Interaction-based evolution: How natural selection and nonrandom mutation work together

Biology Direct

Volumn 8, Issue 1, 2013, Pages

  Livnat, Adi ^a  

^a VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

Adaptive evolution; de novo genes; Epistasis; Evolvability; Junk DNA; Mutation bias; Neutral theory; Sex and recombination; Transcriptional promiscuity

Indexed keywords

LAMARCKIA; SCAEVIUS MILII;

ADAPTATION; BIOLOGICAL MODEL; EVOLUTION; GENETIC SELECTION; MUTATION;

ADAPTATION, BIOLOGICAL; BIOLOGICAL EVOLUTION; MODELS, GENETIC; MUTATION; SELECTION, GENETIC;

EID: 84888012771     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-8-24     Document Type: Article

References (271)

1. Lewontin RC, Hubby JL. A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics 1966, 54:595-609. 1211186, 5968643.
2. Harris H. Enzyme polymorphisms in man. Proc R Soc Lond B 1966, 164:298-310. 10.1098/rspb.1966.0032, 4379519.
3. The ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74. 10.1038/nature11247, 3439153, 22955616, The ENCODE Project Consortium.
4. Ohno S. So much "junk" DNA in our genome. Brookhaven Symp Biol 1972, 23:366-370.
5. Orgel LE, Crick FH. Selfish DNA: the ultimate parasite. Nature 1980, 284:604-607. 10.1038/284604a0, 7366731.
6. Doolittle WF, Sapienza C. Selfish genes, the phenotype paradigm and genome evolution. Nature 1980, 284:601-603. 10.1038/284601a0, 6245369.
7. Graur D, Zheng Y, Price N, Azevedo RBR, Zufall RA, Elhaik E. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 2013, 5:578-590. 10.1093/gbe/evt028, 3622293, 23431001.
8. Doolittle W. Is junk DNA bunk? A critique of ENCODE. P Natl Acad Sci USA 2013, 110:5294-5300.
9. Cai J, Zhao R, Jiang H, Wang W. De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 2008, 179:487-496. 10.1534/genetics.107.084491, 2390625, 18493065.
10. Knowles DG, McLysaght A. Recent de novo origin of human protein-coding genes. Genome Res 2009, 19:1752-1759. 10.1101/gr.095026.109, 2765279, 19726446.
11. Heinen TJAJ, Staubach F, Häming D, Tautz D. Emergence of a new gene from an intergenic region. Curr Biol 2009, 19:1527-1531. 10.1016/j.cub.2009.07.049, 19733073.
12. Li CY, Zhang Y, Wang Z, Zhang Y, Cao C, Zhang PW, Lu SJ, Li XM, Yu Q, Zheng X, Du Q, Uhl GR, Liu QR, Wei L. A human-specific de novo protein-coding gene associated with human brain functions. PLoS Comput Biol 2010, 6:e1000734. 10.1371/journal.pcbi.1000734, 2845654, 20376170.
13. Li D, Dong Y, Jiang Y, Jiang H, Cai J, Wang W. A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand. Cell Res 2010, 20:408-420. 10.1038/cr.2010.31, 20195295.
14. Jacob F. Evolution and tinkering. Science 1977, 196:1161-1166. 10.1126/science.860134, 860134.
15. Lynch VJ, Leclerc RD, May G, Wagner GP. Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nat Genet 2011, 43:1154-1159. 10.1038/ng.917, 21946353.
16. Doolittle WF. Understanding introns: origins and functions. Intervening Sequences in Evolution and Development 1990, 43-62. New York: Oxford University Press, Stone EM, Schwartz RJ.
17. Graur D, Li WH. Fundamentals of Molecular Evolution 2000, Sunderland: Sinauer Associates.
18. Heard E, Tishkoff S, Todd JA, Vidal M, Wagner GP, Wang J, Weigel D, Young R. Ten years of genetics and genomics: what have we achieved and where are we heading?. Nat Rev Genet 2010, 11:723-733. 10.1038/nrg2878, 3004366, 20820184.
19. Fedoroff NV. Presidential address. Transposable elements, epigenetics, and genome evolution. Science 2012, 338:758-767. 10.1126/science.338.6108.758, 23145453.
20. West-Eberhard MJ. Developmental Plasticity and Evolution 2003, New York: Oxford University Press.
21. Fisher RA. The Genetical Theory of Natural Selection 1930, Oxford: The Clarendon Press.
22. Sniegowski PD. The origin of adaptive mutants: Random or nonrandom?. J Mol Evol 1995, 40:94-101.
23. Futuyma DJ. Evolution, 2nd edition 2009, Sunderland: Sinauer Associates.
24. Barton NH, Charlesworth B. Why sex and recombination?. Science 1998, 281:1986-1990.
25. Wade MJ, Goodnight CJ. Perspective: The theories of Fisher and Wright in the context of metapopulations: when nature does many small experiments. Evolution 1998, 52:1537-1553.
26. Muller HJ. Some genetic aspects of sex. Am Nat 1932, 66:118-138.
27. Muller HJ. The relation of recombination to mutational advance. Mutation Res 1964, 1:2-9.
28. Levin DA. Pest pressure and recombination systems in plants. Am Nat 1975, 109:437-451.
29. Jaenike J. A hypothesis to account for the maintenance of sex within populations. Evol Theory 1978, 3:191-194.
30. Kondrashov A. Selection against harmful mutations in large sexual and asexual populations. Genet Res 1982, 40:325-332. 10.1017/S0016672300019194, 7160619.
31. West SA, Lively CM, Read AF. A pluralist approach to sex and recombination. J Evol Biol 1999, 12:1003-1012.
32. Feldman MW, Otto SP, Christiansen FB. Population genetic perspectives on the evolution of recombination. Annu Rev Genet 1997, 30:261-295.
33. Stearns SC, Hoekstra RF. Evolution: An Introduction 2005, New York: Oxford University Press.
34. Wright S. Evolution in Mendelian populations. Genetics 1931, 16:97-159. 1201091, 17246615.
35. Wright S. The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proc 6th Int Cong Genet 1932, 1:356-366.
36. Provine W. Sewall Wright and Evolutionary Biology 1986, Chicago: The University of Chicago Press.
37. Barton N, Rouhani S. Adaptation and the 'shifting balance'. Genet Res 1993, 61:57-74.
38. Coyne JA, Barton NH, Turelli M. Perspective: A critique of Sewall Wright's shifting balance theory of evolution. Evolution 1997, 51:643-671.
