Drosophila yakuba

Summary

Alias:

Top Publications

  1. Bradley R, Li X, Trapnell C, Davidson S, Pachter L, Chu H, et al. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol. 2010;8:e1000343 pubmed publisher
    ..along the anterior-posterior axis in embryos of two closely related species: Drosophila melanogaster and Drosophila yakuba. Where we observe binding by a factor in one species, we almost always observe binding by that factor to the ..
  2. Ding Y, Zhao L, Yang S, Jiang Y, Chen Y, Zhao R, et al. A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes. PLoS Genet. 2010;6:e1001255 pubmed publisher
    ..of the corresponding cis-regulatory elements of the parental gene kep1 in the pre-duplication species Drosophila yakuba indicate that kep1 might not be ancestrally required for male functions and that nsr possibly has ..
  3. Obbard D, Jiggins F, Halligan D, Little T. Natural selection drives extremely rapid evolution in antiviral RNAi genes. Curr Biol. 2006;16:580-5 pubmed
    ..This is a signature of host-pathogen arms races and implies that the ancient battle between RNA viruses and host antiviral RNAi genes is active and significant in shaping RNAi function. ..
  4. Meyer W, Schreiber S, Guo Y, Volkmann T, Welte M, Müller H. Overlapping functions of argonaute proteins in patterning and morphogenesis of Drosophila embryos. PLoS Genet. 2006;2:e134 pubmed
    ..Our findings argue against a strict separation of Ago1 and Ago2 functions and suggest that these proteins act in concert to control key steps of the midblastula transition and of segmental patterning. ..
  5. Fowlkes C, Eckenrode K, Bragdon M, Meyer M, Wunderlich Z, Simirenko L, et al. A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. PLoS Genet. 2011;7:e1002346 pubmed publisher
    ..of such changes, we used high-resolution imaging methods to measure mRNA expression in blastoderm embryos of Drosophila yakuba and Drosophila pseudoobscura and assembled these data into cellular resolution atlases, where expression ..
  6. Ludwig M, Patel N, Kreitman M. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development. 1998;125:949-58 pubmed
    ..This view allows for a slow but continual turnover of functionally important changes in the stripe 2 enhancer. ..
  7. Ludwig M, Bergman C, Patel N, Kreitman M. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature. 2000;403:564-7 pubmed
    ..Sequence differences between species have functional consequences, therefore, but they are masked by other co-evolved differences. On the basis of these results, we present a model for the evolution of eukaryotic regulatory sequences. ..
  8. Celotto A, Graveley B. Alternative splicing of the Drosophila Dscam pre-mRNA is both temporally and spatially regulated. Genetics. 2001;159:599-608 pubmed
    ..In addition, this work provides a framework to determine the mechanisms by which complex alternative splicing events are regulated. ..
  9. Andrioli L, Vasisht V, Theodosopoulou E, Oberstein A, Small S. Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms. Development. 2002;129:4931-40 pubmed
    ..These results suggest a common mechanism for preventing anterior activation of three different eve enhancers. ..
  10. Zhang J, Dean A, Brunet F, Long M. Evolving protein functional diversity in new genes of Drosophila. Proc Natl Acad Sci U S A. 2004;101:16246-50 pubmed
    ..These data suggest that protein functional diversity can expand rapidly under the joint forces of exon shuffling, gene duplication, and natural selection. ..

Detail Information

Publications132 found, 100 shown here

  1. Bradley R, Li X, Trapnell C, Davidson S, Pachter L, Chu H, et al. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol. 2010;8:e1000343 pubmed publisher
    ..along the anterior-posterior axis in embryos of two closely related species: Drosophila melanogaster and Drosophila yakuba. Where we observe binding by a factor in one species, we almost always observe binding by that factor to the ..
  2. Ding Y, Zhao L, Yang S, Jiang Y, Chen Y, Zhao R, et al. A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes. PLoS Genet. 2010;6:e1001255 pubmed publisher
    ..of the corresponding cis-regulatory elements of the parental gene kep1 in the pre-duplication species Drosophila yakuba indicate that kep1 might not be ancestrally required for male functions and that nsr possibly has ..
