The genetic impact of translocations and habitat fragmentation in chamois (Rupicapra) spp.

Journal of Heredity

Volumn 100, Issue 6, 2009, Pages 691-708

  Crestanello, Barbara ^a,b   Pecchioli, Elena ^a   Vernesi, Cristiano ^a   Mona, Stefano ^b   Martínková, Natalia ^c   Janiga, Marian ^d   Hauffe, Heidi C ^a   Bertorelle, Giorgio ^b  

^a RESEARCH AND INNOVATION CENTRE   (Italy)

^b UNIVERSITY OF FERRARA   (Italy)

^c INSTITUTE OF VERTEBRATE BIOLOGY   (Czech Republic)

^d UNIVERSITY OF ILINA   (Slovakia)

Author keywords

Conservation; Hybridization; Management; Microsatellites; MtDNA; Taxonomy

Indexed keywords

CYTOCHROME B; MITOCHONDRIAL DNA;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; GENE FLOW; GENE LOCUS; GENE TRANSLOCATION; GENETIC ANALYSIS; GENETIC DRIFT; GENETIC EROSION; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HABITAT FRAGMENTATION; INTERSPECIFIC HYBRIDIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RUPICAPRA; SPECIES DISTRIBUTION; UNINDEXED SEQUENCE;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; COMPUTATIONAL BIOLOGY; CONSERVATION OF NATURAL RESOURCES; DEMOGRAPHY; DNA, MITOCHONDRIAL; ECOSYSTEM; EUROPE; EVOLUTION, MOLECULAR; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; LIKELIHOOD FUNCTIONS; MICROSATELLITE REPEATS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; RUPICAPRA; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

RUPICAPRA; RUPICAPRA PYRENAICA ORNATA; RUPICAPRA PYRENAICA PYRENAICA; RUPICAPRA RUPICAPRA;

EID: 71049132672     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esp053     Document Type: Article

References (87)

1. Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr. 19:716-723.
2. Anderson CN, Ramakrishnan U, Chan YL, Hadly EA. 2005. Serial SimCoal: A population genetics model for data from multiple populations and points in time. Bioinformatics 21(8):1733-1734.
3. Arctander P, Johansen C, Coutellec-Vreto MA. 1999. Phylogeography of three closely related African bovids (tribe Alcelaphini). Mol Biol Evol. 16:1724-1739.
4. Arevalo E, Holder DA, Derr JN, Bhebhe E, Linn RA, Ruvana F, Davis SK, Taylor JF. 1994. Caprine microsatellite dinucleotide repeat polymorphisms at the SR-CRSP-1, SR-CRSP-2, SR-CRSP-3, SR-CRSP-4 and SR-CRSP-5 loci. Anim Genet. 25:202.
5. Bandelt H-J, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16:37-48.
6. Barendse W, Armitage SM, Kossarek LM, Shalom A, Kirkpatrick BW, Ryan AM, Clayton D, Li L, Neibergs HL, Zhang N, et al. 1994. A genetic linkage map of the bovine genome. Nat Genet. 6:227-235.
7. Beaumont MA. 2008. Joint determination of topology, divergence time, and immigration in population trees. In: Matsumura S, Forster P, Renfrew C, editors. Simulation, genetics, and human prehistory. Cambridge: McDonald Institute Press.
8. Beaumont MA, Zhang W, Balding DJ. 2002. Approximate Bayesian computation in population genetics. Genetics 162:2025-2035.
9. Belkhir K, Borsa P, Goudet J, Chikhi L, Bonhomme F. 1999. GENETIX, logiciel sous WindowsTM pour la génétique des populations. [Internet]. Montpellier (France): Université de Montpellier II. Available from: www.genetix.univ-montp2.fr/genetix/
10. Beniston M. 2006. Mountain weather and climate: A general overview and a focus on climatic change in the Alps. Hydrobiologia 562:3-16.
11. Bertorelle G, Papetti C, Hauffe HC, Boitani L. 2009. Monitoring and detecting translocations using genetic data. In: Bertorelle G, Bruford MW, Rizzoli A, Hauffe HC, Vernesi C, editors. Population genetics for animal conservation. Cambridge: Cambridge University Press. p. 145-166.
12. Blahout M. 1972. Zur taxonomie der population von Rupicapra rupicapra (Linné, 1785) in der Hohen Tatra. Zool Listy. 21:115-132.
13. Brookfield JFY. 1996. A simple new method for estimating null allele frequency from heterozygote deficiency. Mol Ecol. 5:453-455.
14. Brown JH. 2001. Mammals on mountainsides: Elevational patterns of diversity. Glob Ecol Biogeogr. 10:101-109.
15. Camerano L. 1914. Ricerche intorno ai camosci. Mem R Accad Sci Torino (Cl Sci Fis Mat Nat II). 65:1-82.
16. Caughley G, Gunn A. 1996. Conservation biology in theory and practice. Cambridge: Blackwell Science.
17. Chakraborty R, De Andrade M, Daiger SP, Budowle B. 1992. Apparent heterozygote deficiencies observed in DNA typing data and their implications in forensic applications. Ann Hum Genet. 56:45-47.
18. Couturier MAJ. 1938. Le chamois. Grenoble (France): B. Arthaud-Editeur.
19. DeYoung RW, Demarais S, Honeycutt RL, Rooney AP, Gonzales RA, Gee KL. 2003. Genetic consequences of white-tailed deer (Odocoileus virginianus) restoration in Mississippi. Mol Ecol. 12:3237-3252.
20. Dolan JM. 1963. Beitrag zur systematischen Gliederung des Tribus Rupicaprini Simpson, 1945. Z Zool Syst Evolutionsforsch. 1:311-407.
21. Douzery E, Randi E. 1997. The mitochondrial control region of Cervidae: Evolutionary patterns and phylogenetic content. Mol Biol Evol. 14:1154-1166.
22. El Mousadik A, Petit RJ. 1996. High levels of genetic differentiation for allelic richness among populations of the argan tree (Argania spinosa Skeels) endemic to Morocco. Theor Appl Genet. 92:832-839.
23. Excoffier L, Slatkin M. 1998. Incorporating genotypes of relatives into a test of linkage disequilibrium. Am J Hum Genet. 62:171-180.
24. Excoffier L, Smouse PE, Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplogroups: Applications to human mitochondrial DNA restriction data. Genetics 131:479-491.
25. Felsenstein J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol. 17:368-376.
26. Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
27. Felsenstein J. 2004. Inferring phylogenies. Sunderland (MA): Sinauer.
28. Fitch WM. 1971. Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zoo. 20:406-416.
29. Forbes SH, Hogg JT. 1999. Assessing population structure at high levels of differentiation: microsatellite comparisons of bighorn sheep and large carnivores. Anim Conserv. 2:223-233.
30. Gaillard JM. 1992. Some demographic characteristics in ungulate populations and their implications for management and conservation. Ongulés/Ungulates 91:493-495.
31. Goudet J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). [Internet]. Available from: http:// www.unil.ch/izea/softwares/fstat.html