39. Leigh Jr EG Introduction. The Causes of Evolution/by J.S.B. Haldane; with a new Preface and Afterword by E. G. Leigh. 1990, Princeton: Princeton University Press, Leigh Jr EG.
40. Haig D. Weismann rules! OK? Epigenetics and the Lamarckian temptation. Biol Philos 2007, 22:415-428.
41. Berg LS. Nomogenesis; or, Evolution Determined by Law 1926, London: Constable & Company.
42. Dougherty EC. Comparative evolution and the origin of sexuality. Syst Zool 1955, 4:145-190.
43. Vrijenhoek RC. Genetic and ecological constraints on the origins and establishment of unisexual vertebrates. Evolution and Ecology of Unisexual Vertebrates 1989, 24-31. Albany: New York State Museum, Dawley RM, Bogart JP.
44. Stebbins GL. Variation and Evolution in Plants 1950, New York: Columbia University Press.
45. Van Valen L. Group selection, sex, and fossils. Evolution 1975, 29:87-94.
46. Maynard-Smith J. The Evolution of Sex 1978, Cambridge: Cambridge University Press.
47. Bell G. The Masterpiece of Nature: The Evolution and Genetics of Sexuality 1982, Berkeley: University of California Press.
48. Williams GC. Adaptation and Natural Selection 1966, Princeton: Princeton University Press, (8th edition 1996).
49. Stebbins GL. Self fertilization and population variability in the higher plants. Am Nat 1957, 91:337-354.
50. Judson OP, Normark BB. Ancient asexual scandals. Trends Ecol Evol 1996, 11:41-46. 10.1016/0169-5347(96)81040-8, 21237759.
51. Hurst LD, Hamilton WD, Ladle RJ. Covert sex. Trends Ecol Evol 1992, 7:144-145. 10.1016/0169-5347(92)90205-P, 21235987.
52. Meselson M. Molecular and cellular biology, faculty profiles. https://www.mcb.harvard.edu/mcb/faculty/profile/matthew-s-meselson/ Accessed 1/7/2013.
53. Meselson M "Sex and death in bdelloid rotifers." The Second Annual Arthur W. Galston Memorial Lecture given for the Yale Interdisciplinary Center for Bioethics on April 16, 2010. http://archive.org/details/MathewMeselsonSexandDeathinBdelloidRotifers Accessed 1/7/2013, Meselson M.
54. Woese CR. On the evolution of cells. P Natl Acad Sci USA 2002, 99:8742-8747.
55. Brosius J. Gene duplication and other evolutionary strategies: from the RNA world to the future. J Struct Funct Genomics 2003, 3:1-17. 10.1023/A:1022627311114, 12836680.
56. Brosius J. Echoes from the past - are we still in an RNP world?. Cytogenet Genome Res 2005, 110:8-24. 10.1159/000084934, 16093654.
57. Vetsigian K, Woese C, Goldenfeld N. Collective evolution and the genetic code. P Natl Acad Sci USA 2006, 103:10696-10701.
58. Merriam-Webster Online Convergence. http://www.merriam-webster.com/dictionary/convergence Accessed 1/7/2013, Merriam-Webster Online.
59. Oxford English Dictionary Online Converge. http://oxforddictionaries.com/us/definition/american_english/converge?q=converge Accessed 1/7/2013, Oxford English Dictionary Online.
60. Darwin C. The Origin of Species by Means of Natural Selection, Or The Preservation of Favoured Races in the Struggle for Life, 6th edition, Chapter V 1876, London: John Murray.
61. Nei M. Modification of linkage intensity by natural selection. Genetics 1967, 57:625-641. 1211753, 5583732.
62. Feldman MW. Selection for linkage modification. I. Random mating populations. Theor Popul Biol 1972, 3:324-346. 10.1016/0040-5809(72)90007-X, 4667090.
63. Feldman MW, Christiansen FB, Brooks LD. Evolution of recombination in a constant environment. P Natl Acad Sci USA 1980, 77:4838-4841.
64. Avise JC. Clonality: The Genetics, Ecology, and Evolution of Sexual Abstinence in Vertebrate Animals 2008, New York: Oxford University Press.
65. Neaves WB. Tetraploidy in a hybrid lizard of the genus Cnemidophorus (Teiidae). Breviora 1971, 381:1-25.
66. Cole CJ. Evolution of parthenogenetic species of reptiles. Intersexuality in the Animal Kingdom 1975, 340-355. Berlin: Springer-Verlag, Reinboth R.
67. Darevsky IS. Evolution and ecology of parthenogenesis in reptiles. Soc Study Amphib Reptiles Contr Herpetol 1992, 9:21-39.
68. Lande R, Schemske DW. The evolution of self-fertilization and inbreeding depression in plants. I. Genetic models. Evolution 1985, 39:24-40.
69. Goodwillie C, Kalisz S, Eckert CG. The evolutionary enigma of mixed mating systems in plants: Occurrence, theoretical explanations, and empirical evidence. Annu Rev Ecol Evol Syst 2005, 36:47-79.
70. Jarne P, Charlesworth D. The evolution of the selfing rate in functionally hermaphrodite plants and animals. Annu Rev Ecol Syst 1993, 24:441-466.
71. Tian-Bi YNT, N'Goran EK, N'Guetta SP, Matthys B, Sangare A, Jarne P. Prior selfing and the selfing syndrome in animals: an experimental approach in the freshwater snail Biomphalaria pfeifferi. Genet Res 2008, 90:61-72.
72. Winn AA, Moriuchi KS. The maintenance of mixed mating by cleistogamy in the perennial violet Viola septemloba (Violaceae). Am J Bot 2009, 96:2074-2079. 10.3732/ajb.0900048, 21622326.
73. Barrett SCH, Eckert CG. Variation and evolution of mating systems in seed plants. Biological Approaches and Evolutionary Trends in Plants 1990, 229-254. Tokyo: Academic Press, Kawano S.
