosophila Antimicrobial Peptides
Tóm tắt
Từ khóa
Tài liệu tham khảo
Alcaide, 2011, Molecular evolution of the Toll-like receptor multigene family in birds, Mol Biol Evol, 28, 1703, 10.1093/molbev/msq351
Anderson, 1981, The population dynamics of microparasites and their invertebrate hosts, Philos Trans R Soc Lond B Biol Sci, 291, 451, 10.1098/rstb.1981.0005
Behrman, 2018, Rapid seasonal evolution in innate immunity of wild Drosophila melanogaster, Proc R Soc B, 285, 20172599, 10.1098/rspb.2017.2599
Benachour, 2009, Association of human cathelicidin (hCAP-18/LL-37) gene expression with cardiovascular disease risk factors, Nutr Metab Cardiovasc Dis, 19, 720, 10.1016/j.numecd.2009.01.001
Bergland, 2014, Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila, PLoS Genet, 10, e1004775., 10.1371/journal.pgen.1004775
Bernatchez, 2003, MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years?, J Evol Biol, 16, 363, 10.1046/j.1420-9101.2003.00531.x
Brockhurst, 2003, Population mixing accelerates coevolution, Ecol Lett, 6, 975, 10.1046/j.1461-0248.2003.00531.x
Brogden, 2005, Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria?, Nat Rev Microbiol, 3, 238, 10.1038/nrmicro1098
Bulet, 2005, Insect antimicrobial peptides: structures, properties and gene regulation, Protein Pept Lett, 12, 3, 10.2174/0929866053406011
Cagliani, 2008, The signature of long-standing balancing selection at the human defensin beta-1 promoter, Genome Biol, 9, R143, 10.1186/gb-2008-9-9-r143
Cagliani, 2010, Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 gene, Hum Genet, 128, 577, 10.1007/s00439-010-0884-6
Chan, 2012, Genome-wide fine-scale recombination rate variation in Drosophila melanogaster, PLoS Genet, 8, e1003090., 10.1371/journal.pgen.1003090
Chapman, 2016, The evolution of innate immune genes: purifying and balancing selection on β-defensins in waterfowl, Mol Biol Evol, 33, 3075, 10.1093/molbev/msw167
Charlesworth, 2009, Effective population size and patterns of molecular evolution and variation, Nat Rev Genet, 10, 195, 10.1038/nrg2526
Charlesworth, 2006, Balancing selection and its effects on sequences in nearby genome regions, PLoS Genet, 2, e64., 10.1371/journal.pgen.0020064
Clark, 2007, Evolution of genes and genomes on the Drosophila phylogeny, Nature, 450, 203, 10.1038/nature06341
Comeron, 2014, Background selection as baseline for nucleotide variation across the Drosophila genome, PLoS Genet, 10, e1004434., 10.1371/journal.pgen.1004434
Croze, 2016, Balancing selection on immunity genes: review of the current literature and new analysis in Drosophila melanogaster, Zoology, 119, 322, 10.1016/j.zool.2016.03.004
Croze, 2017, A genome-wide scan for genes under balancing selection in Drosophila melanogaster, BMC Evol Biol, 17, 10.1186/s12862-016-0857-z
David, 1988, Genetic variation of Drosophila melanogaster natural populations, Trends Genet, 4, 106, 10.1016/0168-9525(88)90098-4
De Gregorio, 2002, The Toll and Imd pathways are the major regulators of the immune response in Drosophila, EMBO J, 21, 2568, 10.1093/emboj/21.11.2568
DeGiorgio, 2014, A model-based approach for identifying signatures of ancient balancing selection in genetic data, PLoS Genet, 10, e1004561., 10.1371/journal.pgen.1004561
Dostert, 2005, The Jak-STAT signaling pathway is required but not sufficient for the antiviral response of Drosophila, Nat Immunol, 6, 946, 10.1038/ni1237
Downing, 2009, Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus, BMC Evol Biol, 9, 136., 10.1186/1471-2148-9-136
Downing, 2009, Contrasting evolution of diversity at two disease-associated chicken genes, Immunogenetics, 61, 303, 10.1007/s00251-009-0359-x
Downing, 2010, The differential evolutionary dynamics of avian cytokine and TLR gene classes, J Immunol, 184, 6993, 10.4049/jimmunol.0903092
Early, 2017, Survey of global genetic diversity within the Drosophila immune system, Genetics, 205, 353, 10.1534/genetics.116.195016
