Development and testing of an optimized method for DNA-based identification of jaguar (Panthera onca) and puma (Puma concolor) faecal samples for use in ecological and genetic studies

Genetica

Volumn 136, Issue 3, 2009, Pages 505-512

  Haag, Taiana ^a,b   Santos, Anelisie S ^b   De Angelo, Carlos ^c   Srbek Araujo, Ana Carolina ^d   Sana, Dênis A ^e   Morato, Ronaldo G ^e,f   Salzano, Francisco M ^a   Eizirik, Eduardo ^b,g  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^b PONTIFICAL CATHOLIC UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^c Centro de Investigaciones del Bosque Atlantico Puerto Iguazu   (Argentina)

^d VALE S A   (Brazil)

^e Instituto Pro Carnivoros   (Brazil)

^f CENAP/ICMBio   (Brazil)

^g NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Faecal DNA; Mitochondrial DNA; Panthera onca; Puma concolor; Species identification

Indexed keywords

FELIDAE; PANTHERA; PANTHERA ONCA; PUMA CONCOLOR;

DNA; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; ECOLOGY; FECES; FORESTRY; GENETICS; HAPLOTYPE; METHODOLOGY; PANTHERA; PHYLOGENY; PUMA; REPRODUCIBILITY; SOUTH AMERICA; SPECIES DIFFERENCE;

ANIMALS; DNA; DNA, MITOCHONDRIAL; ECOLOGY; FECES; FORESTRY; HAPLOTYPES; PANTHERA; PHYLOGENY; PUMA; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SOUTH AMERICA; SPECIES SPECIFICITY;

EID: 67651092350     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10709-008-9347-6     Document Type: Article

References (35)

