, Volume 62, Issue 10, pp 667–679 | Cite as

MHC class I and MHC class II DRB gene variability in wild and captive Bengal tigers (Panthera tigris tigris)

  • Ina Pokorny
  • Reeta Sharma
  • Surendra Prakash Goyal
  • Sudanshu Mishra
  • Ralph Tiedemann
Original Paper


Bengal tigers are highly endangered and knowledge on adaptive genetic variation can be essential for efficient conservation and management. Here we present the first assessment of allelic variation in major histocompatibility complex (MHC) class I and MHC class II DRB genes for wild and captive tigers from India. We amplified, cloned, and sequenced alpha-1 and alpha-2 domain of MHC class I and beta-1 domain of MHC class II DRB genes in 16 tiger specimens of different geographic origin. We detected high variability in peptide-binding sites, presumably resulting from positive selection. Tigers exhibit a low number of MHC DRB alleles, similar to other endangered big cats. Our initial assessment—admittedly with limited geographic coverage and sample size—did not reveal significant differences between captive and wild tigers with regard to MHC variability. In addition, we successfully amplified MHC DRB alleles from scat samples. Our characterization of tiger MHC alleles forms a basis for further in-depth analyses of MHC variability in this illustrative threatened mammal.


Adaptive variability Balancing selection Bengal tiger Conservation genetics MHC 



We thank Carolin Doering, Madlen Stange, and Fanny Wegner for laboratory help. Financial support is acknowledged from the University of Potsdam. We would like to express sincere thanks to Shri P.R. Sinha, Director and Dr. V.B. Mathur, Dean of the Wildlife Institute of India for providing all required support for the work on tiger genetics. We thank two anonymous reviewers for helpful comments on the manuscript.


