메뉴 건너뛰기




Volumn 3, Issue 1, 2009, Pages 222-248

Modeling substitution and indel processes for AFLP marker evolution and phylogenetic inference

Author keywords

Amplified fragment length polymorphism; Insertion and deletion; Markov chain Monte Carlo; Phylogeny; Statistical phylogenetics

Indexed keywords


EID: 84865368596     PISSN: 19326157     EISSN: 19417330     Source Type: Journal    
DOI: 10.1214/08-AOAS212     Document Type: Article
Times cited : (4)

References (27)
  • 1
    • 0033609147 scopus 로고    scopus 로고
    • Phylogeny of a rapidly evolving clade: The cichlid fishes of Lake Malawi, East Africa
    • Albertson, R. C., Markert, J. A., Danley, P. D. and Kocher, T. D. (1996). Phylogeny of a rapidly evolving clade: The cichlid fishes of Lake Malawi, East Africa. Proc. Natl. Acad. Sci. USA 96 5107-5110.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 5107-5110
    • Albertson, R.C.1    Markert, J.A.2    Danley, P.D.3    Kocher, T.D.4
  • 2
    • 0026443745 scopus 로고
    • Phylogenies from restriction sites: A maximum-likelihood approach
    • Felsenstein, J. (1992). Phylogenies from restriction sites: A maximum-likelihood approach. Evolution 46 159-173.
    • (1992) Evolution , vol.46 , pp. 159-173
    • Felsenstein, J.1
  • 3
    • 0003991673 scopus 로고    scopus 로고
    • Sinauer Associates, Inc., Sunderland, MA
    • Felsenstein, J. (2004). Inferring Phylogenies 251-256. Sinauer Associates, Inc., Sunderland, MA.
    • (2004) Inferring Phylogenies , pp. 251-256
    • Felsenstein, J.1
  • 4
    • 84865392475 scopus 로고    scopus 로고
    • Downloaded in May, 2007
    • FlyBase (2007). http://flybase.bio.indiana.edu. Downloaded in May, 2007.
    • (2007) FlyBase
  • 5
    • 84972492387 scopus 로고
    • Inference from iterative simulation using multiple sequences
    • Gelman, A. and Rubin, D. B. (1992). Inference from iterative simulation using multiple sequences. Statist. Sci. 7 457-511.
    • (1992) Statist. Sci. , vol.7 , pp. 457-511
    • Gelman, A.1    Rubin, D.B.2
  • 6
    • 77956889087 scopus 로고
    • Reversible jump Markov chain Monte Carlo computation and Bayesian model determination
    • Green, P. J. (1995). Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82 711-732.
    • (1995) Biometrika , vol.82 , pp. 711-732
    • Green, P.J.1
  • 7
    • 0346641850 scopus 로고    scopus 로고
    • Trans-dimensional Markov chain Monte Carlo
    • In, (P. J. Green, N. L. Hjort and S. Richardson, eds.). Oxford Univ. Press, Oxford
    • Green, P. J. (2003). Trans-dimensional Markov chain Monte Carlo. In Highly Structured Stochastic Systems (P. J. Green, N. L. Hjort and S. Richardson, eds.) 179-198. Oxford Univ. Press, Oxford.
    • (2003) Highly Structured Stochastic Systems , pp. 179-198
    • Green, P.J.1
  • 8
    • 33747060544 scopus 로고    scopus 로고
    • 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, eds.). Rancho Santa Ana Botanic Garden, Claremont, CA
    • Hipp, A. L., Rothrock, P. E., Reznicek, A. A. and Berry, P. E. (2006). Chromosome number changes associated with speciation in sedges: A phylogenetic study in Carex section Ovales (Cyperaceae) using AFLP data. In Monocots: Comparative Biology and Evolution (J. T. Columbus, E. A. Friar, J. M. Porter, L. M. Prince and M. G. Simpson, eds.). Rancho Santa Ana Botanic Garden, Claremont, CA.
    • (2006) Monocots: Comparative Biology and Evolution
    • Hipp, A.L.1    Rothrock, P.E.2    Reznicek, A.A.3    Berry, P.E.4
  • 9
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck, J. P. and Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 11
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • In (H. N. Munro, ed.). Academic Press, New York
