The efficacy of divergence hitchhiking in generating genomic islands during ecological speciation

Evolution

Volumn 64, Issue 6, 2010, Pages 1729-1747

  Feder, Jeffrey L ^a,b,c   Nosil, Patrik ^b  

^a UNIVERSITY OF NOTRE DAME   (United States)

^b INSTITUTE FOR ADVANCED STUDY   (United States)

^c UNIVERSITY OF COLORADO   (United States)

Author keywords

Divergent selection; Gene flow; Recombination; Simulations; Speciation islands

Indexed keywords

CHROMOSOME; DIVERGENCE; EFFECTIVE POPULATION SIZE; GENE FLOW; GENETIC VARIATION; GENOMICS; NATURAL SELECTION; NUMERICAL MODEL; SPECIATION (BIOLOGY);

ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE FLOW; GENE LOCUS; GENETIC SELECTION; GENOMIC ISLAND; SPECIES DIFFERENTIATION;

COMPUTER SIMULATION; GENE FLOW; GENETIC LOCI; GENETIC SPECIATION; GENOMIC ISLANDS; MODELS, GENETIC; SELECTION, GENETIC;

EID: 77952690357     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2009.00943.x     Document Type: Article

References (71)

1. Achere V, Favre J M, Besnard G, Jeandroz S. Genomic organization of molecular differentiation in Norway spruce (Picea abies). Mol. Ecol. 2005, 14:3191-3201.
2. Avise J. Phylogeography: the history and formation of new species 2000, Harvard Univ. Press, Cambridge, MA
3. Barrett R D H, Schluter D. Adaptation from standing genetic variation. Trends Ecol. Evol. 2008, 23:38-44.
4. Barton N H. Gene flow past a cline. Heredity 1979, 43:333-340.
5. Barton N H. Multilocus clines. Evolution 1983, 37:454-471.
6. Barton N H. Genetic hitchhiking. Philos. Trans. R. Soc. Lond. B 2000, 355:1553-1562.
7. Barton N H, Bengtsson B O. The barrier to genetic exchange between hybridizing populations. Heredity 1986, 57:357-376.
8. Beaumont M A. Adaptation and speciation: what can F-st tell us?. Trends Ecol. Evol. 2005, 20:435-440.
9. Bengtsson B O. The flow of genes through a genetic barrier. Evolution essays in honor of John Maynard Smith 1985, 31-42. Greenwood J JHarvey P HSlatkin M. Pp, , eds, Cambridge Univ. Press, Cambridge
10. Berlocher S H, Feder J L. Sympatric speciation in phytophagous insects: moving beyond controversy?. Annual Review of Entomology 2002, 47:773-815.
11. Butlin R K. Population genomics and speciation. 2008, 10.1007/s10709-008-9321-3, Genetica online Sept. 6. DOI
12. Charlesworth D, Charlesworth B. Theoretical genetics of Batesian mimicry II. Evolution of supergenes. J. Theor. Biol. 1975, 55:305-324.
13. Charlesworth B, Nordborg M, Charlesworth D. The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. Genet. Res. 1997, 70:155-174.
14. Coyne J A, Orr H A. Speciation 2004, Sinauer Associates, Inc, Sunderland, MA
15. Dopman E B, Perez L, Bogdanowicz S M, Harrison R G. Consequences of reproductive barriers for genealogical discordance in the European corn borer. Proc. Natl. Acad. Sci. USA 2005, 102:14706-14711.
16. Egan S P, Nosil P, Funk D J. Selection and genomic differentiation during ecological speciation: isolating the contributions of host-association via a comparative genome scan of Neochlamisus bebbianae leaf beetles. Evolution 2008, 62:1162-1181.
17. Emelianov I, Marec F, Mallet J. Genomic evidence for divergence with gene flow in host races of the larch budmoth. Proc. R. Soc. Lond. B 2004, 271:97-105.
18. Feder J L. The apple maggot fly, Rhagoletis pomonella: flies in the face of conventional wisdom about speciation?. Endless forms: species and speciation 1998, 130-144. Howard DBerlocher S H. Pp, , eds, Oxford Univ. Press, London
19. Feder J L, Nosil P. Chromosomal inversions and species differences: where are genes affecting adaptive divergence and reproductive isolation expected to reside within inversions?. Evolution 2009, 63:3061-3075.
