European Journal of Wildlife Research

, Volume 57, Issue 3, pp 449–456 | Cite as

Mitochondrial and nuclear DNA analyses reveal pronounced genetic structuring in Tunisian wild boar Sus scrofa

  • Ghaiet El Mouna HajjiEmail author
  • Frank E. Zachos
Original Paper


We analysed 74 wild boars from Tunisia with respect to patterns of genetic differentiation and diversity based on sequences of the mitochondrial control region and genotypes at eight nuclear microsatellite loci. Analysis of molecular variance for both marker systems and Bayesian structure analysis of our microsatellite data revealed a clear break between northern and southern populations. Southern wild boar were monomorphic for one of three mtDNA haplotypes; the other two (one of which only occurred in three individuals) were confined to the north. A comparison with published sequences showed all three haplotypes to belong to the major European clade E1. Microsatellite diversity was similar to that found in earlier studies of wild boar (expected heterozygosity of 0.695 and 0.597 for the north and south, respectively). Contrary to the mtDNA results, we did not find unequivocal evidence of a bottleneck in Tunisian wild boar based on our microsatellite data. The clear distinction between northern and southern populations may be due to an Algerian origin of the southern animals.


Genetic diversity Microsatellites mtDNA Sus scrofa Tunisia 



We are grateful to all managers in the “Direction Générale des Forêts- Ministère d´Agriculture de Tunis” for their help in contacting hunters and sample collection. We are also grateful to the Alexander von Humboldt Foundation in Germany for financial support and granting to G. E. M. Hajji for a research stay at the Zoological Institute in Kiel.


