Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits

Genetics

Volumn 199, Issue 4, 2015, Pages 991-1005

  Kessner, Darren ^a   Novembre, John ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

Artificial selection; Evolve and resequence; Forward simulation; Power analysis; Quantitative traits

Indexed keywords

ALLELE; ARTICLE; ARTIFICIAL SELECTION; DROSOPHILA MELANOGASTER; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC VARIABILITY; GENOME; HAPLOTYPE; NONHUMAN; POPULATION SIZE; POWER ANALYSIS; PRIORITY JOURNAL; QUANTITATIVE GENETICS; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS; SIMULATION; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; DROSOPHILA; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIATION; GENETICS; INSECT GENOME;

ALGORITHMS; ANIMALS; DROSOPHILA; GENETIC VARIATION; GENOME, INSECT; MODELS, GENETIC; QUANTITATIVE TRAIT LOCI; RECOMBINATION, GENETIC; SELECTION, GENETIC;

EID: 84926435494     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.175075     Document Type: Article

References (42)

1. Baldwin-Brown, J. G., A. D. Long, and K. R. Thornton, 2014 The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms. Mol. Biol. Evol. 31(4): 1040–1055
2. Burke, M. K., J. P. Dunham, P. Shahrestani, K. R. Thornton, M. R. Rose et al., 2010 Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature 467(7315): 587–590
3. Comeron, J. M., R. Ratnappan, and S. Bailin, 2012 The many landscapes of recombination in Drosophila melanogaster. PLoS Genet. 8(10): e1002905
4. Crow, J. F., 2007 Haldane, Bailey, Taylor and recombinant-inbred lines. Genetics 176: 729–732
5. Darvasi, A., and M. Soller, 1995 Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141: 1199–1207
6. Ehrenreich, I. M., N. Torabi, Y. Jia, J. Kent, S. Martis et al., 2010 Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature 464(7291): 1039–1042
7. Ewens, W. J., 2004 Mathematical Population Genetics 1: Theoretical Introduction (Interdisciplinary Applied Mathematics, Vol. 1), Ed. 2 Springer-Verlag, Berlin/Heidelberg, Germany/New York.
8. Falconer, D. S., 1992 Early selection experiments. Annu. Rev. Genet. 26: 1–14
9. Falconer, D. S., and T. F. Mackay, 1996 Introduction to Quantitative Genetics, Ed. 4 Benjamin-Cummings, Menlo Park, CA.
10. Felsenstein, J., 1974 The evolutionary advantage of recombination. Genetics 78: 737–756
11. Felsenstein, J., 1987 Sex and the evolution of recombination, pp. 74–86 in The Evolution of Sex: An Examination of Current Ideas, edited by R. E. Michod, and B. R. Levin. Sinauer Associates, Sunderland, MA.
12. Futschik, A., and C. Schlotterer, 2010 The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics 186: 207–218
13. Garland, T., and M. R. Rose (Editors), 2009 Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. University of California Press, Berkeley, California.
14. Gillespie, J. H., 1991 The Causes of Molecular Evolution (Oxford Series in Ecology and Evolution). Oxford University Press, London/New York/Oxford.
15. Grossman, S. R., I. Shlyakhter, I. Shylakhter, E. K. Karlsson, E. H. Byrne et al., 2010 A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327(5967): 883–886
16. Hill, W. G., and A. Robertson, 1966 The effect of linkage on limits to artificial selection. Genet. Res. 8(3): 269–294
17. Johansson, A. M., M. E. Pettersson, P. B. Siegel, and O. Carlborg, 2010 Genome-wide effects of long-term divergent selection. PLoS Genet. 6(11): e1001188
18. Keightley, P. D., and G. Bulfield, 1993 Detection of quantitative trait loci from frequency changes of marker alleles under selection. Genet. Res. 62(3): 195–203
19. Kessner, D., and J. Novembre, 2014 forqs: forward-in-time simulation of recombination, quantitative traits and selection. Bioinformatics 30(4): 576–577
20. Kessner, D., T. L. Turner, and J. Novembre, 2013 Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data. Mol. Biol. Evol. 30(5): 1145–1158
