Publications

selection and constraint on regulatory elements in drosophila simulans.	we utilized available drosophila simulans molecular population genomic data to characterize sequence polymorphism in noncoding regulatory regions and their corresponding transcribed target genes or interacting transcription factors. we highlight two properties of regulatory evolution. first, we find that sequence divergence between d. melanogaster and d. simulans is greater at regulatory sites than expected from levels of intraspecific polymorphism, suggestive of positive selection. second, we c ...	2011	21904868
a general method for calculating likelihoods under the coalescent process.	analysis of genomic data requires an efficient way to calculate likelihoods across very large numbers of loci. we describe a general method for finding the distribution of genealogies: we allow migration between demes, splitting of demes [as in the isolation-with-migration (im) model], and recombination between linked loci. these processes are described by a set of linear recursions for the generating function of branch lengths. under the infinite-sites model, the probability of any configuratio ...	2011	21900266
empirical evidence for son-killing x chromosomes and the operation of sa-zygotic drive.	diploid organisms have two copies of all genes, but only one is carried by each haploid gamete and diploid offspring. this causes a fundamental genetic conflict over transmission rate between alternative alleles. single genes, or gene clusters, only rarely code for the complex phenotypes needed to give them a transmission advantage (drive phenotype). however, all genes on a male's x and y chromosomes co-segregate, allowing different sex-linked genes to code for different parts of the drive pheno ...	2011	21858149
rapid rise and fall of selfish sex-ratio x chromosomes in drosophila simulans: spatiotemporal analysis of phenotypic and molecular data.	sex-ratio drive, which has been documented in several drosophila species, is induced by x-linked segregation distorters. contrary to mendel's law of independent assortment, the sex-ratio chromosome (x(sr)) is inherited by more than half the offspring of carrier males, resulting in a female-biased sex ratio. this segregation advantage allows x(sr) to spread in populations, even if it is not beneficial for the carriers. in the cosmopolitan species d. simulans, the paris sex-ratio is caused by rece ...	2011	21498605
females with a mutation in a nuclear-encoded mitochondrial protein pay a higher cost of survival than do males in drosophila.	males and females age at different rates in a variety of species, but the mechanisms underlying the difference is not understood. in this study, we investigated sex-specific costs of a naturally occurring mildly deleterious deletion (dtrp85, dval86) in cytochrome c oxidase subunit 7a (cox7a) in drosophila simulans. we observed that females and males homozygous for the mutation had 30% and 26% reduced cox activity, respectively, compared with wild type. furthermore, 4-day-old females had 34%-42% ...	2011	21498433
functional conservatism among drosophila simulans flies experiencing different thermal regimes and mitochondrial dna introgression.	drosophila simulans possesses three different mitochondrial haplotypes (sii, ii and iii) that are nonrandomly geographically subdivided with a 3% interhaplogroup variation. the aim of this study was to determine whether perturbation of mitochondrial metabolism and ros management by temperature variation and mtdna introgression would influence the development of aerobic capacity and the intensity of oxidative stress in d. simulans at different ages. environmental temperature divergences during de ...	2011	21462313
thermal sensitivity of mitochondrial functions in permeabilized muscle fibers from two populations of drosophila simulans with divergent mitotypes.	in ectotherms, the external temperature is experienced by the mitochondria, and the mitochondrial respiration of different genotypes is likely to change as a result. using high-resolution respirometry with permeabilized fibers (an in situ approach), we tried to identify differences in mitochondrial performance and thermal sensitivity of two drosophila simulans populations with two different mitochondrial types (siii and siiii) and geographical distributions. maximal state 3 respiration rates obt ...	2011	21451139
pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in drosophila simulans.	in drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. all suffer from confounding factors, however, such that the interpretation of the evidence-in particular, conclusions about the rate and strength of beneficial substitutions-remains tentative. here, we use genome-wide polymorphism data in d. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive ...	2011	21347283
genetic mapping of adaptive wing size variation in drosophila simulans.	many ecologically important traits exhibit latitudinal variation. body size clines have been described repeatedly in insects across multiple continents, suggesting that similar selective forces are shaping these geographical gradients. it is unknown whether these parallel clinal patterns are controlled by the same or different genetic mechanism(s). we present here, quantitative trait loci (qtl) analysis of wing size variation in drosophila simulans. our results show that much of the wing size va ...	2011	21157499
