Drosophila yakuba

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Alias:

Top Publications

  1. 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 ..
  2. 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. ..
  3. 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
    ..Such isoform variation may be a general strategy for adapting a common regulatory mechanism to specifically control motion and positioning of multiple organelles. ..
  4. 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)...
  5. 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. ..
  6. 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...
  7. 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. ..
  8. 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
  9. 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. ..

More Information

Publications176 found, 100 shown here

  1. 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...
  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. 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...
  4. 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...
  5. 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. ..
  6. 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
  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. 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...
  11. 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...
  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. 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...
  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. 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 ..
  16. Llopart A, Herrig D, Brud E, Stecklein Z. Sequential adaptive introgression of the mitochondrial genome in Drosophila yakuba and Drosophila santomea. Mol Ecol. 2014;23:1124-36 pubmed publisher
    ..Here we report the sequences of 46 complete mitochondrial genomes of Drosophila yakuba and Drosophila santomea, two sister species known to produce hybrids in nature (~3%)...
  17. Rogers R, Cridland J, Shao L, Hu T, Andolfatto P, Thornton K. Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans. Mol Biol Evol. 2014;31:1750-66 pubmed publisher
    ..used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of Drosophila yakuba and 20 isofemale lines of D...
  18. Yassin A, Debat V, Bastide H, Gidaszewski N, David J, Pool J. Recurrent specialization on a toxic fruit in an island Drosophila population. Proc Natl Acad Sci U S A. 2016;113:4771-6 pubmed publisher
    ..We discovered on the island of Mayotte a population of the generalist fly Drosophila yakuba that is strictly associated with noni (Morinda citrifolia)...
  19. Peluffo A, Nuez I, Debat V, Savisaar R, Stern D, Orgogozo V. A Major Locus Controls a Genital Shape Difference Involved in Reproductive Isolation Between Drosophila yakuba and Drosophila santomea. G3 (Bethesda). 2015;5:2893-901 pubmed publisher
    ..We conclude that the genetic architecture of genitalia morphology divergence may not always be as complex as suggested by previous studies. ..
  20. Chen Z, Lu L, Lu M, Du Y. Comparative mitogenomic analysis of Aposthonia borneensis and Aposthonia japonica (Embioptera: Oligotomidae) reveals divergent evolution of webspinners. Sci Rep. 2017;7:8279 pubmed publisher
    ..The mtDNA map in A. borneensis is similar to Drosophila yakuba, but distinctly different from A. japonica, which has extensive rearrangement...
  21. Chen Z, Du Y. The first two mitochondrial genomes from Taeniopterygidae (Insecta: Plecoptera): Structural features and phylogenetic implications. Int J Biol Macromol. 2018;111:70-76 pubmed publisher
    ..of the two taeniopterygids and other stoneflies was identical with the putative ancestral mitogenome of Drosophila yakuba. Most PCGs used standard ATN start codons and TAN termination codons...
  22. Denis B, Rouzic A, Wicker Thomas C. Hydrocarbon Patterns and Mating Behaviour in Populations of Drosophila yakuba. Insects. 2015;6:897-911 pubmed publisher
    b>Drosophila yakuba is widespread in Africa. Here we compare the cuticular hydrocarbon (CHC) profiles and mating behavior of mainland (Kounden, Cameroon) and island (Mayotte, Sao-Tome, Bioko) populations...
  23. Comeault A, Venkat A, Matute D. Correlated evolution of male and female reproductive traits drive a cascading effect of reinforcement in Drosophila yakuba. Proc Biol Sci. 2016;283: pubmed publisher
    ..Here we address this issue in the fruit fly Drosophila yakuba, a species that hybridizes with its sister species D...
  24. Llopart A, Brud E, Pettie N, Comeron J. Support for the Dominance Theory in Drosophila Transcriptomes. Genetics. 2018;210:703-718 pubmed publisher
    ..Here, we study genome-wide patterns of gene expression in females and males of Drosophila yakuba, Drosophila santomea and their hybrids...
  25. Shibata H, Yamazaki T. A comparative study of the enzymological features of alpha-amylase in the Drosophila melanogaster species subgroup. Jpn J Genet. 1994;69:251-8 pubmed
    ..We found clear differences in the enzymological features between the species. Thus these differences might reflect an adaptation of the amylase enzyme system to speciation in this species subgroup. ..
