How many genetic markers to tag an individual? An empirical assessment of false matching rates among close relatives

Ecological Applications

Volumn 21, Issue 3, 2011, Pages 877-887

  Rew, Mary Beth ^a,d   Robbins, Jooke ^b   Mattila, David ^b,e   Palsbøll, Per J ^a,c   Bérubé, Martine ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CENTER FOR COASTAL STUDIES   (United States)

^c STOCKHOLM UNIVERSITY   (Sweden)

^d OREGON STATE UNIVERSITY   (United States)

^e Hawaiian Islands Humpback Whale National Marine Sanctuary   (United States)

Author keywords

Abundance estimation; Conservation; Error rates; Genetic tagging; Humpback whale; Mark recapture; Megaptera novaeangliae; Microsatellite; Monitoring; Number of loci; Probability of identity; Relatedness

Indexed keywords

DNA; MICROSATELLITE DNA;

ABUNDANCE; ASSESSMENT METHOD; EMPIRICAL ANALYSIS; ENVIRONMENTAL MONITORING; ERROR ANALYSIS; ESTIMATION METHOD; GENETIC MARKER; GENOTYPE; IDENTIFICATION METHOD; LABORATORY METHOD; MARK-RECAPTURE METHOD; PARENT-OFFSPRING INTERACTION; RELATEDNESS; WHALE;

ANIMAL; ARTICLE; FEMALE; GENE LOCUS; GENETIC MARKER; GENETICS; GENOTYPE; HUMPBACK WHALE;

ANIMALS; DNA; FEMALE; GENETIC LOCI; GENETIC MARKERS; GENOTYPE; HUMPBACK WHALE; MICROSATELLITE REPEATS;

MEGAPTERA; MEGAPTERA NOVAEANGLIAE;

EID: 79955508550     PISSN: 10510761     EISSN: None     Source Type: Journal    
DOI: 10.1890/10-0348.1     Document Type: Article

References (38)

