Effects of genotyping protocols on success and errors in identifying individual river otters (Lontra canadensis) from their faeces

Molecular Ecology Resources

Volumn 8, Issue 2, 2008, Pages 282-289

  Hansen, Heidi ^a   Ben David, Merav ^b   Mcdonald, David B ^b  

^a NATIONAL PARK SERVICE   (United States)

^b UNIVERSITY OF WYOMING   (United States)

Author keywords

Allelic dropout; Blood; Multiple alleles; Multiple tubes; Noninvasive genetic sampling; Population estimates

Indexed keywords

CARNIVORA; LONTRA CANADENSIS; LUTRA CANADENSIS;

EID: 38949155479     PISSN: 1755098X     EISSN: 14718286     Source Type: Journal    
DOI: 10.1111/j.1471-8286.2007.01992.x     Document Type: Article

References (44)

1. Banks SC, Piggott MP, Hansen BD et al 2002) Wombat coprogenetics: enumerating a common wombat population by microsatellite analysis of faecal DNA. Australian Journal of Zoology, 50, 193 204.
2. Bayes MK, Smith KL, Alberts SC et al 2000) Testing the reliability of microsatellite typing from faecal DNA in the savannah baboon. Conservation Genetics, 1, 173 176.
3. Beheler AS, Fike JA, Murfitt LM et al 2004) Development of polymorphic microsatellite loci for North American river otters (Lontra canadensis) and amplification in related mustelids. Molecular Ecology Resources, 4, 56 58.
4. Ben-David M, Duffy LK, Bowyer RT (2001) Biomarker responses in river otters experimentally exposed to oil contamination. Journal of Wildlife Diseases, 37, 489 508.
5. Ben-David M, Williams TM, Ormseth OA (2000) Effects of oiling on exercise physiology and diving behavior of river otters: a captive study. Canadian Journal of Zoology, 78, 1380 1390.
6. Blundell GM, Ben-David M, Groves P et al 2002) Characteristics of sex-biased dispersal and gene flow in coastal river otters: implications for natural recolonization of extirpated populations. Molecular Ecology, 11, 289 303.
7. Blundell GM, Ben-David M, Groves P et al 2004) Kinship and sociality in coastal river otters: are they related? Behavioral Ecology, 15, 705 714.
8. Bonin A, Bellemain E, Eidesen PB et al 2004) How to track and assess genotyping errors in population genetics studies. Molecular Ecology, 13, 3261 3273.
9. Bradley BJ, Vigilant L (2002) False alleles derived from microbial DNA pose a potential source of error in microsatellite genotyping of DNA from faeces. Molecular Ecology Resources, 2, 602 605.
10. Broquet T, Petit E (2004) Quantifying genotyping errors in noninvasive population genetics. Molecular Ecology, 13, 3601 3608.
11. Creel S, Spong G, Sands JL et al 2003) Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes. Molecular Ecology, 12, 2003 2009.
12. Dallas JF, Coxon KE, Sykes T et al 2003) Similar estimates of population genetic composition and sex ratio derived from carcasses and faeces of Eurasian otter Lutra lutra. Molecular Ecology, 12, 275 282.
13. Dallas JF, Piertney SB (1998) Microsatellite primers for the Eurasian otter. Molecular Ecology, 7, 1247 1251.
14. Ernest HB, Penedo MCT, May BP et al 2000) Molecular tracking of mountain lions in the Yosemite Valley region in California: genetic analysis using microsatellites and faecal DNA. Molecular Ecology, 9, 433 441.
15. Fernando P, Vidya TNC, Rajapakse C et al 2003) Reliable noninvasive genotyping: fantasy or reality? Journal of Heredity, 94, 115 123.
16. Frantz AC, Pope LC, Carpenter PJ et al 2003) Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Molecular Ecology, 12, 1649 1661.
17. Frantzen MAJ, Silk JB, Ferguson JWH et al 1998) Empirical evaluation of preservation methods for faecal DNA. Molecular Ecology, 7, 1423 1428.
18. Gagneux P, Boesch C, Woodruff DS (1997) Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair. Molecular Ecology, 6, 861 868.
19. Gerloff U, Schlötterer C, Rassmann K et al 1995) Amplification of hypervariable simple sequence repeats (microsatellites) from excremental DNA of wild living bonobos (Pan paniscus). Molecular Ecology, 4, 515 518.
