Unbiased estimate of synonymous and nonsynonymous substitution rates with nonstationary base composition

Molecular Biology and Evolution

Volumn 35, Issue 3, 2018, Pages 734-742

  Guéguen, Laurent ^a   Duret, Laurent ^a  

^a UNIVERSITÉ LYON 1   (France)

Author keywords

Nonsynonymous substitutions; Selection; Stochastic mapping.; Synonymous substitutions

Indexed keywords

ARTICLE; CLADISTICS; CODON; DNA BASE COMPOSITION; MAXIMUM LIKELIHOOD METHOD; SIMULATION; STOCHASTIC MODEL;

EID: 85045952410     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msx308     Document Type: Article

References (48)

1. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F. 1985. The mosaic genome of warm-blooded vertebrates. Science 228(4702): 953–958.
2. Bolivar P, Mugal CF, Nater A, Ellegren H. 2016. Recombination rate variation modulates gene sequence evolution mainly via GC-biased gene conversion, not Hill–Robertson interference, in an avian system. Mol Biol Evol. 33(1): 216–227.
3. Dhar A, Minin VN. 2017. Calculating higher-order moments of phylogenetic stochastic mapping summaries in linear time. J Comput Biol. 24(5): 377–399.
4. Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann IM, Barbe V, Duprat S, Galperin MY, Koonin EV, Gall FL, et al. 2003. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A. 100(17): 10020–10025.
5. Dufresne A, Garczarek L, Partensky F. 2005. Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol. 6(2): 1–10.
6. Duret L, Arndt PF. 2008. The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet. 4(5): e1000071.
7. Dutheil J, Pupko T, Jean-Marie A, Galtier N. 2005. A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol. 22(9): 1919–1928.
8. Dutheil JY, Galtier N, Romiguier J, Douzery EJ, Ranwez V, Boussau B. 2012. Efficient selection of branch-specific models of sequence evolution. Mol Biol Evol. 29(7): 1861–1874.
9. Figuet E, Nabholz B, Bonneau M, Mas Carrio E, Nadachowska-Brzyska K, Ellegren H, Galtier N. 2016. Life history traits, protein evolution, and the nearly neutral theory in amniotes. Mol Biol Evol. 33(6): 1517–1527.
10. Galtier N, Schierup MH. 2016. Adaptive protein evolution in animals and the effective population size hypothesis. PLoS Genet. 12(1): e1005774.
11. Galtier N, Duret L, Glemin S, Ranwez V. 2009. GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends Genet. 25(1): 1–5.
12. Goldman N, Yang Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol. 11(5): 725–736.
13. Guéguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette N, Bigot T, Fournier D, Pouyet F, Cahais V, et al. 2013. Bio þþ: efficient extensible libraries and tools for computational molecular evolution. Mol Biol Evol. 30(8): 1745–1750.
14. Guindon S, Rodrigo AG, Dyer KA, Huelsenbeck JP. 2004. Modeling the site-specific variation of selection patterns along lineages. Proc Natl Acad Sci U S A. 101(35): 12957–12962.
15. Hobolth A, Stone E. 2009. Simulation from endpoint-conditioned, continuous-time Markov chains on a finite state space, with applications to molecular evolution. Ann Appl Stat. 3(3): 1204.
16. Holmes I, Rubin G. 2002. An expectation maximization algorithm for training hidden substitution models. J Mol Biol. 317(5): 753–764.
17. Itoh T, Martin W, Nei M. 2002. Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts. Proc Natl Acad Sci U S A. 99(20): 12944–12948.
18. Kosakovsky Pond SL, Frost SD. 2005. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 22(5): 1208–1222.
19. Pond SLK, Frost SDW, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21(5): 676–679.
20. Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A. 2008. Patterns of positive selection in six mammalian genomes. PLoS Genet. 4(8): e1000144.
21. Kumar S. 2005. Molecular clocks: four decades of evolution. Nat Rev Genet. 6(8): 654–662.
22. Kumar S, Subramanian S. 2002. Mutation rates in mammalian genomes. Proc Natl Acad Sci U S A. 99(2): 803–808.
23. Lemey P, Minin VN, Bielejec F, Kosakovsky Pond SL, Suchard MA. 2012. A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. Bioinformatics 28(24): 3248–3256.
24. Li WH, Wu CI, Luo CC. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol. 2(2): 150–174.
25. Messier W, Stewart CB. 1997. Episodic adaptive evolution of primate lysozymes. Nature 385(6612): 151–154.
26. Minin V, Suchard M. 2008. Fast, accurate and simulation-free stochastic mapping. Philos Trans Roy Soc B. 363(1512): 3985–3995.
27. Moran NA. 1996. Accelerated evolution and Muller’s rachet in endo-symbiotic bacteria. Proc Natl Acad Sci U S A. 93(7): 2873–2878.
28. Moran NA, McCutcheon JP, Nakabachi A. 2008. Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet. 42(1): 165–190.
29. Mouchiroud D, D’Onofrio G, Aïssani B, Macaya G, Gautier C, Bernardi G. 1991. The distribution of genes in the human genome. Gene 100:181–187.
30. Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 3(5): 418–426.
31. Nielsen R. 2002. Mapping mutations on phylogenies. Syst Biol. 51(5): 729–739.
32. O’Brien J, Minin V, Suchard M. 2009. Learning to count: Robust estimates for labeled distances between molecular sequences. Mol Biol Evol. 26(4): 801–814.
33. Paul S, Dutta A, Bag SK, Das S, Dutta C. 2010. Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria Prochlorococcus. BMC Genomics 11(1): 103.
34. Prez-Brocal V, Gil R, Ramos S, Lamelas A, Postigo M, Michelena JM, Silva FJ, Moya A, Latorre A. 2006. A small microbial genome: the end of a long symbiotic relationship? Science 314(5797): 312–313.
35. Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, et al. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424(6952): 1042–1047.
36. Romiguier J, Ranwez V, Douzery E, Galtier N. 2010. Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Res. 20(8): 1001–1009.
37. Romiguier J, Figuet E, Galtier N, Douzery EJP, Boussau B, Dutheil JY, Ranwez V, Liberles D. 2012. Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping. PLoS One 7(3): 1–10.
38. Tataru P, Hobolth A. 2011. Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains. BMC Bioinformatics 12(1): 465–475.
39. van Ham RCHJ, Kamerbeek J, Palacios C, Rausell C, Abascal F, Bastolla U, Fernandez JM, Jiménez L, Postigo M, Silva FJ, et al. 2003. Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci U S A. 100(2): 581–586.,
40. Weber CC, Nabholz B, Romiguier J, Ellegren H. 2014. Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biol. 15(12): 542.
41. Wernegreen JJ, Moran NA. 1999. Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes. Mol Biol Evol. 16(1): 83–97.
42. Wolfe KH, Sharp PM, Li WH. 1989. Mutation rates differ among regions of the mammalian genome. Nature 337(6204): 283–285.
43. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24(8): 1586–1591.
44. Yang Z, Bielawski JP. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 15(12): 496–503.
45. Yang Z, Nielsen R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol. 46(4): 409–418.
46. Yang Z, Nielsen R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol. 17(1): 32–43.
47. Yang Z, Nielsen R, Goldman N, Pedersen AM. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155(1): 431–449.
48. Yu T, Li J, Yang Y, Qi L, Chen B, Zhao F, Bao Q, Wu J. 2012. Codon usage patterns and adaptive evolution of marine unicellular cyanobacteria Synechococcus and Prochlorococcus. Mol Phylogenet Evol. 62(1): 206–213.