Sea turtle stock estimation using genetic markers: Accounting for sampling error of rare genotypes

Ecological Applications

Volumn 13, Issue 3, 2003, Pages 763-775

  Bolker, Benjamin ^a   Okuyama, Toshinori ^a   Bjorndal, Karen ^a   Bolten, Alan ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

Bootstrap; Caretta caretta; Chelonia mydas; Markov Chain Monte Carlo; Maximum likelihood; Migration; mtDNA; Sea turtle; Stock analysis; Uncertainty

Indexed keywords

ERROR ANALYSIS; GENETIC MARKER; GENOTYPE; STOCK ASSESSMENT; TURTLE;

AMPHIBIA; CARETTA CARETTA; CHELONIA MYDAS; CHELONIIDAE; MYDAS; REPTILIA; TESTUDINES;

EID: 0348252409     PISSN: 10510761     EISSN: None     Source Type: Journal    
DOI: 10.1890/1051-0761(2003)013[0763:STSEUG]2.0.CO;2     Document Type: Article

References (23)

1. Bass, A. L., and W. N. Witzell. 2000. Demographic composition of immature green turtles Chelonia mydas from the east central Florida coast: evidence from mtDNA markers. Herpetologica 56:357-367.
2. Bjorndal, K. A., A. B. Bolten, and H. R. Martins. 2000. Somatic growth model of juvenile loggerhead sea turtles Caretta caretta: duration of pelagic stage. Marine Ecology Progress Series 202:265-272.
3. Bolten, A. B., K. A. Bjorndal, H. R. Martins, T. Dellinger, M. J. Biscotio, S. E. Encalada, and B. W. Bowen. 1998. Transatlantic developmental migrations of loggerhead sea turtles demonstrated by mtDNA sequence analysis. Ecological Applications 8:1-7.
4. Bowen, B. W., A. L. Bass, A. Graica-Rodriquez, C. E. Diez, R. van Dam, A. B. Bolten, K. A. Bjorndal, M. M. Miyamoto, and R. J. Ferl. 1996. Origin of hawksbill turtles in a Caribbean feeding area as indicated by genetic markers. Ecological Applications 6:566-572.
5. Bowen, B. W., and S. A. Karl. 1997. Population genetics, phylogeography, and molecular evolution. Pages 29-50 in P. L. Lutz and J. A. Musick, editors. The biology of sea turtles. CRC Press, Boca Raton, Florida, USA.
6. Dennis, B. 1996. Discussion: should ecologists become Bayesians? Ecological Applications 6:1095-1103.
7. Edwards, D. 1996. Comment: the first data analysis should be journalistic. Ecological Applications 6:1090-1094.
8. Gelman, A., J. B. Carlin, H. S. Stern, and D. B. Rubin. 1995. Bayesian data analysis. Chapman and Hall, New York, New York, USA.
9. Geyer, C. J. 1996. Estimation and optimization of functions. Pages 241-258 in W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, editors. Markov Chain Monte Carlo in practice. Chapman and Hall, London, UK.
10. Gibson, G. J. 1997. Markov Chain Monte Carlo methods for fitting spatiotemporal stochastic models in plant epidemiology. Journal of the Royal Statistical Society Series C 46:215-233.
11. Gibson, G. J., and E. Renshaw. 1998. Estimating parameters in stochastic compartmental models using Markov chain methods. IMA [Institute of Mathematics and its Applications] Journal of Mathematics Applied in Medicine and Biology 15:19-40.
12. Gottwald, T. R., G. J. Gibson, S. M. Garnsey, and M. Irey. 1999. Examination of the effect of aphid vector population composition on the spatial dynamics of citrus tristeza virus spread by stochastic modeling. Phytopathology 89:603-608.
13. Ihaka, R., and R. Gentleman. 1996. R: a language for data analysis and graphics. Journal of Computational and Graphical Statistics 5:299-314.
14. Lahanas, P. N., K. A. Bjorndal, A. B. Bolten, S. E. Encalada, M. M. Miyamoto, R. A. Valverde, and B. W. Bowen. 1998. Genetic composition of a green turtle (Chelonia mydas) feeding ground population: evidence for multiple origins. Marine Biology 130:345-352.
15. Miller, R. B. 1987. Maximum likelihood estimation of mixed stock fishery composition. Canadian Journal of Fisheries and Aquatic Sciences 44:583-590.
16. Mollié, A. 1996. Bayesian mapping of disease. Pages 359-379, in W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, editors. Markov Chain Monte Carlo in practice. Chapman and Hall, London, UK.
17. Pella, J., and M. Masuda. 2001. Bayesian methods for analysis of stock mixtures from genetic characters. Fisheries Bulletin 99:151-167.
18. Pella, J. J., and G. B. Milner. 1987. Use of genetic markers in stock composition analysis. Pages 247-276 in N. Ryman and F. W. Utter, editors. Population genetics and fisheries management. University of Washington Press, Seattle, Washington, USA.
19. Raftery, A. E., and S. M. Lewis. 1996. Implementing MCMC. Pages 115-130 in W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, editors. Markov Chain Monte Carlo in practice. Chapman and Hall, London, UK.
20. Smouse, P. E., R. S. Waples, and J. A. Tworek. 1990. A genetic mixture analysis for use with incomplete source population data. Canadian Journal of Fisheries and Aquatic Sciences 47:620-634.
21. Spiegelhalter, D. J., A. Thomas, N. Best, and W. R. Gilks. 1995. BUGS: Bayesian inference using Gibbs sampling, version 0.50. Technical report. Medical Research Council Biostatistics Unit, Institute of Public Health, Cambridge University, Cambridge, UK. [Online, URL: 〈www.mrc-bsu.cam.ac.uk/ bugs/〉.]
22. Utter, F., and N. Ryman. 1993. Genetic markers and mixed stock fisheries. Fisheries 18:11-21.
23. Walsh, P. D. 2000. Sample size for the diagnosis of conservation units. Conservation Biology 14:1533-1537.