| hybrid lethal systems in the drosophila melanogaster species complex. ii. the zygotic hybrid rescue (zhr) gene of d. melanogaster. | hybrid females from drosophila simulans females x drosophila melanogaster males die as embryos while hybrid males from the reciprocal cross die as larvae. we have recovered a mutation in melanogaster that rescues the former hybrid females. it was located on the x chromosome at a position close to the centromere, and it was a zygotically acting gene, in contrast with mhr (maternal hybrid rescue) in simulans that rescues the same hybrids maternally. we named it zhr (zygotic hybrid rescue). the gen ... | 1993 | 8436277 |
| structure of the transcriptional regulatory network correlates with regulatory divergence in drosophila. | transcriptional control of gene expression is regulated by biochemical interactions between cis-regulatory dna sequences and trans-acting factors that form complex regulatory networks. genetic changes affecting both cis- and trans-acting sequences in these networks have been shown to alter patterns of gene expression as well as higher-order organismal phenotypes. here, we investigate how the structure of these regulatory networks relates to patterns of polymorphism and divergence in gene express ... | 2017 | 28333240 |
| genetic and transgenic reagents for drosophila simulans, d. mauritiana, d. yakuba, d. santomea, and d. virilis. | species of the drosophila melanogaster species subgroup, including the species d. simulans, d. mauritiana, d. yakuba, and d. santomea, have long served as model systems for studying evolution. however, studies in these species have been limited by a paucity of genetic and transgenic reagents. here, we describe a collection of transgenic and genetic strains generated to facilitate genetic studies within and between these species. we have generated many strains of each species containing mapped pi ... | 2017 | 28280212 |
| does pupal communication influence wolbachia-mediated cytoplasmic incompatibility? | wolbachia are widespread endosymbiotic bacteria found in terrestrial arthropods and filarial nematodes [1]. in insects, wolbachia generally rely on diverse strategies to manipulate their host's reproduction and favor their own vertical transmission through infected eggs [2]. one such mechanism is a sterility syndrome called 'cytoplasmic incompatibility'. cytoplasmic incompatibility occurs at fertilization, when a spermatozoon from a wolbachia-infected male fertilizes an uninfected egg. in this c ... | 2017 | 28118585 |
| sequence analysis of active mariner elements in natural populations of drosophila simulans. | active and inactive mariner elements from natural and laboratory populations of drosophila simulans were isolated and sequenced in order to assess their nucleotide variability and to compare them with previously isolated mariner elements from the sibling species drosophila mauritiana and drosophila sechellia. the active elements of d. simulans are very similar among themselves (average 99.7% nucleotide identity), suggesting that the level of mariner expression in different natural populations is ... | 1992 | 1312979 |
| naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation. | significant differences in levels of copia [drosophila long terminal repeat (ltr) retrotransposon] expression exist among six species representing the drosophila melanogaster species complex (d. melanogaster, drosophila mauritiana, drosophila simulans, drosophila sechellia, drosophila yakuba, and drosophila erecta) and a more distantly related species (drosophila willistoni). these differences in expression are correlated with major size variation mapping to putative regulatory regions of the co ... | 1996 | 8692951 |
| a genome-wide survey of hybrid incompatibility factors by the introgression of marked segments of drosophila mauritiana chromosomes into drosophila simulans. | in hybrids between drosophila simulans and d. mauritiana, males are sterile and females are fertile, in compliance with haldane's rule. the genetic basis of this phenomenon was investigated by introgression of segments of the mauritiana genome into a simulans background. a total of 87 positions throughout the mauritiana genome were marked with p-element insertions and replicate introgressions were made by repeated backcrossing to simulans for 15 generations. the fraction of hemizgyous x chromoso ... | 1996 | 8849890 |
| sex-biased transcriptome divergence along a latitudinal gradient. | sex-dependent gene expression is likely an important genomic mechanism that allows sex-specific adaptation to environmental changes. among drosophila species, sex-biased genes display remarkably consistent evolutionary patterns; male-biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. however, comparatively little is known of the evolutionary process shaping sex-biased expression within species. latitu ... | 2017 | 28100025 |
| a genomic approach to identify hybrid incompatibility genes. | uncovering the genetic and molecular basis of barriers to gene flow between populations is key to understanding how new species are born. intrinsic postzygotic reproductive barriers such as hybrid sterility and hybrid inviability are caused by deleterious genetic interactions known as hybrid incompatibilities. the difficulty in identifying these hybrid incompatibility genes remains a rate-limiting step in our understanding of the molecular basis of speciation. we recently described how whole gen ... | 2016 | 27230814 |
| hybrid dysgenesis in drosophila simulans associated with a rapid invasion of the p-element. | in a classic example of the invasion of a species by a selfish genetic element, the p-element was horizontally transferred from a distantly related species into drosophila melanogaster. despite causing 'hybrid dysgenesis', a syndrome of abnormal phenotypes that include sterility, the p-element spread globally in the course of a few decades in d. melanogaster. until recently, its sister species, including d. simulans, remained p-element free. here, we find a hybrid dysgenesis-like phenotype in th ... | 2016 | 26982327 |
| crossing-over in the female hybrids between drosophila simulans and drosophila mauritiana. | the cross between d. simulans and d. mauritiana yields fertile hybrid females. crossing-over occurs in such female hybrids. this system allows the transfer of pieces of chromosomes from one species into another, thus providing an experimental tool to analyze the genetic basis of evolutionary problems, as well as the regulation of gene expression during development. | 1982 | 7200915 |
| evolution of drosophila mitochondrial dna and the history of the melanogaster subgroup. | the nucleotide sequences of a common region of 15 mitochondrial dnas (mtdnas) sampled from the drosophila melanogaster subgroup were determined. the region is 2527 base pairs long, including most of the nadh dehydrogenase subunit 2 and cytochrome oxidase subunit 1 genes punctuated by three trna genes. the comparative study revealed (i) the extremely low saturation level of transitional differences, (ii) recombination or variable substitution rates even within species, (iii) long persistence time ... | 1990 | 2124697 |
| genetics of sexual isolation between two sibling species, drosophila simulans and drosophila mauritiana. | drosophila simulans and drosophila mauritiana are sibling species that show substantial sexual isolation in one of their two reciprocal hybridizations. genetic analysis reveals that in females this isolation is caused by at least one recessive gene on each autosome, while the x chromosome has little or no effect. our results, combined with those of previous studies, show that in drosophila the genetics of sexual isolation differs from that of postzygotic reproductive isolation, which invariably ... | 1989 | 2748596 |
