Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity

Nature Genetics

Volumn 44, Issue 3, 2012, Pages 285-290

  Andersen, Erik C ^a   Gerke, Justin P ^a,c   Shapiro, Joshua A ^a   Crissman, Jonathan R ^a,b   Ghosh, Rajarshi ^a   Bloom, Joshua S ^a   Félix, Marie Anne ^a   Kruglyak, Leonid ^a,b  

^a PRINCETON UNIVERSITY   (United States)

^b A DuPont Business   (United States)

^c ECOLE NORMALE SUPÉRIEURE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; CYTOLOGY; DEVELOPMENTAL BIOLOGY; GENETIC STRAIN; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; MOLECULAR BIOLOGY; NONHUMAN; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CAENORHABDITIS ELEGANS; CHROMOSOMES; CLUSTER ANALYSIS; DEMOGRAPHY; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; GENOME; HAPLOTYPES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC;

CAENORHABDITIS ELEGANS;

EID: 84857551173     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.1050     Document Type: Article

References (44)

1. Félix, M.A. & Braendle, C. The natural history of Caenorhabditis elegans. Curr. Biol. 20, R965-R969 (2010).
2. Riddle, D.L., Blumenthal, T., Meyer, B.J. & Priess, J.R. C. Elegans II, xvii, 1222 (Cold Spring Harbor Laboratory Press, Plainview, New York, USA, 1997).
3. Barrière, A. & Felix, M.A. High local genetic diversity and low outcrossing rate in Caenorhabditis elegans natural populations. Curr. Biol. 15, 1176-1184 (2005). (Pubitemid 40950514)
4. Barrière, A. & Felix, M.A. Temporal dynamics and linkage disequilibrium in natural Caenorhabditis elegans populations. Genetics 176, 999-1011 (2007). (Pubitemid 46961102)
5. Cutter, A.D. & Payseur, B.A. Selection at linked sites in the partial selfer Caenorhabditis elegans. Mol. Biol. Evol. 20, 665-673 (2003). (Pubitemid 36539002)
6. Cutter, A.D. Nucleotide polymorphism and linkage disequilibrium in wild populations of the partial selfer Caenorhabditis elegans. Genetics 172, 171-184 (2006). (Pubitemid 43345481)
7. Cutter, A.D., Baird, S.E. & Charlesworth, D. High nucleotide polymorphism and rapid decay of linkage disequilibrium in wild populations of Caenorhabditis remanei. Genetics 174, 901-913 (2006). (Pubitemid 44656477)
8. Cutter, A.D., Felix, M.A., Barriere, A. & Charlesworth, D. Patterns of nucleotide polymorphism distinguish temperate and tropical wild isolates of Caenorhabditis briggsae. Genetics 173, 2021-2031 (2006). (Pubitemid 44285680)
9. Denver, D.R., Morris, K. & Thomas, W.K. Phylogenetics in Caenorhabditis elegans: an analysis of divergence and outcrossing. Mol. Biol. Evol. 20, 393-400 (2003). (Pubitemid 36427174)
10. Dolgin, E.S., Felix, M.A. & Cutter, A.D. Hakuna nematoda: genetic and phenotypic diversity in African isolates of Caenorhabditis elegans and C. briggsae. Heredity 100, 304-315 (2008). (Pubitemid 351282131)
11. Graustein, A., Gaspar, J.M., Walters, J.R. & Palopoli, M.F. Levels of DNA polymorphism vary with mating system in the nematode genus Caenorhabditis. Genetics 161, 99-107 (2002). (Pubitemid 34564039)
12. Haber, M. et al. Evolutionary history of Caenorhabditis elegans inferred from microsatellites: evidence for spatial and temporal genetic differentiation and the occurrence of outbreeding. Mol. Biol. Evol. 22, 160-173 (2005). (Pubitemid 39628553)
13. Sivasundar, A. & Hey, J. Population genetics of Caenorhabditis elegans: the paradox of low polymorphism in a widespread species. Genetics 163, 147-157 (2003). (Pubitemid 36222660)
14. Sivasundar, A. & Hey, J. Sampling from natural populations with RNAi reveals high outcrossing and population structure in Caenorhabditis elegans. Curr. Biol. 15, 1598-1602 (2005). (Pubitemid 41219601)
15. Rockman, M.V., Skrovanek, S.S. & Kruglyak, L. Selection at linked sites shapes heritable phenotypic variation in C. elegans. Science 330, 372-376 (2010).
