References

  1. Lewontin RC, Moore JA, Provine WB, Wallace B, Eds: Dobzhansky's Genetics of Natural Populations I-XLIII.

    New York: Columbia University Press 1981. OpenURL

  2. Patterson JT, Stone WS: Evolution in the Genus Drosophila.

    New York: Macmillan 1952. OpenURL

  3. Lewontin RC, Hubby JL: A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural population of D. pseudoobscura.

    Genetics 1966, 54:595-609. PubMed Abstract OpenURL

  4. Kreitman M: Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster.

    Nature 1983, 304:412-417. PubMed Abstract OpenURL

  5. Blackman RK, Meselson M: Interspecific nucleotide sequence comparisons used to identify regulatory and structural features of the Drosophila hsp82 gene.

    J Mol Biol 1986, 188:499-515. PubMed Abstract OpenURL

  6. Bray SJ, Hirsh J: The Drosophila virilis dopa decarboxylase gene is developmentally regulated when integrated into Drosophila melanogaster.

    EMBO J 1986, 5:2305-2311. PubMed Abstract OpenURL

  7. Powell JR: Progress and Prospects in Evolutionary Biology: The Drosophila Model.

    Oxford: Oxford University Press 1997. OpenURL

  8. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, et al.: The genome sequence of Drosophila melanogaster.

    Science 2000, 287:2185-2195. PubMed Abstract | Publisher Full Text OpenURL

  9. Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, Patel S, Adams M, Champe M, Dugan SP, Frise E, et al.: Finishing a whole-genome shotgun: Release 3 of the Drosophila euchromatic genome sequence.

    Genome Biol 2002, 3:research0079.1-0079.14. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  10. Human genome sequencing center at Baylor College of Medicine: Drosophila genome project [http://www.hgsc.bcm.tmc.edu/projects/drosophila/update.html]
  11. Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, et al.: The genome sequence of the malaria mosquito Anopheles gambiae.

    Science 2002, 298:129-149. PubMed Abstract | Publisher Full Text OpenURL

  12. Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris NL, Marshall B, Shu S, Kaminker JS, Prochnik SE, et al.: An integrated computational pipeline and database to support whole-genome sequence annotation.

    Genome Biol 2002, 3:research0081.1-0081.11. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  13. Lewis SE, Searle SMJ, Harris N, Gibson ML, Iyer VR, Richter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, et al.: Apollo: a sequence annotation editor.

    Genome Biol 2002, 3:research0082.1-0082.14. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  14. Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, et al.: Annotation of the Drosophila euchromatic genome: a systematic review.

    Genome Biol 2002, 3:research0083.1-0083.22. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  15. Lozovskaya ER, Petrov DA, Hartl DL: A combined molecular and cytogenetic approach to genome evolution in Drosophila using large-fragment DNA cloning.

    Chromosoma 1993, 102:253-266. PubMed Abstract OpenURL

  16. Novichkov PS, Gelfand MS, Mironov AA: Gene recognition in eukaryotic DNA by comparison of genomic sequences.

    Bioinformatics 2001, 17:1011-1018. PubMed Abstract | Publisher Full Text OpenURL

  17. Reese MG, Kulp D, Tammana H, Haussler D: Genie - gene finding in Drosophila melanogaster.

    Genome Res 2000, 10:529-538. PubMed Abstract | Publisher Full Text OpenURL

  18. Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA.

    J Mol Biol 1997, 268:78-94. PubMed Abstract | Publisher Full Text OpenURL

  19. Carulli JP, Chen DM, Stark WS, Hartl DL: Phylogeny and physiology of Drosophila opsins.

    J Mol Evol 1994, 38:250-262. PubMed Abstract OpenURL

  20. Nekrutenko A, Makova KD, Li WH: The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study.

    Genome Res 2002, 12:198-202. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  21. Li W-H: Molecular Evolution.

    Sunderland, MA: Sinauer 1997. OpenURL

  22. Yang Z: Phylogenetic Analysis by Maximum Likelihood (PAML) 3.0.

    London, University College London 2000. OpenURL

  23. Zdobnov EM, Von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, et al.: Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.

    Science 2002, 298:149-159. PubMed Abstract | Publisher Full Text OpenURL

  24. Cirera S, Martin-Campos JM, Segarra C, Aguade M: Molecular characterization of the breakpoints of an inversion fixed between Drosophila melanogaster and D. subobscura.

    Genetics 1995, 139:321-326. PubMed Abstract OpenURL

  25. Maier D, Preiss A, Powell JR: Regulation of the segmentation gene fushi tarazu has been functionally conserved in Drosophila.

