Population Genomics of Inversion Polymorphisms in Drosophila melanogaster

PLoS Genetics

Volumn 8, Issue 12, 2012, Pages

  Corbett Detig, Russell B ^a   Hartl, Daniel L ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANIMAL EXPERIMENT; ARTICLE; CHROMOSOME BREAKAGE; CHROMOSOME INVERSION; CHROMOSOME POLYMORPHISM; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; FEMALE; GENE INTERACTION; GENE SEGREGATION; GENE SEQUENCE; HAPLOTYPE; INSECT CHROMOSOME; INSECT GENOME; MALE; NONHUMAN; PARASITE TRANSMISSION; POPULATION GENETIC STRUCTURE; QUALITATIVE ANALYSIS; SEGREGATION ANALYSIS; SEGREGATION DISTORTION; SEQUENCE ANALYSIS; SEX RATIO;

ANIMALS; BASE SEQUENCE; BIOLOGICAL EVOLUTION; CHROMOSOME INVERSION; DROSOPHILA MELANOGASTER; FEMALE; HAPLOTYPES; LINKAGE DISEQUILIBRIUM; MALE; METAGENOMICS; POLYMORPHISM, GENETIC; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA;

DROSOPHILA MELANOGASTER;

EID: 84872022907     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003056     Document Type: Article

References (61)

