Roles of mutation and selection in speciation: From hugo de vries to the modern genomic era

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 812-829

  Nei, Masatoshi ^a   Nozawa, Masafumi ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Chromosomal mutation; Dobzhansky Muller model; Hybrid inviability; Hybrid sterility; Oka model; Polyploidy

Indexed keywords

ANGIOSPERM; ANIMAL; BIOLOGICAL MODEL; DROSOPHILA; FEMALE; FUNGUS; GENETIC SELECTION; GENETICS; GENOMICS; HISTORY; MOLECULAR EVOLUTION; MUTATION; PHYSIOLOGY; REPRODUCTION; REVIEW; SPECIES DIFFERENTIATION;

ANGIOSPERMS; ANIMALS; DROSOPHILA; EVOLUTION, MOLECULAR; FEMALE; FUNGI; GENETIC SPECIATION; GENETICS; GENOMICS; HISTORY, 19TH CENTURY; HISTORY, 20TH CENTURY; MODELS, GENETIC; MUTATION; REPRODUCTION; SELECTION, GENETIC;

EID: 84555170186     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr028     Document Type: Article

References (134)

1. Adams KL, Wendel JF. 2005. Polyploidy and genome evolution in plants. Curr Opin Plant Biol. 8:135-141. (Pubitemid 40323541)
2. Allen GE. 1969. Hugo de Vries and the reception of the "mutation theory". J Hist Biol. 2:55-87.
3. Badaeva ED, et al. 2007. Chromosomal rearrangements in wheat: their types and distribution. Genome 50:907-926. (Pubitemid 350158292)
4. Barr CM, Fishman L. 2010. The nuclear component of a cytonuclear hybrid incompatibility in Mimulus maps to a cluster of pentatrico-peptide repeat genes. Genetics 184:455-465.
5. Bateson W. 1909. Heredity and variation in modern lights. In: Seward AC, editor. Darwin and modern science. Cambridge: Cambridge University Press. p. 85-101.
6. Bayes JJ, Malik HS. 2009. Altered heterochromatin binding by a hybrid sterility protein in Drosophila sibling species. Science 326:1538-1541.
7. Bentolila S, Alfonso AA, Hanson MR. 2002. A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. Proc Natl Acad Sci U S A. 99:10887-10892.
8. Bikard D, et al. 2009. Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana. Science 323:623-626.
9. Bomblies K, et al. 2007. Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants. PLoS Biol. 5:e236.
10. Boss PK, Bastow RM, Mylne JS, Dean C. 2004. Multiple pathways in the decision to flower: enabling, promoting, and resetting. Plant Cell. 16:S18-S31. (Pubitemid 38774214)
11. Brideau NJ, et al. 2006. Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila. Science 314:1292-1295. (Pubitemid 44846401)
12. Brown JD, O'Neill RJ. 2010. Chromosomes, conflict, and epigenetics: chromosomal speciation revisited. Annu Rev Genomics Hum Genet. 11:291-316.
13. Case AL, Willis JH. 2008. Hybrid male sterility in Mimulus (Phrymaceae) is associated with a geographically restricted mitochondrial rearrangement. Evolution 62:1026-1039. (Pubitemid 351634365)
14. Chase CD. 2007. Cytoplasmic male sterility: a window to the world of plant mitochondrial-nuclear interactions. Trends Genet. 23:81-90. (Pubitemid 46161215)
15. Chen J, et al. 2008. A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica-japonica hybrids in rice. Proc Natl Acad Sci USA. 105:11436-11441.
16. Chen KY, Cong B, Wing R, Vrebalov J, Tanksley SD. 2007. Changes in regulation of a transcription factor lead to autogamy in cultivated tomatoes. Science 318:643-645. (Pubitemid 350014837)
17. Chou JY, Hung YS, Lin KH, Lee HY, Leu JY 2010. Multiple molecular mechanisms cause reproductive isolation between three yeast species. PLoS Biol. 8:e1000432.
18. Cleland RE. 1923. Chromosome arrangements during meiosis in certain Oenotherae. Am Nat. 57:562-566.
19. Cleland RE. 1972. Oenothera: cytogenetics and evolution. New York: Academic Press.
20. Coyne JA. 1992. Genetics and speciation. Nature. 355:511-515.
21. Coyne JA, Orr HA. 2004. Speciation. Sunderland (MA): Sinauer Associates.
22. Darwin C. 1859. On the origin of species. London: Murray.
23. Davis BM. 1912. Genetical studies on Oenothera III. Further hybrids of Oenothera biennis and O. grandiflora that resemble O. lamarckiana. Am Nat. 46:377-427.
