Hahn MW, Han MV, Han S-G: Gene family evolution across 12 Drosophila genomes. PLoS Genet. 2007, 3 (11): e197-
Article
PubMed
PubMed Central
Google Scholar
Demuth JP, Hahn MW: The life and death of gene families. BioEssays. 2009, 31 (1): 29-39.
Article
PubMed
Google Scholar
Sanchez-Gracia A, Vieira FG, Rozas J: Molecular evolution of the major chemosensory gene families in insects. Heredity. 2009, 103 (3): 208-216.
Article
CAS
PubMed
Google Scholar
Bailey JA, Eichler EE: Primate segmental duplications: crucibles of evolution, diversity and disease. Nat Rev Genet. 2006, 7 (7): 552-564.
Article
CAS
PubMed
Google Scholar
Lynch M, Conery JS: The evolutionary fate and consequences of duplicate genes. Science. 2000, 290 (5494): 1151-1155.
Article
CAS
PubMed
Google Scholar
Conant GC, Wolfe KH: Turning a hobby into a job: How duplicated genes find new functions. Nat Rev Genet. 2008, 9 (12): 938-950.
Article
CAS
PubMed
Google Scholar
Shigenobu S, Bickel RD, Brisson JA, Butts T, Chang Cc, Christiaens O, Davis GK, Duncan EJ, Ferrier DEK, Iga M, et al: Comprehensive survey of developmental genes in the pea aphid, Acyrthosiphon pisum: frequent lineage-specific duplications and losses of developmental genes. Insect Mol Biol. 2010, 19: 47-62.
Article
CAS
PubMed
Google Scholar
Lespinet O, Wolf YI, Koonin EV, Aravind L: The role of lineage-specific gene family expansion in the evolution of Eukaryotes. Genome Res. 2002, 12 (7): 1048-1059.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wurmbach E, Wech I, Preiss A: The Enhancer of split complex of Drosophila melanogaster harbors three classes of Notch responsive genes. Mech Dev. 1999, 80 (2): 171-180.
Article
CAS
PubMed
Google Scholar
Cooper MTD, Tyler DM, Furriols M, Chalkiadaki A, Delidakis C, Bray S: Spatially restricted factors cooperate with Notch in the regulation of Enhancer of Split genes. Dev Biol. 2000, 221 (2): 390-403.
Article
CAS
PubMed
Google Scholar
Lai EC: Notch signaling: control of cell communication and cell fate. Development. 2004, 131 (5): 965-973.
Article
CAS
PubMed
Google Scholar
Lai EC, Bodner R, Kavaler J, Freschi G, Posakony JW: Antagonism of notch signaling activity by members of a novel protein family encoded by the bearded and enhancer of split gene complexes. Development. 2000, 127 (2): 291-306.
CAS
PubMed
Google Scholar
Bailey AM, Posakony JW: Suppressor of hairless directly activates transcription of enhancer of split complex genes in response to Notch receptor activity. Genes Dev. 1995, 9 (21): 2609-2622.
Article
CAS
PubMed
Google Scholar
Delidakis C, Preiss A, Hartley DA, Artavanis-Tsakonas S: Two genetically and molecularly distinct functions involved in early neurogenesis reside within the Enhancer of split locus of Drosophila melanogaster. Genetics. 1991, 129 (3): 803-823.
CAS
PubMed
PubMed Central
Google Scholar
Nakao K, Campos-Ortega JA: Persistent expression of genes of the Enhancer of split complex suppresses neural development in Drosophila. Neuron. 1996, 16 (2): 275-286.
Article
CAS
PubMed
Google Scholar
Lai EC, Bodner R, Posakony JW: The enhancer of split complex of Drosophila includes four Notch-regulated members of the bearded gene family. Development. 2000, 127 (16): 3441-3455.
