Evidence for selection at cytokine loci in a natural population of field voles (Microtus agrestis)

Individuals in natural populations are frequently exposed to a wide range of pathogens. Given the diverse profile of gene products involved in responses to different types of pathogen, this potentially results in complex pathogen‐specific selection pressures acting on a broad spectrum of immune system genes in wild animals. Thus far, studies into the evolution of immune genes in natural populations have focused almost exclusively on the Major Histocompatibility Complex (MHC). However, the MHC represents only a fraction of the immune system and there is a need to broaden research in wild species to include other immune genes. Here, we examine the evidence for natural selection in a range of non‐MHC genes in a natural population of field voles (Microtus agrestis). We concentrate primarily on genes encoding cytokines, signalling molecules critical in eliciting and mediating immune responses and identify signatures of natural selection acting on several of these genes. In particular, genetic diversity within Interleukin 1 beta and Interleukin 2 appears to have been maintained through balancing selection. Taken together with previous findings that polymorphism within these genes is associated with variation in resistance to multiple pathogens, this suggests that pathogen‐mediated selection may be an important force driving genetic diversity at cytokine loci in voles and other natural populations. These results also suggest that, along with the MHC, preservation of genetic variation within cytokine genes should be a priority for the conservation genetics of threatened wildlife populations.

[1]  Nova Scotia ANTAGONISTIC PLEIOTROPY, DOMINANCE, AND GENETIC VARIATION* , 1982 .

[2]  D. Balding,et al.  Identifying adaptive genetic divergence among populations from genome scans , 2004, Molecular ecology.

[3]  Pablo Librado,et al.  DnaSP v5: a software for comprehensive analysis of DNA polymorphism data , 2009, Bioinform..

[4]  M. Nei Molecular Evolutionary Genetics , 1987 .

[5]  Jacob A. Tennessen,et al.  Balancing Selection at a Frog Antimicrobial Peptide Locus: Fluctuating Immune Effector Alleles? , 2008, Molecular biology and evolution.

[6]  T. A. Hall,et al.  BIOEDIT: A USER-FRIENDLY BIOLOGICAL SEQUENCE ALIGNMENT EDITOR AND ANALYSIS PROGRAM FOR WINDOWS 95/98/ NT , 1999 .

[7]  J. Pemberton,et al.  Major histocompatibility complex variation associated with juvenile survival and parasite resistance in a large unmanaged ungulate population (Ovis aries L.) , 1998 .

[8]  A. Pedersen,et al.  The role of infectious diseases in biological conservation , 2009 .

[9]  P. Fédérici,et al.  Antagonistic effects of a Mhc class I allele on malaria-infected house sparrows. , 2008, Ecology letters.

[10]  J. Welch,et al.  Quantifying Adaptive Evolution in the Drosophila Immune System , 2009, PLoS genetics.

[11]  H. Okamura,et al.  Interleukin 18 together with interleukin 12 inhibits IgE production by induction of interferon-gamma production from activated B cells. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[12]  M Bennett,et al.  Parasite interactions in natural populations: insights from longitudinal data , 2008, Parasitology.

[13]  M. Kreitman,et al.  Adaptive protein evolution at the Adh locus in Drosophila , 1991, Nature.

[14]  D. Lynn,et al.  Contrasting evolution of diversity at two disease-associated chicken genes , 2009, Immunogenetics.

[15]  Lewis G. Spurgin,et al.  How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings , 2010, Proceedings of the Royal Society B: Biological Sciences.

[16]  M. Begon,et al.  Mycobacterium microti Infection (Vole Tuberculosis) in Wild Rodent Populations , 2002, Journal of Clinical Microbiology.

[17]  D. Coltman,et al.  Detecting the signature of selection on immune genes in highly structured populations of wild sheep (Ovis dalli) , 2006, Molecular ecology.

[18]  D. Emilie,et al.  [Cytokines and autoimmunity]. , 1994, La Revue du praticien.

[19]  W. Ollier Cytokine genes and disease susceptibility. , 2004, Cytokine.

[20]  S. Reed TGF-β in infections and infectious diseases , 1999 .

[21]  L. Cavalli-Sforza Population structure and human evolution , 1966, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[22]  Julio A. Rozas Liras,et al.  DnaSP v 5 : a software for comprehensive analysis of DNA polymorphism data , 2009 .

