Species-specific mitochondrial DNA markers for identification of non-invasive samples from sympatric carnivores in the Iberian Peninsula

Conservation Genetics

Volumn 9, Issue 3, 2008, Pages 681-690

  Fernandes, Carlos A ^a   Ginja, Catarina ^a   Pereira, Iris ^a   Tenreiro, Rogério ^c   Bruford, Michael W ^b   Santos Reis, Margarida ^a  

^a UNIVERSITY OF LISBON   (Portugal)

^b CARDIFF UNIVERSITY   (United Kingdom)

^c UNIVERSITY OF LISBON   (Portugal)

Author keywords

Genetic species identification; Iberian Peninsula; Monitoring surveys; Non invasive DNA sampling; Sympatric carnivores

Indexed keywords

CARNIVORE; GENETIC DIFFERENTIATION; IDENTIFICATION METHOD; INVASIVE SPECIES; MITOCHONDRIAL DNA; PHYLOGENETICS; POPULATION GENETICS; SAMPLING; SURVEY; SYMPATRY;

EURASIA; EUROPE; IBERIAN PENINSULA; SOUTHERN EUROPE;

EID: 42549083316     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-007-9364-5     Document Type: Article

References (56)

1. Ayyadevara S, Thaden JJ, Reis RJS (2000) Discrimination of primer 3′-nucleotide mismatch by Taq DNA polymerase during polymerase chain reaction. Anal Biochem 284:11-18
2. Bartlett SE, Davidson WS (1992) FINS (forensically informative nucleotide sequencing): a procedure for identifying the animal origin of biological specimens. Biotechniques 12:408-411
3. Bensasson D, Zhang DX, Hartl DL et al (2001) Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol Evol 16:314-321
4. Cabral MJ, Almeida J, Almeida PR et al (eds) (2005) Livro Vermelho dos Vertebrados de Portugal. Instituto da Conservação da Natureza, Lisboa
5. Colli L, Cannas R, Deiana AM et al (2005) Identification of mustelids (Carnivora: Mustelidae) by mitochondrial DNA markers. Mamm Biol 70:384-389
6. Cracraft J, Feinstein J, Vaughn J et al (1998) Sorting out tigers (Panthera tigris): mitochondrial sequences, nuclear inserts, systematics, and conservation genetics. Anim Conserv 1:63-74
7. Dalén L, Gotherstrom A, Angerbjorn A (2004) Identifying species from pieces of faeces. Conserv Genet 5:109-111
8. Davison A, Birks JDS, Griffiths HI et al (1999) Hybridization and the phylogenetic relationship between polecats and domestic ferrets in Britain. Biol Conserv 87:155-162
9. Davison A, Griffiths HI, Brookes RC et al (2000) Mitochondrial DNA and palaeontological evidence for the origins of endangered European mink, Mustela lutreola. Anim Conserv 4:345-355
10. Davison A, Birks JDS, Brookes RC et al (2001) Mitochondrial phylogeography and population history of pine martens Martes martes compared with polecats Mustela putorius. Mol Ecol 10:2479-2488
11. Davison A, Birks JDS, Brookes RC et al (2002) On the origin of faeces: morphological versus molecular methods for surveying rare carnivores from their scats. J Zool 257:141-143
12. Delisle I, Strobeck C (2002) Conserved primers for rapid sequencing of the complete mitochondrial genome from carnivores, applied to three species of bears. Mol Biol Evol 19:357-361
13. Farrell LE, Roman J, Sunquist ME (2000) Dietary separation of sympatric carnivores identified by molecular analysis of scats. Mol Ecol 9:1583-1590
14. Ferrando A, Ponsa M, Marmi J et al (2004) Eurasian otters, Lutra lutra, have a dominant mtDNA haplotype from the Iberian Peninsula to Scandinavia. J Hered 95:430-435
15. Foran DR, Crooks KR, Minta SC (1997a) Species identification from scat: an unambiguous genetic method. Wildl Soc B 25:835-839
