Core set approach to reduce uncertainty of gene trees

BMC Evolutionary Biology

Volumn 6, Issue , 2006, Pages

  Okabayashi, Takahisa ^a   Kitazoe, Yasuhiro ^a   Kishino, Hirohisa ^b   Watabe, Teruaki ^a   Nakajima, Noriaki ^a   Okuhara, Yoshiyasu ^a   O'Loughlin, Samantha ^c   Walton, Catherine ^c  

^a KOCHI UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA SEQUENCE; GENE FREQUENCY; GENE FUNCTION; GENE SEQUENCE; HAPLOTYPE; HUMAN IMMUNODEFICIENCY VIRUS; MITOCHONDRION; NONHUMAN; PARSIMONY ANALYSIS; PHYLOGENETIC TREE; PHYLOGENY; SIMULATION; SPECIES DIFFERENCE; ANIMAL; ANOPHELES; BIOLOGICAL MODEL; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR EVOLUTION; UNCERTAINTY;

ANOPHELES DIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

ANIMALS; ANOPHELES; EVOLUTION, MOLECULAR; HIV-1; MODELS, GENETIC; PHYLOGENY; UNCERTAINTY;

EID: 33745987930     PISSN: 14712148     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-6-41     Document Type: Article

References (33)

1. Bush RM, Bender CA, Sbbararo K, Cox NJ, Fitch WM: Predicting the evolution of human influenza A. Science 1999, 268:1921-1925.
2. Frost SDW, Günthard HF, Wong JK, Havlir D, Richman DD, Leigh Brown AJ: Evidence for positive selection driving the evolution of HIV-1 env under potent therapy. Virology 2001, 284:250-258.
3. de S Leal E, Holmes EC, PM de A Zanotto : Distinct patterns of natural selection in the reverse transcriptase gene of HIV-1 in the presence and absence of antiretroviral therapy. Virology 2004, 325:181-191.
4. Pagel M: Inferring the historical patterns of biological evolution. Nature 1999, 401:877-884.
5. Ross HA, Rodrigo A: Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J Virol 2002, 76:11715-11719.
6. Williamson S: Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol Biol Evol 2003, 20:1318-1325.
7. Yang Z, Nielsen R, Goldman N, Pedersen AMK: Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 2000, 155:431-449.
8. Fitch WM: Toward defining the course of evolution: minimum change for a specified tree topology. Systematic Zoology 1971, 20:406-416.
9. Swofford DL: PAUP* Phylogenetic Analysis Using Parsimony (* and Other Methods). In ver 4.0b10 Sinauer Associates; 2002.
10. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-425.
11. Adachi J, Hasegawa M: MOLPHY: Programs for molecular phylogenetics. In ver 2.3 Institute of Statistical Mathematics, Tokyo; 1996.
12. Felsenstein J: PHYLIP. In ver 3.572 Univ of Washington Seattle; 1996.
13. Templeton AR, Crandall KA, Sing CF: A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 1992, 132:619-633.
14. Antunes A, Templeton AR, Guyomard R, Alexandrino P: The role of nuclear genes in intraspecific evolutionary inference: genealogy of the transferrin gene in the brown trout. Mol Biol Evol 2002, 19:1272-87.
15. Crandall KA: Intraspecific cladogram estimation: accuracy at higher levels of divergence. Sys Biol 1994, 43:222-235.
16. Crandall KA, Templeton AR: Applications of intraspecific phylogenies. In New uses for new phylogenies Edited by: Harvey P, Brown AJL, Smith JM, Nee S. Oxford University Press. Oxford, U. K; 1996:81-99.
17. Templeton AR, Sing CF: A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics 1993, 134:659-669.
18. Bandelt HJ, Dress AW: Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol Phylogenet Evol 1992, 1:242-52.
19. Excoffier L, Smouse PE: Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: Molecular variance parsimony. Genetics 1994, 136:343-359.
20. Fitch WM: Networks and viral evolution. J Mol Evol 1997, 44(Suppl 1):S65-75.
21. Johnson JB, Jordan S: Phylogenetic divergence in leatherside chub (Gila copei) inferred from mitochondrial cytochrome b sequences. Molecular Ecology 2000, 9:1029-1035.
22. Templeton AR, Routman E, Phillips CA: Separating population structure from population history: a cladistic analysis of geographical distribution of mitochondrial DNA haplotypes in the tiger salamander. Ambystoma tigrimum Genetics 1995, 140:767-782.
23. Templeton AR: Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology 1998, 7:381-397.
24. Turner TF, Trexler JC, Harris JL, Haynes JL: Nested cladistic analysis indicates population fragmentation shapes genetic diversity in a freshwater mussel. Genetics 2000, 154:777-785.
25. Kitazoe Y, Kurihara Y, Narita Y, Okuhara Y, Tominaga A, Suzuki T: A New Theory of Phylogeny Inference Through Construction of Multidimensional Vector Space. Mol Biol Evol 2001, 18:812-828.
26. Kitazoe Y, Kishino H, Okabayashi T, Watabe T, Nakajima N, Okuhara Y, Kurihara Y: Multidimensional vector space representation for convergent evolution and molecular phylogeny. Mol Biol Evol 2005, 22:704-715.
27. Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, Gupta P, Rinaldo CR, Learn GH, He X, Huang XL, Mullins JI: Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol 1999, 73:10489-10502.
28. Clement M, Posada D, Crandall KA: PROGRAM NOTE. TCS: a computer program to estimate gene genealogies. Molecular Ecology 2000, 9:1657-1659.
29. Sheridan I, Pybus OG, Holmes EC, Klenerman P: High resolution phylogenetic analysis of hepatitis C virus adaptation and its relationship to disease progression. J Virol 2004, 78:3447-3454.
30. O'Loughlin S, Walton C, et al.: . to be submitted
31. Walton C, Handley JM, Tun-Lin W, Collins FH, Harback RE, Baimai V, Butlin RK: Population structure and population history of Anopheles dirus mosquitoes in Southeast Asia. Mol Biol Evol 2000, 17:962-974.
32. Templeton AR, Clark AG, Weiss KM, Nickerson DA, Boerwinkle E, Sing CF: Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am J Hum Genet 2000, 66:69-83.
33. Templeton AR, Reichert RA, Weisstein AE, Yu XF, Markham RB: Selection in context: patterns of natural selection in the glycoprotein 120 region of human immunodeficiency virus 1 within infected individuals. Genetics 2004, 167:1547-61.