a re-examination of wolbachia-induced cytoplasmic incompatibility in california drosophila simulans.	in california drosophila simulans, the maternally inherited riverside strain wolbachia infection (wri) provides a paradigm for rapid spread of wolbachia in nature and rapid evolutionary change. wri induces cytoplasmic incompatibility (ci), where crosses between infected males and uninfected females produce reduced egg-hatch. the three parameters governing wri infection-frequency dynamics quantify: the fidelity of maternal transmission, the level of cytoplasmic incompatibility, and the relative f ...	2011	21799900
wolbachia-mediated antibacterial protection and immune gene regulation in drosophila.	the outcome of microbial infection of insects is dependent not only on interactions between the host and pathogen, but also on the interactions between microbes that co-infect the host. recently the maternally inherited endosymbiotic bacteria wolbachia has been shown to protect insects from a range of microbial and eukaryotic pathogens. mosquitoes experimentally infected with wolbachia have upregulated immune responses and are protected from a number of pathogens including viruses, bacteria, pla ...	2011	21980455
the bacteriophage woric is the active phage element in wri of drosophila simulans and represents a conserved class of wo phages.	the alphaproteobacterium wolbachia pipientis, the most common endosymbiont in eukaryotes, is found predominantly in insects including many drosophila species. although wolbachia is primarily vertically transmitted, analysis of its genome provides evidence for frequent horizontal transfer, extensive recombination and numerous mobile genetic elements. the genome sequence of wolbachia in drosophila simulans riverside (wri) is available along with the integrated bacteriophages, enabling a detailed e ...	2011	22085419
wolbachia infections in anopheles gambiae cells: transcriptomic characterization of a novel host-symbiont interaction.	the endosymbiotic bacterium wolbachia is being investigated as a potential control agent in several important vector insect species. recent studies have shown that wolbachia can protect the insect host against a wide variety of pathogens, resulting in reduced transmission of parasites and viruses. it has been proposed that compromised vector competence of wolbachia-infected insects is due to up-regulation of the host innate immune system or metabolic competition. anopheles mosquitoes, which tran ...	2011	21379333
inter-island divergence within drosophila mauritiana, a species of the d. simulans complex: past history and/or speciation in progress?	speciation with gene flow may be more common than generally thought, which makes detailed understanding of the extent and pattern of genetic divergence between geographically isolated populations useful. species of the drosophila simulans complex provide a good model for speciation and evolutionary studies, and hence understanding their population genetic structure will increase our understanding of the context in which speciation has occurred. here, we describe genetic diversity and genetic dif ...	2011	21599771
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
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
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
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
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
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
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
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
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
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
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
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
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
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
cis- and trans-acting genetic factors contribute to heterogeneity in the rate of crossing over between the drosophila simulans clade species.	in the genus drosophila, variation in recombination rates has been found within and between species. genetic variation for both cis- and trans-acting factors has been shown to affect recombination rates within species, but little is known about the genetic factors that affect differences between species. here, we estimate rates of crossing over for seven segments that tile across the euchromatic length of the x chromosome in the genetic backgrounds of three closely related drosophila species. we ...	2012	22817673
a comparison of frost expression among species and life stages of drosophila.	frost (fst) is a gene associated with cold exposure in drosophila melanogaster. we used real-time pcr to assess whether cold exposure induces expression of fst in 10 different life stages of d. melanogaster, and adults of seven other drosophila species. we exposed groups of individuals to 0 °c (2 h), followed by 1 h recovery (22 °c). frost was significantly upregulated in response to cold in eggs, third instar larvae, and 2- and 5-day-old male and female adults in d. melanogaster. life stages in ...	2012	21955087