  3. Obbard D, Jiggins F, Halligan D, Little T. Natural selection drives extremely rapid evolution in antiviral RNAi genes. Curr Biol. 2006;16:580-5 pubmed
    ..This is a signature of host-pathogen arms races and implies that the ancient battle between RNA viruses and host antiviral RNAi genes is active and significant in shaping RNAi function. ..
  4. Meyer W, Schreiber S, Guo Y, Volkmann T, Welte M, Müller H. Overlapping functions of argonaute proteins in patterning and morphogenesis of Drosophila embryos. PLoS Genet. 2006;2:e134 pubmed
    ..Our findings argue against a strict separation of Ago1 and Ago2 functions and suggest that these proteins act in concert to control key steps of the midblastula transition and of segmental patterning. ..
  5. Fowlkes C, Eckenrode K, Bragdon M, Meyer M, Wunderlich Z, Simirenko L, et al. A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. PLoS Genet. 2011;7:e1002346 pubmed publisher
    ..of such changes, we used high-resolution imaging methods to measure mRNA expression in blastoderm embryos of Drosophila yakuba and Drosophila pseudoobscura and assembled these data into cellular resolution atlases, where expression ..
  6. Ludwig M, Patel N, Kreitman M. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development. 1998;125:949-58 pubmed
    ..This view allows for a slow but continual turnover of functionally important changes in the stripe 2 enhancer. ..
  7. Ludwig M, Bergman C, Patel N, Kreitman M. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature. 2000;403:564-7 pubmed
    ..Sequence differences between species have functional consequences, therefore, but they are masked by other co-evolved differences. On the basis of these results, we present a model for the evolution of eukaryotic regulatory sequences. ..
  8. Celotto A, Graveley B. Alternative splicing of the Drosophila Dscam pre-mRNA is both temporally and spatially regulated. Genetics. 2001;159:599-608 pubmed
    ..In addition, this work provides a framework to determine the mechanisms by which complex alternative splicing events are regulated. ..
  9. Andrioli L, Vasisht V, Theodosopoulou E, Oberstein A, Small S. Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms. Development. 2002;129:4931-40 pubmed
    ..These results suggest a common mechanism for preventing anterior activation of three different eve enhancers. ..
  10. Zhang J, Dean A, Brunet F, Long M. Evolving protein functional diversity in new genes of Drosophila. Proc Natl Acad Sci U S A. 2004;101:16246-50 pubmed
    ..These data suggest that protein functional diversity can expand rapidly under the joint forces of exon shuffling, gene duplication, and natural selection. ..
  11. Ludwig M, Palsson A, Alekseeva E, Bergman C, Nathan J, Kreitman M. Functional evolution of a cis-regulatory module. PLoS Biol. 2005;3:e93 pubmed
    ..Our findings have implications for understanding enhancer structure-function, mechanisms of speciation and computational identification of regulatory modules. ..
  12. Graveley B. Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures. Cell. 2005;123:65-73 pubmed
  13. Schmid K, Nigro L, Aquadro C, Tautz D. Large number of replacement polymorphisms in rapidly evolving genes of Drosophila. Implications for genome-wide surveys of DNA polymorphism. Genetics. 1999;153:1717-29 pubmed
  14. Lu J, Fu Y, Kumar S, Shen Y, Zeng K, Xu A, et al. Adaptive evolution of newly emerged micro-RNA genes in Drosophila. Mol Biol Evol. 2008;25:929-38 pubmed publisher
    ..melanogaster is indicative of hitchhiking under positive selection. Thus, a large number of adaptive changes over a long period of time may be essential for the evolution of newly emerged miRNA genes. ..
  15. Clary D, Wolstenholme D. The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J Mol Evol. 1985;22:252-71 pubmed
    The sequence of the 16,019 nucleotide-pair mitochondrial DNA (mtDNA) molecule of Drosophila yakuba is presented...