20. Fry J D. Multilocus models of sympatric speciation: Bush vs. Rice vs. Felsenstein. Evolution 2003, 57:1735-1746.
21. Gavrilets S. Single locus clines. Evolution 1997, 51:979-983.
22. Gavrilets S. Fitness landscapes and the origin of species 2004, Princeton Univ. Press, Princeton, NJ
23. Gavrilets S, Cruzan M B. Neutral gene flow across single locus clines. Evolution 1998, 52:1277-1284.
24. Gavrilets S, Vose A. Dynamic patterns of adaptive radiation. Proc. Natl. Acad. Sci. USA 2005, 102:18040-18045.
25. Geraldes A, Ferrand N, Nachman N W. Contrasting patterns of introgression at X-linked loci across the hybrid zone between subspecies of the European rabbit (Oryctolagus cuniculus). Genetics 2006, 173:919-933.
26. Grahame J W, Wilding C S, Butlin R K. Adaptation to a steep environmental gradient and an associated barrier to gene exchange in Littorina saxatilis. Evolution 2006, 60:268-278.
27. Harr B. Genomic islands of differentiation between house mouse subspecies. Genome Res. 2006, 16:730-737.
28. Harrison R G, Rand D M. Mosaic hybrid zones and the nature of species boundaries. Speciation and its consequences 1989, 111-133. Otte D, Endler J A. Pp, , eds, Sinauer, Sunderland, MA
29. Hawthorne D J, Via S. Genetic linkage of ecological specialization and reproductive isolation in pea aphids. Nature 2001, 412:904-907.
30. Hermisson J, Pennings P S. Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 2005, 169:2335-2352.
31. Hudson R R. Gene genealogies and the coalescent process. Oxf. Surv. Evol. Biol. 1990, 7:1-45.
32. Kimura M. A model of genetic system which leads to closer linkage by natural selection. Evolution 1956, 10:278-287.
33. Kouyos R D, Otto S P, Bonhoeffer S. Effect of varying epistasis on the evolution of recombination. Genetics 2006, 173:589-597.
34. Lewontin R C, Krakauer J. Distribution of gene frequency as a test of the theory of selective neutrality of polymorphisms. Genetics 1973, 74:175-195.
35. Machado C A, Haselkorn T S, Noor M A F. Evaluation of the genomic extent of effects of fixed inversion differences on intraspecific variation and interspecific gene flow in Drosophila pseudoobscura and D. persimilis. Genetics 2007, 175:1289-1306.
36. Mäkinen H S, Cano J M, Merilä J. Identifying footprints of directional and balancing selection in marine and freshwater threespine stickleback (Gasterosteus aculeatus) populations. Mol. Ecol. 2008a, 17:3565-3582.
37. Mäkinen H S, Shikano T, Cano J M, Merilä J. Hitchhiking mapping reveals a candidate genomic region for natural selection in three-spined stickleback chromosome VIII. Genetics 2008b, 178:435-465.
38. Mallet J. What has Drosophila genetics revealed about speciation?. Trends Ecol. Evol. 2006, 21:186-193.
39. Navarro A, Barton N H. Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation. Evolution 2003, 57:447-459.
40. Nielsen R. Molecular signatures of natural selection. Annu. Rev. Genet. 2005, 39:197-218.
41. Noor M A F, Feder J L. Speciation genetics: evolving approaches. Nat. Rev. Genet. 2006, 7:851-861.
42. Noor M A F, Garfield D A, Schaeffer S W, Machado C A. Divergent between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions. Genetics 2007, 177:1417-1428.
43. Nosil P. Reproductive isolation caused by visual predation on migrants between divergent environments. Proc. R. Soc. Lond. B 2004, 271:1521-1528.
44. Nosil P, Vines T H, Funk D J. Perspective: reproductive isolation caused by natural selection against immigrants from divergent habitats. Evolution 2005, 59:705-719.
45. Nosil P, Egan S P, Funk D J. Heterogeneous genomic differentiation between walking-stick ecotypes: 'isolation-by-adaptation' and multiple roles for divergent selection. Evolution 2008, 62:316-336.
