Diversity and duplication of DQB and DRB-like genes of the MHC in baleen whales (suborder: Mysticeti)

Immunogenetics

Volumn 58, Issue 4, 2006, Pages 283-296

  Baker, C S ^a   Vant, M D ^a   Dalebout, M L ^a   Lento, G M ^a   O'Brien, S J ^b   Yuhki, N ^b  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Cetaceans; Diversity; Dolphins; Overdominant selection

Indexed keywords

HLA ANTIGEN CLASS 2; HLA DQ ANTIGEN; HLA DR ANTIGEN;

ALLELE; AMINO ACID SEQUENCE; ANIMAL TISSUE; ARTICLE; BALEEN WHALE; BOWHEAD WHALE; CATTLE; CONVERGENT EVOLUTION; DQB LIKE GENE; DRB LIKE GENE; GENE; GENE AMPLIFICATION; GENE CONVERSION; GENE DISRUPTION; GENE DUPLICATION; GENE FUNCTION; GENE LOSS; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC SIMILARITY; GENETIC VARIABILITY; HUMPBACK WHALE; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR CLONING; MYSTICETI; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION RESEARCH; PRIORITY JOURNAL; PROTEIN BINDING; SOUTHERN RIGHT WHALE; SPECIES COMPARISON; SUBORDER; TAXONOMIC RANK; TOOTHED WHALE; WHALE;

AMINO ACID SEQUENCE; ANIMALS; EVOLUTION; GENE DUPLICATION; GENES, MHC CLASS II; HLA-DQ ANTIGENS; HLA-DR ANTIGENS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS); WHALES;

ANIMALIA; BALAENA MYSTICETUS; BALAENIDAE; BOS TAURUS; CETACEA; EUBALAENA AUSTRALIS; MAMMALIA; MEGAPTERA; MEGAPTERA NOVAEANGLIAE; MYSTICETI; ODONTOCETI; ONCORHYNCHUS GORBUSCHA;

EID: 33646384409     PISSN: 00937711     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00251-006-0080-y     Document Type: Article

References (54)