| maternally inherited transposon excision in drosophila simulans. | a mutation in the white gene of drosophila mauritiana resulting from insertion of the transposable element mariner exhibits genetic instability in germline and somatic cells. the instability is greatly enhanced in the presence of the trans-acting autosomal factor mos, giving eye-color mosaics with pigmented sectors of tissue on an otherwise peach-colored background. the mos factor, when introduced into the genome of the sibling species drosophila simulans, exhibited a dramatic maternal effect on ... | 1988 | 2832948 |
| intraspecific diversity of nucleotide sequences within the adenine + thymine-rich region of mitochondrial dna molecules of drosophila mauritiana, drosophila melanogaster and drosophila simulans. | mitochondrial dna (mtdna) molecules from drosophila mauritiana, d. melanogaster, and d. simulans contain a single adenine + thymine (a+t)-rich region, which is similarly located in all molecules, but varies in size among these species. using agarose gel electrophoresis and electron microscopy, a difference in occurrence of one ecori site, and a difference in size (approximately 0.7 kb) of the a+t-rich regions was found between mtdna molecules of flies of two female lines of d. mauritiana. in het ... | 1980 | 6258143 |
| the recent invasion of natural drosophila simulans populations by the p-element. | the p-element is one of the best understood eukaryotic transposable elements. it invaded drosophila melanogaster populations within a few decades but was thought to be absent from close relatives, including drosophila simulans. five decades after the spread in d. melanogaster, we provide evidence that the p-element has also invaded d. simulans. p-elements in d. simulans appear to have been acquired recently from d. melanogaster probably via a single horizontal transfer event. expression data ind ... | 2015 | 25964349 |
| the taste of togetherness. | the larvae of fruit flies produce pheromones to control whether they are attracted to others of the same species or whether they avoid members of a different species. | 2014 | 25497434 |
| nonrandom partition of mitochondria in heteroplasmic drosophila. | in order to understand the status of heteroplasmy and its evolution within the drosophila melanogaster subgroup, cytoplasm microinjections between eggs were performed involving three lineages of drosophila simulans, carrying the sii, siii or siiii mtdna type, respectively, and two strains of drosophila mauritiana carrying the mai or maii mtdna type. progeny of eggs from all combinations of injection were analysed. the maii or sii molecules, when provided by the donor, were never detected in the ... | 1997 | 9418268 |
| nucleotide sequence divergence in the a+t-rich region of mitochondrial dna in drosophila simulans and drosophila mauritiana. | we have determined the nucleotide sequences of two regions within the a+t-rich region of mitochondrial dna (mtdna) in the siiii type of drosophila simulans and the mai type of d. mauritiana. the sequences of the two regions in siiii and mai are almost identical. the sequences include elements corresponding to the type i and type ii repeats elements and the t-stretches as reported in d. melanogaster; an approximately 340-bp region (a region) adjacent to the trna(ile) gene includes a part of the t ... | 1997 | 9254919 |
| normal segregation of a foreign-species chromosome during drosophila female meiosis despite extensive heterochromatin divergence. | the abundance and composition of heterochromatin changes rapidly between species and contributes to hybrid incompatibility and reproductive isolation. heterochromatin differences may also destabilize chromosome segregation and cause meiotic drive, the non-mendelian segregation of homologous chromosomes. here we use a range of genetic and cytological assays to examine the meiotic properties of a drosophila simulans chromosome 4 (sim-iv) introgressed into d. melanogaster. these two species differ ... | 2015 | 25406466 |
| identification of nucleotide substitutions necessary for trans-activation of mariner transposable elements in drosophila: analysis of naturally occurring elements. | six copies of the mariner element from the genomes of drosophila mauritiana and drosophila simulans were chosen at random for dna sequencing and functional analysis and compared with the highly active element mos1 and the inactive element peach. all elements were 1286 base pairs in length, but among them there were 18 nucleotide differences. as assayed in drosophila melanogaster, three of the elements were apparently nonfunctional, two were marginally functional, and one had moderate activity th ... | 1991 | 1655567 |
| the role of rdl in resistance to phenylpyrazoles in drosophila melanogaster. | extensive use of older generation insecticides may result in pre-existing cross-resistance to new chemical classes acting at the same target site. phenylpyrazole insecticides block inhibitory neurotransmission in insects via their action on ligand-gated chloride channels (lgccs). phenylpyrazoles are broad-spectrum insecticides widely used in agriculture and domestic pest control. so far, all identified cases of target site resistance to phenylpyrazoles are based on mutations in the rdl (resistan ... | 2014 | 25193377 |
| a test of double interspecific introgression of nucleoporin genes in drosophila. | in interspecific hybrids between drosophila melanogaster and drosophila simulans, the d. simulans nucleoporin-encoding nup96(sim) and nup160(sim) can cause recessive lethality if the hybrid does not also inherit the d. simulans x chromosome. in addition, nup160(sim) leads to recessive female sterility in the d. melanogaster genetic background. here, we conducted carefully controlled crosses to better understandthe relationship between nup96(sim) and nup160(sim). nup96(sim) did not lead to female ... | 2014 | 25172915 |
| genomic patterns of geographic differentiation in drosophila simulans. | geographic patterns of genetic differentiation have long been used to understand population history and to learn about the biological mechanisms of adaptation. here we present an examination of genomic patterns of differentiation between northern and southern populations of australian and north american drosophila simulans, with an emphasis on characterizing signals of parallel differentiation. we report on the genomic scale of differentiation and functional enrichment of outlier snps. while, ov ... | 2016 | 26801179 |
| comparative population genomics of latitudinal variation in drosophila simulans and drosophila melanogaster. | examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. here, we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of drosophila simulans and drosophila melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatia ... | 2016 | 26523848 |
| introduction of the transposable element mariner into the germline of drosophila melanogaster. | a chimeric white gene (wpch) and other constructs containing the transposable element mariner from drosophila mauritiana were introduced into the germline of drosophila melanogaster using transformation mediated by the p element. in the absence of other mariner elements, the wpch allele is genetically stable in both germ cells and somatic cells, indicating that the peach element (i.e., the particular copy of mariner inserted in the wpch allele) is inactive. however, in the presence of the active ... | 1991 | 1649067 |
