Establishment of new mutations under divergence and genome hitchhiking

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 367, Issue 1587, 2012, Pages 461-474

  Feder, Jeffrey L ^a,b   Gejji, Richard ^a,c   Yeaman, Sam ^d   Nosil, Patrik ^b,e  

^a UNIVERSITY OF NOTRE DAME   (United States)

^b Institute for Advanced Study   (Germany)

^c OHIO STATE UNIVERSITY   (United States)

^d UNIVERSITY OF NEUCHÂTEL   (Switzerland)

^e UNIVERSITY OF COLORADO   (United States)

Author keywords

Divergence hitchhiking; Genome hitchhiking; Mutations; Standing genetic variation

Indexed keywords

DIVERGENCE; GENE FLOW; GENETIC DIFFERENTIATION; GENETIC STRUCTURE; GENOMICS; MUTATION; NATURAL SELECTION; PROBABILITY; SPECIATION (BIOLOGY);

EID: 84255177701     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2011.0256     Document Type: Article

References (82)

1. Coyne, J. A. & Orr, H. A. 2004 Speciation. Sunderland, MA: Sinauer Associates.
2. Mallet, J. 1995 A species definition for the modern synthesis. Trends Ecol. Evol. 10, 294-299. (doi:10.1016/0169-5347(95)90031-4)
3. Schluter, D. 2001 Ecology and the origin of species. Trends Ecol. Evol. 16, 372-380. (doi:10.1016/S0169-5347(01)02198-X)
4. Schluter, D. 2009 Evidence for ecological speciation and its alternative. Science 323, 737-741. (doi:10.1126/science.1160006)
5. Rundle, H. D. & Nosil, P. 2005 Ecological speciation. Ecol. Lett. 8, 336-352. (doi:10.1111/j.1461-0248.2004.00715.x)
6. Feder, J. L., Xie, X. F., Rull, J., Velez, S., Forbes, A., Leung, B., Dambroski, H., Filchak, K. E. & Aluja, M. 2005 Mayr, Dobzhansky, and Bush and the complexities of sympatric speciation in Rhagoletis. Proc. Natl Acad. Sci. USA 102, 6573-6580. (doi:10.1073/pnas.0502099102)
7. Presgraves, D. C. 2007 Speciation genetics: epistasis, conflict and the origin of species. Curr. Biol. 17, R125-R127. (doi:10.1016/j.cub.2006.12.030)
8. Wu, C. I. & Ting, C. T. 2004 Genes and speciation. Nat. Rev. Genet. 5, 114-122. (doi:10.1038/nrg1269)
9. Orr, H. A. 2005 The genetic basis of reproductive isolation: insights from Drosophila. Proc. Natl Acad. Sci. USA 102, 6522-6526. (doi:10.1073/pnas.0501893102)
10. Rieseberg, L. H. & Blackman, B. K. 2010 Speciation genes in plants. Ann. Bot. 106, 439-455. (doi:10.1093/aob/mcq126)
11. Nosil, P. & Schluter, D. 2011 The genes underlying the process of speciation. Trends Ecol. Evol. 26, 160-167. (doi:10.1016/j.tree.2011.01.001)
12. Nosil, P. & Feder, J. L. 2012 Genomic divergence during speciation: causes and consequences. Phil. Trans. R. Soc. B 367, 332-342. (doi:10.1098/rstb.2011.0263)
13. Mayr, E. 1942 Systematics and the origin of species. New York, NY: Columbia University Press.
14. Mayr, E. 1963 Animal species and evolution. Harvard, MA: Harvard University Press.
15. Orr, H. A. & Turelli, M. 2001 The evolution of postzygotic isolation: accumulating Dobzhansky-Muller incompatibilities. Evolution 55, 1085-1094.
16. Orr, H. A. 1995 The population-genetics of speciation: the evolution of hybrid incompatibilities. Genetics 139, 1805-1813.
17. Gavrilets, S. 2004 Fitness landscapes and the origin of species (eds S. A. Levin & H. S. Horn). Princeton, NJ: Princeton University Press.
18. Nosil, P., Funk, D. J. & Ortiz-Barrientos, D. 2009 Divergent selection and heterogeneous genomic divergence. Mol. Ecol. 18, 375-402. (doi:10.1111/j.1365-294X.2008.03946.x)
19. Noor, M. A. F. & Feder, J. L. 2006 Speciation genetics: evolving approaches. Nat. Rev. Genet. 7, 851-861. (doi:10.1038/nrg1968)
20. Nielsen, R. 2005 Molecular signatures of natural selection. Ann. Rev. Genet. 39, 197-218. (doi:10.1146/annurev.genet.39.073003.112420)