Edwards, 1998, Evolution and ecology of MHC molecules: from genomics to sexual selection, Trends Ecol Evol, 13, 305, 10.1016/S0169-5347(98)01416-5
Ekblom, 2010, Evolutionary analysis and expression profiling of Zebra Finch immune genes, Genome Biol Evol, 2, 781, 10.1093/gbe/evq061
Ferguson, 2012, Long-term balancing selection at the antiviral gene OAS1 in Central African chimpanzees, Mol Biol Evol, 29, 1093, 10.1093/molbev/msr247
Ferguson, 2008, Long-term balancing selection at the West Nile virus resistance gene, Oas1b, maintains transspecific polymorphisms in the house mouse, Mol Biol Evol, 25, 1609, 10.1093/molbev/msn106
Ferrer-Admetlla, 2008, Balancing selection is the main force shaping the evolution of innate immunity genes, J Immunol, 181, 1315, 10.4049/jimmunol.181.2.1315
Ferretti, 2012, Neutrality tests for sequences with missing data, Genetics, 191, 1397, 10.1534/genetics.112.139949
Fish, 2015, Contrasted patterns of variation and evolutionary convergence at the antiviral OAS1 gene in old world primates, Immunogenetics, 67, 487, 10.1007/s00251-015-0855-0
Fox, 2011, An R Companion to Applied Regression
Franzoi, 2017, Structural insights into the mode of action of the peptide antibiotic Copsin, Biochemistry, 56, 4992, 10.1021/acs.biochem.7b00697
Fumagalli, 2009, Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions, J Exp Med, 206, 1395, 10.1084/jem.20082779
Gandon, 2002, Local adaptation, evolutionary potential and host-parasite coevolution: interactions between migration, mutation, population size and generation time, J Evol Biol, 15, 451, 10.1046/j.1420-9101.2002.00402.x
Gao, 2015, Footprints of ancient-balanced polymorphisms in genetic variation data from closely related species, Evolution, 69, 431, 10.1111/evo.12567
Garrigan, 2003, Perspective: detecting adaptive molecular polymorphism: lessons from the MHC, Evolution, 57, 1707, 10.1111/j.0014-3820.2003.tb00580.x
Gilliet, 2008, Antimicrobial peptides and self-DNA in autoimmune skin inflammation, Curr Opin Immunol, 20, 401, 10.1016/j.coi.2008.06.008
Gilroy, 2017, Toll-like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the ‘ghost of selection past’ and quantify the ‘drift debt’, J Evol Biol, 30, 1276, 10.1111/jeb.13077
Glinka, 2003, Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach, Genetics, 165, 1269, 10.1093/genetics/165.3.1269
Gosset, 2014, Evidence for adaptation from standing genetic variation on an antimicrobial peptide gene in the mussel Mytilus edulis, Mol Ecol, 23, 3000, 10.1111/mec.12784
Gossmann, 2014, Fluctuating selection models and McDonald–Kreitman type analyses, PLoS One, 9, e84540., 10.1371/journal.pone.0084540
Halldórsdóttir, 2015, Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species, PeerJ, 3, e976., 10.7717/peerj.976
Hanson, 2016, Immune genes and divergent antimicrobial peptides in flies of the subgenus Drosophila, BMC Evol Biol, 16, 10.1186/s12862-016-0805-y
Hartl, 2006, Principles of Population Genetics
Heger, 2007, Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes, Genome Res, 17, 1837, 10.1101/gr.6249707
Hellgren, 2011, Locus-specific protocol for nine different innate immune genes (antimicrobial peptides: β-defensins) across passerine bird species reveals within-species coding variation and a case of trans-species polymorphisms, Mol Ecol Resour, 11, 686, 10.1111/j.1755-0998.2011.02995.x
Hellgren, 2010, In vitro tests of natural allelic variation of innate immune genes (avian β-defensins) reveal functional differences in microbial inhibition, J Evol Biol, 23, 2726, 10.1111/j.1420-9101.2010.02115.x
Hill, 2019, The genome of Drosophila innubila reveals lineage-specific patterns of selection in immune genes, Mol Biol Evol, 36, 1405, 10.1093/molbev/msz059
Hollox, 2008, Directional and balancing selection in human beta-defensins, BMC Evol Biol, 8, 113., 10.1186/1471-2148-8-113
