Combining experimental evolution with next-generation sequencing: A powerful tool to study adaptation from standing genetic variation

Heredity

Volumn 114, Issue 5, 2015, Pages 431-440

  Schlotterer C ^a   Kofler, R ^a   Versace, E ^a,b   Tobler, R ^a,c   Franssen, S U ^a  

^a Institute für Populationsgenetik   (Austria)

^b UNIVERSITY OF TRENTO   (Italy)

^c Vienna Graduate School of Economics   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; EVOLUTIONARY BIOLOGY; GENETIC VARIATION; IDENTIFICATION KEY; PHENOTYPE;

ADAPTATION; ANIMAL; DROSOPHILA MELANOGASTER; EVOLUTION; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENETICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; PHENOTYPE; SINGLE NUCLEOTIDE POLYMORPHISM;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; BIOLOGICAL EVOLUTION; DROSOPHILA MELANOGASTER; GENE FREQUENCY; GENETIC ASSOCIATION STUDIES; GENETIC VARIATION; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; RESEARCH DESIGN;

EID: 84928214396     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2014.86     Document Type: Review

References (48)

1. Aulard S, Monti L, Chaminade N, Lemeunier F (2004). Mitotic and polytene chromosomes: comparisons between Drosophila melanogaster and Drosophila simulans. Genetica 120: 137-150.
2. Baldwin-Brown JG, Long AD, Thornton KR (2014). The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms. Mol Biol Evol 31: 1040-1055.
3. Beissinger TM, Hirsch CN, Vaillancourt B, Deshpande S, Barry K, Buell CR et al. (2014). A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number. Genetics 196: 829-840.
4. Burke MK, Dunham JP, Shahrestani P, Thornton KR, Rose MR, Long AD (2010). Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature 467: 587-590.
5. Chevin LM, Hospital F (2008). Selective sweep at a quantitative trait locus in the presence of background genetic variation. Genetics 180: 1645-1660.
6. Cutter AD, Baird SE, Charlesworth D (2006). High nucleotide polymorphism and rapid decay of linkage disequilibrium in wild populations of Caenorhabditis remanei. Genetics 174: 901-913.
7. Elena SF, Lenski RE (2003). Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 4: 457-469.
8. Futschik A, Schlötterer C (2010). The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics 186: 207-218.
9. Garland T, Rose MR (2009). Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. University of California Press: Berkeley.
10. Hollis B, Houle D, Yan Z, Kawecki TJ, Keller L (2014). Evolution under monogamy feminizes gene expression in Drosophila melanogaster. Nat Commun 5: 3482.
11. Hu TT, Eisen MB, Thornton KR, Andolfatto P (2013). A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Res 23: 89-98.
12. Illingworth CJ, Parts L, Schiffels S, Liti G, Mustonen V (2012). Quantifying selection acting on a complex trait using allele frequency time series data. Mol Biol Evol 29: 1187-1197.
13. Jalvingh KM, Chang PL, Nuzhdin SV, Wertheim B (2014). Genomic changes under rapid evolution: selection for parasitoid resistance. Proc Biol Sci R Soc 281: 20132303.
14. Johansson AM, Pettersson ME, Siegel PB, Carlborg O (2010). Genome-wide effects of longterm divergent selection. PLoS Genet 6: e1001188.
15. Kapun M, van Schalkwyk H, McAllister B, Flatt T, Schlötterer C (2014). Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster. Mol Ecol 23: 1813-1827.
16. Kawecki TJ, Lenski RE, Ebert D, Hollis B, Olivieri I, Whitlock MC (2012). Experimental evolution. Trends Ecol Evol 27: 547-560.
17. Kelly JK, Koseva B, Mojica JP (2013). The genomic signal of partial sweeps in Mimulus guttatus. Genome Biol Evol 5: 1457-1469.
18. Kessner D, Novembre J (2014a). forqs: forward-in-time simulation of recombination, quantitative traits and selection. Bioinformatics 30: 576-577.
19. Kessner D, Novembre J (2014b). Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits. bioRxiv http://dx.doi.org/10.1101/005892.
20. Kessner D, Turner TL, Novembre J (2013). Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data. Mol Biol Evol 30: 1145-1158.
21. Kofler R, Schlötterer C (2014). A guide for the design of evolve and resequencing studies. Mol Biol Evol 31: 474-483.
22. Liu W, Yuan JS, Stewart CN Jr. (2013). Advanced genetic tools for plant biotechnology. Nat Rev Genet 14: 781-793.
23. Magwire MM, Fabian DK, Schweyen H, Cao C, Longdon B, Bayer F et al. (2012). Genomewide association studies reveal a simple genetic basis of resistance to naturally coevolving viruses in Drosophila melanogaster. PLoS Genet 8: e1003057.
