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further studies on gene polymorphism in the mainbody and geographically isolated populations of drosophila pseudoobscura.we have examined polymorphism at 22 additional loci in the populations from the mainbody of drosophila pseudoobscura and an isolated population from bogotá, columbia, which also shows partial reproductive isolation from mainbody populations. these studies extend our previous observations of reduced gene polymorphism and apparent lack of unique allele in the bogotá population.1977863242
population genetics of mexican drosophila. i. chromosomal variation in natural populations of drosophila pseudoobscura from central mexico.drosophila pseudoobscura populations of central mexico are chromosomally highly polymorphic. five gene arangements in the third chromosome are endemic, including the two newly described in the present article. the phylogenetic tree of the gene arrangements known in the species is shown in figure 1. the ones found in central mexico all belong to the santa cruz "phylad", while in the northern part of the species area both santa cruz and standard phylads are widespread. some inferences concerning t ...19751165399
the effects of anthranilic acid on gene expression.1. a drosophila pseudoobscura amylase gene cloned in escherichia coli is expressed at high levels. the expression of this gene is repressed when glucose (0.5% final concentration) is added to a starch minimal medium culture of e. coli cells containing the amylase plasmid. 2. addition of anthranilic acid (5 and 7 mm final exogenous concentration) to catabolite repressed cells mimics the action of adenosine 3'5' cyclic monophosphate (camp) by depressing the expression of the amylase. 3. the result ...19901691993
four decades of inversion polymorphism in drosophila pseudoobscura.we report data that continue the studies of dobzhansky and others on the frequencies of third-chromosome inversions in natural populations of drosophila pseudoobscura in north america. the common gene arrangements continue to be present in frequencies similar to those described four decades ago, and the broad geographic patterns also remain unchanged. there is only one pronounced trend over time: the increase in frequency of the tree line inversion in pacific coast populations.19911946458
is there selection on rflp differences in mitochondrial dna?experimental populations of drosophila simulans were established for the purpose of detecting the presence or absence of selection on a restriction fragment length polymorphism in mitochondrial dna (mtdna). it was then discovered that the founding strains differed with respect to the rickettsia-mediated incompatibility system in this species, which is maternally transmitted together with the mtdna differences. a population model was constructed using the known fitness effects of the incompatibil ...19901974225
nucleotide sequence analysis of adh genes estimates the time of geographic isolation of the bogota population of drosophila pseudoobscura.the population of drosophila pseudoobscura at bogota, columbia, is geographically and partially reproductively isolated from populations in the main body of the species in north america. the degree of genetic differentiation and time of divergence between populations at bogota and apple hill, ca, were estimated by comparison of 3388 nucleotides in the alcohol dehydrogenase region (adh and adh-dup genes) of 18 strains. of the 146 polymorphic nucleotide sites detected, 68 and 31 were unique to the ...19912068088
an amylase gene from drosophila pseudoobscura is expressed in escherichia coli. functional selection and biochemical comparisons of the fly- and clone-produced amylases.an amylase gene from drosophila pseudoobscura was isolated from a genomic library constructed in pbr322 and cloned in escherichia coli by selecting for the ability of its product to hydrolyze starch, a carbon source not normally utilized by e. coli. hybridization of pamy17f to d. pseudoobscura polytene chromosomes shows a positive signal at the amylase pseudogene locus (bank 78, chromosome 3). the chimeric plasmid pamy17f, has been altered in such a way as to increase amylase expression. souther ...19872443177
chromosomal and behavioral studies of mexican drosophila. iii. inversion polymorphism of d. pseudoobscura.four new gene arrangements of chromosome 3 of drosophila pseudoobscura are reported, as well as an updated phylogenetic sequence of the inversion polymorphism in this species. evidence that the tree line gene arrangement of chromosome 3 was the original form in d. pseudoobscura, and that central mexico is the center of distribution of this species is discussed.19854031462
genetic analysis of hybrid sterility within the species drosophila pseudoobscura. 19744413557
origin of reproductive isolation in the absence of apparent genic differentiation in a geographic isolate of drosophila pseudoobscura.f(1) males obtained from the cross of d. pseudoobscura females from bogotá (colombia) x males of this species from mainland, i.e. populations from various locations in the united states and from guatemala, are sterile. this sterility is due to genes located on the x chromosome and the autosomes; the y chromosome is not involved. the percentage of sterile males in backcrosses can be explained by assuming an interaction between two loci on the bogotá x chromosome and probably two loci, one each on ...19725073854
studies on the pathogenicity of spiroplasmas for drosophila pseudoobscura.representatives of several currently available spiroplasma serovars were used in feeding and injection experiments involving drosophila pseudoobscura adult flies in order to evaluate the host-range of the spiroplasmas and to determine their pathogenicity for flies. many of the isolates injected into flies either do not survive or grow poorly, and have no negative effects on longevity or fecundity. two spiroplasma strains, honey-bee (serovar i-2) and cornstunt (serovar i-3), can grow to high titr ...19846712059
a critical examination of the dual system theory in ostrinia nubilalis.beck's dual system theory (dst) is examined theoretically and experimentally by investigating the oviposition rhythm of ostrinia nubilalis and its entrainment by light cycles. several well-known circadian phenomena are not accounted for by the dst. 1) it does not generate transient cycles when light pulses fall during the advance portion of the circadian cycle. this is also reflected in dst-predicted phase-response curves (prc's) for both drosophila pseudoobscura and o. nubilalis. steady-state p ...19817304776
conservation and function of the transcriptional regulatory protein runt.a phylogenetic approach was used to identify conserved regions of the transcriptional regulator runt. alignment of the deduced protein sequences from drosophila melanogaster, drosophila pseudoobscura, and drosophila virilis revealed eight blocks of high sequence homology separated by regions with little or no homology. the largest conserved block contains the runt domain, a dna and protein binding domain conserved in a small family of mammalian transcription factors. the functional properties of ...19957568078