1. Baker, C. S., J. G. Cooke, S. Lavery, M. L. Dalebout, Y. U. Ma, N. Funahashi, C. Carraher, and R. L. Brownell. 2007. Estimating the number of whales entering trade using DNA profiling and capture-recapture analysis of market products. Molecular Ecology 16:2617-2626. (Pubitemid 47012147)
2. Bérubé, M., A. Aguilar, D. Dendanto, F. Larsen, G. Notarbartolo-di-Sciara, R. Sears, J. Sigurjónsson, J. Urban- Ramirez, and P. J. Palsbøll. 1998. Population genetic structure of North Atlantic, Mediterranean Sea and Sea of Cortez fin whales, Balaenoptera physalus (Linnaeus, 1758): analysis of mitochondrial and nuclear loci. Molecular Ecology 7:585-600.
3. Bérubé , M., H. Jørgensen, R. McEwing, and P. J. Palsbøll. 2000. Polymorphic di-nucleotide microsatellite loci isolated from the humpback whale, Megaptera novaeangliae. Molecular Ecology 9:2181-2182. (Pubitemid 32053365)
4. Blouin, M. S. 2003. DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends in Ecology and Evolution 18:503-511. (Pubitemid 37143677)
5. Bonin, A., E. Bellemain, P. B. Eidesen, F. Pompanon, C. Brochmann, and P. Taberlet. 2004. How to track and assess genotyping errors in population genetics studies. Molecular Ecology 13:3261-3273. (Pubitemid 39415663)
6. Clapham, P., J. Barlow, M. Bessinger, T. Cole, D. Mattila, R. Pace, D. Palka, J. Robbins, and R. Seton. 2003. Abundance and demographic parameters of humpback whales from the Gulf of Maine, and stock definition relative to the Scotian Shelf. Journal of Cetacean Research and Management 5:13-22. (Pubitemid 36905380)
7. Clapham, P. J., and C. A. Mayo. 1987. Reproduction and recruitment of individually identified humpback whales, Megaptera novaeangliae, observed in Massachusetts Bay, 1979-1985. Canadian Journal of Zoology 65:2853-2863. (Pubitemid 19318355)
8. Creel, S., G. Spong, J. L. Sands, J. Rotella, J. Zeigle, L. Joe, K. M. Murphy, and D. Smith. 2003. Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes. Molecular Ecology 12:2003-2009. (Pubitemid 36815033)
9. Kalinowski, S. T., A. P. Wagner, and M. L. Taper. 2006. MLRELATE: a computer program for maximum likelihood estimation of relatedness and relationship. Molecular Ecology Notes 6:576-579. (Pubitemid 43780797)
10. Katona, S. K., and J. A. Beard. 1991. Humpback whales (Megaptera novaeangliae) in the western North Atlantic Ocean. Memoirs of the Queensland Museum 30:307-321.
11. Katona, S. K., and H. P. Whitehead. 1981. Identifying humpback whales using their natural markings. Polar Record 20:439-444.
12. Kendall, K. C., J. B. Stetz, J. Boulanger, A. C. Macleod, D. Paetkau, and G. C. White. 2009. Demography and genetic structure of a recovering grizzly bear population. Journal of Wildlife Management 73:3-17.
13. McKelvey, K. S., and M. K. Schwartz. 2004. Genetic errors associated with population estimation using non-invasive molecular tagging: problems and new solutions. Journal of Wildlife Management 68:439-448. (Pubitemid 39033498)
14. Mills, L. S., J. J. Citta, K. P. Lair, M. K. Schwartz, and D. A. Tallmon. 2000. Estimating animal abundance using noninvasive DNA sampling: promise and pitfalls. Ecological Applications 10:283-294. (Pubitemid 30086660)
15. Paetkau, D. 2003. An empirical exploration of data quality in DNA-based population inventories. Molecular Ecology 12: 1375-1387. (Pubitemid 36708446)
16. Paetkau, D. 2004. The optimal number of markers in genetic capture-mark-recapture studies. Journal of Wildlife Management 68:449-452. (Pubitemid 39033499)
17. Paetkau, D., W. Calvert, I. Stirling, and C. Strobeck. 1995. Microsatellite analysis of population-structure in Canadian polar bears. Molecular Ecology 4:347-354.
18. Paetkau, D., and C. Strobeck. 1994. Microsatellite analysis of genetic variation in black bear populations. Molecular Ecology 3:489-495. (Pubitemid 2152897)
19. Palsbøll, P. J., et al. 1997a. Genetic tagging of humpback whales. Nature 388:676-679.
20. Palsbøll, P. J., M. Bérubé , A. H. Larsen, and H. Jørgensen. 1997b. Primers for the amplification of tri- and tetramer microsatellite loci in cetaceans. Molecular Ecology 6:893-895. (Pubitemid 27378147)
21. Pearse, D. E., C. M. Eckerman, F. J. Janzen, and J. C. Avise. 2001. A genetic analogue of "mark-recapture" methods for estimating population size: an approach based on molecular parentage assessments. Molecular Ecology 10:2711-2718. (Pubitemid 33136574)
22. Peery, M. Z., S. R. Beissinger, R. F. House, M. Berube, L. A. Hall, A. Sellas, and P. J. Palsbøll. 2008. Characterizing source-sink dynamics with genetic parentage assignments. Ecology 89:2746-2759.
23. Pompanon, F., A. Bonin, E. Bellemain, and P. Taberlet. 2005. Genotyping errors: causes, consequences and solutions. Nature Reviews Genetics 6:847-859.
24. Roon, D. A., L. P. Waits, and K. C. Kendall. 2005. A simulation test of the effectiveness of several methods for error-checking non-invasive genetic data. Animal Conservation 8:203-215. (Pubitemid 40742781)
25. Sambrook, J., and D. W. Russell. 2001. Molecular cloning. A laboratory manual. Third edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA.
26. Schwartz, M. K., G. Luikart, and R. S. Waples. 2007. Genetic monitoring as a promising tool for conservation and management. Trends in Ecology and Evolution 22:25-33. (Pubitemid 44959168)
27. Swenson, J. E., F. Sandegren, A. Bjärvall, A Söderberg, P. Wabakken, and F. R. Franzen. 1994. Size, trend, distribution and conservation of the brown bear Ursus arctos population in Sweden. Biological Conservation 70:9-17.
28. Taberlet, P., S. Griffin, B. Goossens, S. Questiau, V. Manceau, N. Escaravage, L. P. Waits, and J. Bouvet. 1996. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research 24:3189-3194. (Pubitemid 26278559)
29. Taberlet, P., L. P. Waits, and G. Luikart. 1999. Noninvasive genetic sampling: look before you leap. Trends in Ecology and Evolution 14:323-327. (Pubitemid 29334432)
30. Thompson, E. A. 1975. Estimation of pairwise relationships. Annals of Human Genetics 39:173-188.
31. Valiere, N., and P. Taberlet. 2000. Urine collected in the field as a source of DNA for species and individual identification. Molecular Ecology 9:2150-2152. (Pubitemid 32053349)
32. Valsecchi, E., and W. Amos. 1996. Microsatellite markers for the study of cetacean populations. Molecular Ecology 5:151-156.
33. Waits, J. L., and P. L. Leberg. 2000. Biases associated with population estimation using molecular tagging. Animal Conservation 3:191-199.
34. Waits, L. P., G. Luikart, and P. Taberlet. 2001. Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Molecular Ecology 10:249-256. (Pubitemid 32097545)
35. Waits, L. P., and D. Paetkau. 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.
36. Waldick, R. C., M. W. Brown, and B. N. White. 1999. Characterization and isolation of microsatellite loci from the endangered North Atlantic right whale. Molecular Ecology 8:1763-1765. (Pubitemid 29514722)
37. Woods, J. G., D. Paetkau, D. Lewis, B. N. McLellan, M. Proctor, and C. Strobeck. 1999. Genetic tagging of freeranging black and brown bears. Wildlife Society Bulletin 27: 616-627. (Pubitemid 30008019)
38. Wright, J. A., R. J. Barker, M. R. Schofield, A. C. Frantz, A. E. Byrom, and D. M. Gleeson. 2009. Incorporating genotype uncertainty into mark-recapture-type models for estimating abundance using DNA samples. Biometrics 65:833-840.