Huerta-Sanchez, 2008, Population genetics of polymorphism and divergence under fluctuating selection, Genetics, 178, 325, 10.1534/genetics.107.073361
Hughes, 2005, High level of functional polymorphism indicates a unique role of natural selection at human immune system loci, Immunogenetics, 57, 821, 10.1007/s00251-005-0052-7
Hughes, 1997, Coordinated amino acid changes in the evolution of mammalian defensins, J Mol Evol, 44, 675, 10.1007/PL00006191
Hultmark, 1993, Immune reactions in Drosophila and other insects: a model for innate immunity, Trends Genet, 9, 178, 10.1016/0168-9525(93)90165-E
Janssens, 2003, Role of Toll-like receptors in pathogen recognition, Clin Microbiol Rev, 16, 637, 10.1128/CMR.16.4.637-646.2003
Keller, 2007, Drosophila melanogaster's history as a human commensal, Curr Biol, 17, R77, 10.1016/j.cub.2006.12.031
Kingsolver, 2007, Patterns and power of phenotypic selection in nature, Bioscience, 57, 561, 10.1641/B570706
Kloch, 2018, Signatures of balancing selection in toll-like receptor (TLRs) genes—novel insights from a free-living rodent, Sci Rep, 8, 8361, 10.1038/s41598-018-26672-2
Kofler, 2011, PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals, PLoS One, 6, e15925, 10.1371/journal.pone.0015925
Kosiol, 2008, Patterns of positive selection in six mammalian genomes, PLoS Genet, 4, e1000144, 10.1371/journal.pgen.1000144
Lack, 2016, A thousand fly genomes: an expanded Drosophila Genome Nexus, Mol Biol Evol, 33, 3308, 10.1093/molbev/msw195
Lambrechts, 2006, Coevolutionary interactions between host and parasite genotypes, Trends Parasitol, 22, 12, 10.1016/j.pt.2005.11.008
Lamiable, 2016, Cytokine Diedel and a viral homologue suppress the IMD pathway in Drosophila, Proc Natl Acad Sci U S A, 113, 698, 10.1073/pnas.1516122113
Lemaitre, 2007, The host defense of Drosophila melanogaster, Annu Rev Immunol, 25, 697, 10.1146/annurev.immunol.25.022106.141615
Lemaitre, 1997, Drosophila host defense: differential induction of antimicrobial peptide genes after infection by various classes of microorganisms, Proc Natl Acad Sci U S A, 94, 14614, 10.1073/pnas.94.26.14614
Li, 2006, Inferring the demographic history and rate of adaptive substitution in Drosophila, PLoS Genet, 2, e166., 10.1371/journal.pgen.0020166
Llaurens, 2017, Genetic architecture and balancing selection: the life and death of differentiated variants, Mol Ecol, 26, 2430, 10.1111/mec.14051
Mackay, 2001, The genetic architecture of quantitative traits, Annu Rev Genet, 35, 303, 10.1146/annurev.genet.35.102401.090633
Mackay, 2012, The Drosophila melanogaster Genetic Reference Panel, Nature, 482, 173, 10.1038/nature10811
Maneerat, 2016, Increased alpha-defensin expression is associated with risk of coronary heart disease: a feasible predictive inflammatory biomarker of coronary heart disease in hyperlipidemia patients, Lipids Health Dis, 15, 117., 10.1186/s12944-016-0285-5
McTaggart, 2012, Immune genes undergo more adaptive evolution than non-immune system genes in Daphnia pulex, BMC Evol Biol, 12, 63., 10.1186/1471-2148-12-63
Miura, 2013, Random fluctuation of selection coefficients and the extent of nucleotide variation in human populations, Proc Natl Acad Sci U S A, 110, 10676, 10.1073/pnas.1308462110
Newman, 2006, Balancing selection and the evolution of functional polymorphism in Old World monkey TRIM5α, Proc Natl Acad Sci U S A, 103, 19134, 10.1073/pnas.0605838103
Nielsen, 2005, A scan for positively selected genes in the genomes of humans and chimpanzees, PLoS Biol, 3, e170, 10.1371/journal.pbio.0030170
Nolte, 2013, Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana, Genome Res, 23, 99, 10.1101/gr.139873.112
Obbard, 2006, Natural selection drives extremely rapid evolution in antiviral RNAi genes, Curr Biol, 16, 580, 10.1016/j.cub.2006.01.065
Obbard, 2009, Quantifying adaptive evolution in the Drosophila immune system, PLoS Genet, 5, e1000698., 10.1371/journal.pgen.1000698
