Incorporating genotyping error into non-invasive DNA-Based Mark-recapture population estimates

Journal of Wildlife Management

Volumn 73, Issue 4, 2009, Pages 598-604

  Knapp, Shannon M ^a   Craig, Bruce A ^a   Waits, Lisette P ^b  

^a PURDUE UNIVERSITY   (United States)

^b UNIVERSITY OF IDAHO   (United States)

Author keywords

DNA markers; Genotyping error; Markreleaserecapture; Microsatellite; Non invasive sampling; Population size estimation

Indexed keywords

ALLELE; CANID; DNA; ERROR ANALYSIS; GENETIC MARKER; GENOTYPE; MARK-RECAPTURE METHOD; POPULATION SIZE; SAMPLING;

CANIS FAMILIARIS; CANIS RUFUS;

EID: 77749292461     PISSN: 0022541X     EISSN: None     Source Type: Journal    
DOI: 10.2193/2007-156     Document Type: Article

References (30)

1. Adams, J. R., and L. P. Waits. 2007. An efficient method for screening faecal DNA genotypes and detecting new individuals and hybrids in the red wolf (Canis rufus) experimental population area. Conservation Genetics 8:123-131.
2. Bellemain, E., J. E. Swenson, D. Tallmon, S. Brunberg, and P. Taberlet. 2005. Estimating population size of elusive animals with DNA from hunter-collected feces: four methods for brown bears. Conservation Biology 19:150-161.
3. Burnham, K. P., and W. S. Overton. 1979. Robust estimation of population size when capture probabilities vary among animals. Ecology 60:927-936.
4. Chao, A. 1988. Estimating animal abundance with capture frequency data. Journal of Wildlife Management 52:295-300.
5. 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.
6. Frantz, A. C., L. C. Pope, P. J. Carpenter, T. J. Roper, G. J. Wilson, R. J. Delahay, and T. Burke. 2003. Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Molecular Ecology 12: 1649-1661.
7. Kalinowski, S. T., M. L. Taper, and S. Creel. 2006. Using DNA from noninvasive samples to identify individuals and census populations: an evidential approach tolerant of genotyping errors. Conservation Genetics 7:319-329.
8. Knapp, S. M. 2007. Incorporating uncertainty into non-invasive DNAbased mark-recapture population estimates. Dissertation, Purdue University, West Lafayette, Indiana, USA.
9. Kohn, M., F. Knauer, A. Stoffella, W. Schroder, and S. Paabo. 1995. Conservation genetics of the European brown bear-a study using the excremental PCR of nuclear and mitochondrial sequences. Molecular Ecology 4:95-103.
10. Lukacs, P. M. 2005. Statistical aspects of using genetic markers for individual identification in capture-recapture studies. Dissertation, Colorado State University, Fort Collins, USA.
11. Lukacs, P. M., and K. P. Burnham. 2005. Estimating population size from DNA-based closed capture-recapture data incorporating genotyping error. Journal of Wildlife Management 69:396-403.
12. 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.
13. Miller, C. R., P. Joyce, and L. P. Waits. 2002. Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics 160:357-366.
14. Miller, C. R., P. Joyce, and L. P. Waits. 2005. A new method for estimating the size of small populations from genetic mark-recapture data. Molecular Ecology 14:1991-2005.
15. 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.
16. Navidi, W., N. Arnheim, and M. S. Waterman. 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.
17. Paetkau, D. 2003. An empirical exploration of data quality in DNA-based population inventories. Molecular Ecology 12:1375-1387.
18. Paetkau, D., L. P. Waits, P. L. Clarkson, L. Craighead, and C. Strobeck. 1997. An empirical evaluation of genetic distance statistics using microsatellite data from bear (Ursidae) populations. Genetics 147: 1943-1957.
19. Petit, E., and N. Valiere. 2006. Estimating population size with noninvasive capture-mark-recapture data. Conservation Biology 20: 1062-1073.
20. Pledger, S. 2000. Unified maximum likelihood estimates for closed capturerecapture models using mixtures. Biometrics 56:434-442.
21. Seber, G. A. F. 1982. The estimation of animal abundance and related parameters. Second edition. Macmillan, New York, New York, USA.
22. 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.
23. Taberlet, P., L. P. Waits, and G. Luikart. 1999. Noninvasive genetic sampling: look before you leap. Trends in Ecology and Evolution 14:323-327.
24. Tredick, C. A., M. R. Vaughan, D. F. Stauffer, S. L. Simek, and T. Eason. 2007. Sub-sampling genetic data to estimate black bear population size: a case study. Ursus 18:179-188.
25. Waits, J. L., and P. L. Leberg. 2000. Biases associated with population estimation using molecular tagging. Animal Conservation 3:191-199.
26. Waits, L. P. 2004. Using non-invasive genetic sampling to detect and estimate abundance of rare wildlife species. Pages 211-228 in W. Thompson, editor. Sampling rare or elusive species. Island Press, Washington, D.C., USA.
27. 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.
28. Waits, L. P., and D. Paetkau. 2005. Noninvasive genetic sampling tools for wildlife biologists: a view of applications and recommendations for accurate data collection. Journal of Wildlife Management 69:1419-1433.
29. Weiss, N. A. 2006. A course in probability. Pearson Education Inc., Boston, Massachusetts, USA.
30. White, G. C., D. R. Anderson, K. P. Burnham, and D. L. Otis. 1982. Capture-recapture and removal methods for sampling closed populations. Los Alamos National Laboratory LA-8787-NERP, Los Alamos, New Mexico, USA.