Conservation Genetics

, Volume 14, Issue 2, pp 401–412 | Cite as

Population genetics of chamois in the contact zone between the Alps and the Dinaric Mountains: uncovering the role of habitat fragmentation and past management

  • Elena V. BuzanEmail author
  • Josef Bryja
  • Barbora Zemanová
  • Boris Kryštufek
Research Article


The chamois is a habitat specialist ungulate occupying “continental archipelagos” of fragmented rocky habitats which are frequently restricted to high altitudes. It is not clear whether forest habitats separating such population fragments act as barriers to gene flow. We studied the genetic makeup of the chamois in a topographically diverse landscape at the contact zone of two mountain ranges in Slovenia. Based on sequences of mitochondrial DNA, all Slovenian populations belong to a Northern chamois (Rupicapra r. rupicapra) subspecies. The range of chamois in Slovenia encompasses three different regions, each with unique topography, habitat connectivity and abundance of chamois: the Alps, the Dinaric Mts., and the Pohorje Mts. The habitat of the chamois is extensive and more or less continuous in the Alps, but suboptimal and fragmented in the remaining regions. In agreement with neutral genetic theory, large Northern chamois populations tended to have higher allelic richness and observed heterozygosity. Spatial clustering bears the differentiation into four geographically associated clusters within Slovenia and also revealed a strong substructure within all mountain ranges with suboptimal chamois habitat. Surprisingly, some small Dinaric populations have stayed genetically isolated in restricted habitat patches, even if they are geographically very close to each other. The four clusters, each having a unique demographic history, should be regarded as independent units for management purposes.


Rupicapra rupicapra Microsatellites Population structure Fragmentation Conservation management 



We would like to thank the authorities from the Slovenian Hunting Organisation, Triglav National Park and Rearing Hunting Ground Kozorog, Kamnik for helping to interpret past chamois management. We are grateful to the Hunter Families Log Pod Mangartom, Idrija, Postojna, Ig, Rakitna, Osilnica, Puščava, and Pohorje for collecting the tissue samples. Our thanks also to the Department of Forestry, Biotechnical Faculty, at the University of Ljubljana for providing the map and Peter Glasnović for cartography. Part of the research was sponsored by bilateral project between Slovenia and the Czech Republic (project Contact No: MEB 091023). JB and BZ worked with institutional support RVO: 68081766. We thank Mrs. Karollyn Close for English editing and two anonymous referees for valuable suggestions.

Supplementary material

10592_2013_469_MOESM1_ESM.pdf (96 kb)
Supplementary material 1 (PDF 95 kb)
10592_2013_469_MOESM2_ESM.pdf (51 kb)
Supplementary material 2 (PDF 50 kb)


