On the possibility of constructive neutral evolution

Journal of Molecular Evolution

Volumn 49, Issue 2, 1999, Pages 169-181

  Stoltzfus, Arlin ^a,b  

^a DALHOUSIE UNIVERSITY   (Canada)

^b UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

Author keywords

Complexity; Gene duplication; Neutral evolution; RNA editing; Scrambling; Spliceosomal introns

Indexed keywords

RNA;

ALLELE; ARTICLE; BIODIVERSITY; GENE; GENE STRUCTURE; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; MOLECULAR MODEL; RNA EDITING; SPLICEOSOME; THEORY;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CILIOPHORA; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, PROTOZOAN; INTRONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; RNA EDITING; RNA SPLICING; RNA, PROTOZOAN; SPLICEOSOMES;

CILIOPHORA;

EID: 0032770725     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006540     Document Type: Article

References (98)

1. Alberch P, Gale EA (1985) A developmental analysis of an evolutionary trend: Digital reduction in amphibians. Evolution 39:8-23
2. Alfonzo JD, Thiemann O, Simpson L (1997) The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria. Nucleic Acids Res 25:3751-3759
3. Amundson R (1994) Two concepts of constraint: Adaptationism and the challenge from developmental biology. Philos Sci 61:556-578
4. Antonovics J, van Tienderen PH (1991) Ontoecoenophyloconstraints? The chaos of constraint terminoloy. Trends Ecol Evol 6:166-168
5. Armbruster WS (1996) Exaptation, adaptation, and homoplasy: Evolution of ecological traits in Dalechampia vines. In: Sanderson MJ, Hufford L (eds) Homoplasy: The recurrence of similarity in evolution. Academic Press, San Diego, pp 227-243
6. Avila HA, Simpson L (1995) Organization and complexity of minicircle-encoded guide RNAs in Trypanosoma cruzi. RNA I: 939-947
7. Baurén G, Wieslander L (1994) Splicing of balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell 76:183-192
8. Berry RJ (1982) Neo-Darwinism. Edward Arnold, London
9. Beyer AL, Osheim YN (1988) Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes Dev 2:754-765
10. Biessmann H, Mason JM (1997) Telomere maintenance without telomerase. Chromosoma 106:63-69
11. Bonen L (1993) Trans-splicing of pre-mRNA in plants, animals and protists. FASEB J 7:40-46
12. Brandon RN (1990) Adaptation and environment. Princeton University Press, Princeton, NJ
13. Britten RJ (1996) DNA sequence insertion and evolutionary variation in gene regulation. Proc Natl Acad Sci USA 93:9374-9377
14. Bull JJ, Charnov EL (1985) On irreversible evolution. Evolution 39: 1149-1155
15. Buth DG (1983) Duplicate isozyme loci in fishes: Origins, distribution, phyletic consequences, and locus nomenclature. In: Rattazzi MC, Scandalios JG, Whitt GS (eds) Isozymes: Current topics in biological and medical research. Alan R. Liss, New York, pp 381-400
16. Cavalier-Smith T (1991) Intron phylogeny: A new hypothesis. Trends Genet 7:145-148
17. Cavalier-Smith T (1997) Cell and genome coevolution: Facultative anaerobiosis, glycosomes and kinetoplastan RNA editing. Trends Genet 13:6-9
18. Coetzee T, Herschlag D, Belfort M (1994) Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones. Genes Dev 8:1575-1588
19. Copertino DW, Hallick RB (1993) Group II and group III introns of twintrons: Potential relationships with nuclear pre-mRNA introns. Trends Biochem 18:467-471
20. Covello PS, Gray MW (1993) On the evolution of RNA editing. Trends Genet 9:265-268
21. Cronin H (1991) The ant and the peacock. Cambridge University Press, Cambridge
22. Cruz-Reyes J, Sollner-Webb B (1996) Trypanosome U-deletional RNA editing involves guide RNA-directed endonuclease cleavage, terminal U exonuclease, and RNA ligase activities. Proc Natl Acad Sci USA 93:8901-8906
23. Csink AK, Henikoff S (1998) Something from nothing: The evolution and utility of satellite repeats. Trends Genet 14:200-204
24. Cunningham CW, Jeng K, Husti J, et al. (1997) Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7. Mol Biol Evol 14:113-116
25. de Jong WW, Ryden L (1981) Causes of more frequent deletions than insertions in mutations and protein evolution. Nature 290:157-159
26. Dover GA (1992) Observing development through evolutionary eyes: A practical approach. Bioessays 14:281-287