| expression divergence of chemosensory genes between drosophila sechellia and its sibling species and its implications for host shift. | drosophila sechellia relies exclusively on the fruits of morinda citrifolia, which are toxic to most insects, including its sibling species drosophila melanogaster and drosophila simulans. although several odorant binding protein (obp) genes and olfactory receptor (or) genes have been suggested to be associated with the d. sechellia host shift, a broad view of how chemosensory genes have contributed to this shift is still lacking. we therefore studied the transcriptomes of antennae, the main org ... | 2015 | 26430061 |
| seasonal variation in life history traits in two drosophila species. | seasonal environmental heterogeneity is cyclic, persistent and geographically widespread. in species that reproduce multiple times annually, environmental changes across seasonal time may create different selection regimes that may shape the population ecology and life history adaptation in these species. here, we investigate how two closely related species of drosophila in a temperate orchard respond to environmental changes across seasonal time. natural populations of drosophila melanogaster a ... | 2015 | 26174167 |
| a drosophila model for mito-nuclear diseases generated by an incompatible interaction between trna and trna synthetase. | communication between the mitochondrial and nuclear genomes is vital for cellular function. the assembly of mitochondrial enzyme complexes, which produce the majority of cellular energy, requires the coordinated expression and translation of both mitochondrially and nuclear-encoded proteins. the joint genetic architecture of this system complicates the basis of mitochondrial diseases, and mutations both in mitochondrial dna (mtdna)- and nuclear-encoded genes have been implicated in mitochondrial ... | 2015 | 26035388 |
| lineage-specific evolution of the complex nup160 hybrid incompatibility between drosophila melanogaster and its sister species. | two genes encoding protein components of the nuclear pore complex nup160 and nup96 cause lethality in f2-like hybrid genotypes between drosophila simulans and drosophila melanogaster. in particular, d. simulans nup160 and nup96 each cause inviability when hemizygous or homozygous in species hybrids that are also hemizygous (or homozygous) for the d. melanogaster x chromosome. the hybrid lethality of nup160, however, is genetically complex, depending on one or more unknown additional factors in t ... | 2015 | 26022241 |
| genetic basis of male sterility in hybrids between two closely related species of drosophila. | drosophila simulans and drosophila mauritiana are closely related sibling species, the former cosmopolitan and the latter restricted to the small oceanic island of mauritius. genetic analysis of male sterility in hybrids between these species shows that at least five loci (one on each chromosome arm) are responsible for this reproductive isolation. this is the most loci that could have been detected with the techniques used and implies that the true genetic divergence for sterility is even great ... | 1984 | 6589604 |
| a pair of centromeric proteins mediates reproductive isolation in drosophila species. | speciation involves the reproductive isolation of natural populations due to the sterility or lethality of their hybrids. however, the molecular basis of hybrid lethality and the evolutionary driving forces that provoke it remain largely elusive. the hybrid male rescue (hmr) and the lethal hybrid rescue (lhr) genes serve as a model to study speciation in drosophilids because their interaction causes lethality in male hybrid offspring. here, we show that hmr and lhr form a centromeric complex nec ... | 2013 | 24239514 |
| selectivity and plasticity in a sound-evoked male-male interaction in drosophila. | during courtship, many animals, including insects, birds, fish, and mammals, utilize acoustic signals to transmit information about species identity. although auditory communication is crucial across phyla, the neuronal and physiologic processes are poorly understood. sound-evoked chaining behavior, a display of homosexual courtship behavior in drosophila males, has long been used as an excellent model for analyzing auditory behavior responses, outcomes of acoustic perception and higher-order br ... | 2013 | 24086330 |
| more accurate phylogenies inferred from low-recombination regions in the presence of incomplete lineage sorting. | when speciation events occur in rapid succession, incomplete lineage sorting (ils) can cause disagreement among individual gene trees. the probability that ils affects a given locus is directly related to its effective population size (ne ), which in turn is proportional to the recombination rate if there is strong selection across the genome. based on these expectations, we hypothesized that low-recombination regions of the genome, as well as sex chromosomes and nonrecombining chromosomes, shou ... | 2013 | 23888858 |
| using near-infrared spectroscopy to resolve the species, gender, age, and the presence of wolbachia infection in laboratory-reared drosophila. | the aim of the study was to determine the accuracy of near-infrared spectroscopy (nirs) in determining species, gender, age, and the presence of the common endosymbiont wolbachia in laboratory-reared drosophila. nirs measures the absorption of light by organic molecules. initially, a calibration model was developed for each study. an independent set with flies not involved in initial cross-validation was then used to validate the accuracy of each calibration model. flies from the independent set ... | 2012 | 22973543 |
| a second-generation assembly of the drosophila simulans genome provides new insights into patterns of lineage-specific divergence. | we create a new assembly of the drosophila simulans genome using 142 million paired short-read sequences and previously published data for strain w(501). our assembly represents a higher-quality genomic sequence with greater coverage, fewer misassemblies, and, by several indexes, fewer sequence errors. evolutionary analysis of this genome reference sequence reveals interesting patterns of lineage-specific divergence that are different from those previously reported. specifically, we find that dr ... | 2013 | 22936249 |
| major role of positive selection in the evolution of conservative segments of drosophila proteins. | slow evolution of conservative segments of coding and non-coding dna is caused by the action of negative selection, which removes new mutations. however, the mode of selection that affects the few substitutions that do occur within such segments remains unclear. here, we show that the fraction of allele replacements that were driven by positive selection, and the strength of this selection, is the highest within the conservative segments of drosophila protein-coding genes. the mcdonald-kreitman ... | 2012 | 22673359 |
| individual genetic contributions to genital shape variation between drosophila simulans and d. mauritiana. | external genitalia are one of the most rapidly evolving morphological features in insects. in the drosophila melanogaster species subgroup, males possess a nonfertilizing external genital structure, called the posterior lobe, which is highly divergent among even closely related species. a previous study on this subgroup mapped two genomic regions that affect lobe size and four that affect lobe shape differences between d. mauritiana and d. sechellia; none of the regions affected both size and sh ... | 2014 | 25313344 |