  16. Llopart A, Elwyn S, Lachaise D, Coyne J. Genetics of a difference in pigmentation between Drosophila yakuba and Drosophila santomea. Evolution. 2002;56:2262-77 pubmed
    b>Drosophila yakuba is a species widespread in Africa, whereas D. santomea, its newly discovered sister species, is endemic to the volcanic island of São Tomé in the Gulf of Guinea...
  17. Begun D, Lindfors H, Thompson M, Holloway A. Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics. 2006;172:1675-81 pubmed publisher
    ..We found no evidence that these novel genes are attributable primarily to duplication and divergence, which suggests the possibility that Acp's or other genes coding for small proteins may originate from ancestrally noncoding DNA...
  18. Begun D, Lindfors H, Kern A, Jones C. Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics. 2007;176:1131-7 pubmed publisher
    ..Here we use testis-derived expressed sequence tags (ESTs) from Drosophila yakuba to identify genes that have likely arisen either in D. yakuba or in the D. yakuba/D. erecta ancestor...
  19. Russo C, Takezaki N, Nei M. Molecular phylogeny and divergence times of drosophilid species. Mol Biol Evol. 1995;12:391-404 pubmed publisher
    ..melanogaster groups apparently diverged about 25 Mya. Many of the D. repleta group species studied here have two functional Adh genes (Adh-1 and Adh-2), and these duplicated genes can be explained by two duplication events...
  20. Tautz D, Nigro L. Microevolutionary divergence pattern of the segmentation gene hunchback in Drosophila. Mol Biol Evol. 1998;15:1403-11 pubmed publisher
    ..melanogaster, as well as from the closely related species Drosophila sechellia, Drosophila orena, and Drosophila yakuba. We find a relatively low degree of sequence variation in D. melanogaster (theta = 0...
  21. Guo Y, Jangi S, Welte M. Organelle-specific control of intracellular transport: distinctly targeted isoforms of the regulator Klar. Mol Biol Cell. 2005;16:1406-16 pubmed publisher
    ..Such isoform variation may be a general strategy for adapting a common regulatory mechanism to specifically control motion and positioning of multiple organelles...
  22. Loppin B, Lepetit D, Dorus S, Couble P, Karr T. Origin and neofunctionalization of a Drosophila paternal effect gene essential for zygote viability. Curr Biol. 2005;15:87-93 pubmed publisher
    ..We present a detailed case history of the origin and evolution of a new essential gene and, in so doing, provide the first molecular identification of a Drosophila paternal effect gene, ms(3)K81 (K81)...
  23. ten Bosch J, Benavides J, Cline T. The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription. Development. 2006;133:1967-77 pubmed publisher
  24. Kalamegham R, Sturgill D, Siegfried E, Oliver B. Drosophila mojoless, a retroposed GSK-3, has functionally diverged to acquire an essential role in male fertility. Mol Biol Evol. 2007;24:732-42 pubmed publisher
    ..We postulate that mjl has undergone functional diversification and is now under stabilizing selection in the Drosophila genus...
  25. Cao J, Wu X, Jin Y. Lower GC-content in editing exons: implications for regulation by molecular characteristics maintained by selection. Gene. 2008;421:14-9 pubmed publisher
    ..Thus, relations between molecular characteristics of DNA, RNA editing and purifying selection might be present...
  26. Walrad P, Hang S, Joseph G, Salas J, Gergen J. Distinct contributions of conserved modules to Runt transcription factor activity. Mol Biol Cell. 2010;21:2315-26 pubmed publisher
    ..These results provide a foundation for further studies on the molecular interactions that contribute to the context-dependent properties of Runx proteins as developmental regulators...
  27. Renault A, Axton J. Identification of plu genes and cis-acting elements of PCNA in the Drosophila genus using conservation of gene order. Gene. 2003;307:77-86 pubmed
    ..Of the transcriptional control elements of D. melanogaster PCNA, we found that three motifs 5' to the PCNA transcription unit are conserved in Drosophila species. ..