27. Ferns SD, Whitt GS (1979) Evolution of the differential regulation of duplicate genes after polyploidization. J Mol Evol 12:267-317
28. Fitch WM (1972) Rate of change of concomitantly variable codons. J Mol Evol 1:84-96
29. Foster PG, Jermiin LS, Hickey DA (1997) Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J Mol Evol 44:282-288
30. Frazetta TH (1975) Complex adaptations in evolving populations. Sinauer Associates, Sunderland, MA
31. Galis F (1996) The application of functional morphology to evolutionary studies. Trends Ecol Evol 11:124-129
32. Gillham NW (1994) Organelle genes and genomes. Oxford University Press, New York
33. Gojobori T, Li W-H, Graur D (1982) Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 17:245-250
34. Golding GB (1987) Nonrandom patterns of mutation are reflected in evolutionary divergence and may cause some of the unusual patterns observed in sequences. In: Loeschcke V (ed) Genetic constraints on adaptive evolution. Springer-Verlag, Berlin, pp 151-172
35. Goldschmidt-Clermont M, Choquet Y, Girard-Bascou J, Michel F, Schirmer-Rahire M, Rochaix JD (1991) A small chloroplast RNA may be required for trans-splicing in Chlamydomonas reinhardtii. Cell 65:135-143
36. Gould SJ (1997) The exaptive excellence of spandrels as a term and prototype. Proc Natl Acad Sci USA 94:10750-10755
37. Gould SJ, Lewontin RC (1979) The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist program. Proc Roy Soc London B 205:581-598
38. Gould SJ, Vrba ES (1982) Exaptation - A missing term in the science of form. Paleobiology 8:4-15
39. Gu X, Hewett-Emmett D, Li W-H (1998) Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria. Genetica 102/103:383-391
40. Hajduk SL, Harris JE, Pollard VW (1993) RNA editing in kinetoplastid mitochondria. FASEB J 7:54-63
41. Haldane JBS (1932) The causes of evolution. Longmans, Green and Co., New York
42. Hartl DL, Dykhuizen DE, Dean AM (1985) Limits of adaptation: The evolution of selective neutrality. Genetics 111:655-674
43. Hecht MK, Hoffman A (1986) Why not neo-Darwinism? A critique of paleobiological challenges. Oxford Surv Evol Biol 3:1-47
44. Herschlag D, Khosla M, Tsuchihashi Z, Karpel RL (1994) An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis. [Erratum appears in EMBO J 13(16): 3926, 1994]. EMBO J 13:2913-2924
45. Hetzer M, Wurzer G, Schweyen RJ, Mueller MW (1997) Tranactivation of group II intron splicing by nuclear U5 snRNA. Nature 386:417-420
46. Hughes AL (1994) The evolution of functionally novel proteins after gene duplication. Proc R Soc Lond B 256:119-124
47. Hughes AL, Hughes MK (1993) Adaptive evolution in the rat olfactory receptor gene family. J Mol Evol 36:249-254
48. Iida S, Meyer J, Arber W (1983) Prokaryotic IS elements. In: Shapiro JA (ed) Mobile genetic elements. Academic Press, New York
49. Inoue R (1994) Time to change partners. Nature 370:99-100
50. Jarrell KA, Dietrich RC, Perlman PS (1988) Group II intron domain 5 facilitates a trans-splicing reaction. Mol Cell Biol 8:2361-2366
51. Kauffman SA (1993) The origins of order: Self-organization and evolution. Oxford University Press, New York
52. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
53. Lambowitz AM, Perlman PS (1990) Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing. Trends Biochem Sci 15:440-444
54. Lamond AI (1993) The spliceosome. Bioessays 15:595-603
55. Lande R (1976) Natural selection and random genetic drift in phenotypic evolution. Evolution 30:314-334
56. Landweber LF (1992) The evolution of RNA editing in kinetoplastic protozoa. BioSystems 28:41-45
57. Lang KM, Spritz RA (1987) In vitro splicing pathways of pre-mRNAs containing multiple intervening sequences. Mol Cell Biol 7:3428 3437
58. Li W-H (1980) Rate of gene silencing at duplicate loci: A theoretical study and interpretation of data from tetraploid fishes. Genetics 95:237-258
59. Li W-H (1997) Molecular evolution. Sinauer, Sunderland, MA
60. Macey JR, Larson A, Ananjeva NB, Papenfuss TJ (1997) Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs. Mol Biol Evol 14:30-39
61. Malek O, Lättig K, Hiesel R, Brennicke A, Knoop A (1996) RNA editing in bryophyles and a molecular phylogeny of land plants. EMBO J 15:1403-1411
62. Maxwell ES, Fournier MJ (1995) The small nucleolar RNAs. Annu Rev Biochem 64:897-934
63. Maynard Smith J, Szathmary E (1995) The major transitions in evolution. W.H. Freeman, Oxford
