A human-specific allelic group of the MHC DRB1 gene in primates

Journal of Physiological Anthropology

Volumn 33, Issue 1, 2014, Pages

  Yasukochi, Yoshiki ^a   Satta, Yoko ^b  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

Allelic lineage; Balancing selection; HLA; Out of Africa; Pathogen; Trans species polymorphism

Indexed keywords

HLA ANTIGEN CLASS 2; HLA DRB1 ANTIGEN;

ANIMAL; ARTICLE; CLASSIFICATION; GENETIC SELECTION; GENETICS; HUMAN; MOLECULAR EVOLUTION; PAN TROGLODYTES; PHYLOGENY; SPECIES DIFFERENCE;

ANIMALS; EVOLUTION, MOLECULAR; HISTOCOMPATIBILITY ANTIGENS CLASS II; HLA-DRB1 CHAINS; HUMANS; PAN TROGLODYTES; PHYLOGENY; SELECTION, GENETIC; SPECIES SPECIFICITY;

EID: 84902068950     PISSN: 18806791     EISSN: 18806805     Source Type: Journal    
DOI: 10.1186/1880-6805-33-14     Document Type: Article

References (46)

1. Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, Mcdonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper R, Kwiatkowski D, Ward R, Lander ES: Detecting recent positive selection in the human genome from haplotype structure. Nature 2002, 419:832-837.
2. Hill AV: The immunogenetics of human infectious diseases. Annu Rev Immunol 1998, 16:593-617.
3. The MHC sequencing consortium: Complete sequence and gene map of a human major histocompatibility complex. Nature 1999, 401:921-923.
4. Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, Wiley DC: The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens. Nature 1987, 329:512-518.
5. Brown JH, Jardetzky TS, Gorga JC, Stern LJ, Urban RG, Strominger JL, Wiley DC: Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 1993, 364:33-39.
6. Hughes AL, Nei M: Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc Natl Acad Sci U S A 1989, 86:958-962.
7. Hughes AL, Nei M: Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 1988, 335:167-170.
8. Takahata N, Satta Y, Klein J: Polymorphism and balancing selection at major histocompatibility complex loci. Genetics 1992, 130:925-938.
9. Satta Y, O'hUigin C, Takahata N, Klein J: Intensity of natural selection at the major histocompatibility complex loci. Proc Natl Acad Sci U S A 1994, 91:7184-7188.
10. Klein J, Sato A, Nikolaidis N: MHC, TSP, and the origin of species: from immunogenetics to evolutionary genetics. Annu Rev Genet 2007, 41:281-304.
11. Takahata N, Nei M: Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics 1990, 124:967-978.
12. Satta Y, O'hUigin C, Takahata N, Klein J: The synonymous substitution rate of the major histocompatibility complex loci in primates. Proc Natl Acad Sci U S A 1993, 90:7480-7484.
13. Muchmore EA: Chimpanzee models for human disease and immunobiology. Immunol Rev 2001, 183:86-93.
14. Kenter M, Otting N, Anholts J, Jonker M, Schipper R, Bontrop RE: Mhc-DRB diversity of the chimpanzee (Pan troglodytes). Immunogenetics 1992, 37:1-11.
15. Mayer WE, O'hUigin C, Zaleska-Rutczynska Z, Klein J: Trans-species origin of Mhc-DRB polymorphism in the chimpanzee. Immunogenetics 1992, 37:12-23.
16. Bontrop RE, Otting N, de Groot NG, Doxiadis GGM: Major histocompatibility complex class II polymorphisms in primates. Immunol Rev 1999, 167:339-350.
17. Yasukochi Y, Satta Y: Current perspectives on the intensity of natural selection of MHC loci. Immunogenetics 2013, 65:479-483.
18. Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh SGE: The IMGT/HLA database. Nucleic Acids Res 2011, 39:D1171-D1176.
19. Robinson J, Waller MJ, Stoehr P, Marsh SGE: IPD-the immuno polymorphism database. Nucleic Acids Res 2005, 33:D523-D526.
20. Satta Y: Balancing selection at HLA loci. In Proceedings of the 17th Taniguchi Symposium. Edited by Takahata N. Tokyo: Japan Science Society Press; 1992:111-131.
21. Kusaba M, Nishio T, Satta Y, Hinata K, Ockendon D: Striking sequence similarity in inter-and intra-specific comparisons of class I SLG alleles from Brassica oleracea and Brassica campestris: implications for the evolution and recognition mechanism. Proc Natl Acad Sci U S A 1997, 94:7673-7678.