1. JR Adams BT Kelly LP Waits 2003 Using faecal DNA sampling and GIS to monitor hybridization between red wolves (Canis rufus) and coyotes (Canis latrans) Mol Ecol 12 2175 2186 10.1046/j.1365-294X.2003.01895.x
2. RA Bergl L Vigilant 2007 Genetic analysis reveals population structure and recent migration within the highly fragmented ranger of the Cross River gorilla (Gorilla gorilla diehli) Mol Ecol 16 501 516 10.1111/j.1365-294X.2006. 03159.x
3. J Bhagavatula L Singh 2006 Genotyping faecal samples of Bengal tiger Panthera tigris tigris for population estimation: a pilot study BMC Genet 7 48 10.1186/1471-2156-7-48
4. M Chame 2003 Terrestrial mammal feces: a morphometric summary and description Mem Inst Oswaldo Cruz 98 71 94 10.1590/S0074-02762003000900014 (Pubitemid 38019680)
5. A Davison JDS Birks RC Brookes TC Braithwaite JE Messenger 2002 On the origin of faeces: morphological versus molecular methods for surveying rare carnivores from their scats J Zool (Lond) 257 141 143 10.1017/S0952836902000730
6. LH Emmons 1987 Comparative feeding ecology of felids in a Neotropical rainforest Behav Ecol Sociobiol 20 271 283 10.1007/BF00292180
7. HB Ernest WM Boyce VC Bleich SJ Stiver ST Torres 2003 Genetic structure of mountain lion (Puma concolor) populations in California Conserv Genet 4 353 366 10.1023/A:1024069014911
8. LE Farrell J Romant ME Sunquist 2000 Dietary separation of sympatric carnivores identified by molecular analysis of scats Mol Ecol 9 1583 1590 10.1046/j.1365-294x.2000.01037.x
9. Johnson WE, Eizirik E, Roelke-Parker M, O'Brien SJ (2001) Applications of genetic concepts and molecular methods to carnivore conservation. In: Gittleman JL, Funk SM, MacDonald D, Wayne RK (eds) Carnivore conservation. Cambridge University Press, Cambridge, pp 335-358
10. J-H Kim A Antunes S-J Luo 2006 Evolutionary analysis of a large mtDNA translocation (Numt) into the nuclear genome of the Panthera genus species Gene 366 292 302 10.1016/j.gene.2005.08.023
11. MH Kohn EC York DA Kamradt G Haught RM Sauvajot RK Wayne 1999 Estimating population size by genotyping faeces Proc R Soc Lond B Biol Sci 266 657 663 10.1098/rspb.1999.0686 (Pubitemid 29161040)
12. S Kumar K Tamura M Nei 2004 MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment briefings Bioinformatics 5 150 163 10.1186/1471-2105-5-150
13. L Lucentini F Vercillo A Palomba F Panara B Ragni 2007 A PCR-RFLP method on faecal samples to distinguish Martes martes, Martes foina, Mustela putorius and Vulpes vulpes Conserv Genet 8 757 759 10.1007/s10592-006-9203-0
14. RA Miotto FP Rodrigues G Ciocheti PM Galetti Jr 2007 Determination of the minimum population size of pumas (Puma concolor) through fecal DNA analysis in two protected Cerrado areas in the brazilian southeast Biotropica 39 647 654 10.1111/j.1744-7429.2007.00315.x
15. Novack AJ (2003) Impacts of subsistence hunting on the foraging ecology of jaguar and puma in the Maya Biosphere Reserve, Guatemala. M.Sc. Thesis, University of Florida
16. AJ Novack MB Main ME Sunquist RF Labisky 2005 Foraging ecology of jaguar (Panthera onca) and puma (Puma concolor) in hunted and non-hunted sites within the Maya Biosphere Reserve, Guatemala J Zool (Lond) 267 167 178 10.1017/S0952836905007338
17. Nowell K, Jackson P (1996) Wilds cats: status survey and conservation action plan. IUCN, Gland
18. D Onorato C White P Zager LP Waits 2006 Detection of predator presence at elk mortality sites using mtDNA analysis of hair and scat samples Wildl Soc Bull 34 815 882 10.2193/0091-7648(2006)34[815:DOPPAE]2.0.CO;2
19. F Palomares JA Godoy A Piriz SJ O'Brien WE Johnson 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 10.1046/j.1365-294X.2002.01608.x
20. KM Parsons 2001 Reliable microsatellite genotyping of dolphin DNA from faeces Mol Ecol Notes 1 341 344 (Pubitemid 33691755)
21. KL Pilgrim KS Mckelvey AE Riddle MK Schwartz 2005 Felid sex identification based on noninvasive genetic samples Mol Ecol 5 60 61 (Pubitemid 40350879)
22. M Pilot B Gralak J Goszczynski M Postuszny 2007 A method of genetic identification of pine marten (Martes martes) and stone marten (Marten foina) and its application to faecal samples J Zool (Lond) 271 140 147 10.1111/j.1469-7998.2006.00179.x
23. Polisar J (2002) Componentes de la base de presas de jaguar y puma en Piñero, Venezuela. In: Medellín RA, Equihua C, Chetkiewicz CL, Crawshaw PG Jr, Rabinowitz A, Redford KH, Robinson JG, Sanderson EW, Taber AB (eds) El Jaguar en el nuevo milenio. Universidad Nacional Autonoma de Mexico/Wildlife Conservation Society, México, pp 151-182
24. JZ Reed DJ Tollit PM Thompson W Amos 1997 Molecular scatology: the use of molecular genetic analysis to assign species, sex and individual identify to seal faeces Mol Ecol 6 225 234 10.1046/j.1365-294X.1997.00175.x (Pubitemid 27126670)
25. JE Reed RJ Baker WB Ballard BT Kelly 2004 Differentiating Mexican gray wolf and coyote seats using DNA analysis Wildl Soc Bull 32 685 692 10.2193/0091-7648(2004)032[0685:DMGWAC]2.0.CO;2
26. N Saitou M Nei 1987 The Neighbor-joining method: a new method for reconstructing phylogenetic trees J Mol Evol 9 945 967
27. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning, 2nd edn. Cold Spring Harbor Laboratory Press, New York
28. Silveira L (2004) Ecologia comparada e conservação da onça-pintada (Panthera onca) e onça-parda (Puma concolor), no Cerrado e Pantanal. Ph.D. Thesis, University of Brasília
29. MA Sloane P Sunnucks D Alpers LB Beheregaray AC Taylor 2000 Highly reliable genetic identification of individual northern hairy-nosed wombats from single remotely collected hairs: a feasible censuring method Mol Ecol 9 1233 1240 10.1046/j.1365-294x.2000.00993.x
30. P Taberlet LP Waits G Luikart 1999 Noninvasive genetic sampling: look before you leap Trends Ecol Evol 14 323 327 10.1016/S0169-5347(99)01637-7
31. TC Trigo TR Freitas G Kunzler L Cardoso JC Silva WE Johnson SJ O'Brien SL Bonatto E Eizirik 2008 Inter-species hybridization among Neotropical cats of the genus Leopardus, and evidence for an introgressive hybrid zone between L. geoffroyi and L. tigrinus in southern Brazil Mol Ecol 17 4317 4317
32. QH Wan SG Fang GF Chen 2003 Use of oligonucleotide fingerprinting and faecal DNA in identifying the distribution of the Chinese tiger (Panthera tigris amoyensis Hilzheimer) Biodivers Conserv 12 1641 1648 10.1023/A:1023693613608
33. SK Wasser CS Houston GM Koehler GG Cadd SR Fain 1997 Techniques for application of faecal DNA methods to filed studies of Ursids Mol Ecol 6 1091 1097 10.1046/j.1365-294X.1997.00281.x (Pubitemid 27498890)
34. M Weckel W Giuliano S Silver 2006 Jaguar diet in the Cockscomb Basin Wildlife Sanctuary, Belize Biotropica 38 687 690 10.1111/j.1744-7429.2006.00190. x
35. D-X Zhang GM Hewitt 1996 Nuclear integration: challenges for mitochondrial DNA markers Trends Ecol Evol 11 247 251 10.1016/0169-5347(96) 10031-8