Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping

PLoS ONE

Volumn 7, Issue 3, 2012, Pages

  Romiguier, Jonathan ^a   Figuet, Emeric ^a   Galtier, Nicolas ^a   Douzery, Emmanuel J P ^a   Boussau, Bastien ^b,d   Dutheil, Julien Y ^a   Ranwez, Vincent ^a,c  

^a INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^b UNIVERSITÉ LYON 1   (France)

^c UMR AGAP   (France)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 18S;

AMINO ACID SUBSTITUTION; ARTICLE; COMPUTER SIMULATION; DNA SEQUENCE; HIGH THROUGHPUT SEQUENCING; MATHEMATICAL COMPUTING; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; NUCLEIC ACID BASE SUBSTITUTION; SEQUENCE ANALYSIS; SEQUENCE EVOLUTION; SUBSTITUTION MAPPING;

AMINO ACID SUBSTITUTION; ANIMALS; BASE COMPOSITION; CODON; COMPUTER SIMULATION; DNA MUTATIONAL ANALYSIS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC HETEROGENEITY; HUMANS; MODELS, GENETIC; RNA, RIBOSOMAL, 18S; TIME FACTORS;

EID: 84858975960     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0033852     Document Type: Article

References (48)

1. Dutheil J, Pupko T, Jean-Marie A, Galtier N, (2005) A model-based approach for detecting coevolving positions in a molecule. Molecular biology and evolution 22: 1919-1928.
2. Dimmic MW, Hubisz MJ, Bustamante CD, Nielsen R, (2005) Detecting coevolving amino acid sites using Bayesian mutational mapping. Bioinformatics 21 (Suppl 1): i126-i135.
3. Dutheil J, (2008) Detecting site-specific biochemical constraints through substitution mapping. Journal of molecular evolution 67: 257-265 doi:10.1007/s00239-008-9139-8.
4. Mayrose I, Otto SP, (2011) A likelihood method for detecting trait-dependent shifts in the rate of molecular evolution. Molecular biology and evolution 28: 759-770 doi:10.1093/molbev/msq263.
5. Zhai W, Slatkin M, Nielsen R, (2007) Exploring Variation in the dN/dS Ratio Among Sites and Lineages Using Mutational Mappings: Applications to the Influenza Virus. Journal of Molecular Evolution 65: 340-348-348 doi:10.1007/s00239-007-9019-7.
6. Lartillot N, (2006) Conjugate Gibbs sampling for Bayesian phylogenetic models. Journal of computational biology a journal of computational molecular cell biology 13: 1701-1722.
7. Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL, (2003) Protein evolution with dependence among codons due to tertiary structure. Molecular Biology and Evolution 20: 1692-1704.
8. Shindyalov IN, Kolchanov NA, Sander C, (1994) Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Engineering 7: 349-358.
9. Nielsen R, (2002) Mapping mutations on phylogenies. Systematic biology 51: 729-739 doi:10.1080/10635150290102393.
10. Dutheil J, Galtier N, (2007) Detecting groups of coevolving positions in a molecule: a clustering approach. BMC Evolutionary Biology 7: 242.
11. Felsenstein J, (2004) Inferring Phylogenies. Sinauer As. Sinauer Associates Inc., U.S.
12. Yang Z, (2006) Computational molecular evolution. Oxford University Press.
13. Rodrigue N, Philippe H, Lartillot N, (2008) Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models. Bioinformatics 24: 56-62.
14. Hobolth A, Stone EA, (2009) Simulation from endpoint-conditioned, continuous-time Markov chains on a finite state space, with applications to molecular evolution. The Annals of Applied Statistics.
15. Tataru P, Hobolth A, (2011) Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains. BMC Bioinformatics 12: 465.
16. Minin VN, Suchard MA, (2008) Fast, accurate and simulation-free stochastic mapping. Philosophical transactions of the Royal Society of London Series B, Biological sciences 363: 3985-3995 doi:10.1098/rstb.2008.0176.
17. Hobolth A, Jensen J, (2005) Applications of hidden Markov models for comparative gene structure prediction. J Comput Biology 12: 186-203.
18. Jobson RW, Nabholz B, Galtier N, (2010) An evolutionary genome scan for longevity-related natural selection in mammals. Molecular Biology and Evolution 27: 840-847.
19. Duret L, Arndt PF, (2008) The impact of recombination on nucleotide substitutions in the human genome. PLoS genetics 4.
20. Paland S, Lynch M, (2006) Transitions to asexuality result in excess amino acid substitutions. Science (New York, N Y) 311: 990-992 doi:10.1126/science.1118152.