  1. Adamic M, Jerina K (2010) Ungulate management in Europe in the XXI century Slovenia. In: Apollonio M, Andersen R, Putman R (Eds) European ungulates and their management in the 21st century, Cambridge University,Cambride, pp 507–527Google Scholar
  2. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (1996–2004) GENETIX 4.05, logiciel sous Windows TM pour la ge′ne′tique des populations. Laboratoire Ge′nome, Populations, Interactions, CNRS UMR 5000, Universite′ de Montpellier II, Montpellier (France).
  3. Blanco-Aguiar JA, Gonzàlez-Jara P, Ferrero ME, Sànchez-Barbudo I, Virgós E, Villafuerte R, Davila JA (2008) Assessment of game restocking contributions to anthropogenic hybridization: the case of the Iberian red-legged partridge. Anim Conserv 11:535–545CrossRefGoogle Scholar
  4. Brook BW, Tonkyn DW, O’Grady JJ, Frankham R (2002) Contribution of inbreeding to extinction risk in threatened species. Ecol Soc 6(1):16–23Google Scholar
  5. Brown JH (2001) Mammals on mountainsides: elevational patterns of diversity. Glob Ecol Biogeogr 10:101–109CrossRefGoogle Scholar
  6. Buzan EV, Forster DW, Searle JB, Kryštufek B (2010) A new cytochrome b phylogroup of the common vole (Microtus arvalis) endemic to the Balkans and its implications for the evolutionary history of the species. Biol J Linn Soc 100:788–796CrossRefGoogle Scholar
  7. Chapuis M-P, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24(3):621–631PubMedCrossRefGoogle Scholar
  8. Corander J, Sirén J, Arjas E (2008) Bayesian spatial modeling of genetic population structure. Comput Stat 23:111–129CrossRefGoogle Scholar
  9. Corlatti L, Lorenzini R, Lovari S (2011) The conservation of the chamois Rupicapra spp. Mammal Rev 41(2):163–174CrossRefGoogle Scholar
  10. Crestanello B, Pecchioli E, Vernesi C, Mona C, Martínková N, Janiga M, Hauffe HC, Bertorelle G (2009) The genetic impact of translocations and habitat fragmentation in chamois (Rupicapra spp). J Hered 100:691–708PubMedCrossRefGoogle Scholar
  11. Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772PubMedCrossRefGoogle Scholar
  12. Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361CrossRefGoogle Scholar
  13. Epperson BK (1995) Spatial distributions of genotypes under isolation by distance. Genetics 140:1431–1440PubMedGoogle Scholar
  14. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620PubMedCrossRefGoogle Scholar
  15. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using Phred I. Accuracy Assess Gen Res 8:175–185Google Scholar
  16. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Res 10:564–567CrossRefGoogle Scholar
  17. Ezard THG, Travis JMJ (2006) The impact of habitat loss and fragmentation on genetic drift and fixation time. Oikos 114:367–375CrossRefGoogle Scholar
  18. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587PubMedGoogle Scholar
  19. Frantz AC, Tigel Pourtois J, Heuertz M, Schley L, Flamand MC, Krier A, Bertouille S, Chaumont F, Burke T (2006) Genetic structure and assignment tests demonstrate illegal translocation of red deer (Cervus elaphus) into a continuous population. Mol Ecol 15:3191–3203PubMedCrossRefGoogle Scholar
  20. Frantz AC, Cellina S, Krier A, Schley L, Burke T (2009) Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance. J Appl Ecol 46:493–505CrossRefGoogle Scholar
  21. Fuchs K, Deutz A, Gressmann G (2000) Detection of space–time clusters and epidemiological examinations of scabies in chamois. Vet Parasitol 92:63–73PubMedCrossRefGoogle Scholar
  22. Goudet J (2001) FSTAT, a programme to estimate and test gene diversities and fixation indices (version 2.9.3), 2003.
  23. Grubb P (2005) Order artiodactyla. In: Wilson DE, Reeder DAM (eds) Mammal species of the world. A taxonomic and geographic reference, vol 1. John Hopkins University, Baltimore, pp 637–743Google Scholar
  24. Guindon S, Gascuel O (2003) A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood”. Sys Biol 52:696–704CrossRefGoogle Scholar
  25. Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature 405:907–913PubMedCrossRefGoogle Scholar
  26. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754–755PubMedCrossRefGoogle Scholar
  27. Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806PubMedCrossRefGoogle Scholar
  28. Kryštufek B (1991) Mammals of Slovenia. Prirodoslovni muzej Slovenije, Ljubljana 294 ppGoogle Scholar
  29. Kryštufek B (2004) A quantitative assessment of Balkan mammal diversity. In: Griffiths HI, Kryštufek B, Reed JM (eds) Balkan Biodiversity: Process and Pattern in the European hotspot. Kluwer Academic Publ, Dordrecht, NL, pp 79–108CrossRefGoogle Scholar
  30. Kryštufek B, Grifiths HI (2003) Anatomy of a human : brown bear conflict. Case study from Slovenia in 1999–2000. In: Kryštfek B, Flajšman B, Griffiths HI (eds) Living with bears: a large European carnivore in a shrinking world. Ljubljana, Ecological form LDS, pp 127–153Google Scholar
