A bayesian model of AFLP marker evolution and phylogenetic inference

Statistical Applications in Genetics and Molecular Biology

Volumn 6, Issue 1, 2007, Pages

  Luo, Ruiyan ^a   Hipp, Andrew L ^b   Larget, Bret ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b MORTON ARBORETUM   (United States)

Author keywords

Amplified fragment length polymorphism; Markov chain Monte Carlo; Phylogeny; Restriction site; Statistical phylogenetics

Indexed keywords

DNA FRAGMENT; GENOMIC DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BAYES THEOREM; CYPERACEAE; GENE AMPLIFICATION; GENETIC MARKER; MODEL; MOLECULAR EVOLUTION; MONTE CARLO METHOD; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PHYLOGENY; PROBABILITY; STATISTICAL ANALYSIS; BIOLOGICAL MODEL; BIOLOGY; COMPARATIVE STUDY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

CAREX;

BASE SEQUENCE; BAYES THEOREM; COMPUTATIONAL BIOLOGY; CYPERACEAE; EVOLUTION, MOLECULAR; GENETIC MARKERS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH;

EID: 34247359152     PISSN: None     EISSN: 15446115     Source Type: Journal    
DOI: 10.2202/1544-6115.1152     Document Type: Article

References (33)

1. Albertson, R. C., J. A. Markert, P. D. Danley, and T. D. Kocher (1996). Phylogeny of a rapidly evolving clade: The cichlid fishes of Lake Malawi, East Africa. In Proceedings of the National Academy of Sciences of the United States of America, pages 5107-5110.
2. Alfaro, M. E., S. Zoller, and F. Lutzoni (2003). Bayes or Bootstrap? a simulation study comparing the preformance of Bayesian Markov Chain Monte Carlo sampling and Bootstrapping in assessing phylogenetic confidence. Molecular Biology and Evolution 20: 255-266.
3. Drozdek, A. (2001). Data Structures and Algorithms in Java, pages 214-215. Brooks/Cole, Pacific Grove, CA 93950.
4. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Biology 17: 368-376.
5. _ (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
6. _ (1989). PHYLIP: Phylogeny inference package (Version 3.2). Cladistics 5: 164-166.
7. _ (1992). Phylogenies from restriction sites: a maximum-likelihood approach. Evolution 46: 159-173.
8. _ (2004). Inferring phylogenies, chapter 15, pages 239-241. Sinauer Associates, Inc., Sunderland, Massachusetts.
9. Gascuel, O. and M. Steel (2006). Neighbor-Joining revealed. Molecular Biology and Evolution 23: 1997-2000.
10. Green, P. J. (1995). Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82: 711-732.
11. _ (2003). Trans-dimensional Markov chain Monte Carlo. In P. J. Green, N. L. Hjort, and S. Richardson, editors, Highly Structured Stochastic Systems, pages 179-196. Oxford University Press.
12. Hartl, D. and E. Jones (1998). Genetics: Principles and Analysis, chapter 5, pages 207-208. Jones and Bartlett Publishers, fourth edition.
13. Hastings, W. K. (1970). Monte Carlo sampling methods using Markov chains and their applications. Biometrika.
14. Hipp, A. L., P. E. Rothrock, A. A. Reznicek, and P. E. Berry (2006). Chromosome number changes associated with speciation in sedges: A phylogenetic study in Carex section Ovales (Cyperaceae) using AFLP data. In J. T. Columbus, E. A. Friar, J. M. Porter, L. M. Prince, and M. G. Simpson, editors, Monocots: Comparative biology and evolution. Rancho Santa Ana Botanic Garden, Claremont, CA.
15. Holder, M., P. Lewis, D. Swofford, and B. Larget (2005). Hastings ratio of the local proposal used in bayesian phylogenetics. Systematic Biology 54: 961-965.
16. Huelsenbeck, J. P. and F. Ronquist (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
17. Innan, H. R., G. Terauchi, G. Kahl, and F. Tajima (1999). A method for estimating nucleotide diversity from AFLP data. Genetics 151: 1157-1164.
18. Jones, C. J., K. J. Edwards, S. Castaglione, M. O. Winfield, F. Sala, C. van de Wiel, G. Bredemeijer, B. Vosman, M. Matthes, A. Daly, R. Brettschneider, P. Bettini, M. Buiatti, E. Maestri, A. Malcevschi, N. Marmiroli, R. Aert, G. Volckaert, J. Rueda, R. Linacero, A. Vazquez, and A. Karp (1997). Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Molecular Breeding 3: 381-390.
19. Jukes, T. H. and C. R. Cantor (1969). Mammalian protein metabolism, volume 3, chapter Evolution of protein molecules, pages 21-132. Academic Press.
20. Landry, P. A. and F. J. Lapointe (1996). RAPD problems in phylogenetics. Zoologica Scripta 25: 283-252.
21. Larget, B. and D. L. Simon (1999). Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology and Evolution 16: 750-759.
22. Mau, B. and M. A. Newton (1997). Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo. Journal of Computational and Graphical Statistics 6: 122-131.
23. Metropolis, N. A., A. W. Rosenbluth, M. N. Rosenbluth, A. W. Teller, and E. Teller (1953). Equations of state calulations by fast computing machines. Journal of Chemical Physics 21: 1087-1092.
24. Mueller, U. G. and L. L. Wolfenbarger (1999). AFLP genotyping and finger-printing. Trends in Ecology and Evolution 14: 389-394.
25. Nei, M. and W.-H. Li (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. In Proceedings of the National Academy of Sciences, volume 76, pages 5269-5273.
26. Powell, W., M. Morgante, C. Andre, M. Hanafey, J. Vogel, S. Tingey, and A. Rafalski (1996). The comparison of RFLP, RAPD, AFLP and SSR markers for germplasm analysis. Molecular Breeding 2: 225-238.
27. Rzhetsky, A. and M. Nei (1992). A simple method for estimating and testing minimum-evolution trees. Molecular Biology Evolution 9: 945-967.
28. Saitou, N. and M. Nei (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406-425.
29. Shimodaira, H. and M. Hasegawa (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16: 1114-1116.
30. Smouse, P. E. and W. H. Li (1987). Likelihood analysis of mitochondrial restriction-cleavage patterns for the human-chimpanzee-gorilla trichotomy. Evolution 41: 1162-1176.
31. Vekemans, X., T. Beauwens, M. Lemaire, and I. Roldan-Ruiz (2002). Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Molecular Ecology 11: 139-151.
32. Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. van de Lee, M. Hornes, A. Frijters, J. Pot, J. Peleman, M. Kuiper, and M. Zabeau (1995). AFLP: A new technique for DNA fingerprinting. Nucleic Acids Research 23: 4407-4414.
33. Wolfe, A. D. and A. Liston (1998). Molecular systematics of plants II, chapter 2, pages 43-86. Kluwer Academic Pub.