Experimental evidence for ecological selection on genome variation in the wild

Ecology Letters

Volumn 17, Issue 3, 2014, Pages 369-379

  Gompert, Zachariah ^a   Comeault, Aaron A ^b   Farkas, Timothy E ^b   Feder, Jeffrey L ^c   Parchman, Thomas L ^d   Buerkle, C Alex ^e   Nosil, Patrik ^b  

^a UTAH STATE UNIVERSITY   (United States)

^b UNIVERSITY OF SHEFFIELD   (United Kingdom)

^c UNIVERSITY OF NOTRE DAME   (United States)

^d UNIVERSITY OF NEVADA   (United States)

^e UNIVERSITY OF WYOMING   (United States)

Author keywords

Adaptation; Climate; Ecological speciation; Genome evolution; Genomics; Natural selection; Next generation sequencing; Population genomics; Timema cristinae

Indexed keywords

PHASMATODEA; TIMEMA CRISTINAE;

ADAPTATION; ANIMAL; BIOLOGICAL MODEL; CLIMATE; COMPARATIVE STUDY; DNA SEQUENCE; ECOLOGICAL SPECIATION; ECOSYSTEM; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC DRIFT; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GENOME; GENOME EVOLUTION; GENOMICS; INSECT; LETTER; MOLECULAR GENETICS; NATURAL SELECTION; NEXT-GENERATION SEQUENCING; NUCLEOTIDE SEQUENCE; PHENOTYPE; PIGMENTATION; POPULATION GENOMICS; TIMEMA CRISTINAE; UNITED STATES;

ADAPTATION; CLIMATE; ECOLOGICAL SPECIATION; GENOME EVOLUTION; GENOMICS; NATURAL SELECTION; NEXT-GENERATION SEQUENCING; POPULATION GENOMICS; TIMEMA CRISTINAE;

ANIMALS; BASE SEQUENCE; CALIFORNIA; ECOSYSTEM; GENE FREQUENCY; GENETIC DRIFT; GENETIC VARIATION; GENOME; INSECTS; LINKAGE DISEQUILIBRIUM; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; PHENOTYPE; PIGMENTATION; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84892674349     PISSN: 1461023X     EISSN: 14610248     Source Type: Journal    
DOI: 10.1111/ele.12238     Document Type: Article

References (46)