32. Guo SW, Thompson EA. 1992. Performing the exact test of Hardy- Weinberg proportion for multiple alleles. Biometrics 48:361-372.
33. Gutiérrez-Espeleta GA, Kalinowski ST, Boyce WM, Hedrick PW. 2000. Genetic variation and population structure in desert bighorn sheep: Implications for conservation. Conserv Genet. 1:3-15.
34. Hammer S, Nadlinger K, Hartl GB. 1995. Mitochondrial-DNA differentiation in chamois (genus Rupicapra): Implications for taxonomy, conservation, and management. Acta Theriol. (Suppl 3):145-155.
35. Hasegawa M, Kishino K, Yano T. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22:160-174.
36. Holm S. 1979. A simple sequentially rejective multiple test procedure. Scand J Stat. 6:65-70.
37. Huelsenbeck JP, Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
38. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
39. Hundertmark KJ, Shields GF, Udina IG, Bowyer RT, Schwartz CC. 2002. Mitochondrial phylogeography of moose (Alces alces): late Pleistocene divergence and population expansion. Mol Phylogenet Evol. 22:375-387.
40. IUCN, 2008. 2008 IUCN Red List of Threatened Species. [Internet]. Available from: www.iucnredlist.org
41. Jurdíková N. 2000. The decline of the Tatra chamois. Caprinae, Newsletter of the IUCN/SSC Caprinae Specialist Group. December 2000.
42. Kemp SJ, Hishida O, Wambugu J, Rink A, Longeri ML, Ma RZ, Da Y, Lewin HA, Barendse W, Teale AJ. 1995. A panel of polymorphic bovine, ovine and caprine microsatellite markers. Anim Genet. 26:299-306.
43. King TL, Burke T. 2000. Special issue on gene conservation: Identification and management of genetic diversity. Introduction. Mol Ecol. 8:S1-S3.
44. Kirstein F, Gray JS. 1996. A molecular marker for the identification of the zoonotic reservoirs of Lyme borreliosis by analysis of the blood meal in its European vector Ixodes ricinus. Appl Environ Microbiol. 62:4060-4065.
45. Kogi J, Yeh CC, Bhebhe E, Burns BM, Ruvuna F, Davis SK, Taylor JF. 1995. Caprine microsatellite dinucleotide repeat polymorphisms at the SR-CRSP-11, SR-CRSP-12, SR-CRSP-13, SR-CRSP-14 and SR-CRSP-15 loci. Anim Genet. 26:449.
46. Lalueza-Fox C, Castresana J, Sampietro L, Marquès-Bonet T, Alcover JA, Bertranpetit J. 2005. Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal. BMC Evol Biol. 5:70.
47. Loehr J, Worley K, Grapputo A, Carey J, Veitch A, Coltman DW. 2006. Evidence for cryptic glacial refugia from North American mountain sheep mitochondrial DNA. J Evol Biol. 19:419-430.
48. Loison A, Jullien J-M, Menaut P. 1999. Subpopulation structure and dispersal in two populations of chamois. J Mammal. 80:620-632.
49. Lomolino MV, Davis R. 1997. Biogeographic scale and biodiversity of mountain forest mammals of western North America. Glob Ecol Biogeogr. 6:57-76.
50. Lorenzen ED, Siegismund HR. 2004. No suggestion of hybridization between the vulnerable black-faced impala (Aepyceros melampus petersi) and the common impala (A. m. melampus) in Etosha NP, Namibia. Mol Ecol. 13:3007-3019.
51. Lovari S, Sacconi F, Trivellini G. 2006. Do alternative strategies of space use occur in male Alpine chamois? Ethol Ecol Evol. 18:221-231.
52. Lovari S, Scala C. 1980. Revision of Rupicapra Genus. I. A statistical reevaluation of Couturier's data on the morphometry of six chamois subspecies. Boll Zool. 47:113-124.
53. Lydekker R. 1913. Artiodactyla, family Bovidae, subfamilies Bovinae to Ovibovinae (cattle, sheep, goats, chamois, serows, takin, musk-oxen, etc.). In: Catalogue of the ungulate mammals in the British Museum (Natural History). Vol I. London: Trustees of the British Museum (Nat. Hist.).
54. Mannen H, Nagata Y, Tsuji S. 2001. Mitochondrial DNA reveal that domestic goat (Capra hircus) are genetically affected by two subspecies of Bezoar (Capra aegagurus). Biochem Genet. 39:145-154.
55. Masini F, Lovari S. 1988. Systematics, phylogenetic relationships and dispersal of the chamois (Rupicapra spp.). Quat Res. 30:339-349.
56. Maudet C, Miller C, Bassano B, Breitenmoser-Würsten C, Gauthier D, Obexer-Ruff G, Michallet J, Taberlet P, Luikart G. 2002. Microsatellite DNA and recent statistical methods in wildlife conservation management: Applications in Alpine ibex [Capra ibex (ibex)]. Mol Ecol. 11:421-436.
57. Mitchell-Jones AJ, Amori G, Bogdanowicz W, Krystufek B, Reijnders PJH, Spitzenberger F, Stubbe M, Thissen JBM, Vohralik V, Zima J. 1999. Atlas of European mammals. London: Academic Press.
58. Moore SS, Sargeant LL, King TJ, Mattick JS, Georges M, Hetzel DJ. 1991. The conservation of dinucleotide microsatellites among mammalian genomes allows the use of heterologous PCR primer pairs in closely related species. Genomics 10:654-660.