24. Martins N, Faria V, Nolte V, Schlötterer C, Teixeira L, Sucena E et al. (2014). Host adaptation to viruses relies on few genes with different cross-resistance properties. Proc Natl Acad Sci USA 111: 5938-5943.
25. Nuzhdin SV, Keightley PD, Pasyukova EG (1993). The use of retrotransposons as markers for mapping genes responsible for fitness differences between related Drosophila melanogaster strains. Genet Res 62: 125-131.
26. Nuzhdin SV, Turner TL (2013). Promises and limitations of hitchhiking mapping. Curr Opin Genet Dev 23: 694-699.
27. Orozco-terWengel P, Kapun M, Nolte V, Kofler R, Flatt T, Schlötterer C (2012). Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol Ecol 21: 4931-4941.
28. Palmieri N, Nolte V, Chen J, Schlötterer C (2014). Genome assembly and annotation of a Drosophila simulans strain from Madagascar. Mol Ecol Resour (e-pub ahead of print 24 June 2014; doi:10.1111/1755-0998.12297).
29. Parts L, Cubillos FA, Warringer J, Jain K, Salinas F, Bumpstead SJ et al. (2011). Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res 21: 1131-1138.
30. Rellstab C, Zoller S, Tedder A, Gugerli F, Fischer MC (2013). Validation of SNP allele frequencies determined by pooled next-generation sequencing in natural populations of a non-model plant species. PLoS ONE 8: e80422.
31. Remolina SC, Chang PL, Leips J, Nuzhdin SV, Hughes KA (2012). Genomic basis of aging and life-history evolution in Drosophila melanogaster. Evolution 66: 3390-3403.
32. Ronen R, Udpa N, Halperin E, Bafna V (2013). Learning natural selection from the site frequency spectrum. Genetics 195: 181-193.
33. Rubin CJ, Zody MC, Eriksson J, Meadows JR, Sherwood E, Webster MT et al. (2010). Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464: 587-591.
34. Schlötterer C, Tobler R, Kofler R, Nolte V (2014). Sequencing pools of individuals-mining genome-wide polymorphism data without big funding. Nature Rev. Genet. http://dx.doi.org/10.1038/nrg3803.
35. Smith JM (1968). "Haldane's dilemma" and the rate of evolution. Nature 219: 1114-1116.
36. Teotonio H, Carvalho S, Manoel D, Roque M, Chelo IM (2012). Evolution of outcrossing in experimental populations of Caenorhabditis elegans. PLoS ONE 7: e35811.
37. Teotonio H, Chelo IM, Bradic M, Rose MR, Long AD (2009). Experimental evolution reveals natural selection on standing genetic variation. Nat Genet 41: 251-257.
38. Terhorst J, Song YS (2014). Multi-locus analysis of genomic time series data from experimental evolution. bioRxiv http://dx.doi.org/10.1101/006734.
39. Terns RM, Terns MP (2014). CRISPR-based technologies: prokaryotic defense weapons repurposed. Trends Genet 30: 111-118.
40. Tobler R, Franssen SU, Kofler R, Orozco-terWengel P, Nolte V, Hermisson J et al. (2013). Massive habitat-specific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments. Mol Biol Evol 31: 364-375.
41. Topa H, Jónás Á, Kofler R, Kosiol C, Honkela A (2014). Gaussian process test for high-throughput sequencing time series: application to experimental evolution. Preprint at http://arXiv.org/1403.4086.
42. Turner TL, Miller PM (2012). Investigating natural variation in Drosophila courtship song by the evolve and resequence approach. Genetics 191: 633-642.
43. Turner TL, Miller PM, Cochrane VA (2013). Combining genome-wide methods to investigate the genetic complexity of courtship song variation in Drosophila melanogaster. Mol Biol Evol 30: 2113-2120.
44. Turner TL, Stewart AD, Fields AT, Rice WR, Tarone AM (2011). Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster. PLoS Genet 7: e1001336.
45. Versace E, Nolte V, Pandey RV, Tobler R, Schlötterer C (2014). Experimental evolution reveals habitat-specific fitness dynamics among Wolbachia clades in Drosophila melanogaster. Mol Ecol 23: 802-814.
46. Weber KE (1996). Large genetic change at small fitness cost in large populations of Drosophila melanogaster selected for wind tunnel flight: rethinking fitness surfaces. Genetics 144: 205-213.
47. Yampolsky LY, Glazko GV, Fry JD (2012). Evolution of gene expression and expression plasticity in long-term experimental populations of Drosophila melanogaster maintained under constant and variable ethanol stress. Mol Ecol 21: 4287-4299.
48. Zhou D, Udpa N, Gersten M, Visk DW, Bashir A, Xue J et al. (2011). Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc Natl Acad Sci USA 108: 2349-2354.