Conservation Genetics

, Volume 17, Issue 5, pp 1171–1182 | Cite as

Limited diversity associated with duplicated class II MHC-DRB genes in the red squirrel population in the United Kingdom compared with continental Europe

  • Keith T. BallingallEmail author
  • Angeline McIntyre
  • Zhenzhen Lin
  • Naomi Timmerman
  • Erik Matthysen
  • Peter W.W. Lurz
  • Lynsey Melville
  • Amy Wallace
  • Anna L. Meredith
  • Claudia Romeo
  • Lucas A. Wauters
  • Anthony W. Sainsbury
  • Colin J. McInnes
Research Article


The red squirrel (Sciurus vulgaris) population in the United Kingdom has declined over the last century and is now on the UK endangered species list. This is the result of competition from the eastern grey squirrel (S. carolinensis) which was introduced in the 19th century. However, recent evidence suggests that the rate of population decline is enhanced by squirrelpox disease, caused by a viral infection carried asymptomatically by grey squirrels but to which red squirrels are highly susceptible. Population genetic diversity provides some resilience to rapidly evolving or exotic pathogens. There is currently no data on genetic diversity of extant UK squirrel populations with respect to genes involved in disease resistance. Diversity is highest at loci involved in the immune response including genes clustered within the major histocompatibility complex (MHC). Using the class II DRB locus as a marker for diversity across the MHC region we genotyped 110 red squirrels from locations in the UK and continental Europe. Twenty-four Scvu-DRB alleles at two functional loci; Scvu-DRB1 and Scvu-DRB2, were identified. High levels of diversity were identified at both loci in the continental populations. In contrast, no diversity was observed at the Scvu-DRB2 locus in the mainland UK population while a high level of homozygosity was observed at the Scvu-DRB1 locus. The red squirrel population in the UK appears to lack the extensive MHC diversity associated with continental populations, a feature which may have contributed to their rapid decline.


Red squirrel MHC DRB Population UK Diversity Squirrelpox virus Disease 



The authors acknowledge all those who contributed genetic material to this study. KB and CM are supported by the Scottish Government Rural and Environment Science and Analytical Services (RESAS) Division.

Supplementary material

10592_2016_852_MOESM1_ESM.pptx (172 kb)
Supplementary material 1 (PPTX 172 kb)
10592_2016_852_MOESM2_ESM.docx (22 kb)
Supplementary material 2 (DOCX 21 kb)