74. Jarne P, Auld JR. Animals mix it up too: The distribution of self-fertilization among hermaphroditic animals. Evolution 2006, 60:1816-1824.
75. Moritz C, Brown WM, Densmore LD, Wright JW, Vyas D, Donnellan S Genetic diversity and the dynamics of hybrid parthenogenesis in Cnemidophorus (Teiidae) and Heteronotia (Gekkonidae). Evolution and Ecology of Unisexual Vertebrates 1989, 87-112. Albany: New York State Museum: Dawley RM, Bogart JP, Donnellan S.
76. Darevsky IS, Kupriyanova LA, Uzzell T Parthenogenesis in reptiles. Biol Reptilia, Volume 15 1985, 411-526. New York: Wiley, Gans C, Billett F, Uzzell T.
77. Holsinger KE. Mass-action models of plant mating systems: The evolutionary stability of mixed mating systems. Am Nat 1991, 138:606-622.
78. Porcher E, Lande R. The evolution of self-fertilization and inbreeding depression under pollen discounting and pollen limitation. J Evol Biol 2005, 18:497-508. 10.1111/j.1420-9101.2005.00905.x, 15842479.
79. Johnston MO Evolution of intermediate selfing rates in plants: Pollination ecology versus deleterious mutations. Genetica 1998, 102/103:267-278. Johnston MO.
80. Harder LD, Wilson WG. A clarification of pollen discounting and its joint effects with inbreeding depression on mating system evolution. Am Nat 1998, 152:684-695. 10.1086/286199, 18811343.
81. Vallejo-Marin M, Uyenoyama MK. On the evolutionary costs of self-incompatibility: Incomplete reproductive compensation due to pollen limitation. Evolution 2004, 58:1924-1935.
82. Morgan MT, Wilson WG. Self-fertilization and the escape from pollen limitation in variable pollination environments. Evolution 2005, 59:1143-1148.
83. Sakai S, Ishii HS. Why be completely outcrossing? Evolutionary stable outcrossing strategies in an environment where outcross-pollen availability is unpredictable. Evol Ecol Res 1999, 1:211-222.
84. Cheptou PO. Allee effect and self-fertilization in hermaphrodites: reproductive assurance in demographically stable populations. Evolution 2004, 58:2613-2621.
85. Pannell JR. On the problems of a closed marriage: celebrating Darwin 200. Biol Lett 2009, 5:332-335. 10.1098/rsbl.2009.0142, 2679940, 19386650.
86. Kiontke K, Gavin NP, Raynes Y, Roehrig C, Piano F, Fitch DHA. Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. P Natl Acad Sci USA 2004, 101:9003-9008.
87. Sassaman C, Weeks SC. The genetic mechanism of sex determination in the conchostracan shrimp Eulimnadia texana. Am Nat 1993, 141:314-328. 10.1086/285475, 19426084.
88. Mackiewicz M, Tatarenkov A, Taylor DS, Turner BJ, Avise JC. Extensive outcrossing and androdioecy in a vertebrate species that otherwise reproduces as a self-fertilizing hermaphrodite. P Natl Acad Sci USA 2006, 103:9924-9928.
89. Otto SP, Sassaman C, Feldman MW. Evolution of sex determination in the conchostracan shrimp Eulimnadia texana. Am Nat 1993, 141:329-337. 10.1086/285476, 19426085.
90. Darwin C. The Different Forms of Flowers on Plants of the Same Species 1877, New York: Appleton and Co.
91. Lord EM. Cleistogamy: a tool for the study of floral morphogenesis, function and evolution. Bot Rev 1981, 47:421-449.
92. Culley TM, Klooster MR. The cleistogamous breeding system: a review of its frequency, evolution, and ecology in angiosperms. Bot Rev 2007, 73:1-30.
93. de Nettancourt D. Incompatibility and Incongruity in Wild and Cultivated Plants 2001, New York: Springer Verlag.
94. Franklin-Tong VE. Self-incompatibility in Flowering Plants: Evolution, Diversity, and Mechanisms 2008, Berlin: Springer Verlag.
95. Lloyd DG. Self- and cross-fertilization in plants. II. The selection of self-fertilization. Int J Plant Sci 1992, 153:370-380.
96. Feldman MW, Christiansen FB. Population genetic theory of the cost of inbreeding. Am Nat 1984, 123:642-653.
97. Ramsey FP. A mathematical theory of saving. Econ J 1928, 38:543-559.
98. Stearns SC. The Evolution of Life Histories 1992, Oxford: Oxford University Press.
99. Evans HE. The Comparative Ethology and Evolution of the Sand Wasps 1966, Cambridge: Harvard University Press.
100. Tsuneki K. Comparative studies on the nesting biology of the genus Sphex (s.l.) in East Asia (Hymenoptera, Sphecidae). Mem Fac Lib Arts, Fukui Univ Ser II 1963, 13:13-78.
101. Evans HE. The accessory burrows of digger wasps. Science 1966, 152:465-471. 10.1126/science.152.3721.465, 17815073.
102. Schmalhausen II. Factors of Evolution 1947, Philadelphia: Blakiston.
103. Waddington CH. The Strategy of the Genes 1957, London: George Allen and Unwin Ltd. Publishers.
104. Wagner GP, Booth G, Bagheri-Chaichian H. A population genetic theory of canalization. Evolution 1997, 51:329-347.
105. Virgen CA, Kratovac Z, Bieniasz PD, Hatziioannou T. Independent genesis of chimeric TRIM5-cyclophilin proteins in two primate species. P Natl Acad Sci USA 2008, 105:3563-3568.
106. Johnson WE, Sawyer SL. Molecular evolution of the antiretroviral TRIM5 gene. Immunogenetics 2009, 61:163-176. 10.1007/s00251-009-0358-y, 19238338.
107. Nisole S, Lynch C, Stoye JP, Yap MW. A Trim5-cyclophilin A fusion protein found in owl monkey kidney cells can restrict HIV-1. P Natl Acad Sci USA 2004, 101:13324-13328.
108. Sayah DM, Sokolskaja E, Berthoux L, Luban J. Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1. Nature 2004, 430:569-573. 10.1038/nature02777, 15243629.
109. Liao CH, Kuang YQ, Liu HL, Zheng YT, Su B. A novel fusion gene, TRIM5-Cyclophilin A in the pig-tailed macaque determines its susceptibility to HIV-1 infection. Aids 2007, 21(Suppl 8):S19-S26.