59. Nascetti G, Lovari S, Lanfranchi P, Berducou C, Matteucci S, Rossi L, Bullini L. 1985. Revision of Rupicapra Genus. III. Electrophoretic studies demonstrating species distinction of chamois populations of the Alps from those of the Apennines and Pyrenees. In: Lovari S, editor. The biology and management of mountain ungulates. London: Croom Helm. p. 56-62.
60. Pérez T, Albornoz J, Dominguez A. 2002. Phylogeography of chamois (Rupicapra spp.) inferred from microsatellites. Mol Phylogenet Evol. 25:524-534.
61. Posada D, Crandall KA. 1998. MODELTEST: Testing the model of DNA substitutions. Bioinformatics 14:817-818.
62. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
63. Randi E, Alves PC, Carranza J, Milosevic-Zlatanovic S, Sfougaris A, Mucci N. 2004. Phylogeography of roe deer (Capreolus capreolus) populations: The effects of historical genetic subdivisions and recent nonequilibrium dynamics. Mol Ecol. 13:3071-3083.
64. Rannala B, Yang Z. 1996. Probability distribution of molecular evolutionary trees: A new method for phylogenetic inference. J Mol Evol. 43:304-311.
65. R Development Core Team. 2008. R: A language and environment for statistical computing [Internet]. Vienna (Austria): R Foundation for Statistical Computing. Available from: http://www.R-project.org
66. Rodríguez F, Hammer S, Pérez T, Suchentrunk F, Lorenzini R, Michallet J, Martinkova M, Albornoz J, Domínguez 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.
67. Roucher F. 1999. The fate of the Chartreuse chamois. Caprinae, Newsletter of the IUCN/SSC Caprinae Specialist Group. January 1999.
68. Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
69. 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.
70. Schneider S, Roessli D, Excoffier L. 2000. Arlequin. A software for population genetic data analysis, Version 2.0. Switzerland: Genetics and Biometry Laboratory, Department of Anthropology and Ecology, University of Geneva.
71. Sfougaris AI, Giannakopoulos A, Goumas H, Tsachalidis E. 1999. Status and management needs of a Balkan chamois population in the Rodopi Mountains. Caprinae, Newsletter of the IUCN/SSC Caprinae Specialist Group. May 1999.
72. Simonsen BT, Siegismund HR, Arctander P. 1998. Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation. Mol Ecol. 7:225-237.
73. Slatkin M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457-462.
74. Solinas-Toldo S, Fries R. 1993. Physically mapped, cosmid-derived microsatellite markers as anchor loci on bovine chromosomes. Mamm Genome 4:720-727.
75. Steffen P, Eggen A, Dietz AB, Womack JE, Stranzinger G, Fries R. 1993. Isolation and mapping of polymorphic microsatellites in cattle. Anim Genet. 24:121-124.
76. Swofford D. 2000. PAUP*: Phylogenetic analysis using parsimony (*and other methods). Version 4.0b8. Sunderland (MA): Sinauer Associates.
77. 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. 10:512-526.
78. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The Clustal-x windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876-4882.
79. Tosi G, Perco F. 1981. Camoscio Rupicapra rupicapra Linnaeus, 1758. In: Pavan D, editor. Distribuzione e biologia di 22 specie di Mammiferi in Italia. Rome (Italy): CNR. p. 177-184.
80. Vaiman D, Mercier D, Moazami-Goudarzi K, Eggen A, Ciampolini R, Lépingle A, Velmala R, Kaukinen J, Varvio SL, Martin P, et al. 1994. A set of 99 cattle microsatellites: Characterization, synteny mapping, and polymorphism. Mamm Genome 5:288-297.
81. Vaiman D, Osta R, Mercier D, Grohs C, Leveziel H. 1992. Characterization of five new bovine dinucleotide repeats. Anim Genet. 23:537-541.
82. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P. 2004. MICROCHECKER: Software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes. 4:535-538.
83. Vernesi C, Crestanello B, Pecchioli E, Tartari D, Caramelli D, Hauffe H, Bertorelle G. 2003. The genetic impact of population decline and reintroduction in the wild boar (Sus scrofa): A microsatellite analysis. Mol Ecol. 12:585-595.
84. Vernesi C, Pecchioli E, Caramelli D, Tiedemann R, Randi E, Bertorelle G. 2002. The genetic structure of natural and reintroduced roe deer (Capreolus capreolus) populations in the Alps and Central Italy, with reference to the mitochondrial DNA phylogeography of Europe. Mol Ecol. 11:1285-1297.
85. Weir BS, Cockerham CC. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.
86. Worley K, Strobeck C, Arthur S, Carey J, Schwantje H, Veitch A, Coltman DW. 2004. Population genetic structure of North American thinhorn sheep (Ovis dalli). Mol Ecol. 13:2545-2556.
87. Wright S. 1951. The genetical structure of populations. Ann Eugen. 1:323-334.