16. Foran DR, Minta SC, Heinemeyer KS (1997b) DNA-based analysis of hair to identify species and individuals for population research and monitoring. Wildl Soc B 25:840-847
17. Frantz AC, Schaul M, Pope LC et al (2004) Estimating population size by genotyping remotely plucked hair: the Eurasian badger. J Appl Ecol 41:985-995
18. Frantzen MAJ, Silk JB, Ferguson JWH et al (1998) Empirical evaluation of preservation methods for faecal DNA. Mol Ecol 7:1423-1428
19. Frati F, Hartl GB, Lovari S et al (1998) Quaternary radiation and genetic structure of the red fox Vulpes vulpes in the Mediterranean Basin, as revealed by allozymes and mitochondrial DNA. J Zool 245:43-52
20. Gese EM (2001) Monitoring of terrestrial carnivore populations. In: Gittleman JL, Funk SM, MacDonald DW, Wayne RK (eds) Carnivore conservation. Cambridge University Press, Cambridge
21. Gómez-Moliner BJ, Cabria MT, Rubines J et al (2004) PCR-RFLP identification of mustelids species: European mink (Mustela lutreola), American mink (M. vison), and polecat (M. putorius) by analysis of excremental DNA. J Zool 262:311-316
22. Hansen MM, Jacobsen L (1999) Identification of mustelids species: otter (Lutra lutra), American mink (Mustela vison) and polecat (Mustela putorius), by analysis of DNA from faecal samples. J Zool 247:177-181
23. Ishiguro N, Nakajima A, Horiuchi M et al (2002) Multiple nuclear pseudogenes of mitochondrial DNA exist in the canine genome. Mamm Genome 13:365-372
24. Johnson WE, Godoy JA, Palomares F et al (2004) Phylogenetic and phylogeographic analysis of Iberian lynx populations. J Hered 95:19-28
25. Kohn MH, York EC, Kamradt DA et al (1999) Estimating population size by genotyping faeces. Proc R Soc B Biol Sci 266:657-663
26. Kurose N, Masuda R, Tatara M (2005) Fecal DNA analysis for identifying species and sex of sympatric carnivores: a noninvasive method for conservation on the Tsushima Islands, Japan. J Hered 96:688-697
27. Lecis R, Pierpaoli M, Biro ZS et al (2006) Bayesian analysis of admixture in wild and domestic cats (Felis silvestris) using linked microsatellite loci. Mol Ecol 15:119-131
28. Lopez JV, Cevario S, O'Brien SJ (1996) Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome. Genomics 33:229-246
29. López-Giráldez F, Gómez-Moliner BJ, Marmi J et al (2005) Genetic distinction of American and European mink (Mustela vison and M. lutreola) and European polecat (M. putorius) hair samples by detection of a species-specific SINE and a RFLP assay. J Zool 265:405-410
30. Lucentini L, Vercillo F, Palomba A et al (2007) A PCR-RFLP method on faecal samples to distinguish Martes martes, Martes foina, Mustela putorius and Vulpes vulpes. Conserv Genet 8:757-759
31. MacDonald D, Barrett P (1993) Mammals of Britain and Europe. Harper Collins, London
32. Michaux JR, Hardy OJ, Justy F et al (2005) Conservation genetics and population history of the threatened European mink Mustela lutreola, with an emphasis on the west European population. Mol Ecol 14:2373-2388
33. Mills LS, Pilgrim KL, Schwartz MK et al (2000) Identifying lynx and other North American felids based on mtDNA analysis. Conserv Genet 1:285-288
34. Mukherjee S, Goyal SP, Johnsingh AJT et al (2004) The importance of rodents in the diet of jungle cat (Felis chaus), caracal (Caracal caracal) and golden jackal (Canis aureus) in Sariska Tiger Reserve, Rajasthan, India. J Zool 262:405-411
35. Mundy NI, Unitt P, Woodruff DS (1997) Skin from feet of museum specimens as a non-destructive source of DNA for avian genotyping. Auk 114:126-128