| a comparative analysis of the amounts and dynamics of transposable elements in natural populations of drosophila melanogaster and drosophila simulans. | genes are important in defining genetic variability, but they do not constitute the largest component of genomes, which in most organisms contain large amounts of various repeated sequences including transposable elements (tes), which have been shown to account for most of the genome size. tes contribute to genetic diversity by their mutational potential as a result of their ability to insert into genes or gene regulator regions, to promote chromosomal rearrangements, and to interfere with gene ... | 2012 | 22659421 |
| differential responses to artificial selection on oviposition site preferences in drosophila melanogaster and d. simulans. | the preference-performance relationship in plant-insect interactions is a central theme in evolutionary ecology. among many insects, eggs are vulnerable and larvae have limited mobility, making the choice of an appropriate oviposition site one of the most important decisions for a female. we investigated the evolution of oviposition preferences in drosophila melanogaster meigen and drosophila simulans sturtevant by artificially selecting for the preference for 2 natural resources, grape and quin ... | 2015 | 25263841 |
| partitioning transcript variation in drosophila: abundance, isoforms, and alleles. | multilevel analysis of transcription is facilitated by a new array design that includes modules for assessment of differential expression, isoform usage, and allelic imbalance in drosophila. the ∼2.5 million feature chip incorporates a large number of controls, and it contains 18,769 3' expression probe sets and 61,919 exon probe sets with probe sequences from drosophila melanogaster and 60,118 snp probe sets focused on drosophila simulans. an experiment in d. simulans identified genes different ... | 2011 | 22384353 |
| abundant genetic variability in drosophila simulans for hybrid female lethality in interspecific crosses to drosophila melanogaster. | intrinsic postzygotic reproductive isolation is thought to result from the substitution of multiple harmless or beneficial genetic differences between species that are incidentally deleterious when combined in species hybrids, causing hybrid sterility or inviability. genetic variability for hybrid sterility or inviability phenotypes is, however, rarely assessed in natural populations. here, we assess variation for drosophila simulans-encoded maternal factor(s) that cause lethality in d. simulans ... | 2012 | 22353244 |
| high anti-viral protection without immune upregulation after interspecies wolbachia transfer. | wolbachia, endosymbionts that reside naturally in up to 40-70% of all insect species, are some of the most prevalent intracellular bacteria. both wolbachia wau, naturally associated with drosophila simulans, and wmel, native to drosophila melanogaster, have been previously described to protect their hosts against viral infections. wmel transferred to d. simulans was also shown to have a strong antiviral effect. here we directly compare one of the most protective wmel variants and wau in d. melan ... | 2014 | 24911519 |
| allelic imbalance in drosophila hybrid heads: exons, isoforms, and evolution. | unraveling how regulatory divergence contributes to species differences and adaptation requires identifying functional variants from among millions of genetic differences. analysis of allelic imbalance (ai) reveals functional genetic differences in cis regulation and has demonstrated differences in cis regulation within and between species. regulatory mechanisms are often highly conserved, yet differences between species in gene expression are extensive. what evolutionary forces explain widespre ... | 2012 | 22319150 |
| functional evidence that a recently evolved drosophila sperm-specific gene boosts sperm competition. | in many species, both morphological and molecular traits related to sex and reproduction evolve faster in males than in females. ultimately, rapid male evolution relies on the acquisition of genetic variation associated with differential reproductive success. many newly evolved genes are associated with novel functions that might enhance male fitness. however, functional evidence of the adaptive role of recently originated genes in males is still lacking. the sperm dynein intermediate chain mult ... | 2012 | 22308475 |
| the genetics of cuticular hydrocarbon profiles in the fruit fly drosophila simulans. | female mate choice is one mechanism of sexual selection and, provided there is adequate genetic variation in the male traits that are the target of this selection, they will evolve via female choice. cuticular hydrocarbons (chcs) are important in drosophila mate choice, but relatively little is known about the underlying genetic architecture of chc profiles in drosophila simulans. here, we used gas chromatography-mass spectrometry to investigate patterns of genetic variation in the chc profiles ... | 2012 | 22268163 |
| neural representations of courtship song in the drosophila brain. | acoustic communication in drosophilid flies is based on the production and perception of courtship songs, which facilitate mating. despite decades of research on courtship songs and behavior in drosophila, central auditory responses have remained uncharacterized. in this study, we report on intracellular recordings from central neurons that innervate the drosophila antennal mechanosensory and motor center (ammc), the first relay for auditory information in the fly brain. these neurons produce gr ... | 2012 | 22262877 |
| drosophila duplication hotspots are associated with late-replicating regions of the genome. | duplications play a significant role in both extremes of the phenotypic spectrum of newly arising mutations: they can have severe deleterious effects (e.g. duplications underlie a variety of diseases) but can also be highly advantageous. the phenotypic potential of newly arisen duplications has stimulated wide interest in both the mutational and selective processes shaping these variants in the genome. here we take advantage of the drosophila simulans-drosophila melanogaster genetic system to fu ... | 2011 | 22072977 |
| widespread polymorphism in the positions of stop codons in drosophila melanogaster. | the mechanisms underlying evolutionary changes in protein length are poorly understood. protein domains are lost and gained between species and must have arisen first as within-species polymorphisms. here, we use drosophila melanogaster population genomic data combined with between species divergence information to understand the evolutionary forces that generate and maintain polymorphisms causing changes in protein length in d. melanogaster. specifically, we looked for protein length variations ... | 2012 | 22051795 |
| genomic regions harboring insecticide resistance-associated cyp genes are enriched by transposable element fragments carrying putative transcription factor binding sites in two sibling drosophila species. | in the present study, an in silico analysis was performed to identify transposable element (te) fragments inserted in cyps with functions associated with resistance to insecticides and developmental regulation as well as in neighboring genes in two sibling species, drosophila melanogaster and drosophila simulans. the cyps associated with insecticide resistance and their neighboring non-cyp genes have accumulated a greater number of te fragments than the other cyps or a random sample of genes, pr ... | 2014 | 24361809 |
| temporally variable selection on proteolysis-related reproductive tract proteins in drosophila. | in order to gain further insight into the processes underlying rapid reproductive protein evolution, we have conducted a population genetic survey of 44 reproductive tract-expressed proteases, protease inhibitors, and targets of proteolysis in drosophila melanogaster and drosophila simulans. our findings suggest that positive selection on this group of genes is temporally heterogeneous, with different patterns of selection inferred using tests sensitive at different time scales. such variation i ... | 2012 | 21940639 |