structural changes in the antennapedia complex of drosophila pseudoobscura.the discovery of the striking positional conservation between the antennapedia and bithorax homeotic gene complexes (ant-c and bx-c) in drosophila melanogaster and the murine hox and human hox clusters has had a substantial impact on our understanding of the evolution of development and its genetic regulation. structural differences do exist among the mammalian hox complexes and the ant-c in d. melanogaster. to gain further insight into the evolutionary changes among these complexes, the ant-c w ...19938099892
p1 clones from drosophila melanogaster as markers to study the chromosomal evolution of muller's a element in two species of the obscura group of drosophila.thirty p1 clones from the x chromosome (muller's a element) of drosophila melanogaster were cross-hybridized in situ to drosophila subobscura and drosophila pseudoobscura polytene chromosomes. an additional recombinant phage lambda dsuby was also used as a marker. twenty-three (77%) of the p1 clones gave positive hybridization on d. pseudoobscura chromosomes but only 16 (53%) did so with those of d. subobscura. eight p1 clones gave more than one hybridization signal on d. pseudoobscura and/or d. ...19958585990
cytoplasmic incompatibility and mating preference in colombian drosophila pseudoobscura.macrae and anderson observed a large frequency change of mitochondrial dna (mtdna) haplotypes in a population initiated with two allopatric strains of drosophila pseudoobscura, boger from colombia and ah162 from california. they concluded that mtdna haplotypes in d. pseudoobscura are not always selectively neutral. nigro and prout suggested, however, that a maternally transmitted incompatibility system, similar to the one they observed in two strains of d. simulans from italy, could account for ...19968770596
mitochondrial gene divergence of colombian drosophila pseudoobscura.isolated populations of drosophila pseudoobscura, separated from north american populations by about 2,400 km, were found in colombia in 1960. we compared for sequences of the small ribosomal rna (srrna) gene on the mitochondria between north american and colombian d. pseudoobscura in order to clarify the age of the colombian isolates. the north american populations were not genetically different from each other but were genetically different from the colombian populations. the mexican strains r ...19968896379
the 5' regulatory region from the drosophila pseudoobscura hsp82 gene results in a high level of reporter gene expression in lucilia cuprina embryos.we have previously examined the efficiency of two drosophila melanogaster promoters to enable reporter gene expression in embryos of the australian sheep blowfly, lucilia cuprina. both the hsp70 heat-shock promoter and the actin5c promoter resulted in low levels of expression of a reporter gene in these embryos. in this study, the d. pseudoobscura hsp82 promoter (phsp82) was tested for its ability to direct the expression of the escherichia coli chloramphenicol acetyltransferase-encoding gene (c ...19968917099
the correlation between synonymous and nonsynonymous substitutions in drosophila: mutation, selection or relaxed constraints?codon usage bias, the preferential use of particular codons within each codon family, is characteristic of synonymous base composition in many species, including drosophila, yeast, and many bacteria. preferential usage of particular codons in these species is maintained by natural selection acting largely at the level of translation. in drosophila, as in bacteria, the rate of synonymous substitution per site is negatively correlated with the degree of codon usage bias, indicating stronger select ...19989755207
strong founder effect in drosophila pseudoobscura colonizing new zealand from north america.the north american native species drosophila pseudoobscura was first identified in new zealand in the last few decades. here, we have studied the genetic consequences of its spread across the pacific ocean. using 10 microsatellites that are highly variable in north american populations, we found that the new zealand population has substantially fewer alleles, a much lower average heterozygosity, and significantly different allele frequencies at these loci. we have discussed the relative sensitiv ...200212642641
effects of temperature and temperature-steps on circadian locomotor rhythmicity in the blow fly calliphora vicina.the free-running period (in darkness) of the locomotor activity rhythm in adult blow flies (calliphora vicina) was temperature-compensated between 15 and 25 degrees c, showing q(10) values between 0.98 and 1.04. single steps-up (20 to 25 degrees c) or steps-down (20 to 15 degrees c) in temperature caused stable phase shifts of the activity rhythm, giving rise to temperature-step phase response curves (prcs) with both advances and delays. phase advances, however, were dominant for steps-up, and p ...200012770234
evolutionary genomics of inversions in drosophila pseudoobscura: evidence for epistasis.drosophila pseudoobscura harbors a rich polymorphism for paracentric inversions on the third chromosome, and the clines in the inversion frequencies across the southwestern united states indicate that strong natural selection operates on them. isogenic inversion strains were made from isofemale lines collected from four localities, and eight molecular markers were mapped on the third chromosome. nucleotide diversity was measured for these loci and formed the basis of an evolutionary genomic anal ...200312824467
microrna targets in drosophila.the recent discoveries of microrna (mirna) genes and characterization of the first few target genes regulated by mirnas in caenorhabditis elegans and drosophila melanogaster have set the stage for elucidation of a novel network of regulatory control. we present a computational method for whole-genome prediction of mirna target genes. the method is validated using known examples. for each mirna, target genes are selected on the basis of three properties: sequence complementarity using a position- ...200314709173
the drosophila gene start1: a putative cholesterol transporter and key regulator of ecdysteroid synthesis.human metastatic lymph node 64 (mln64) is a transmembrane protein that shares homology with the cholesterol-binding vertebrate steroid acute regulatory protein (star)-related lipid transfer domain (start) and is involved in cholesterol traffic and steroid synthesis. we identified a drosophila melanogaster gene whose putative protein product shows extensive homology with mln64 and that we name start1 (flybase cg3522). the putative start1 protein, derived from start1 cdna sequences, contains an ad ...200414745013
"plus-c" odorant-binding protein genes in two drosophila species and the malaria mosquito anopheles gambiae.olfaction plays a crucial role in many aspects of insect behaviour, including host selection by agricultural pests and vectors of human disease. insect odorant-binding proteins (obps) are thought to function as the first step in molecular recognition and the transport of semiochemicals. the whole genome sequence of the fruit fly drosophila melanogaster has been completed and a large number of genes have been annotated as obps, based on the presence of six conserved cysteine residues and a conser ...200414960367