  28. Wong A, Christopher A, Buehner N, Wolfner M. Immortal coils: conserved dimerization motifs of the Drosophila ovulation prohormone ovulin. Insect Biochem Mol Biol. 2010;40:303-10 pubmed publisher
  29. Wunderlich Z, Bragdon M, Vincent B, White J, Estrada J, DePace A. Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers. Cell Rep. 2015;12:1740-7 pubmed publisher
    ..we analyzed expression driven by orthologous pairs of shadow enhancers from Drosophila melanogaster, Drosophila yakuba, and Drosophila pseudoobscura that control expression of Krüppel, a transcription factor that patterns ..
  30. Clark J, Altheide T, Schlosser M, Kidwell M. Molecular evolution of P transposable elements in the genus Drosophila. I. The saltans and willistoni species groups. Mol Biol Evol. 1995;12:902-13 pubmed publisher
    ..Such explanations are not mutually exclusive, and each may be involved to varying degrees in the maintenance of P elements in natural populations of Drosophila...
  31. Long M, Wang W, Zhang J. Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila. Gene. 1999;238:135-41 pubmed
    ..We name this duplicate gene in Drosophila teissieri and Drosophila yakuba and its orthologous gene in Drosophila melanogaster as yellow-emperor (ymp)...
  32. Spokony R, Restifo L. Anciently duplicated Broad Complex exons have distinct temporal functions during tissue morphogenesis. Dev Genes Evol. 2007;217:499-513 pubmed publisher
    ..The sequential action of BRC isoforms indicates subfunctionalization of duplicated ZBRC exons even when they contribute to common developmental processes...
  33. Palsson A, Wesolowska N, Reynisdóttir S, Ludwig M, Kreitman M. Naturally occurring deletions of hunchback binding sites in the even-skipped stripe 3+7 enhancer. PLoS ONE. 2014;9:e91924 pubmed publisher
    ..The data reveal segregating variation in regulatory elements, which may reflect evolutionary turnover of characterized TFBS due to drift or co-evolution. ..
  34. Rosato E, Trevisan A, Sandrelli F, Zordan M, Kyriacou C, Costa R. Conceptual translation of timeless reveals alternative initiating methionines in Drosophila. Nucleic Acids Res. 1997;25:455-8 pubmed
    ..Given the current interest in TIM regulation in D. melanogaster, it is important to correctly define the N-terminus in this species...
  35. Bretman A, Rouse J, Westmancoat J, Chapman T. The role of species-specific sensory cues in male responses to mating rivals in Drosophila melanogaster fruitflies. Ecol Evol. 2017;7:9247-9256 pubmed publisher
    ..minimize "off-target" responses to heterospecific males that they might encounter (Drosophila simulans, Drosophila yakuba, Drosophila pseudoobscura, or Drosophila virilis). Focal D...
  36. Dorit R, Ayala F. ADH evolution and the phylogenetic footprint. J Mol Evol. 1995;40:658-62 pubmed
  37. O Grady P, Clark J, Kidwell M. Phylogeny of the Drosophila saltans species group based on combined analysis of nuclear and mitochondrial DNA sequences. Mol Biol Evol. 1998;15:656-64 pubmed publisher
    ..As with previous morphological studies, phylogenetic relationships within the saltans subgroup were not satisfactorily resolved by the molecular data...
  38. Lazzaro B. Elevated polymorphism and divergence in the class C scavenger receptors of Drosophila melanogaster and D. simulans. Genetics. 2005;169:2023-34 pubmed publisher
    ..Interestingly, Sr-CIII and Sr-CIV are polymorphic for premature stop codons. Sr-CIV is also polymorphic for an in-frame 101-codon deletion and for the absence of one intron...
  39. Long M, Langley C. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science. 1993;260:91-5 pubmed
    ..This novel chimeric gene, jingwei, differs from its parent Adh gene in both its pattern of expression and rate of molecular evolution. Natural selection participated in the origin and subsequent evolution of this gene...
  40. Maka owski W. Genomic scrap yard: how genomes utilize all that junk. Gene. 2000;259:61-7 pubmed
    ..As such, repetitive elements should be called genomic scrap yard rather than junk DNA. Tables listing examples of recruited (exapted) transposable elements are available at http://www.ncbi.nlm.gov/Makalowski/ScrapYard/..
