Home LiteratureArticle Details
PMID: 15756546 Published · ppublish English Journal Article

Recombination and the origin of sequence diversity in the DRB MHC class II locus in chamois (Rupicapra spp.).

Immunogenetics ·Vol. 57 ·No. 1-2 ·2005-04-00 ·Pages 108-15

Schaschl H, Suchentrunk F, Hammer S, Goodman SJ

Abstract

We examined the evolutionary processes contributing to genetic diversity at the major histocompatibility complex (MHC) class II DRB locus in chamois (Rupicapra spp., subfamily Caprinae). We characterised the pattern of intragenic recombination (or homologous gene conversion) and quantified the amount of recombination in the genealogical history of the two chamois species, Pyrenean chamois (Rupicapra pyrenaica) and Alpine chamois (Rupicapra rupicapra). We found evidence for intragenic recombination, and the estimated amount of population recombination suggests that recombination has been a significant process in generating DRB allelic diversity in the genealogical history of the genus Rupicapra. Moreover, positive selection appears to act on the same peptide-binding residues in both analysed chamois species, but not in identical intensity. Recombination coupled with positive selection drives the rapid evolution at the peptide-binding sites in the MHC class II DRB gene. Many chamois MHC class II DRB alleles are thus much younger than previously assumed.

MeSH Terms
Alleles Amino Acid Sequence Animals Evolution, Molecular Genes, MHC Class II Genetic Variation Polymorphism, Genetic Recombination, Genetic Rupicapra/genetics Sequence Alignment
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Schaschl Helmut
Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK. [email protected]
Suchentrunk Franz
Hammer Sabine
Goodman Simon J
References (40)
40 references, click to expand
  1. Generation of MHC class II diversity by intra- and intergenic recombination.
    Immunol Rev. 1995 Feb;143:5-12 PMID: 7558082
  2. Codon-substitution models for heterogeneous selection pressure at amino acid sites.
    Genetics. 2000 May;155(1):431-49 PMID: 10790415
  3. Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1.
    Nature. 1993 Jul 1;364(6432):33-9 PMID: 8316295
  4. Quantifying the degree of convergence in primate Mhc-DRB genes.
    Immunol Rev. 1995 Feb;143:123-40 PMID: 7558073
  5. Nomenclature for the major histocompatibility complexes of different species: a proposal.
    Immunogenetics. 1990;31(4):217-9 PMID: 2329006
  6. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.
    Proc Natl Acad Sci U S A. 1990 Mar;87(6):2264-8 PMID: 2315319
  7. Allelic diversity is generated by intraexon sequence exchange at the DRB1 locus of primates.
    Proc Natl Acad Sci U S A. 1991 May 1;88(9):3686-90 PMID: 2023919
  8. Recent origin of HLA-DRB1 alleles and implications for human evolution.
    Nat Genet. 1998 Mar;18(3):237-42 PMID: 9500545
  9. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene.
    Genetics. 1998 Mar;148(3):929-36 PMID: 9539414
  10. The fine-scale structure of recombination rate variation in the human genome.
    Science. 2004 Apr 23;304(5670):581-4 PMID: 15105499
  11. A coalescent-based method for detecting and estimating recombination from gene sequences.
    Genetics. 2002 Mar;160(3):1231-41 PMID: 11901136
  12. Spatial patterns of mitochondrial and nuclear gene pools in chamois (Rupicapra r. rupicapra) from the Eastern Alps.
    Heredity (Edinb). 2003 Aug;91(2):125-35 PMID: 12886279
  13. Mhc-DRB genes evolution in lemurs.
    Immunogenetics. 2002 Sep;54(6):403-17 PMID: 12242591
  14. The nature of selection on the major histocompatibility complex.
    Crit Rev Immunol. 1997;17(2):179-224 PMID: 9094452
  15. Two-locus sampling distributions and their application.
    Genetics. 2001 Dec;159(4):1805-17 PMID: 11779816
  16. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.
