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

Conservation Genetics

Volumn 14, Issue 2, 2013, Pages 401-412

  Buzan, Elena V ^a   Bryja, Josef ^b,c   Zemanová, Barbora ^b,c   Kryštufek, Boris ^a  

^a UNIVERSITY OF PRIMORSKA   (Slovenia)

^b INSTITUTE OF VERTEBRATE BIOLOGY   (Czech Republic)

^c MASARYK UNIVERSITY   (Czech Republic)

Author keywords

Conservation management; Fragmentation; Microsatellites; Population structure; Rupicapra rupicapra

Indexed keywords

CONTACT ZONE; GOAT; HABITAT FRAGMENTATION; HABITAT MANAGEMENT; MOUNTAIN; POPULATION GENETICS; SUBTROPICAL REGION;

ALPS; DINARIC ALPS; EASTERN ALPS; SLOVENIA;

RUPICAPRA; RUPICAPRA RUPICAPRA; UNGULATA;

EID: 84875714259     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-013-0469-8     Document Type: Article

References (56)

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 507-527.
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). http://www. genetix. univ-montp2. fr/genetix/intro. htm.
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: 535-545.
4. Brook BW, Tonkyn DW, O'Grady JJ, Frankham R (2002) Contribution of inbreeding to extinction risk in threatened species. Ecol Soc 6(1): 16-23.
5. Brown JH (2001) Mammals on mountainsides: elevational patterns of diversity. Glob Ecol Biogeogr 10: 101-109.
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: 788-796.
7. Chapuis M-P, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24(3): 621-631.
8. Corander J, Sirén J, Arjas E (2008) Bayesian spatial modeling of genetic population structure. Comput Stat 23: 111-129.
9. Corlatti L, Lorenzini R, Lovari S (2011) The conservation of the chamois Rupicapra spp. Mammal Rev 41(2): 163-174.
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: 691-708.
11. Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9: 772.
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: 359-361.
13. Epperson BK (1995) Spatial distributions of genotypes under isolation by distance. Genetics 140: 1431-1440.
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: 2611-2620.
15. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using Phred I. Accuracy Assess Gen Res 8: 175-185.
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: 564-567.
17. Ezard THG, Travis JMJ (2006) The impact of habitat loss and fragmentation on genetic drift and fixation time. Oikos 114: 367-375.
18. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
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: 3191-3203.
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: 493-505.
21. Fuchs K, Deutz A, Gressmann G (2000) Detection of space-time clusters and epidemiological examinations of scabies in chamois. Vet Parasitol 92: 63-73.
22. Goudet J (2001) FSTAT, a programme to estimate and test gene diversities and fixation indices (version 2. 9. 3), 2003. http://www2. unil. ch/izea/softwares/fstat. html.
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 637-743.
24. Guindon S, Gascuel O (2003) A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Sys Biol 52: 696-704.
25. Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature 405: 907-913.
26. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogeny. Bioinformatics 17: 754-755.
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: 1801-1806.
28. Kryštufek B (1991) Mammals of Slovenia. Prirodoslovni muzej Slovenije, Ljubljana 294 pp.
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 79-108.
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 127-153.
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 138-143.
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: 485-492.
33. Mares MA, Lacher TE (1987) Ecological, morphological and behavioral convergence in rockdwelling mammals. Curr Mammal 1: 307-348.
34. Masini F, Lovari S (1988) Systematics, phylogenetic relationships, and dispersal of the chamois (Rupicapra spp.). Quaternary Res 30: 339-349.
35. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583-590.
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 90-108.
37. Pérez T, Albornoz J, Domínguez A (2002) Phylogeography of chamois (Rupicapra spp.) inferred from microsatellites. Mol Phylogenet Evol 25: 524-534.
38. Rambaud A, Drummond AJ (2007) Tracer, version 1. 4. http://beast. bio. ed. ac. uk/Tracer.
39. Raymond M, Rousset F (1995) GENEPOP (version 1. 2): population genetics software for exact tests and ecumenicism. J Heredity 86: 248-249.
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: 47-55.
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: 214-222.
42. Ronquist F, Huelsenbeck JP (2003) Mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
43. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Not 4: 137-138.
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: 233-240.
45. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145(4): 1219-1228.
46. Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resources 8: 103-106.
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: 125-135.
48. Shackleton DM (1997) Wild sheep and goats and their relatives. International Union for Conservation of Nature, Gland.
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): 845-854.
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: 15261-15264.
51. Švigelj L (1961) Medved v Sloveniji (Brown bear in Slovenia). Mladinska knjiga, Ljubljana (in Slovene).
52. Tamura K, Dudley J, Nei M, Kumar S (2011) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol 24: 1596-1599.
53. Weir BS, Cockerham CC (1984) Estimating F-Statistics for the analysis of population structure. Evolution 38: 1358-1370.
54. Whitlock MC (2003) Fixation probability and time in subdivided populations. Genetics 164: 767-779.
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): 534-542.
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: 70-80.