detection of stabilizing selection in favor of the santa cruz homokaryotype in drosophila pseudoobscura populations from the high plateau of the colombian andes.chromosome 3 rearrangements were studied in five drosophila pseudoobscura populations from the high plateau of the colombian andes. as in previous studies, the santa cruz and tree line rearrangements were predominant in these populations, but for the first time other rearrangements such as the olympic, cuernavaca and a rearrangement similar to the endemic mexican amecameca rearrangement were also discovered. researchers in the early 1960's showed that colombian d. pseudoobscura populations were ...200214963809
computational identification of microrna targets.recent experiments have shown that the genomes of organisms such as worm, fly, human, and mouse encode hundreds of microrna genes. many of these micrornas are thought to regulate the translational expression of other genes by binding to partially complementary sites in messenger rnas. phenotypic and expression analysis suggests an important role of micrornas during development. therefore, it is of fundamental importance to identify microrna targets. however, no experimental or computational high ...200415013811
conservation of dna methylation in dipteran insects.dna methylation is a central mechanism of epigenetic regulation. whereas vertebrate dna methylation requires at least four different dna methyltransferases, drosophila melanogaster only utilizes a single, dnmt2-like enzyme. this profound difference has raised the question of the evolutionary significance of the drosophila methylation system. we have now identified dnmt2-like open reading frames in the genome sequences of drosophila pseudoobscura and anopheles gambiae. these genes represent the o ...200415056358
molecular evolution of x-linked accessory gland proteins in drosophila pseudoobscura.in drosophila melanogaster and drosophila simulans, positive darwinian selection drives high rates of evolution of male reproductive genes, and accessory gland proteins (acps) in particular. here, we tested whether 13 x-linked male-specific genes, 4 acps and 9 non-acps, are under selective forces in the drosophila pseudoobscura species group, much as those in the d. melanogaster group. we observed a statistically significant correlation in relative rates of nonsynonymous evolution between the tw ...200415073226
evolution of the trans-splicing drosophila locus mod(mdg4) in several species of diptera and lepidoptera.the modifier of mdg4 (mod[mdg4]) locus of drosophila melanogaster (dme) encodes chromatin proteins which are involved in position effect variegation, establishment of chromatin boundaries, nerve pathfinding, meiotic chromosome pairing and apoptosis. it was recently shown that mrna trans-splicing is involved in the generation of at least 26 different mod(mdg4) transcripts. here, we show that a similar complex mod(mdg4) locus exists in drosophila pseudoobscura (dps), drosophila virilis (dvi), anop ...200415094203
analysis of the insect os-d-like gene family.insect os-d-like proteins, also known as chemosensory (csp) or sensory appendage proteins (sap), are broadly expressed in various insect tissues, where they are thought to bind short to medium chain length fatty acids and their derivatives. although their specific function remains uncertain, os-d-like members have been isolated from sensory organs (including the sensillum lymph in some cases), and a role in olfaction similar to that of the insect odorant binding proteins (obp) has been suggested ...200415274438
comparison of the oxidative phosphorylation (oxphos) nuclear genes in the genomes of drosophila melanogaster, drosophila pseudoobscura and anopheles gambiae.in eukaryotic cells, oxidative phosphorylation (oxphos) uses the products of both nuclear and mitochondrial genes to generate cellular atp. interspecies comparative analysis of these genes, which appear to be under strong functional constraints, may shed light on the evolutionary mechanisms that act on a set of genes correlated by function and subcellular localization of their products.200515693940
phylogenetic and structural analysis of the drosophila melanogaster p21-activated kinase dmpak3.p21-activated kinases (paks) are a family of serine/threonine kinases whose diverse cellular functions in cytoskeletal reorganisation, cell motility, transformation and cell death are regulated both by the binding of the small rhogtpases rac and cdc42 and by rhogtpase independent mechanisms. the genome of drosophila melanogaster encodes three different pak proteins: dmpak1, dmmbt (dmpak2) and dmpak3. although structurally related, dmpak and dmmbt control different developmental processes and als ...200515777717
ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mrna splicing.recently, we identified a large number of ultraconserved (uc) sequences in noncoding regions of human, mouse, and rat genomes that appear to be essential for vertebrate and amniote ontogeny. here, we used similar methods to identify ultraconserved genomic regions between the insect species drosophila melanogaster and drosophila pseudoobscura, as well as the more distantly related anopheles gambiae. as with vertebrates, ultraconserved sequences in insects appear to occur primarily in intergenic a ...200515899965
conserved genomic organisation of group b sox genes in insects.sox domain containing genes are important metazoan transcriptional regulators implicated in a wide rage of developmental processes. the vertebrate b subgroup contains the sox1, sox2 and sox3 genes that have early functions in neural development. previous studies show that drosophila group b genes have been functionally conserved since they play essential roles in early neural specification and mutations in the drosophila dichaete and soxn genes can be rescued with mammalian sox genes. despite th ...200515943880
a cellular drosophila melanogaster protein with similarity to baculovirus f envelope fusion proteins.baculovirus f (fusion) proteins are found in the envelopes of budded virions. recently a drosophila melanogaster gene (cg4715) that encodes a protein with sequence similarity to baculovirus f proteins was discovered. to examine similarities and differences with baculovirus f proteins, we cloned the d. melanogaster cellular f (dm-cf) protein gene and analyzed dm-cf expression and localization. the predicted dm-cf protein sequence lacks a furin cleavage site, and transiently expressed dm-cf showed ...200515956544
the coevolution of insect muscle tpnt and tpni gene isoforms.in bilaterians, the main regulator of muscle contraction is the troponin (tpn) complex, comprising three closely interacting subunits (c, t, and i). to understand how evolutionary forces drive molecular change in protein complexes, we have compared the gene structures and expression patterns of tpn genes in insects. in this class, while tpnc is encoded by multiple genes, tpnt and tpni are encoded by single genes. their isoform expression pattern is highly conserved within the drosophilidae, and ...200516049195
evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes.comparative analysis of alternative splicing of orthologous genes from fruit flies (drosophila melanogaster and drosophila pseudoobscura) and mosquito (anopheles gambiae) demonstrated that both in the fruit fly genes and in fruit fly-mosquito comparisons, constitutive exons and splicing sites are more conserved than alternative ones. while >97% of constitutive d. melanogaster exons are conserved in d. pseudoobscura, only approximately 80% of alternative exons are conserved. similarly, 77% of con ...200616520458
the structural role of high molecular weight tropomyosins in dipteran indirect flight muscle and the effect of phosphorylation.in drosophila melanogaster two high molecular weight tropomyosin isoforms, historically named heavy troponins (tnh-33 and tnh-34), are encoded by the tm1 tropomyosin gene. they are specifically expressed in the indirect flight muscles (ifm). their n-termini are conventional and complete tropomyosin sequences, but their c-termini consist of different ifm-specific domains that are rich in proline, alanine, glycine and glutamate. the evidence indicates that in diptera these ifm-specific isoforms ar ...200616752200
periplaneta americana arginine kinase as a major cockroach allergen among thai patients with major cockroach allergies.periplaneta americana is the predominant cockroach (cr) species and a major source of indoor allergens in thailand. nevertheless, data on the nature and molecular characteristics of its allergenic components are rare. we conducted this study to identify and characterize the p. americana allergenic protein. a random heptapeptide phage display library and monoclonal antibody (mab) specific to a the p. americana component previously shown to be an allergenic molecule were used to identify the mab-b ...200616759988
the mitodrome database annotates and compares the oxphos nuclear genes of drosophila melanogaster, drosophila pseudoobscura and anopheles gambiae.the oxidative phosphorylation (oxphos) is the primary energy-producing process of all aerobic organisms and the only cellular function under the dual control of both the mitochondrial and the nuclear genomes. functional characterization and evolutionary study of the oxphos system is of great importance for the understanding of many as yet unclear aspects of nucleus-mitochondrion genomic co-evolution and co-regulation gene networks. the mitodrome database is a web-based database which provides ge ...200616982216
fine-scale crossover rate heterogeneity in drosophila pseudoobscura.broad-scale differences in crossover rate across the genome have been characterized in most genomes studied. fine-scale differences, however, have only been examined in a few taxa, such as arabidopsis, yeast, humans, and mice. no prior studies have directly looked for fine-scale recombination rate heterogeneity in drosophila. we produced 370 drosophila pseudoobscura containing a crossover event within the 2-megabase (mb) region between the genes yellow and white. we then examined 19 intervals wi ...200717160365
genetic variation for dispersal by drosophila pseudoobscura and drosophila persimilis.release-recapture experiments using drosophila pseudoobscura and d. persimilis strains of different karyotypes were performed in a heterogeneous environment. the heterogeneity was due to both spatial variation and the species of yeast used to attract the released flies. no karyotypic-specific habitat preferences were detected. however, in all releases, different strains did behave differently with respect to one or both of the heterogeneous factors. these results indicate there is variation for ...198617246313
evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life.selenocysteine (sec) is a selenium-containing amino acid that is co-translationally inserted into nascent polypeptides by recoding uga codons. selenoproteins occur in both eukaryotes and prokaryotes, but the selenoprotein content of organisms (selenoproteome) is highly variable and some organisms do not utilize sec at all.200717880704
fine-scale mapping of recombination rate in drosophila refines its correlation to diversity and divergence.regional rates of recombination often correlate with levels of nucleotide diversity, and either selective or neutral hypotheses can explain this relationship. regional recombination rates also correlate with nucleotide differences between human and chimpanzee, consistent with models where recombination is mutagenic; however, a lack of correlation is observed in the drosophila melanogaster group, consistent with models invoking natural selection. here, we revisit the relationship among recombinat ...200818621713
the insect snmp gene family.snmps are membrane proteins observed to associate with chemosensory neurons in insects; in drosophila melanogaster, snmp1 has been shown to be essential for the detection of the pheromone cis-vaccenyl acetate (cva). snmps are one of three insect gene clades related to the human fatty acid transporter cd36. we previously characterized the cd36 gene family in 4 insect orders that effectively cover the holometabola, or some 80% of known insect species and the 300 million years of evolution since th ...200919364529
molecular evolution of a drosophila homolog of human brca2.the human cancer susceptibility gene, brca2, functions in double-strand break repair by homologous recombination, and it appears to function via interaction of a repetitive region ("brc repeats") with rad-51. a putatively simpler homolog, dmbrca2, was identified in drosophila melanogaster recently and also affects mitotic and meiotic double-strand break repair. in this study, we examined patterns of repeat variation both within drosophila pseudoobscura and among available drosophila genome seque ...200919554456
enrichment of mrna-like noncoding rnas in the divergence of drosophila males.with the advent of transcriptome data, it has become clear that mrna-like noncoding rnas (mlncrnas) are widespread in eukaryotes. although their functions are poorly understood, these transcripts may play an important role in development and could thus be involved in determining developmental complexity and phenotypic diversification. however, few studies have assessed their potential roles in the divergence of closely related species. here, we identify and study patterns of sequence and express ...201021041796
macromolecular interaction and the electrophoretic mobility of esterase-5 from drosophila pseudoobscura.esterase-5 is one of the most polymorphic loci in drosophila pseudoobscura. some variants reportedly produce a dimeric enzyme, while a few produce a monomeric form. this paper reports the finding that during electrophoresis esterase-5 exists in a dynamic equilibrium between monomers and dimers, an equilibrium that is dependent on the running temperature of the gels. this is shown by a series of analytical electrophoresis experiments in which the apparent molecular weights of several variants are ...20133606564
variable rates of evolution among drosophila opsin genes.dna sequences and chromosomal locations of four drosophila pseudoobscura opsin genes were compared with those from drosophila melanogaster, to determine factors that influence the evolution of multigene families. although the opsin proteins perform the same primary functions, the comparisons reveal a wide range of evolutionary rates. amino acid identities for the opsins range from 90% for rh2 to more than 95% for rh1 and rh4. variation in the rate of synonymous site substitution is especially st ...20051398053