  1. Amadou C (1999) Evolution of the MHC class I region: the framework hypothesis. Immunogenetics 49:362–367CrossRefPubMedGoogle Scholar
  2. Apanius V, Penn D, Slev PR, Ruff LR, Potts WK (1997) The nature of selection on major histocompatibility complex. Crit Rev Immunol 17:179–224PubMedGoogle Scholar
  3. Beck TW, Menninger J, Voigt G, Newmann K, Nishigaki Y, Nash WG, Stephens RM, Wang Y, de Jong P, O’Brien SJ, Yuhki N (2001) Comparative feline genomics: a BAC/PAC contig map of the major histocompatibility class II region. Genomics 71:282–295CrossRefPubMedGoogle Scholar
  4. Beck TW, Menninger J, Murphy WJ, Nash WG, O’Brien SJ, Yuhki N (2005) The feline major histocompatibility complex is rearranged by an inversion with a breakpoint in the distal class I region. Immunogenetics 56:702–709CrossRefPubMedGoogle Scholar
  5. Bernatchez L, Landry C (2003) MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years? J Evol Biol 16:363–377CrossRefPubMedGoogle Scholar
  6. Bjorkman PM, Parham P (1990) Structure, function, and diversity of class I major histocompatibility complex molecules. Annu Rev Biochem 59:253–288CrossRefPubMedGoogle Scholar
  7. Brown JH, Jardetzky TS, Gorga JC, Stern LJ, Urban RG, Strominger JL, Wiley DC (1993) Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 364:33–39CrossRefPubMedGoogle Scholar
  8. Casola C, Hahn MW (2009) Gene conversion among paralogs results in moderate false detection of positive selection using likelihood methods. J Mol Evol 68:679–687CrossRefPubMedGoogle Scholar
  9. Drake GJC, Kennedy LJ, Auty HK, Ryvar R, Ollier WER, Kitchener AC, Freeman AR, Radford AD (2004) The use of reference strand-mediated conformational analysis for the study of cheetah (Acinonyx jubatus) feline leucocyte antigen class II DRB polymorphisms. Mol Ecol 13:221–229CrossRefPubMedGoogle Scholar
  10. Graumann MB, DeRose SA, Ostrander EA, Storb R (1998) Polymorphism analysis of four canine MHC class I genes. Tissue Antigens 51:374–381CrossRefPubMedGoogle Scholar
  11. Hall TA (1999) BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98Google Scholar
  12. Hedrick PW (1994) Evolutionary genetics of the major histocompatibility complex. Am Nat 143:945–964CrossRefGoogle Scholar
  13. Hedrick PW (2002) Pathogen resistance and genetic variation at MHC loci. Evolution 56:1902–1908PubMedGoogle Scholar
  14. Hendrickson SL, Mayer GC, Wallen EP, Quigley K (2000) Genetic variability and geographic structure of three subspecies of tigers (Panthera tigris) based on MHC class I variation. Anim Conserv 3:135–143CrossRefGoogle Scholar
  15. Herrington S (1987) Subspecies and the conservation of Panthera tigris. In: Tilson RL, Seal US (eds) Tigers of the world: the biology, biopolitics, management and conservation of an endangered species. Noyes, Park Ridge, pp 51–60Google Scholar
  16. Hughes AL, Hughes MK (1995) Natural selection on the peptide-binding regions of major histocompatibility complex molecules. Immunogenetics 42:233–243CrossRefPubMedGoogle Scholar
  17. Hughes AL, Nei M (1989a) Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc Nat Acad Sci USA 86:958–962CrossRefPubMedGoogle Scholar
  18. Hughes AL, Nei M (1989b) Evolution of the major histocompatibility complex: independent origin of nonclassical class I genes in different groups of mammals. Mol Biol Evol 6:559–579PubMedGoogle Scholar
  19. Huson DH (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14:68–73CrossRefPubMedGoogle Scholar
  20. Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267, CrossRefPubMedGoogle Scholar
  21. Jackson P (1997) The status of the tiger in 1997 and threats in the future. Cat News 27:8–10Google Scholar
  22. Jhala YV, Gopal R, Qureshi Q (2008) Status of the tigers, co-predators, and prey in India. National Tiger Conservation Authority, Government of India, New Dehli, Wildlife Institute of India Dehradun, TR 08/001, 151Google Scholar
  23. Judo MSB, Wedel AB, Wilson C (1998) Stimulation and suppression of PCR-mediated recombination. Nucleic Acids Res 26:1819–1825CrossRefPubMedGoogle Scholar
  24. Kaufman J, Salomonsen J, Flajnik M (1994) Evolutionary conservation of MHC class I and class II molecules—different yet the same. Semin Immunol 6:411–424CrossRefPubMedGoogle Scholar
  25. Kennedy LJ, Ryvar R, Gaskell RM, Addie DD, Willoughby K, Carter SD, Thomson W, Ollier WER, Radford AD (2002) Sequence analysis of MHC DRB alleles in domestic cats from the United Kingdom. Immunogenetics 54:348–352CrossRefPubMedGoogle Scholar
  26. Kennedy LJ, Ryvar R, Brown JJ, Ollier WER, Radford AD (2003) Resolution of complex feline leukocyte antigen DRB loci by reference strand-mediated conformational analysis (RSCA). Tissue Antigens 62:313–323CrossRefPubMedGoogle Scholar
  27. Klein J (1986) Natural history of the major histocompatibility complex. Wiley, New YorkGoogle Scholar
  28. Klein J (1997) Immunology. Blackwell Science, OxfordGoogle Scholar
  29. Klein J, Bontrop RE, Dawkins RL et al (1990) Nomenclature for the major histocompatibility complex in different species: a proposal. Immunogenetics 31:217–219PubMedGoogle Scholar
  30. Knapp LA (2005) Facts, faeces and setting the standards for the study of MHC genes using noninvasive samples. Mol Ecol 14:1597–1599CrossRefPubMedGoogle Scholar
  31. Korber B (2000) HIV Signature and sequence variation analysis. In: Rodrigo AG, Learn GH (eds) Computational analysis of HIV molecular sequences, chapter 4. Kluwer Academic, The Netherlands, pp 55–72Google Scholar
  32. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163CrossRefPubMedGoogle Scholar