1. Anderson, J.T., Lee, C.-R. & Mitchell-Olds, T. (2013). Strong selection genome-wide enhances fitness tradeoffs across environments and episodes of selection. Evolution, DOI: 10.1111/evo.12259.
2. Araya, C.L., Payen, C., Dunham, M.J. & Fields, S. (2010). Whole-genome sequencing of a laboratory-evolved yeast strain. BMC Genomics, 11, 88.
3. Barrett, R.D.H. & Hoekstra, H.E. (2011). Molecular spandrels: tests of adaptation at the genetic level. Nat. Rev. Genet., 12, 767-780.
4. Barrett, R.D.H. & Schluter, D. (2008). Adaptation from standing genetic variation. Trends Ecol. Evol., 23, 38-44.
5. Barrick, J.E., Yu, D.S., Yoon, S.H., Jeong, H., Oh, T.K., Schneider, D. et al. (2009). Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature, 461, 1243-1247.
6. Burke, M.K. (2012). How does adaptation sweep through the genome? Insights from long-term selection experiments. Proc. Biol. Sci., 279, 5029-5038.
7. Burke, M.K., Dunham, J.P., Shahrestani, P., Thornton, K.R., Rose, M.R. & Long, A.D. (2010). Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature, 467, 587-590.
8. Butler, J., MacCallum, L., Kleber, M., Shlyakhter, I.A., Belmonte, M.K., Lander, E.S. et al. (2008). ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Research, 18, 810-820.
9. Ellegren, H., Smeds, L., Burri, R., Olason, P.I., Backström, N., Kawakami, T. et al. (2012). The genomic landscape of species divergence in Ficedula flycatchers. Nature, 491, 756-760.
10. Endler, J.A. (1986). Natural selection in the wild. Princeton University Press, Princeton, NJ.
11. Farkas, T.E., Mononen, T., Comeault, A.A., Hanski, I. & Nosil, P. (2013). Evolution of camouflage drives rapid ecological change in an insect community. Curr. Biol., 23, 1835-1843.
12. Fournier-Level, A., Korte, A., Cooper, M.D., Nordborg, M., Schmitt, J. & Wilczek, A.M. (2011). A map of local adaptation in arabidopsis thaliana. Science, 333, 86-89.
13. Funk, D.J., Nosil, P. & Etges, W.J. (2006). Ecological divergence exhibits consistently positive associations with reproductive isolation across disparate taxa. Proc. Natl. Acad. Sci. USA, 103, 3209-3213.
14. Gavrilets, S. & Hastings, A. (1996). Founder effect speciation: a theoretical reassessment. Am. Nat., 147, 466-491.
15. Gould, S.J. (2002). The structure of evolutionary theory. Belknap Press, Harvard.
16. Hancock, A.M., Brachi, B., Faure, N., Horton, M.W., Jarymowycz, L.B., Sperone, F.G. et al. (2011). Adaptation to climate across the Arabidopsis thaliana genome. Science, 333, 83-86.
17. Hanski, I. & Mononen, T. (2011). Eco-evolutionary dynamics of dispersal in spatially heterogeneous environments. Ecol. Lett., 14, 1025-1034.
18. Heliconius Genome Consortium (2012). Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature, 487, 94-98.
19. Hendry, A.P., Grant, P.R., Grant, B.R., Ford, H.A., Brewer, M.J. & Podos, J. (2006). Possible human impacts on adaptive radiation: beak size bimodality in Darwin's finches. Proc. Biol. Sci., 273, 1887-1894.
20. Hermisson, J. & Pennings, P.S. (2005). Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics, 169, 2335-2352.
21. Hohenlohe, P.A., Bassham, S., Etter, P.D., Stiffler, N., Johnson, E.A. & Cresko, W.A. (2010). Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags. PLoS Genet., 6, e1000862.
22. Jones, F.C., Grabherr, M.G., Chan, Y.F., Russell, P., Mauceli, E., Johnson, J. et al. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484, 55-61.
23. Kingsolver, J.G., Hoekstra, H.E., Hoekstra, J.M., Berrigan, D., Vignieri, S.N., Hill, C.E. et al. (2001). The strength of phenotypic selection in natural populations. Am. Nat., 157, 245-261.
24. Kolbe, J.J., Leal, M., Schoener, T.W., Spiller, D.A. & Losos, J.B. (2012). Founder Effects Persist Despite Adaptive Differentiation: A Field Experiment with Lizards. Science, 335, 1086-1089.
25. Lawniczak, M.K.N., Emrich, S.J., Holloway, A.K., Regier, A.P., Olson, M., White, B. et al. (2010). Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences. Science, 330, 512-514.
26. Li, Y.F., Costello, J.C., Holloway, A.K. & Hahn, M.W. (2008). 'Reverse ecology' and the power of population genomics. Evolution, 62, 2984-2994.
27. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N. et al. & Genome Project Data P. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
28. Moran, P.A.P. (1950). Notes on continuous stochastic phenomena. Biometrika, 37, 17-23.
29. Nielsen, R. (2005). Molecular signatures of natural selection. Annu. Rev. Genet., 39, 197-218.
30. Nosil, P. (2004). Reproductive isolation caused by visual predation on migrants between divergent environments. Proc. Biol. Sci., 271, 1521-1528.
31. Nosil, P. (2007). Divergent host plant adaptation and reproductive isolation between ecotypes of Timema cristinae walking sticks. Am. Nat., 169, 151-162.
32. Nosil, P. & Crespi, B.J. (2006). Experimental evidence that predation promotes divergence in adaptive radiation. Proc. Natl. Acad. Sci. USA, 103, 9090-9095.
33. Nosil, P., Gompert, Z., Farkas, T.E., Comeault, A.A., Feder, J.L., Buerkle, C.A. et al. (2012). Genomic consequences of multiple speciation processes in a stick insect. Proc. Biol. Sci., 279, 5058-5065.
34. Paterson, S., Vogwill, T., Buckling, A., Benmayor, R., Spiers, A.J., Thomson, N.R. et al. (2010). Antagonistic coevolution accelerates molecular evolution. Nature, 464, 275-278.
35. Pelletier, F., Garant, D. & Hendry, A.P. (2009). Eco-evolutionary dynamics introduction. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 364, 1483-1489.
36. Pespeni, M.H., Sanford, E., Gaylordb, B., Hill, T.M., Hosfelt, J.D., Jarisa, H.K. et al. (2013). Evolutionary change during experimental ocean acidification. Proc. Natl. Acad. Sci. USA, 110, 6937-6942.
37. Post, D.M. & Palkovacs, E.P. (2009). Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 364, 1629-1640.
38. Roesti, M., Hendry, A.P., Salzburger, W. & Berner, D. (2012). Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs. Mol. Ecol., 21, 2852-2862.
39. Sandoval, C.P. (1994). The effects of relative geographical scales of gene flow and selection on morph frequencies in the walking-stick Timema cristinae. Evolution, 48, 1866-1879.
40. Sandoval, C. (2000). Persistence of a walking-stick population (Phasmatoptera: Timematodea) after a wildfire. Southwest. Nat., 45, 123-127.
41. Schluter, D. (2001). Ecology and the origin of species. Trends Ecol. Evol., 16, 372-380.
42. Schluter, D. & Nagel, L.M. (1995). Parallel speciation by natural-selection. Am. Nat., 146, 292-301.
43. Seehausen, O., Takimoto, G., Roy, D. & Jokela, J. (2008). Speciation reversal and biodiversity dynamics with hybridization in changing environments. Mol. Ecol., 17, 30-44.
44. Siepielski, A.M., DiBattista, J.D. & Carlson, S.M. (2009). It's about time: the temporal dynamics of phenotypic selection in the wild. Ecol. Lett., 12, 1261-1276.
45. Siepielski, A.M., Gotanda, K., Morrissey, M., Diamond, S., DiBattista, J. & Carlson, S.M. (2013). Spatial patterns of directional phenotypic selection. Ecol. Lett., 16, 1382-1392.
46. Weir, B.S. (1979). Inferences about linkage disequilibrium. Biometrics, 35, 235-254.