    EMBO J 1990, 9:3957-3966. PubMed Abstract OpenURL

  26. Krimbas CB, Powell JR, Eds: Drosophila Inversion Polymorphism.

    Boca Raton, FL: CRC Press 1992. OpenURL

  27. Moschetti R, Caggese C, Barsanti P, Caizzi R: Intra- and interspecies variation among Bari-1 elements of the melanogaster species group.

    Genetics 1998, 150:239-250. PubMed Abstract | Publisher Full Text OpenURL

  28. de Frutos R, Peterson KR, Kidwell MG: Distribution of Drosophila melanogaster transposable element sequences in species of the obscura group.

    Chromosoma 1992, 101:293-300. PubMed Abstract OpenURL

  29. Neufeld TP, Carthew RW, Rubin GM: Evolution of gene position: chromosomal arrangement and sequence comparison of the Drosophila melanogaster and Drosophila virilis sina and Rh4 genes.

    Proc Natl Acad Sci USA 1991, 88:10203-10207. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  30. Gonzalez J, Ranz JM, Ruiz A: Chromosomal elements evolve at different rates in the Drosophila genome.

    Genetics 2002, 161:1137-1154. PubMed Abstract | Publisher Full Text OpenURL

  31. Bolshakov VN, Topalis P, Blass C, Kokoza E, della Torre A, Kafatos FC, Louis C: A comparative genomic analysis of two distant diptera, the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae.

    Genome Res 2002, 12:57-66. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  32. Thomasova D, Ton LQ, Copley RR, Zdobnov EM, Wang X, Hong YS, Sim C, Bork P, Kafatos FC, Collins FH: Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae.

    Proc Natl Acad Sci USA 2002, 99:8179-8184. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  33. Zeng LW, Comeron JM, Chen B, Kreitman M: The molecular clock revisited: the rate of synonymous versus replacement change in Drosophila.

    Genetica 1998, 102-103:369-382. PubMed Abstract | Publisher Full Text OpenURL

  34. Schmid KJ, Tautz D: A screen for fast evolving genes from Drosophila.

    Proc Natl Acad Sci USA 1997, 94:9746-9750. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  35. Jeffs PS, Holmes EC, Ashburner M: The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup.

    Mol Biol Evol 1994, 11:287-304. PubMed Abstract | Publisher Full Text OpenURL

  36. Rodriguez-Trelles F, Tarrio R, Ayala FJ: Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group.

    Genetics 1999, 153:339-350. PubMed Abstract | Publisher Full Text OpenURL

  37. Rodriguez-Trelles F, Tarrio R, Ayala FJ: Fluctuating mutation bias and the evolution of base composition in Drosophila.

    J Mol Evol 2000, 50:1-10. PubMed Abstract | Publisher Full Text OpenURL

  38. Shields DC, Sharp PM, Higgins DG, Wright F: 'Silent' sites in Drosophila genes are not neutral: evidence of selection among synonymous codons.

    Mol Biol Evol 1988, 5:704-716. PubMed Abstract | Publisher Full Text OpenURL

  39. Laird CD: DNA of Drosophila chromosomes.

    Annu Rev Genet 1973, 7:177-204. PubMed Abstract | Publisher Full Text OpenURL

  40. Moriyama EN, Hartl DL: Codon usage bias and base composition of nuclear genes in Drosophila.

    Genetics 1993, 134:847-858. PubMed Abstract OpenURL

  41. Anderson CL, Carew EA, Powell JR: Evolution of the Adh locus in the Drosophila willistoni group: the loss of an intron, and shift in codon usage.

    Mol Biol Evol 1993, 10:605-618. PubMed Abstract | Publisher Full Text OpenURL

  42. Visualization tools for alignments [http://www-gsd.lbl.gov/vista/details_avid.htm]
  43. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, Dubchak I: VISTA: visualizing global DNA sequence alignments of arbitrary length.

    Bioinformatics 2000, 16:1046-1047. PubMed Abstract | Publisher Full Text OpenURL

  44. Bergman CM, Kreitman M: Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.

    Genome Res 2001, 11:1335-1345. PubMed Abstract | Publisher Full Text OpenURL

  45. Clark AG: The search for meaning in noncoding DNA.

    Genome Res 2001, 11:1319-1320. PubMed Abstract | Publisher Full Text OpenURL

  46. Bergman CM: Evolutionary Analyses of Transcriptional Control Sequences in Drosophila.

    Chicago: University of Chicago 2001. OpenURL

  47. Webb CT, Shabalina SA, Ogurtsov AY, Kondrashov AS: Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae.

    Nucleic Acids Res 2002, 30:1233-1239. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  48. Petrov DA, Lozovskaya ER, Hartl DL: High intrinsic rate of DNA loss in Drosophila.