  33. Kuwahara Y, Kitoh K, Kobayashi R, Iwata J, Ohne R, Hosokawa-Kanai T, Matsumoto Y, Kitagawa H, Sasaki Y (2000) Genotyping of feline MHC (FLA) class II DRB by PCR-RFLP method using group-specific primers. J Vet Med Sci 62:1283–1289CrossRefPubMedGoogle Scholar
  34. Lenz TL, Becker S (2008) Simple approach to reduce PCR artifact formation leads to reliable genotyping of MHC and other highly polymorphic loci—implications for evolutionary analysis. Gene 427:117–123CrossRefPubMedGoogle Scholar
  35. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452CrossRefPubMedGoogle Scholar
  36. Lukas D, Vigilant L (2005) Reply: facts, faeces and setting the standards for the study of MHC genes using noninvasive samples. Mol Ecol 14:1601–1602CrossRefGoogle Scholar
  37. Lukas D, Bradley BJ, Nsubuga AM, Doran-Sheehy D, Robbins MM, Vigilant L (2004) Major histocompatibility complex and microsatellite variation in two populations of wild gorillas. Mol Ecol 13:3389–3402CrossRefPubMedGoogle Scholar
  38. Luo SJ, Kim JH, Johnson WE et al (2004) Phylogeography and genetic ancestry of tigers (Panthera tigris). PLoS Biol 2:2275–2293Google Scholar
  39. Mazak V (1981) Panthera tigris. Mamm Species 152:1–8CrossRefGoogle Scholar
  40. Meyers LA, Bull JJ (2002) Fighting change with change: adaptive variation in an uncertain world. Trends Ecol Evol 17:551–557CrossRefGoogle Scholar
  41. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New YorkGoogle Scholar
  42. Nielson R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929–936Google Scholar
  43. O’Brien SJ, Yuhki N (1999) Comparative genome organization of the major histocompatibility complex: lessons from the Felidae. Immunol Rev 167:133–144CrossRefPubMedGoogle Scholar
  44. O’Brien SJ, Wildt DE, Goldman D, Merril CR, Bush M (1983) The cheetah is depauperate in genetic variation. Science 221:459–462CrossRefPubMedGoogle Scholar
  45. Ouborg NJ, Pertoldi C, Loeschcke V, Bijlsma R, Hedrick PW (2010) Conservation genetics in transition to conservation genomics. Trends Genet 26:177–187CrossRefPubMedGoogle Scholar
  46. Pääbo S, Irwin DM, Wilson AC (1990) DNA damage promotes jumping between templates during enzymatic amplification. J Biol Chem 265:4718–47121PubMedGoogle Scholar
  47. Piertney SB, Oliver MK (2006) The evolutionary ecology of the major histocompatibility complex. Heredity 96:7–21PubMedGoogle Scholar
  48. Sachdev M, Sankaranarayanan R, Reddanna P, Thangaraj K, Singh L (2005) Major histocompatibility complex class I polymorphism in Asiatic lions. Tissue Antigens 66:9–18CrossRefPubMedGoogle Scholar
  49. Sharma R, Stuckas H, Bhaskar R, Rajput S, Khan I, Goyal SP, Tiedemann R (2009) mtDNA indicates profound population structure in Indian tiger (Panthera tigris tigris). Conserv Genet 10:909–914CrossRefGoogle Scholar
  50. Sommer S (2005) The importance of immune gene variability (MHC) in evolutionary ecology and conservation. Front Zool 2:1–18CrossRefGoogle Scholar
  51. Wan QH, Zhu L, Wu H, Fang SG (2006) Major histocompatibility complex class II variation in giant panda (Ailuropoda melanoleuca). Mol Ecol 15:2441–2450CrossRefPubMedGoogle Scholar
  52. Wang Q, Wu X, Yan P, Zheng S (2008) Sequence variability analysis on major histocompatibility complex class II DRB alleles in three felines. Front Biol China 3:55–62CrossRefGoogle Scholar
  53. Wei K, Zhang Z, Wang X, Zhang W, Xu X, Shen F, Yue B (2010) Lineage pattern, trans-species polymorphism, and selection pressure among major lineages of feline MHC-DRB peptide-binding region. Immunogenetics 62:307–317CrossRefPubMedGoogle Scholar
  54. Wong WS, Yang Z, Goldman N, Nielsen R (2004) Accuracy and power of statistical methods detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168:1041–1051CrossRefPubMedGoogle Scholar
  55. Yang Z (2000) Phylogenetic analysis by maximum likelihood (PAML), version 3.0. University College London, London, Google Scholar
  56. Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591CrossRefPubMedGoogle Scholar
  57. Yuhki N, O’Brien SJ (1990a) DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history. Proc Natl Acad Sci USA 87:836–840CrossRefPubMedGoogle Scholar
  58. Yuhki N, O’Brien SJ (1990b) DNA recombination and natural selection pressure sustain genetic sequence diversity of the feline MHC class I genes. J Exp Med 172:621–630CrossRefPubMedGoogle Scholar
  59. Yuhki N, O’Brien SJ (1994) Exchanges of short polymorphic DNA segments predating speciation in feline major histocompatibility complex class I genes. J Mol Evol 39:22–33CrossRefPubMedGoogle Scholar
  60. Yuhki N, O’Brien SJ (1997) Nature and origin of polymorphism in feline MHC class II DRA and DRB genes. J Immunol 158:2822–2833PubMedGoogle Scholar
  61. Yuhki N, Beck T, Stephens RM, Nishigaki Y, Newmann K, O’Brien SJ (2003) Comparative genome organization of human, murine, and feline MHC class II region. Genome Res 13:1169–1179CrossRefPubMedGoogle Scholar
  62. Yuhki N, Mullikin JC, Beck T, Stephens R, O’Brien SJ (2008) Sequences, annotation and single nucleotide polymorphism of major histocompatibility complex in the domestic cat. PLoS ONE 3(7):e2674. doi: 10.1371/journal.pone.0002674 CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Ina Pokorny
    • 1
  • Reeta Sharma
    • 2
    • 3
  • Surendra Prakash Goyal
    • 2
  • Sudanshu Mishra
    • 2
  • Ralph Tiedemann
    • 1
  1. 1.Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
  2. 2.Wildlife Institute of IndiaDehradunIndia
  3. 3.Instituto Gulbenkian de CiênciaOeirasPortugal

Personalised recommendations