Strong Purifying Selection at Synonymous Sites in

English version České info

Synonymous sites are generally assumed to be subject to weak selective constraint. For this reason, they are often neglected as a possible source of important functional variation. We use site frequency spectra from deep population sequencing data to show that, contrary to this expectation, 22% of four-fold synonymous (4D) sites in Drosophila melanogaster evolve under very strong selective constraint while few, if any, appear to be under weak constraint. Linking polymorphism with divergence data, we further find that the fraction of synonymous sites exposed to strong purifying selection is higher for those positions that show slower evolution on the Drosophila phylogeny. The function underlying the inferred strong constraint appears to be separate from splicing enhancers, nucleosome positioning, and the translational optimization generating canonical codon bias. The fraction of synonymous sites under strong constraint within a gene correlates well with gene expression, particularly in the mid-late embryo, pupae, and adult developmental stages. Genes enriched in strongly constrained synonymous sites tend to be particularly functionally important and are often involved in key developmental pathways. Given that the observed widespread constraint acting on synonymous sites is likely not limited to Drosophila, the role of synonymous sites in genetic disease and adaptation should be reevaluated.

Vyšlo v časopise: Strong Purifying Selection at Synonymous Sites in. PLoS Genet 9(5): e32767. doi:10.1371/journal.pgen.1003527
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003527

Souhrn

Zdroje

1. KimuraM (1968) Evolutionary rate at the molecular level. Nature 217(5129): 624.

2. KingJL, JukesTH (1969) Non-darwinian evolution. Science 164(881): 788–798.

3. McDonaldJH, KreitmanM (1991) Adaptive protein evolution at the adh locus in drosophila. Nature 351(6328): 652–654.

4. SawyerSA, HartlDL (1992) Population genetics of polymorphism and divergence. Genetics 132(4): 1161–1176.

5. BustamanteCD, Fledel-AlonA, WilliamsonS, NielsenR, HubiszMT, et al. (2005) Natural selection on protein-coding genes in the human genome. Nature 437(7062): 1153–1157.

6. Eyre-WalkerA, KeightleyPD (1999) High genomic deleterious mutation rates in hominids. Nature 397(6717): 344–347.

7. YangZ (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24(8): 1586–1591.

8. IkemuraT (1981) Correlation between the abundance of escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 151(3): 389–409.

9. GranthamR, GautierC, GouyM, JacobzoneM, MercierR (1981) Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res 9(1): 213–213.

10. GouyM, GautierC (1982) Codon usage in bacteria: Correlation with gene expressivity. Nucleic Acids Res 10(22): 7055–7074.

11. SharpPM, DevineKM (1989) Codon usage and gene expression level in dictyosteiium discoidtum: Highly expressed genes do [prefer [optimal codons. Nucleic Acids Res 17(13): 5029–5040.

12. AkashiH, Eyre-WalkerA (1998) Translational selection and molecular evolution. Curr Opin Genet Dev 8(6): 688–693.

13. PlotkinJB, KudlaG (2010) Synonymous but not the same: The causes and consequences of codon bias. Nature Reviews Genetics 12(1): 32–42.

14. HershbergR, PetrovDA (2009) General rules for optimal codon choice. PLoS Genet 5: e1000556 doi:10.1371/journal.pgen.1000556.

15. AkashiH (2001) Gene expression and molecular evolution. Curr Opin Genet Dev 11(6): 660–666.

16. DrummondDA, WilkeCO (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134(2): 341–352.

17. AkashiH (1994) Synonymous codon usage in drosophila melanogaster: Natural selection and translational accuracy. Genetics 136(3): 927–935.

18. StoletzkiN, Eyre-WalkerA (2007) Synonymous codon usage in escherichia coli: Selection for translational accuracy. Mol Biol Evol 24(2): 374–381.