24. Davis BM. 1943. An amphidiploid in the F1 generation from the cross Oenothera Franciscana x Oenothera Biennis, and its progeny. Genetics 28:275-285.
25. De Bodt S, Maere S, Van de Peer Y 2005. Genome duplication and the origin of angiosperms. Trends Ecol Evol. 20:591-597. (Pubitemid 41502811)
26. de Vries H. 1901-1903.Die mutationstheorie. Vol. I and II. Leipzig (Germany): Verlag von Veit and Company.
27. de Vries H. 1909. The mutation theory: experiments and observations on the origin of species in the vegetable kingdom. Vol. I. The origin of species by mutation. English translation by J. B. Farmer and A. D. Darbishire. Chicago (IL): Open Court Publishing Company.
28. de Vries H. 1910. The mutation theory: experiments and observations on the origin of species in the vegtable kingdom. Vol. II. The origin of varieties by mutation. English translation by J. B. Farmer and A. D. Darbishire. Chicago (IL): Open Court Publishing Company.
29. Delneri D, et al. 2003. Engineering evolution to study speciation in yeasts. Nature 422:68-72.
30. Des Marais MD, Rausher DL. 2010. Parallel evolution at multiple levels in the origin of hummingbird pollinated flowers in Ipomoea. Evolution 64:2044-2054.
31. Desiderio UV, Zhu X, Evans JP. 2010. ADAM2 interactions with mouse eggs and cell lines expressing alpha4/alpha9 (ITGA4/ITGA9) integrins: implications for integrin-based adhesion and fertilization. PLoS One. 5:e13744.
32. Dobzhansky T. 1937. Genetics and the origin of species. New York: Columbia University Press.
33. Doyle JJ, et al. 2008. Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet. 42:443-461.
34. Evans JP, Florman HM. 2002. The state of the union: the cell biology of fertilization. Nat Cell Biol. 4(Suppl):s57-s63. (Pubitemid 35175935)
35. Ferree PM, Barbash DA. 2009. Species-specific heterochromatin prevents mitotic chromosome segregation to cause hybrid lethality in Drosophila. PLoS Biol. 7:e1000234.
36. Flagel LE, Wendel JF. 2009. Gene duplication and evolutionary novelty in plants. New Phytol. 183:557-564.
37. Frank SA. 1991. Divergence of meiotic drive-suppression systems as an explanation for sex-biased hybrid sterility and inviability. Evolution 45:262-267.
38. Fujii S, Toriyama K. 2009. Suppressed expression of retrograde-regulated male sterility restores pollen fertility in cytoplasmic male sterile rice plants. Proc Natl Acad Sci U S A. 106:9513-9518.
39. Galindo BE, Vacquier VD, Swanson WJ. 2003. Positive selection in the egg receptor for abalone sperm lysin. Proc Natl Acad Sci U S A. 100:4639-4643. (Pubitemid 36469240)
40. Gates RR. 1908. The chromosomes of Oenothera. Science 27:193-195.
41. Grant V. 1981. Plant speciation. New York: Columbia University Press.
42. Greig D, Travisano M, Louis EJ, Borts RH. 2003. A role for the mismatch repair system during incipient speciation in Saccharomyces. J Evol Biol. 16:429-437. (Pubitemid 36567973)
43. Haldane JB. 1922. Sex-ratio and unidirectional sterility in hybrid animals. J Genet. 12:101-109.
44. Hartl DL. 1969. Dysfunctional sperm production in Drosophila mela-nogaster males homozygous for the segregation distorter elements. Proc Natl Acad Sci U S A. 63:782-789.
45. Henikoff S, Malik HS. 2002. Centromeres: selfish drivers. Nature 417:227.
46. Hirsch N, Zimmerman LB, Grainger RM. 2002. Xenopus, the next generation: X. tropicalis genetics and genomics. Dev Dyn. 225:422-433. (Pubitemid 35429726)
47. Hoballah ME, et al. 2007. Single gene-mediated shift in pollinator attraction in Petunia. Plant Cell. 19:779-790. (Pubitemid 46953227)
48. Hunter N, Chambers SR, Louis EJ, Borts RH. 1996. The mismatch repair system contributes to meiotic sterility in an interspecific yeast hybrid. Embo J. 15:1726-1733. (Pubitemid 26112395)
49. Hurst LD, Pomiankowski A. 1991. Causes of sex ratio bias may account for unisexual sterility in hybrids: a new explanation of Haldane's rule and related phenomena. Genetics 128:841-858.