21. Beaumont, M. A. 2005 Adaptation and speciation: what can F-st tell us? Trends Ecol. Evol. 20, 435-440. (doi:10.1016/j.tree.2005.05.017)
22. Kirkpatrick, M., Johnson, T. & Barton, N. 2002 General models of multilocus evolution. Genetics 161, 1727-1750.
23. Kirkpatrick, M. & Ravigné, V. 2002 Speciation by natural and sexual selection: models and experiments. Am. Nat. 159, S22-S35. (doi:10.1086/338370)
24. Gavrilets, S. 2003 Perspective. Models of speciation: what have we learned in 40 years? Evolution 57, 2197-2215.
25. Nosil, P. & Flaxman, S. M. 2011 Conditions for mutationorder speciation. Proc. R. Soc. B 278, 399-407. (doi:10.1098/rspb.2010.1215)
26. Barton, N. H. 2001 The role of hybridization in evolution. Mol. Ecol. 10, 551-568. (doi:10.1046/j.1365-294x.2001.01216.x)
27. Feder, J. L., Geji, R., Powell, T. H. Q. & Nosil, P. 2011 Adaptive chromosomal divergence driven by mixed geographic mode of evolution. Evolution 65, 2157-2170. (doi:10.1111/j.1558-5646.2011.01321.x)
28. Felsenstein, J. 1981 Skepticism towards Santa Rosalia, or why are there so few kinds of animals? Evolution 35, 124-138. (doi:10.2307/2407946)
29. Servedio, M., Van Doorn, S., Kopp, M., Frame, A. & Nosil, P. 2011 Magic traits in speciation: 'magic' but not rare? Trends Ecol. Evol. 26, 389-397. (doi:10.1016/j.tree.2011.04.005)
30. Via, S. 2009 Natural selection in action during speciation. Proc. Natl Acad. Sci. USA 106, 9939-9946. (doi:10.1073/pnas.0901397106)
31. Via, S. & West, J. 2008 The genetic mosaic suggests a new role for hitchhiking in ecological speciation. Mol. Ecol. 17, 4334-4345. (doi:10.1111/j.1365-294X.2008.03921.x)
32. Turner, T. L., Hahn, M. W. & Nuzhdin, S. V. 2005 Genomic islands of speciation in Anopheles gambiae. PLoS Biol. 3, 1572-1578. (doi:10.1371/journal.pbio.0030285)
33. Via, S. 2012 Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow. Phil. Trans. R. Soc. B 367, 451-460. (doi:10.1098/rstb.2011.0260)
34. Bush, G. L. 1969 Sympatric host race formation and speciation in frugivorous flies of genus Rhagoletis (Diptera, Tephritidae). Evolution 23, 237-251. (doi:10.2307/2406788)
35. Bush, G. L. 1969 Mating behavior, host specificity, and ecological significance of sibling species in frugivorous flies of genus Rhagoletis (Diptera-Tephritidae). Am. Nat. 103, 661-672. (doi:10.1086/282634)
36. Kimura, M. 1956 A model of a genetic system which leads to closer linkage by natural selection. Evolution 10, 278-287. (doi:10.2307/2406012)
37. Nosil, P., Crespi, B. J., Sandoval, C. P. & Kirkpatrick, M. 2006 Migration and the genetic covariance between habitat preference and performance. Am. Nat. 167, E66-E78. (doi:10.1086/499383)
38. Rice, W. R. 1984 Disruptive selection on habitat preference and the evolution of reproductive isolation: a simulation study. Evolution 38, 1251-1260. (doi:10.2307/2408632)
39. Rice, W. R. 1985 Disruptive selection on habitat preference and the evolution of reproductive isolation: an exploratory experiment. Evolution 39, 645-656. (doi:10.2307/2408659)
40. Rice, W. R. & Hostert, E. E. 1993 Laboratory experiments on speciation: what have we learned in 40 years? Evolution 47, 1637-1653. (doi:10.2307/2410209)
41. Smith, T. B., Calsbeek, R., Wayne, R. K., Holder, K. H., Pires, D. & Bardeleben, C. 2005 Testing alternative mechanisms of evolutionary divergence in an African rain forest passerine bird. J. Evol. Biol. 18, 257-268. (doi:10.1111/j.1420-9101.2004.00825.x)
42. Smith, T. B., Wayne, R. K., Girman, D. J. & Bruford, M. W. 1997 A role for ecotones in generating rainforest biodiversity. Science 276, 1855-1857. (doi:10.1126/science.276.5320.1855)