21. Popadin K, Polishchuk LV, Mamirova L, Knorre D, Gunbin K, (2007) Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals. Proceedings of the National Academy of Sciences of the United States of America 104: 13390-13395 doi:10.1073/pnas.0701256104.
22. Boussau B, Blanquart S, Necsulea A, Lartillot N, Gouy M, (2008) Parallel adaptations to high temperatures in the Archaean eon. Nature 456: 942-945 doi:10.1038/nature07393.
23. Romiguier J, Ranwez V, Douzery EJP, Galtier N, (2010) Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes. Genome research pp. 1001-1009 doi:10.1101/gr.104372.109.
24. Galtier N, Gouy M, (1998) Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Molecular biology and evolution 15: 871-879.
25. Nielsen R, Yang Z, (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
26. Lartillot N, Poujol R, (2011) A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. Molecular Biology and Evolution 28: 729-744.
27. Yang Z, (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular biology and evolution 15: 568-573.
28. Proux E, Studer RA, Moretti S, Robinson-Rechavi M, (2009) Selectome: a database of positive selection. Nucleic Acids Research 37: D404-D407.
29. Ranwez V, Delsuc F, Ranwez S, Belkhir K, Tilak M-K, et al. (2007) {OrthoMaM:} A database of orthologous genomic markers for placental mammal phylogenetics. {BMC} Evolutionary Biology 7: 241 doi:10.1186/1471-2148-7-241.
30. Jukes TH, Cantor CR, (1969) Evolution of protein molecules. In: Munro HN, editors. Mammalian Protein Metabolism pp. 21-132 Academic Press, Vol. 3.
31. Tamura K, (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C content biases. Molecular Biology and Evolution 9: 678-687.
32. Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, et al. (2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443: 167-172 doi:10.1038/nature05113.
33. Ohta T, (1973) Slightly deleterious mutant substitutions in evolution. Nature 246: 96-98.
34. Barraclough TG, Fontaneto D, Ricci C, Herniou EA, (2007) Evidence for inefficient selection against deleterious mutations in cytochrome oxidase I of asexual bdelloid rotifers. Molecular Biology and Evolution 24: 1952-1962.
35. Neiman M, Hehman G, Miller JT, Logsdon JM, Taylor DR, (2010) Accelerated mutation accumulation in asexual lineages of a freshwater snail. Molecular biology and evolution 27: 954-963 doi:10.1093/molbev/msp300.
36. Pond SLK, Frost SDW, Muse SV, (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679 doi:10.1093/bioinformatics/bti079.
37. Dutheil J, Boussau B, (2008) Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evolutionary Biology 8: 255.
38. Escobar JS, Glémin S, Galtier N, (2011) GC-Biased Gene Conversion Impacts Ribosomal DNA Evolution in Vertebrates, Angiosperms and Other Eukaryotes. Molecular Biology.
39. Duret L, Galtier N, (2009) Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes. Annual Review of Genomics and Human Genetics 10: 285-311 doi:10.1146/annurev-genom-082908-150001.
40. Nickel GC, Tefft D, Adams MD, (2008) Human PAML browser: a database of positive selection on human genes using phylogenetic methods. Nucleic acids research 36: D800.
41. Liberles D, Schreiber D, Govindarajan S, Chamberlin S, Benner S, (2001) The Adaptive Evolution Database (TAED). Genome Biology 2.
42. Genome 10K Community of Scientists (2009) Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. The Journal of heredity 100: 659-674 doi:10.1093/jhered/esp086.
43. Dutheil J, Gaillard S, Bazin E, Glémin S, Ranwez V, et al. (2006) Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinformatics.
44. Pupko T, Sharan R, Hasegawa M, Shamir R, Graur D, (2003) Detecting excess radical replacements in phylogenetic trees. Gene 319: 127-135.
45. Galtier N, Boursot P, (2000) A new method for locating changes in a tree reveals distinct nucleotide polymorphism vs divergence patterns in mouse mitochondrial control region. Journal of Molecular Evolution 50: 224-231 doi:10.1007/s002399910025.
46. Felsenstein J, (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17: 368-376.
47. De Magalhaes J, Costa J, (2009) A database of vertebrate longevity records and their relation to other life-history traits. Journal of Evolutionary Biology 22: 1770-1774 doi:10.1111/j.1420-9101.2009.01783.x.
48. Team RDC (2008) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing 1: ISBN 3-900051-07-0.