36. Palomares F, Godoy JA, Piriz A et al (2002) Faecal genetic analysis to determine the presence and distribution of elusive carnivores: design and feasibility for the Iberian lynx. Mol Ecol 11:2171-2182
37. Palomo LJ, Gisbert J (eds) (2002) Atlas de los mamíferos terrestres de España. Dirección General de la Conservación de la Naturaleza-SECEM-SECEMU, Madrid
38. Parson W, Pegoraro K, Niederstatter H et al (2000) Species identification by means of the cytochrome b gene. Int J Leg Med 114:23-28
39. Paxinos E, McIntosh C, Ralls K et al (1997) A noninvasive method for distinguishing among canid species: amplification and enzyme restriction of DNA from dung. Mol Ecol 6:483-486
40. Pertoldi C, Breyne P, Cabria MT et al (2006) Genetic structure of the European polecat (Mustela putorius) and its implication for conservation strategies. J Zool 270:102-115
41. Pilot M, Gralak B, Goszczynski J et al (2007) A method of genetic identification of pine marten (Martes martes) and stone marten (Martes foina) and its applications to faecal samples. J Zool. 271:140-147
42. Prugh LR, Ritland CE (2005) Molecular testing of observer identification of carnivore feces in the field. Wildl Soc B 33:189-194
43. Randi E, Pierpaoli M, Beaumont M et al (2001) Genetic identification of wild and domestic cats (Felis silvestris) and their hybrids using Bayesian clustering methods. Mol Biol Evol 18:1679-1693
44. Riddle AE, Pilgrim KL, Mills LS et al (2003) Identification of mustelids using mitochondrial DNA and non-invasive sampling. Conserv Genet 4:241-243
45. Roeder AD, Archer FI, Poinar HN et al (2004) A novel method for collection and preservation of faeces for genetic studies. Mol Ecol Notes 4:761-764
46. Rosalino LM, Torres J, Santos-Reis M (2006) A survey of helminth infection in Eurasian badgers (Meles meles) in relation to their foraging behaviour in a Mediterranean environment in southwest Portugal. Eur J Wildl Res 52:202-206
47. Sadlier LMJ, Webbon CC, Baker PJ et al (2004) Methods of monitoring red foxes Vulpes vulpes and badgers Meles meles: are field signs the answer? Mammal Rev 34:75-98
48. Seutin G, White BN, Boag PT (1991) Preservation of avian blood and tissue samples for DNA analyses. Can J Zool 69:82-90
49. Verardi A, Lucchini V, Randi E (2006) Detecting introgressive hybridisation between free-ranging domestic dogs and wild wolves (Canis lupus) by admixture linkage disequilibrium analysis. Mol Ecol 15:2845-2855
50. Vercillo F, Lucentini L, Mucci N et al (2004) A simple and rapid PCR-RFLP method to distinguish Martes martes and Martes foina. Conserv Genet 5:869-871
51. Waits LP, Paetkau D (2005) Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection. J Wildl Manage 69:1419-1433
52. Walsh PS, Metzger DA, Higuchi R (1991) Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10:506-513
53. Wan Q, Fang S (2003) Application of species-specific polymerase chain reaction in the forensic identification of tiger species. Forensic Sci Int 131:75-78
54. Wayne RK, Vila C (2001) Phylogeny and origin of the domestic dog. In: Ruvinsky A, Sampson J (eds) The genetics of the dog. CABI Publishing, Wallingford
55. Woischnik M, Moraes CT (2002) Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. Genome Res 12:885-893
56. Zhan X, Li M, Zhang Z et al (2006) Molecular censusing doubles giant panda population estimate in a key nature reserve. Curr Biol 16:R436-R437