Abstract
The major histocompatibility complex is one of the best studied systems in vertebrates providing evidence for the long-term action of selection. Here, we examined the intra- and inter-population genetic diversity of the MHC class II DRB locus in European brown hare (Lepus europaeus) and correlated the results with genetic variability already estimated from the MHC DQA locus and from maternally (mitochondrial DNA (mtDNA)) and biparentally (allozymes, microsatellites) inherited loci. L. europaeus showed remarkable genetic polymorphism in both DQA and DRB1 loci. The Anatolian populations exhibited the highest genetic polymorphism for both loci. Balancing selection has established increased variability in the European populations despite the founder effects after the last glaciation. Different evolutionary rates were traced for DRB1 and DQA loci, as evidenced by the higher number of common DRB1 than DQA alleles and the greater differences between DRB1 alleles with common origin in comparison with DQA alleles. The high number of rare alleles with low frequencies detected implies that frequency-dependent selection drives MHC evolution in the brown hare through the advantage of rare alleles. Both loci were under the influence of positive selection within the peptide-binding region. The functional polymorphism, recorded as amino acid substitutions within the binding pockets, fell also within distinct geographic patterns, yet it was much narrower than the genetic polymorphism. We hypothesize that certain structural and functional characteristics of the binding pockets set limitations to the actual shape of genetic polymorphism in MHC.
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs00251-014-0772-7/MediaObjects/251_2014_772_Fig1_HTML.gif)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs00251-014-0772-7/MediaObjects/251_2014_772_Fig2_HTML.gif)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs00251-014-0772-7/MediaObjects/251_2014_772_Fig3_HTML.gif)
Similar content being viewed by others
References
Acevedo-Whitehouse K, Cunningham AA (2006) Is MHC enough for understanding wildlife immunogenetics? Trends Ecol Evol 21:433–438
Averdam A, Kuschal C, Otto N, Westphal N, Roos C, Reinhardt R, Walter L (2011) Sequence analysis of the grey mouse lemur (Microcebus murinus) MHC class II DQ and DR region. Immunogenetics 63:85–93
Beck K (1984) Coevolution: mathematical analysis of host-parasite interactions. J Math Biol 19:63–77
Belkhir K (1999) GENETIX, logiciel sous Windows pour la génétique des populations, Laboratoire Génome et Populations, CNRS UPR 9060. Université de Montpellier II, Montpellier (France)
Ben Slimen H, Suchentrunk F, Stamatis C, Mamuris Z, Sert H, Alves PC, Kryger U, Shahin AB, Ben Ammar Elgaaied A (2008) Population genetics of cape and brown hares (Lepus capensis and L. europaeus): a test of Petter’s hypothesis of conspecificity. Biochem Syst Ecol 36:22–39
Bernatchez L, Landry C (2003) MHC studies in non model vertebrates: what have we learned about natural selection in 15 years? J Evol Biol 16:363–377
Bodmer W (1972) Evolutionary significance of the HL-A system. Nature 237:139–145
Bondinas GP, Moustakas AK, Papadopoulos GK (2007) The spectrum of HLA-DQ and HLA-DR alleles, 2006: a listing correlating sequence and structure with function. Immunogenetics 59:539–553
Borghans JAM, Beltman JB, De Boer RJ (2004) MHC polymorphism under host-pathogen coevolution. Immunogenetics 55(732–7):39
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 364:33–39
Campos JL, Goüy de Bellocq J, Schaschla H, Suchentrunk F (2011) MHC class II DQA gene variation across cohorts of brown hares (Lepus europaeus) from eastern Austria: testing for different selection hypotheses. Mamm Biol 76:251–257
Cárdenas C, Villaveces JL, Suárez C, Obregón M, Ortiz M, Patarroyo ME (2005) A comparative study of MHC Class-II HLA-DRb1*0401-Col II and HLA-DRb1*0101-HA complexes: a theoretical point of view. J Struct Biol 149:38–52
Cheylan G (1991) Patterns of Pleistocene turnover, current distribution and speciation among Mediterranean mammals. In: Groves RH, Di Castri F (eds) Biogeography of Mediterranean invasion. Cambridge University Press, Cambridge, pp 227–262
Doherty PC, Zingernagel R (1975) Enhanced immunologic surveillance in mice heterozygous at the H2 complex. Nature 256:50–52