110. Brennan G, Kozyrev Y, Hu SL. TRIMCyp expression in Old World primates Macaca nemestrina and Macaca fascicularis. P Natl Acad Sci USA 2008, 105:3569-3574.
111. Wilson SJ, Webb BL, Ylinen LM, Verschoor E, Heeney JL, Towers GJ. Independent evolution of an antiviral TRIMCyp in rhesus macaques. P Natl Acad Sci USA 2008, 105:3557-3562.
112. Newman RM, Hall L, Kirmaier A, Pozzi LA, Farzan M, O'Neil SP, Johnson W, Pery E Evolution of a TRIM5-CypA splice isoform in old world monkeys. PLoS Pathog 2008, 4:e1000003. 10.1371/journal.ppat.1000003, 2279257, 18389077, Pery E.
113. Dennett DC. Darwin's Dangerous Idea: Evolution and the Meaning of Life 1996, New York: Simon & Schuster.
114. Roth JR, Kofoid E, Roth FP, Berg OG, Seger J, Andersson DI. Regulating general mutation rates: examination of the hypermutable state model for Cairnsian adaptive mutation. Genetics 2003, 163:1483-1496. 1462528, 12702691.
115. Koonin EV. The Logic of Chance: The Nature and Origin of Biological Evolution 2011, Upper Saddle River: FT Press.
116. Kaessmann H, Vinckenbosch N, Long M. RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet 2009, 10:19-31. 3690669, 19030023.
117. Muller HJ. Bar duplication. Science 1936, 83:528-530.
118. Nei M. Mutation-Driven Evolution 2013, Oxford: Oxford University Press.
119. Doolittle WF. What introns have to tell us: hierarchy in genome evolution. Cold Spring Harb Symp Quant Biol 1987, 52:907-913. 10.1101/SQB.1987.052.01.099, 2456888.
120. Haldane JBS. The cost of natural selection. J Genet 1957, 55:511-524.
121. Kimura M. Evolutionary rate at the molecular level. Nature 1968, 217:624-626. 10.1038/217624a0, 5637732.
122. Bryson V, Vogel HJ. (Eds): Evolving Genes and Proteins: A Symposium Held at the Institute of Microbiology of Rutgers, with Support from the National Science Foundation 1965, New York: Academic Press.
123. Gu W, Zhang F, Lupski JR. Mechanisms for human genomic rearrangements. PathoGenetics 2008, 1:4. 10.1186/1755-8417-1-4, 2583991, 19014668.
124. Zhang F, Gu W, Hurles ME, Lupski JR. Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 2009, 10:451-481. 10.1146/annurev.genom.9.081307.164217, 19715442.
125. Mani RS, Chinnaiyan AM. Triggers for genomic rearrangements: insights into genomic, cellular and environmental influences. Nat Rev Genet 2010, 11:819-829.
126. Lupski JR. Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet 1998, 14:417-422. 10.1016/S0168-9525(98)01555-8, 9820031.
127. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. Recent segmental duplications in the human genome. Science 2002, 297:1003-1007. 10.1126/science.1072047, 12169732.
128. Stankiewicz P, Lupski JR. Genome architecture, rearrangements and genomic disorders. Trends Genet 2002, 18:74-82. 10.1016/S0168-9525(02)02592-1, 11818139.
129. Sharp AJ, Cheng Z, Eichler EE. Structural variation of the human genome. Annu Rev Genomics Hum Genet 2006, 7:407-442. 10.1146/annurev.genom.7.080505.115618, 16780417.
130. Wells RD. Non-B DNA conformations, mutagenesis and disease. Trends Biochem Sci 2007, 32:271-278. 10.1016/j.tibs.2007.04.003, 17493823.
131. Zhao J, Bacolla A, Wang G, Vasquez KM. Non-B DNA structure-induced genetic instability and evolution. Cell Mol Life Sci 2010, 67:43-62. 10.1007/s00018-009-0131-2, 3017512, 19727556.
132. Pfeiffer P, Goedecke W, Obe G. Mechanisms of DNA double-strand break repair and their potential to induce chromosomal aberrations. Mutagenesis 2000, 15:289-302. 10.1093/mutage/15.4.289, 10887207.
133. De Raedt T, Stephens M, Heyns I, Brems H, Thijs D, Messiaen L, Stephens K, Lazaro C, Wimmer K, Kehrer-Sawatzki H, Vidaud D, Kluwe L, Marynen P, Legius E. Conservation of hotspots for recombination in low-copy repeats associated with the NF1 microdeletion. Nat Genet 2006, 38:1419-1423. 10.1038/ng1920, 17115058.
134. Lindsay SJ, Khajavi M, Lupski JR, Hurles ME. A chromosomal rearrangement hotspot can be identified from population genetic variation and is coincident with a hotspot for allelic recombination. Am J Hum Genet 2006, 79:890-902. 10.1086/508709, 1698570, 17033965.
135. Wahls WP, Davidson MK. Discrete DNA sites regulate global distribution of meiotic recombination. Trends Genet 2010, 26:202-208. 10.1016/j.tig.2010.02.003, 2860662, 20381894.
136. Rass E, Grabarz A, Plo I, Gautier J, Bertrand P, Lopez BS. Role of Mre11 in chromosomal nonhomologous end joining in mammalian cells. Nat Struct Mol Biol 2009, 16:819-824. 10.1038/nsmb.1641, 19633668.
137. Woodward KJ, Cundall M, Sperle K, Sistermans EA, Ross M, Howell G, Gribble SM, Burford DC, Carter NP, Hobson DL, Garbern JY, Kamholz J, Heng H, Hodes ME, Malcolm S, Hobson GM. Heterogeneous duplications in patients with Pelizaeus-Merzbacher disease suggest a mechanism of coupled homologous and nonhomologous recombination. Am J Hum Genet 2005, 77:966-987. 10.1086/498048, 1285180, 16380909.
138. Lee JA, Inoue K, Cheung SW, Shaw CA, Stankiewicz P, Lupski JR. Role of genomic architecture in PLP1 duplication causing Pelizaeus-Merzbacher disease. Hum Mol Genet 2006, 15:2250-2265. 10.1093/hmg/ddl150, 16774974.
