Data deposited at Dryad: doi:10.5061/dryad.8sc8b
Spatially explicit models of divergence and genome hitchhiking
Version of Record online: 30 OCT 2012
© 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology
Journal of Evolutionary Biology
Volume 25, Issue 12, pages 2633–2650, December 2012
How to Cite
Flaxman, S. M., Feder, J. L. and Nosil, P. (2012), Spatially explicit models of divergence and genome hitchhiking. Journal of Evolutionary Biology, 25: 2633–2650. doi: 10.1111/jeb.12013
- Issue online: 16 NOV 2012
- Version of Record online: 30 OCT 2012
- Manuscript Accepted: 9 SEP 2012
- Manuscript Revised: 24 AUG 2012
- Manuscript Received: 11 JUN 2012
- National Science Foundation. Grant Number: CNS-0821794
- University of Colorado Boulder
- 1979. Dynamics of hybrid zones. Heredity 43: 341–359.
- 1983. Multilocus clines. Evolution 37: 454–471.
- 1995. Linkage and the limits to natural selection. Genetics 140: 821–841.
- 1998. The effect of hitch-hiking on neutral genealogies. Genet. Res. 72: 123–133.
- 2000. Genetic hitchhiking. Philos. Trans. R. Soc. Lond. B Biol. Sci. 355: 1553–1562.
- 2001. The role of hybridization in evolution. Mol. Ecol. 10: 551–568.
- 2008. The effect of a barrier to gene flow on patterns of geographic variation. Genet Res 90: 139–149.
- 1986. The barrier to genetic exchange between hybridizing populations. Heredity 57: 357–376. &
- 1985. Analysis of hybrid zones. Annu. Rev. Ecol. Syst. 16: 113–148. &
- 2010. Genomic hotspots for adaptation: the population genetics of Müllerian mimicry in the Heliconius melpomene clade. PLoS Genet. 6: e1000794. , , , , , et al.
- 2005. Adaptation and speciation: what can Fst tell us? Trends Ecol. Evol. 20: 435–440.
- 2002. Sympatric speciation in phytophagous insects: moving beyond controversy? Annu. Rev. Entomol. 47: 773–815. &
- 2010. The distinctive footprints of local hitchhiking in a varied environment and global hitchhiking in a subdivided population. Evolution 64: 3254–3272.
- 2007. Sympatric speciation: models and empirical evidence. Annu. Rev. Ecol. Evol. Syst. 38: 459–487. &
- 2009. Phenotypic-dependent native habitat preference facilitates divergence between parapatric lake and stream stickleback. Evolution 63: 2004–2016. , , , , &
- 1999. Reinforcing selection is effective under a relatively broad set of conditions in a mosaic hybrid zone. Evolution 53: 1343–1353. , &
- 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. , &
- 2003. The effects of genetic and geographic structure on neutral variation. Annu. Rev. Ecol. Evol. Syst. 34: 99–125. , &
- 2010. Genomic hotspots for adaptation: the population genetics of Müllerian mimicry in Heliconius erato. PLoS Genet. 6: e1000796. , , , , , et al.
- 2003. Speciation along environmental gradients. Nature 421: 259–264. &
- 1977. Geographic Variation, Speciation, and Clines. Princeton University Press, Princeton, NJ.
- 2010. The efficacy of divergence hitchhiking in generating genomic islands during ecological speciation. Evolution 64: 1729–1747. &
- 2012. Establishment of new mutations under divergence and genome hitchhiking. Philos. Trans. R. Soc. Lond. B Biol. Sci. 367: 461–474. , , &
- 1981. Skepticism towards Santa Rosalia, or why are there so few kinds of animals? Evolution 35: 124–138.
- 2008. What, if anything, is sympatric speciation? J. Evol. Biol. 21: 1452–1459. , &
- 2009. Tracking prey or tracking the prey's resource? Mechanisms of movement and optimal habitat selection by predators. J. Theor. Biol. 256: 187–200. &
- 2011. Evolutionary ecology of movement by predators and prey. Theor. Ecol. 4: 255–267. , &
- 2008. A genome-scan method to identify selected loci appropriate for both dominant and codominant Markers: a Bayesian perspective. Genetics 180: 977–993. &
- 2003. Multilocus models of sympatric speciation: Bush versus Rice versus Felsenstein. Evolution 57: 1735–1746.
- 2003. Perspective: models of speciation: what have we learned in 40 years? Evolution 57: 2197–2215.
- 2004. Fitness Landscapes and the Origin of Species. Princeton University Press, Princeton, NJ.
- 2011. A hierarchical Bayesian model for next-generation population genomics. Genetics 187: 903–917. &
- 2007. Principles of Population Genetics, Fourth Edition. Sinauer, Sunderland, MA. &
- 1991. A multidimensional coalescent process applied to multi-allelic selection models and migration models. Theor. Popul. Biol. 39: 30–48.
- 1996. Conditions for sympatric speciation: a diploid model incorporating habitat fidelity and non-habitat assortative mating. Evol. Ecol. 10: 187–205. , , &
- 1991. The coalescent process in models with selection, recombination and geographic subdivision. Genet. Res. 57: 83–91. , &
- 2011. Hitchhiking effect of a beneficial mutation spreading in a subdivided population. Genetics 189: 213–226. &
- 2010. Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences. Science 330: 512–514. , , , , , et al.
