Frail Hypotheses in Evolutionary Biology

1. WellesJF

1984 The survival advantage of stupidity. Speculations Sci Technol 7 17 21

2. StensethNC

1985 On the evolution of cannibalism. J Theor Biol 115 161 177

3. KimuraM

1983 The neutral theory of molecular evolution. London, UK Cambridge University Press

4. OhtaT

1973 Slightly deleterious substitutions in evolution. Nature 246 96 98

5. MillerJH

2005 Perspective on mutagenesis and repair: The standard model and alternate modes of mutagenesis. Crit Rev Biochem Mol Biol 40 155 179

6. McClintockB

1984 The significance of responses of the genome to challenges. Science 226 792 801

7. HerbertA

RichA

1999 RNA processing in evolution. The logic of soft-wired genomes. Ann N Y Acad Sci 870 119 132

8. ShapiroJA

1999 Genome system architecture and natural genetic engineering in evolution. Ann N Y Acad Sci 870 23 35

9. ChayotR

MontagneB

MazelD

RicchettiM

2010 An end-joining repair mechanism in Escherichia coli. Proc Natl Acad Sci U S A 107 2141 2146

10. BrinkRA

StylesED

AxtellJD

1968 Paramutation: directed genetic change. Science 159 161 170

11. CasadesúsJ

d'AriR

2002 Memory in bacteria and phage. Bioessays 24 512 518

12. HollidayR

1987 The inheritance of epigenetic defects. Science 238 163 170

13. JablonkaE

LambMJ

2008 Soft inheritance: challenging the modern synthesis. Genet Mol Biol 31 389 395

14. GerhardtJ

KirschnerM

2007 The theory of facilitated variation. Proc Natl Acad Sci U S A 104 suppl. 1 8582 8589

15. LynchM

2007 The frailty of adaptive hypotheses for the origin of organismal complexity. Proc Natl Acad Sci U S A 104 suppl. 1 8597 8604

16. KreitmanM

1996 The neutral theory is dead. Long live the neutral theory. Bioessays 18 678 683

17. DrakeJW

CharlesworthB

CharlesworthD

CrowJF

1998 Rates of spontaneous mutations. Genetics 148 1667 1686

18. WakeleyJ

2005 The limits of theoretical population genetics. Genetics 169 1 7

19. TenaillonO

ToupanceB

Le NagardH

TaddeiF

GodelleB

1999 Mutators, population size, adaptive landscape and the adaptation of asexual populations of bacteria. Genetics 152 485 493

20. KibotaTT

LynchM

1996 Estimate of the genomic mutation rate deleterious to overall fitness in E. coli. Nature 381 694 696

21. GerrishPJ

LenskiRE

1998 The fate of competing beneficial mutations in an asexual population. Genetica 102/ 103 127 144

22. BershteinS

TawfikDS

2008 Ohno's model revisited: measuring the frequency of potentially adaptive mutations under various mutational drifts. Mol Biol Evol 25 2311 2318

23. HorwitzMSZ

LoebLA

1988 DNA sequences of random origin as probes of Escherichia coli promoter architecture. J Biol Chem 263 14724 14731

24. OkadaH

NegoroS

KimuraH

NakamuraS

1983 Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers. Nature 306 203 206

25. KondrashovAS

1995 Contamination of the genomes by very slightly deleterious mutations. Why have we not died 100 times over? J Theor Biol 175 583 594

26. CrowJ

1999 The odds of losing at genetic roulette. Nature 39 293 294

27. Eyre-WalkerA

KeightleyPD

1999 High genomic deleterious mutation rates in hominids. Nature 397 344 347

28. SturtevantAH

1937 Essays on Evolution. I. On the effects of selection on mutation rate. Quart Rev Biol 12 464 467

29. ChaoL

CoxEC

1983 Competition between high and low mutating strains of Escherichia coli. Evolution 37 125 134

30. MillerJH

YeungA

FunchainP

MaoE

StewartJ

2000 Temporary and permanent mutators lacking the mismatch repair system: the enhancement of mutators in cell populations. Cold Spring Harb Symp Quant Biol 65 241 252

31. ShaverAC

DombrowskiPG

SweeneyJY

TreisT

ZappalaRM

2002 Fitness evolution and the rise of mutator alleles in experimental Escherichia coli populations. Genetics 162 557 566