19. HershbergR, PetrovDA (2008) Selection on codon bias. Annu Rev Genet 42: 287–299.

20. IkemuraT (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2(1): 13–34.

21. IkemuraT (1982) Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. differences in synonymous codon choice patterns of yeast and escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J Mol Biol 158(4): 573–597.

22. YangZ, NielsenR (2008) Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol 25(3):568–579.

23. HartlDL, MoriyamaEN, SawyerSA (1994) Selection intensity for codon bias. Genetics 138(1): 227–234.

24. AndolfattoP, WongKM, BachtrogD (2011) Effective population size and the efficacy of selection on the X chromosomes of two closely related drosophila species. Genome Biology and Evolution 3: 114.

25. ClementeF, VoglC (2012) Evidence for complex selection on four-fold degenerate sites in drosophila melanogaster. J Evol Biol 25: 2582–2595.

26. VoglC, ClementeF (2012) The allele-frequency spectrum in a decoupled moran model with mutation, drift, and directional selection, assuming small mutation rates. Theor Popul Biol 81(3): 197–209.

27. ZengK, CharlesworthB (2009) Estimating selection intensity on synonymous codon usage in a nonequilibrium population. Genetics 183(2): 651–662.

28. ZengK, CharlesworthB (2010) Studying patterns of recent evolution at synonymous sites and intronic sites in drosophila melanogaster. J Mol Evol 70(1): 116–128.

29. ChamaryJ, ParmleyJL, HurstLD (2006) Hearing silence: Non-neutral evolution at synonymous sites in mammals. Nature Reviews Genetics 7(2): 98–108.

30. NielsenR, DuMontVLB, HubiszMJ, AquadroCF (2007) Maximum likelihood estimation of ancestral codon usage bias parameters in drosophila. Mol Biol Evol 24(1): 228–235.

31. AkashiH (1995) Inferring weak selection from patterns of polymorphism and divergence at “silent” sites in drosophila DNA. Genetics 139(2): 1067–1076.

32. LawrieDS, PetrovDA, MesserPW (2011) Faster than neutral evolution of constrained sequences: The complex interplay of mutational biases and weak selection. Genome Biology and Evolution 3: 383.

33. SinghND, DuMontVLB, HubiszMJ, NielsenR, AquadroCF (2007) Patterns of mutation and selection at synonymous sites in drosophila. Mol Biol Evol 24(12): 2687–2697.

34. AkashiH (1996) Molecular evolution between drosophila melanogaster and D. simulans: Reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics 144(3): 1297–1307.

35. EőryL, HalliganDL, KeightleyPD (2010) Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Mol Biol Evol 27(1): 177–192.

36. KünstnerA, NabholzB, EllegrenH (2011) Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positive selection. Genome Biology and Evolution 3: 1381.

37. PollardKS, HubiszMJ, RosenbloomKR, SiepelA (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 20(1): 110–121.

38. McVeanGAT, VieiraJ (2001) Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in drosophila. Genetics 157(1): 245–257.

39. ZhouT, GuW, WilkeCO (2010) Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol Biol Evol 27(8): 1912–1922.

40. HaddrillPR, ZengK, CharlesworthB (2011) Determinants of synonymous and nonsynonymous variability in three species of drosophila. Mol Biol Evol 28(5): 1731–1743.

41. Eyre-WalkerA, WoolfitM, PhelpsT (2006) The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics 173(2): 891–900.

42. BoykoAR, WilliamsonSH, IndapAR, DegenhardtJD, HernandezRD, et al. (2008) Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet 4: e1000083 doi:10.1371/journal.pgen.1000083.

43. WrightS (1938) The distribution of gene frequencies under irreversible mutation. Proc Natl Acad Sci U S A 24(7): 253.

44. FisherRA (1930) The distribution of gene ratios for rare mutations. Proceedings of the Royal Society of Edinburgh 50: 205–220.