  26. Lunetti P, Cappello A, Marsano R, Pierri C, Carrisi C, Martello E, et al. Mitochondrial glutamate carriers from Drosophila melanogaster: biochemical, evolutionary and modeling studies. Biochim Biophys Acta. 2013;1827:1245-55 pubmed publisher
  27. Clary D, Wahleithner J, Wolstenholme D. Sequence and arrangement of the genes for cytochrome b, URF1, URF4L, URF4, URF5, URF6 and five tRNAs in Drosophila mitochondrial DNA. Nucleic Acids Res. 1984;12:3747-62 pubmed
    The nucleotide sequence of a segment of the mtDNA molecule of Drosophila yakuba has been determined, within which have been identified the 3' end of the large rRNA gene and the entire genes for tRNAleuCUN , URF1 , tRNAserUCN , cytochrome ..
  28. Zhan Z, Ding Y, Zhao R, Zhang Y, Yu H, Zhou Q, et al. Rapid functional divergence of a newly evolved polyubiquitin gene in Drosophila and its role in the trade-off between male fecundity and lifespan. Mol Biol Evol. 2012;29:1407-16 pubmed publisher
    ..These results suggest that CG11700 might have experienced neofunctionalization and evolved important functions in the trade-off between male fecundity and lifespan and that CG32744 likely has retained the ancestral function. ..
  29. Casso D, Liu S, Biehs B, Kornberg T. Expression and characterization of Drosophila signal peptide peptidase-like (sppL), a gene that encodes an intramembrane protease. PLoS ONE. 2012;7:e33827 pubmed publisher
    ..This was unexpected given that genetic knockdown phenotypes in other organisms suggested significant roles for Spp-related proteases. ..
  30. Schmidt P, Duvernell D, Eanes W. Adaptive evolution of a candidate gene for aging in Drosophila. Proc Natl Acad Sci U S A. 2000;97:10861-5 pubmed publisher
    ..Together, these consistently nonneutral patterns of inter- and intraspecific variation suggest adaptive evolution of a signal transduction pathway that may modulate lifespan in nature...
  31. Meyerowitz E, Martin C. Adjacent chromosomal regions can evolve at very different rates: evolution of the Drosophila 68C glue gene cluster. J Mol Evol. 1984;20:251-64 pubmed
    ..melanogaster glue mRNAs. The highly conserved region is at least 13,000 bp long, and is not known to code for any RNAs. ..
  32. Okuyama E, Shibata H, Tachida H, Yamazaki T. Molecular evolution of the 5'-flanking regions of the duplicated Amy genes in Drosophila melanogaster species subgroup. Mol Biol Evol. 1996;13:574-83 pubmed
    ..From these observations, we discuss a possibility of positive selection acting on the subregion immediately upstream of the Amy coding region to cause divergence of regulatory elements of the paralogous genes. ..
  33. Katoh T, Tamura K, Aotsuka T. Phylogenetic position of the subgenus Lordiphosa of the genus Drosophila (Diptera: Drosophilidae) inferred from alcohol dehydrogenase (Adh) gene sequences. J Mol Evol. 2000;51:122-30 pubmed publisher
  34. Verrelli B, Eanes W. Extensive amino acid polymorphism at the pgm locus is consistent with adaptive protein evolution in Drosophila melanogaster. Genetics. 2000;156:1737-52 pubmed
    ..Like G6pd, Pgm shows strong evidence for a branch point enzyme that exhibits adaptive protein evolution...
  35. Balakirev E, Ayala F. Pseudogenes: are they "junk" or functional DNA?. Annu Rev Genet. 2003;37:123-51 pubmed publisher
    ..We agree with the proposal that pseudogenes be considered as potogenes, i.e., DNA sequences with a potentiality for becoming new genes...
  36. Llopart A, Lachaise D, Coyne J. An anomalous hybrid zone in Drosophila. Evolution. 2005;59:2602-7 pubmed
    ..Here we describe a classic hybrid zone in Drosophila that involves two sister species, Drosophila yakuba and D. santomea, on the island of São Tomé...
  37. Murawska M, Kunert N, van Vugt J, L ngst G, Kremmer E, Logie C, et al. dCHD3, a novel ATP-dependent chromatin remodeler associated with sites of active transcription. Mol Cell Biol. 2008;28:2745-57 pubmed publisher
    ..Unlike dMi-2, dCHD3 exists as a monomer. Nevertheless, both proteins colocalize with RNA polymerase II to actively transcribed regions on polytene chromosomes, suggesting that both remodelers participate in the process of transcription...