| adaptive evolution of a novel drosophila lectin induced by parasitic wasp attack. | drosophila melanogaster has long been used as a model for the molecular genetics of innate immunity. such work has uncovered several immune receptors that recognize bacterial and fungal pathogens by binding unique components of their cell walls and membranes. drosophila also act as hosts to metazoan pathogens such as parasitic wasps, which can infect a majority of individuals in natural populations, but many aspects of their immune responses against these more closely related pathogens are poorl ... | 2012 | 21873297 |
| desiccation resistance and mating behaviour in laboratory populations of drosophila simulans originating from the opposing slopes of lower nahal oren (israel). | lower nahal oren in northern israel, often referred to as 'evolution canyon', has been proposed as a microscale model site for ecological evolution. however, conflicting stress resistance and mating assay results contribute to controversy over the nahal oren model. in this study, we further tested the nahal oren model, while extending its focus from drosophila melanogaster to its sister species, drosophila simulans. using fly populations derived from the opposing canyon slopes and acclimated to ... | 2011 | 21696478 |
| adaptive evolution and the birth of ctcf binding sites in the drosophila genome. | changes in the physical interaction between cis-regulatory dna sequences and proteins drive the evolution of gene expression. however, it has proven difficult to accurately quantify evolutionary rates of such binding change or to estimate the relative effects of selection and drift in shaping the binding evolution. here we examine the genome-wide binding of ctcf in four species of drosophila separated by between ∼2.5 and 25 million years. ctcf is a highly conserved protein known to be associated ... | 2012 | 23139640 |
| evidence for complex selection on four-fold degenerate sites in drosophila melanogaster. | we considered genome-wide four-fold degenerate sites from an african drosophila melanogaster population and compared them to short introns. to include divergence and to polarize the data, we used its close relatives drosophila simulans, drosophila sechellia, drosophila erecta and drosophila yakuba as outgroups. in d. melanogaster, the gc content at four-fold degenerate sites is higher than in short introns; compared to its relatives, more at than gc is fixed. the former has been explained by cod ... | 2012 | 23020078 |
| transposable elements and insecticide resistance. | transposable elements (tes) are mobile dna sequences that are able to copy themselves within a host genome. they were initially characterized as selfish genes because of documented or presumed costs to host fitness, but it has become increasingly clear that not all tes reduce host fitness. a good example of tes benefiting hosts is seen with insecticide resistance, where in a number of cases, te insertions near specific genes confer resistance to these man-made products. this is particularly true ... | 2012 | 22980922 |
| does positive selection drive transcription factor binding site turnover? a test with drosophila cis-regulatory modules. | transcription factor binding site(s) (tfbs) gain and loss (i.e., turnover) is a well-documented feature of cis-regulatory module (crm) evolution, yet little attention has been paid to the evolutionary force(s) driving this turnover process. the predominant view, motivated by its widespread occurrence, emphasizes the importance of compensatory mutation and genetic drift. positive selection, in contrast, although it has been invoked in specific instances of adaptive gene expression evolution, has ... | 2011 | 21572512 |
| comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes. | transposable elements (tes) are indwelling components of genomes, and their dynamics have been a driving force in genome evolution. although we now have more information concerning their amounts and characteristics in various organisms, we still have little data from overall comparisons of their sequences in very closely-related species. while the drosophila melanogaster genome has been extensively studied, we have only limited knowledge regarding the precise te sequences in the genomes of the r ... | 2011 | 21156200 |
| the effect of developmental temperature on the genetic architecture underlying size and thermal clines in drosophila melanogaster and d. simulans from the east coast of australia. | body size and thermal tolerance clines in drosophila melanogaster occur along the east coast of australia. however the extent to which temperature affects the genetic architecture underlying the observed clinal divergence remains unknown. clinal variation in these traits is associated with cosmopolitan chromosome inversions that cline in d. melanogaster. whether this association influences the genetic architecture for these traits in d. melanogaster is unclear. drosophila simulans shows linear c ... | 2011 | 21091469 |
| introgression of drosophila simulans nuclear pore protein 160 in drosophila melanogaster alone does not cause inviability but does cause female sterility. | we have been analyzing genes for reproductive isolation by replacing drosophila melanogaster genes with homologs from drosophila simulans by interspecific backcrossing. among the introgressions established, we found that a segment of the left arm of chromosome 2, int(2l)s, carried recessive genes for hybrid sterility and inviability. that nuclear pore protein 160 (nup160) in the introgression region is involved in hybrid inviability, as suggested by others, was confirmed by the present analysis. ... | 2010 | 20647504 |
| recognition and detoxification of the insecticide ddt by drosophila melanogaster glutathione s-transferase d1. | gstd1 is one of several insect glutathione s-transferases capable of metabolizing the insecticide ddt. here we use crystallography and nmr to elucidate the binding of ddt and glutathione to gstd1. the crystal structure of drosophila melanogaster gstd1 has been determined to 1.1 a resolution, which reveals that the enzyme adopts the canonical gst fold but with a partially occluded active site caused by the packing of a c-terminal helix against one wall of the binding site for substrates. this hel ... | 2010 | 20417639 |
| transgenic drosophila simulans strains prove the identity of the speciation gene lethal hybrid rescue. | speciation genes are responsible for genetic incompatibilities in hybrids of incipient species and therefore participate in reproductive isolation leading to complete speciation. hybrid males between drosophila melanogaster females and d. simulans males die at late larval or prepupal stages due to a failure in chromosome condensation during mitosis. however a mutant male of d. simulans, named lethal hybrid rescue (lhr), produces viable hybrid males when crossed to females of d. melanogaster. rec ... | 2009 | 20154422 |
| incorporating sequence quality data into alignment improves dna read mapping. | new dna sequencing technologies have achieved breakthroughs in throughput, at the expense of higher error rates. the primary way of interpreting biological sequences is via alignment, but standard alignment methods assume the sequences are accurate. here, we describe how to incorporate the per-base error probabilities reported by sequencers into alignment. unlike existing tools for dna read mapping, our method models both sequencer errors and real sequence differences. this approach consistently ... | 2010 | 20110255 |