Ellis SA, Bontrop RE, Antczak DF, Ballingall K, Davies CJ, Kaufman J, Kennedy LJ, Robinson J, Smith DM, Stear MJ, Stet RJM, Waller MJ, Walter L, Marsh SGE (2006) ISAG/IUIS-VIC Comparative MHC Nomenclature Committee report, 2005. Immunogenetics 57:953–958
Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial-DNA restriction data. Genetics 131:479–491
Fickel J, Lieckfeldt D, Pitra C (1999) Analysis of genetic diversity and structure in neighboring populations of the European brown hare (Lepus europaeus, Pallas 1778). Z Jagdwiss 45:230–237
Fickel J, Schmidt A, Putze M, Spittler H, Ludwig A, Streich WJ, Pitra C (2005) Genetic structure of populations of European brown hare: implications for management. J Wildl Manag 69:760–770
Fickel J, Hauffe HC, Pecchioli E, Soriguer R, Vapa L, Pitra C (2008) Cladogenesis of the European brown hare (Lepus europaeus Pallas, 1778). Eur J Wildl Res 54:495–510
Flux ECJ (2007) Notes on New Zealand mammals 3. Brown hare signals to cat. N Z J Zool 34:159–160
Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). http://www2.unil.ch/popgen/softwares/fstat.html. Updated from Goudet 1995
Goüy de Bellocq J, Suchentrunk F, Baird SJE, Schaschl H (2009) Evolutionary history of an MHC gene in two leporid species: characterisation of Mhc-DQA in the European brown hare and comparison with the European rabbit. Immunogenetics 61:131–144
Gyllensten UB, Erlich HA (1989) Ancient roots for polymorphism at the HLA-DQ locus in primates. Proc Natl Acad Sci U S A 86:9986–9990
Hasegawa M, Kishino M, Yano T (1985) Dating the human–ape split by a molecular clock of mitochondrial DNA. J Mol Evol 22:160–174
Hedrick PW, Thompson G (1983) Evidence for balancing selection at HLA. Genetics 104:449–456
Hedrick PW, Thompson G (1988) Maternal-fetal interactions and the maintenance of HLA polymorphism. Genetics 119:205–212
Hedrick PW, Lee RN, Parker KM (2000) Major histocompatibility complex (MHC) variation in the endangered Mexican wolf and related canids. Heredity 85:617–624
Hedrick PW, Lee RN, Garrigan D (2002) Major histocompatibility complex variation in red wolves: evidence for common ancestry with coyotes and balancing selection. Mol Ecol 10:1905–1913
Hughes AL, Nei M (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167–170
Hughes AL, Nei M (1989) Nucleotide substitution at major histocompatibility complex class II-loci—evidence for overdominant selection. Proc Natl Acad Sci U S A 86:958–962
Hughes A, Yeager M, Carrington M (1996) Peptide binding function and the paradox of HLA disease associations. Immunol Cell Biol 74:444–448
Iacovakis C, Mamuris Z, Moutou KA, Touloudi A, Hammer AS, Valiakos C-G, Giannoulis T, Stamatis C, Spyrou V, Athanasiou LV, Kantere M, Asferg T, Giannakopoulos A, Salomonsen CM, Bogdanos D, Birtsas P, Petrovska L, Hannant D, Billinis C (2013) Polarisation of Major Histocompatibility Complex ii host genotype with pathogenesis of European brown hare syndrome virus. PLoS One 8(9):e74360
Janeway CA, Travers P, Walport M, Shlomchik MJ (2005) Immunobiology, 6th edn. Garland Science, London, pp 183–201
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic, New York, pp 21–123
Kasapidis P, Suchentrunk F, Magoulas A, Kotoulas G (2005) The sha** of mitochondrial DNA phylogeographic patterns of the brown hare (Lepus europaeus) under the combined influence of Late Pleistocene climatic fluctuations and anthropogenic translocations. Mol Phylogenet Evol 34:55–66
Klein J, Sato A, Nagl S, O’hUigin C (1998) Molecular trans-species polymorphism. Annu Rev Ecol Syst 29:1–21
Koutsogiannouli EA, Moutou KA, Sarafidou T, Stamatis C, Spyrou V, Mamuris Z (2009) Major histocompatibility complex variation at class II DQA locus in the brown hare (Lepus europaeus). Mol Ecol 18:4631–4649
Koutsogiannouli EA, Moutou KA, Stamatis C, Mamuris Z (2012) Analysis of MC1R genetic variation in Lepus species in Mediterranean refugia. Mamm Biol 77:428–433
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
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
Lohm J, Grahn M, Langefors A, Andersen O, Storset A, von Schantz T (2002) Experimental evidence for major histocompatibility complex—allele-specific resistance to a bacterial infection. P Roy Soc Lond B Biol 269:2029–2033
Mamuris Z, Sfougaris AI, Stamatis C (2001) Genetic structure of Greek brown hare (Lepus europaeus) populations as revealed by mtDNA RFLP-PCR analysis: implications for conserving genetic diversity. Biol Conserv 101:187–196