139. Streisinger G, Okada Y, Emrich J, Newton J, Tsugita A, Terzaghi E, Inouye M. Frameshift mutations and the genetic code. Cold Spring Harb Symp Quant Biol 1966, 31:77-84. 10.1101/SQB.1966.031.01.014, 5237214.
140. Chen JM, Chuzhanova N, Stenson PD, Férec C, Cooper DN. Complex gene rearrangements caused by serial replication slippage. Hum Mutat 2005, 26:125-134. 10.1002/humu.20202, 15977178.
141. Lee JA, Carvalho CMB, Lupski JR. A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 2007, 131:1235-1247. 10.1016/j.cell.2007.11.037, 18160035.
142. Hastings PJ, Ira G, Lupski JR. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 2009, 5:e1000327. 10.1371/journal.pgen.1000327, 2621351, 19180184.
143. Zhang F, Carvalho CMB, Lupski JR. Complex human chromosomal and genomic rearrangements. Trends Genet 2009, 25:298-307. 10.1016/j.tig.2009.05.005, 19560228.
144. Voineagu I, Narayanan V, Lobachev KS, Mirkin SM. Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins. P Natl Acad Sci 2008, 105:9936-9941.
145. Carvalho CM, Zhang F, Liu P, Patel A, Sahoo T, Bacino CA, Shaw C, Peacock S, Pursley A, Tavyev YJ, Ramocki MB, Nawara M, Obersztyn E, Vianna-Morgante AM, Stankiewicz P, Zoghbi HY, Cheung SW, Lupski JR. Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching. Human Mol Genet 2009, 18:2188-2203.
146. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders ACE, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M. Paired-end mapping reveals extensive structural variation in the human genome. Science 2007, 318:420-426. 10.1126/science.1149504, 2674581, 17901297.
147. Lupski JR. Genome structural variation and sporadic disease traits. Nat Genet 2006, 38:974-976. 10.1038/ng0906-974, 16941003.
148. Shapiro JA. Evolution: A View from the 21st Century 2011, Upper Saddle River: FT Press.
149. Dawkins R. The Selfish Gene 1976, Oxford: Oxford University Press.
150. Brosius J, Gould SJ. On "genomenclature" : A comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA" P Natl Acad Sci USA 1992, 89:10706-10710.
151. Brosius J. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 1999, 238:115-134. 10.1016/S0378-1119(99)00227-9, 10570990.
152. Bailey JA, Liu G, Eichler EE. An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet 2003, 73:823-834. 10.1086/378594, 1180605, 14505274.
153. Kim PM, Lam HYK, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M, Gerstein MB. Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res 2008, 18:1865-1874. 10.1101/gr.081422.108, 2593581, 18842824.
154. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tuzun E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, et al. Mapping and sequencing of structural variation from eight human genomes. Nature 2008, 453:56-64. 10.1038/nature06862, 2424287, 18451855.
155. Hodgkinson A, Eyre-Walker A. Variation in the mutation rate across mammalian genomes. Nat Rev Genet 2011, 12:756-766. 10.1038/nrg3098, 21969038.
156. Fryxell KJ, Moon WJ. CpG mutation rates in the human genome are highly dependent on local GC content. Mol Biol Evol 2005, 22:650-658.
157. Bird AP. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 1980, 8:1499-1504. 10.1093/nar/8.7.1499, 324012, 6253938.
158. Cohen NM, Kenigsberg E, Tanay A. Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection. Cell 2011, 145:773-786. 10.1016/j.cell.2011.04.024, 21620139.
159. Deaton AM, Bird A. CpG islands and the regulation of transcription. Genes Dev 2011, 25:1010-1022. 10.1101/gad.2037511, 3093116, 21576262.
160. Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008, 9:465-476.
161. Arnheim N, Calabrese P. Understanding what determines the frequency and pattern of human germline mutations. Nat Rev Genet 2009, 10:478-488. 2744436, 19488047.
162. Qu W, Hashimoto S, Shimada A, Nakatani Y, Ichikawa K, Saito TL, Ogoshi K, Matsushima K, Suzuki Y, Sugano S, Takeda H, Morishita S. Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns. Genome Res 2012, 22:1419-1425. 10.1101/gr.140236.112, 3409255, 22689467.
163. Walser JC, Ponger L, Furano AV. CpG dinucleotides and the mutation rate of non-CpG DNA. Genome Res 2008, 18:1403-1414. 10.1101/gr.076455.108, 2527700, 18550801.
164. Walser JC, Furano AV. The mutational spectrum of non-CpG DNA varies with CpG content. Genome Res 2010, 20:875-882. 10.1101/gr.103283.109, 2892088, 20498119.
165. Panchin AY, Mitrofanov SI, Alexeevski AV, Spirin SA, Panchin YV. New words in human mutagenesis. BMC Bioinformatics 2011, 12:268-274. 10.1186/1471-2105-12-268, 3152918, 21718472.
166. Hodgkinson A, Ladoukakis E, Eyre-Walker A. Cryptic variation in the human mutation rate. PLoS Biol 2009, 7:226-232.
167. Johnson PL, Hellmann I. Mutation rate distribution inferred from coincident SNPs and coincident substitutions. Genome Biol Evol 2011, 3:842-850. 10.1093/gbe/evr044, 3172574, 21572094.
168. Seplyarskiy VB, Kharchenko P, Kondrashov AS, Bazykin GA. Heterogeneity of the transition/transversion ratio in Drosophila and Hominidae genomes. Mol Biol Evol 2012, 29:1943-1955. 10.1093/molbev/mss071, 22337862.
169. Hodgkinson A, Eyre-Walker A. The genomic distribution and local context of coincident SNPs in human and chimpanzee. Genome Biol Evol 2010, 2:547-557. 10.1093/gbe/evq039, 2997558, 20675616.
170. Stoneking M. Hypervariable sites in the mtDNA control region are mutational hotspots. Am J Hum Genet 2000, 67:1029-1032. 10.1086/303092, 1287875, 10968778.
171. Bazykin GA, Kondrashov FA, Brudno M, Poliakov A, Dubchak I, Kondrashov AS. Extensive parallelism in protein evolution. Biol Direct 2007, 2:20. 10.1186/1745-6150-2-20, 2020468, 17705846.