nucleotide sequence of the adh gene region of drosophila pseudoobscura: evolutionary change and evidence for an ancient gene duplication.the alcohol dehydrogenase (adh) locus (adh; alcohol: nad+ oxidoreductase, ec 1.1.1.1) of drosophila pseudoobscura was cloned and sequenced. forty-five percent of the "effectively silent sites" have changed between adh in d. pseudoobscura of the obscura species group and the homologous dna sequence in d. mauritiana, the latter representing the melanogaster species group. the untranslated leader sequence of the adult transcript of d. pseudoobscura has two deletions relative to the d. mauritiana me ...20133666441
molecular heterosis for heat-sensitive enzyme alleles.heat denaturation studies were carried out and revealed hidden genic variants with the same net charge at the octanol dehydrogenase-1 locus in drosophila pseudoobscura. studies of several genetic crosses between strains with different heat-sensitivity alleles showed that the f(1) retained more in vitro enzyme activity after being heat-treated for a specified amount of time at a given temperature than the heat-resistant parent. we call this phenomenon "heterosis for heat-stability of enzyme activ ...20154525464
temperature sensitive events between photoreceptor and circadian clock?the phase shifting action of low temperature pulses of 6 degrees c and 2 h duration administered to the various phases of the drosophila pseudoobscura circadian rhythm and the action of light pulses given 30 min after the beginning of these low temperature pulses have been investigated. the phase response curve obtained from experiments with light pulses during low temperature cannot be explained on the basis of a straightforward and sequential phase shifting of the oscillation by the various tr ...2002125969
inbreeding and mating patterns in drosophila pseudoobscura. 2004539969
distinguishing the forces controlling genetic variation at the xdh locus in drosophila pseudoobscura.fifty-eight isochromosomal lines sampled from two natural populations of drosophila pseudoobscura in california and one from bogota, colombia, were examined using four-cutter restriction mapping. a 4.6-kb region of the xanthine dehydrogenase locus was probed and 66 of 135 restriction sites scored were polymorphic. this predicts that on average every 12th bp would be polymorphic in this region for the genes surveyed if polymorphism occurred randomly along the coding region. in addition, there wer ...20082583480
cytogenetic mapping of marker genes on the chromosome elements c and e of drosophila pseudoobscura and d. subobscura.enzyme loci, visible marker genes and lambda-cloned dna-sequences from a d. miranda library were mapped cytologically on the chromosome elements c and e of d. pseudoobscura and d. subobscura. new data are incorporated into the linkage maps of the two species. homologous segments can now be localized in the polytene chromosomes with these markers. a comparison of the chromosome elements e of d. melanogaster and d. subobscura shows 12 conserved subsections which have been rearranged by paracentric ...20123504805
genetics of male and female sterility in hybrids of drosophila pseudoobscura and d. persimilis.the genetic basis of male and female sterility in hybrids of drosophila pseudoobscura-drosophila persimilis was studied using backcross analysis. previous studies indirectly assessed male fertility by measuring testis size; these studies concluded that male sterility results from an x chromosome-autosome imbalance. by directly scoring for the production of motile sperm, male sterility is shown to be largely due to an incompatibility between genes on the x and y chromosomes of these two species. ...20133623079
behavior in different environments of populations of drosophila, pseudoobscura selected for phototaxis and geotaxis.when tested in hirsch-hadler mazes, drosophila pseudoobscura descended from natural populations is phototactically and geotactically neutral on the average. decidedly positive and negative populations have been obtained by artificial selection. the behavior is independent of temperature (15-27 degrees ) and age (2-17 days). the flies perceive light as weak as 0.2 lux; from 7 to 3000 lux the behavior difference between positive and negative strains increases little, and perhaps decreases at 8000 ...20154525308
synthesis of an attached autosome, c(3)rm, in drosophila pseudoobscura.drosophila pseudoobscura has three acrocentric autosomes. in the experiments reported, homologous arms of the third chromosome were attached to the same centromere. this is a 'reversed metacentric compound' third chromosome, denoted by c(3)rm. this compound chromosome is relatively fertile in within-strain crosses (ca. 50% egg hatch) but sterile when outcrossed to a normal karyotype. when constructing translocations for this experiment, the behavior of the y-autosome translocations suggested tha ...20082323568
genic heterogeneity within electrophoretic "alleles" and the pattern of variation among loci in drosophila pseudoobscura.an investigation, similar to our previously reported xanthine dehydrogenase study, was undertaken to examine the extent of hidden genic variation at nine loci (five larval proteins, three esterases and one aldehyde oxidase) by sequential application of various electrophoretic criteria employing ph, gel concentration and buffer variation. polymorphic loci appear to fall into two distinct groups: weakly polymorphic, including larval protein 6, 7, 8, 10 and 13 and esterase-1 and -6; and highly poly ...1966546677
figaro: a novel statistical method for vector sequence removal.sequences produced by automated sanger sequencing machines frequently contain fragments of the cloning vector on their ends. software tools currently available for identifying and removing the vector sequence require knowledge of the vector sequence, specific splice sites and any adapter sequences used in the experiment-information often omitted from public databases. furthermore, the clipping coordinates themselves are missing or incorrectly reported. as an example, within the approximately 1.2 ...200818202027
origin and evolution of y chromosomes: drosophila tales.classically, y chromosomes are thought to originate from x chromosomes through a process of degeneration and gene loss. now, the availability of 12 drosophila genomes provides an opportunity to study the origin and evolution of y chromosomes in an informative phylogenetic context. surprisingly, the majority of drosophila y-linked genes are recent acquisitions from autosomes and y chromosome gene gains are more frequent than gene losses. moreover, the drosophila pseudoobscura y chromosome lacks h ...200919443075
the insect chemoreceptor superfamily in drosophila pseudoobscura: molecular evolution of ecologically-relevant genes over 25 million years.the insect chemoreceptor superfamily, consisting of the odorant receptor (or) and gustatory receptor (gr) families, exhibits patterns of evolution ranging from highly conserved proteins to lineage-specific gene subfamily expansions when compared across insect suborders and orders. here their evolution across the timespan of 25 million years is examined which yield orthologous divergences ranging from 5-50%. they also reveal the beginnings of lineage-specific gene subfamilies as multiple duplicat ...019613461