Mamuris Z, Sfougaris AI, Stamatis C, Suchentrunk F (2002) Genetic structure of Greek brown hare (Lepus europaeus) populations based on the random amplified polymorphic DNA (RAPD) method. Biochem Genet 40:323–338
McFarland BJ, Beeson C (2002) Binding interactions between peptides and proteins of the class II major histocompatibility complex. Med Res Rev 22:168–203
Meyer-Lucht Y, Sommer S (2009) Number of MHC alleles is related to parasite loads in natural populations of yellow necked mice, Apodemus flavicollis. Evol Ecol Res 11:1085–1097
Mona S, Crestanello B, Bankhead-Dronnet S, Pecchioli E, Ingrosso S, D’Ameli S, Rossi L, Meneguz PG, Bertorelle G (2008) Disentangling the effects of recombination, selection, and demography on the genetic variation at a major histocompatibility complex class II gene in the alpine chamois. Mol Ecol 17:4053–4067
Musolf K, Meyer-Lucht Y, Sommer S (2004) Evolution of MHC-DRB class II polymorphism in the genus Apodemus and a comparison of DRB sequences within the family Muridae (Mammalia: Rodentia). Immunogenetics 56:420–426
Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:18–426
Nei M, Hughes AL (1991) Polymorphism and evolution of the major histocompatibility complex in mammals. In: Selander RK, Clark AG, Whittam TS (eds) Evolution at the molecular level. Sinauer, Sunderland, pp 222–247
Ohta T (1982) Allelic and nonallelic homology of a supergene family. Proc Natl Acad Sci U S A 79:3251–3254
Parham P, Adams EJ, Arnett KL (1995) The Origins of HLA-A, B, C Polymorphism. Immunol Rev 143:141–180
Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818
Reche PA, Reinherz EL (2003) Sequence variability analysis of human Class I and Class II MHC molecules: functional and structural correlates of amino acid polymorphisms. J Mol Biol 331(3):623–641
Seddon JM, Ellegren H (2002) MHC class II genes in European wolves: a comparison with dogs. Immunogenetics 54:490–500
Sert H, Suchentrunk F, Erdogăn A (2005) Genetic diversity within Anatolian brown hares (Lepus europaeus Pallas, 1778) and differentiation among Anatolian and European populations. Mamm Biol 70:171–186
Smith S, Goüy de Bellocq J, Suchentrunk F, Schaschl H (2011) Evolutionary genetics of MHC class II beta genes in the brown hare, Lepus europaeus. Immunogenetics 63:743–751
Stamatis C, Suchentrunk F, Moutou KA, Giacometti M, Haerer G, Djan M, Vapa L, Vukovic M, Tvrtkovič N, Sert H, Alve PC, Mamuris Z (2009) Phylogeography of the brown hare (Lepus europaeus) in Europe: a legacy of south-eastern Mediterranean refugia? J Biogeogr 36:515–528
Suchentrunk F, Michailo C, Markov G, Haiden A (2000) Population genetics of Bulgarian brown hares Lepus europaeus: allozymic diversity at zoogeographical crossroads. Acta Theriol 45:1–12
Suchentrunk F, Mamuris Z, Sfougaris AI, Stamatis C (2003) Biochemical genetic variability in brown hares (Lepus europaeus) from Greece. Biochem Genet 41:127–140
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Tennessen JA (2005) Molecular evolution of animal antimicrobial peptides: widespread moderate positive selection. J Evol Biol 18:1387–1394
Wan Q-H, Zhu L, Wu H, Fang S-G (2006) Major histocompatibility complex class II variation in the giant panda (Ailuropoda melanoleuca). Mol Ecol 15:2441–2450
Yamazaki K, Boyse EA, Mike V, Thaler HT, Mathieson BJ, Abbott J, Boyse J, Zayas ZA, Thomas L (1976) Control of mating preferences in mice by genes in the major histocompatibility complex. J Exp Med 114:1324–1335
Yeager M, Hughes AL (1999) Evolution of the mammalian MHC: natural selection, recombination, and convergent evolution. Immunol Rev 167:45–58
Acknowledgments
This work was supported financially by the PYTHAGORAS–EPEAEK II framework, Ministry of Education and Religious Affairs, Greece. The authors thank Professor K. Mathiopoulos for fruitful discussions; the Greek hunting associations for help in collecting the samples throughout Greece; M. Giacometti, G. Haerer and F. Suchentrunk for providing the European samples; and H. Sert for providing the Anatolian samples.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Koutsogiannouli, E.A., Moutou, K.A., Stamatis, C. et al. Genetic variation in the major histocompatibility complex of the European brown hare (Lepus europaeus) across distinct phylogeographic areas. Immunogenetics 66, 379–392 (2014). https://doi.org/10.1007/s00251-014-0772-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00251-014-0772-7