172. Hodgkinson A, Eyre-Walker A. Human triallelic sites: Evidence for a new mutational mechanism?. Genetics 2010, 184:233-241. 10.1534/genetics.109.110510, 2815919, 19884308.
173. Lercher MJ, Hurst LD. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet 2002, 18:337-340. 10.1016/S0168-9525(02)02669-0, 12127766.
174. Webster MT, Hurst LD. Direct and indirect consequences of meiotic recombination: implications for genome evolution. Trends Genet 2012, 28:101-109. 10.1016/j.tig.2011.11.002, 22154475.
175. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P. A fine-scale map of recombination rates and hotspots across the human genome. Science 2005, 310:321-324. 10.1126/science.1117196, 16224025.
176. Duret L, Arndt PF. The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet 2008, 4:e1000071. 10.1371/journal.pgen.1000071, 2346554, 18464896.
177. Caporale LH. Darwin in the Genome: Molecular Strategies in Biological Evolution 2003, New York: McGraw-Hill.
178. Caporale LH. Natural selection and the emergence of a mutation phenotype: An update of the evolutionary synthesis considering mechanisms that affect genome variation. Annu Rev Microbiol 2003, 57:467-485. 10.1146/annurev.micro.57.030502.090855, 14527288.
179. Chuang JH, Li H. Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome. PLoS Biol 2004, 2:253-263.
180. Nguyen DQ, Webber C, Ponting C. Bias of selection on human copy-number variants. PLoS Genet 2006, 2:198-207.
181. 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. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 2003, 302:1960-1963. 10.1126/science.1088821, 14671302.
182. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, Sninsky JJ, Adams MD, Cargill M. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 2005, 3:976-985.
183. Woodward SR, Cruz LJ, Olivera BM, Hillyard DR. Constant and hypervariable regions in conotoxin propeptides. EMBO J 1990, 9:1015-1020. 551772, 1691090.
184. Olivera BM, Walker C, Cartier GE, Hooper D, Santos AD, Schoenfeld R, Shetty R, Watkins M, Bandyopadhyay P, Hillyard DR. Speciation of cone snails and interspecific hyperdivergence of their venom peptides: potential evolutionary significance of introns. Ann NY Acad Sci 1999, 870:223-237. 10.1111/j.1749-6632.1999.tb08883.x, 10415486.
185. Crow KD, Amemiya CT, Roth J, Wagner GP. Hypermutability of HoxA13a and functional divergence from its paralog are associated with the origin of a novel developmental feature in zebrafish and related taxa (cypriniformes). Evolution 2009, 63:1574-1592. 10.1111/j.1558-5646.2009.00657.x, 19222565.
186. Inoue K, Lupski J. Molecular mechanisms for genomic disorders. Annu Rev Genom Hum G 2002, 3:199-242.
187. Veltman JA, Brunner HG. De novo mutations in human genetic disease. Nat Rev Genet 2012, 13:565-575. 10.1038/nrg3241, 22805709.
188. Voight BF, Kudaravalli S, Wen X, Pritchard JK. A map of recent positive selection in the human genome. PLoS Biol 2006, 4:446-458.
189. Crespi BJ, Summers K. Positive selection in the evolution of cancer. Biol Rev 2006, 81:407-424.
190. Dawkins R. The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design 1986, New York: WW Norton & Company.
191. Ohno S. Evolution by Gene Duplication 1970, Heidelberg: Springer-Verlag.
192. Siepel A. Darwinian alchemy: Human genes from noncoding DNA. Genome Res 2009, 19:1693-1695. 10.1101/gr.098376.109, 2765273, 19797681.
193. Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ. Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. P Natl Acad Sci USA 2006, 103:9935-9939.
194. Begun DJ, Lindfors HA, Kern AD, Jones CD. Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics 2007, 176:1131-1137. 1894579, 17435230.
195. Chen ST, Cheng HC, Barbash DA, Yang HP. Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster. PLoS Genet 2007, 3:1131-1143.
196. Zhou Q, Zhang G, Zhang Y, Xu S, Zhao R, Zhan Z, Li X, Ding Y, Yang S, Wang W. On the origin of new genes in Drosophila. Genome Res 2008, 18:1446-1455. 10.1101/gr.076588.108, 2527705, 18550802.
197. Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Alba MM. Origin of primate orphan genes: A comparative genomics approach. Mol Biol Evol 2009, 26:603-612.
198. Wu DD, Irwin DM, Zhang YP. De novo origin of human protein-coding genes. PLoS Genet 2011, 7:e1002379. 10.1371/journal.pgen.1002379, 3213175, 22102831.
199. Tautz D, Domazet-Lošo T. The evolutionary origin of orphan genes. Nat Rev Genet 2011, 12:692-702.
200. Zhang YE, Liu CJ, Li Y, Zhang R, Wei L, Li CY, Xie C Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs. PLoS Genet 2012, 8:e1002942. 10.1371/journal.pgen.1002942, 3441637, 23028352, Xie C.
201. Neme R, Tautz D Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC Genomics 2013, 14. doi:10.1186/1471-2164-14-117, Tautz D.
202. Babushok DV, Ohshima K, Ostertag EM, Chen X, Wang Y, Mandal PK, Okada N, Abrams CS, Kazazian Jr HH. A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids. Genome Res 2007, 17:1129-1138. 10.1101/gr.6252107, 1933510, 17623810.
203. Zhang Y, Lu S, Zhao S, Zheng X, Long M, Wei L. Positive selection for the male functionality of a co-retroposed gene in the hominoids. BMC Evol Biol 2009, 9:252. 10.1186/1471-2148-9-252, 2773790, 19832993.
204. Lynch VJ, Nnamani M, Brayer KJ, Emera D, Wertheim JO, Kosakovsky-Pond SL, Grutzner F, Bauersachs S, Graf A, Kapusta A, Feschotte C, Wagner GP. Lineage-specific transposons drove massive gene expression recruitments during the evolution of pregnancy in mammals. arXiv preprint 2012, arXiv, 1208.4639.
205. Emera D, Wagner GP. Transposable element recruitments in the mammalian placenta: impacts and mechanisms. Brief Funct Genomics 2012, 11:267-276. 10.1093/bfgp/els013, 22753775.