22. Yasukochi Y, Kurosaki T, YonedaM, Koike H, Satta Y: MHC class II DQB diversity in the Japanese black bear: Ursus thibetanus japonicus. BMC Evol Biol 2012, 12:230.
23. Stern LJ, Brown JH, Jardetzky TS, Gorga JC, Urban RG, Strominger JL, Wiley DC: Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature 1994, 368:215-221.
24. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739.
25. Hasegawa M, Kishino H, Yano T: Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985, 22:160-174.
26. Zhang J, Rosenberg HF, Nei M: Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci U S A 1998, 95:3708-3713.
27. Jukes T, Cantor C: Evolution of protein molecules. In Mammalian Protein Metabolism. Edited by Munro H. New York: Academic; 1969:21-132.
28. Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B: The immune epitope database 2.0. Nucleic Acids Res 2010, 38:D854-D862.
29. Meyer D, Single R, Mack S, Lancaster A, Nelson M, Erlich H, Fernandez-Vina M, Thomson G: Single locus polymorphism of classical HLA genes. In Immunobiolology of the Human MHC: Proceedings of the 13th International Histocompatibility Workshop and Conference, Volume I. Edited by Hansen JA. Seattle, WA: IHWG Press; 2007:653-704.
30. Klein J: Origin of major histocompatibility complex polymorphism: the trans-species hypothesis. Hum Immunol 1987, 19:155-162.
31. Klein J, Sato A, Nagl S, O'hUigin C: Molecular trans-species polymorphism. Annu Rev Ecol Syst 1998, 29:1-21.
32. Satta Y, Hickerson M, Watanabe H, O'hUigin C, Klein J: Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and BAC end sequences. J Mol Evol 2004, 59:478-487.
33. Steiper ME, Young NM: Primate molecular divergence dates. Mol Phylogenet Evol 2006, 41:384-394.
34. Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, et al: Insights into hominid evolution from the gorilla genome sequence. Nature 2012, 483:169-175.
35. Takahata N: Evolutionary genetics of human paleo-populations. In Mechanisms of molecular evolution. Edited by Takahata N, Clark A. Sunderland, Massachusetts: Sinauer Associates; 1993:1-21.
36. Takahata N, Satta Y, Klein J: Divergence time and population size in the lineage leading to modern humans. Theor Popul Biol 1995, 48:198-221.
37. Satta Y: Comparison of DNA and protein polymorphisms between humans and chimpanzees. Genes Genet Syst 2001, 76:159-168.
38. Kim HL, Igawa T, Kawashima A, Satta Y, Takahata N: Divergence, demography and gene loss along the human lineage. Philos Trans R Soc Lond B Biol Sci 2010, 365:2451-2457.
39. Riley-Vargas RC, Gill DB, Kemper C, Liszewski MK, Atkinson JP: CD46: expanding beyond complement regulation. Trends Immunol 2004, 25:496-503.
40. Guiso N: Bordetella pertussis and pertussis vaccines. Clin Infect Dis 2009, 49:1565-1569.
41. Osterhaus A, Rimmelzwaan G, Martina B, Bestebroer T, Fouchier R: Influenza B virus in seals. Science 2000, 288:1051-1053.
42. De Groot NG, Otting N, Doxiadis GGM, Balla-Jhagjhoorsingh SS, Heeney JL, van Rood JJ, Gagneux P, Bontrop RE: Evidence for an ancient selective sweep in the MHC class I gene repertoire of chimpanzees. Proc Natl Acad Sci U S A 2002, 99:11748-11753.
43. Gyllensten UB, Sundvall M, Erlich HA: Allelic diversity is generated by intraexon sequence exchange at the DRB1 locus of primates. Proc Natl Acad Sci U S A 1991, 88:3686-3690.
44. Bak EJ, Ishii Y, Omatsu T, Kyuwa S, Tetsuya T, Hayasaka I, Yoshikawa Y: Identification and analysis of MHC class II DRB1 (Patr-DRB1) alleles in chimpanzees. Tissue Antigens 2006, 67:134-142.
45. De Zorzi M, Caggiari L, Ahlenstiel G, Rehermann B, De Re V: Description of two new major histocompatibility complex (MHC) class II DRB1 [Pan troglodytes (Patr)-DRB1] alleles. Tissue Antigens 2008, 71:490-492.
46. Wilson D, Reeder D: Mammal Species of the World: A Taxonomic and Geographic Reference. 3rd edition. Baltimore: Johns Hopkins University Press; 2005.