    Nature 1996, 384:346-349. PubMed Abstract | Publisher Full Text OpenURL

  49. Petrov DA, Hartl DL: High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups.

    Mol Biol Evol 1998, 15:293-302. PubMed Abstract | Publisher Full Text OpenURL

  50. Fujioka M, Emi-Sarker Y, Yusibova GL, Goto T, Jaynes JB: Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients.

    Development 1999, 126:2527-2538. PubMed Abstract | Publisher Full Text OpenURL

  51. Sackerson C, Fujioka M, Goto T: The even-skipped locus is contained in a 16-kb chromatin domain.

    Dev Biol 1999, 211:39-52. PubMed Abstract | Publisher Full Text OpenURL

  52. Cohen B, McGuffin ME, Pfeifle C, Segal D, Cohen SM: apterous, a gene required for imaginal disc development in Drosophila encodes a member of the LIM family of developmental regulatory proteins.

    Genes Dev 1992, 6:715-729. PubMed Abstract OpenURL

  53. Rincon-Limas DE, Lu CH, Canal I, Calleja M, Rodriguez-Esteban C, Izpisua-Belmonte JC, Botas J: Conservation of the expression and function of apterous orthologs in Drosophila and mammals.

    Proc Natl Acad Sci USA 1999, 96:2165-2170. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  54. Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, et al.: Comparison of the complete protein sets of worm and yeast: orthology and divergence.

    Science 1998, 282:2022-2028. PubMed Abstract | Publisher Full Text OpenURL

  55. Rubin GM, Hong L, Brokstein P, Evans-Holm M, Frise E, Stapleton M, Harvey DA: A Drosophila complementary DNA resource.

    Science 2000, 287:2222-2224. PubMed Abstract | Publisher Full Text OpenURL

  56. The Arabidopsis Genome Intiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

    Nature 2000, 408:796-815. PubMed Abstract | Publisher Full Text OpenURL

  57. International Human Genome Consortium: Initial sequencing and analysis of the human genome.

    Nature 2001, 409:860-921. PubMed Abstract | Publisher Full Text OpenURL

  58. Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O, Salzberg SL: Full-length messenger RNA sequences greatly improve genome annotation.

    Genome Biol 2002, 3:research0029.1-0029.12. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  59. Schmid KJ, Aquadro CF: The evolutionary analysis of 'orphans' from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes.

    Genetics 2001, 159:589-598. PubMed Abstract | Publisher Full Text OpenURL

  60. Ashburner M, Misra S, Roote J, Lewis SE, Blazej R, Davis T, Doyle C, Galle R, George R, Harris N, et al.: An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region.

    Genetics 1999, 153:179-219. PubMed Abstract | Publisher Full Text OpenURL

  61. Ranz JM, Casals F, Ruiz A: How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila.

    Genome Res 2001, 11:230-239. PubMed Abstract | Publisher Full Text OpenURL

  62. Coghlan A, Wolfe KH: Fourfold faster rate of genome rearrangement in nematodes than in Drosophila.

    Genome Res 2002, 12:857-867. PubMed Abstract | Publisher Full Text OpenURL

  63. Lyttle TW, Haymer DS: The role of the transposable element hobo in the origin of endemic inversions in wild populations of Drosophila melanogaster.

    Genetica 1992, 86:113-126. PubMed Abstract OpenURL

  64. Andolfatto P, Wall JD, Kreitman M: Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster.

    Genetics 1999, 153:1297-1311. PubMed Abstract | Publisher Full Text OpenURL

  65. Caceres M, Puig M, Ruiz A: Molecular characterization of two natural hotspots in the Drosophila buzzatii genome induced by transposon insertions.

    Genome Res 2001, 11:1353-1364. PubMed Abstract | Publisher Full Text OpenURL

  66. Mathiopoulos KD, della Torre A, Predazzi V, Petrarca V, Coluzzi M: Cloning of inversion breakpoints in the Anopheles gambiae complex traces a transposable element at the inversion junction.

    Proc Natl Acad Sci USA 1998, 95:12444-12449. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  67. Pachter L, Alexandersson M, Cawley S: Applications of generalized pair hidden Markov models to alignment and gene finding problems.

    J Comput Biol 2002, 9:389-399. PubMed Abstract | Publisher Full Text OpenURL

  68. Hardison RC: Conserved noncoding sequences are reliable guides to regulatory elements.

    Trends Genet 2000, 16:369-372. PubMed Abstract | Publisher Full Text OpenURL

  69. Ishihara K, Hatano N, Furuumi H, Kato R, Iwaki T, Miura K, Jinno Y, Sasaki H: Comparative genomic sequencing identifies novel tissue-specific enhancers and sequence elements for methylation-sensitive factors implicated in Igf2/H19 imprinting.