46. Nosil P, Funk D J, Ortiz-Barrientos D. Divergent selection and heterogeneous genomic divergence. Mol. Ecol. 2009a, 18:375-402.
47. Nosil P, Harmon L, Seehausen O. Ecological explanations for (incomplete) speciation. Trends Ecol. Evol. 2009b, 24:145-156.
48. Orr H A, Betancourt e. Haldane's sieve and adaptation from standing genetic variation. Genetics 2001, 157:875-844.
49. Payseur B A, Krenz J G, Nachman M W. Differential patterns of introgression across the X chromosome in a hybrid zone between two species of house mice. Evolution 2004, 58:2064-2078.
50. Przeworski M, Graham C, Wall J D. The signature of positive selection on standing genetic variation. Evolution 2005, 59:2312-2323.
51. Petry D. The effect on netral gene flow of selection at a linked locus. Theor. Popul. Biol. 1983, 23:300-313.
52. Pialek J, Barton N H. The spread of an advantageous allele across a barrier: the effects of random drift and selection against heterozygotes. Genetics 1997, 145:493-504.
53. Rice W R, Hostert E E. Laboratory experiments in speciation: what have we learned in 40 years?. Evolution 1993, 47:1637-1653.
54. Rogers S M, Bernatchez L. The genetic architecture of ecological speciation and the association with signatures of selection in natural lake whitefish (Coregonus sp. Salmonidae). Mol. Biol. Evol. 2007, 24:1423-1438.
55. Schluter D. The ecology of adaptive radiation 2000, Oxford Univ. Press, Oxford, U.K
56. Scotti-Saintagne C, Mariette S, Porth I, Goicoechea P G, Barreneche T, Bodenes K, Burg K, Kremer A. Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q. petraea (Matt.) Liebl.]. Genetics 2004, 168:1615-1626.
57. Slatkin M. Inbreeding coefficients and coalescence times. Genet. Res. 1991, 58:167-175.
58. Smadja C, Galindo J, Butlin R K. Hitching a lift on the road to speciation. Mol. Ecol. 2008, 17:4177-4180.
59. Strasburg J L, Scotti-Saintagne C, Scotti I, Lai Z, Rieseberg L H. Genomic patterns of adaptive divergence between chromosomally differentiated sunflower species. Mol. Biol. Evol. 2009, 26:1341-1355.
60. Templeton A. Mechanisms of speciation - A population genetic approach. Annu. Rev. Ecol. Syst. 1981, 12:23-48.
61. Turner T L, Hahn M W. Locus- and population specific selection and differentiation between incipient species of Anopholes gambiae. Mol. Biol. Evol. 2007, 24:2132-2138.
62. Turner T L, Hahn M W, Nuzhdin S V. Genomic islands of speciation in Anopheles gambiae. PLOS Biol. 2005, 3:1572-1578.
63. Turner T L, Levine M T, Eckert M L, Begun D J. Genomic analysis of adaptive differentiation in Drosophila melanogaster. Genetics 2008, 179:455-475.
64. Via S. Sympatric speciation in animals: the ugly duckling grows up. Trends Ecol. Evol. 2001, 16:381-390.
65. Via S. Natural selection in action during speciation. Proc. Natl. Acad. Sci. USA 2009, 106:9939-9946.
66. Via S, West J. The genetic mosaic suggests a new role for hitchhiking in ecological speciation. Mol. Ecol. 2008, 17:4334-4345.
67. White B J, Hahn M W, Pombi M, Cassone B J, Lobo N F, Simard F, Besansky N J. Localization of candidate regions maintaining a common polymorphic inversion (2La) in Anopheleles gambiae. PLoS Genet. 2007, 3:e217.
68. Wood H M, Grahame J W, Humphray S, Rogers J, Butlin R K. Sequence differentiation in regions identified by a genome scan for local adaptation. Mol. Ecol. 2008, 17:3123-3135.
69. Wu C-I. The genic view of the process of speciation. J. Evol. Biol. 2001, 14:851-865.
70. Wu C-I, Ting C-T. Genes and speciation. Nat. Rev. Genet. 2004, 5:114-122.
71. Yatabe Y, Kane N C, Scotti-Saintagne C, Rieseberg L H. Rampant gene exchange across a strong reproductive barrier between the annual sunflowers, Helianthus annuus and H. petiolaris. Genetics 2007, 175:1883-1893.