64. Maynard Smith J, Burian R, Kauffman S, et al. (1985) Developmental constraints and evolution. Q Rev Biol 60:265-287
65. Mayr E (1983) How to carry out the adaptationist program? Am Nat 121:324-334
66. Nadeau JH, Sankoff D (1997) Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution. Genetics 147:1259-1266
67. Nedelcu AM (1997) Fragmented and scrambled mitochondrial ribosomal RNA coding regions among green algae: a model for their origin and evolution. Mol Biol Evol 14:506-517
68. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
69. Nitecki MH, Hoffman A (1987) Neutral models in biology. Oxford University Press, New York
70. Ohno S (1970) Evolution by gene duplication. Springer-Verlag, New York
71. Ohta T (1994) Further examples of evolution by gene duplication revealed through DNA sequence comparisons. Genetics 138:1331-1337
72. Ohta T (1996) The current significance and standing of neutral and nearly neutral theories. Bioessays 18:673-677
73. Osawa S, Jukes TH, Watanabe K, Muto A (1992) Recent evidence for evolution of the genetic code. Microbiol Rev 56:229-264
74. Patthy L (1987) Intron-dependent evolution: Preferred types of exons and introns. FEBS Lett 214:1-7
75. Phillips PC (1998) The language of gene interaction. Genetics 149: 1167-1171
76. Prescott DM (1997) Origin, evolution, and excision of internal elimination segments in germline genes of ciliates. Curr Opin Genet Dev 7:807-813
77. Prescott DM, Greslin AF (1992) Scrambled actin 1 gene in the micronucleus of Oxytricha nova. Dev Genet 13:66-74
78. Rennell D, Bouvier SE, Hardy LW, Potecte AR (1991) Systematic mutation of bacteriophage T4 lysozyme. J Mol Biol 222:67-87
79. Riedl R (1978) Order in living organisms. John Wiley & Sons, New York
80. Robeson JP, Goldschmidt RM, Curtiss R, III (1980) Potential of Escherichiu coli isolated from nature to propagate cloning vectors. Nature 283:104-106
81. Schmidt U, Podar M, Stahl U, Perlman PS (1996) Mutations of the two-nucleotide bulge of D5 of a group II intron block splicing in vitro and in vivo: Phenotypes and suppressor mutations. RNA 2: 1161-1172
82. Schug MD, Hutter CM, Wetterstrand KA, Gaudette MS, Mackay TFC, Aquadro CF (1998) The mutation rates of di-, tri-and tetranucleotide repeats in Drosophila melanogaster. Mol Biol Evol 15:1751-1760
83. Sommer SS, Kettterling RP (1994) How precisely can data from transgenic mouse mutation-detection systems be extrapolated to humans? Lesions from the human factor IX gene. Mutat Res 307: 517-531
84. Stern S, Powers T, Changchien L-M, Nollier HF (1989) RNA-protein interactions in 30S ribosomal subunits: Folding and function of 16S rRNA. Science 244:783-790
85. Stuart K (1991) RNA editing in mitochondrial mRNA of trypanosomatids. TIBS 16:68-72
86. Stuart K, Allen TE, Heidmann S, Seiwert SD (1997) RNA editing in kinetoplastid protozoa. Microbiol Mol Biol Rev 61:105-120
87. Thomas DC, Roberts JD, Sabatino RD, et al. (1991) Fidelity of mammalian DNA replication and replicative DNA polymerases. Biochemistry 30:11751-11759
88. Thomson KS (1985) Essay review: The relationship between development and evolution. Oxford Surv Evol Biol 2:220-233
89. Vrba ES, Eldredge N (1984) Individuals, hierarchies and processes: Towards a more complete evolutionary theory. Paleobiology 10: 146-171
90. Wallace B (1991) The manly art of self-defense: On the neutrality of fitness components. Q Rev Biol 66:455-465
91. Weeks KM, Cech TR (1996) Assembly of a ribonucleoprotein catalyst by tertiary structure capture. Science 271:345-348
92. Weissman C, Cattaneo R, Billeter MA (1990) Sometimes an editor makes sense. Nature 343:697-699
93. Williams GC (1966) Adaptation and natural selection: A critique of some current evolutionary thought. Princeton University Press, Princeton, NJ
94. Wilson RJ, Williamson DH (1997) Extrachromosomal DNA in the Apicomplexa. Microbiol Mol Biol Rev 61:1-16
95. Wolfe KH (1989) Mutation rates differ among regions of the mammalian genome. Nature 337:283-285
96. Yost HJ, Petersen RB, Lindquist S (1990) RNA metabolism: Strategies for regulation in the heat shock response. Trends Genetics 6:223-227
97. Zuckerkandl E (1992) Revisiting junk DNA. J Mol Evol 34:259-271
98. Zuckerkandl E (1997) Neutral and nonneutral mutations: The creative mix - Evolution of complexity in gene interaction systems. J Mol Evol 44:S2-S8