Stacks: An analysis tool set for population genomics

Molecular Ecology

Volumn 22, Issue 11, 2013, Pages 3124-3140

  Catchen, Julian ^a   Hohenlohe, Paul A ^a,b   Bassham, Susan ^a   Amores, Angel ^a   Cresko, William A ^a  

^a UNIVERSITY OF OREGON   (United States)

^b UNIVERSITY OF IDAHO   (United States)

Author keywords

GBS; genetics; next generation sequencing; population genomics; RAD seq

Indexed keywords

ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC MARKER; GENOTYPE; HIGH THROUGHPUT SEQUENCING; INFORMATION PROCESSING; METAGENOMICS; METHODOLOGY; NUCLEIC ACID DATABASE; SINGLE NUCLEOTIDE POLYMORPHISM;

AUTOMATIC DATA PROCESSING; DATABASES, NUCLEIC ACID; GENETIC MARKERS; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SOFTWARE;

HARNESS;

EID: 84878461613     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12354     Document Type: Article

References (98)

1. Amish SJ, Hohenlohe PA, Painter S, et al,. (2012) RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays. Molecular Ecology Resources, 12, 653-660.
2. Andersen EC, Gerke JP, Shapiro JA, et al,. (2012) Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity. Nature Genetics, 44, 285-290.
3. Anderson JL, Rodriguez Mari A, Braasch I, et al,. (2012) Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics. PLoS ONE, 7, e40701.
4. Andrew RL, Kane NC, Baute GJ, Grassa CJ, Rieseberg LH, (2013) Recent nonhybrid origin of sunflower ecotypes in a novel habitat. Molecular Ecology, 22, 799-813.
5. Baird NA, Etter PD, Atwood TS, et al,. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE, 3, e3376.
6. Balding DJ, (2006) A tutorial on statistical methods for population association studies. Nature Reviews Genetics, 7, 781-791.
7. Barchi L, Lanteri S, Portis E, et al,. (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics, 12, 304.
8. Barchi L, Lanteri S, Portis E, et al,. (2012) A RAD tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation. PLoS ONE, 7, e43740.
9. Baxter SW, Davey JW, Johnston JS, et al,. (2011) Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS ONE, 6, e19315.
10. Beaumont MA, Balding DJ, (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13, 969-980.
11. Bell MA, Foster SA, (1994) The Evolutionary Biology of the Threespine Stickleback. Oxford University Press, Oxford, 571.
12. Boitard S, Kofler R, Françoise P, Robelin D, Schlötterer C, Futschik A, (2013) Pool-hmm: a python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples. Molecular Ecology Resources, 13, 337-340. doi: 10.1111/1755-0998.12063.
13. Bonin A, (2008) Population genomics: a new generation of genome scans to bridge the gap with functional genomics. Molecular Ecology, 17, 3583-3584.
14. Bruneaux M, Johnston SE, Herczeg G, Merila J, Primmer CR, Vasemagi A, (2013) Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach. Molecular Ecology, 22, 565-582.
15. Buerkle AC, Gompert Z, (2012) Population genomics based on low coverage sequencing: how low should we go? Molecular Ecology. doi: 10.1111/mec.12105.
16. Bus A, Hecht J, Huettel B, Reinhardt R, Stich B, (2012) High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing. BMC Genomics, 13, 281.
17. Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH, (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1, 171-182.
18. Catchen J, Bassham S, Wilson T, et al,. (2013) The population structure and recent colonization history of Oregon threespine stickleback determined using RAD-seq. Molecular Ecology, 22, 2864-2883.
19. Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, et al,. (2011) Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics, 12, 4.
20. Cresko W, McGuigan K, Phillips P, Postlethwait J, (2007) Studies of threespine stickleback developmental evolution: progress and promise. Genetica, 129, 105-126.
21. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML, (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12, 499-510.
22. Davey JW, Cezard T, Fuentes-Utrilla P, Eland C, Gharbi K, Blaxter ML, (2012) Special features of RAD sequencing data: implications for genotyping. Molecular Ecology. doi: 10.1111/mec.12084.
23. Elshire RJ, Glaubitz JC, Sun Q, et al,. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6, e19379.
24. Emerson KJ, Merz CR, Catchen JM, et al,. (2010) Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Sciences, 107, 16196-16200.
25. Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA, (2011a) Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS ONE, 6, e18561.
26. Etter PD, Bassham S, Hohenlohe PA, Johnson EA, Cresko WA, (2011b) SNP discovery and genotyping for evolutionary genetics using RAD sequencing. Methods in Molecular Biology, 772, 157-178.
27. Everett MV, Miller MR, Seeb JE, (2012) Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing. BMC Genomics, 13, 521.
28. Excoffier L, Lischer HEL, (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
29. Falush D, Stephens M, Pritchard JK, (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
30. Falush D, Stephens M, Pritchard JK, (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes, 7, 574-578.
31. Foll M, Gaggiotti O, (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics, 180, 977-993.