206. Emera D, Wagner GP. Transformation of a transposon into a derived prolactin promoter with function during human pregnancy. P Natl Acad Sci USA 2012, 109:11246-11251.
207. McClintock B. Components of action of the regulators Spm and Ac. Carnegie Inst Wash Yearbook 1965, 64:527-534.
208. Britten RJ, Davidson EH. Gene regulation for higher cells: A theory. Science 1969, 165:349-357. 10.1126/science.165.3891.349, 5789433.
209. Georgiev GP. Mobile genetic elements in animal cells and their biological significance. Eur J Biochem 1984, 145:203-220. 10.1111/j.1432-1033.1984.tb08541.x, 6209137.
210. Brosius J. Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica 1999, 107:209-238. 10.1023/A:1004018519722, 10952214.
211. Eddy SR. The ENCODE project: Missteps overshadowing a success. Curr Biol 2013, 23:R259-R261.
212. Kleene KC. Sexual selection, genetic conflict, selfish genes, and the atypical patterns of gene expression in spermatogenic cells. Dev Biol 2005, 277:16-26. 10.1016/j.ydbio.2004.09.031, 15572136.
213. Kan Z, Garrett-Engele PW, Johnson JM, Castle JC. Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles. Nucleic Acids Res 2005, 33:5659-5666. 10.1093/nar/gki834, 1240112, 16195578.
214. Elliott DJ, Grellscheid SN. Alternative RNA splicing regulation in the testis. Reproduction 2006, 132:811-819. 10.1530/REP-06-0147, 17127741.
215. Thomson T, Lin H. The biogenesis and function of PIWI proteins and piRNAs: Progress and prospect. Annu Rev Cell Dev Biol 2009, 25:355-376. 10.1146/annurev.cellbio.24.110707.175327, 2780330, 19575643.
216. Kaessmann H. Origins, evolution, and phenotypic impact of new genes. Genome Res 2010, 20:1313-1326. 10.1101/gr.101386.109, 2945180, 20651121.
217. Miller D, Brinkworth M, Iles D. The testis as a conduit for genomic plasticity: an advanced interdisciplinary workshop. Biochem Soc Trans 2007, 35:605-608. 10.1042/BST0350605, 17511661.
218. Old LJ. Cancer/Testis (CT) antigens-a new link between gametogenesis and cancer. Cancer Immunity 2001, 1:1.
219. Simpson A, Caballero O, Jungbluth A, Chen YT, Old L. Cancer/testis antigens, gametogenesis and cancer. Nat Rev Cancer 2005, 5:615-625. 10.1038/nrc1669, 16034368.
220. She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W, Schwartz S, Eichler EE. The structure and evolution of centromeric transition regions within the human genome. Nature 2004, 430:857-864. 10.1038/nature02806, 15318213.
221. Vinckenbosch N, Dupanloup I, Kaessmann H. Evolutionary fate of retroposed gene copies in the human genome. P Natl Acad Sci USA 2006, 103:3220-3225.
222. Marques AC, Dupanloup I, Vinckenbosch N, Reymond A, Kaessmann H. Emergence of young human genes after a burst of retroposition in primates. PLoS Biol 2005, 3:e357. 10.1371/journal.pbio.0030357, 1251493, 16201836.
223. Nei M. Selectionism and neutralism in molecular evolution. Mol Biol Evol 2005, 22:2318-2342. 10.1093/molbev/msi242, 1513187, 16120807.
224. Landry J, Pyl PT, Rausch T, Zichner T, Tekkedil MM, Stütz AM, Jauch A, Aiyar RS, Pau G, Delhomme N, Gagneur J, Korbel JO, Huber W, Steinmetz LM. The genomic and transcriptomic landscape of a HeLa cell line. G3 2013, 3:1213-1224. 2013, 3737162, 23550136.
225. Pauling L, Itano HA, Singer SJ, Wells IC. Sickle-cell anemia, a molecular disease. Science 1949, 110:543-548. 10.1126/science.110.2865.543, 15395398.
226. Ingram VM. How do genes act?. Sci Am 1958, 198:68-76.
227. Allison AC. Polymorphisms and natural selection in human populations. Cold Spring Harb Symp Quant Biol 1964, 29:137-149. 10.1101/SQB.1964.029.01.018, 14278460.
228. Hill AV, Allsopp CE, Kwiatkowski D, Anstey NM, Twumasi P, Rowe PA, Bennett S, Brewster D, McMichael AJ, Greenwood BM. Common West African HLA antigens are associated with protection from severe malaria. Nature 1991, 352:595-600. 10.1038/352595a0, 1865923.
229. Haldane JBS. Disease and evolution. La Ricera Scientifica Suppl A 1949, 19:68-76.
230. Behe MJ. The Edge of Evolution: The Search for the Limits of Darwinism 2007, New York: Free Press.
231. Flint J, Harding RM, Boyce AJ, Clegg JB. The population genetics of the haemoglobinopathies. Baillière's Clin Haem 1998, 11:1-51.
232. Kwiatkowski DP. How malaria has affected the human genome and what human genetics can teach us about malaria. Am J Hum Genet 2005, 77:171-192. 10.1086/432519, 1224522, 16001361.
233. Flint J, Harding RM, Clegg JB, Boyce AJ. Why are some genetic diseases common?. Hum Genet 1993, 91:91-117.
234. Borg J, Georgitsi M, Aleporou-Marinou V, Kollia P, Patrinos GP. Genetic recombination as a major cause of mutagenesis in the human globin gene clusters. Clin Biochem 2009, 42:1839-1850. 10.1016/j.clinbiochem.2009.07.014, 19631200.
235. Giordano PC, Harteveld CL, Michiels JJ, Terpstra W, Schelfhout LJDM, Appel IM, Batelaan D, van D, Plug RJ, Bernini LF. Phenotype variability of the dominant β-thalassemia induced in four Dutch families by the rare cd121 (G→ T) mutation. Ann Hematol 1998, 77:249-255. 10.1007/s002770050453, 9875660.
236. Holloway K, Lawson VE, Jeffreys AJ. Allelic recombination and de novo deletions in sperm in the human β-globin gene region. Human Mol Genet 2006, 15:1099-1111.