  38. Morozov P, Sitnikova T, Churchill G, Ayala F, Rzhetsky A. A new method for characterizing replacement rate variation in molecular sequences. Application of the Fourier and wavelet models to Drosophila and mammalian proteins. Genetics. 2000;154:381-95 pubmed
    ..We illustrate the application of the new method by analyzing human immunoglobulin and Drosophilid alcohol dehydrogenase sequences...
  39. Jones C, Custer A, Begun D. Origin and evolution of a chimeric fusion gene in Drosophila subobscura, D. madeirensis and D. guanche. Genetics. 2005;170:207-19 pubmed publisher
    ..We present a model for the origin of this new gene and discuss genetic and evolutionary factors affecting the evolution of new genes and functions...
  40. Wu Y, Dai R, Zhan H, Qu L. Complete mitochondrial genome of Drabescoides nuchalis (Hemiptera: Cicadellidae). Mitochondrial DNA A DNA Mapp Seq Anal. 2016;27:3626-7 pubmed publisher
    ..The anticodons are identical to those of Drosophila yakuba. The phylogenetic tree confirms D...
  41. Yurlova A, Makunin I, Kolesnikova T, Posukh O, Belyaeva E, Zhimulev I. Conservation of domain structure in a fast-evolving heterochromatic SUUR protein in drosophilids. Genetics. 2009;183:119-29 pubmed publisher
    ..The C terminus contains interlacing conserved and variable motifs. Our results suggest that SUUR domains evolve with different rates and patterns but maintain their features. ..
  42. Sorourian M, BETRAN E. Turnover and lineage-specific broadening of the transcription start site in a testis-specific retrogene. Fly (Austin). 2010;4:3-11 pubmed
    ..This work reveals the difficulties of studying gene regulation in one species and extrapolating those findings to close relatives. ..
  43. Beck E, Thompson A, Sharbrough J, Brud E, Llopart A. Gene flow between Drosophila yakuba and Drosophila santomea in subunit V of cytochrome c oxidase: A potential case of cytonuclear cointrogression. Evolution. 2015;69:1973-86 pubmed publisher
    ..Previous genetic analyses of the Drosophila yakuba-D. santomea hybrid zone showed that the mitochondrial genome of D. yakuba had introgressed into D...
  44. Langley C, Montgomery E, Quattlebaum W. Restriction map variation in the Adh region of Drosophila. Proc Natl Acad Sci U S A. 1982;79:5631-5 pubmed
    ..006. The relative distributions of restriction sites and insertion/deletion variations among subpopulations and species suggest that the insertion/deletion variation may be mildly deleterious. ..
  45. Matsumoto H, Tsuzuki S, Date Ito A, Ohnishi A, Hayakawa Y. Characteristics common to a cytokine family spanning five orders of insects. Insect Biochem Mol Biol. 2012;42:446-54 pubmed publisher
    ..These data indicate that these small cytokines belonging to one family are present in at least five insect orders. ..
  46. Turissini D, Liu G, David J, Matute D. The evolution of reproductive isolation in the Drosophila yakuba complex of species. J Evol Biol. 2015;28:557-75 pubmed publisher
    ..Our results open the possibility of studying the history of introgression in the yakuba species complex and dissecting the genetic basis of interspecific differences between these three species by genetic mapping. ..
  47. Matute D. Noisy neighbors can hamper the evolution of reproductive isolation by reinforcing selection. Am Nat. 2015;185:253-69 pubmed publisher
    ..In areas of secondary contact with Drosophila santomea, Drosophila yakuba females show reinforcement of gametic isolation but not behavioral isolation, despite the fact that both ..
  48. Parsch J, Meiklejohn C, Hauschteck Jungen E, Hunziker P, Hartl D. Molecular evolution of the ocnus and janus genes in the Drosophila melanogaster species subgroup. Mol Biol Evol. 2001;18:801-11 pubmed publisher
    ..These results are consistent with previous studies that have detected an increased rate of evolution in genes with reproductive function...
  49. Date Ito A, Kasahara K, Sawai H, Chigusa S. Rapid evolution of the male-specific antibacterial protein andropin gene in Drosophila. J Mol Evol. 2002;54:665-70 pubmed publisher
    ..The series of present results suggests that Andropin was born in the course of constructing the Drosophila Cecropin gene family and then started to evolve rapidly, in contrast to Cecropins...