CAS
PubMed
Google Scholar
Chanet S, Vodovar N, Mayau V, Schweisguth F: Genome engineering-based analysis of Bearded family genes reveals both functional redundancy and a nonessential function in lateral inhibition in Drosophila. Genetics. 2009, 182 (4): 1101-1108.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heitzler P, Bourouis M, Ruel L, Carteret C, Simpson P: Genes of the Enhancer of split and achaete-scute complexes are required for a regulatory loop between Notch and Delta during lateral signalling in Drosophila. Development. 1996, 122 (1): 161-171.
CAS
PubMed
Google Scholar
Ziemer A, Tietze K, Knust E, Campos-Ortega JA: Genetic analysis of Enhancer of split, a locus involved in neurogenesis in Drosophila melanogaster. Genetics. 1988, 119 (1): 63-74.
CAS
PubMed
PubMed Central
Google Scholar
Maier D, Marte BM, Schäfer W, Yu Y, Preiss A: Drosophila evolution challenges postulated redundancy in the E(spl) gene complex. Proc Natl Acad Sci USA. 1993, 90 (12): 5464-5468.
Article
CAS
PubMed
PubMed Central
Google Scholar
de Celis JF, de Celis J, Ligoxygakis P, Preiss A, Delidakis C, Bray S: Functional relationships between Notch, Su(H) and the bHLH genes of the E(spl) complex: the E(spl) genes mediate only a subset of Notch activities during imaginal development. Development. 1996, 122 (9): 2719-2728.
CAS
PubMed
Google Scholar
Ligoxygakis P, Yu SY, Delidakis C, Baker NE: A subset of notch functions during Drosophila eye development require Su(H) and the E(spl) gene complex. Development. 1998, 125 (15): 2893-2900.
CAS
PubMed
Google Scholar
Kafri R, Springer M, Pilpel Y: Genetic redundancy: New tricks for old genes. Cell. 2009, 136 (3): 389-392.
Article
CAS
PubMed
Google Scholar
Nellesen DT, Lai EC, Posakony JW: Discrete enhancer elements mediate selective responsiveness of Enhancer of split complex genes to common transcriptional activators. Dev Biol. 1999, 213 (1): 33-53.
Article
CAS
PubMed
Google Scholar
Maeder ML, Polansky BJ, Robson BE, Eastman DA: Phylogenetic footprinting analysis in the upstream regulatory regions of the Drosophila Enhancer of split genes. Genetics. 2007, 177 (3): 1377-1394.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cave J, Xia L, Caudy M: The Daughterless N-terminus directly mediates synergistic interactions with Notch transcription complexes via the SPS+A DNA transcription code. BMC Research Notes. 2009, 2 (1): 65-
Article
PubMed
PubMed Central
Google Scholar
Cave JW, Loh F, Surpris JW, Xia L, Caudy MA: A DNA transcription code for cell-specific gene activation by Notch signaling. Curr Biol. 2005, 15 (2): 94-104.
Article
CAS
PubMed
Google Scholar
Castro B, Barolo S, Bailey AM, Posakony JW: Lateral inhibition in proneural clusters: cis-regulatory logic and default repression by Suppressor of Hairless. Development. 2005, 132 (15): 3333-3344.
Article
CAS
PubMed
Google Scholar
Cave JW, Xia L, Caudy M: Differential regulation of transcription through distinct Suppressor of Hairless DNA binding site architectures during Notch signaling in proneural clusters. Mol Cell Biol. 2011, 31 (1): 22-29.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lai EC, Tam B, Rubin GM: Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs. Genes Dev. 2005, 19 (9): 1067-1080.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lai EC, Burks C, Posakony JW: The K box, a conserved 3' UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts. Development. 1998, 125 (20): 4077-4088.
CAS
PubMed
Google Scholar
Lai EC, Posakony JW: The Bearded box, a novel 3' UTR sequence motif, mediates negative post-transcriptional regulation of Bearded and Enhancer of split Complex gene expression. Development. 1997, 124 (23): 4847-4856.