  41. Pasini M, Intra J, Pavesi G. Expression study of an alpha-l-fucosidase gene in the Drosophilidae family. Gene. 2008;420:23-33 pubmed publisher
    ..These findings support the hypothesis that the enzyme is involved in the molecular events of primary gamete interactions that are conserved among drosophilids belonging to Drosophila genus. ..
  42. Rogers R, Cridland J, Shao L, Hu T, Andolfatto P, Thornton K. Tandem Duplications and the Limits of Natural Selection in Drosophila yakuba and Drosophila simulans. PLoS ONE. 2015;10:e0132184 pubmed publisher
    ..Here, we describe evolutionary impacts of recently-derived, segregating tandem duplications in Drosophila yakuba and Drosophila simulans...
  43. Sirot L, Findlay G, Sitnik J, Frasheri D, Avila F, Wolfner M. Molecular characterization and evolution of a gene family encoding both female- and male-specific reproductive proteins in Drosophila. Mol Biol Evol. 2014;31:1554-67 pubmed publisher
    ..After duplication and male co-option of one paralog, the evolution of the interacting proteins could have resulted in differential strengths or effects of each paralog. ..
  44. Sawyer S, Hartl D. Population genetics of polymorphism and divergence. Genetics. 1992;132:1161-76 pubmed
    ..the sample configurations of nucleotides in the alcohol dehydrogenase gene (Adh) in Drosophila simulans and Drosophila yakuba. Assuming a synonymous mutation rate of 1...
  45. Takahashi A. Effect of exonic splicing regulation on synonymous codon usage in alternatively spliced exons of Dscam. BMC Evol Biol. 2009;9:214 pubmed publisher
  46. Kogan G, Usakin L, Ryazansky S, Gvozdev V. Expansion and evolution of the X-linked testis specific multigene families in the melanogaster species subgroup. PLoS ONE. 2012;7:e37738 pubmed publisher
  47. Hodar C, Zúñiga A, Pulgar R, Travisany D, Chacón C, Pino M, et al. Comparative gene expression analysis of Dtg, a novel target gene of Dpp signaling pathway in the early Drosophila melanogaster embryo. Gene. 2014;535:210-7 pubmed publisher
    ..These results suggest that Dtg was recruited as a new component of the network that controls dorsal ectoderm patterning in the lineage leading to higher Cyclorrhaphan flies, such as D. melanogaster and M. domestica. ..
  48. Kerekes E, Kókai E, Páldy F, Dombradi V. Functional analysis of the glycogen binding subunit CG9238/Gbs-70E of protein phosphatase 1 in Drosophila melanogaster. Insect Biochem Mol Biol. 2014;49:70-9 pubmed publisher
    ..Our results prove that Gbs-70E functions as the glycogen binding subunit of protein phosphatase 1 that regulates glycogen content and plays a role in the development of eggs in D. melanogaster. ..
  49. Clary D, Goddard J, Martin S, Fauron C, Wolstenholme D. Drosophila mitochondrial DNA: a novel gene order. Nucleic Acids Res. 1982;10:6619-37 pubmed
    Part of the replication origin-containing A+T-rich region of the Drosophila yakuba mtDNA molecule and segments on either side of this region have been sequenced, and the genes within them identified...
  50. Begun D, Whitley P. Adaptive evolution of relish, a Drosophila NF-kappaB/IkappaB protein. Genetics. 2000;154:1231-8 pubmed
    ..melanogaster. The adaptive evolution appears to be restricted to the IkappaB domain. A possible explanation for these results is that Relish is a site of evolutionary conflict between flies and their microbial pathogens...
  51. Andersen S. Studies on resilin-like gene products in insects. Insect Biochem Mol Biol. 2010;40:541-51 pubmed publisher
    ..Gene products which are predicted to possess long-range elasticity, but do not contain a chitin-binding region, should not be classified as pro-resilin-like proteins until it has been established that they are cuticular proteins...