| species-specific heterochromatin prevents mitotic chromosome segregation to cause hybrid lethality in drosophila. | postzygotic reproductive barriers such as sterility and lethality of hybrids are important for establishing and maintaining reproductive isolation between species. identifying the causal loci and discerning how they interfere with the development of hybrids is essential for understanding how hybrid incompatibilities (his) evolve, but little is known about the mechanisms of how hi genes cause hybrid dysfunctions. a previously discovered drosophila melanogaster locus called zhr causes lethality in ... | 2009 | 19859525 |
| drosophila melanogaster males respond differently at the behavioural and genome-wide levels to drosophila melanogaster and drosophila simulans females. | drosophila melanogaster are found in sympatry with drosophila simulans, and matings between the species produce nonfertile hybrid offspring at low frequency. evolutionary theory predicts that females choose mates, so males should alter their behaviour in response to female cues. we show that d. melanogaster males quickly decrease courtship towards d. simulans females. courtship levels are reduced within 5 min of exposure to a heterospecific female, and overall courtship is significantly lower th ... | 2009 | 19765174 |
| limited gene misregulation is exacerbated by allele-specific upregulation in lethal hybrids between drosophila melanogaster and drosophila simulans. | misregulation of gene expression is often observed in interspecific hybrids and is generally attributed to regulatory incompatibilities caused by divergence between the two genomes. however, it has been challenging to distinguish effects of regulatory divergence from secondary effects including developmental and physiological defects common to hybrids. here, we use rna-seq to profile gene expression in f1 hybrid male larvae from crosses of drosophila melanogaster to its sibling species d. simula ... | 2014 | 24723419 |
| positive and negative selection on noncoding dna in drosophila simulans. | there is now a wealth of evidence that some of the most important regions of the genome are found outside those that encode proteins, and noncoding regions of the genome have been shown to be subject to substantial levels of selective constraint, particularly in drosophila. recent work has suggested that these regions may also have been subject to the action of positive selection, with large fractions of noncoding divergence having been driven to fixation by adaptive evolution. however, this wor ... | 2008 | 18515263 |
| the genomic response to courtship song stimulation in female drosophila melanogaster. | courtship behaviour involves a complex exchange of signals and responses. these are usually studied at the phenotypic level, and genetic or transcriptional responses to courtship are still poorly understood. here, we examine the gene-expression changes in drosophila melanogaster females in response to one of the key male courtship signals in mate recognition, song produced by male wing vibration. using long oligonucleotide microarrays, we identified several genes that responded differentially to ... | 2012 | 21976688 |
| interspecific y chromosome introgressions disrupt testis-specific gene expression and male reproductive phenotypes in drosophila. | the drosophila y chromosome is a degenerated, heterochromatic chromosome with few functional genes. nonetheless, natural variation on the y chromosome in drosophila melanogaster has substantial trans-acting effects on the regulation of x-linked and autosomal genes. however, the contribution of y chromosome divergence to gene expression divergence between species is unknown. in this study, we constructed a series of y chromosome introgression lines, in which y chromosomes from either drosophila s ... | 2011 | 21969588 |
| adaptive protein evolution of x-linked and autosomal genes in drosophila: implications for faster-x hypotheses. | patterns of sex chromosome and autosome evolution can be used to elucidate the underlying genetic basis of adaptative change. evolutionary theory predicts that x-linked genes will adapt more rapidly than autosomes if adaptation is limited by the availability of beneficial mutations and if such mutations are recessive. in drosophila, rates of molecular divergence between species appear to be equivalent between autosomes and the x chromosome. however, molecular divergence contrasts are difficult t ... | 2007 | 17884828 |
| species-specific positive selection of the male-specific lethal complex that participates in dosage compensation in drosophila. | in many taxa, males and females have unequal ratios of sex chromosomes to autosomes, which has resulted in the invention of diverse mechanisms to equilibrate gene expression between the sexes (dosage compensation). failure to compensate for sex chromosome dosage results in male lethality in drosophila. in drosophila, a male-specific lethal (msl) complex of proteins and noncoding rnas binds to hundreds of sites on the single male x chromosome and up-regulates gene expression. here we use populati ... | 2007 | 17878295 |
| geographic differentiation in the house fly estimated by microsatellite and mitochondrial variation. | gene flow over very large geographic scales has been investigated in few species. examples include drosophila melanogaster, drosophila subobscura, drosophila simulans, and the mediterranean fruit fly (ceratitis capitata). the cosmopolitan house fly, a highly vagile, fecund, colonizing species offers an additional exemplar. genotypes at seven microsatellite loci were scored in 14 widely separated natural house fly populations from the nearctic, neotropics, afrotropics, palearctic, and asia. allel ... | 2008 | 16135710 |
| the drosulfakinin 0 (dsk 0) peptide encoded in the conserved dsk gene affects adult drosophila melanogaster crop contractions. | we report that the drosulfakinin 0 (dsk 0; nqktmsfnh2) structure and genomic organization are conserved. the dsk 0 c-terminus, sfnh2, is widely distributed in the animal kingdom suggesting it defines a novel peptide family. we also report the first description of dsk 0 activity. dsk 0, i (dsk i, fddyghmrfnh2), and ii (dsk ii, ggddqfddyghmrfnh2) are encoded in sulfakinin (dsk). drosophila erecta, drosophila sechellia, drosophila simulans, and drosophila yakuba shared 62.5-87.5% identity to drosop ... | 2007 | 17632121 |
| recent ltr retrotransposon insertion contrasts with waves of non-ltr insertion since speciation in drosophila melanogaster. | ltr and non-ltr retrotransposons exhibit distinct patterns of abundance within the drosophila melanogaster genome, yet the causes of these differences remain unknown. here we investigate whether genomic differences between ltr and non-ltr retrotransposons reflect systematic differences in their insertion history. we find that for 17 ltr and 10 non-ltr retrotransposon families that evolve under a pseudogene-like mode of evolution, most elements from ltr families have integrated in the very recent ... | 2007 | 17592135 |
| canalization of segmentation and its evolution in drosophila. | segmentation in drosophila embryogenesis occurs through a hierarchical cascade of regulatory gene expression driven by the establishment of a diffusion-mediated morphogen gradient. here, we investigate the response of this pattern formation process to genetic variation and evolution in egg size. specifically, we ask whether spatial localization of gap genes kruppel (kr) and giant (gt) and the pair-rule gene even-skipped (eve) during cellularization is robust to genetic variation in embryo length ... | 2007 | 17569783 |
| prevalence of positive selection among nearly neutral amino acid replacements in drosophila. | we have estimated the selective effects of amino acid replacements in natural populations by comparing levels of polymorphism in 91 genes in african populations of drosophila melanogaster with their divergence from drosophila simulans. the genes include about equal numbers whose level of expression in adults is greater in males, greater in females, or approximately equal in the sexes. markov chain monte carlo methods were used to sample key parameters in the stationary distribution of polymorphi ... | 2007 | 17409186 |
| adaptive evolution of metabolic pathways in drosophila. | the adaptive significance of enzyme variation has been of central interest in population genetics. yet, how natural selection operates on enzymes in the larger context of biochemical pathways has not been broadly explored. a basic expectation is that natural selection on metabolic phenotypes will target enzymes that control metabolic flux, but how adaptive variation is distributed among enzymes in metabolic networks is poorly understood. here, we use population genetic methods to identify enzyme ... | 2007 | 17379620 |
| systems-level analysis and evolution of the phototransduction network in drosophila. | networks of interacting genes are responsible for generating life's complexity and for mediating how organisms respond to their environment. thus, a basic understanding of genetic variation in gene networks in natural populations is important for elucidating how changes at the genetic level map to higher levels of biological organization. here, using the well-characterized phototransduction network in drosophila, we analyze variation in gene expression within and between two closely related spec ... | 2007 | 17360639 |
| adaptive genic evolution in the drosophila genomes. | determining the extent of adaptive evolution at the genomic level is central to our understanding of molecular evolution. a suitable observation for this purpose would consist of polymorphic data on a large and unbiased collection of genes from two closely related species, each having a large and stable population. in this study, we sequenced 419 genes from 24 lines of drosophila melanogaster and its close relatives. together with data from drosophila simulans, these data reveal the following. ( ... | 2007 | 17284599 |
| drosophila flies in "evolution canyon" as a model for incipient sympatric speciation. | the genetic basis of population divergence leading to adaptive radiation and speciation is a major unresolved problem of evolutionary biology. molecular elucidation of "speciation genes" advanced recently, yet it remains without clear identification of the gene complexes participating in reproductive isolation between natural populations, particularly, in sympatry. genetic divergence was discovered between drosophila melanogaster populations inhabiting ecologically contrasting, opposite slopes i ... | 2006 | 17108081 |
| lethality in drosophila melanogaster/drosophila simulans species hybrids is not associated with substantial transcriptional misregulation. | the cross of drosophila melanogaster females to drosophila simulans males produces lethal f1 hybrid males. these lethal phenotypes can be suppressed by mutations in the d. melanogaster gene hybrid male rescue (hmr), demonstrating that hmr has a major role in causing lethality in this hybridization. we performed parallel crosses to generate viable (hmr-) and lethal (hmr+) hybrid male larvae and used microarrays to compare whole-genome transcriptional profiles between these two samples. this compa ... | 2007 | 17075830 |
| phylogenetic incongruence in the drosophila melanogaster species group. | drosophila melanogaster and its close relatives are used extensively in comparative biology. despite the importance of phylogenetic information for such studies, relationships between some melanogaster species group members are unclear due to conflicting phylogenetic signals at different loci. in this study, we use twelve nuclear loci (eleven coding and one non-coding) to assess the degree of phylogenetic incongruence in this model system. we focus on two nodes: (1) the node joining the drosophi ... | 2007 | 17071113 |
| pervasive adaptive evolution among interactors of the drosophila hybrid inviability gene, nup96. | nup96 is involved in a lethal hybrid incompatibility between 2 fruit fly species, drosophila melanogaster and drosophila simulans. recurrent adaptive evolution drove the rapid functional divergence of nup96 in both the d. melanogaster and the d. simulans lineages. functional divergence of nup96 between these 2 species is unexpected as nup96 encodes part of the nup107 subcomplex, an architectural component of nuclear pore complexes, the macromolecular channels in nuclear envelopes that mediate nu ... | 2007 | 17056646 |
| recurrent positive selection at bgcn, a key determinant of germ line differentiation, does not appear to be driven by simple coevolution with its partner protein bam. | surveys of nucleotide sequence polymorphism in drosophila melanogaster and drosophila simulans were performed at 2 interacting loci crucial for gametogenesis: bag-of-marbles (bam) and benign gonial cell neoplasm (bgcn). at the polymorphism level, both loci appear to be evolving under the expectations of the neutral theory. however, ratios of polymorphism and divergence for synonymous and nonsynonymous mutations depart significantly from neutral expectations for both loci consistent with a previo ... | 2007 | 17056645 |
| maximum likelihood estimation of ancestral codon usage bias parameters in drosophila. | we present a likelihood method for estimating codon usage bias parameters along the lineages of a phylogeny. the method is an extension of the classical codon-based models used for estimating dn/ds ratios along the lineages of a phylogeny. however, we add one extra parameter for each lineage: the selection coefficient for optimal codon usage (s), allowing joint maximum likelihood estimation of s and the dn/ds ratio. we apply the method to previously published data from drosophila melanogaster, d ... | 2007 | 17041152 |
| ubiquitous selective constraints in the drosophila genome revealed by a genome-wide interspecies comparison. | non-coding dna comprises approximately 80% of the euchromatic portion of the drosophila melanogaster genome. non-coding sequences are known to contain functionally important elements controlling gene expression, but the proportion of sites that are selectively constrained is still largely unknown. we have compared the complete d. melanogaster and drosophila simulans genome sequences to estimate mean selective constraint (the fraction of mutations that are eliminated by selection) in coding and n ... | 2006 | 16751341 |
| proteomic identification of drosophila melanogaster male accessory gland proteins, including a pro-cathepsin and a soluble gamma-glutamyl transpeptidase. | in drosophila melanogaster, the male seminal fluid contains proteins that are important for reproductive success. many of these proteins are synthesised by the male accessory glands and are secreted into the accessory gland lumen, where they are stored until required. previous studies on the identification of drosophila accessory gland products have largely focused on characterisation of male-specific accessory gland cdnas from d. melanogaster and, more recently, drosophila simulans. in the pres ... | 2006 | 16670001 |
