Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples

Molecular Ecology Resources

Volumn 9, Issue 1, 2009, Pages 28-36

  Arandjelovic, M ^a   Guschanski, K ^a   Schubert, G ^a   Harris, T R ^a   Thalmann, O ^a   Siedel, H ^a   Vigilant, L ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

Author keywords

Black and white colobus; Chimpanzee; Genotyping errors; Gorilla; Low quantity DNA; Multiplex pre amplification method

Indexed keywords

COLOBINAE; COLOBUS; GORILLA GORILLA BERINGEI; PAN;

EID: 58949083369     PISSN: 1755098X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2008.02387.x     Document Type: Article

References (34)

1. Ball MC, Pither R, Manseau M et al 2007) Characterization of target nuclear DNA from faeces reduces technical issues associated with the assumption of low-quality and quantity template. Conservation Genetics, 8, 577 586.
2. Banks SC, Piggott MP, Hansen BD, Robinson NA, Taylor AC (2002) Wombat coprogenetics: enumerating a common wombat population by microsatellite analysis of faecal DNA. Australian Journal of Zoology, 50, 193 204.
3. Bayes MK, Smith KL, Alberts SC, Altman J, Bruford MW (2000) Testing the reliability of microsatellite typing from fecal DNA in the savannah baboon. Conservation Genetics, 1, 173 176.
4. Bellemain E, Taberlet P (2004) Improved noninvasive genotyping method: application to brown bear (Ursus arctos) faeces. Molecular Ecology Notes, 4, 519 522.
5. Bellemain E, Swenson JE, Tallmon D, Brunberg S, Taberlet P (2005) Estimating population size of elusive animals with DNA from hunter-collected feces: four methods for brown bears. Conservation Biology, 19, 150 161.
6. Bonhomme M, Blancher A, Crouau-Roy B (2005) Mutiplexed microsatellites for rapid identification and characterization of individuals and populations of Cercopithecidae. American Journal of Primatology, 67, 385 391.
7. Broquet T, Petit E (2004) Quantifying genotyping errors in noninvasive population genetics. Molecular Ecology, 13, 3601 3608.
8. Chamberlain JS, Gibbs RA, Ranier JE, Nguyen PN, Caskey CT (1988) Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. Nucleic Acids Research, 16, 11141 11156.
9. Flagstad O, Røed K, Stacy JE, Jakobsen KS (1999) Reliable noninvasive genotyping based on excremental PCR of nuclear DNA purified with a magnetic bead protocol. Molecular Ecology, 8, 879 883.
10. Frantzen MAJ, Silk JB, Ferguson JWH, Wayne RK, Kohn MH (1998) Empirical evaluation of preservation methods for faecal DNA. Molecular Ecology, 7, 1423 1428.
11. Hansen H, Ben-David M, McDonald DB (2008) Effects of genotyping protocols on success and errors in identifying individual river otters (Lontra Canadensis) from their feces. Molecular Ecology Resources, 8, 282 289.
12. Hedmark E, Ellegren H (2006) A test of the multiplex pre-amplification approach in microsatellite genotyping of wolverine faecal DNA. Conservation Genetics, 7, 289 293.
13. Hedmark E, Flagstad O, Segerström P et al 2004) DNA-based individual and sex identification from wolverine (Gulo Gulo) faeces and urine. Conservation Genetics, 5, 405 410.
14. Kohn MH, York EC, Kamradt DA et al 1999) Estimating population size by genotyping faeces. Proceedings of the Royal Society B: Biological Sciences, 266, 657 663.
15. Lampa S, Gruber B, Henle K, Hoehn M (2008) An optimisation approach to increase DNA amplification success of otter faeces. Conservation Genetics, 9, 201 210.
16. Miquel C, Bellemain E, Poillot C et al 2006) Quality indexes to assess the reliability of genotypes in studies using noninvasive sampling and multiple-tube approach. Molecular Ecology Notes, 6, 985 988.
17. Monteiro L, Bonnemaison D, Vekris A et al 1997) Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. Journal of Clinical Microbiology, 35, 995 998.
18. Morin PA, Chambers KE, Boesch C, Vigilant L (2001) Quantitative PCR analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus). Molecular Ecology, 10, 1835 1844.
19. Murphy MA, Waits LP, Kendall KC et al 2002) An evaluation of long-term preservation methods for brown bear (Ursus arctos) faecal DNA samples. Conservation Genetics, 3, 435 440.
20. Navidi W, Arnheim N, Waterman MS (1992) A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR: statistical considerations. American Journal of Human Genetics, 50, 347 359.
21. Nsubuga AM, Robbins MM, Roeder A et al 2004) Factors affecting the amount of genomic DNA extracted from ape feces and the identification of an improved sample storage method. Molecular Ecology, 13, 2089 2094.
22. Piggot MP, Bellemain E, Taberlet P, Taylor AC (2004) A multiplex pre-amplification method that significantly improves microsatellite amplification and error rate for faecal DNA in limiting conditions. Conservation Genetics, 5, 417 420.
23. Piggott MP, Banks SC, Stone N, Banffy C, Taylor AC (2006) Estimating population size of endangered brush-tailed rock-wallaby (Petrogale penicillata) colonies using faecal DNA. Molecular Ecology, 15, 81 91.
24. Puechmaille SJ, Petit EJ (2007) Empirical evaluation of non-invasive capture-mark-recpature estimation of population size based on a single sampling session. Journal of Applied Ecology, 44, 843 852.
25. Puechmaille SJ, Mathy G, Petit EJ (2007) Good DNA from bat droppings. Acta Chiropterologica, 9, 269 276.
26. Roeder AD, Archer FI, Poinar HN, Morin PA (2004) A novel method for collection and preservation of faeces for genetic studies. Molecular Ecology Notes, 4, 761 764.
27. Roeder AD, Jeffery K, Bruford MW, the INPRIMAT consortium (2006) A universal microsatellite multiplex kit for genetic analysis of great apes. Folia Primatologica, 77, 240 245.
28. Roempler H, Dear PH, Krause J et al 2006) Multiplex amplification of ancient DNA. Nature Protocols, 1, 720 728.
29. Roon DA, Waits LP, Kendall KC (2003) A quantitative evaluation of two methods for preserving hair samples. Molecular Ecology Notes, 3, 163 166.
30. Sloane MA, Sunnucks P, Alpers D, Beheregaray B, Taylor AC (2000) Highly reliable genetic identification of individual northern hairy-nosed wombats from single remotely collected hairs: a feasible censusing method. Molecular Ecology, 9, 1233 1240.
31. Taberlet P, Griffin S, Goossens B et al 1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research, 26, 3189 3194.
32. Taberlet P, Waits LP, Luikart G (1999) Noninvasive genetic sampling: look before you leap. Trends in Ecology & Evolution, 14, 321 325.
33. Vigilant L, Hofreiter M, Siedel H, Boesch C (2001) Paternity and relatedness in wild chimpanzee communities. Proceedings of the National Academy of Sciences, USA, 98, 12890 12895.
34. Wehausen JD, Ramey RR, Epps CW (2004) Experiments in DNA extraction and PCR amplification from bighorn sheep feces: the importance of DNA extraction method. Journal of Heredity, 95, 503 509.