Abstract
One method for diagnosing the mode of sequence evolution considers the ratio of nonsynonymous substitutions per nonsynonymous site (K A) to the corresponding figure for synonymous substitutions (K S). A ratio (K A/K S) greater than unity is taken as evidence for positive selection. This, however, need not necessarily be the case. Notably, there is one instance of a high intragenic K A/K S peak, revealed by sliding window analysis and observed in two pairwise comparisons, better accounted for by localised purifying selection on synonymous mutations that affect splicing. Is this example exceptional? To address this we isolate intragenic domains with K A/K S > 1 from more than 1000 long mouse-rat orthologues. Approximately one K A/K S > 1 peak is found per 12–15 kb of coding sequence. Surprisingly, low synonymous substitution rates underpin more incidences than do high nonsynonymous rates. Several reasons, however, prevent us from supposing that the low synonymous rates reflect purifying selection on synonymous mutations. First, for many peaks, the null that the peak is no higher than expected given the underlying rates of evolution, cannot be rejected. Second, of 18 statistically significant incidences with unusually low K S values, only 3 are repeatable across independent comparisons. At least two of these are within alternatively spliced exons. We conclude that repeatable statistically significant intragenic domains of low intragenic K S are rare. As so few K A/K S peaks reflect increased rates of protein evolution and so few hold statistical support, we additionally conclude that sliding window analysis to infer domains of positive selection is highly error-prone.
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References
Carlini DB, Genut JE (2006) Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers. J Mol Evol 62:89–98
Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA (2005) Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res 15:1553–1565
Cartegni L, Chew SL, Krainer AR (2002) Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 3:285–298
Chamary JV, Hurst LD (2005a) Biased codon usage near mtron-exon junctions: selection on splicing enhancers, splice-site recognition or something else? Trends Genet 21:256–259
Chamary JV, Hurst LD (2005b) Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol 6:R75
Chamary J-V, Parmley JL, Hurst LD (2006) Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7:98–108
Chen FC, Wang SS, Chen CJ, Li WH, Chuang TJ (2006) Alternatively and constitutively spliced exons are subject to different evolutionary forces. Mol Biol Evol 23:675–682
Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, Todd MA, Tanenbaum DM, Civello D, Lu F, Murphy B, Ferriera S, Wang G, Zheng X, White TJ, Sninsky JJ, Adams MD, Cargill M (2003) Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302:1960–1963
Duan JB, Wainright MS, Comeron JM, Saitou N, Sanders AR, Gelerrifer J, Gejman PV (2003) Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum Mol Genet 12:205–216
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Endo T, Ikeo K, Gojobori T (1996) Large-scale search for genes on which positive selection may operate. Mol Biol Evol 13:685–690
Ermakova EO, Nurtdinov RN, Gelfand MS (2006) Fast rate of evolution in alternatively spliced coding regions of mammalian genes. BMC Genomics 7:84
Fairbrother WG, Yeh RF, Sharp PA, Burge CB (2002) Predictive identification of exonic splicing enhancers in human genes. Science 297:1007–l013
Fairbrother WG, Holste D, Burge CB, Sharp PA (2004a) Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol 2:E268
Fairbrother WG, Yeo GW, Yeh R, Goldstein P, Mawson M, Sharp PA, Burge CB (2004b) RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res 32:W187–W190
Fares MA (2004) SWAPSC: sliding window analysis procedure to detect selective constraints. Bioinformatics 20:2867–2868
Fares MA, Elena SF, Ortiz J, Moya A, Barrio E (2002) A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses. J Mol Evol 55:509–521
Filatov DA (2002) PROSEQ: A software for preparation and evolutionary analysis of DNA sequence data sets. Mol Ecol Notes 2:621–624
Gissen P, Johnson CA, Gentle D, Hurst LD, Doherty AJ, O’Kane CJ, Kelly DA, Maher ER (2005) Comparative evolutionary analysis of VPS33 homologues: genetic and functional insights. Hum Mol Genet 14:1261–1270