  52. Sanfilippo P, Wen J, Lai E. Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species. Genome Biol. 2017;18:229 pubmed publisher
    ..and divergence of APA patterns, we generate developmental and tissue-specific 3'-seq libraries from Drosophila yakuba and Drosophila virilis...
  53. Clary D, Wahleithner J, Wolstenholme D. Transfer RNA genes in Drosophila mitochondrial DNA: related 5' flanking sequences and comparisons to mammalian mitochondrial tRNA genes. Nucleic Acids Res. 1983;11:2411-25 pubmed
    Genes for tRNAgly and tRNAserUCN have been identified within sequences of mtDNA of Drosophila yakuba. The tRNAgly gene lies between the genes for cytochrome c oxidase subunit III and URF3, and all three of these genes are contained in ..
  54. Yassin A. Drosophila yakuba mayottensis, a new model for the study of incipient ecological speciation. Fly (Austin). 2017;11:37-45 pubmed publisher
    ..recent study, we described an early stage of ecological speciation in a population of the generalist species Drosophila yakuba (melanogaster subgroup) on the island of Mayotte (Indian Ocean)...
  55. Ayala F, Hartl D. Molecular drift of the bride of sevenless (boss) gene in Drosophila. Mol Biol Evol. 1993;10:1030-40 pubmed
    ..The data also imply that random genetic drift has been responsible for virtually all of the observed differences in the portion of the boss gene analyzed among the four species. ..
  56. Llopart A, Comeron J, Brunet F, Lachaise D, Long M. Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection. Proc Natl Acad Sci U S A. 2002;99:8121-6 pubmed publisher
    ..Forward simulations suggest that the intensity of this selection is weak to moderate, roughly equal to the selection intensity on most replacement mutations in Drosophila...
  57. Duvernell D, Schmidt P, Eanes W. Clines and adaptive evolution in the methuselah gene region in Drosophila melanogaster. Mol Ecol. 2003;12:1277-85 pubmed
    ..However, Ka : Ks ratios indicate a difference in levels of functional constraint at the two methuselah, loci with mth2 exhibiting a five- to six-fold reduction in levels of amino acid divergence relative to mth...
  58. Presgraves D, Balagopalan L, Abmayr S, Orr H. Adaptive evolution drives divergence of a hybrid inviability gene between two species of Drosophila. Nature. 2003;423:715-9 pubmed publisher
    ..These results show that a lethal hybrid incompatibility has evolved as a by-product of adaptive protein evolution...
  59. Tchoubrieva E, Gibson J. Conserved (CT)n.(GA)n repeats in the non-coding regions at the Gpdh locus are binding sites for the GAGA factor in drosophila melanogaster and its sibling species. Genetica. 2004;121:55-63 pubmed
    ..Using in vitro DNA-footprint analyses we show that the GAGA factor binds to these multiple closely spaced and overlapping conserved (CT)n.(GA)n repeats in D. melanogaster and D. erecta...
  60. Maheshwari S, Barbash D. An indel polymorphism in the hybrid incompatibility gene lethal hybrid rescue of Drosophila is functionally relevant. Genetics. 2012;192:683-91 pubmed publisher
    ..Through a series of transgenic constructs we demonstrate that the ancestral deletion state contributes to the rescue activity of Lhr(2). This indel is thus a polymorphism that can affect the HI function of Lhr. ..
  61. Reinhardt J, Jones C. Two rapidly evolving genes contribute to male fitness in Drosophila. J Mol Evol. 2013;77:246-59 pubmed publisher
    ..Together these data provide a clear case where a lack of sequence conservation does not imply a lack of conservation of expression or function. ..
  62. Wang Z, Schmid K, Ackerman S. The Drosophila gene 2A5 complements the defect in mitochondrial F1-ATPase assembly in yeast lacking the molecular chaperone Atp11p. FEBS Lett. 1999;452:305-8 pubmed
    ..cerevisiae Atp11p. A cDNA encoding the putative Atp11p from Drosophila yakuba was shown to complement the respiratory deficient phenotype of yeast harboring an atp11::HIS3 disruption ..