45. KimuraM (1962) On the probability of fixation of mutant genes in a population. Genetics 47(6): 713.

46. KeightleyPD, Eyre-WalkerA (2007) Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177(4): 2251–2261.

47. KeightleyPD, HalliganDL (2011) Inference of site frequency spectra from high-throughput sequence data: Quantification of selection on nonsynonymous and synonymous sites in humans. Genetics 188(4): 931–940.

48. MackayTFC, RichardsS, StoneEA, BarbadillaA, AyrolesJF, et al. (2012) The drosophila melanogaster genetic reference panel. Nature 482(7384): 173–178.

49. ClementeF, VoglC (2012) Unconstrained evolution in short introns?–An analysis of genome-wide polymorphism and divergence data from drosophila. J Evol Biol 25: 1975–1990.

50. ParschJ, NovozhilovS, Saminadin-PeterSS, WongKM, AndolfattoP (2010) On the utility of short intron sequences as a reference for the detection of positive and negative selection in drosophila. Mol Biol Evol 27(6): 1226–1234.

51. SinghND, ArndtPF, ClarkAG, AquadroCF (2009) Strong evidence for lineage and sequence specificity of substitution rates and patterns in drosophila. Mol Biol Evol 26(7): 1591–1605.

52. HaddrillPR, CharlesworthB, HalliganDL, AndolfattoP (2005) Patterns of intron sequence evolution in drosophila are dependent upon length and GC content. Genome Biol 6(8): R67.

53. ClarkAG, EisenMB, SmithDR, BergmanCM, OliverB, et al. (2007) Evolution of genes and genomes on the drosophila phylogeny. Nature 450(7167): 203–218.

54. HershbergR, PetrovDA (2010) Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet 6: e1001115 doi:10.1371/journal.pgen.1001115.

55. LynchM, SungW, MorrisK, CoffeyN, LandryCR, et al. (2008) A genome-wide view of the spectrum of spontaneous mutations in yeast. Proceedings of the National Academy of Sciences 105(27): 9272–9277.

56. HildebrandF, MeyerA, Eyre-WalkerA (2010) Evidence of selection upon genomic GC-content in bacteria. PLoS Genet 6: e1001107 doi:10.1371/journal.pgen.1001107.

57. PetrovDA, HartlDL (1999) Patterns of nucleotide substitution in drosophila and mammalian genomes. Proceedings of the National Academy of Sciences 96(4): 1475–1479.

58. SellaG, PetrovDA, PrzeworskiM, AndolfattoP (2009) Pervasive natural selection in the drosophila genome? PLoS Genet 5: e1000495 doi:10.1371/journal.pgen.1000495.

59. HaddrillPR, HalliganDL, TomarasD, CharlesworthB (2007) Reduced efficacy of selection in regions of the drosophila genome that lack crossing over. Genome Biol 8(2): R18.

60. AndolfattoP (2007) Hitchhiking effects of recurrent beneficial amino acid substitutions in the drosophila melanogaster genome. Genome Res 17(12): 1755–1762.

61. MacphersonJM, SellaG, DavisJC, PetrovDA (2007) Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in drosophila. Genetics 177(4): 2083–2099.

62. SmithJM, HaighJ (1974) The hitch-hiking effect of a favourable gene. Genet Res 23(1): 23–35.

63. CharlesworthB, MorganM, CharlesworthD (1993) The effect of deleterious mutations on neutral molecular variation. Genetics 134(4): 1289–1303.

64. SekelskyJJ, BrodskyMH, BurtisKC (2000) DNA repair in drosophila insights from the drosophila genome sequence. J Cell Biol 150(2): F31–F36.

65. HernandezRD, WilliamsonSH, BustamanteCD (2007) Context dependence, ancestral misidentification, and spurious signatures of natural selection. Mol Biol Evol 24(8): 1792–1800.

66. ArndtPF, BurgeCB, HwaT (2003) DNA sequence evolution with neighbor-dependent mutation. Journal of Computational Biology 10(3–4): 313–322.