| molecular population genetics and evolution of drosophila meiosis genes. | while many functional elements of the meiotic process are well characterized in model organisms, the genetic basis of most of the natural phenotypic variation observed in meiotic pathways has not been determined. to begin to address this issue, we characterized patterns of polymorphism and divergence in the protein-coding regions of 33 genes across 31 lines of drosophila melanogaster and 6 lines of drosophila simulans. we sequenced genes known to be involved in chromosome segregation, recombinat ... | 2009 | 18984573 |
| starvation resistance is positively correlated with body lipid proportion in five wild caught drosophila simulans populations. | stress resistance traits in drosophila often show clinal variation, suggesting that selection affects resistance traits either directly or indirectly. one of the most common causes of stress for animals is the shortage or suboptimal quality of food, and individuals within many species must survive periods of starvation or exposure to nutritionally imbalanced diets. this study determines the relationship between starvation resistance, body lipid content, and lifespan in five recently collected dr ... | 2008 | 18706419 |
| ongoing loss of the tirant transposable element in natural populations of drosophila simulans. | tirant is a long terminal repeat (ltr) retrotransposon with an average of 11 insertion sites on the chromosome arms of drosophila melanogaster flies collected from natural populations worldwide. in the sibling species drosophila simulans, tirant is found only in african populations, which harbor a few insertion sites (1 to 5) on the chromosome arms, although some tirant sequences are present in the heterochromatin of most populations. this distribution in d. simulans reflects either the recent g ... | 2006 | 16626897 |
| recurrent tandem gene duplication gave rise to functionally divergent genes in drosophila. | tandem gene duplication is one of the major gene duplication mechanisms in eukaryotes, as illustrated by the prevalence of gene family clusters. tandem duplicated paralogs usually share the same regulatory element, and as a consequence, they are likely to perform similar biological functions. here, we provide an example of a newly evolved tandem duplicate acquiring novel functions, which were driven by positive selection. cg32708, cg32706, and cg6999 are 3 clustered genes residing in the x chrom ... | 2008 | 18408233 |
| divergence times in caenorhabditis and drosophila inferred from direct estimates of the neutral mutation rate. | accurate inference of the dates of common ancestry among species forms a central problem in understanding the evolutionary history of organisms. molecular estimates of divergence time rely on the molecular evolutionary prediction that neutral mutations and substitutions occur at the same constant rate in genomes of related species. this underlies the notion of a molecular clock. most implementations of this idea depend on paleontological calibration to infer dates of common ancestry, but taxa wi ... | 2008 | 18234705 |
| evolution of a desaturase involved in female pheromonal cuticular hydrocarbon biosynthesis and courtship behavior in drosophila. | drosophila species exhibit polymorphism in female pheromonal cuticular hydrocarbons, with 7-monoenes produced in drosophila simulans and 7,11-dienes in most populations of drosophila melanogaster (5,9-dienes in several african populations). a female-biased desaturase, desatf, expressed only in d. melanogaster is involved in the synthesis of 7,11-dienes. we investigated the role of desatf in 5,9-diene flies. we constructed a 5,9-diene strain knock-down for desatf and showed that desatf is involve ... | 2008 | 18207084 |
| adaptive protein evolution and regulatory divergence in drosophila. | two recent studies demonstrated a positive correlation between divergence in gene expression and protein sequence in drosophila. this correlation could be driven by positive selection or variation in functional constraint. to distinguish between these alternatives, we compared patterns of molecular evolution for 1,862 genes with two previously reported estimates of expression divergence in drosophila. we found a slight negative trend (nonsignificant) between positive selection on protein sequenc ... | 2006 | 16537654 |
| quantitative trait loci for cuticular hydrocarbons associated with sexual isolation between drosophila simulans and d. sechellia. | the identification of genes with large effects on sexual isolation and speciation is an important link between classic evolutionary genetics and molecular biology. few genes that affect sexual isolation and speciation have been identified, perhaps because many traits influencing sexual isolation are complex behaviors. cuticular hydrocarbons (chs) of species of the drosophila melanogaster group play a large role in sexual isolation by functioning as contact pheromones influencing mate recognition ... | 2005 | 16143629 |
| patterns of intron sequence evolution in drosophila are dependent upon length and gc content. | introns comprise a large fraction of eukaryotic genomes, yet little is known about their functional significance. regulatory elements have been mapped to some introns, though these are believed to account for only a small fraction of genome wide intronic dna. no consistent patterns have emerged from studies that have investigated general levels of evolutionary constraint in introns. | 2005 | 16086849 |
| evidence for a functional interaction between the bari1 transposable element and the cytochrome p450 cyp12a4 gene in drosophila melanogaster. | previous studies of the genomic distribution of the transposon bari1 in drosophila melanogaster have revealed an element which is fixed at division 91f in over 90 lab and natural populations. here we report about the structural and transcriptional features of the insertion site which was studied in sublines isolated from an exceptional drosophila line polymorphic for the presence/absence of bari1 at 91f. the insert is located at the 3' end of the cyp12a4 gene that belongs to the cytochrome p450 ... | 2005 | 16076534 |
| rapid evolution of genomic acp complement in the melanogaster subgroup of drosophila. | unusual properties of molecular evolution in reproduction-related drosophila genes, including atypically rapid rates of protein evolution, support the idea that natural selection plays an important role in divergence of reproductive function in drosophila. we used subtractive hybridization to investigate another potential side of evolution of the male reproductive transcriptome. we carried out a screen for genes with much greater transcript abundance in drosophila simulans reproductive tracts th ... | 2005 | 15987879 |
| prospects for identifying functional variation across the genome. | the genetic factors contributing to complex trait variation may reside in regulatory, rather than protein-coding portions of the genome. within noncoding regions, snps in regulatory elements are more likely to contribute to phenotypic variation than those in nonregulatory regions. thus, it is important to be able to identify and annotate noncoding regulatory elements. dna conservation among diverged species successfully identifies noncoding regulatory regions. however, because rapidly evolving r ... | 2005 | 15851675 |
| similar mating and sperm displacement patterns in two highly divergent d. simulans populations from africa and europe. | the frequency of remating in drosophila melanogaster is affected by both genetic and ecological factors. we studied the remating behaviour in one european (italy) and one african (uganda) drosophila simulans population using six highly polymorphic microsatellite markers. despite that the populations were genetically distinct (f(st) = 0.18) and originated from very dissimilar ecological settings with different population densities, we inferred a very similar mating pattern. the remating parameter ... | 2005 | 15813788 |