  1. Anisimova M, Gascuel O (2006) Approximate likelihood ratio test for branches: a fast, accurate and powerful alternative. Syst Biol 55:539–552CrossRefPubMedGoogle Scholar
  2. Babik W, Durka W, Radwan J (2005) Sequence diversity of the MHC DRB gene in the Eurasian beaver (Castor fiber). Mol Ecol 14:4249–4257CrossRefPubMedGoogle Scholar
  3. Barratt EM, Gurnell J, Malarky G, Deaville R, Bruford MW (1999) Genetic structure of fragmented populations of red squirrel (Sciurus vulgaris) in the UK. Mol Ecol 8:55–63CrossRefGoogle Scholar
  4. Barreiro LB, Quintana-Murci L (2010) From evolutionary genetics to human immunology: how selection shapes host defense genes. Nature Rev Genet 11:17–30CrossRefPubMedGoogle 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. Bertolino S, Lurz PWW, Sanderson R, Rushton SP (2008) Predicting the spread of the American grey squirrel (Sciurus carolinensis) in Europe: a call for a co-ordinated European approach. Biol Conserv 141:2564–2575CrossRefGoogle Scholar
  7. Bertolino S, Cordero di Montezemolo N, Wauters LA, Martinoli A (2014) A grey future for Europe: Sciurus carolinensis is replacing red squirrels in Italy. Biol Invasions 16:53–62CrossRefGoogle Scholar
  8. Biedrzycka A, Radwan J (2008) Population fragmentation and major histocompatibility complex variation in the spotted suslik, Spermophilus suslicus. Mol Ecol 17:4801–4811CrossRefPubMedGoogle Scholar
  9. Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, Wiley DC (1987) Structure of human class I histocompatibility antigen. Nature 329:506–512CrossRefPubMedGoogle Scholar
  10. 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
  11. Charlesworth D, Willis JH (2009) The genetics of inbreeding depression. Nat Rev Genet 10:783–796CrossRefPubMedGoogle Scholar
  12. Cížková D, Gouy de Bellocq J, Baird SJ, Piálek J, Bryja J (2011) Genetic structure and contrasting selection pattern at two major histocompatibility complex genes in wild house mouse populations. Heredity 106:727–740CrossRefPubMedGoogle Scholar
  13. Darby AC, McInnes CJ, Kjær KH, Wood AR, Hughes M, Martensen PM, Radford AD, Hall N, Chantrey J (2014) Novel host-related virulence factors are encoded by squirrelpox virus, the main causative agent of epidemic disease in red squirrels in the UK. PLoS ONE 9:e96439CrossRefPubMedPubMedCentralGoogle Scholar
  14. Ellegren H, Hartman G, Johansson M, Andersson L (1993) Major histocompatibility complex monomorphism and low-levels of DNA fingerprinting variability in a reintroduced and rapidly expanding population of beavers. Proc Natl Acad Sci USA 90:8150–8153CrossRefPubMedPubMedCentralGoogle Scholar
  15. Everest DJ, Shuttleworth CM, Stidworthy MF, Grierson SS, Duff JP, Kenward RE (2014) Adenovirus: an emerging factor in red squirrel Sciurus vulgaris conservation. Mammal Rev 44:225–233CrossRefGoogle Scholar
  16. Frankham R, Ralls K (1998) Inbreeding leads to extinction. Nature 392:441–442CrossRefGoogle Scholar
  17. Germain RN, Margulies DH (1993) The biochemistry and cell biology of antigen processing and presentation. Annu Rev Immunol 11:403–450CrossRefPubMedGoogle Scholar
  18. Grill A, Amori G, Aloise G, Lisi I, Tosi G, Wauters LA, Randi E (2009) Molecular phylogeography of European Sciurus vulgaris: refuge within refugia? Mol Ecol 18:2687–2699CrossRefPubMedGoogle Scholar
  19. Gurnell J, Clark MJ, Lurz PWW, Shirley MDF, Rushton SP (2002) Conserving red squirrels (Sciurus vulgaris): mapping and forecasting habitat suitability using a geographic information systems approach. Biol Conserv 105:53–64CrossRefGoogle Scholar
  20. Gurnell J, Wauters LA, Lurz PW, Tosi G (2004) Alien species and interspecific competition: effects of introduced eastern grey squirrels on red squirrel population dynamics. J Anim Ecol 73:26–35CrossRefGoogle Scholar
  21. Hale ML, Lurz PWW, Shirley MDF, Rushton S, Fuller RM, Wolff K (2001) Impact of landscape management on the genetic structure of red squirrel populations. Science 293:2246–2248CrossRefPubMedGoogle Scholar
  22. Hale ML, Lurz PWW, Wolff K (2004) Patterns of genetic diversity in the red squirrel: footprints of biogeographic history and artificial introductions. Conserv Genet 5:167–179CrossRefGoogle Scholar