    Genome Res 2000, 10:664-671. PubMed Abstract | Publisher Full Text OpenURL

  70. Crowley EM, Roeder K, Bina M: A statistical model for locating regulatory regions in genomic DNA.

    J Mol Biol 1997, 268:8-14. PubMed Abstract | Publisher Full Text OpenURL

  71. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB: Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.

    Proc Natl Acad Sci USA 2002, 99:757-762. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  72. Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence C: Human-mouse genome comparisons to locate regulatory sites.

    Nat Genet 2000, 26:225-228. PubMed Abstract | Publisher Full Text OpenURL

  73. Tucson Drosophila Species Stock Center [http://stockcenter.arl.arizona.edu]
  74. Kim UJ, Shizuya H, de Jong PJ, Birren B, Simon MI: Stable propagation of cosmid sized human DNA inserts in an F factor based vector.

    Nucleic Acids Res 1992, 20:1083-1085. PubMed Abstract OpenURL

  75. BACPAC Resources Center [http://www.chori.org/bacpac]
  76. Ross MT, LaBrie J, McPherson VP, Stanton P Jr: Screening large insert libraries by hybridization.

    In Current Protocols in Human Genetics (Edited by: Dracopoli NC, Haines JL, Korf BR, Moir DT, Morton CC, Seidman CE, Seidman JG, Smith DR). New York: Wiley and Sons 1999, 1:5.6.1-5.6.52. OpenURL

  77. Washington University BLAST archives [http://blast.wustl.edu]
  78. Kent WJ: BLAT - the BLAST-like alignment tool.

    Genome Res 2002, 12:656-664. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  79. Morgenstern B: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.

    Bioinformatics 1999, 15:211-218. PubMed Abstract | Publisher Full Text OpenURL

  80. Walker DR, Koonin EV: SEALS: a system for easy analysis of lots of sequences.

    Proc Int Conf Intell Syst Mol Biol 1997, 5:333-339. PubMed Abstract OpenURL

  81. Yang Z, Nielsen R: Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.

    Mol Biol Evol 2000, 17:32-43. PubMed Abstract | Publisher Full Text OpenURL

  82. Rubin GM, Spradling AC: Genetic transformation of Drosophila with transposable element vectors.

    Science 1982, 218:348-353. PubMed Abstract OpenURL

  83. Hoskins RA, Smith CD, Carlson JW, Carvalho AB, Halpern A, Kaminker JS, Kennedy C, Mungall CJ, Sullivan BA, Sutton GG, et al.: Heterochromatic sequences in a Drosophila whole-genome shotgun assembly.

    Genome Biol 2002, 3:research0085.1-0085.16. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  84. Gaunt MW, Miles MA: An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks.

    Mol Biol Evol 2002, 19:748-761. PubMed Abstract | Publisher Full Text OpenURL

  85. Powers TP, Hogan J, Ke Z, Dymbrowski K, Wang X, Collins FH, Kaufman TC: Characterization of the Hox cluster from the mosquito Anopheles gambiae (Diptera: Culicidae).

    Evol Dev 2000, 2:311-325. PubMed Abstract | Publisher Full Text OpenURL

  86. Devenport MP, Blass C, Eggleston P: Characterization of the Hox gene cluster in the malaria vector mosquito, Anopheles gambiae.

    Evol Dev 2000, 2:326-339. PubMed Abstract | Publisher Full Text OpenURL

  87. Brown SJ, Fellers JP, Shippy TD, Richardson EA, Maxwell M, Stuart JJ, Denell RE: Sequence of the Tribolium castaneum homeotic complex: the region corresponding to the Drosophila melanogaster antennapedia complex.

    Genetics 2002, 160:1067-1074. PubMed Abstract | Publisher Full Text OpenURL

  88. Jiang J, Hoey T, Levine M: Autoregulation of a segmentation gene in Drosophila: combinatorial interaction of the even-skipped homeo box protein with a distal enhancer element.

    Genes Dev 1991, 5:265-277. PubMed Abstract OpenURL

  89. Stanojevic D, Small S, Levine M: Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo.

    Science 1991, 254:1385-1387. PubMed Abstract OpenURL

  90. Small S, Blair A, Levine M: Regulation of two pair-rule stripes by a single enhancer in the Drosophila embryo.

    Dev Biol 1996, 175:314-324. PubMed Abstract | Publisher Full Text OpenURL

  91. Capovilla M, Kambris Z, Botas J: Direct regulation of the muscle-identity gene apterous by a Hox protein in the somatic mesoderm.

    Development 2001, 128:1221-1230. PubMed Abstract | Publisher Full Text OpenURL

  92. Stapleton M, Carlson J, Brokstein P, Yu C, Champe M, George R, Guarin H, Kronmiller B, Pacleb J, Park S, et al.: A Drosophila full-length cDNA resource.

    Genome Biol 2002, 3:research0080.1-0080.8. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL