Erratum: Contrasting evolution of diversity at two disease-associated chicken genes (Immunogenetics DOI: 10.1007/s00251-009-0359-x);Contrasting evolution of diversity at two disease-associated chicken genes

Immunogenetics

Volumn 61, Issue 4, 2009, Pages 303-314

  Downing, Tim ^a   Lynn, David J ^b   Connell, Sarah ^a   Lloyd, Andrew T ^a   Bhuiyan, Ak Fazlul Haque ^c   Silva, Pradeepa ^d   Naqvi, Arifa N ^e   Sanfo, Rahamame ^f   Sow, Racine Samba ^g   Podisi, Baitsi ^h   O'Farrelly, Cliona ^a   Hanotte, Olivier ⁱ   Bradley, Daniel G ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

^b SIMON FRASER UNIVERSITY   (Canada)

^c BANGLADESH AGRICULTURAL UNIVERSITY   (Bangladesh)

^d UNIVERSITY OF PERADENIYA   (Sri Lanka)

^e PAKISTAN AGRICULTURAL RESEARCH COUNCIL   (Pakistan)

^f INSTITUT DE L ENVIRONNEMENT ET DE RECHERCHES AGRICOLES INERA   (Burkina Faso)

^g Institut Senegalais de Recherches AgrEcoles Dakar   (Senegal)

^h Department of Agricultural Research ^*  (Botswana)

ⁱ INTERNATIONAL LIVESTOCK RESEARCH INSTITUTE   (Kenya)

Author keywords

Chicken; Interferon gamma; Interleukin 1 beta; Population genetics; Selection

Indexed keywords

GAMMA INTERFERON; INTERLEUKIN 1BETA;

ALLELE; ARTICLE; AVIAN GENETICS; BANGLADESH; BOTSWANA; BURKINA FASO; CHICKEN; CONTROLLED STUDY; DISEASE ASSOCIATION; FOWL; GENE FREQUENCY; GENE FUNCTION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; HAPLOTYPE; IMMUNE RESPONSE; KENYA; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PAKISTAN; PHYLOGENY; PRIORITY JOURNAL; SENEGAL; SRI LANKA; ANIMAL; GENETIC SELECTION; GENETICS; IMMUNOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CHICKENS; GENETIC VARIATION; INTERFERON-GAMMA; INTERLEUKIN-1BETA; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION (GENETICS);

EID: 64149123814     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-009-0367-x     Document Type: Erratum

References (82)