comparative genome sequencing of drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.we have sequenced the genome of a second drosophila species, drosophila pseudoobscura, and compared this to the genome sequence of drosophila melanogaster, a primary model organism. throughout evolution the vast majority of drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. a repetitive sequence is found in the d. pseudoobscura genome at many junctions b ...015632085
computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in drosophila melanogaster and drosophila pseudoobscura.the identification of sequences that control transcription in metazoans is a major goal of genome analysis. in a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. nine of these clusters overlapped known ...200415345045
transcription of drosophila troponin i gene is regulated by two conserved, functionally identical, synergistic elements.the drosophila wings-up a gene encodes troponin i. two regions, located upstream of the transcription initiation site (upstream regulatory element) and in the first intron (intron regulatory element), regulate gene expression in specific developmental and muscle type domains. based on lacz reporter expression in transgenic lines, upstream regulatory element and intron regulatory element yield identical expression patterns. both elements are required for full expression levels in vivo as indicate ...200414718563
molecular evolution of drosophila cdc6, an essential dna replication-licensing gene, suggests an adaptive choice of replication origins.increased size of eukaryotic genomes necessitated the use of multiple origins of dna replication, and presumably selected for their efficient spacing to ensure rapid dna replication. the sequence of these origins remains undetermined in metazoan genomes, leaving important questions about the selective constraints acting on replication origins unanswered. we have chosen to study the evolution of proteins that recognize and define these origins every cell cycle, as a surrogate to the direct analys ...018618020
epistasis modifies the dominance of loci causing hybrid male sterility in the drosophila pseudoobscura species group.speciation, the evolution of reproductive isolation between populations, serves as the driving force for generating biodiversity. postzygotic barriers to gene flow, such as f(1) hybrid sterility and inviability, play important roles in the establishment and maintenance of biological species. f(1) hybrid incompatibilities in taxa that obey haldane's rule, the observation that the heterogametic sex suffers greater hybrid fitness problems than the homogametic sex, are thought to often result from i ...200919686263
mind the gap: upgrading genomes with pacific biosciences rs long-read sequencing technology.many genomes have been sequenced to high-quality draft status using sanger capillary electrophoresis and/or newer short-read sequence data and whole genome assembly techniques. however, even the best draft genomes contain gaps and other imperfections due to limitations in the input data and the techniques used to build draft assemblies. sequencing biases, repetitive genomic features, genomic polymorphism, and other complicating factors all come together to make some regions difficult or impossib ...201223185243
molecular coevolution within a drosophila clock gene.the period (per) gene in drosophila melanogaster provides an integral component of biological rhythmicity and encodes a protein that includes a repetitive threonine-glycine (thr-gly) tract. similar repeats are found in the frq and wc2 clock genes of neurospora crassa and in the mammalian per homologues, but their circadian functions are unknown. in drosophilids, the length of the thr-gly repeat varies widely between species, and sequence comparisons have suggested that the repeat length coevolve ...19989539762
comparative gene expression analysis of dtg, a novel target gene of dpp signaling pathway in the early drosophila melanogaster embryo.in the early drosophila melanogaster embryo, dpp, a secreted molecule that belongs to the tgf-β superfamily of growth factors, activates a set of downstream genes to subdivide the dorsal region into amnioserosa and dorsal epidermis. here, we examined the expression pattern and transcriptional regulation of dtg, a new target gene of dpp signaling pathway that is required for proper amnioserosa differentiation. we showed that the expression of dtg was controlled by dpp and characterized a 524-bp e ...201424321690
how hot are drosophila hotspots? examining recombination rate variation and associations with nucleotide diversity, divergence, and maternal age in drosophila pseudoobscura.fine scale meiotic recombination maps have uncovered a large amount of variation in crossover rate across the genomes of many species, and such variation in mammalian and yeast genomes is concentrated to <5kb regions of highly elevated recombination rates (10-100x the background rate) called "hotspots." drosophila exhibit substantial recombination rate heterogeneity across their genome, but evidence for these highly-localized hotspots is lacking. we assayed recombination across a 40kb region of ...201323967224
ancestral polymorphisms in drosophila pseudoobscura and drosophila miranda.ancestral polymorphisms are defined as variants that arose by mutation prior to the speciation event that generated the species in which they segregate. their presence may complicate the interpretation of molecular data and lead to incorrect phylogenetic inferences. they may also be used to identify regions of the genome that are under balancing selection. it is thus important to take into account the contribution of ancestral polymorphisms to variability within species and divergence between sp ...201121767458
a multispecies approach for comparing sequence evolution of x-linked and autosomal sites in drosophila.population genetics models show that, under certain conditions, the x chromosome is expected to be under more efficient selection than the autosomes. this could lead to 'faster-x evolution', if a large proportion of mutations are fixed by positive selection, as suggested by recent studies in drosophila. we used a multispecies approach to test this: muller's element d, an autosomal arm, is fused to the ancestral x chromosome in drosophila pseudoobscura and its sister species, drosophila affinis. ...200819061532
a novel dataset for identifying sex-biased genes in drosophila.phenotypic differences between males and females of sexually dimorphic species are caused in large part by differences in gene expression between the sexes, most of which occurs in the gonads. to accurately identify genes differentially expressed between males and females in drosophila, we sequenced the testis and ovary transcriptomes of d. yakuba, d. pseudoobscura, and d. ananassae and used them to identify sex-biased genes in the latter two species. we highlight the increased sensitivity and i ...201425031657