20. Goossens B, Chikhi L, Utami SS et al 2000) A multi-samples, multi-extracts approach for microsatellite analysis of faecal samples in an arboreal ape. Conservation Genetics, 1, 157 162.
21. Huber S, Bruns U, Arnold W (2003) Genotyping herbivore feces facilitating their further analyses. Wildlife Society Bulletin, 31, 692 697.
22. Johnson LB (2006) Assessing the feasibility of using hair snares and DNA analysis to determine the dispersal of American martens (Martes americana) among old-growth reserves on Prince of Wales Island, Alaska. MS Thesis, University of Wyoming, Laramie, Wyoming.
23. Kohn M, Knauer F, Stoffella A et al 1995) Conservation genetics of the European brown bear - a study using excremental PCR of nuclear and mitochondrial sequences. Molecular Ecology, 4, 95 103.
24. Kohn MH, Wayne RK (1997) Facts from feces revisited. Trends in Ecology & Evolution, 12, 223 227.
25. Lucchini V, Fabbri E, Marucco F et al 2002) Noninvasive molecular tracking of colonizing wolf (Canis lupus) packs in the western Italian Alps. Molecular Ecology, 11, 857 868.
26. Lukacs PM, Burnham KN (2005a) Estimating population size from DNA-based closed capture-recapture data incorporating genotyping error. Journal of Wildlife Management, 69, 396 403.
27. Lukacs PM, Burnham KN (2005b) Review of capture-recapture methods applicable to noninvasive genetic sampling. Molecular Ecology, 14, 3909 3919.
28. McKelvey KS, Schwartz MK (2004a) Genetic errors associated with population estimation using non-invasive molecular tagging: problems and new solutions. Journal of Wildlife Management, 68, 439 448.
29. McKelvey KS, Schwartz MK (2004b) Providing reliable and accurate genetic capture-mark-recapture estimates in a cost effective way. Journal of Wildlife Management, 68, 453 456.
30. Miller CR, Joyce P, Waits LP (2002) Assessing allelic drop-out and genotype reliability using maximum likelihood. Genetics, 160, 357 366.
31. Mills LS, Citta JJ, Lair KP et al 2000) Estimating animal abundance using noninvasive DNA sampling: promise and pitfalls. Ecological Applications, 10, 283 294.
32. Morin PA, Chambers KE, Boesch C et al 2001) Quantitative polymerase chain reaction analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus). Molecular Ecology, 10, 1835 1844.
33. 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.
34. Paetkau D (2003) An empirical exploration of data quality in DNA-based population inventories. Molecular Ecology, 12, 1375 1387.
35. Paetkau D (2004) The optimal number of markers in genetic capture-mark-recapture studies. Journal of Wildlife Management, 68, 449 452.
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. Molecular Ecology, 11, 2171 2182.
37. Prigioni C, Remonti L, Balestrieri A et al 2006) Estimation of European otter (Lutra lutra) population size by fecal DNA typing in southern Italy. Journal of Mammalogy, 87, 855 858.
38. Taberlet P, Griffin S, Goossens B et al 1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research, 2, 3189 3194.
39. Taberlet P, Luikart G (1999) Non-invasive genetic sampling and individual identification. Biological Journal of the Linnean Society, 68, 41 55.
40. Taberlet P, Waits LP, Luikart G (1999) Noninvasive genetic sampling: look before you leap. Trends in Ecology & Evolution, 14, 323 327.
41. Valière N (2002) gimlet: a computer program for analysing genetic individual identification data. Molecular Ecology Resources, 2, 377 379.
42. Waits LP (2004) Using genetic sampling to estimate abundance of rare wild species. In : Sampling Rare or Elusive Species: Concepts, Designs, and Techniques for Estimating Population Parameters (ed. Thompson WL pp. 211 228. Island Press, Washington D.C.
43. Waits LP, Paetkau D (2005) Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection. Journal of Wildlife Management, 69, 1419 1433.
44. Zar JH (1999) Biostatistical Analysis. Prentice Hall, Upper Saddle River, New Jersey.