    Genetics. 2003 Jul;164(3):1229-36 PMID: 12871927
  17. Low major histocompatibility complex class II diversity in European and North American moose.
    Proc Natl Acad Sci U S A. 1995 May 9;92(10):4259-63 PMID: 7753793
  18. Phylogeography of chamois (Rupicapra spp.) inferred from microsatellites.
    Mol Phylogenet Evol. 2002 Dec;25(3):524-34 PMID: 12450756
  19. Major histocompatibility complex variation in the Arabian oryx.
    Evolution. 2000 Dec;54(6):2145-51 PMID: 11209789
  20. Estimating recombination rates from population genetic data.
    Genetics. 2001 Nov;159(3):1299-318 PMID: 11729171
  21. Linkage disequilibrium and recombination in hominid mitochondrial DNA.
    Science. 1999 Dec 24;286(5449):2524-5 PMID: 10617471
  22. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
    Nucleic Acids Res. 1997 Dec 15;25(24):4876-82 PMID: 9396791
  23. Sarcoptic mange in Spanish ibex from Spain.
    J Wildl Dis. 1999 Oct;35(4):647-59 PMID: 10574523
  24. Is the decline of desert bighorn sheep from infectious disease the result of low MHC variation?
    Heredity (Edinb). 2001 Apr;86(Pt 4):439-50 PMID: 11520344
  25. Sequence analysis of the MHC class II DRB alleles in Alpine chamois (Rupicapra r. rupicapra).
    Dev Comp Immunol. 2004 Mar;28(3):265-77 PMID: 14642892
  26. Class II B Mhc motifs in an evolutionary perspective.
    Immunol Rev. 1995 Feb;143:89-111 PMID: 7558084
  27. Natural selection at major histocompatibility complex loci of vertebrates.
    Annu Rev Genet. 1998;32:415-35 PMID: 9928486
  28. The epizootiology of sarcoptic mange in chamois, Rupicapra rupicapra, from the Italian eastern Alps.
    Parassitologia. 1995 Dec;37(2-3):233-40 PMID: 8778664
  29. IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex.
    Nucleic Acids Res. 2003 Jan 1;31(1):311-4 PMID: 12520010
  30. Evolution of MHC class II E beta diversity within the genus Peromyscus.
    Genetics. 2003 May;164(1):289-97 PMID: 12750340
  31. Statistical tests for detecting gene conversion.
    Mol Biol Evol. 1989 Sep;6(5):526-38 PMID: 2677599
  32. Characterization of Mhc-DRB allelic diversity in white-tailed deer (Odocoileus virginianus) provides insight into Mhc-DRB allelic evolution within Cervidae.
    Immunogenetics. 1999 May;49(5):429-37 PMID: 10199919
  33. PAML: a program package for phylogenetic analysis by maximum likelihood.
    Comput Appl Biosci. 1997 Oct;13(5):555-6 PMID: 9367129
  34. Relative roles of mutation and recombination in generating allelic polymorphism at an MHC class II locus in Peromyscus maniculatus.
    Genet Res. 2003 Oct;82(2):89-99 PMID: 14768893
  35. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
    Mol Biol Evol. 1986 Sep;3(5):418-26 PMID: 3444411
  36. Evaluation of methods for detecting recombination from DNA sequences: empirical data.
    Mol Biol Evol. 2002 May;19(5):708-17 PMID: 11961104
  37. Monomorphism and polymorphism at Mhc DRB loci in domestic and wild ruminants.
    Immunol Rev. 1999 Feb;167:169-78 PMID: 10319259
  38. Single-strand conformational polymorphism and sequence polymorphism of Mhc-DRB in Latxa and Karrantzar sheep: implications for Caprinae phylogeny.
    Immunogenetics. 2000 Sep;51(11):887-97 PMID: 11003382
  39. Selection, convergence, and intragenic recombination in HLA diversity.
    Genetica. 1998;102-103(1-6):157-69 PMID: 9720277
  40. Consequences of recombination on traditional phylogenetic analysis.
    Genetics. 2000 Oct;156(2):879-91 PMID: 11014833
Article Info
Journal
Immunogenetics
Abbr.
Immunogenetics
ISSN
0093-7711
DOI
10.1007/s00251-005-0784-4
Email
[email protected]
Published
2005-04-00
Epub
2005-00-09
Pages
108-15
Language
English
Region
United States
NLM ID
0420404
Subset
IM
External Links
PubMed source DOI: 10.1007/s00251-005-0784-4 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2