237. Sicard D, Lieurzou Y, Lapoumeroulie C, Labie D. High genetic polymorphism of hemoglobin disorders in Laos. Hum Genet 1979, 50:327-336. 10.1007/BF00399399, 489017.
238. Kazazian Jr HH, Boehm CD. Molecular basis and prenatal diagnosis of β-thalassemia. Blood 1988, 72:1107-1116.
239. Thein SL, Hesketh C, Taylor P, Temperley IJ, Hutchinson RM, Old JM, Wood WG, Clegg JB, Weatherall DJ. Molecular basis for dominantly inherited inclusion body β-thalassemia. P Natl Acad Sci USA 1990, 87:3924-3928.
240. Kazazian Jr HH, Dowling CE, Hurwitz RL, Coleman M, Adams JGI. Thalassemia mutations in exon 3 of the β-globin gene often cause a dominant form of thalassemia and show no predilection for malarial-endemic regions. Am J Hum Genet 1989, 45:A242.
241. Kazazian Jr HH, Orkin SH, Boehm CD, Goff SC, Wong C, Dowling CE, Newburger PE, Knowlton RG, Brown V, Donis-Keller H. Characterization of a spontaneous mutation to a β-thalassemia allele. Am J Hum Genet 1986, 38:860-867. 1684845, 3014870.
242. Troland LT. The chemical origin and regulation of life. The Monist 1914, 24:92-133.
243. Muller HJ. The gene as the basis of life. Proc. 1st Int Congr Plant Sci, Ithaca 1926, 1:897-921.
244. Dyson FJ. Origins of Life 1985, Cambridge: Cambridge University Press.
245. Ospovat D. The Development of Darwin's Theory: Natural History, Natural Theology, and Natural Selection, 1838-1859 1995, Cambridge: Cambridge University Press.
246. Galton F. Natural Inheritance 1889, London: Macmillan and Co.
247. Gayon J. Darwinism's Struggle for Survival: Heredity and the Hypothesis of Natural Selection 1998, Cambridge: Cambridge University Press.
248. Mayr E. Animal Species and Evolution 1963, Cambridge: Belknap Press.
249. Stoltzfus A. On the possibility of constructive neutral evolution. J Mol Evol 1999, 49:169-181. 10.1007/PL00006540, 10441669.
250. Yampolsky LY, Stoltzfus A. Bias in the introduction of variation as an orienting factor in evolution. Evol Dev 2001, 3:73-83. 10.1046/j.1525-142x.2001.003002073.x, 11341676.
251. Stoltzfus A. Mutationism and the dual causation of evolutionary change. Evol Dev 2006, 8:304-317. 10.1111/j.1525-142X.2006.00101.x, 16686641.
252. Stoltzfus A, Yampolsky L. Climbing mount probable: Mutation as a cause of nonrandomness in evolution. J Hered 2009, 100:637-647. 10.1093/jhered/esp048, 19625453.
253. Lenski RE, Mittler JE. The directed mutation controversy and neo-Darwinism. Science 1993, 259:188-194. 10.1126/science.7678468, 7678468.
254. Hall BG. On the specificity of adaptive mutations. Genetics 1997, 145:39-44. 1207782, 9017388.
255. Rosenberg SM. Evolving responsively: Adaptive mutation. Nat Rev Genet 2001, 2:504-515.
256. Fang W, Landweber LF. RNA-mediated genome rearrangement: Hypotheses and evidence. BioEssays 2013, 35:84-87. 10.1002/bies.201200140, 23281134.
257. Bracht JR, Fang W, Goldman AD, Dolzhenko E, Stein EM, Landweber LF. Genomes on the edge: Programmed genome instability in ciliates. Cell 2013, 152:406-416. 10.1016/j.cell.2013.01.005, 23374338.
258. Koonin EV, Wolf YI. Is evolution Darwinian or/and Lamarckian?. Biol Direct 2009, 4:42. 10.1186/1745-6150-4-42, 2781790, 19906303.
259. Gladyshev EA, Meselson M, Arkhipova IR. Massive horizontal gene transfer in bdelloid rotifers. Science 2008, 320:1210-1213. 10.1126/science.1156407, 18511688.
260. Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EGJ, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthélémy RM, Bast J, Bazykin GA, Chabrol O, Couloux A, DaRocha M, DaSilva C, Gladyshev E, Gouret P, Hallatschek O, Hecox-Lea B, Labadie K, Lejeune B, Piskurek O, Poulain J, Rodriguez F, Ryan JF, Vakhrusheva OA, Wajnberg E, et al. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature 2013, 500:453-457. 10.1038/nature12326, 23873043.
261. Jenkin HCF. Darwin and the origin of species. Papers Literary, Scientific etc., Volume I 1887, 215-263. London: Longmans, Green & Company, Colvin S, Ewing JA.
262. Goldschmidt R. Some aspects of evolution. Science 1933, 78:539-547. 10.1126/science.78.2033.539, 17811930.
263. Leigh Jr EG. Natural selection and mutability. Am Nat 1970, 104:301-305.
264. Feldman MW, Liberman U. An evolutionary reduction principle for genetic modifiers. P Natl Acad Sci USA 1986, 83:4824-4827.
265. Altenberg L, Feldman MW. Selection, generalized transmission and the evolution of modifier genes. I. The reduction principle. Genetics 1987, 117:559-572. 1203230, 3692141.
266. Bergman A, Feldman MW. More on selection for and against recombination. Theor Popul Biol 1990, 38:68-92. 10.1016/0040-5809(90)90004-F, 2205018.
267. Barton N. A general model for the evolution of recombination. Genet Res 1995, 65:123-144. 10.1017/S0016672300033140, 7605514.
268. Charlesworth B. Directional selection and the evolution of sex and recombination. Genet Res 1993, 61:205-224. 10.1017/S0016672300031372, 8365658.
269. Kimura M. On the evolutionary adjustment of spontaneous mutation rates. Genet Res 1967, 9:23-34.
270. Wenzel JW. Behavioral homology and phylogeny. Annu Rev Ecol Syst 1992, 23:361-381.
271. Lorenz K. Comparative studies of the motor patterns of Anatinae. Studies in Animal and Human Behavior, Volume II (1941), Rome and London: Butler & Tanner Ltd; 1971, Lorenz K.