48. Jeong Y, El-Jaick K, Roessler E, Muenke M, Epstein DJ (2006) A functional screen for sonic hedgehog regulatory elements across a 1 Mb interval identifies long-range ventral forebrain enhancers. Development 133: 761–772. 49. Dekker T, Ibba I, Siju KP, Stensmyr MC, Hansson BS (2006) Olfactory shifts parallel superspecialism for toxic fruit in Drosophila melanogaster sibling, D. sechellia. Curr Biol 16: 101–109. 50. Ruebenbauer A, Schlyter F, Hansson BS, Lofstedt C, Larsson MC (2008) Genetic variability and robustness of host odor preference in Drosophila melanogaster. Curr Biol 18: 1438–1443. 51. Mackay TF, Heinsohn SL, Lyman RF, Moehring AJ, Morgan TJ, et al. (2005) Genetics and genomics of Drosophila mating behavior. Proc Natl Acad Sci U S A 102 Suppl 1: 6622–6629. 52. Shevelyov YY, Lavrov SA, Mikhaylova LM, Nurminsky ID, Kulathinal RJ, et al. (2009) The B-type lamin is required for somatic repression of testis-specific gene clusters. Proc Natl Acad Sci U S A 106: 3282–3287. 53. Lupski JR (1998) Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet 14: 417–422. 54. Stankiewicz P, Lupski JR (2002) Genome architecture, rearrangements and genomic disorders. Trends Genet 18: 74–82. 55. Szankasi P, Gysler C, Zehntner U, Leupold U, Kohli J, et al. (1986) Mitotic recombination between dispersed but related rRNA genes of Schizosaccharomyces pombe generates a reciprocal translocation. Molecular General Genetics 202: 394–402. 56. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241–254. 57. Hill CW, Gray JA (1988) Effects of chromosomal inversion on cell fitness in Escherichia coli K-12. Genetics 119: 771–778. 58. Liu SL, Sanderson KE (1995) Rearrangements in the genome of the bacterium Salmonella typhi. Proc Natl Acad Sci U S A 92: 1018–1022. 59. Gonzalez J, Casals F, Ruiz A (2004) Duplicative and conservative transpositions of larval serum protein 1 genes in the genus Drosophila. Genetics 168: 253–264. 60. Ranz JM, D´ıaz-Castillo C, Petersen R (2011) Conserved gene order at the nuclear periphery in Drosophila. Mol Biol Evol. 61. Mathog D, Sedat JW (1989) The three-dimensional organization of polytene nuclei in male Drosophila melanogaster with compound XY or ring X chromosomes. Genetics 121: 293–311. 62. Pickersgill H, Kalverda B, de Wit E, Talhout W, Fornerod M, et al. (2006) Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet 38: 1005–1014. 63. Lefevre G (1976) A photographic representation and interpretation of the polytene chromosomes of Drosophila melanogaster salivary glands. In: Ashburner MA, Novitski E, eds. The Genetics and Biology of Drosophila. London: Academic Press. pp 31–66. 64. Anderson WW, Arnold J, Sammons SA, Yardley DG (1986) Frequency- dependent viabilities of Drosophila pseudoobscura karyotypes. Heredity 56: 7–17. 65. Anholt RR, Lyman RF, Mackay TF (1996) Effects of single P-element insertions on olfactory behavior in Drosophila melanogaster. Genetics 143: 293–301. 66. Miquel J, Lundgren PR, Bensch KG, Atlan H (1976) Effects of temperature on the life span, vitality and fine structure of Drosophila melanogaster. Mech Ageing Dev 5: 347–370. 67. Gong WJ, Golic KG (2006) Loss of Hsp70 in Drosophila is pleiotropic, with effects on thermotolerance, recovery from heat shock and neurodegeneration. Genetics 172: 275–286. 68. Gibbs AG, Chippindale AK, Rose MR (1997) Physiological mechanisms of evolved desiccation resistance in Drosophila melanogaster. J Exp Biol 200: 1821–1832. Collinearity Conservation in Eukaryotes 69. Faul F, Erdfelder E, Lang AG, Buchner A (2007) G*Power 3: a flexible statistical power analysis program for the social, behavioral, and biomedical sciences. Behav Res Methods 39: 175–191. 70. Xia XQ, McClelland M, Porwollik S, Song W, Cong X, et al. (2009) WebArrayDB: cross-platform microarray data analysis and public data repository. Bioinformatics 25: 2425–2429. 71. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, et al. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30: e15. 72. Smyth GK (2005) Limma: linear models for microarray data. In: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W, eds. Bioinformatics and Computational Biology Solutions using R and Bioconductor. New York: Springer. pp 397–420. 73. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc Ser B 57: 289–300. 74. Hothorn T, Bretz F, Westfall P (2008) Simultaneous inference in general parametric models. Biom J 50: 346–363. 75. Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44–57. 76. Ohler U (2006) Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. Nucleic Acids Res 34: 5943–5950. 77. Haider S, Ballester B, Smedley D, Zhang J, Rice P, et al. (2009) BioMart Central Portal–unified access to biological data. Nucleic Acids Res 37: W23–27. 78. Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, et al. (2009) VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res 37: D583–587. 79. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol. 80. 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. 81. Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18: 691–699. 82. Engstrom PG, Fredman D, Lenhard B (2008) Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol 9: R34. 83. Gaunt MW, Miles MA (2002) An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks. Mol Biol Evol 19: 748–761. 84. Krzywinski J, Grushko OG, Besansky NJ (2006) Analysis of the complete mitochondrial DNA from Anopheles funestus: an improved dipteran mitochon- drial genome annotation and a temporal dimension of mosquito evolution. Mol Phylogenet Evol 39: 417–423. 85. Vieira FG, Sanchez-Gracia A, Rozas J (2007) Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution. Genome Biol 8: R235. 86. Klemenz R, Weber U, Gehring WJ (1987) The white gene as a marker in a new P-element vector for gene transfer in Drosophila. Nucleic Acids Res 15: 3947–3959. PLoS Genetics | www.plosgenetics.org 14 February 2012 | Volume 8 | Issue 2 | e1002475