1. Altschul S, Gish W, Miller W, Myers E, Lipman D (1990) Basic local alignment tool. J Mol Biol 215:403-410
2. Ammer H, Schwaiger F, Kammerbauer C, Gomolka M, Arriens A, Lazary S, Epplen J (1992) Exonic polymorphism vs intronic simple repeat hypervariability in MHC-DRB genes. Immunogenetics 35:332-340
3. Andersson L, Mikko S (1995) Generation of MHC class II diversity by intra- and intergenic recombination. Immunol Rev 143:5-12
4. Atha DH, Wenz H-M, Morehead H, Tiang J, O'Connell CD (1998) Detection of p53 point mutations by single strand conformation polymorphism: analysis by capillary electrophoresis. Electrophoresis 19:172-179
5. Baker CS, Clapham P (2004) Modelling the past and future of whales and whaling. Trends Ecol Evol 19:365-371
6. Baker CS, Perry A, Bannister JL, Weinrich MT, Abernethy RB, Calambokidis J, Lien J, Lambertsen RH, Urban-Ramirez J, Vasquez O, Clapham PJ, Alling A, O'Brien SJ, Palumbi SR (1993) Abundant mitochondrial DNA variation and world-wide population structure in humpback whales. Proc Natl Acad Sci U S A 90:8239-8243
7. Baker CS, Slade RW, Bannister JL, Abernethy RB, Weinrich MT, Lien J, Urban-Ramirez J, Corkeron P, Calambokidis J, Vasquez O, Palumbi SR (1994) Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide. Mol Ecol 3:313-327
8. Barnes WM (1992) The fidelity of Taq polymerase catalysing PCR is improved by an N-terminal deletion. Gene 112:29-35
9. Barnes LG, Domming DP, Ray CF (1985) Status of studies on fossil marine mammals. Mar Mamm Sci 1:15-53
10. Beck S, Trowsdale J (1999) Sequence organisation of the class II region of the human MHC. Immunol Rev 167:201-210
11. Bodmer JG, Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Charron D, Dupont B, Erlich HA, Fauchet R, Mach B, Mayr WR, Parham P, Sasazuki T, Schreuder GMT, Strominger JL, Svejgaard A, Terasaki PI (1997) Nomenclature for factors of the HLA system 1996. Hum Immunol 53:98-128
12. Brown J, Jardetzky T, Gorga J, Stern L, Urban R, Strominger J, Wiley D (1993) Three-dimensional structure of the human class II histocompatibility antigen HLA-DR. Nature 364:33-39
13. Cassens I, Vicario S, Waddell VG, Balchowsky H, Van Belle D, Ding W, Fan C, Lal Mohan RS, Simones-Lopes PC, Bastida R, Meyer A, Stanhope MJ, Milinkovitch MC (2000) Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages. Proc Natl Acad Sci U S A 97:11343-11347
14. Dalebout M, Hooker S, Christensen I (2001) Genetic diversity and population structure among northern bottlenose whales. Can J Zool 79:478-484
15. Ellis G (1999) Cattle MHC: evolution in action? Immunol Rev 167:159-168
16. EMBL-EBI (2005) IMGT/HLA Sequence Database. http://www.ebi.ac.uk/imgt/hla/stats.html
17. Flores-Ramirez S, Urban-Ramirez J, Miller RD (2000) Major histocompatibility complex class I loci from the gray whale (Eschrichtius robustus). J Hered 91:279-282
18. Groenen MAM, van der Poel JJ, Dijkhof RJM, Giphart MJ (1990) The nucleotide sequence of bovine MHC class II DQB and DRB gene. Immunogenetics 31:37-44
19. Gyllensten U, Sundvall M, Ezcurra I, Erlich H (1991) Genetic diversity at class II DRB loci of the primate MHC. J Immunol 146:4368-4376
20. Hayashi K, Nishida S, Yoshida H, Goto M, Pastene LA, Koike H (2003) Sequence variation of the DQB allele in the cetacean MHC. Mamm Study 28:89-96
21. Hughes AL, Nei M (1988) Patterns of nucleotide substitution at major histocompatibility complex class I loci reveal overdominant selection. Nature 335:167-170
22. Klein J (1986) The natural history of the major histocompatibility complex. Wiley, New York
23. Kumar S, Tamura K, Jacobsen IB, Nei M (2001) MEGA, molecular evolutionary genetics analysis. Arizona State University, Tempe, AZ, USA
24. Lambertsen RH (1987) A biopsy system for large whales and its use for cytogenetics. J Mammal 68:443-445
25. Lawlor DA, Ward FE, Ennis PD, Jackson AP, Parham P (1988) HLA-A and B polymorphisms predate the divergence of humans and chimpanzees. Nature 335:268-271
26. Lento GM, Baker CS, David V, Yuhki N, Gales NJ, O'Brien SJ (2003) Automated single-strand conformation polymorphism reveals low diversity of a major histocompatibility complex class II gene in the threatened New Zealand sea lion. Mol Ecol Notes 3:346-349
27. Maddison DR, Maddison WP (2000) MacClade: analysis of phylogeny and character evolution. Sinauer, Sunderland, Massachusetts
28. Martin A, Palumbi SR (1993) Body size, metabolic rate, generation time, and the molecular clock. Proc Natl Acad Sci U S A 90:4087-4091
29. McCallum HI, Kuris A, Harvell CD, Lafferty KD, Smith GW, Porter J (2004) Does terrestrial epidemiology apply to marine systems? Trends Ecol Evol 19:585-591
30. Mikko S, Road K, Schmutz S, Andersson L (1999) Monomorphism and polymorphism at the Mhc DRB loci in domestic and wild ruminants. Immunol Rev 167:169-178
31. Muggli-Cockett NE, Stone RT (1989) Partial nucleotide sequence of a bovine major histocompatibility class II DR beta-like gene. Anim Genet 20:361-369
32. Murray BW, White BN (1998) Sequence variation at the major histocompatibility complex DRB loci in beluga (Delphinapterus leucas) and narwhal (Monodon monoceros). Immunogenetics 48:242-252
33. Murray BW, Malik S, White BN (1995) Sequence variation at the major histocompatibility complex locus DQB in beluga whales (Delphinaterus leucas). Mol Biol Evol 12:582-593
34. Nei M (1987) Molecular evolutionary genetics. Columbia Univ. Press, New York
35. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418-426
36. O'Brien SJ, Roelke ME, Marker L, Newman A, Winkler CA, Meltzer D, Cody L, Everman JF, Bush M, Wildt DE (1985) Genetic basis for species vulnerability in the cheetah. Science 227:1428-1434
37. Parham P (1999) Virtual reality in the MHC. Immunol Rev 167:5-15
38. Parham P, Ohta T (1996) Population biology of antigen presentation by MHC class 1 molecules. Science 272:67-74
39. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818
40. Rice DW (1998) Marine mammals of the world: systematics and distribution. Society for Marine Mammalogy, Lawrence, Kansas
41. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
42. Schlotterer C, Amos B, Tautz D (1991) Conservation of polymorphic simple sequence loci in cetacean species. Nature 354:63-65
43. Seddon JM, Ellegren H (2002) MHC class II genes in European wolves: a comparison with dogs. Immunogenetics 54:490-500
44. Shirai K, Sakai T, Oike T (1998) Molecular cloning of bottle-nosed dolphin (Tursiops truncatus) MHC class I cDNA. J Vet Med Sci 60:1093-1096
45. Sigurdardottir S, Borsch C, Gustafsson K, Andersson L (1991) Cloning and sequence analysis of 14 DRB alleles of the bovine major histocompatibility complex by using the polymerase chain reaction. Anim Genet 22:199-209
46. Slade RW, McCallum HI (1992) Overdominant vs. frequency-dependent selection at MHC loci. Genetics 132:861-862
47. Swofford DL (2000) PAUP*: Phylogenetic analysis using parsimony (*and other methods). Sinauer, Sunderland, MA
48. Takahashi K, Rooney A, Nei M (2000) Origins and divergence times of mammalian class II MHC gene clusters. J Hered 91:198-204
49. Tindall (1988) Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry 27:6008-6013
50. Trowsdale J, Groves V, Arnason A (1989) Limited MHC polymorphism in whales. Immunogenetics 29:19-24
51. Yang G, Yan J, Zhou K, Wei F (2005) Sequence variation and gene duplication at the MHC DQB Loci of baiji (Lipotes vexillifer), a Chinese river dolphin. J Hered 96:310-317
52. Yeager M, Hughes AL (1999) Evolution of the mammalian MHC: natural selection, recombination, and convergent evolution. Immunol Rev 167:45-58
53. Yuhki N, O'Brien SJ (1990) DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history. Proc Natl Acad Sci U S A 87:836-840
54. Yuhki N, O'Brien SJ (1997) Nature and origin of polymorphism in feline MHC class II DRA and DRB genes. J Immunol 158:2822-2833