43. Ogden, R. & Thorpe, R. S. 2002 Molecular evidence for ecological speciation in tropical habitats. Proc. Natl Acad. Sci. USA 99, 13612-13615. (doi:10.1073/pnas.212248499)
44. Thibert-Plante, X. & Hendry, A. P. 2009 Five questions on ecological speciation addressed with individual-based simulations. J. Evol. Biol. 22, 109-123. (doi:10.1111/j.1420-9101.2008.01627.x)
45. Thibert-Plante, X. & Hendry, A. P. 2010 When can ecological speciation be detected with neutral loci? Mol. Ecol. 19, 2301-2314. (doi:10.1111/j.1365-294X.2010.04641.x)
46. Feder, J. L. & Nosil, P. 2010 The efficacy of divergence hitchhiking in generating genomic islands during ecological speciation. Evolution 64, 1729-1747. (doi:10.1111/j.1558-5646.2009.00943.x)
47. Nosil, P., Egan, S. P. & Funk, D. J. 2008 Heterogeneous genomic differentiation between walking-stick ecotypes: 'isolation by adaptation' and multiple roles for divergent selection. Evolution 62, 316-336. (doi:10.1111/j.1558-5646.2007.00299.x)
48. Noor, M. A. F. & Bennett, S. M. 2010 Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species (Correction to Heredity, 2009, vol. 103, p. 434). Heredity 104, 418. (doi:10.1038/hdy.2010.13)
49. Turner, T. L. & Hahn, M. W. 2010 Genomic islands of speciation or genomic islands and speciation? Mol. Ecol. 19, 848-850. (doi:10.1111/j.1365-294X.2010.04532.x)
50. Nosil, P., Vines, T. H. & Funk, D. J. 2005 Perspective reproductive isolation caused by natural selection against immigrants from divergent habitats. Evolution 59, 705-719. (doi:10.1554/04-428)
51. Strasburg, J. L., Sherman, N. A., Wright, K. M., Moyle, L. C., Willis, J. H. & Rieseberg, L. H. 2012 What can patterns of differentiation across plant genomes tell us about adaptation and speciation? Phil. Trans. R. Soc. B 367, 364-373. (doi:10.1098/rstb.2011.0199)
52. Michel, A. P., Sim, S., Powell, T. H. Q., Taylor, M. S., Nosil, P. & Feder, J. L. 2010 Widespread genomic divergence during sympatric speciation. Proc. Natl Acad. Sci. USA 107, 9724-9729. (doi:10.1073/pnas.1000939107)
53. Nosil, P., Harmon, L. J. & Seehausen, O. 2009 Ecological explanations for (incomplete) speciation. Trends Ecol. Evol. 24, 145-156. (doi:10.1016/j.tree.2008.10.011)
54. Emelianov, I., Marec, F. & Mallet, J. 2004 Genomic evidence for divergence with gene flow in host races of the larch budmoth. Proc. R. Soc. Lond. B 271, 97-105. (doi:10.1098/rspb.2003.2574)
55. Lawniczak, M. K. N. et al. 2010 Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences. Science 330, 512-514. (doi:10.1126/science.1195755)
56. Charlesworth, B., Nordborg, M. & Charlesworth, D. 1997 The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. Genet. Res. 70, 155-174. (doi:10.1017/S0016672397002954)
57. Barton, N. & Bengtsson, B. O. 1986 The barrier to genetic exchange between hybridizing populations. Heredity 57, 357-376. (doi:10.1038/hdy.1986.135)
58. Bengtsson, B.O. (ed.) 1985 The flow of genes through a genetic barrier. Cambridge, UK: Cambridge University Press.
59. Pialek, J. & Barton, N. H. 1997 The spread of an advantageous allele across a barrier: the effects of random drift and selection against heterozygotes. Genetics 145, 493-504.
60. Gavrilets, S. & Cruzan, M. B. 1998 Neutral gene flow across single locus clines. Evolution 52, 1277-1284. (doi:10.2307/2411297)
61. Yeaman, S. & Otto, S. P. 2011 Establishment and maintenance of adaptive genetic divergence under migration, selection, and drift. Evolution 65, 2123-2129. (doi:10.1111/j.1558-5646.2011.01277.x)