67. SiepelA, HausslerD (2004) Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol 21(3): 468–488.

68. LöytynojaA, GoldmanN (2008) Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320(5883): 1632–1635.

69. Markova-RainaP, PetrovD (2011) High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 drosophila genomes. Genome Res 21(6): 863–874.

70. GuindonS, DufayardJF, LefortV, AnisimovaM, HordijkW, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst Biol 59(3): 307–321.

71. VicarioS, MoriyamaEN, PowellJR (2007) Codon usage in twelve species of drosophila. BMC Evolutionary Biology 7(1): 226.

72. CooperGM, StoneEA, AsimenosG, GreenED, BatzoglouS, et al. (2005) Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 15(7): 901–913.

73. DavydovEV, GoodeDL, SirotaM, CooperGM, SidowA, et al. (2010) Identifying a high fraction of the human genome to be under selective constraint using GERP. PLoS Comput Biol 6: e1001025 doi:10.1371/journal.pcbi.1001025.

74. GnadF, ParschJ (2006) Sebida: A database for the functional and evolutionary analysis of genes with sex-biased expression. Bioinformatics 22(20): 2577–2579.

75. ChenX, ChenZ, ChenH, SuZ, YangJ, et al. (2012) Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes. Science 335(6073): 1235–1238.

76. DaiZ, DaiX, XiangQ (2011) Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast. Bioinformatics 27(13): 1758–1764.

77. PrendergastJGD, SempleCAM (2011) Widespread signatures of recent selection linked to nucleosome positioning in the human lineage. Genome Res 21(11): 1777–1787.

78. WarneckeT, BatadaNN, HurstLD (2008) The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet 4: e1000250 doi:10.1371/journal.pgen.1000250.

79. WarneckeT, SupekF, LehnerB (2012) Nucleoid-associated proteins affect mutation dynamics in E. coli in a growth phase-specific manner. PLoS Comput Biol 8: e1002846 doi:10.1371/journal.pcbi.1002846.

80. MavrichTN, JiangC, IoshikhesIP, LiX, VentersBJ, et al. (2008) Nucleosome organization in the drosophila genome. Nature 453(7193): 358–362.

81. MoriyamaEN, PowellJR (1998) Gene length and codon usage bias in drosophila melanogaster, saccharomyces cerevisiae and escherichia coli. Nucleic Acids Res 26(13): 3188–3193.

82. SinghND, DavisJC, PetrovDA (2005) X-linked genes evolve higher codon bias in drosophila and caenorhabditis. Genetics 171(1): 145–155.

83. SinghND, LarracuenteAM, ClarkAG (2008) Contrasting the efficacy of selection on the X and autosomes in drosophila. Mol Biol Evol 25(2): 454–467.

84. GraveleyBR, BrooksAN, CarlsonJW, DuffMO, LandolinJM, et al. (2010) The developmental transcriptome of drosophila melanogaster. Nature 471(7339): 473–479.

85. VicarioS, MasonCE, WhiteKP, PowellJR (2008) Developmental stage and level of codon usage bias in drosophila. Mol Biol Evol 25(11): 2269–2277.

86. Da Wei HuangBTS, LempickiRA (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4(1): 44–57.

87. ShermanBT, LempickiRA (2009) Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37(1): 1–13.

88. Messer PW, Petrov DA. (2012) The McDonald-kreitman test and its extensions under frequent adaptation: Problems and solutions. arXiv Preprint arXiv:1211.0060 [Q-Bio.PE].

89. DuMontVB, FayJC, CalabresePP, AquadroCF (2004) DNA variability and divergence at the notch locus in drosophila melanogaster and D. simulans: A case of accelerated synonymous site divergence. Genetics 167(1): 171–185.

90. DuMontVLB, SinghND, WrightMH, AquadroCF (2009) Locus-specific decoupling of base composition evolution at synonymous sites and introns along the drosophila melanogaster and drosophila sechellia lineages. Genome Biology and Evolution 1: 67.