  31. Kryštufek B, Milenkovic M, Rapaic Z, Tvrtkovic N (1997) Status and distribution of Caprinae in Former Yugoslavia. In: Shackleton DM (ed) Wild Sheep and Goats and their Relatives. IUCN, Cambridge, UK, pp 138–143Google Scholar
  32. Latch EK, Harveson LA, King JS, Hobson MD, Rhodes OE (2006) Assessing hybridization in wildlife populations using molecular markers: a case study in wild Turkeys. J Wildl Manage 70:485–492CrossRefGoogle Scholar
  33. Mares MA, Lacher TE (1987) Ecological, morphological and behavioral convergence in rockdwelling mammals. Curr Mammal 1:307–348Google Scholar
  34. Masini F, Lovari S (1988) Systematics, phylogenetic relationships, and dispersal of the chamois (Rupicapra spp.). Quaternary Res 30:339–349CrossRefGoogle Scholar
  35. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedGoogle Scholar
  36. Onderscheka K (1982) Etat actuel de la recherche sur la gale du chamois. In: Gindré C (ed) Proceedings: Simposium sur le Chamois. Office National de la Chasse, Ljubljana, pp 90–108Google Scholar
  37. Pérez T, Albornoz J, Domínguez A (2002) Phylogeography of chamois (Rupicapra spp.) inferred from microsatellites. Mol Phylogenet Evol 25:524–534PubMedCrossRefGoogle Scholar
  38. Rambaud A, Drummond AJ (2007) Tracer, version 1.4.
  39. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Heredity 86:248–249Google Scholar
  40. Rodríguez F, Hammer S, Pérez T, Suchentrunk F, Lorenzini R, Michallet J, Mantinkova N, Albornoz J, Dominguez A (2009) Cytochrome b phylogeography of chamois (Rupicapra spp.). Population contractions, expansions and hybridizations governed the diversification of the genus. J Hered 100:47–55PubMedCrossRefGoogle Scholar
  41. Rodríguez F, Pérez T, Hammer S, Albornoz J, Domínguez A (2010) Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois. BMC Evol Biol 10:214–222CrossRefGoogle Scholar
  42. Ronquist F, Huelsenbeck JP (2003) Mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574PubMedCrossRefGoogle Scholar
  43. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Not 4:137–138CrossRefGoogle Scholar
  44. Rossi L, Meneguz PG, DeMartin P, Rodolfi M (1995) The epizootiology of sarcoptic mange in chamois Rupicapra rupicapra, from the Italian Eastern Alps. Parassitologia 37:233–240PubMedGoogle Scholar
  45. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145(4):1219–1228PubMedGoogle Scholar
  46. Rousset F (2008) Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resources 8:103–106CrossRefGoogle Scholar
  47. Schaschl H, Kaulfus D, Hammer S, Suchentrunk F (2003) Spatial patterns of mitochondrial and nuclear gene pools in chamois (Rupicapra r. rupicapra) from the Eastern Alps. Heredity 91:125–135PubMedCrossRefGoogle Scholar
  48. Shackleton DM (1997) Wild sheep and goats and their relatives. International Union for Conservation of Nature, GlandGoogle Scholar
  49. Soglia D, Rossi L, Cauvin E, Citterio C, Ferroglio E, Maione S, Meneguz PG, Spalenza V, Rasero R, Sacchi P (2010) Population genetic structure of alpine chamois (Rupicapra r. rupicapra) in the Italian Alps. Eur J Wildl Res 56(6):845–854CrossRefGoogle Scholar
  50. Spielman D, Brook BW, Frankham R (2004) Most species are not driven to extinction before genetic factors impact them. Proc Natl Acad Sci USA 101:15261–15264PubMedCrossRefGoogle Scholar
  51. Švigelj L (1961) Medved v Sloveniji (Brown bear in Slovenia). Mladinska knjiga, Ljubljana (in Slovene)Google Scholar
  52. Tamura K, Dudley J, Nei M, Kumar S (2011) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefGoogle Scholar
  53. Weir BS, Cockerham CC (1984) Estimating F-Statistics for the analysis of population structure. Evolution 38:1358–1370CrossRefGoogle Scholar
  54. Whitlock MC (2003) Fixation probability and time in subdivided populations. Genetics 164:767–779PubMedGoogle Scholar
  55. Willi Y, Van Buskirk J, Schmid B, Fischer M (2006) Genetic isolation of fragmented populations is exacerbated by drift and selection. J Evol Biol 20(2):534–542CrossRefGoogle Scholar
  56. Zemanová B, Hájková P, Bryja J, Zima J, Hájková A, Zima J Jr (2011) Development of multiplex microsatellite sets for noninvasive population genetic study of the endangered Tatra chamois. Fol Zool 60:70–80Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Elena V. Buzan
    • 1
    Email author
  • Josef Bryja
    • 2
    • 3
  • Barbora Zemanová
    • 2
    • 3
  • Boris Kryštufek
    • 1
  1. 1.University of Primorska, Science and Research Centre of KoperKoperSlovenia
  2. 2.Department of Population BiologyInstitute of Vertebrate Biology AS CRBrnoCzech Republic
  3. 3.Department of Botany and ZoologyFaculty of Science, Masaryk UniversityBrnoCzech Republic

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