An information-theoretic method for the treatment of plural ancestry in phylogenetics

Molecular Biology and Evolution

Volumn 25, Issue 6, 2008, Pages 1199-1208

  Munshaw, Supriya ^a,b   Kepler, Thomas B ^a,c  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b DUKE UNIVERSITY   (United States)

^c DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Gene conversion; MDL; Phylogenetic networks; Recombination

Indexed keywords

ARTICLE; CLADISTICS; DNA SEQUENCE; EVOLUTIONARY ADAPTATION; GENE CONVERSION; GENE MUTATION; GENE SEQUENCE; GENETIC RECOMBINATION; INHERITANCE; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; PLESIOMORPHY; PLURAL ANCESTRY; SEQUENCE ALIGNMENT; SIMULATION; UNINDEXED SEQUENCE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; EVALUATION; GENETICS; HUMAN; METHODOLOGY;

VIRUS ENVELOPE PROTEIN;

COMPUTATIONAL BIOLOGY; ENV GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; GENE CONVERSION; HUMANS; MODELS, BIOLOGICAL; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 44149123106     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn066     Document Type: Article

References (27)

1. Chaitin G. 1966. On the length of programs for computing finite binary sequences. J ACM. 13:547-569.
2. Crandall KA, Kelsey CR, Imamichi H, Lane HC, Salzman NP. 1999. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol Biol Evol. 16(3):372-382.
3. Darwin CR. 1859. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. Issue 1, 1st ed. London: John Murray. p. 413.
4. Felsenstein J. 1978. The number of evolutionary trees. Syst Zool. 27(1):27-33.
5. Felsenstein J. 1988. Phylogenies from molecular sequence: inference and reliability. Annu Rev Genet. 22:521-565.
6. Grassly NC, Holmes EC. 1997. A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol Biol Evol. 14:239-247.
7. Grünwald PD. 2007. The minimum description length principle. Cambridge (MA): MIT Press.
8. Hein J. 1990. Reconstructing evolution of sequences subject to recombination using parsimony. Math Biosci. 98(2):185-200.
9. Hein J. 1993. A heuristic method to reconstruct the history of sequences subject to recombination. J Mol Evol. 36(4):396-405.
10. Hudson RR, Kaplan NL. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics. 111(1):147-164.
11. Jin G, Nakhleh L, Snir S, Tuller T. 2006. Maximum likelihood of phylogenetic networks. Bioinformatics. 22(21):2604-2611.
12. Kirkpatrick S, Gelatt CD, Vecchi MP. 1983. Optimization by simulated annealing. Science. 220:671-680.
13. Kolmogorov A. 1965. Three approaches to the quantitative definition of information. Probl Inf Transm. 1:1-7.
14. MacQueen JB. 1967. Some methods for classification and analysis of multivariate observations. In: LeCam LM, Newman J, editors. Proceedings of 5th Berkeley Symposium on Mathematical Statistics and Probability. Berkeley (CA): University of California Press. p. 281-297.
15. Maynard Smith J. 1989. Trees, bundles or nets? Trends Ecol Evol. 4:302-304.
16. Pancer Z, Amemiya CT, Ehrhardt GR, Ceitlin J, Gartland GL, Cooper MD. 2004. Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature. 430:174-180.
17. Ren F, Tanaka H, Gojobori T. 1995. Construction of molecular evolutionary phylogenetic trees from DNA sequences based on minimum complexity principle. Comput. Methods Programs Biomed. 46:121-130.
18. Rissanen J. 1987. Stochastic complexity. J R Stat Soc Ser B. 49:223-239.
19. Robertson DL, Sharp PM, McCutchan FE, Hahn BH. 1995. Recombination in HIV-1. Nature. 374:124-126.
20. Sawyer S. 1989. Statistical tests for detecting gene conversion. Mol Biol Evol. 6:528-538.
21. Schierup MH, Hein J. 2000. Consequences of recombination on traditional phylogenetic analysis. Genetics. 156:879-891.
22. Shankarappa R, Margolick JB, Gange SJ, et al. (11 co-authors). 1999. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type I infection. J Virol. 73(12):10489-10502.
23. Solomonoff R. 1964. A formal theory of inductive inference. Inf Control. 7:1-22.
24. Strimmer K, Moulton V. 2000. Likelihood analysis of phylogenetic networks using directed graphical models. Mol Biol Evol. 17(6):875-881.
25. Tonegawa S. 1983. Somatic generation of antibody diversity. Nature. 302:575-581.
26. Woelk CH, Frost SDW, Richman DD, Higley PE, Kosakovsky Pond SL. 2007. Evolution of the interferon alpha gene family in eutherian mammals. Gene. 397:38-50.
27. Zhang SM, Adema CM, Kepler TB, Loker ES. 2004. Diversification of Ig superfamily genes in an invertebrate. Science. 305:251-254.