91. SaunaZE, Kimchi-SarfatyC (2011) Understanding the contribution of synonymous mutations to human disease. Nature Reviews Genetics 12(10): 683–691.

92. DeanaA, BelascoJG (2005) Lost in translation: The influence of ribosomes on bacterial mRNA decay. Genes Dev 19(21): 2526–2533.

93. PurvisIJ, BettanyAJE, SantiagoTC, CogginsJR, DuncanK, et al. (1987) The efficiency of folding of some proteins is increased by controlled rates of translation in vivo: A hypothesis. J Mol Biol 193(2): 413–417.

94. ZhangG, IgnatovaZ (2011) Folding at the birth of the nascent chain: Coordinating translation with co-translational folding. Curr Opin Struct Biol 21(1): 25–31.

95. IngoliaNT, LareauLF, WeissmanJS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147(4): 789–802.

96. NovoaEM, Ribas de PouplanaL (2012) Speeding with control: Codon usage, tRNAs, and ribosomes. Trends in Genetics 28(11): 574–581.

97. StoletzkiN (2008) Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures. BMC Evolutionary Biology 8(1): 224.

98. GuW, ZhouT, WilkeCO (2010) A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol 6: e1000664 doi:10.1371/journal.pcbi.1000664.

99. GuW, WangX, ZhaiC, XieX, ZhouT (2012) Selection on synonymous sites for increased accessibility around miRNA binding sites in plants. Mol Biol Evol 29(10): 3037–3044.

100. TullerT, Veksler-LublinskyI, GazitN, KupiecM, RuppinE, et al. (2011) Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol 12(11): R110.

101. TullerT, CarmiA, VestsigianK, NavonS, DorfanY, et al. (2010) An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 141(2): 344–354.

102. PechmannS, FrydmanJ (2013) Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. Nature Structural & Molecular Biology 20: 237–243.

103. ZurH, TullerT (2012) Strong association between mRNA folding strength and protein abundance in S. cerevisiae. EMBO Rep 13: 272–277.

104. TullerT, WaldmanYY, KupiecM, RuppinE (2010) Translation efficiency is determined by both codon bias and folding energy. Proceedings of the National Academy of Sciences 107(8): 3645–3650.

105. KatzL, BurgeCB (2003) Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res 13(9): 2042–2051.

106. ParkC, ChenX, YangJ, ZhangJ (2013) Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly. Proceedings of the National Academy of Sciences 110(8): E678–E686.

107. LiF, ZhengQ, RyvkinP, DragomirI, DesaiY, et al. (2012) Global analysis of RNA secondary structure in two metazoans. Cell Rep 1: 69–82.

108. BartelDP (2009) MicroRNAs: Target recognition and regulatory functions. Cell 136(2): 215–233.

109. KusendaB, MrazM, MayerJ, PospisilovaS (2009) MicroRNA biogenesis, functionality and cancer relevance. Biomedical Papers 150(2): 205–215.

110. ZhangG, HubalewskaM, IgnatovaZ (2009) Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nature Structural & Molecular Biology 16(3): 274–280.

111. Deana MassafernoAE, Ehrlich SzalmianRM, ReissC (1996) Synonymous codon selection controls in vivo turnover and amount of mRNA in escherichia coli bla and ompA genes. J Bacteriol 2718: 2720.

112. DeanaA, EhrlichR, ReissC (1998) Silent mutations in the escherichia coli ompA leader peptide region strongly affect transcription and translation in vivo. Nucleic Acids Res 26(20): 4778–4782.

113. QianW, YangJR, PearsonNM, MacleanC, ZhangJ (2012) Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet 8: e1002603 doi:10.1371/journal.pgen.1002603.

114. StadlerM, FireA (2011) Wobble base-pairing slows in vivo translation elongation in metazoans. RNA 17(12): 2063–2073.

