A Bayesian model for gene family evolution

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Liu, Liang ^a   Yu, Lili ^b   Kalavacharla, Venugopal ^c   Liu, Zhanji ^c  

^a UNIVERSITY OF GEORGIA   (United States)

^b GEORGIA SOUTHERN UNIVERSITY   (United States)

^c DELAWARE STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN HYPOTHESIS TESTS; BIRTH AND DEATH PROCESS; BIRTH-AND-DEATH MODEL; ESTIMATING PARAMETERS; EXTRACT INFORMATIONS; MAXIMUM LIKELIHOOD ESTIMATE; MAXIMUM LIKELIHOOD METHODS; STATISTICAL TECHNIQUES;

BAYESIAN NETWORKS; BIOINFORMATICS; ESTIMATION; GENES; MAXIMUM LIKELIHOOD ESTIMATION; PARAMETER ESTIMATION; STATISTICAL TESTS; TREES (MATHEMATICS); YEAST;

POPULATION STATISTICS;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; GENETICS; HUMAN; MOLECULAR EVOLUTION; PHYLOGENY; STATISTICAL MODEL; YEAST;

ANIMALS; BAYES THEOREM; EVOLUTION, MOLECULAR; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; YEASTS;

EID: 80055038986     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-426     Document Type: Article

References (40)