Hanchard NA, Rockett KA, Spencer C, Coop G, Pinder M, Jallow M, Kimber M, McVean G, Mott R, Kwiatkowski DP (2006) Screening for recently selected alleles by analysis of human haplotype similarity. Am J Hum Genet 78:153–159
Hartigan JA, Hartigan PM (1985) The dip test of unimodality. Ann Stat 13:70–84
Hartigan PM (1985) Computation of the dip statistic to test for unimodality. J Roy Stat Soc C App Stat 34:320–325
Hurst LD (2006) Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals. J Mol Evol 63:174–182
Hurst LD, Pal C (2001) Evidence for purifying selection acting on silent sites in BRCA1. Trends Genet l7:62–65
Hutter S, Vilella AJ, Rozas J (2006) Genome-wide DNA polymorphism analyses using VariScan. BMC Biomform 7:409
Huttley GA, Easteal S, Southey MC, Tesoriero A, Giles GG, McCredie MRE, Hopper JL, Venter DJ (2000) Adaptive evolution of the tumour suppressor BRCA 1 in humans and chimpanzees. Nat Genet 25:410–413
Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM (2007) A “silent” polymorphism in the MDR1 gene changes substrate specificity. Science 315:525–528
Le Texier V, Riethoven JJ, Kumanduri V, Gopalakrishnan C, Lopez F, Gautheret D, Thanaraj TA (2006) AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. BMC Bioinform 7:169
Li W-H (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36:96–99
Liang H, Zhou W, Landweber LF (2006) SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis. Nucleic Acids Res 34:W382–384
Nackley AG, Shabalina SA, Tchivileya IE, Satterfield K, Korchynskyi O, Makarov SS, Maixner W, Diatchenko L (2006) Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 314:1930–1933
Orban TI, Olah E (2001) Purifying selection on silent sites—a constraint from splicing regulation? Trends Genet 17:252–253
Palsson S (2004) On the effects of background selection in small populations on comparisons of molecular variation. Hereditas 141:74–80
Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol 10:271–281
Parmley JL, Chamary JV, Hurst LD (2006) Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol 23:301–309
Plass M, Eyras E (2006) Differentiated evolutionary rates in alternative exons and the implications for splicing regulation. BMC Evol Bio 6:50
Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174–175
Schattner P, Diekhans M (2006) Regions of extreme synonymous codon selection in mammalian genes. Nucl Acids Res 34:1700–l710
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29:308–311
Stamm S, Riethoven JJ, Le Texier V, Gopalakrishnan C, Kumanduri V, Tang Y, Barbosa-Morais NL, Thanaraj TA (2006) ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res 34:D46–D55
Talbert P, Bryson T, Henikoff S (2004) Adaptive evolution of centromere proteins in plants and animals. J Biol 3:18
Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4:e72
Willie E, Majewski J (2004) Evidence for codon bias selection at the pre-mRNA level in eukaryotes. Trends Genet 20:534–538
Xing Y, Lee C (2005a) Assessing the application of Ka/Ks ratio test to alternatively spliced exons. Bioinformatics 21:3701–3703
Xing Y, Lee C (2005b) Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc Natl Acad Sci USA 102:13526–13531
Xing Y, Lee C (2006a) Alternative splicing and RNA selection pressure—evolutionary consequences for eukaryotic genomes. Nat Rev Genet 7:499–509
Xing Y, Lee C (2006b) Can RNA selection pressure distort the measurement of Ka/Ks? Gene 370:1–5
Yeo G, Hoon S., Venkatesh B, Burge CB (2004) Variation in sequence and organization of splicing regulatory elements in vertebrate genes. Proc Natl Acad Sci USA 101:15700–15705
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We wish to thank the editor and two referees for constructive comments on an early version of the manuscript. J.L.P. is funded by the Biotechnology and Biological Sciences Research Council.
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[Reviewing Editor: Dr. Manyuan Long]
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Parmley, J.L., Hurst, L.D. How Common Are Intragene Windows with K A > K S Owing to Purifying Selection on Synonymous Mutations?. J Mol Evol 64, 646–655 (2007). https://doi.org/10.1007/s00239-006-0207-7
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DOI: https://doi.org/10.1007/s00239-006-0207-7