  63. Hsu S, Yonekura S, Ting C, Robertson H, Iwai Y, Uemura T, et al. Conserved alternative splicing and expression patterns of arthropod N-cadherin. PLoS Genet. 2009;5:e1000441 pubmed publisher
    ..Ectopic muscle expression of either isoform beyond the time it normally ceases leads to paralysis and lethality. Together, our results offer an example of well-conserved alternative splicing increasing cellular diversity in metazoans...
  64. Alvi Z, Chu T, Schawaroch V, Klaus A. Protamine-like proteins in 12 sequenced species of Drosophila. Protein Pept Lett. 2013;20:17-35 pubmed
    ..This study represents the first large-scale, single-genus dataset for protamine-like proteins and provides the basis for a fine-grained analysis of their evolution...
  65. Jeffs P, Ashburner M. Processed pseudogenes in Drosophila. Proc Biol Sci. 1991;244:151-9 pubmed publisher
    ..Remarkably, the pattern of base substitution in the pseudogenes differs between sites that correspond to degenerate and non-degenerate codon positions in their functional paralogs...
  66. Clary D, Wolstenholme D. Genes for cytochrome c oxidase subunit I, URF2, and three tRNAs in Drosophila mitochondrial DNA. Nucleic Acids Res. 1983;11:6859-72 pubmed
    ..tRNAtyr and cytochrome c oxidase subunit I (COI) have been identified within a sequenced segment of the Drosophila yakuba mtDNA molecule. The five genes are arranged in the order given...
  67. Eanes W, Kirchner M, Yoon J, Biermann C, Wang I, McCartney M, et al. Historical selection, amino acid polymorphism and lineage-specific divergence at the G6pd locus in Drosophila melanogaster and D. simulans. Genetics. 1996;144:1027-41 pubmed
    ..Lineage-specific differences in mutation fixation are inconsistent with neutral expectations and suggest the interaction of species-specific population size differences with both weakly advantageous and deleterious selection...
  68. Capy P. Evolutionary biology. A plastic genome. Nature. 1998;396:522-3 pubmed publisher
  69. Cariou M, Silvain J, Daubin V, Da Lage J, Lachaise D. Divergence between Drosophila santomea and allopatric or sympatric populations of D. yakuba using paralogous amylase genes and migration scenarios along the Cameroon volcanic line. Mol Ecol. 2001;10:649-60 pubmed
    ..Despite their different modes of evolution and different functions, the Amyrel and Amy genes provide remarkably consistent topologies and hence reflect the same history, that of the species...
  70. Manheim E, Jang J, Dominic D, McKim K. Cytoplasmic localization and evolutionary conservation of MEI-218, a protein required for meiotic crossing-over in Drosophila. Mol Biol Cell. 2002;13:84-95 pubmed publisher
    ..We propose that mei-218 is a molecular link between oocyte differentiation and meiosis...
  71. Skaer N, Pistillo D, Gibert J, 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;18:399-405 pubmed
    ..This probably coincided in time with gene duplication events, raising the possibility that an increase in gene copy number might have provided the flexibility necessary for more complex transcriptional regulation...
  72. Ohta T. Near-neutrality in evolution of genes and gene regulation. Proc Natl Acad Sci U S A. 2002;99:16134-7 pubmed publisher
    ..In addition to the effective population size, molecular chaperones such as heat shock protein 90 have significant effects on the range of near neutrality...
  73. Lee C, Kim N, Roy M, Graveley B. Massive expansions of Dscam splicing diversity via staggered homologous recombination during arthropod evolution. RNA. 2010;16:91-105 pubmed publisher
    ..These data provide a remarkably detailed picture of how complex gene structure evolves and reveal the molecular mechanism behind this process...
  74. Moses A. Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites. BMC Evol Biol. 2009;9:286 pubmed publisher
    ..This demonstrates that it is possible to develop tests for selection on regulatory regions based on the specific functional constrains on these sequences...
  75. Baumann A, Fujiwara Y, Wilson T. Evolutionary divergence of the paralogs Methoprene tolerant (Met) and germ cell expressed (gce) within the genus Drosophila. J Insect Physiol. 2010;56:1445-55 pubmed publisher
    ..Our results suggest that Drosophila Met and gce experienced divergent evolutionary pressures following the duplication of an ancestral gce-like gene found in less derived holometabolous insects...