1. Sturtevant AH, (1917) Genetic factors affecting the strength of linkage in Drosophila. Proc Natl Acad Sci U S A 3: 555-558.
2. Noor MAF, Grams KL, Bertucci LA, Reiland J, (2001) Chromosomal inversions and the reproductive isolation of species. Proc Natl Acad Sci U S A 98: 12084-88.
3. Rieseberg LH, (2001) Chromosomal rearrangements and speciation. Trends Ecol. Evol 16: 351-58.
4. Kirkpatrick M, Barton N, (2006) Chromosome inversions, local adaptation and speciation. Genetics 173: 419-34.
5. Sandler L, Hiraizumi Y, Sandler I, (1959) Meiotic drive in natural populations of Drosophila melanogaster. I. The cytogenetic basis of segregation distortion. Genetics 44: 233-250.
6. Jaenike J, (2001) Sex chromosome meiotic drive. Ann Rev Ecol System 32: 25-49.
7. Presgraves DC, Gerard PR, Cherukuri A, Lyttle TW, (2009) Large-scale selective sweep among segregation distorter chromosomes in African populations of Drosophila melanogaster. PLoS Genet 5: e1000463.
8. Hoffmann AA, Rieseberg LH, (2008) Revisiting the impact of inversions in evolution: from population genetic markers to drivers of adaptive shifts and speciation? Annu Rev Ecol Evol Syst 39: 21-42.
9. White MJD (1973) Animal Cytology and Evolution, Third Ed. Cambridge University Press, London.
10. Krimbas CB, Powell JR (1992) Drosophila Inversion Polymorphism. CRC Press, Boca Raton, FL.
11. Sperlich D, Pfriem P (1986) Chromosomal polymorphism in natural and experimental populations. 257-309 in The Genetics and Biology of Drosophila. Eds. Ashburner M, Carson HL, Thomson JN. Academic Press, New York, NY.
12. Stalker HD, (1976) Chromosome studies in wild populations of Drosophila melanogaster. Genetics 82: 323-347.
13. Mettler LE, Voelker RA, Mukai T, (1977) Inversion clines in populations of Drosophila melanogaster. Genetics 87: 169-176.
14. Stalker HD, (1980) Chromosome studies in wild populations of Drosophila melanogaster. II. Relationship of inversion frequencies to latitude, season, wing loading and flight activity. Genetics 95: 211-223.
15. Knibb WR, Oakenshot JG, Gibson JB, (1981) Chromosome inversion polymorphism in Drosophila melanogaster.1. Latitudinal clines and associations between inversions in Australasian populations. Genetics 98: 833-847.
16. Inoue Y, (1979) Seasonal changes of inversion frequencies of Drosophila melanogaster. Annual Report of the National Institute of Genetics (Japan) 29: 77.
17. Watanabe T, (1969) Frequency of deleterious chromosomes and allelism between lethal genes in Japanese natural populations of Drosophila melanogaster. Japanese J Genet 44: 171-187.
18. Watanabe TK, Watanabe T, (1973) Fertility genes in natural populations of Drosophila melanogaster. III. Superiority of inversion heterozygotes. Evolution 27: 468-475.
19. Andolfatto P, Wall JD, Kreitman M, (1999) Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster. Genetics 153: 1297-311.
20. Matzkin LM, Merritt TJS, Zhu CT, Eanes WF, (2005) The structure and population genetics of the breakpoints associated with the cosmopolitan chromosomal inversion In(3R)Payne in Drosophila melanogaster. Genetics 170: 1143-52.
21. Wesley CS, Eanes WF, (1994) Isolation and analysis of the breakpoint sequences of chromosome inversion In(3L)Payne in Drosophila melanogaster. Proc Natl Acad Sci U S A 91: 3132-3136.
22. Hasson E, Eanes WF, (1996) Contrasting histories of three gene regions associated with In(3L)Payne of Drosophila melanogaster. Genetics 144: 1565-1575.
23. Corbett-Detig RB, Cardeno C, Langley CH, (2012) Sequence-based detection and breakpoint assembly of polymorphic inversions. Genetics 192: 131-7.
24. Aulard S, David JR, Lemeunier F, (2002) Chromosomal inversion polymorphism in Afrotropical populations of Drosophila melanogaster. Genet Res 79: 49-63.
25. Pool JE, Corbett-Detig RB, Sugino RP, Stevens KA, Cardeno CM, et al. (2012) Population genomics of sub-Saharan Drosophila melanogaster: African diversity and non-African admixture. Cosubmission.
26. Mackay TFC, Richards S, Stone EA, Barbadilla A, Ayroles JF, et al. (2012) The Drosophila melanogaster genetic reference panel. Nature 482: 173-178.
27. Li H, Stephan W, (2006) Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet 2: e166.
28. Thornton KR, Andolfatto P, (2006) Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
29. Glinka S, Ometto L, Mousset S, Stephan W, De Lorenzo D, (2003) Demography and natural selection have shaped genetic variation in Drosophila melanogaster a multi-locus approach. Genetics 165: 1269-1278.
30. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 2078-2079.
31. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
32. Maynard Smith J, Haigh J, (1974) The hitch-hiking effect of a favourable gene. Genet Res Camb 23: 23-35.
33. Langley CH, Stevens K, Cardeno C, Lee YCG, Schrider DR, et al. (2012) Genomic variation in natural populations of Drosophila melanogaster. Genetics, revisions submitted.
34. Wallace AG, Detweiler D, Schaeffer SW, (2011) Evolutionary History of the Third Chromosome Gene Arrangements of Drosophila pseudoobscura Inferred from Inversion Breakpoints. Mol Biol Evol 28 (8):: 2219-2229.
35. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
36. Schaeffer SW, (2002) Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura. Gen Res 80: 163-175.
37. Pritchard JK, Seielstad MT, Perez-Lezaun A, Feldman MW, (1999) Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol Biol Evol 16: 1791-1798.
38. Beaumont MA, Zhang W, Balding DJ, (2002) Approximate Bayesian computation in population genetics. Genetics 162: 2025-2035.
39. Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, et al. (2005) Genomic scans for selective sweeps using SNP data. Genome Res 15: 1566-1575.
40. Andolfatto P, Depaulis F, Navarro A, (2001) Inversion polymorphisms and nucleotide variability in Drosophila. Genet Res 77: 1-8.
41. Aulard S, Monti L, Chaminade N, Lemeunier F, (2004) Mitotic and polytene chromosomes: comparisons between Drosophila melanogaster and Drosophila simulans. Genetica 120: 137-150.
42. Ranz JM, Maurin D, Chan YS, Grotthuss MV, Hillier LM, et al. (2007) Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biol 5: 1366-1381.
43. Pool JE, Aquadro CF, (2006) History and structure of sub-Saharan populations of Drosophila melanogaster. Genetics 174: 915-929.
44. Navarro A, Betran E, Barbadilla A, Ruiz A, (1997) Recombination and gene flux caused by gene conversion and crossing over in inversion heterokaryotypes. Genetics 146: 695-709.
45. Patterson N, Price AL, Reich D, (2006) Population structure and eigenanalysis. PLoS Genet 2 (12):: e190.
46. Kulathinal RJ, Stevison LS, Noor MAF, (2009) The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing. PLoS Genet 5: e1000550.
47. Payne F, (1924) Crossover modifiers in the third chromosome of Drosophila melanogaster. Genetics 9: 327-342.
48. Navarro A, Barbadilla A, Ruiz A, (2000) Effect of inversion polymorphism on the neutral nucleotide variability of linked chromosomal regions in Drosophila. Genetics 155: 685-698.
49. Baudry E, Viginier B, Veuille M, (2004) Non-African populations of Drosophila melanogaster have a unique origin. Mol Biol Evol 21: 1482-1491.
50. Dobzhansky, T., 1951 Genetics and the Origin of Species, Ed. 3. Columbia University Press, New York.
51. Maynard Smith J, Haigh J, (1974) The hitch-hiking effect of a favourable gene. Genet Res 23: 23-35.
52. Charlesworth B, (1994) The Effect of Background Selection Against Deleterious Mutations on Weakly Selected, Linked Variants. Genet. Res 63: 213-227.
53. Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, et al. (2005) Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Res 15: 1-18.
54. Reed FA, Reeves RG, Aquadro CF, (2005) Evidence of susceptibility and resistance to cryptic X-linked meiotic drive in natural populations of Drosophila melanogaster. Evolution 59: 1280-1291.
55. Novitski E, Hanks GD, (1961) The analysis of irradiated Drosophila populations for instances of meiotic drive. Nature 190: 989-990.
56. Hanks GD, (1968) RD (Recovery Disrupter) activity associated with various wild-type X chromosomes. Dros Inf Ser 43: 98.
57. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, et al. (2000) The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
58. Thompson JD, Higgins DG, Gibson TJ, (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
59. Hu TT, Eisen MB, Thornton KR, Andolfatto P, (2012) A second generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Res Published in Advance August 30. doi:10.1101/gr.141689.112.
60. Hudson RR, (2002) Generating samples under a Wright-Fisher neutral model. Bioinformatics 18: 337-338.
61. Hudson RR, Slatkin M, Maddison WP, (1992) Estimation of levels of gene flow from DNA-sequence data. Genetics 132: 583-589.