115. AndréS, SeedB, EberleJ, SchrautW, BültmannA, et al. (1998) Increased immune response elicited by DNA vaccination with a synthetic gp120 sequence with optimized codon usage. J Virol 72(2): 1497–1503.

116. KimCH, OhY, LeeTH (1997) Codon optimization for high-level expression of human erythropoietin (EPO) in mammalian cells. Gene 199(1–2): 293–301.

117. ZolotukhinS, PotterM, HauswirthWW, GuyJ, MuzyczkaN (1996) A “humanized” green fluorescent protein cDNA adapted for high-level expression in mammalian cells. J Virol 70(7): 4646–4654.

118. NagataT, UchijimaM, YoshidaA, KawashimaM, KoideY (1999) Codon optimization effect on translational efficiency of DNA vaccine in mammalian cells: Analysis of plasmid DNA encoding a CTL epitope derived from microorganisms. Biochem Biophys Res Commun 261(2): 445–451.

119. CarliniDB, StephanW (2003) In vivo introduction of unpreferred synonymous codons into the drosophila adh gene results in reduced levels of ADH protein. Genetics 163(1): 239–243.

120. DuanJ, WainwrightMS, ComeronJM, SaitouN, SandersAR, et al. (2003) Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum Mol Genet 12(3): 205–216.

121. GriseriP, BourcierC, HieblotC, Essafi-BenkhadirK, ChamoreyE, et al. (2011) A synonymous polymorphism of the tristetraprolin (TTP) gene, an AU-rich mRNA-binding protein, affects translation efficiency and response to herceptin treatment in breast cancer patients. Hum Mol Genet 20(23): 4556–4568.

122. Kimchi-SarfatyC, OhJM, KimIW, SaunaZE, CalcagnoAM, et al. (2007) A “silent” polymorphism in the MDR1 gene changes substrate specificity. Science 315(5811): 525–528.

123. KomarAA, LesnikT, ReissC (1999) Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. FEBS Lett 462(3): 387–391.

124. LetzringDP, DeanKM, GrayhackEJ (2010) Control of translation efficiency in yeast by codon–anticodon interactions. RNA 16(12): 2516–2528.

125. PaganiF, RaponiM, BaralleFE (2005) Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution. Proc Natl Acad Sci U S A 102(18): 6368–6372.

126. KudlaG, MurrayAW, TollerveyD, PlotkinJB (2009) Coding-sequence determinants of gene expression in escherichia coli. Science 324(5924): 255–258.

127. AgasheD, Martinez-GomezNC, DrummondDA, MarxCJ (2013) Good codons, bad transcript: Large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme. Mol Biol Evol 30(3): 549–560.

128. WaldmanYY, TullerT, KeinanA, RuppinE (2011) Selection for translation efficiency on synonymous polymorphisms in recent human evolution. Genome Biology and Evolution 3: 749.

129. IngvarssonPK (2010) Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in populus tremula. Mol Biol Evol 27(3): 650–660.

130. VishnoiA, SethupathyP, SimolaD, PlotkinJB, HannenhalliS (2011) Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in saccharomyces paradoxus. Mol Biol Evol 28(9): 2615–2627.

131. dos ReisM, SavvaR, WernischL (2004) Solving the riddle of codon usage preferences: A test for translational selection. Nucleic Acids Res 32(17): 5036–5044.

132. McQuiltonP, PierreSES, ThurmondJ (2012) FlyBase 101–the basics of navigating FlyBase. Nucleic Acids Res 40(D1): D706–D714.

133. NelderJA, MeadR (1965) A simplex method for function minimization. The Computer Journal 7(4): 308–313.

134. MeyerLR, ZweigAS, HinrichsAS, KarolchikD, KuhnRM, et al. (2013) The UCSC genome browser database: Extensions and updates 2013. Nucleic Acids Res 41(D1): D64–D69.

135. HasegawaM, KishinoH, YanoT (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22(2): 160–174.