21. Kim, Y., and W. Stephan, 1999 Allele frequency changes in artificial selection experiments: statistical power and precision of QTL mapping. Genet. Res. 73: 177–184
22. King, E. G., C. M. Merkes, C. L. McNeil, S. R. Hoofer, S. Sen et al., 2012 Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Res. 22 (8): 1558–1566
23. Kofler, R., and C. Schlotterer, 2014 A guide for the design of evolve and resequencing studies. Mol. Biol. Evol. 31(2): 474–483
24. Laurie, C. C., S. D. Chasalow, J. R. LeDeaux, R. McCarroll, D. Bush et al., 2004 The genetic architecture of response to long-term artificial selection for oil concentration in the maize kernel. Genetics 168: 2141–2155
25. Long, Q., D. C. Jeffares, Q. Zhang, K. Ye, V. Nizhynska et al., 2011 Poolhap: inferring haplotype frequencies from pooled samples by next generation sequencing. PLoS ONE 6(1): e15292
26. Mackay, T. F., 2010 Mutations and quantitative genetic variation: lessons from Drosophila. Philos. Trans. R. Soc. Lond. B Biol. Sci. 365(1544): 1229–1239
27. Mackay, T. F. C., S. Richards, E. A. Stone, A. Barbadilla, J. F. Ayroles et al., 2012 The Drosophila melanogaster Genetic Reference Panel. Nature 482(7384): 173–178
28. Magwire, M. M., D. K. Fabian, H. Schweyen, C. Cao, B. Longdon et al., 2012 Genome-wide association studies reveal a simple genetic basis of resistance to naturally coevolving viruses in Drosophila melanogaster. PLoS Genet. 8(11): e1003057
29. Nuzhdin, S. V., L. G. Harshman, M. Zhou, and K. Harmon, 2007 Genome-enabled hitchhiking mapping identifies QTLs 1004 D. for stress resistance in natural Drosophila. Heredity 99(3): 313–321
30. Orozco-terWengel, P., M. Kapun, V. Nolte, R. Kofler, T. Flatt et al., 2012 Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol. Ecol. 21(20): 4931–4941
31. Orr, H. A., 1998 The population genetics of adaptation: the distribution of factors fixed during adaptive evolution. Evolution 52(4): 935–949
32. Otto, S. P., and C. D. Jones, 2000 Detecting the undetected: estimating the total number of loci underlying a quantitative trait. Genetics 156: 2093–2107
33. Parts, L., F. A. Cubillos, J. Warringer, K. Jain, F. Salinas et al., 2011 Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res. 21(7): 1131–1138
34. Remolina, S. C., P. L. Chang, J. Leips, S. V. Nuzhdin, and K. A. Hughes, 2012 Genomic basis of aging and life-history evolution in Drosophila melanogaster. Evolution 66(11): 3390–3403
35. Rice, S. H., 2004 Evolutionary Theory. Sinauer Associates, Sunderland, MA.
36. Teotonio, H., and I. M. Chelo, M. Bradić, M. R. Rose, and A. D. Long, 2009 Experimental evolution reveals natural selection on standing genetic variation. Nat. Genet. 41(2): 251–257
37. Thornton, K. R., A. J. Foran, and A. D. Long, 2013 Properties and modeling of GWAS when complex disease risk is due to noncomplementing, deleterious mutations in genes of large effect. PLoS Genet. 9(2): e1003258
38. Turner, T. L., and P. M. Miller, 2012 Investigating natural variation in Drosophila courtship song by the evolve and resequence approach. Genetics 191: 633–642
39. Turner, T. L., A. D. Stewart, A. T. Fields, W. R. Rice, and A. M. Tarone, 2011 Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster. PLoS Genet. 7(3): e1001336
40. Utsunomiya, Y. T., A. M. Perez O’Brien, T. S. Sonstegard, C. P. Van Tassell, A. S. do Carmo et al., 2013 Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods. PLoS ONE 8(5): e64280.
41. Mackay, T. F. and Lyman, R. F. (2005). Drosophila bristles and the nature of quantitative genetic variation. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 360(1459), 1513-1527.
42. Marriage, T. N., King, E. G., Long, A. D., and Macdonald, S. J. (2014). Fine-mapping nicotine resistance loci in Drosophila using a multiparent advanced generation inter-cross population. Genetics, 198(1), 45-57.