32. DenamurE

LecointreG

DarluP

AcquavivaC

SayadaC

2000 Evolutionary implications of the frequent horizontal transfer of mismatch repair genes. Cell 103 711 721

33. DrakeJW

2009 Avoiding dangerous missense: thermophiles display especially low mutation rates. PLoS Genet 5 e1000520 doi:10.1371/journal.pgen.1000520

34. NinioJ

1991 Transient mutators: a semi-quantitative analysis of the influence of translation and transcription errors on mutation rates. Genetics 129 957 962

35. NinioJ

1996 Gene conversion as a focusing mechanism for correlated mutations: a hypothesis. Mol Gen Genet 251 503 508

36. NinioJ

2000 Illusory defects and mismatches: why must DNA repair always be (slightly) error prone? Bioessays 22 396 401

37. LecomtePJ

NinioJ

1988 Nucleotide excision by E. coli DNA polymerase I in proofreading and non-proofreading modes. Biochim Biophys Acta 951 225 260

38. DrakeJW

2007 Too many mutants with multiple mutations. Crit Rev Biochem Mol Biol 42 247 258

39. HodgkinsonA

LadoukakisE

Eyre-WalkerA

2009 Cryptic variation in the human mutation rate. PLoS Biology 7 e1000027 doi:10.1371/journal.pbio.1000027

40. BerdalKG

JohansenRF

SeebergE

1998 Release of normal bases from intact DNA by a native DNA repair enzyme. EMBO J 17 363 367

41. HolmquistGP

1998 Endogenous lesions, S-phase-independent spontaneous mutations, and evolutionary strategies for base excision repair. Mut Res 400 59 68

42. MuramatsuM

KinoshitaK

FagarasanS

YamadaS

ShinkaiY

2000 Class switch recombination and hypermutation require activation induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 102 553 563

43. HarrisRS

Petersen-MahrtSK

NeubergerMS

2002 RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol Cell 10 1247 1253

44. SchanzS

CastorD

FischerF

JiricnyJ

2009 Interference of mismatch and base excision repair during the processing of adjacent U/G mispairs may play a key role in somatic hypermutation. Proc Natl Acad Sci U S A 106 5593 5598

45. NinioJ

1991 Connections between translation, transcription and replication error-rates. Biochimie 73 1517 1523

46. NinioJ

1997 The evolutionary design of error-rates and the fast fixation enigma. Orig Life Evol Biosph 27 609 621

47. HallBG

1989 Selection, adaptation, and bacterial operons. Genome 31 265 271

48. RoscheWA

FosterPL

with an appendix by CairnsJ

1999 The role of transient hypermutators in adaptive mutation in Escherichia coli. Proc Natl Acad Sci U S A 96 6862 6867

49. RothJR

KugelbergE

ReamsAB

KofoidE

AnderssonDI

2006 Origin of mutations under selection: the adaptive mutation controversy. Annu Rev Microbiol 60 477 501

50. GalhardoRS

HastingsPJ

RosenbergSM

2007 Mutation as a stress response and the regulation of evolvability. Crit Rev Biochem Mol Biol 42 399 435

51. TimmsAR

BridgesBA

1993 Double, independent mutational events in the rpsL gene of Escherichia coli: an example of hypermutability? Mol Microbiol 9 335 342

52. ChenJ-M

CooperDN

ChuzhanovaN

FérecC

PatrinosGP

2007 Gene conversion: mechanisms, evolution and human disease. Nature Rev Genet 8 762 775

53. StrathernJN

ShaferBK

McGillCB

1995 DNA synthesis errors associated with double-strand break repair. Genetics 140 965 972

54. KuzminovA

1995 Collapse and repair of replication forks in Escherichia coli. Mol Microbiol 16 373 384

55. DuretL

GaltierN

2009 Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet 10 285 311

56. WincklerW

MyersSR

RichterDJ

OnofrioRC

McDonaldGJ

2005 Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308 107 111

57. BortsRH

LeungW-Y

KramerW

KramerB

WilliamsonM

1990 Mismatch repair-induced meiotic recombination requires the PMS1 gene product. Genetics 124 573 581

58. BollagRJ

ElwoodDR

TobinED

GodwinAR

LiskayRM

1992 Formation of heteroduplex DNA during mammalian intrachromosomal gene conversion. Mol Cell Biol 12 1546 1552

59. ManivasakamP

RosenbergSM

HastingsPJ

1996 Poorly repaired mismatches in heteroduplex DNA are hyper-recombinagenic in Saccharomyces cerevisiae. Genetics 142 407 416

60. DoverG

1982 Molecular drive: a cohesive mode of species evolution. Nature 299 111 117

61. RubinszteinDC

AmosW

LeggoJ

GoodburnS

JainS

1994 Microsatellite evolution - evidence for directionality and variation in rate between species. Nat Genet 10 337 343

62. AmosW

2009 Heterozygosity and mutation rate: evidence for an interaction and its implications. Bioessays 32 82 90

63. GiverCR

GrosovskyAJ

1997 Single and coincident intragenic mutations attributable to gene conversion in a human cell line. Genetics 146 1429 1439

64. CarrasquilloMM

ZlotogoraJ

BargesS

ChakravartiA

1997 Two different connexin 26 mutations in an inbred kindred segregating non-syndromic deafness: Implications for genetic studies in isolated populations. Hum Mol Genet 6 2163 2172

65. FeingoldJ

1998 Multiple mutations in a specific gene in a small population. C R Acad Sci III 321 553 555

66. PatrinosGP

KolliaP

Loutradi-AnagnostouA

LoukopoulosD

PapadakisM

1998 The Cretan type of non-deletional hereditary persistence of fetal hemoglobin [Aγ-158C→T] results from two independent gene conversion events. Hum genet 102 629 634

67. BachinskyAG

1980 Mathematical models of evolutionary processes (in Russian) (Ratner VA, ed.), Novosibirsk (USSR): Academy of Sciences Press. 49 65 Chapter, The qualitative estimation of the influence of template processes ambiguity on the population fitness

68. NinioJ

1983 Molecular approaches to evolution. Princeton, New Jersey Princeton University Press

69. WhiteheadDJ

WilkeCO

VernazobresD

Bornberg-BauerE

2008 The look-ahead effect of phenotypic mutations. Biology Direct 3 18

70. ConradM

1978 Lecture notes in mathematics, vol. 21:Theoretical approaches to complex systems (Heim R, Palm G, eds). 147 169 Berlin (Germany): Springer-Verlag. Chapter, Evolution of the adaptive landscape

71. NinioJ

1986 Accuracy in Molecular Processes (Kirkwood TBL, Rosenberger R, Galas DJ, eds). London (UK) Chapman & Hall 381 391 Chapter, Diversity and accuracy in evolution: sketches past, present and future

72. CluneJ

MisevicD

OfriaC

LenskiRE

ElenaSF

2008 Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. PLoS Comput Biol 4 e1000187 doi:10.1371/journal.pcbi.1000187

73. d'AriR

CasadesúsJ

1998 Underground metabolism. Bioessays 20 181 186

74. PatelPH

LoebLA

2000 DNA polymerase active site is highly mutable: evolutionary consequences. Proc Natl Acad Sci U S A 97 5095 5100

75. KacserH

BurnsJA

1981 The molecular basis of dominance. Genetics 97 639 666

76. Cornish-BowdenA

1987 Dominance is not inevitable. J Theor Biol 125 333 338

77. DeanACR

HinshelwodCN

1955 Reaction patterns of a coliform organism. Prog Biophys Biophys Chem 5 1 40

78. WoeseCR

1974 The custom fitting problem and the evolution of developmental systems. J Mol Evol 3 109 113

79. SangsterTA

LindquistS

QueitschC

2004 Under cover: causes, effects and implications of Hsp90-mediated genetic capacitance. Bioessays 26 348 362

80. RutherfordS

HirateY

SwallaBJ

2007 The Hsp90 capacitor, developmental, remodeling, and evolution: the robustness of gene networks and the curious evolvability of metamorphosis. Crit Rev Biochem Mol Biol 42 355 372

81. NinioJ

BokorV

1986 Stratégies d'adaptation moléculaire. La vie des Sciences 3 121 136

82. BaldwinJM

1896 A new factor in evolution. Am Nat 30 441 451;536–553

83. PiagetJ

1974 Adaptation vitale et psychologie de l'intelligence. Chicago, Illinois University of Chicago Press Paris (France); Hermann. English translation (1980) Adaptation and intelligence: organic selection and phenocopy.

84. GordonAJE

HallidayJA

BlankschienMD

BurnsPA

YatagaiF

2009 Transcriptional infidelity promotes heritable phenotypic change in a bistable gene network. PLoS Biol 7 e1000044 doi:10.1371/journal.pbio.1000044

85. HeinemanRH

BullJJ

MolineuxIJ

2009 Layers of evolvability in a becteriophage life history trait. Mol Biol Evol 26 1289 1298