  23. Harris S, Morris P, Wray S (1995) A review of British mammals: population estimates and conservation status of British mammals other than cetaceans. Report to the Joint Nature Conservation Committee, PeterboroughGoogle Scholar
  24. Horton R, Wilming L, Rand V, Lovering RC, Bruford EA, Khodiyar VK, Lush MJ, Povey S, Talbot CC Jr, Wright MJ, Wain HM, Trowsdale J, Ziegler A, Beck S (2004) Gene map of the extended human MHC. Nature Rev Genet 5:889–899CrossRefPubMedGoogle Scholar
  25. Hughes AL, Nei M (1989) Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc Natl Acad Sci USA 86:948–962CrossRefGoogle Scholar
  26. Hughes AL, Yeager M (1998) Natural selection at major histocompatibility complex loci of vertebrates. Annu Rev Genet 32:415–434CrossRefPubMedGoogle Scholar
  27. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism III. Academic Press, New York, pp 21–132CrossRefGoogle Scholar
  28. Keller L, Waller D (2002) Inbreeding effects in wild populations. Trends Ecol Evol 17:230–241CrossRefGoogle Scholar
  29. Kenward RE, Holm JL (1993) On the replacement of the red squirrel in Britain: a phytotoxic explanation. Proc R Soc B- Biolog Sci 251:187–194CrossRefGoogle Scholar
  30. Klein J, Bontrop RE, Dawkins RL, Erlich HA, Gyllensten UB, Heise ER, Jones PP, Parham P, Wakeland EK, Watkins DI (1990) Nomenclature for the major histocompatibility complexes of different species: a proposal. Immunogenetics 31:217–219PubMedGoogle Scholar
  31. Kumanovics A, Takada T, Lindahl KF (2003) Genomic organization of the mammalian MHC. Annu Rev Immunol 21:629–657CrossRefPubMedGoogle Scholar
  32. La-Rose JP, Meredith AL, Everest DJ, Fiegna C, McInnes CJ, Shaw DJ, Milne EM (2010) Epidemiological and postmortem findings in 262 red squirrels (Sciurus vulgaris) in Scotland, 2005 to 2009. Vet Rec 167:297–302CrossRefGoogle Scholar
  33. Mainguy J, Worley K, Cote SD (2007) Low MHC DRB class II diversity in the mountain goat: past bottlenecks and possible role of pathogens and parasites. Conserv Genet 8:885–891CrossRefGoogle Scholar
  34. Martinoli A, Bertolino B, Preatoni DG, Balduzzi A, Marsan A, Genovesi P, Tosi G, Wauters LA (2010) Headcount 2010: the multiplication of the grey squirrel populations introduced in Italy. Hystrix Ital J Mammal 21:127–136Google Scholar
  35. McInnes CJ, Wood AR, Thomas K, Sainsbury AW, Gurnell J, Dein FJ, Nettleton PF (2006) Genomic characterization of a novel poxvirus contributing to the decline of the red squirrel (Sciurus vulgaris) in the UK. J Gen Virol 87:2115–2125CrossRefPubMedGoogle Scholar
  36. Meredith A, Del Pozo J, Smith S, Milne E, Stevenson K, McLuckie J (2014) Leprosy in red squirrels in Scotland. Vet Rec 175:285–286CrossRefPubMedGoogle Scholar
  37. Meyer D, Thomson G (2001) How selection shapes variation on the human major histocompatibility complex: a review. Annals of Human Genet 65:1–26CrossRefGoogle Scholar
  38. Middleton AD (1930) Ecology of the American gray squirrel in the British Isles. Proc Zool Soc Lond 100:809–843CrossRefGoogle Scholar
  39. Mikko S, Andersson L (1995) Low major histocompatibility complex class-II diversity in European and North-American moose. Proc Natl Acad Sci USA 92:4259–4263CrossRefPubMedPubMedCentralGoogle Scholar
  40. Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF, Wright F (2008) TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 25:126–127CrossRefPubMedPubMedCentralGoogle Scholar
  41. O’Brien SJ, Roelke ME, Marker L, Newman A, Winkler CA, Meltzer D, Colly L, Evermann JF, Bush M, Wildt DE (1985) Genetic basis for species vulnerability in the cheetah. Science 227:1428–1434CrossRefPubMedGoogle Scholar
  42. Osborne AJ, Pearson J, Negro SS, Chilvers BL, Kennedy MA, Gemmell NJ (2015) Heterozygote advantage at MHC DRB may influence response to infectious disease epizootics. Mol Ecol 24:1419–1432CrossRefPubMedGoogle Scholar
  43. Radwan J, Biedrzyck A, Babik W (2010) Does reduced MHC diversity decrease viability of vertebrate populations? Biol Conserv 143:537–544CrossRefGoogle Scholar
  44. 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 331:623–641CrossRefPubMedGoogle Scholar
  45. Ricanova S, Bryja J, Cosson J-F, Gedeon C, Choleva LS, Ambros M, Sedlacek F (2011) Depleted genetic variation of the European ground squirrel in Central Europe in both microsatellites and the major histocompatibility complex gene: implications for conservation. Conserv Genet 12:1115–1129CrossRefGoogle Scholar
