A composite-likelihood method for detecting incomplete selective sweep from population genomic data

Genetics

Volumn 200, Issue 2, 2015, Pages 633-649

  Vy, Ha My T ^a   Kim, Yuseob ^a  

^a Ewha Womans University   (South Korea)

Author keywords

Composite likelihood; Polymorphism; Positive selection; Selective sweep

Indexed keywords

ACCURACY; ANIMAL EXPERIMENT; ARTICLE; COMPOSITE LIKELIHOOD RATIO; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE SEQUENCE; GENE STRUCTURE; GENETIC RECOMBINATION; GENETIC SCREENING; GENETIC VARIABILITY; GENOMICS; HAPLOTYPE; INSECT GENOME; NEXT GENERATION SEQUENCING; NONHUMAN; POINT MUTATION; POPULATION GENETICS; POPULATION SIZE; PRIORITY JOURNAL; PROBABILITY; REPRODUCTION; SELECTIVE SWEEP; SEQUENCE ALIGNMENT; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; COMPUTER SIMULATION; EVOLUTION; GENE LOCUS; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETICS; HOMOZYGOTE; PROCEDURES; STATISTICAL MODEL;

DROSOPHILA MELANOGASTER;

ALGORITHMS; ANIMALS; BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; DROSOPHILA MELANOGASTER; GENETIC LOCI; GENETICS, POPULATION; GENOMICS; HAPLOTYPES; HOMOZYGOTE; LIKELIHOOD FUNCTIONS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, GENETIC; SELECTION, GENETIC;

EID: 84931312654     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.175380     Document Type: Article

References (34)

1. Akey, J. M., 2009 Constructing genomic maps of positive selection in humans: Where do we go from here? Genome Res. 19: 711– 722.
2. Barton, N. H., 1998 The effect of hitch-hiking on neutral genealogies. Genet. Res. 72: 123–133.
3. Biswas, S., and J. M. Akey, 2006 Genomic insights into positive selection. Trends Genet. 22: 437–446.
4. Chan, A. H., P. A. Jenkins, and Y. S. Song, 2012 Genome-wide fine-scale recombination variation in Drosophila melanogaster. PLoS Genet. 8: e1003090.
5. Comeron, J. M., R. Ratnappan, and S. Bailin, 2012 The many landscapes of recombination in Drosophila melanogaster. PLoS Genet. 8: e1002905.
6. Etheridge, A., P. Pfaffelhuber, and A. Wakolbinger, 2006 An approximate sampling formula under genetic hitchhiking. Ann. Appl. Probab. 16: 685–729.
7. Ewing, G., and J. Hermisson, 2010 MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics 26: 2064–2065.
8. Fay, J. C., and C. I. Wu, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405–1413.
9. Ferrer-Admetlla, A., M. Liang, T. Korneliussen, and R. Nielsen, 2014 On detecting incomplete soft or hard selective sweeps using haplotype structure. Mol. Biol. Evol. 31: 1275–1291.
10. Fu, Y.-X., and W.-H. Li, 1993 Statistical tests of neutrality of mu tations. Genetics 133: 693–709.
11. Gautier, M., and R. Vitalis, 2012. rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics 28: 1176–1177.
12. Hill, W. G., and A. Robertson, 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38: 473–485.
13. Hudson, R. R., K. Bailey, D. Skarecky, J. Kwiatowski, and F. J. Ayala, 1994 Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136: 1329–1340.
14. Innan, H., and Y. Kim, 2008 Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populations. Genetics 179: 1713–1720.
15. Kaplan, N. L., R. R. Hudson, and C. H. Langley, 1989 The “hitchhiking effect” revisited. Genetics 123: 887–899.
16. Kim, Y., and R. Nielsen, 2004 Linkage disequilibrium as a signature of selective sweeps. Genetics 167: 1513–1524.
17. Kim, Y., and W. Stephan, 2002 Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765–777.
18. Maynard Smith, J., and J. Haigh, 1974 The hitch-hiking effect of a favorable gene. Genet. Res. 23: 23–35.
19. Meiklejohn, C. D., Y. Kim, D. L. Hartl, and J. Parsch, 2004 Identification of a locus under complex positive selection in Drosophila simulans by haplotype mapping and compositelikelihood estimation. Genetics 168: 265–279.
20. Nielsen, R., 2005 Molecular signatures of natural selection. Annu. Rev. Genet. 39: 197–218.
21. Nielsen, R., S. Williamson, Y. Kim, M. J. Hubisz, A. G. Clark et al., 2005 Genomic scans for selective sweeps using SNP data. Genome Res. 15: 1566.
22. Pool, J. E., R. B. Corbett-Detig, R. P. Sugino, K. A. Stevens, C. M. Cardeno et al., 2012 Population genomics of sub-Saharan Drosophila melanogaster: African diversity and non-African admixture. PLoS Genet. 8: e1003080.
23. Przeworski, M., 2002 The signature of positive selection at randomly chosen loci. Genetics 160: 1179–1189.
24. Quesada, H., U. E. Ramírez, J. Rozas, and M. Aguadé, 2003 Largescale adaptive hitchhiking upon high recombination in Drosophila simulans. Genetics 165: 895–900.
25. Sabeti, P. C., D. E. Reich, J. M. Higgins, H. Z. Levine, D. J. Richter et al., 2002 Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832–837.
26. Sabeti, P. C., S. F. Schaffner, B. Fry, J. Lohmueller, P. Varilly et al., 2006 Positive natural selection in the human lineage. Science 312: 1614–1620.
27. Saunders, M. A., J. M. Good, E. C. Lawrence, R. E. Ferrell, W.-H. Li et al., 2006 Human adaptive evolution at myostatin (GDF8), a regulator of muscle growth. Am. J. Hum. Genet. 79: 1089–1097.
28. Sellis, D., B. J. Callahan, D. A. Petrov, and P. W. Messer, 2011 Heterozygote advantage as a natural consequence of adaptation in diploids. Proc. Natl. Acad. Sci. USA 108: 20666–20671.
29. Stephan, W., 2010 Detecting strong positive selection in the genome. Mol. Ecol. Res. 10: 863–872.
30. Stephan, W., T. H. E. Wiehe, and M. W. Lenz, 1992 The effect of strongly selected substitutions on neutral polymorphism: analytic results based on diffusion theory. Theor. Popul. Biol. 41: 237–254.
31. Stephan, W., Y. S. Yun, and C. H. Langley, 2006 The hitchhiking effect on linkage disequilibrium between linked neutral loci. Genetics 172: 2647–2663.
32. Tajima, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.
33. Toomajian, C., R. S. Ajioka, L. B. Jorde, J. P. Kushner, and M. Kreitman, 2003 A method for detecting recent selection in the human genome from allele age estimates. Genetics 165: 287–297.
34. Voight, B. F., S. Kudaravalli, X. Wen, and J. K. Pritchard, 2006 A map of recent positive selection in the human genome. PLoS Biol. 4: e72.