CAS
PubMed
Google Scholar
Duncan EJ, Dearden PK: Evolution of a genomic regulatory domain: The role of gene co-option and gene duplication in the Enhancer of split complex. Genome Res. 2010, 20 (7): 917-928.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schlatter R, Maier D: The Enhancer of split and Achaete-Scute complexes of Drosophilids derived from simple ur-complexes preserved in mosquito and honeybee. BMC Evol Biol. 2005, 5 (1): 67-
Article
PubMed
PubMed Central
Google Scholar
Baker RH, Morgan J, Wang X, Boore JL, Wilkinson GS: Genomic analysis of a sexually-selected character: EST sequencing and microarray analysis of eye-antennal imaginal discs in the stalk-eyed fly Teleopsis dalmanni (Diopsidae). BMC Genomics. 2009, 10 (361): 1-20.
Google Scholar
Baker RH, Wilkinson GS: Comparative Genomic Hybridization (CGH) reveals a neo-X chromosome and biased gene movement in stalk-eyed flies (genus Teleopsis). PLoS Genet. 2010, 6 (9): e1001121-
Article
PubMed
PubMed Central
Google Scholar
Yeates DK, Wiegmann BM: Phylogeny and evolution of Diptera: Recent insights and new perspectives. The Evolutionary Biology of Flies. Edited by: Yeates DK, Wiegmann BM. 2005, New York: Columbia University Press, 14-44.
Google Scholar
Gibson JF, Skevington JH, Kelso S: Placement of Conopidae (Diptera) within Schizophora based on mtDNA and nrDNA gene regions. Mol Phylogenet Evol. 2010, 56 (1): 91-103.
Article
CAS
PubMed
Google Scholar
Han HY, Ro KE: Molecular phylogeny of the superfamily Tephritoidea (Insecta: Diptera): new evidence from the mitochondrial 12S, 16S and COII genes. Mol Phylogenet Evol. 2005, 34: 416-430.
Article
CAS
PubMed
Google Scholar
Wiegmann BM, Trautwein MD, Winkler IS, Barr NB, Kim J-W, Lambkin C, Bertone MA, Cassel BK, Bayless KM, Heimberg AM, et al: Episodic radiations in the fly tree of life. Proc Natl Acad Sci USA. 2011, 108 (14): 5690-5695.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cameron SL, Lambkin CL, Barker SC, Whiting MF: A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision. Syst Entomol. 2007, 32 (1): 40-59.
Article
Google Scholar
Baker RH, Wilkinson GS, DeSalle R: The phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae). Syst Biol. 2001, 50: 87-105.
Article
CAS
PubMed
Google Scholar
Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998, 8: 186-194.
Article
CAS
PubMed
Google Scholar
Ewing B, Hillier L, Wendl MC, Green P: Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998, 8: 175-185.
Article
CAS
PubMed
Google Scholar
Green P: Phrap Documentation. 1996
Google Scholar
Gordon D, Abajian C, Green P: Consed: A graphical tool for sequence finishing. Genome Res. 1998, 8 (3): 195-202.
Article
CAS
PubMed
Google Scholar
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I: VISTA: computational tools for comparative genomics. Nucl Acids Res. 2004, 32 (suppl_2): W273-279.
Article
CAS
PubMed
PubMed Central
Google Scholar
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 (11): 1046-1047.
Article
CAS
PubMed
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32 (5): 1792-1797.
Article
CAS
PubMed
PubMed Central
Google Scholar
Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Heled J, Kearse M, Moir R, Stones-Havas S, Sturrock S, et al: Geneious v5.1. 2010, [http://www.geneious.com]
Google Scholar
Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52: 696-704.
Article
PubMed
Google Scholar
Suyama M, Torrents D, Bork P: PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006, 34: W609-W612.