comparative genomic analysis of allatostatin-encoding (ast) genes in drosophila species and prediction of regulatory elements by phylogenetic footprinting.the role of the yxfgla family of allatostatin (ast) peptides in dipterans is not well-established. the recent completion of sequencing of genomes for multiple drosophila species provides an opportunity to study the evolutionary variation of the allatostatins and to examine regulatory elements that control gene expression. we performed comparative analyses of ast genes from seven drosophila species (drosophila melanogaster, drosophila simulans, drosophila ananassae, drosophila yakuba, drosophila ...200717175069
amyrel, a paralogous gene of the amylase gene family in drosophila melanogaster and the sophophora subgenus.we describe a gene from drosophila melanogaster related to the alpha-amylase gene amy. this gene, which exists as a single copy, was named amyrel. it is strikingly divergent from amy because the amino acid divergence is 40%. the coding sequence is interrupted by a short intron at position 655, which is unusual in amylase genes. amyrel has also been cloned in drosophila ananassae, drosophila pseudoobscura, and drosophila subobscura and is likely to be present throughout the sophophora subgenus, b ...19989618501
an intron loss of dfak gene in species of the drosophila melanogaster subgroup and phylogenetic analysis.drosophila focal adhesion kinase (dfak) gene is a single-copy nuclear gene. previous study revealed that drosophila melanogaster and drosophila simulans had lost an intron precisely within the tyrosine kinase (tyk) domain of this gene. however, this did not happen in several other drosophila species, including drosophila elegans, drosophila ficusphila, drosophila biarmipes, drosophila jambulina, drosophila prostipennis, drosophila takahashii, and drosophila pseudoobscura. in the current study, h ...200918310070
the adh genomic region of drosophila ambigua: evolutionary trends in different species.the study of individual genes is essential to a comprehensive understanding of genome evolution. the wealth of information on alcohol dehydrogenase (adh) in drosophila makes this gene particularly suitable for such analysis. we have characterized more than 4 kb of the genomic adh region in drosophila ambigua and compared this region to drosophila mauritiana and drosophila pseudoobscura. the presence of two genes, adh and 3'orf (open reading frame), has been confirmed and some of their essential ...19911908016
comparative expression dynamics of intergenic long noncoding rnas in the genus drosophila.thousands of long noncoding rnas (lncrnas) have been annotated in eukaryotic genomes, but comparative transcriptomic approaches are necessary to understand their biological impact and evolution. to facilitate such comparative studies in drosophila, we identified and characterized lncrnas in a second drosophilid-the evolutionary model drosophila pseudoobscura using rna-seq and computational filtering of protein-coding potential, we identified 1,589 intergenic lncrna loci in d. pseudoobscura we su ...201627189981
winter is coming: hibernation reverses the outcome of sperm competition in a fly.sperm commonly compete within females to fertilize ova, but research has focused on short-term sperm storage: sperm that are maintained in a female for only a few days or weeks before use. in nature, females of many species store sperm for months or years, often during periods of environmental stress, such as cold winters. here we examine the outcome of sperm competition in the fruit fly drosophila pseudoobscura, simulating the conditions in which females survive winter. we mated females to two ...201626565889
krüppel expression levels are maintained through compensatory evolution of shadow enhancers.many developmental genes are controlled by shadow enhancers—pairs of enhancers that drive overlapping expression patterns. we hypothesized that compensatory evolution can maintain the total expression of a gene, while individual shadow enhancers diverge between species. to test this hypothesis, 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 fac ...201526344774
assessment of rival males through the use of multiple sensory cues in the fruitfly drosophila pseudoobscura.environments vary stochastically, and animals need to behave in ways that best fit the conditions in which they find themselves. the social environment is particularly variable, and responding appropriately to it can be vital for an animal's success. however, cues of social environment are not always reliable, and animals may need to balance accuracy against the risk of failing to respond if local conditions or interfering signals prevent them detecting a cue. recent work has shown that many mal ...201525849643
evidence for stabilizing selection on codon usage in chromosomal rearrangements of drosophila pseudoobscura.there has been a renewed interest in investigating the role of stabilizing selection acting on genome-wide traits such as codon usage bias. codon bias, when synonymous codons are used at unequal frequencies, occurs in a wide variety of taxa. standard evolutionary models explain the maintenance of codon bias through a balance of genetic drift, mutation and weak purifying selection. the efficacy of selection is expected to be reduced in regions of suppressed recombination. contrary to observations ...201425326424
faster-x effects in two drosophila lineages.under certain circumstances, x-linked loci are expected to experience more adaptive substitutions than similar autosomal loci. to look for evidence of faster-x evolution, we analyzed the evolutionary rates of coding sequences in two sets of drosophila species, the melanogaster and pseudoobscura clades, using whole-genome sequences. one of these, the pseudoobscura clade, contains a centric fusion between the ancestral x chromosome and the autosomal arm homologous to 3l in d. melanogaster. this of ...201425323954
the heritability of mating behaviour in a fly and its plasticity in response to the threat of sperm competition.phenotypic plasticity is a key mechanism by which animals can cope with rapidly changeable environments, but the evolutionary lability of such plasticity remains unclear. the socio-sexual environment can fluctuate very rapidly, affecting both the frequency of mating opportunities and the level of competition males may face. males of many species show plastic behavioural responses to changes in social environment, in particular the presence of rival males. for example, drosophila pseudoobscura ma ...201424587294
hundreds of putatively functional small open reading frames in drosophila.the relationship between dna sequence and encoded information is still an unsolved puzzle. the number of protein-coding genes in higher eukaryotes identified by genome projects is lower than was expected, while a considerable amount of putatively non-coding transcription has been detected. functional small open reading frames (smorfs) are known to exist in several organisms. however, coding sequence detection methods are biased against detecting such very short open reading frames. thus, a subst ...201122118156
a conserved developmental patterning network produces quantitatively different output in multiple species of drosophila.differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between closely related species. to assess the scope of such changes, we used high-resolution imaging methods to measure mrna expression in blastoderm embryos of drosophila yakuba and drosophi ...201122046143