50. Inoue N, Ikawa M, Isotani A, Okabe M. 2005. The immunoglobulin superfamily protein Izumo is required for sperm to fuse with eggs. Nature 434:234-238. (Pubitemid 40388056)
51. Jaenike J. 2001. Sex chromosome meiotic drive. Annu Rev Ecol Syst. 32:25-49. (Pubitemid 34043155)
52. Jaillon O, et al. 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957.
53. Kamei N, Glabe CG. 2003. The species-specific egg receptor for sea urchin sperm adhesion is EBR1, a novel ADAMTS protein. Genes Dev. 17:2502-2507. (Pubitemid 37271419)
54. Kazama T, Toriyama K. 2003. A pentatricopeptide repeat-containing gene that promotes the processing of aberrant atp6 RNA of cytoplasmic male-sterile rice. FEBS Lett. 544:99-102. (Pubitemid 36628043)
55. Kellis M, Birren BW, Lander ES. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-624. (Pubitemid 38524797)
56. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.
57. Kusano A, Staber C, Chan HY, Ganetzky B. 2003. Closing the (Ran) GAP on segregation distortion in Drosophila. Bioessays 25:108-115. (Pubitemid 36222381)
58. Lee HY, et al. 2008. Incompatibility of nuclear and mitochondrial genomes causes hybrid sterility between two yeast species. Cell 135:1065-1073.
59. Li WH, Nei M. 1977. Persistence of common alleles in two related populations or species. Genetics 86:901-914. (Pubitemid 8184453)
60. Liti G, Barton DB, Louis EJ. 2006. Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics 174: 839-850. (Pubitemid 44656472)
61. Long Y, et al. 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc Natl Acad Sci U S A. 105:18871-18876.
62. Lurin C, et al. 2004. Genome-wide analysis of Arabidopsis pentatrico-peptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell. 16:2089-2103. (Pubitemid 39059730)
63. Lutz AM. 1907. A preliminary note on the chromosomes of Oenothera Lamarckiana and one of its mutants, O. gigas. Science 26:151-152.
64. Lynch M, Force A. 2000. Gene duplication and the origin of interspecific genomic incompatibility. Am Nat. 156:590-605. (Pubitemid 32013275)
65. Lyon JD, Vacquier VD. 1999. Interspecies chimeric sperm lysins identify regions mediating species-specific recognition of the abalone egg vitelline envelope. Dev Biol. 214:151-159. (Pubitemid 29463363)
66. Lyttle TW. 1991. Segregation distorters. Annu Rev Genet. 25:511-557. (Pubitemid 21903732)
67. Maheshwari S, Wang J, Barbash DA. 2008. Recurrent positive selection of the Drosophila hybrid incompatibility gene Hmr. Mol Biol Evol. 25:2421-2430.
68. Masly JP, Jones CD, Noor MA, Locke J, Orr HA. 2006. Gene transposition as a cause of hybrid sterility in Drosophila. Science 313:1448-1450. (Pubitemid 44360275)
69. Mayr E. 1963. Animal species and evolution. Cambridge: Harvard University Press.
70. Mayr E. 1980. Prologue: some thoughts on the history of the evolutionary synthesis. In: Mayr E, Provine WB, editors. The evolutionary synthesis. Cambridge (MA): Harvard University Press. p. 1-48.
71. McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654. (Pubitemid 21896661)
72. Mizuta Y, Harushima Y, Kurata N. 2010. From the Cover: rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes. Proc Natl Acad Sci U S A. 107:20417-20422.
73. Muller HJ. 1925. Why polyploid is rarer in animals than in plants. Am Nat. 59:346-353.
74. Muller HJ. 1940. Bearing of the Drosophila work on systematics. In: Huxley J, editor. The new systematics. Oxford: Clarendon Press.
75. Muller HJ. 1942. Isolating mechanisms, evolution and temperature. Biol Symp. 6:71-125.
76. Nandi HK. 1936. The chromosome morphology, secondary association and origin of cultivated rice. J Genet. 33:316-336.
77. Nei M. 1969. Gene duplication and nucleotide substitution in evolution. Nature 221:40-42.
78. Nei M. 1976. Mathematical models of speciation and genetic distance. In: Karlin S, Nevo E, editors. Population genetics and ecology. New York: Academic Press. p. 723-765.