Obbard, 2012, Estimating divergence dates and substitution rates in the Drosophila phylogeny, Mol Biol Evol, 29, 3459, 10.1093/molbev/mss150
Park, 2014, Functional characterization of naturally occurring melittin peptide isoforms in two honey bee species, Apis mellifera and Apis cerana, Peptides, 53, 185, 10.1016/j.peptides.2014.01.026
Paterson, 2010, Antagonistic coevolution accelerates molecular evolution, Nature, 464, 275, 10.1038/nature08798
Pool, 2012, Population genomics of sub-Saharan Drosophila melanogaster: African diversity and non-African admixture, PLoS Genet, 8, e1003080, 10.1371/journal.pgen.1003080
Quéméré, 2015, Immunogenetic heterogeneity in a widespread ungulate: the European roe deer (Capreolus capreolus), Mol Ecol, 24, 3873, 10.1111/mec.13292
Quéméré, 2018
R Core Team, 2017, R: a language and environment for statistical computing
Sackton, 2007, Dynamic evolution of the innate immune system in Drosophila, Nat Genet, 39, 1461, 10.1038/ng.2007.60
Schlenke, 2003, Natural selection drives Drosophila immune system evolution, Genetics, 164, 1471, 10.1093/genetics/164.4.1471
Schmitt, 2016, An intimate link between antimicrobial peptide sequence diversity and binding to essential components of bacterial membranes, Biochim Biophys Acta Biomembr, 1858, 958, 10.1016/j.bbamem.2015.10.011
Schulte, 2010, Multiple reciprocal adaptations and rapid genetic change upon experimental coevolution of an animal host and its microbial parasite, Proc Natl Acad Sci U S A, 107, 7359, 10.1073/pnas.1003113107
Shai, 2002, Mode of action of membrane active antimicrobial peptides, Pept Sci, 66, 236, 10.1002/bip.10260
Shapiro, 2007, Adaptive genic evolution in the Drosophila genomes, Proc Natl Acad Sci U S A, 104, 2271, 10.1073/pnas.0610385104
Siewert, 2017, Detecting long-term balancing selection using allele frequency correlation, Mol Biol Evol, 34, 2996, 10.1093/molbev/msx209
Stahl, 1999, Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis, Nature, 400, 667, 10.1038/23260
Sukumaran, 2010, DendroPy: a Python library for phylogenetic computing, Bioinformatics, 26, 1569, 10.1093/bioinformatics/btq228
Tennessen, 2008, Balancing selection at a frog antimicrobial peptide locus: fluctuating immune effector alleles?, Mol Biol Evol, 25, 2669, 10.1093/molbev/msn208
Tennessen, 2009, Variations in the expressed antimicrobial peptide repertoire of northern leopard frog (Rana pipiens) populations suggest intraspecies differences in resistance to pathogens, Dev Comp Immunol, 33, 1247, 10.1016/j.dci.2009.07.004
Thrall, 2012, Rapid genetic change underpins antagonistic coevolution in a natural host–pathogen metapopulation, Ecol Lett, 15, 425, 10.1111/j.1461-0248.2012.01749.x
True, 1996, Differences in crossover frequency and distribution among three sibling species of Drosophila, Genetics, 142, 507, 10.1093/genetics/142.2.507
Turner, 2012, Evidence for selection at cytokine loci in a natural population of field voles (Microtus agrestis), Mol Ecol, 21, 1632, 10.1111/j.1365-294X.2012.05501.x
Tzou, 2000, Tissue-specific inducible expression of antimicrobial peptide genes in Drosophila surface epithelia, Immunity, 13, 737, 10.1016/S1074-7613(00)00072-8
Unckless, 2016, Convergent balancing selection on an antimicrobial peptide in Drosophila, Curr Biol, 26, 257, 10.1016/j.cub.2015.11.063
Unckless, 2016, The potential for adaptive maintenance of diversity in insect antimicrobial peptides, Philos Trans R Soc B, 371, 20150291., 10.1098/rstb.2015.0291
Velová, 2018, Toll-like receptor evolution in birds: gene duplication, pseudogenization, and diversifying selection, Mol Biol Evol, 35, 2170, 10.1093/molbev/msy119
Wang, 2016, Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication, Cell Res, 26, 556, 10.1038/cr.2016.44
Wilson, 2006, A hallmark of balancing selection is present at the promoter region of interleukin 10, Genes Immun, 7, 680, 10.1038/sj.gene.6364336