    • Jukes, T. H. and Cantor, C. R. (1969). Evolution of protein molecules. InMammalian Protein Metabolism Vol. 3 (H. N. Munro, ed.) 21-132. Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , vol.3 , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 13
    • 34247359152 scopus 로고    scopus 로고
    • A Bayesian model of AFLP marker evolution and phylogenetic inference
    • Article 11
    • Luo, R., Hipp, A. and Larget, B. (2007). A Bayesian model of AFLP marker evolution and phylogenetic inference. Statist. Appl. Genet. Mol. Biol. 6Article 11.
    • (2007) Statist. Appl. Genet. Mol. Biol. , vol.6
    • Luo, R.1    Hipp, A.2    Larget, B.3
  • 15
    • 0031498410 scopus 로고    scopus 로고
    • Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo
    • Mau, B. and Newton, M. A. (1997). Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo. J. Comput. Graph. Statist. 6122-131.
    • (1997) J. Comput. Graph. Statist. , vol.6 , pp. 122-131
    • Mau, B.1    Newton, M.A.2
  • 16
    • 1542510093 scopus 로고    scopus 로고
    • A "long indel" model for evolutionary sequence alignment
    • Miklós, I., Lunter, G. A. and Holmes, I. (2004). A "long indel" model for evolutionary sequence alignment. Mol. Biol. Evol. 21 529-540.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 529-540
    • Miklós, I.1    Lunter, G.A.2    Holmes, I.3
  • 17
    • 84865386238 scopus 로고    scopus 로고
    • Downloaded in May, 2007
    • NCBI (2007). http://www.ncbi.nlm.nih.gov/Genomes/. Downloaded in May, 2007.
    • (2007) NCBI
  • 19
    • 22844450838 scopus 로고    scopus 로고
    • Joint Bayesian estimation of alignment and phylogeny
    • Redelings, B. D. and Suchard, M. A. (2005). Joint Bayesian estimation of alignment and phylogeny. Systematic Biology 54 401-418.
    • (2005) Systematic Biology , vol.54 , pp. 401-418
    • Redelings, B.D.1    Suchard, M.A.2
  • 20
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • Tamura, K. and Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10 512-526.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 21
    • 0026079507 scopus 로고
    • An evolutionary model for maximum likelihood alignment of DNA sequences
    • Thorne, J. L., Kishino, H. and Felsenstein, J. (1991). An evolutionary model for maximum likelihood alignment of DNA sequences. Journal of Molecular Evolution 33 114-124.
    • (1991) Journal of Molecular Evolution , vol.33 , pp. 114-124
    • Thorne, J.L.1    Kishino, H.2    Felsenstein, J.3
  • 22
    • 0026528734 scopus 로고
    • Inching toward reality: An improved likelihood model of sequence evolution
    • Thorne, J. L., Kishino, H. and Felsenstein, J. (1992). Inching toward reality: An improved likelihood model of sequence evolution. Journal of Molecular Evolution 34 3-16.
    • (1992) Journal of Molecular Evolution , vol.34 , pp. 3-16
    • Thorne, J.L.1    Kishino, H.2    Felsenstein, J.3
  • 23
    • 0000576595 scopus 로고
    • Markov chains for exploring posterior distributions
    • Tierney, L. (1994). Markov chains for exploring posterior distributions. Ann. Statist. 22 1701-1728.
    • (1994) Ann. Statist. , vol.22 , pp. 1701-1728
    • Tierney, L.1
  • 26
    • 0027132974 scopus 로고
    • Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • Yang, Z. (1993). Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 101396-1401.
    • (1993) Mol. Biol. Evol. , vol.101 , pp. 396-401
    • Yang, Z.1
  • 27
    • 0028064845 scopus 로고
    • Maximum likelihood estimation of phylogeny from DNA sequences with variable rates over sites: Approximate methods
    • Yang, Z. (1994). Maximum likelihood estimation of phylogeny from DNA sequences with variable rates over sites: Approximate methods. Journal of Computational Evolution 39 306-314.
    • (1994) Journal of Computational Evolution , vol.39 , pp. 306-314
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.