79. Nei M, Maruyama T, Wu CI. 1983. Models of evolution of reproductive isolation. Genetics 103:557-579. (Pubitemid 13125932)
80. Nei M, Rooney AP. 2005. Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39:121-152. (Pubitemid 43011110)
81. Nei M, Roychoudhury AK. 1973. Probability of fixation of nonfunctional genes at duplicate loci. Am Nat. 107:362-372.
82. Nei M, Suzuki Y, Nozawa M. 2010. The neutral theory of molecular evolution in the genomic era. Annu Rev Genomics Hum Genet. 11:265-289.
83. Nei M, Zhang J. 1998. Molecular origin of species. Science 282: 1428-1429. (Pubitemid 28538589)
84. Ohno S. 1970. Evolution by gene duplication. Berlin (Germany): Springer.
85. Ohno S. 1998. The notion of the Cambrian pananimalia genome and a genomic difference that separated vertebrates from invertebrates. Prog Mol Subcell Biol. 21:97-117.
86. Oka HI. 1953. The mechanisms of sterility in the intervarietal hybrids. Phylogenetic differentiation of cultivated rice. VI. (In Japanese with English summary). Japan J Breed. 2:217-224.
87. Oka HI. 1957. Genic analysis for the sterility of hybrids between distantly related varieties of cultivated rice. J Genet. 55:397-409.
88. Oka HI. 1974. Analysis of genes controlling F1 sterility in rice by the use of isogenic lines. Genetics 77:521-534.
89. Oliver PL, et al. 2009. Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genet. 5:e1000753.
90. Orr HA. 1995. The population genetics of speciation: the evolution of hybrid incompatibilities. Genetics 139:1805-1813.
91. Orr HA. 1996. Dobzhansky, Bateson, and the genetics of speciation. Genetics 144:1331-1335. (Pubitemid 127562728)
92. Orr HA, Masly JP, Presgraves DC. 2004. Speciation genes. Curr Opin Genet Dev. 14:675-679. (Pubitemid 39505373)
93. Orr HA, Presgraves DC. 2000. Speciation by postzygotic isolation: forces, genes and molecules. Bioessays 22:1085-1094. (Pubitemid 32010518)
94. Otto SP, Whitton J. 2000. Polyploid incidence and evolution. Annu Rev Genet. 34:401-437. (Pubitemid 32065927)
95. Phadnis N, Orr HA. 2009. A single gene causes both male sterility and segregation distortion in Drosophila hybrids. Science 323:376-379.
96. Pouteau S, et al. 2008. Diversification of photoperiodic response patterns in a collection of early-flowering mutants of Arabidopsis. Plant Physiol. 148:1465-1473. (Pubitemid 352847510)
97. Presgraves DC. 2008. Sex chromosomes and speciation in Drosophila. Trends Genet. 24:336-343.
98. Presgraves DC, Balagopalan L, Abmayr SM, Orr HA. 2003. Adaptive evolution drives divergence of a hybrid inviability gene between two species of Drosophila. Nature 423:715-719. (Pubitemid 36735688)
99. Presgraves DC, Stephan W. 2007. Pervasive adaptive evolution among interactors of the Drosophila hybrid inviability gene, Nup96. Mol Biol Evol. 24:306-314. (Pubitemid 46026303)
100. Redon R, et al. 2006. Global variation in copy number in the human genome. Nature 444:444-454. (Pubitemid 44809057)
101. Renner O. 1917. Versuche uber die gametische Konstitution der Oenotheren. Z Ind Abst Vererb. 18:121-294.
102. Rensing SA, et al. 2008. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319:64-69.
103. Rieseberg LH. 2001. Chromosomal rearrangements and speciation. Trends Ecol Evol. 16:351-358. (Pubitemid 32525775)
104. Rieseberg LH, Willis JH. 2007. Plant speciation. Science. 317:910-914. (Pubitemid 47301311)
105. Sakai K. 1935. Chromosome study of Oryza sativa L. I. The secondary association of hte meiotic chromosomes. Japan J Genet. 44:149-156.
106. Sandler L, Hiraizumi Y, Sandler I. 1959. Meiotic drive in natural populations of Drosophila melanogaster. I. The cytogenetic basis of segregation-distortion. Genetics 44:233-250.