32. Futschik A, Schlötterer C, (2010) The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics, 186, 207-218. doi: 10.1534/genetics.110.114397.
33. Gaggiotti OE, Bekkevold D, Jørgensen HBH, et al,. (2009) Disentangling the effects of evolutionary, demographic, and environmental factors influencing genetic structure of natural populations: Atlantic herring as a case study. Evolution, 63, 2939-2951.
34. Gautier M, Gharbi K, Cezard T, et al,. (2013) The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Molecular Ecology, 22, 3165-3178.
35. Glenn TC, (2011) Field guide to next-generation DNA sequencers. Molecular Ecology Resources, 11, 759-769.
36. Gompert Z, Forister ML, Fordyce JA, Nice CC, Williamson RJ, Buerkle CA, (2010) Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies. Molecular Ecology, 19, 2455-2473.
37. Gompert Z, Lucas LK, Nice CC, Fordyce JA, Forister ML, Buerkle CA, (2012) Genomic regions with a history of divergent selection affect fitness of hybrids between two butterfly species. Evolution; International Journal of Organic Evolution, 66, 2167-2181. doi: 10.1111/j.1558-5646.2012.01587.x.
38. Goudet J, (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. Journal of heredity, 86, 485-486.
39. Hecht BC, Thrower FP, Hale MC, Miller MR, Nichols KM, (2012) Genetic architecture of migration-related traits in rainbow and steelhead trout. Oncorhynchus mykiss, G3 (Bethesda), 2, 1113-1127.
40. Hecht BC, Campbell NR, Holecek DE, Narum SR, (2013) Genome-wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout. Molecular Ecology, 22, 3061-3076.
41. Hohenlohe PA, Phillips PC, Cresko WA, (2010a) Using population genomics to detect selection in natural populations: key concepts and methodological considerations. International Journal of Plant Sciences, 171, 1059-1071.
42. Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA, (2010b) Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genetics, 6, e1000862.
43. Hohenlohe PA, Amish SJ, Catchen JM, Allendorf FW, Luikart G, (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources, 11 (Suppl 1), 117-122.
44. Hohenlohe PA, Catchen J, Cresko WA, (2012a) Population genomic analysis of model and nonmodel organisms using sequenced RAD tags. Methods in Molecular Biology, 888, 235-260.
45. Hohenlohe PA, Bassham S, Currey M, Cresko WA, (2012b) Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes. Philosophical Transactions of the Royal Society of London. Series B, Biological sciences, 367, 395-408.
46. Houston RD, Davey JW, Bishop SC, et al,. (2012) Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon. BMC Genomics, 13, 244.
47. Hubisz M, Falush D, Stephens M, Pritchard JK, (2009) Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources, 9, 1322-1332.
48. Keller I, Wagner CE, Greuter L, et al,. (2013) Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes. Molecular Ecology, 22, 2848-2863.
49. King EG, Macdonald SJ, Long AD, (2012) Properties and power of the Drosophila synthetic population resource for the routine dissection of complex traits. Genetics, 191, 935-949.
50. Kofler R, Orozco-terWengel P, De Maio N, et al,. (2011a) PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS ONE, 6, e15925. doi: 10.1371/journal.pone.0015925.
51. Kofler R, Pandey RV, Schlötterer C, (2011b) PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics (Oxford, England), 27, 3435-3436. doi: 10.1093/bioinformatics/btr589.
52. Kofler R, Betancourt AJ, Schlötterer C, (2012) Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in drosophila melanogaster. PLoS Genetics, 8, e1002487. doi: 10.1371/journal.pgen.1002487.
53. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, R25.
54. Lemmon AR, Lemmon EM, (2012) High-throughput identification of informative nuclear loci for shallow-scale phylogenetics and phylogeography. Systematic Biology, 61, 745-761.
55. Lewontin RC, Krakauer J, (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics, 74, 175-195.
56. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
57. Li H, Handsaker B, Wysoker A, et al,., 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics (Oxford, England), 25, 2078-2079. doi: 10.1093/bioinformatics/ btp352.
58. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
59. Luikart G, England P, Tallmon D, Jordan S, Taberlet P, (2003) The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics, 4, 981-994.
60. Luo L, Boerwinkle E, Xiong M, (2011) Association studies for next-generation sequencing. Genome Research, 21, 1099-1108. doi: 10.1101/gr.115998.110
61. Lynch M, (2009) Estimation of allele frequencies from high-coverage genome-sequencing projects. Genetics, 182, 295-301.
62. Mardis ER, (2008) The impact of next-generation sequencing technology on genetics. Trends in Genetics, 24, 133-141.
63. Maynard Smith J, Haigh J, (1974) The hitch-hiking effect of a favourable gene. Genetical Research, 23, 23-35.
64. McCormack JE, Maley JM, Hird SM, Derryberry EP, Graves GR, Brumfield RT, (2012) Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. Molecular Phylogenetics and Evolution, 62, 397-406.
65. McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT, (2013) Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution, 66, 526-538.
66. McKenna A, Hanna M, Banks E, et al,. (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297-1303.
67. Merz C, Catchen JM, Hanson-Smith V, Emerson KJ, Bradshaw W, Holzapfel C, (2013) Independent replication of phylogeographies: how repeatable are they? Molecular Ecology, in press.
68. Miller MR, Brunelli JP, Wheeler PA, et al,. (2012) A conserved haplotype controls parallel adaptation in geographically distant salmonid populations. Molecular Ecology, 21, 237-249.
69. Mitchell-Olds T, Feder M, Wray G, (2008) Evolutionary and ecological functional genomics. Heredity, 100, 101-102.
70. Nadeau NJ, Martin SH, Kozak KM, et al,. (2013) Genome-wide patterns of divergence and gene flow across a butterfly radiation. Molecular Ecology, 22, 814-826.
71. Nice CC, Gompert Z, Fordyce JA, Forister ML, Lucas LK, Buerkle CA, (2013) Hybrid speciation and independent evolution in lineages of alpine butterflies. Evolution; International Journal of Organic Evolution, 67, 1055-1068. doi: 10.1111/evo.12019.
72. Nielsen R, (2005) Molecular signatures of natural selection. Annual Review of Genetics, 39, 197-218. doi: 10.1146/annurev.genet.39.073003.112420.
73. Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG, (2007) Recent and ongoing selection in the human genome. Nature Reviews Genetics, 8, 857-868. doi: 10.1038/nrg2187.
74. Nosil P, Gompert Z, Farkas TE, et al,. (2012) Genomic consequences of multiple speciation processes in a stick insect. Proceedings of the Royal Society. B, Biological Sciences, 279, 5058-5065. doi: 10.1098/rspb.2012.0813.
75. Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA, (2012) Genome-wide association genetics of an adaptive trait in lodgepole pine. Molecular Ecology, 21, 2991-3005. doi: 10.1111/j.1365-294X.2012.05513.x.
76. Parchman TL, Gompert Z, Braun MJ, et al,. (2013) The genomic consequences of adaptive divergence and reproductive isolation between species of manakins. Molecular Ecology. doi: 10.1111/mec.12201.
77. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE, (2012) Double digest radseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE, 7, e37135.
78. Pfender WF, Saha MC, Johnson EA, Slabaugh MB, (2011) Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. TAG. Theoretical and Applied Genetics, 122, 1467-1480.
79. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
80. Rosenberg NA, Huang L, Jewett EM, Szpiech ZA, Jankovic I, Boehnke M, (2010) Genome-wide association studies in diverse populations. Nature Reviews Genetics, 11, 356-366.
81. Rousset F, (2008) Genepop'07: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources, 8, 103-106.
82. Rowe HC, Renaut S, Guggisberg A, (2011) RAD in the realm of next-generation sequencing technologies. Molecular Ecology, 20, 3499-3502.
83. Rubin BE, Ree RH, Moreau CS, (2012) Inferring phylogenies from RAD sequence data. PLoS ONE, 7, e33394.
84. Scaglione D, Acquadro A, Portis E, Tirone M, Knapp SJ, Lanteri S, (2012) RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. BMC Genomics, 13, 3.
85. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nature Biotechnology, 26, 1135-1145.
86. Stapley J, Reger J, Feulner PG, et al,. (2010) Adaptation genomics: the next generation. Trends in Ecology & Evolution, 25, 705-712.
87. Stolting KN, Nipper R, Lindtke D, et al,. (2013) Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species. Molecular Ecology, 22, 842-855.
88. Storz JF, (2005) Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology, 14, 671-688.
89. Strasburg JL, Sherman NA, Wright KM, Moyle LC, Willis JH, Rieseberg LH, (2012) What can patterns of differentiation across plant genomes tell us about adaptation and speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 367, 364-373.
90. Van Orsouw NJ, Hogers RCJ, Janssen A, et al,. (2007) Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS ONE, 2, e1172.
91. Wagner CE, Keller I, Wittwer S, et al,. (2013) Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology, 22, 787-798.
92. Wang N, Fang L, Xin H, Wang L, Li S, (2012a) Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing. BMC Plant Biology, 12, 148.
93. Wang S, Meyer E, McKay JK, Matz MV, (2012b) 2b-RAD: a simple and flexible method for genome-wide genotyping. Nature Methods, 9, 808-810.
94. Wootton R, (1976) The Biology of the Sticklebacks. Academic Press, London. 387 p.
95. Wu TD, Nacu S, (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics, 26, 873-881.
96. Yang H, Tao Y, Zheng Z, Li C, Sweetingham MW, Howieson JG, (2012a) Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L. BMC Genomics, 13, 318.
97. Yang H, Tao Y, Zheng Z, et al,. (2012b) Rapid development of molecular markers by next-generation sequencing linked to a gene conferring phomopsis stem blight disease resistance for marker-assisted selection in lupin (Lupinus angustifolius L.) breeding. TAG. Theoretical and Applied Genetics, 126, 511-522.
98. Zellmer AJ, Hanes MM, Hird SM, Carstens BC, (2012) Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata. Systematic Biology, 61, 763-777.