  76. Quezada D az J, Muliyil T, R o J, Betr n E. Drcd-1 related: a positively selected spermatogenesis retrogene in Drosophila. Genetica. 2010;138:925-37 pubmed publisher
    ..Analysis of this strain reveals the difficulties that can be encountered in studying the functions of genes with overlapping transcripts. Avenues for studying of the function of this gene are proposed...
  77. Jung I, Kim T, Kim Ha J. Identification of Drosophila SOD3 and its protective role against phototoxic damage to cells. FEBS Lett. 2011;585:1973-8 pubmed publisher
    ..In addition, the dSod3 protein alleviates ultraviolet-induced cellular damage. These results suggest that dSod3 functions as an extracellular SOD3...
  78. Wen M, Shen Y, Shi S, Tang T. miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments. BMC Bioinformatics. 2012;13:140 pubmed publisher
    ..MiREvo is standalone, modular, and freely available at http://evolution.sysu.edu.cn/software/mirevo.htm under the GNU/GPL license...
  79. Wunderlich Z, Bragdon M, Eckenrode K, Lydiard Martin T, Pearl Waserman S, DePace A. Dissecting sources of quantitative gene expression pattern divergence between Drosophila species. Mol Syst Biol. 2012;8:604 pubmed publisher
  80. McDonald J, Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 1991;351:652-4 pubmed publisher
    ..We suggest that these excess replacement substitutions result from adaptive fixation of selectively advantageous mutations...
  81. Luque T, Marfany G, Gonz lez Duarte R. Characterization and molecular analysis of Adh retrosequences in species of the Drosophila obscura group. Mol Biol Evol. 1997;14:1316-25 pubmed publisher
    ..The significance of retrotranscriptional events in the evolution of invertebrate genomes is discussed...
  82. D Amico S, Gerday C, Feller G. Structural similarities and evolutionary relationships in chloride-dependent alpha-amylases. Gene. 2000;253:95-105 pubmed
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    ..We propose that the basic region may mediate DNA binding and that the glycine-rich region may promote the association of MSL complexes to closely adjacent sites on the X chromosome...
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    ..The second gene, CG9997, was previously shown to be essential for normal sperm usage, suggesting that sexual selection may underlie its history of adaptation...
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    ..Large introns could be a reservoir of genetic diversity, because they have a greater number of mutable sites than short introns. Taken together, gene structure can constrain and/or promote gene evolution...
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    ..Single-nucleotide substitutions in these elements dramatically changed the promoter activity. These results provide insight into the molecular mechanism for evolution of adaptive behavior via modulation of OBP expression levels...
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    ..The diversity of Mtn patterns in closely related Drosophila species exemplifies the rapid evolution of a gene regulatory system...
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    ..The screen that yielded new sc alleles also generated autosomal duplications that argue against the textbook view that fruit fly sex signal evolution recruited a set of autosomal signal elements comparable to the XSEs...
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    ..melanogaster. The results suggest that the gtwin element may be an infectious retrovirus able to invade the genome of new species, supporting the gtwin evolutionary picture shown in this work...
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    ..Differences in the pattern of amino acid fixations between these 2 interacting proteins suggest that the detected positive selection is not due to a simple model of coevolution...
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    ..These genes are evolving rapidly, in some cases under directional selection, consistent with models of conflict...
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    ..Drosophila erecta, Drosophila sechellia, Drosophila simulans, and Drosophila yakuba shared 62.5-87.5% identity to Drosophila melanogaster DSK 0; Drosophila pseudoobscura shared 37...
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    ..Disablement of the ran-like gene in D. yakuba indicates turnover of these duplicates. We discuss the possibility that Dntf-2r and ran-like might be involved in genomic conflicts during spermatogenesis...
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    ..Our results provide insight into the molecular mechanisms of feeding acceptance of yeast products and raise the possibility that Gr64e contributes to specific evolutionary variations in appetitive selectivity across Drosophila species...