  50. Gao J, Hu Y, Toda M, Katoh T, Tamura K. Phylogenetic relationships between Sophophora and Lordiphosa, with proposition of a hypothesis on the vicariant divergences of tropical lineages between the Old and New Worlds in the family Drosophilidae. Mol Phylogenet Evol. 2011;60:98-107 pubmed publisher
  51. Parker D, Gardiner A, Neville M, Ritchie M, Goodwin S. The evolution of novelty in conserved genes; evidence of positive selection in the Drosophila fruitless gene is localised to alternatively spliced exons. Heredity (Edinb). 2014;112:300-6 pubmed publisher
    ..Alternative splicing may thus provide a route to gene diversification in key regulatory loci. ..
  52. Wojtas K, von Kalm L, Weaver J, Sullivan D. The evolution of duplicate glyceraldehyde-3-phosphate dehydrogenase genes in Drosophila. Genetics. 1992;132:789-97 pubmed
    ..Species of the subgenus Drosophila have a single Gapdh gene with an intron. Species of the willistoni and saltans groups have a single Gapdh gene that does not contain an intron.(ABSTRACT TRUNCATED AT 250 WORDS) ..
  53. Andersson S, Lambertsson A. Evolution of the dec-1 eggshell locus in Drosophila. I. Restriction site mapping and limited sequence comparison in the melanogaster species subgroup. J Mol Evol. 1991;33:321-31 pubmed
    ..teissieri and D. yakuba. ..
  54. Ross J, Fong P, Cavener D. Correlated evolution of the cis-acting regulatory elements and developmental expression of the Drosophila Gld gene in seven species from the subgroup melanogaster. Dev Genet. 1994;15:38-50 pubmed publisher
    ..Together these data suggest the absence or presence of the TTAGA elements may be responsible for variation in the absence or presence of GLD in the ejaculatory duct among species...
  55. Da Lage J, Renard E, Chartois F, Lemeunier F, Cariou M. Amyrel, a paralogous gene of the amylase gene family in Drosophila melanogaster and the Sophophora subgenus. Proc Natl Acad Sci U S A. 1998;95:6848-53 pubmed
    ..Amyrel evolves about twice as fast as Amy in the several species studied. We suggest that this gene could result from a duplication of Amy followed by accelerated and selected divergence toward a new adaptation. ..
  56. Robin G, Russell R, Cutler D, Oakeshott J. The evolution of an alpha-esterase pseudogene inactivated in the Drosophila melanogaster lineage. Mol Biol Evol. 2000;17:563-75 pubmed publisher
    ..melanogaster populations and single alleles from Drosophila simulans and Drosophila yakuba. All of the DmalphaE4a-Psi alleles contain numerous inactivating mutations, suggesting that pseudogene ..
  57. Lachaise D, Harry M, Solignac M, Lemeunier F, B nassi V, Cariou M. Evolutionary novelties in islands: Drosophila santomea, a new melanogaster sister species from São Tomé. Proc Biol Sci. 2000;267:1487-95 pubmed publisher
    ..period gene and allozymes are provided indicating that it is nonetheless the nearest relative of Drosophila yakuba with which it coexists on the island...
  58. Yang Y, Gupta V, Ho L, Zhou B, Fan Q, Zhu Z, et al. Both upstream and downstream intergenic regions are critical for the mob as tumor suppressor gene activity in Drosophila. FEBS Lett. 2008;582:1766-70 pubmed publisher
    ..Consistent with a model that the downstream intergenic region is critical for mats activity, this sequence contains evolutionarily conserved elements and has enhancer activities. ..
  59. Schmid K, Tautz D. Sequence and expression of DmMKLP1, a homolog of the human MKLP1 kinesin-like protein from Drosophila melanogaster. Dev Genes Evol. 1998;208:474-6 pubmed
    ..Later, the expression becomes increasingly restricted to the developing central nervous system, where it remains expressed at least until the end of embryogenesis. ..
  60. 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...
  61. 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. ..
  62. 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. ..
  63. 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
  64. 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 ..
  65. 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...
  66. 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)...
  67. 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...
  68. 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. ..
  69. 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...
  70. 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...
  71. Dorit R, Ayala F. ADH evolution and the phylogenetic footprint. J Mol Evol. 1995;40:658-62 pubmed
  72. 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...
  73. 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...
  74. 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...
  75. 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/..
  76. 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. ..
  77. 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...
  78. 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. ..
  79. 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...
  80. 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
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    ..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. ..
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    ..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. ..
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    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...
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    ..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...
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    ..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...
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    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 ..
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    ..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. ..
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    ..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...
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    ..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...