62. Yeaman, S. & Whitlock, M. C. 2011 The genetic architecture of adaptation under migration-selection balance. Evolution 65, 1897-1911. (doi:10.1111/j.1558-5646.2011.01269.x)
63. Barrett, R. D. H., M'Gonigle, L. K. & Otto, S. P. 2006 The distribution of beneficial mutant effects under strong selection. Genetics 174, 2071-2079. (doi:10.1534/genetics.106.062406)
64. Peccoud, J., Ollivier, A., Plantegenest, M. & Simon, J. C. 2009 A continuum of genetic divergence from sympatric host races to species in the pea aphid complex. Proc. Natl Acad. Sci. USA 106, 7495-7500. (doi:10.1073/pnas.0811117106)
65. Hendry, A. P., Bolnick, D. I., Berner, D. & Peichel, C. L. 2009 Along the speciation continuum in sticklebacks. J. Fish Biol. 75, 2000-2036. (doi:10.1111/j.1095-8649.2009.02419.x)
66. Mallet, J., Beltran, M., Neukirchen, W. & Linares, M. 2007 Natural hybridization in heliconiine butterflies: the species boundary as a continuum. BMC Evol. Biol. 7, 28. (doi:10.1186/1471-2148-7-28)
67. van Doorn, G. S. & Weissing, F. J. 2001 Ecological versus sexual models of sympatric speciation: a synthesis. Selection 2, 17-40. (doi:10.1556/Select.2.2001.1-2.3)
68. Kirkpatrick, M. & Barton, N. 2006 Chromosome inversions, local adaptation and speciation. Genetics 173, 419-434. (doi:10.1534/genetics.105.047985)
69. Feder, J. L. & Nosil, P. 2009 Chromosomal inversions and species differences: when are genes affecting adaptive divergence and reproductive isolation expected to reside within inversions? Evolution 63, 3061-3075. (doi:10.1111/j.1558-5646.2009.00786.x)
70. Nadeau, N. J. et al. 2012 Genomic islands of divergence in hybridizing Heliconius butterflies identified by largescale targeted sequencing. Phil. Trans. R. Soc. B 367, 343-353. (doi:10.1098/rstb.2011.0198)
71. Orr, H. A. 2005 The genetic theory of adaptation: a brief history. Nat. Rev. Genet. 6, 119-127. (doi:10.1038/nrg1523)
72. Barrett, R. D. H. & Schluter, D. 2008 Adaptation from standing genetic variation. Trends Ecol. Evol. 23, 38-44. (doi:10.1016/j.tree.2007.09.008)
73. Feder, J. L. et al. 2003 Allopatric genetic origins for sympatric host-plant shifts and race formation in Rhagoletis. Proc. Natl Acad. Sci. USA 100, 10314-10319. (doi:10.1073/pnas.1730757100)
74. Orr, H. A. & Betancourt, A. J. 2001 Haldane's sieve and adaptation from the standing genetic variation. Genetics 157, 875-884.
75. Przeworski, M. 2003 Estimating the time since the fixation of a beneficial allele. Genetics 164, 1667-1676.
76. Hermisson, J. & Pennings, P. S. 2005 Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169, 2335-2352. (doi:10.1534/genetics.104.036947)
77. Pennings, P. S. & Hermisson, J. 2006 Soft sweeps III: the signature of positive selection from recurrent mutation. PLoS Genet. 2, 1998-2012. (doi:10.1371/journal.pgen.0020186)
78. Pennings, P. S. & Hermisson, J. 2006 Soft sweeps II: molecular population genetics of adaptation from recurrent mutation or migration. Mol. Biol. Evol. 23, 1076-1084. (doi:10.1093/molbev/msj117)
79. Barton, N. 2010 Understanding adaptation in large populations. PLoS Genet. 6, e1000987. (doi:10.1371/journal.pgen.1000987)
80. Paterson, S. et al. 2010 Antagonistic coevolution accelerates molecular evolution. Nature 464, 275-278. (doi:10.1038/nature08798)
81. Araya, C. L., Payen, C., Dunham, M. J. & Fields, S. 2010 Whole-genome sequencing of a laboratory-evolved yeast strain. BMC Genom. 11, 88. (doi:10.1186/1471-2164-11-88)
82. Barrick, J. E., Yu, D. S., Yoon, S. H., Jeong, H., Oh, T. K., Schneider, D., Lenski, R. E. & Kim, J. F. 2009 Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243-1274. (doi:10.1038/nature08480)