16. Swan, K.A. et al. High-throughput gene mapping in Caenorhabditis elegans. Genome Res. 12, 1100-1105 (2002). (Pubitemid 34785203)
17. Rockman, M.V. & Kruglyak, L. Recombinational landscape and population genomics of Caenorhabditis elegans. PLoS Genet. 5, e1000419 (2009).
18. Baird, N.A. et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3, e3376 (2008).
19. McGrath, P.T. et al. Quantitative mapping of a digenic behavioral trait implicates globin variation in C. elegans sensory behaviors. Neuron 61, 692-699 (2009).
20. Hudson, R.R. Two-locus sampling distributions and their application. Genetics 159, 1805-1817 (2001). (Pubitemid 34087616)
21. Falush, D., Stephens, M. & Pritchard, J.K. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164, 1567-1587 (2003). (Pubitemid 37102217)
22. Pritchard, J.K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945-959 (2000). (Pubitemid 30397141)
23. Cully, D.F. et al. Cloning of an avermectin-sensitive glutamate-gated chloride channel from Caenorhabditis elegans. Nature 371, 707-711 (1994). (Pubitemid 24327331)
24. Koch, R., van Luenen, H.G., van der Horst, M., Thijssen, K.L. & Plasterk, R.H. Single nucleotide polymorphisms in wild isolates of Caenorhabditis elegans. Genome Res. 10, 1690-1696 (2000).
25. Hillier, L.W. et al. Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods 5, 183-188 (2008). (Pubitemid 351181748)
26. Gusev, A. et al. Whole population, genome-wide mapping of hidden relatedness. Genome Res. 19, 318-326 (2009).
27. Sabeti, P.C. et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832-837 (2002). (Pubitemid 35238568)
28. Cutter, A.D. Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Mol. Biol. Evol. 25, 778-786 (2008). (Pubitemid 351398333)
29. Phillips, P.C. One perfect worm. Trends Genet. 22, 405-407 (2006). (Pubitemid 44093765)
30. Khan, A., Taylor, S., Ajioka, J.W., Rosenthal, B.M. & Sibley, L.D. Selection at a single locus leads to widespread expansion of Toxoplasma gondii lineages that are virulent in mice. PLoS Genet. 5, e1000404 (2009).
31. Brenner, S. The genetics of Caenorhabditis elegans. Genetics 77, 71-94 (1974).
32. Kiontke, K. et al. Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Proc. Natl. Acad. Sci. USA 101, 9003-9008 (2004). (Pubitemid 38781600)
33. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
34. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
35. Roberts, A. et al. Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. Bioinformatics 23, i401-i407 (2007). (Pubitemid 47244426)
36. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007). (Pubitemid 47330214)
37. Patterson, N. et al. Methods for high-density admixture mapping of disease genes. Am. J. Hum. Genet. 74, 979-1000 (2004). (Pubitemid 38578397)
38. Kang, H.M. et al. Efficient control of population structure in model organism association mapping. Genetics 178, 1709-1723 (2008).
39. Reddy, K.C., Andersen, E.C., Kruglyak, L. & Kim, D.H. A polymorphism in npr-1 is a behavioral determinant of pathogen susceptibility in C. elegans. Science 323, 382-384 (2009).
40. Tan, M.W., Mahajan-Miklos, S. & Ausubel, F.M. Killing of Caenorhabditis elegans by Pseudomonas aeruginosa used to model mammalian bacterial pathogenesis. Proc. Natl. Acad. Sci. USA 96, 715-720 (1999). (Pubitemid 29061274)
41. Achaz, G. Frequency spectrum neutrality tests: one for all and all for one. Genetics 183, 249-258 (2009).
42. Achaz, G. Testing for neutrality in samples with sequencing errors. Genetics 179, 1409-1424 (2008).
43. Ewing, G. & Hermisson, J. MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics 26, 2064-2065 (2010).
44. Denver, D.R., Morris, K., Lynch, M. & Thomas, W.K. High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature 430, 679-682 (2004). (Pubitemid 39061683)