1. Demuth JP, Hahn MW. The life and death of gene families. BioEssays: news and reviews in molecular, cellular and developmental biology 2009, 31(1):29-39.
2. Ohta T. Evolution of gene families. Gene 2000, 259:45-52. 10.1016/S0378-1119(00)00428-5, 11163960.
3. Ridley M. Evolution. 2003, Hoboken: Wiley-Blackwell.
4. Holmes RS, Lim HA. Gene Families: Structure, Function, Genetics and Evolution. 1996, Singapore: World Scientific Publisher.
5. Hahn MW, Demuth JP, Han SG. Accelerated rate of gene gain and loss in primates. Genetics 2007, 177(3):1941-9. 10.1534/genetics.107.080077, 2147951, 17947411.
6. Basten CJ, Ohta T. Simulation study of a multigene family, with special reference to the evolution of compensatory advantageous mutations. Genetics 1992, 132(1):247-52. 1205123, 1398058.
7. Karev GP, Wolf YI, Berezovskaya FS, Koonin EV. Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models. BMC Evol Biol 2004, 4:32. 10.1186/1471-2148-4-32, 523855, 15357876.
8. Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res 2005, 15(8):1153-60. 10.1101/gr.3567505, 1182228, 16077014.
9. Yanai I, Camacho CJ, DeLisi C. Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. Phys Rev Lett 2000, 85(12):2641-4. 10.1103/PhysRevLett.85.2641, 10978127.
10. Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science 2000, 290(5494):1151-5. 10.1126/science.290.5494.1151, 11073452.
11. Ohta T. An Extension of a Model for the Evolution of Multigene Families by Unequal Crossing over. Genetics 1979, 91(3):591-607. 1216852, 17248900.
12. Arvestad L, Berglund AC, Lagergren J, Sennblad B. Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 2003, 19(Suppl 1):i7-15. 10.1093/bioinformatics/btg1000, 12855432.
13. Nei M, Rooney AP. Concerted and Birth-and-Death Evolution in Multigene Families. Ann Rev Genet 2005, 39:121-152. 10.1146/annurev.genet.39.073003.112240, 1464479, 16285855.
14. Ohta T. Simulating evolution by gene duplication. Genetics 1987, 115(1):207-13. 1203057, 3557113.
15. Fortna A, Kim Y, MacLaren E, Marshall K, Hahn G, Meltesen L, Brenton M, Hink R, Burgers S, Hernandez-Boussard T, Karimpour-Fard A, Glueck D, McGavran L, Berry R, Pollack J, Sikela JM. Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol 2004, 2(7):E207. 10.1371/journal.pbio.0020207, 449870, 15252450.
16. Csuros M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 2010, 26(15):1910-2. 10.1093/bioinformatics/btq315, 20551134.
17. Csuros M, Miklos I. Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. Molecular biology and evolution 2009, 26(9):2087-95. 10.1093/molbev/msp123, 2726834, 19570746.
18. Cohen O, Pupko T. Inference and characterization of horizontally transferred gene families using stochastic mapping. Molecular Biology and Evolution 2010, 27(3):703-13. 10.1093/molbev/msp240, 2822287, 19808865.
19. Feller W. An introduction to probability theory and its application. 1968, New York: John Wiley & Sons.
20. Cohen O, Ashkenazy H, Belinky F, Huchon D, Pupko T. GLOOME: gain loss mapping engine. Bioinformatics 2010, 26(22):2914-5. 10.1093/bioinformatics/btq549, 20876605.
21. Iwasaki W, Takagi T. Reconstruction of highly heterogeneous gene-content evolution across the three domains of life. Bioinformatics 2007, 23(13):i230-9. 10.1093/bioinformatics/btm165, 17646301.
22. Huynen MA, van Nimwegen E. The frequency distribution of gene family sizes in complete genomes. Mol Biol Evol 1998, 15(5):583-9.
23. Hahn MW, Han MV, Han SG. Gene family evolution across 12 Drosophila genomes. PLoS Genet 2007, 3(11):e197. 10.1371/journal.pgen.0030197, 2065885, 17997610.
24. Lauritzen SL. Graphical models. 2001, Oxford, UK: Clarendon Press.
25. Demuth JP, De Bie T, Stajich JE, Cristianini N, Hahn MW. The evolution of mammalian gene families. PLoS One 2006, 1:e85. 10.1371/journal.pone.0000085, 1762380, 17183716.
26. Page RD. GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics 1998, 14(9):819-20. 10.1093/bioinformatics/14.9.819, 9918954.
27. Hahn MW. Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biol 2007, 8(7):R141. 10.1186/gb-2007-8-7-r141, 2323230, 17634151.
28. Meng X. Posterior predictive p-value. Ann Statist 1994, 22:1142-1160.
29. Gelman A, Carlin JB, Stern HS, Rubin DB. Bayesian data analysis. 2003, New York: Chapman and Hall/CRC, 2.
30. Hastings WK. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 1970, 57:97-109.
31. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. Equations of State Calculations by Fast Computing Machines. J Chem Phys 1950, 21:1087-1092.
32. Barber MN, Ninham BW. Random and Restricted Walks: Theory and Applications. 1970, New York: Gordon and Breach Publisher.
33. Cowles MK, Carlin BP. Markov Chain Monte Carlo convergence diagnostics. JASA 1996, 91:883-904.
34. Johnson VE. Studying convergence of Markov Chain Monte Carlo algorithms using coupled sample paths. JASA 1996, 91:154-166.
35. Wallace DL. The Behrens-Fisher and Feiller-Creasy problems. RA Fisher: An appreciation 1980, 119-147. Springer: New York, Fienberg SF, Hinkley DV.
36. Novozhilov AS, Karev GP, Koonin EV. Biological applications of the theory of birth-and-death processes. Briefings in bioinformatics 2006, 7(1):70-85. 10.1093/bib/bbk006, 16761366.
37. Bernardo J, Smith AFM. Bayesian Theory. 1994, New York: John Wiley.
38. Jeffreys H. The Theory of Probability. 1961, UK: Oxford Publisher.
39. De Bie T, Cristianini N, Demuth JP, Hahn MW. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 2006, 22(10):1269-71. 10.1093/bioinformatics/btl097, 16543274.
40. Cohen O, Rubinstein ND, Stern A, Gophna U, Pupko T. A likelihood framework to analyse phyletic patterns. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2008, 363(1512):3903-11. 10.1098/rstb.2008.0177, 2607420, 18852099.