  1. Alves A, Ovilo C, Rodriguez MC, Silio L (2003) Mitochondrial DNA sequence variation and phylogenetic relationships among Iberain pigs and others domestic and wild pig populations. Anim Genet 34:319–324PubMedCrossRefGoogle Scholar
  2. Balloux F, Lugon-Moulin N (2002) The estimation of population differentiation with microsatellite markers. Mol Ecol 11:155–165PubMedCrossRefGoogle Scholar
  3. Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48PubMedGoogle Scholar
  4. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) GENETIX, Windows TM software for population genetics. In: Laboratoire Génome, Populations, Interaction, CNRS UMR 5171. Université de Montpellier II, Montpellier, FranceGoogle Scholar
  5. Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from Allele frequency data. Genetics 144:2001–2014PubMedGoogle Scholar
  6. Dobson M (1998) Mammal distributions in the western Mediterranean: the role of human intervention. Mamm Rev 28:77–88CrossRefGoogle Scholar
  7. Ellegren H, Hartman G, Johasson M, Andersson L (1993) Major histocompatibility complex monomorphism and low levels of DNA fingerprinting variability in a reintroduced and rapidly expanding population of bears. Proc Natl Acad Sci USA 90:8150–8153PubMedCrossRefGoogle Scholar
  8. Ewen KR, Bahlo M, Treloar SA, Levinson DF, Mowry B, Barlow JW, Foote SJ (2000) Identification and analysis of error types in high-throughput genotyping. Am J Hum Genet 67:727–736PubMedCrossRefGoogle Scholar
  9. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50PubMedGoogle Scholar
  10. Ferreira E, Souto L, Soares AMVM, Fonseca C (2009) Genetic structure of the wild boar population in Portugal: evidence of a recent bottleneck. Mamm Biol 74:274–285CrossRefGoogle Scholar
  11. Feulner PGD, Bielfeldt W, Zachos FE, Bradvarovic J, Eckert I, Hartl GB (2004) Mitochondrial DNA and microsatellite analyses of the genetic status of the presumed subspecies Cervus elaphus montanus (Carpathian red deer). Heredity 93:299–306PubMedCrossRefGoogle Scholar
  12. Fickel J, Hohmann U (2006) A methodological approach for non-invasive sampling for population size estimates in wild boar (Sus scrofa). Eur J Wildl Res 52(1):28–33CrossRefGoogle Scholar
  13. Fredholm M, Winterö AK, Christensen K, Kristensen B, Nielsen PB, Davies W, Archlbald A (1993) Characterization of 24 porcine (dA-dC)n- (dT-dG)n microsatellites: genotyping of unrelated animals from four breeds and linkage studies. Mamm Genome 4(4):187–192PubMedCrossRefGoogle Scholar
  14. Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10:305–318PubMedCrossRefGoogle Scholar
  15. Gharaibeh BM (1997) Systematics, distribution and zoogeography of mammals of Tunisia. Dissertation. Faculty of Texas, TexasGoogle Scholar
  16. Goudet J (1995) FSTAT, a computer program to calculate F-statistics. J Hered 86:485–486Google Scholar
  17. Groves CP, Grubb P (1993) Taxonomy and description. In pigs, peccaries and hippos status survey and action plan. IUCN (World Conservation Union), GlandGoogle Scholar
  18. Hajji GM, Zachos FE, Charfi-Cheikrouha F, Hartl GB (2007) Conservation genetics of the imperilled Barbary red deer (Cervus elaphus barbarus) in Tunisia. Anim Conserv 10:229–235CrossRefGoogle Scholar
  19. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  20. Hedrick PW (1999) Highly variable loci and their interpretation in evolution and conservation. Evolution 53:313–318CrossRefGoogle Scholar
  21. Henry P, Miquelle D, Sugimoto T, McCullough DR, Caccone A, Russello MA (2009) In situ population structure and ex situ representation of the endangered Amur tiger. Mol Ecol 18:3173–3184PubMedCrossRefGoogle Scholar
  22. Hmwe SS, Zachos FE, Eckert I, Lorenzini R, Fico R, Hartl GB (2006a) Conservation genetics of the endangered red deer from Sardinia and Mesola with further remarks on the phylogeography of Cervus elaphus corsicanus. Biol J Linn Soc 88:691–701CrossRefGoogle Scholar
  23. Hmwe SS, Zachos FE, Sale JB, Rose HR, Hartl GB (2006b) Genetic variability and differentiation in red deer (Cervus elaphus) from Scotland and England. J Zool 270:479–487CrossRefGoogle Scholar
  24. Koutsogiannouli EA, Moutou KA, Sarafidou T, Stamatis C, Mamuris Z (2010) Detection of hybrids between wild boars (Sus scrofa scrofa) and domestic pigs (Sus scrofa f. domestica) in Greece, using the PCR-RFLP method on melanocortin-1 receptor (MC1R) mutations. Mamm Biol 75:69–73CrossRefGoogle Scholar
  25. Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29:1–10CrossRefGoogle Scholar
  26. Nikolov IS, Gum B, Markov G, Kuehn R (2009) Population genetic structure of wild boar Sus scrofa in Bulgaria as revealed by microsatellite analysis. Acta Theriol 54(3):193–205CrossRefGoogle Scholar
  27. Ojeda A, Rozas J, Folch JM, Pérez-Enciso M (2006) Unexpected high polymorphism at the FABP4 gene unveils a complex history for pig populations. Genetics 174:2119–2127PubMedCrossRefGoogle Scholar
  28. Pemberton J, Slate MJ, Bancroft DR, Barrett JA (1995) Nonamplifying alleles at microsatellite loci: a caution for parentage and population studies. Mol Ecol 4:249–252PubMedCrossRefGoogle Scholar
  29. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818PubMedCrossRefGoogle Scholar
  30. Poteaux C, Baubet E, Kaminski G, Brandt S, Dobson FS, Baudoin C (2009) Socio-genetic structure and mating system of a wild boar population. J Zool 278:116–125CrossRefGoogle Scholar
  31. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959PubMedGoogle Scholar
  32. Ramirez O, Ojeda A, Tomàs A, Gallardo D, Huang LS, Folch JM, Clop A, Sánchez A, Bdaoui B, Hanotte O, Galman-Omitogun O, Makuza SM, Soto H, Cadillo J, Kelly L, Cho IC, Yeghoyan S, Pérez-Enciso M, Amills M (2009) Integrating Y-chromosome, mitochondrial, and autosomal data to analyse the origin of pig breeds. Mol Biol Evol 26(9):2061–2072PubMedCrossRefGoogle Scholar
  33. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249Google Scholar
  34. Robic A, Dalens M, WoloszynN MD, Riquet J, Gellin J (1994) Isolation of 28 new porcine microsatellites revealing polymorphism. Mamm Genome 5(9):580–583PubMedCrossRefGoogle Scholar
  35. Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatic 15:174–175CrossRefGoogle Scholar
  36. Scandura M, Iacolina L, Crestanello B, Pecchioli E, Di Benedetto MF, Russo V, Davoli R, Apollonio M, Bertorelle G (2008) Ancient vs. recent process as factors shaping the genetic variation of the European wild boar: are the effects of the last glaciations still detectable? Mol Ecol 17:1745–1762PubMedCrossRefGoogle Scholar
  37. Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462PubMedGoogle Scholar
  38. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526PubMedGoogle Scholar
  39. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER (Version 2.2.3): software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538CrossRefGoogle Scholar
  40. Vernesi C, Crestanello B, Pecchioli E, Tartari D, Caramelli D, Hauffe H, Bertorelle G (2003) The genetic impact of demographic decline and reintroduction in the wild boar (Sus scrofa): a microsatellite analysis. Mol Ecol 12:585–595PubMedCrossRefGoogle Scholar
  41. Wattier R, Engel CR, Saumitou-Laprade P, Valero M (1998) Short allele dominance as a source of heterozygote deficiency at microsatellite loci: experimental evidence at the dinucleotide locus Gv1CT in Gracilaria gracilis (Rhodophyta). Mol Ecol 7:1569–1573CrossRefGoogle Scholar
  42. Wright S (1951) The genetic structure of populations. Ann Eugen 15:323–354CrossRefGoogle Scholar
  43. Zachos FE, Hmwe SS, Hartl GB (2006) Biochemical and DNA markers yield strikingly different results regarding variability and differentiation of roe deer (Capreolus capreolus, Artiodactyla: Cervidae) populations from northern Germany. J Zool Syst Evol Res 44:167–174CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  1. 1.Zoological InstituteChristian-Albrechts-UniversityKielGermany

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