- 2007. 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 175: 1289–1306. , &
- 2008. Hitchhiking mapping reveals a candidate genomic region for natural selection in three-spined stickleback chromosome VIII. Genetics 178: 453–465. , , &
- 2009. Space, sympatry and speciation. J. Evol. Biol. 22: 2332–2341. , , &
- 1974. Hitch-hiking effect of a favorable gene. Genet. Res. 23: 23–35. &
- 1963. Animal Species and Evolution. Harvard University Press, Harvard, MA.
- 2010. Widespread genomic divergence during sympatric speciation. Proc. Nat. Acad. Sci. 107: 9724–9729. , , , , &
- 2012. Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing. Philos. Trans. R. Soc. Lond. B Biol. Sci. 367: 343–353. , , , , , et al.
- 1975. Conditions for the existence of clines. Genetics 80: 595–615.
- 1976. Clines with variable migration. Genetics 83: 867–886.
- 2005. Molecular signatures of natural selection. Annu. Rev. Genet. 39: 197–218.
- 2006. Speciation genetics: evolving approaches. Nat. Rev. Genet. 7: 851–861. &
- 2007. Divergence between the Drosophila pseudoobscura and D-persimilis genome sequences in relation to chromosomal inversions. Genetics 177: 1417–1428. , , &
- 1996a. The effect of recombination on background selection. Genet. Res. 67: 159–174. , &
- 1996b. Increased levels of polymorphism surrounding selectively maintained sites in highly selfing species. Proc. R. Soc. Lond. B Biol. Sci. 263: 1033–1039. , &
- 2012. Genomic divergence during speciation: causes and consequences. Philos. Trans. R. Soc. Lond. B Biol. Sci. 367: 332–342. &
- 2006. Migration and the genetic covariance between habitat preference and performance. Am. Nat. 167: E66–E78. , , &
- 2009. Divergent selection and heterogeneous genomic divergence. Mol. Ecol. 18: 375–402. , &
- 1983. The effect on neutral gene flow of selection at a linked locus. Theor. Popul. Biol. 23: 300–313.
- 2012. Genome-wide patterns of divergence during speciation: the lake whitefish case study. Philos. Trans. R. Soc. Lond. B Biol. Sci. 367: 354–363. , , , , , et al.
- 1993. Laboratory experiments on speciation – what have we learned in 40 years? Evolution 47: 1637–1653. &
- 2007. The genetic architecture of ecological speciation and the association with signatures of selection in natural lake whitefish (Coregonas sp Salmonidae) species pairs. Mol. Biol. Evol. 24: 1423–1438. &
- 2006. SIMD-oriented Fast Mersenne Twister: a 128-bit pseudorandom number generator. In: Monte Carlo and Quasi-Monte Carlo Methods (A. Keller, S. Heinrich & H. Niederreiter, eds), pp. 607–622. Springer Berlin Heidelberg, Berlin. &
- 2010. Genome scan of hybridizing sunflowers from Texas (Helianthus annuus and H. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation. Mol. Ecol. 19: 521–541. , , , , &
- 2011. Magic traits in speciation: magic but not rare? Trends Ecol. Evol. 26: 389–397. , , , &
- 1973. Gene flow and selection in a cline. Genetics 75: 733–756.
- 2008. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 100: 158–170. &
- 2008. Effects of spatially varying selection on nucleotide diversity and linkage disequilibrium: insights from deer mouse globin genes. Genetics 180: 367–379. &
- 2012. What can patterns of differentiation across plant genomes tell us about adaptation and speciation? Philos. Trans. R. Soc. Lond. B Biol. Sci. 367: 364–373. , , , , &
- 2007. Locus- and population-specific selection and differentiation between incipient species of Anopheles gambiae. Mol. Biol. Evol. 24: 2132–2138. &
- 2005. Genomic islands of speciation in Anopheles gambiae. PLoS Biol. 3: 1572–1578. , &
- 2010. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat. Genet. 42: 260–263. , , , &
- 2001. Sympatric speciation in animals: the ugly duckling grows up. Trends Ecol. Evol. 16: 381–390.
- 2009. Natural selection in action during speciation. Proc. Natl Acad. Sci. USA 106: 9939–9946.
- 2012. Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow. Philos. Trans. R. Soc. Lond. B Biol. Sci. 367: 451–460.
- 2008. The genetic mosaic suggests a new role for hitchhiking in ecological speciation. Mol. Ecol. 17: 4334–4345. &
- 2010. Evolution in heterogeneous populations: from migration models to fixation probabilities. Theor. Popul. Biol. 78: 250–258. , &
- 2004. A separation-of-timescales approach to the coalescent in a continuous population. Genetics 168: 2227–2244.
- 2008. Sequence differentiation in regions identified by a genome scan for local adaptation. Mol. Ecol. 17: 3123–3135. , , , &
- 2001. The genic view of the process of speciation. J. Evol. Biol. 14: 851–865.