Inferring dispersal and migrations from incomplete geochemical baselines: Analysis of population structure using Bayesian infinite mixture models

Methods in Ecology and Evolution

Volumn 4, Issue 9, 2013, Pages 836-845

  Neubauer, Philipp ^a,c   Shima, Jeffrey S ^a   Swearer, Stephen E ^b  

^a VICTORIA UNIVERSITY OF WELLINGTON   (New Zealand)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c Dragonfly Ltd   (New Zealand)

Author keywords

Bayesian mixture; Dirichlet process; Dispersal; Geochemical tags; Stock mixture

Indexed keywords

EID: 84883351872     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12076     Document Type: Article

References (27)

1. Bishop, C. (2007) Pattern Recognition and Machine Learning (Information Science and Statistics). Springer, New York.
2. Bolker, B.M., Okuyama, T., Bjorndal, K.A. & Bolten, A.B. (2007) Incorporating multiple mixed stocks in mixed stock analysis: 'many-to-many' analyses. Molecular Ecology, 16, 685-695.
3. Burton, R.K. & Koch, P.L. (1999) Isotopic tracking of foraging and long-distance migration in northeastern Pacific pinnipeds. Oecologia, 119, 578-585.
4. Campana, S.E., Chouinard, G.A., Hanson, J.M., Frechet, A. & Brattey, J. (2000) Otolith elemental fingerprints as biological tracers of fish stocks. Fisheries Research, 46, 343-357.
5. Celeux, G., Forbes, F., Robert, C.P. & Titterington, D.M. (2006) Deviance information criteria for missing data models. Bayesian Analysis, 1, 651-673.
6. Dawson, K.J. & Belkhir, K. (2009) An agglomerative hierarchical approach to visualization in Bayesian clustering problems. Heredity, 103, 32-45.
7. Dorazio, R.M. (2009) On selecting a prior for the precision parameter of Dirichlet process mixture models. Journal of Statistical Planning and Inference, 139, 3384-3390.
8. Elsdon, T., Wells, B., Campana, S., Gillanders, B., Jones, C., Limburg, K. et al. (2008) Otolith chemistry to describe movements and life-history parameters of fishes. Oceanography and Marine Biology: An Annual Review, 46, 297-330.
9. Fontes, J., Caselle, J.E., Sheehy, M.S., Santos, R.S. & Warner, R.R. (2009) Natal signatures of juvenile Coris julis in the Azores: investigating connectivity scenarios in an oceanic archipelago. Marine Ecology Progress Series, 387, 51-59.
10. Gelman, A., Carlin, J., Stern, H. & Rubin, D. (2003) Bayesian Data Analysis, Second Edition (Chapman & Hall/CRC Texts in Statistical Science). Chapman & Hall, Boca Raton.
11. Gillanders, B.M. & Kingsford, M.J. (2000) Elemental fingerprints of otoliths of fish may distinguish estuarine 'nursery' habitats. Marine Ecology Progress Series, 201, 273-286.
12. Koljonen, M.L., Pella, J.J. & Masuda, M. (2005) Classical individual assignments versus mixture modeling to estimate stock proportions in Atlantic salmon (Salmo salar) catches from DNA microsatellite data. Canadian Journal of Fisheries and Aquatic Sciences, 62, 2143-2158.
13. Miller, J.A. (2007) Scales of variation in otolith elemental chemistry of juvenile staghorn sculpin (Leptocottus armatus) in three Pacific Northwest estuaries. Marine Biology, 151, 483-494.
14. Munch, S.B. & Clarke, L.M. (2008) A Bayesian approach to identifying mixtures from otolith chemistry data. Canadian Journal of Fisheries and Aquatic Sciences, 65, 2742-2751.
15. Neal, R. (1992) Bayesian mixture modeling. Maximum Entropy and Bayesian Methods: Proceedings of the 11th International Workshop on Maximum Entropy and Bayesian Methods of Statistical Analysis, Seattle, 1991 (eds C.R. Smith, G.J. Erickson & P.O. Neudorfer ), pp. 197-211. Kluwer Academic Publishers, Dordrecht.
16. Neubauer, P., Shima, J.S. & Swearer, S.E. (2010) Scale-dependent variability in Forsterygion lapillum hatchling otolith chemistry: implications and solutions for studies of population connectivity. Marine Ecology Progress Series, 415, 263-274.
17. Pella, J. & Masuda, M. (2001) Bayesian methods for analysis of stock mixtures from genetic characters. Fishery Bulletin, 99, 151-167.
18. Pella, J. & Masuda, M. (2006) The Gibbs and split-merge sampler for population mixture analysis from genetic data with incomplete baselines. Canadian Journal of Fisheries and Aquatic Sciences, 63, 576-596.
19. Pflugeisen, B. & Calder, C. (2012) Bayesian hierarchical mixture models for otolith microchemistry analysis. Environmental and Ecological Statistics, 20, 179-190.
20. R Development Core Team (2007) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
21. Rubenstein, D.R. & Hobson, K.A. (2004) From birds to butterflies: animal movement patterns and stable isotopes. Trends in Ecology & Evolution, 19, 256-263.
22. Rubenstein, D.R., Chamberlain, C.P., Holmes, R.T., Ayres, M.P., Waldbauer, J.R., Graves, G.R. et al. (2002) Linking breeding and wintering ranges of a migratory songbird using stable isotopes. Science, 295, 1062-1065.
23. Shima, J.S. & Swearer, S.E. (2009) Larval quality is shaped by matrix effects: implications for connectivity in a marine metapopulation. Ecology, 90, 1255-1267.
24. Smith, S.J. & Campana, S.E. (2010) Integrated stock mixture analysis for continuous and categorical data, with application to genetic-otolith combinations. Canadian Journal of Fisheries and Aquatic Sciences, 67, 1533-1548.
25. Thorrold, S., Jones, C., Swart, P. & Targett, T. (1998) Accurate classification of juvenile weakfish Cynoscion regalis to estuarine nursery areas based on chemical signatures in otoliths. Marine Ecology Progress Series, 173, 253-265.
26. Thorrold, S.R., Latkoczy, C., Swart, P.K. & Jones, C.M. (2001) Natal homing in a marine fish metapopulation. Science, 291, 297-299.
27. White, J.W., Standish, J.D., Thorrold, S.R. & Warner, R.R. (2008) Makov Chain Monte Carlo Methods for assigning larvae to natal sites using natural geochemical tags. Ecological Applications, 18, 1901-1913.