odorant receptor (or) genes: polymorphism and divergence in the d. melanogaster and d. pseudoobscura lineages.in insects, like in most invertebrates, olfaction is the principal sensory modality, which provides animals with essential information for survival and reproduction. odorant receptors are involved in this response, mediating interactions between an individual and its environment, as well as between individuals of the same or different species. the adaptive importance of odorant receptors renders them good candidates for having their variation shaped by natural selection.201020967126
spermatogenic cyst and organ culture in drosophila pseudoobscura.spermatogenesis is a complex series of processes that involves (1) the maintenance of a renewable pool of diploid stem cells within a niche, (2) the mitotic expansion of a subpopulation of stem cells committed to the spermatogenic pathway, and (3) the differentiation of diploid cells into highly specialized, haploid spermatozoa through meiotic and post-meiotic cellular transformations. drosophila melanogaster is a desirable model for studying spermatogenesis, as similarities exist between mammal ...201020694478
evolution of expression patterns of two odorant-binding protein genes, obp57d and obp57e, in drosophila.odorant-binding proteins (obps) function in the perception of chemical signals together with odorant and taste receptors. genes encoding obps form a large family in insect genomes. in drosophila, the evolution of obp gene repertoire has been well studied by comparisons of the whole genome sequences from 12 closely related species. in contrast, their expression patterns are known only in drosophila melanogaster. two obp genes, obp57d and obp57e, arose by gene duplication at the early stage of d. ...201020637846
adverse interactions between micro-rnas and target genes from different species.it is commonly assumed but not proven that micrornas (mirnas) and their targets coevolve. under this assumption, mirnas and targets from different species may interact adversely, resulting in reduced fitness. however, the strength of the adverse interactions may not be detectable because even outright deletions of mirnas often manifest only subtle fitness effects. we tested and measured the strength of heterospecific interactions by carrying out transgenic experiments across drosophila species b ...201020615957
fish mapping of microsatellite loci from drosophila subobscura and its comparison to related species.microsatellites are highly polymorphic markers that are distributed through all the genome being more abundant in non-coding regions. whether they are neutral or under selection, these markers if localized can be used as co-dominant molecular markers to explore the dynamics of the evolutionary processes. their cytological localization can allow identifying genes under selection, inferring recombination from a genomic point of view, or screening for the genomic reorganizations occurring during th ...201020198419
polyandry prevents extinction.females of most animal species are polyandrous, with individual females usually mating with more than one male. however, the ubiquity of polyandry remains enigmatic because of the potentially high costs to females of multiple mating. current theory to account for the high prevalence of polyandry largely focuses on its benefits to individual females. there are also higher-level explanations for the high incidence of polyandry-polyandrous clades may speciate more rapidly. here we test the hypothes ...201020188561
in vivo rnai rescue in drosophila melanogaster with genomic transgenes from drosophila pseudoobscura.systematic, large-scale rna interference (rnai) approaches are very valuable to systematically investigate biological processes in cell culture or in tissues of organisms such as drosophila. a notorious pitfall of all rnai technologies are potential false positives caused by unspecific knock-down of genes other than the intended target gene. the ultimate proof for rnai specificity is a rescue by a construct immune to rnai, typically originating from a related species.201020126626
the "plant drosophila": e.b. babcock, the genus "crepis," and the evolution of a genetics research program at berkeley, 1915-1947.this paper explores the research and administrative efforts of ernest brown babcock, head of the division of genetics in the college of agriculture at the university of california, berkeley, the first academic unit so named in the united states. it explores the rationale for his choice of "model organism," the development--and transformation--of his ambitious genetics research program centering on the weedy plant genus named "crepis" (commonly known as the hawkbeard), along with examining in det ...200920077617
sex ratio drive promotes sexual conflict and sexual coevolution in the fly drosophila pseudoobscura.selfish genetic elements occur in all living organisms and often cause reduced fertility and sperm competitive ability in males. in the fruit fly drosophila pseudoobscura, the presence of a sex-ratio distorting x-chromosome meiotic driver sex ratio (sr) has been shown to promote the evolution of increased female remating rates in laboratory populations. this is favored because it promotes sperm competition, which decreases the risk to females of producing highly female-biased broods and to their ...201019922445
patterns of dna-sequence divergence between drosophila miranda and d. pseudoobscura.contrary to the classical view, a large amount of non-coding dna seems to be selectively constrained in drosophila and other species. here, using drosophila miranda bac sequences and the drosophila pseudoobscura genome sequence, we aligned coding and non-coding sequences between d. pseudoobscura and d. miranda, and investigated their patterns of evolution. we found two patterns that have previously been observed in comparisons between drosophila melanogaster and its relatives. first, there is a ...200919859648
the genomics of speciation in drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing.in nature, closely related species may hybridize while still retaining their distinctive identities. chromosomal regions that experience reduced recombination in hybrids, such as within inversions, have been hypothesized to contribute to the maintenance of species integrity. here, we examine genomic sequences from closely related fruit fly taxa of the drosophila pseudoobscura subgroup to reconstruct their evolutionary histories and past patterns of genic exchange. partial genomic assemblies were ...200919578407
a toolkit for high-throughput, cross-species gene engineering in drosophila.we generated two complementary genomic fosmid libraries for drosophila melanogaster and drosophila pseudoobscura that permit seamless modification of large genomic clones by high-throughput recombineering and direct transgenesis. the fosmid transgenes recapitulated endogenous gene expression patterns. these libraries, in combination with recombineering technology, will be useful to rescue mutant phenotypes, allow imaging of gene products in living flies and enable systematic analysis and manipul ...200919465918
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