107. Sawamura K, Yamamoto MT, Watanabe TK. 1993. Hybrid lethal systems in the Drosophila melanogaster species complex. II. The zygotic hybrid rescue (Zhr) gene of D. melanogaster. Genetics 133:307-313. (Pubitemid 23033486)
108. Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH. 2006. Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440:341-345.
109. Schartl M. 2008. Evolution of Xmrk: an oncogene, but also a speciation gene? Bioessays 30:822-832.
110. Seidel HS, Rockman MV, Kruglyak L. 2008. Widespread genetic incompatibility in C. elegans maintained by balancing selection. Science 319:589-594. (Pubitemid 351197056)
111. Shaw A, Fortes PA, Stout CD, Vacquier VD. 1995. Crystal structure and subunit dynamics of the abalone sperm lysin dimmer: egg envelopes dissociate dimmers, the monomer is the active species. J Cell Biol. 130:1117-1125.
112. Simpson GG, Gendall AR, Dean C. 1999. When to switch to flowering. Annu Rev Cell Dev Biol. 15:519-550. (Pubitemid 32250385)
113. Stebbins GL. 1950. Variation and evolution in plants. New York: Columbia University Press.
114. Stebbins GL. 1966. Processes of organic evolution. Upper Saddle River (NJ): Prentice-Hall.
115. Sun S, Ting CT, Wu CI. 2004. The normal function of a speciation gene, Odysseus, and its hybrid sterility effect. Science 305:81-83. (Pubitemid 38869375)
116. Tang S, Presgraves DC. 2009. Evolution of the Drosophila nuclear pore complex results in multiple hybrid incompatibilities. Science 323:779-782.
117. Tao Y, et al. 2007. A sex-ratio meiotic drive system in Drosophila simulans. II: An X-linked distorter. PLoS Biol. 5:e293.
118. Tao Y, Hartl DL, Laurie CC. 2001. Sex-ratio segregation distortion associated with reproductive isolation in Drosophila. Proc Natl Acad Sci U S A. 98:13183-13188. (Pubitemid 33051338)
119. Tauber CA, Tauber MJ. 1977. Sympatric speciation based on allelic changes at three loci: evidence from natural populations in two habitats. Science 197:1298-1299.
120. Ting CT, Tsaur SC, Wu ML, Wu CI. 1998. A rapidly evolving homeobox at the site of a hybrid sterility gene. Science 282:1501-1504.
121. Wendel JF. 2000. Genome evolution in polyploids. Plant Mol Biol. 42:225-249. (Pubitemid 30096119)
122. Werth CR, Windham MD. 1991. A model for divergent, allopatric speciation of polyploid pteridophytes resulting from silencing of duplicate-gene expression. Am Nat. 137:515-526.
123. White MJD. 1969. Chromosomal rearrangements and speciation in animals. Annu Rev Genet. 3:75-98.
124. Wolfe KH, Shields DC. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713. (Pubitemid 27270611)
125. Wood TE, et al. 2009. The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci U S A. 106:13875-13879.
126. Wright S. 1941. On the probability of fixation of reciprocal translocations. Am Nat. 75:513-522.
127. Wu CI, Hammer MF. 1991. Molecular evolution of ultraselfish genes of meiotic drive systems. In: Selander RK, Whittam TS, Clark AG, editors. Evolution at the molecular level. Sunderland (MA): Sinaur Press. p. 177-203.
128. Wu CI, Lyttle TW, Wu ML, Lin GF. 1988. Association between a satellite DNA sequence and the responder of segregation distorter in D. melanogaster. Cell 54:179-189.
129. Wu CI, Ting CT. 2004. Genes and speciation. Nat Rev Genet. 5:114-122.
130. Yamagata Y, et al. 2010. Mitochondrial gene in the nuclear genome induces reproductive barrier in rice. Proc Natl Acad Sci U S A. 107:1494-1499.
131. Yamamoto E, et al. 2010. Gain of deleterious function causes an autoimmune response and Bateson-Dobzhansky-Muller incompatibility in rice. Mol Genet Genomics. 283:305-315.
132. Yuan YX, et al. 2009. A naturally occurring splicing site mutation in the Brassica rapa FLC1 gene is associated with variation in flowering time. J Exp Bot. 60:1299-1308.
133. Zeh JA, Zeh DW. 2005. Maternal inheritance, sexual conflict and the maladapted male. Trends Genet. 21:281-286. (Pubitemid 40558933)
134. Zhang J, Rosenberg HF, Nei M. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci U S A. 95:3708-3713. (Pubitemid 28173193)