  46. Robinson J, Halliwell JA, McWilliam H, Lopez R, Marsh SG (2013) IPD—the Immuno polymorphism database. Nucleic Acids Res 41:D1234–D1240CrossRefPubMedGoogle Scholar
  47. Rushton SP, Lurz PW, Gurnell J, Nettleton P, Bruemmer C, Shirley MD, Sainsbury AW (2006) Disease threats posed by alien species: the role of a poxvirus in the decline of the native red squirrel in Britain. Epidemiol Infect 134:521–533CrossRefPubMedGoogle Scholar
  48. Sainsbury AW, Nettleton P, Gilray J, Gurnell J (2000) Grey squirrels have a high seroprevalence to a parapoxvirus associated with deaths in red squirrels. Animal Conserv 3:229–233CrossRefGoogle Scholar
  49. Sainsbury AW, Adair B, Graham D (2001) Isolation of a novel adenovirus associated with splenitis, diarrhoea, and mortality in translocated red squirrels. Sciurus vulgaris. Verhandlungsberichte über Erkrankungen der Zootiere 40:265–270Google Scholar
  50. Shorten M (1954) Squirrels. Collins, LondonGoogle Scholar
  51. Shuttleworth CM, Everest DJ, McInnes CJ, Greenwood A, Jackson NL, Rushton S, Kenward RE (2014) Inter-specific viral infections: can the management of captive red squirrel collections help inform scientific research? Hystrix Ital J Mammal 25:18–24Google Scholar
  52. Siddle HV, Kreiss A, Eldridge MD, Noonan E, Clarke CJ, Pyecroft S, Woods GM, Belov K (2007) Transmission of a fatal clonal tumor by biting occurs due to depleted MHC diversity in a threatened carnivorous marsupial. Proc Natl Acad Sci USA 104:6221–16226CrossRefGoogle Scholar
  53. Signorile AL, Wang J, Lurz PWW, Bertolino S, Carbone C, Reuman DC (2014) Do founder size, genetic diversity and structure influence rates of expansion of North American grey squirrels in Europe? Divers Distrib 20:918–930CrossRefGoogle Scholar
  54. Signorile AL, Lurz PWW, Wang J, Reuman DC, Carbone C (2016) Mixture or mosaic? Genetic patterns in UK grey squirrels support a human-mediated ‘long-jump’ invasion mechanism. Divers Distrib 22:566–577CrossRefGoogle Scholar
  55. Simpson VR, Birtles RJ, Bown KJ, Panciera RJ, Butler H, Davison N (2006) Hepatozoon species infection in wild red squirrels (Sciurus vulgaris) on the Isle of Wight. Vet Rec 159:202–205CrossRefPubMedGoogle Scholar
  56. Sommer S (2005) The importance of immune gene variability (MHC) in evolutionary ecology and conservation. Front Zool 2:1–18CrossRefGoogle Scholar
  57. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefPubMedPubMedCentralGoogle Scholar
  58. Thomas K, Tompkins D, Sainsbury A, Wood AR, Dalziel R, Nettleton PF, McInnes CJ (2003) A novel poxvirus lethal to red squirrels (Sciurus vulgaris). J Gen Virol 84:3337–3341CrossRefPubMedGoogle Scholar
  59. Tompkins D, Sainsbury AW, Nettleton P, Buxton D, Gurnell J (2002) Parapoxvirus causes a deleterious disease of red squirrels associated with UK population declines. Proc R Soc Lond 269:529–533CrossRefGoogle Scholar
  60. Trowsdale J (2011) The MHC, disease and selection. Immunol Letters 137:1–8CrossRefGoogle Scholar
  61. Wauters LA, Gurnell J (1999) The mechanism of replacement of red squirrels by grey squirrels: a test of the interference competition hypothesis. Ethology 105:1053–1071CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Keith T. Ballingall
    • 1
    Email author
  • Angeline McIntyre
    • 1
    • 2
    • 7
  • Zhenzhen Lin
    • 1
    • 3
  • Naomi Timmerman
    • 1
    • 6
  • Erik Matthysen
    • 6
  • Peter W.W. Lurz
    • 3
  • Lynsey Melville
    • 1
  • Amy Wallace
    • 1
  • Anna L. Meredith
    • 3
  • Claudia Romeo
    • 4
  • Lucas A. Wauters
    • 5
  • Anthony W. Sainsbury
    • 2
  • Colin J. McInnes
    • 1
  1. 1.Moredun Research Institute, Pentlands Science ParkPenicuik, MidlothianScotland, UK
  2. 2.Institute of ZoologyZoological Society of LondonLondonUK
  3. 3.The Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
  4. 4.Department of Veterinary Sciences and Public HealthUniversity of MilanMilanItaly
  5. 5.Department of Theoretical and Applied SciencesUniversity of InsubriaVareseItaly
  6. 6.Evolutionary Ecology GroupUniversity of AntwerpAntwerpBelgium
  7. 7.Department of Ecosystem and Public HealthUniversity of CalgaryCalgaryCanada

Personalised recommendations