Detecting selective sweeps from pooled next-generation sequencing samples

Molecular Biology and Evolution

Volumn 29, Issue 9, 2012, Pages 2177-2186

  Boitard, Simon ^a   Schlötterer, Christian ^b   Nolte, Viola ^b   Pandey, Ram Vinay ^b   Futschik, Andreas ^c  

^a CEMAGREF   (France)

^b Institute für Populationsgenetik   (Austria)

^c UNIVERSITY OF VIENNA   (Austria)

Author keywords

allele frequency spectrum; Drosophila; hidden Markov model; next generation sequencing; pooled DNA; selective sweeps

Indexed keywords

ARTICLE; CHROMOSOME ANALYSIS; COMPUTER SIMULATION; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE FREQUENCY; GENE POOL; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; SAMPLING; SELECTIVE SWEEP; STATISTICAL ANALYSIS; X CHROMOSOME;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; DROSOPHILA MELANOGASTER; FEMALE; GENE FREQUENCY; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MODELS, GENETIC; MODELS, STATISTICAL; REPRODUCIBILITY OF RESULTS; X CHROMOSOME;

DROSOPHILA MELANOGASTER;

EID: 84864841125     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss090     Document Type: Article

References (30)

1. Achaz G. 2009. Testing for neutrality in samples with sequencing errors. Genetics 179:1409-1424.
2. Andolfatto P, Davison D, Erezyilmaz D, Hu T, Mast J, Sunayama-Morita T, Stern D. 2011. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res. 21:610-617.
3. Bansal V. 2010. A statistical method for the detection of variants from next-generation resequencing of DNA pools. Bioinformatics 26:i318-i324.
4. Beisswanger S, Stephan W, De Lorenzo D. 2006. Evidence for a selective sweep in the wapl region of Drosophila melanogaster. Genetics 172:265-274. (Pubitemid 43345489)
5. Boitard S, Schlötterer C, Futschik A. 2009. Detecting selective sweeps: a new approach based on hidden Markov models. Genetics 181:1567-1578.
6. Cirelli C, Bushey D, Hill S, Huber R, Kreber R, Ganetzky B, Tononi G. 2005. Reduced sleep in Drosophila shaker mutants. Nature 434:1087-1092. (Pubitemid 40663480)
7. DePristo M, Banks E, Poplin R, et al. (18 co-authors). 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 43(5):491-498.
8. Dohm J, Lottaz C, Borodina T, Himmelbauer H. 2008. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36:e105.
9. Druley T, Vallania F, Wegner D, et al. (12 co-authors). 2009. Quantification of rare allelic variants from pooled genomic DNA. Nat Methods. 6:263-265.
10. Elshire R, Glaubitz J, Sun Q, Poland J, Kawamoto K, Buckler E, Mitchell S. 2011. A robust, simple genotyping-by-sequencing (gbs) approach for high diversity species. PLoS One 6(5): e19379.
11. Ewing G, Hermisson J. 2010. MSMS: a coalescent simulation program including recombination, demographic structure, and selection at a single locus. Bioinformatics 26(16):2064-2065.
12. Fiston-Lavier A, Singh N, Lipatov M, Petrov D. 2010. Drosophila melanogaster recombination rate calculator. Gene 463:18-20.
13. Futschik A, Schlötterer C. 2010. The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics 186:207-218.
14. Glinka S, De Lorenzo D, Stephan W. 2006. Evidence of gene conversion associated with a selective sweep in Drosophila melanogaster. Mol Biol Evol. 23(10):1869-1878. (Pubitemid 44412873)
15. Gompert Z, Buerkle C. 2011. A hierarchical Bayesian model for nextgeneration population genomics. Genetics 187:903-917.
16. Gompert Z, Lucas L, Nice C, Fordyce J, Forister M, Buerkle C. 2012. Genomic regions with a history of divergent selection affect fitness of hybrids between two butterfly species. Evolution doi:10.1111/j.1558-5646.2012.01587.x.
17. Haddrill P, Thornton K, Charlesworth B, Andolfatto P. 2005. Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophilia melanogaster populations. Genome Res. 15:790-799. (Pubitemid 41003102)
18. Hohenlohe P, Bassham S, Etter P, Stiffler N, Johnson E, Cresko N. 2010. Population genomics of parallel adaptation in threespine stickleback using sequenced rad tags. PLoS Genet. 6(2):e1000862.
19. Jensen J, Kim Y, Bauer DuMont V, Aquadro C, Bustamante C. 2005. Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170:1401-1410. (Pubitemid 41105491)
20. Jiang R, Tavaré S, Marjoram P. 2009. Population genetic inference from resequencing data. Genetics 181:187-197.
21. Kim Y, Stephan W. 2002. Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160:765-777. (Pubitemid 34194545)
22. Lee J, Choi M, Yan X, Lifton R, Zhao H. 2011. On optimal pooling designs to identify rare variants through massive resequencing. Genet Epidemiol. 35:139-147.
23. Li H. 2011. A statistical framework for snp calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27(21):2987-2993.
24. Li H, Durbin R. 2009. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 25:1754-1760.
25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. Subgroup GPDP. 2009. The sequence alignment/map (sam) format and samtools. Bioinformatics 25:2078-2079.
26. Li H, Stephan W. 2006. Inferring the demographic history and rate of adaptative substitution in drosophilia. PLoS Genet. 2(10):e166.
27. Nielsen R, Williamson L, Kim Y, Hubisz M, Clark A, Bustamante C. 2005. Genomic scans for selective sweeps using SNP data. Genome Res. 15:1566-1575. (Pubitemid 41545010)
28. Rubin C-J, Zody M, Eriksson J, et al. (19 co-authors). 2010. Wholegenome resequencing reveals loci under selection during chicken domestication. Nature 464:587-591.
29. Wei Z, Wang W, Hu P, Lyon G, Hakonarson H. 2011. Snver: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nuclear Acids Res. 39(19):e132.
30. Williamson S, Hubisz M, Clark A, Payseur B, Bustamante C, Nielsen R. 2007. Localizing recent adaptive evolution in the human genome. PLoS Genet. 3(6):e90.