[23]  S. Altizer,et al.  Disease ecology meets ecological immunology: understanding the links between organismal immunity and infection dynamics in natural populations , 2011 .

[24]  Malcolm Bennett,et al.  Cowpox virus infection in natural field vole Microtus agrestis populations: significant negative impacts on survival. , 2008, The Journal of animal ecology.

[25]  M. Stephens,et al.  Accounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-data Imputation , 2022 .

[26]  Shameek Biswas,et al.  Genomic insights into positive selection. , 2006, Trends in genetics : TIG.

[27]  C. Elton,et al.  An Epidemic among Voles (Microtus agrestis) on the Scottish Border in the Spring of 1934 , 1935 .

[28]  François Rousset,et al.  GENEPOP (version 1.2): population genetic software for exact tests and ecumenicism , 1995 .

[29]  H. Tegelström,et al.  MITOCHONDRIAL DNA VARIATION IN THE FIELD VOLE (MICROTUS AGRESTIS): REGIONAL POPULATION STRUCTURE AND COLONIZATION HISTORY , 1996, Evolution; international journal of organic evolution.

[30]  P. Phillips,et al.  Using Population Genomics to Detect Selection in Natural Populations: Key Concepts and Methodological Considerations , 2010, International Journal of Plant Sciences.

[31]  P. Puccetti,et al.  Interleukin-12 in infectious diseases , 1997, Clinical microbiology reviews.

[32]  M. Begon,et al.  Tuberculosis (Mycobacterium microti) in wild field vole populations , 2007, Parasitology.

[33]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[34]  P. Kourilsky,et al.  Cytokine fields and the polarization of the immune response. , 2001, Trends in immunology.

[35]  F. Rousset genepop’007: a complete re‐implementation of the genepop software for Windows and Linux , 2008, Molecular ecology resources.

[36]  K. Else,et al.  Genetic variation in the humoral immune responses of mice to the nematode Trichuris muris , 1989, Parasite immunology.

[37]  W. Bodmer,et al.  Evolutionary Significance of the HL-A System , 1972, Nature.

[38]  M. Hollegaard,et al.  Cytokine gene polymorphism in human disease: on-line databases, Supplement 3 , 2006, Genes and Immunity.

[39]  F. Bonhomme,et al.  Adaptive evolution of interferon-γ in Glire lineage and evidence for a recent selective sweep in Mus. m. domesticus , 2009, Genes and Immunity.

[40]  F. Pociot,et al.  Cytokine gene polymorphism in human disease: on-line databases , 1999, Genes and Immunity.

[41]  P. Donnelly,et al.  A new statistical method for haplotype reconstruction from population data. , 2001, American journal of human genetics.

[42]  Justin C. Fay,et al.  Hitchhiking under positive Darwinian selection. , 2000, Genetics.

[43]  C. Primmer,et al.  Beyond MHC: signals of elevated selection pressure on Atlantic salmon (Salmo salar) immune-relevant loci. , 2010, Molecular ecology.

[44]  B. Weir Inferences about linkage disequilibrium. , 1979, Biometrics.

[45]  M. Benton,et al.  Paleontological evidence to date the tree of life. , 2006, Molecular biology and evolution.

[46]  R. Hudson Gene genealogies and the coalescent process. , 1990 .

[47]  K. Else,et al.  The effects of H-2 and non-H-2 genes on the expulsion of the nematode Trichuris muris from inbred and congenic mice , 1988, Parasitology.

[48]  P. Bork,et al.  Human non-synonymous SNPs: server and survey. , 2002, Nucleic acids research.

[49]  B. Weir,et al.  ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.

[50]  S. Humphries,et al.  Cytokine and cytokine receptor gene polymorphisms and their functionality. , 2009, Cytokine & growth factor reviews.

[51]  R. Lewontin,et al.  Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. , 1973, Genetics.

[52]  M. Begon,et al.  Contrasting dynamics of Bartonella spp. in cyclic field vole populations: the impact of vector and host dynamics , 2006, Parasitology.

[53]  J. Blackwell,et al.  SLC11A1 (formerly NRAMP1) and disease resistance , 2001, Cellular microbiology.

[54]  M. Begon,et al.  Disease dynamics in cyclic populations of field voles (Microtus agrestis): cowpox virus and vole tuberculosis (Mycobacterium microti) , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[55]  J. Pemberton,et al.  Fitness Correlates of Heritable Variation in Antibody Responsiveness in a Wild Mammal , 2010, Science.

[56]  R. Zinkernagel,et al.  Enhanced immunological surveillance in mice heterozygous at the H-2 gene complex , 1975, Nature.

[57]  V. Loeschcke,et al.  Spatially and temporally fluctuating selection at non-MHC immune genes: evidence from TAP polymorphism in populations of brown trout (Salmo trutta, L.) , 2008, Heredity.

[58]  T. Giraud,et al.  Antagonistic pleiotropy may help population-level selection in maintaining genetic polymorphism for transmission rate in a model phytopathogenic fungus , 2007, Heredity.

[59]  Matteo Fumagalli,et al.  Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions , 2009, The Journal of experimental medicine.

[60]  W. Ewens The sampling theory of selectively neutral alleles. , 1972, Theoretical population biology.

[61]  S. Sommer The importance of immune gene variability (MHC) in evolutionary ecology and conservation , 2005, Frontiers in Zoology.

[62]  F. Tajima Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.

[63]  S. Edwards,et al.  Molecular evolution of the toll-like receptor multigene family in birds. , 2011, Molecular biology and evolution.

[64]  F. Sisay-Joof,et al.  Quantification of the relative contribution of major histocompatibility complex (MHC) and non-MHC genes to human immune responses to foreign antigens , 1997, Infection and immunity.

[65]  A. Cunningham,et al.  Is MHC enough for understanding wildlife immunogenetics? , 2006, Trends in ecology & evolution.

[66]  M. Begon,et al.  Cowpox virus infection in natural field vole Microtus agrestis populations: delayed density dependence and individual risk. , 2006, The Journal of animal ecology.

[67]  Saleh M. Ibrahim,et al.  Cytokines and Cytokine Profiles in Human Autoimmune Diseases and Animal Models of Autoimmunity , 2009, Mediators of inflammation.

[68]  X. Lambin,et al.  Cyclic dynamics in field vole populations and generalist predation , 2000 .

[69]  A. T. Lloyd,et al.  The Differential Evolutionary Dynamics of Avian Cytokine and TLR Gene Classes , 2010, The Journal of Immunology.

[70]  R. Coffman,et al.  Two types of murine helper T cell clone. I. Definition according to profiles of lymphokine activities and secreted proteins. , 1986, Journal of immunology.

[71]  O. Bjørnstad,et al.  Transmission consequences of coinfection: cytokines writ large? , 2007, Trends in parasitology.

[72]  A. Hill,et al.  The genomics and genetics of human infectious disease susceptibility. , 2001, Annual review of genomics and human genetics.

[73]  E. Thompson,et al.  Performing the exact test of Hardy-Weinberg proportion for multiple alleles. , 1992, Biometrics.

[74]  D. Roff Variation and Life-History Evolution , 2005 .

[75]  PATHOGEN RESISTANCE AND GENETIC VARIATION AT MHC LOCI , 2002, Evolution; international journal of organic evolution.

[76]  J. Anaya,et al.  Analysis of IL1B, TAP1, TAP2 and IKBL polymorphisms on susceptibility to tuberculosis. , 2006, Tissue antigens.

[77]  Detlef Weigel,et al.  Next Generation Molecular Ecology , 2010, Molecular ecology.

[78]  M. Nachman Detecting Selection at the Molecular Level , 2022 .

[79]  M. Begon,et al.  Trypanosomes, fleas and field voles: ecological dynamics of a host-vector–parasite interaction , 2005, Parasitology.

[80]  T. Marquès-Bonet,et al.  Balancing Selection Is the Main Force Shaping the Evolution of Innate Immunity Genes1 , 2008, The Journal of Immunology.

[81]  J. Ott Genetic data analysis II , 1997 .

[82]  Kenneth M. Murphy,et al.  Functional diversity of helper T lymphocytes , 1996, Nature.

[83]  A. Hill,et al.  The immunogenetics of human infectious diseases. , 1998, Annual review of immunology.

[84]  M. Milinski,et al.  Major histocompatibility complex diversity influences parasite resistance and innate immunity in sticklebacks , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[85]  L. Excoffier,et al.  Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows , 2010, Molecular ecology resources.

[86]  M. Begon,et al.  The analysis of immunological profiles in wild animals: a case study on immunodynamics in the field vole, Microtus agrestis , 2011, Molecular ecology.

[87]  M. Begon,et al.  Species Interactions in a Parasite Community Drive Infection Risk in a Wildlife Population , 2010, Science.

[88]  P. Garnier-Géré,et al.  A computer program for testing pairwise linkage disequilibria in subdivided populations. , 1992, The Journal of heredity.

[89]  H. Westerdahl,et al.  Signatures of selection acting on the innate immunity gene Toll‐like receptor 2 (TLR2) during the evolutionary history of rodents , 2011, Journal of evolutionary biology.

[90]  J. Jackson,et al.  Measuring immune system variation to help understand host-pathogen community dynamics , 2008, Parasitology.

[91]  L. Excoffier,et al.  Detecting loci under selection in a hierarchically structured population , 2009, Heredity.

[92]  J. Howard Disease and evolution , 1991, Nature.

[93]  J. Steinke,et al.  2. Cytokines and chemokines. , 2003, The Journal of allergy and clinical immunology.

[94]  Emily H Turner,et al.  Target-enrichment strategies for next-generation sequencing , 2010, Nature Methods.

[95]  J. Eimes,et al.  Drift and selection influence geographic variation at immune loci of prairie‐chickens , 2011, Molecular ecology.

[96]  G. A. Watterson On the number of segregating sites in genetical models without recombination. , 1975, Theoretical population biology.

[97]  B. Lazzaro,et al.  Immunity in a variable world , 2009, Philosophical Transactions of the Royal Society B: Biological Sciences.

[98]  S. V. van Deventer Cytokine and cytokine receptor polymorphisms in infectious disease , 2000, Intensive care medicine.

[99]  Larry Borish,et al.  Cytokines and chemokines , 2003 .

[100]  G. A. Watterson The homozygosity test of neutrality. , 1978, Genetics.

[101]  M. Milinski,et al.  Female sticklebacks count alleles in a strategy of sexual selection explaining MHC polymorphism , 2001, Nature.

[102]  J. M. Smith,et al.  The hitch-hiking effect of a favourable gene. , 1974, Genetical research.

[103]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[104]  R. Hiorns,et al.  Immunogenetic correlates of susceptibility to infection with Heligmosomoides polygyrus in outbred mice , 1990, Parasitology.

[105]  David A. Elston,et al.  Spatial asynchrony and periodic travelling waves in cyclic populations of field voles , 1998, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[106]  Leo Goodstadt,et al.  Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes , 2004, Genome Biology.

[107]  D. Begun,et al.  Natural selection drives Drosophila immune system evolution. , 2003, Genetics.

[108]  R. Nielsen Molecular signatures of natural selection. , 2005, Annual review of genetics.

[109]  L. Quintana-Murci,et al.  From evolutionary genetics to human immunology: how selection shapes host defence genes , 2010, Nature Reviews Genetics.

[110]  R. Adkins,et al.  Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes. , 2004, Systematic biology.

[111]  W. Li,et al.  Statistical tests of neutrality of mutations. , 1993, Genetics.

[112]  H. Akashi,et al.  Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. , 1995, Genetics.

[113]  W. Black,et al.  A FORTRAN program for the calculation and analysis of two-locus linkage disequilibrium coefficients , 1985, Theoretical and Applied Genetics.

[114]  Timothy B Sackton,et al.  Mutations in smooth muscle α-actin (ACTA2) lead to thoracic aortic aneurysms and dissections , 2007, Nature Genetics.

[115]  M. Begon,et al.  Ecological differences and coexistence in a guild of microparasites: Bartonella in wild rodents. , 2007, Ecology.

[116]  M. Begon,et al.  Genetic Diversity in Cytokines Associated with Immune Variation and Resistance to Multiple Pathogens in a Natural Rodent Population , 2011, PLoS genetics.

[117]  T. Ottenhoff,et al.  Is there a future for TNF promoter polymorphisms? , 2004, Genes and Immunity.

[118]  S. Piertney,et al.  The evolutionary ecology of the major histocompatibility complex , 2006, Heredity.

[119]  R. Schumann,et al.  Single nucleotide polymorphisms of Toll-like receptors and susceptibility to infectious disease. , 2005, The Lancet. Infectious diseases.