Article
CAS
PubMed
PubMed Central
Google Scholar
Subramanian A, Weyer-Menkhoff J, Kaufmann M, Morgenstern B: DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics. 2005, 6 (1): 66-
Article
PubMed
PubMed Central
Google Scholar
Paroush Z, Finley RL, Kidd T, Wainwright SM, Ingham PW, Brent R, Ish-Horowicz D: Groucho is required for Drosophila neurogenesis, segmentation, and sex determination and interacts directly with hairy-related bHLH proteins. Cell. 1994, 79 (5): 805-815.
Article
CAS
PubMed
Google Scholar
Nam Y, Sliz P, Pear WS, Aster JC, Blacklow SC: Cooperative assembly of higher-order Notch complexes functions as a switch to induce transcription. Proc Natl Acad Sci USA. 2007, 104 (7): 2103-2108.
Article
CAS
PubMed
PubMed Central
Google Scholar
Arnett KL, Hass M, McArthur DG, Ilagan MXG, Aster JC, Kopan R, Blacklow SC: Structural and mechanistic insights into cooperative assembly of dimeric Notch transcription complexes. Nat Struct Mol Biol. 2010, 17 (11): 1312-1317.
Article
CAS
PubMed
PubMed Central
Google Scholar
Horvath JE, Gulden CL, Vallente RU, Eichler MY, Ventura M, McPherson JD, Graves TA, Wilson RK, Schwartz S, Rocchi M, et al: Punctuated duplication seeding events during the evolution of human chromosome 2p11. Genome Res. 2005, 15 (7): 914-927.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N: Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 2005, 15 (8): 1153-1160.
Article
CAS
PubMed
PubMed Central
Google Scholar
Simpson P, Marcellini S: The origin and evolution of stereotyped patterns of macrochaetes on the nota of cyclorraphous Diptera. Heredity. 2006, 97 (3): 148-156.
Article
CAS
PubMed
Google Scholar
Marcellini S, Simpson P: Two or four bristles: Functional evolution of an Enhancer of scute in Drosophilidae. PLoS Biol. 2006, 4 (12): e386-
Article
PubMed
PubMed Central
Google Scholar
Skaer N, Pistillo D, Gibert J-M, Lio P, W¸lbeck C, Simpson P: Gene duplication at the achaete-scute complex and morphological complexity of the peripheral nervous system in Diptera. Trends Genet. 2002, 18 (8): 399-405.
Article
CAS
PubMed
Google Scholar
Negre Br, Simpson P: Evolution of the achaete-scute complex in insects: convergent duplication of proneural genes. Trends Genet. 2009, 25 (4): 147-152.
Article
CAS
PubMed
Google Scholar
Macdonald SJ, Long AD: Identifying signatures of selection at the Enhancer of split neurogenic gene complex in Drosophila. Mol Biol Evol. 2005, 22 (3): 607-619.
Article
CAS
PubMed
Google Scholar
Macdonald SJ, Pastinen T, Long AD: The effect of polymorphisms in the Enhancer of split gene complex on bristle number variation in a large wild-caught cohort of Drosophila melanogaster. Genetics. 2005, 171 (4): 1741-1756.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bray S, Furriols M: Notch pathway: Making sense of Suppressor of Hairless. Curr Biol. 2001, 11 (6): R217-R221.
Article
CAS
PubMed
Google Scholar
Filipowicz W, Bhattacharyya SN, Sonenberg N: Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?. Nat Rev Genet. 2008, 9 (2): 102-114.
Article
CAS
PubMed
Google Scholar
Flynt AS, Lai EC: Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat Rev Genet. 2008, 9 (11): 831-842.
Article
CAS
PubMed
PubMed Central
Google Scholar
Didiano D, Cochella L, Tursun B, Hobert O: Neuron-type specific regulation of a 3' UTR through redundant and combinatorially acting cis-regulatory elements. RNA. 2010, 16 (2): 349-363.
Article
CAS
PubMed
PubMed Central
Google Scholar