1. JM Akey MA Eberle MJ Rieder CS Carlson MD Shriver DA Nickerson L Kruglyak 2004 Population history and natural selection shape patterns of genetic variation in 132 genes PLoS Biol 2 10 e286
2. M Anisimova JP Bielawski Z Yang 2001 Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution Mol Biol Evol 18 1585 1592
3. DH Ardell 2004 SCANMS: adjusting for multiple comparisons in sliding window neutrality tests Bioinformatics 20 12 1986 1988
4. D Balkissoon K Staines J McCauley J Wood J Young J Kaufman C Butter 2007 Low frequency of the Mx allele for viral resistance predates recent intensive selection in domestic chickens Immunogenetics 59 8 687 691
5. S Berlin L Qu X Li N Yang H Ellegren 2008 Positive diversifying selection in avian Mx genes Immunogenetics 60 11 689 697
6. E Betrán J Rozas A Navarro A Barbadilla 1997 The estimation of the number and the length distribution of gene conversion tracts from population DNA sequence data Genetics 146 1 89 99
7. J Bratt J Palmblad 1997 Cytokine-induced neutrophil-mediated injury of human endothelial cells J Immunol 159 2 912 918
8. D De Nardo P Masendycz S Ho M Cross AJ Fleetwood EC Reynolds JA Hamilton GM Scholz 2005 A central role for the Hsp90.Cdc37 molecular chaperone module in interleukin-1 receptor-associated-kinase-dependent signaling by Toll-like receptors J Biol Chem 280 11 9813 9822
9. F Depaulis M Veuille 1998 Neutrality tests based on the distribution of haplotypes under an infinite-site model Mol Biol Evol 15 12 1788 1790
10. L Duret PF Arndt 2008 The impact of recombination on nucleotide substitutions in the human genome PLoS Genet 4 5 e1000071
11. H Ellegren 2005 The avian genome uncovered Trends Ecol Evol 20 4 180 186
12. J Eriksson G Larson U Gunnarsson B Bed'hom M Tixier-Boichard L Strömstedt D Wright A Jungerius A Vereijken E Randi P Jensen L Andersson 2008 Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken PLoS Genet 4 2 e1000010
13. B Ewing P Green 1998 Base-calling of automated sequencer traces using phred II. Error probabilities Genome Res 8 3 186 194
14. B Ewing L Hillier MC Wendl P Green 1998 Base-calling of automated sequencer traces using phred. I. Accuracy assessment Genome Res 8 3 175 185
15. L Excoffier PE Smouse JM Quattro 1992 Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data Genetics 131 2 479 491
16. JC Fay CI Wu 2000 Hitchhiking under positive Darwinian selection Genetics 155 3 1405 1413
17. C Ferrer-Costa J Gelpi L Zamakola I Parraga X de la Cruz M Orozco 2005 PMUT: a web-based tool for the annotation of pathological mutations on proteins Bioinformatics 21 3176 3178
18. YX Fu 1997 Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection Genetics 147 2 915 925
19. YX Fu WH Li 1993 Statistical tests of neutrality of mutations Genetics 133 3 693 709
20. A Fumihito T Miyake S Sumi M Takada S Ohno N Kondo 1996 One subspecies of the red junglefowl (Gallus gallus gallus) suffices as the matriarchic ancestor of all domestic breeds Proc Natl Acad Sci USA 91 26 12505 12509
21. A Fumihito T Miyake M Takada R Shingu T Endo T Gojobori N Kondo S Ohno 1994 Monophyletic origin and unique dispersal patterns of domestic fowls Proc Natl Acad Sci USA 93 13 6792 67925
22. JF Goetschy H Zeller J Content MA Horisberger 1989 Regulation of the interferon-inducible IFI-78K gene, the human equivalent of the murine Mx gene, by interferons, double-stranded RNA, certain cytokines, and viruses J Virol 63 6 2616 2622
23. D Gordon C Abajian P Green 1998 Consed: a graphical tool for sequence finishing Genome Res 8 3 195 202
24. Z Gyorfy A Ohnemus B Kaspers E Duda P Staeheli 2003 Truncated chicken interleukin-1beta with increased biologic activity J Interferon Cytokine Res 23 5 223 228
25. ZC Hou GY Xu Z Su N Yang 2007 Purifying selection and positive selection on the myxovirus resistance gene in mammals and chickens Gene 396 1 188 195
26. RR Hudson 1987 Estimating the recombination parameter of a finite population model without selection Genet Res 50 3 245 250
27. RR Hudson 2001 Two-locus sampling distributions and their application Genetics 159 4 1805 1817
28. RR Hudson 2002 Generating samples under a Wright-Fisher neutral model of genetic variation Bioinformatics 18 2 337 338
29. RR Hudson NL Kaplan 1985 Statistical properties of the number of recombination events in the history of a sample of DNA sequences Genetics 111 1 147 164
30. AL Hughes B Packer R Welch SJ Chanock M Yeager 2005 High level of functional polymorphism indicates a unique role of natural selection at human immune system loci Immunogenetics 57 11 821 827
31. International Chicken Genome Sequencing Consortium 2004 Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution Nature 432 695 716
32. International Chicken Polymorphism Map Consortium 2004 A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms Nature 432 717 722
33. V Janardhana ME Ford MP Bruce MM Broadway TE O'Neil AJ Karpala M Asif GF Browning KA Tivendale AH Noormohammadi JW Lowenthal AG Bean 2007 IFN-gamma enhances immune responses to E. coli infection in the chicken J Interferon Cytokine Res 27 11 937 946
34. JD Jensen A Wong CF Aquadro 2007 Approaches for identifying targets of positive selection Trends Genet 23 11 568 577
35. PL Johnson M Slatkin 2005 Inference of population genetic parameters in metagenomics: a clean look at messy data Genome Res 16 10 1320 1327
36. P Kaiser 2007 The avian immune genome-a glass half-full or half-empty? Cytogenet Genome Res 117 221 230
37. P Kaiser L Rothwell M Goodchild N Bumstead 2004 The chicken proinflammatory cytokines interleukin-1beta and interleukin-6: differences in gene structure and genetic location compared with their mammalian orthologues Anim Genet 35 3 169 175
38. VB Kaiser M van Tuinen H Ellegren 2007 Insertion events of CR1 retrotransposable elements elucidate the phylogenetic branching order in galliform birds Mol Biol Evol 24 1 338 347
39. S Kanginakudru M Metta RD Jakati J Nagaraju 2008 Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken BMC Evol Biol 8 174
40. JK Kelly 1997 A test of neutrality based on interlocus associations Genetics 146 3 1197 1206
41. H Kim CJ Schmidt KS Decker MG Emara 2003 A double-screening method to identify reliable candidate non-synonymous SNPs from chicken EST data Anim Genet 34 4 249 254
42. MH Kogut L Rothwell P Kaiser 2005 IFN-gamma priming of chicken heterophils upregulates the expression of proinflammatory and Th1 cytokine mRNA following receptor-mediated phagocytosis of Salmonella enterica serovar enteritidis J Interferon Cytokine Res 25 2 73 81
43. MH Kogut H He P Kaiser 2005 Lipopolysaccharide binding protein/CD14/ TLR4-dependent recognition of salmonella LPS induces the functional activation of chicken heterophils and up-regulation of pro-inflammatory cytokine and chemokine gene expression in these cells Anim Biotechnol 16 2 165 181
44. MH Kogut C Swaggerty H He I Pevzner P Kaiser 2006 Toll-like receptor agonists stimulate differential functional activation and cytokine and chemokine gene expression in heterophils isolated from chickens with differential innate responses Microbes Infect 8 7 1866 1874
45. BT Lee TW Tan S Ranganathan 2003 MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences Nucleic Acids Res 31 13 3533 3536
46. XY Li LJ Qu JF Yao N Yang 2006 Skewed allele frequencies of an Mx gene mutation with potential resistance to avian influenza virus in different chicken populations Poult Sci 85 7 1327 1329
47. YP Liu GS Wu YG Yao YW Miao G Luikart M Baig A Beja-Pereira ZL Ding MG Palanichamy YP Zhang 2006 Multiple maternal origins of chickens: out of the Asian jungles Mol Phylogenet Evol 38 1 12 19
48. JE Long LN Huang ZQ Qin WY Wang D Qu 2004 IFN-gamma increases efficiency of DNA vaccine in protecting ducks against infection World J Gastroenterol 11 32 4967 4973
49. LA Madge JS Pober 2000 A phosphatidylinositol 3-kinase/Akt pathway, activated by tumor necrosis factor or interleukin-1, inhibits apoptosis but does not activate NFkappaB in human endothelial cells J Biol Chem 275 20 15458 15465
50. G McVean P Awadalla P Fearnhead 2002 A coalescent-based method for detecting and estimating recombination from gene sequences Genetics 160 3 1231 1241
51. PC Ng S Henikoff 2003 SIFT: Predicting amino acid changes that affect protein function Nucleic Acids Res 31 13 3812 3814
52. DA Nickerson VO Tobe SL Taylor 1997 PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing Nucleic Acids Res 25 14 2745 2751
53. R Nielsen Z Yang 1998 Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene Genetics 148 929 936
54. M Nishibori T Shimogiri T Hayashi H Yasue 2005 Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius Anim Genet 36 5 367 375
55. C Notredame DG Higgins J Heringa 2000 T-Coffee: a novel method for fast and accurate multiple sequence alignment J Mol Biol 302 1 205 217
56. M Okamura HS Lillehoj RB Raybourne US Babu RA Heckert 2004 Cell-mediated immune responses to a killed Salmonella enteritidis vaccine: lymphocyte proliferation, T-cell changes and interleukin-6 (IL-6), IL-1, IL-2, and IFN-gamma production Comp Immunol Microbiol Infect Dis 27 4 255 272
57. H Quesada UE Ramirez J Rozas M Aguade 2006 Large-scale adaptive hitchhiking upon high recombination in Drosophila simulans Genetics 165 2 895 900
58. V Ramensky P Bork S Sunyaev 2002 Human non-synonymous SNPs: server and survey Nucleic Acids Res 30 17 3894 900
59. J Ronald JM Akey 2005 Genome-wide scans for loci under selection in humans Hum Genomics 2 2 113 125
60. J Rozas R Rozas 1999 DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis Bioinformatics 15 2 174 175
61. J Rozas JC Sanchez-DelBarrio X Messeguer R Rozas 2003 DnaSP, DNA polymorphism analyses by the coalescent and other methods Bioinformatics 19 18 2496 2497
62. JR Sadeyen J Trotereau P Velge J Marly C Beaumont PA Barrow N Bumstead AC Lalmanach 2004 Salmonella carrier state in chicken: comparison of expression of immune response genes between susceptible and resistant animals Microbes Infect 6 14 1278 1286
63. Schneider S, Roessli D, Excoffier L (2000) Arlequin: a software for population genetics data analysis, ver 2.000. Genetics and Biometry Lab, Department of Anthropology, University of Geneva
64. JR Schoenborn CB Wilson 2007 Regulation of interferon-gamma during innate and adaptive immune responses Adv Immunol 96 41 101
65. SF Schaffner C Foo S Gabriel D Reich MJ Daly D Altshuler 2005 Calibrating a coalescent simulation of human genome sequence variation Genome Res 15 11 1576 1583
66. A Simon J Fäh O Haller P Staeheli 1991 Interferon-regulated Mx genes are not responsive to interleukin-1, tumor necrosis factor, and other cytokines J Virol 65 2 968 971
67. CK Smith P Kaiser L Rothwell T Humphrey PA Barrow MA Jones 2004 Campylobacter jejuni-induced cytokine responses in avian cells Infect Immun 73 4 2094 2100
68. BL Spangelo DD Farrimond M Pompilius KL Bowman 2000 Interleukin-1 beta and thymic peptide regulation of pituitary and glial cell cytokine expression and cellular proliferation Ann N Y Acad Sci 917 597 607
69. M Stephens JS Sloan PD Robertson P Scheet DA Nickerson 2006 Automating sequence-based detection and genotyping of SNPs from diploid samples Nat Genet. 38 3 375 381
70. M Stephens N Smith P Donnelly 2001 A new statistical method for haplotype reconstruction from population data Am J Hum Genet 68 978 989
71. F Tajima 1983 Evolutionary relationship of DNA sequences in finite populations Genetics 105 2 437 460
72. F Tajima 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism Genetics 123 3 585 595
73. K Tamura J Dudley M Nei S Kumar 2007 MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0 Mol Biol Evol 24 8 1596 1599
74. GA Watterson 1975 On the number of segregation sites Theor Popul Biol 7 256 276
75. KC Weining C Sick B Kaspers P Staeheli 1998 A chicken homolog of mammalian interleukin-1 beta: cDNA cloning and purification of active recombinant protein Eur J Biochem 258 3 994 1000
76. B West BX Zhou 1989 Did chickens go north? New evidence for domestication World's Poult Sci J 45 3 205 218
77. K Worley M Gillingham P Jensen LJ Kennedy T Pizzari J Kaufman DS Richardson 2008 Single locus typing of MHC class I and class II B loci in a population of red jungle fowl Immunogenetics 60 5 233 247
78. Z Yang 1997 PAML: a program package for phylogenetic analysis by maximum likelihood Comput Appl Biosci 13 555 556
79. Z Yang 2002 Inference of selection from multiple species alignments Curr Opin Genet Dev 12 688 694
80. Z Yang Z Lu A Wang 2001 Study of adaptive mutations in Salmonella typhimurium by using a super-repressing mutant of a trans regulatory gene purR Mutat Res 484 1-2 95 102
81. X Ye S Avendano JC Dekkers SJ Lamont 2006 Association of twelve immune-related genes with performance of three broiler lines in two different hygiene environments Poult Sci 85 9 1555 1569
82. H Zhou AJ Buitenhuis S Weigend SJ Lamont 2001 Candidate gene promoter polymorphisms and antibody response kinetics in chickens: interferon-gamma, interleukin-2, and immunoglobulin light chain Poult Sci 80 12 1679 1689