disruption of redox homeostasis leads to oxidative dna damage in spermatocytes of wolbachia-infected drosophila simulans.	molecular interactions between symbiotic bacteria and their animal hosts are, as yet, poorly understood. the most widespread bacterial endosymbiont, wolbachia pipientis, occurs in high density in testes of infected drosophila simulans and causes cytoplasmic incompatibility (ci), a form of male-derived zygotic lethality. wolbachia grow and divide within host vacuoles that generate reactive oxygen species (ros), which in turn stimulate the up-regulation of antioxidant enzymes. these enzymes appear ...	2012	22831171
witnessing phenotypic and molecular evolution in the fruit fly.	this multi-day exercise is designed for a college genetics and evolution laboratory to demonstrate concepts of inheritance and phenotypic and molecular evolution using a live model organism, drosophila simulans. students set up an experimental fruit fly population consisting of ten white eyed flies and one red eyed fly. having red eyes is advantageous compared to having white eyes, allowing students to track the spread of this advantageous trait over several generations. ultimately, the students ...	2012	23459154
antiviral protection and the importance of wolbachia density and tissue tropism in drosophila simulans.	wolbachia, a maternally transmitted endosymbiont of insects, is increasingly being seen as an effective biological control agent that can interfere with transmission of pathogens, including dengue virus. however, the mechanism of antiviral protection is not well understood. the density and distribution of wolbachia in host tissues have been implicated as contributing factors by previous studies with both mosquitoes and flies. drosophila flies infected with five diverse strains of wolbachia were ...	2012	22843518
high-throughput pcr assays to monitor wolbachia infection in the dengue mosquito (aedes aegypti) and drosophila simulans.	we have developed and validated two new fluorescence-based pcr assays to detect the wolbachia wmel strain in aedes aegypti and the wri and wau strains in drosophila simulans. the new assays are accurate, informative, and cost-efficient for large-scale wolbachia screening.	2012	22522691
loss of reproductive parasitism following transfer of male-killing wolbachia to drosophila melanogaster and drosophila simulans.	wolbachia manipulate insect host biology through a variety of means that result in increased production of infected females, enhancing its own transmission. a wolbachia strain (winn) naturally infecting drosophila innubila induces male killing, while native strains of d. melanogaster and d. simulans usually induce cytoplasmic incompatibility (ci). in this study, we transferred winn to d. melanogaster and d. simulans by embryonic microinjection, expecting conservation of the male-killing phenotyp ...	2012	22892635
antagonistic responses to natural and sexual selection and the sex-specific evolution of cuticular hydrocarbons in drosophila simulans.	natural and sexual selection are classically thought to oppose one another, and although there is evidence for this, direct experimental demonstrations of this antagonism are largely lacking. here, we assessed the effects of sexual and natural selection on the evolution of cuticular hydrocarbons (chcs), a character subject to both modes of selection, in drosophila simulans. natural selection and sexual selection were manipulated in a fully factorial design, and after 27 generations of experiment ...	2012	22380431
drosophilid assemblages at different urbanization levels in the city of porto alegre, state of rio grande do sul, southern brazil.	the present study analyzed the drosophilid assemblages in different levels of urbanization in the city of porto alegre, rio grande do sul, brazil. collections were carried out in 2008 in three different environments: a highly urbanized area-"jardim botânico," a forested area with intermediary urbanization-"parque gabriel knijnik," and in a relatively well-preserved forested area, although threatened by the urban growth-"morro santana." in jardim botânico, 36 species belonging to four genera were ...	2012	23950007
tirant, a newly discovered active endogenous retrovirus in drosophila simulans.	endogenous retroviruses have the ability to become permanently integrated into the genomes of their host, and they are generally transmitted vertically from parent to progeny. with the exception of gypsy, few endogenous retroviruses have been identified in insects. in this study, we describe the tirant endogenous retrovirus in a subset of drosophila simulans natural populations. by focusing on the envelope gene, we show that the entire retroviral cycle (transcription, translation, and retrotrans ...	2012	22278247
phototactic personality in fruit flies and its suppression by serotonin and white.	drosophila typically move toward light (phototax positively) when startled. the various species of drosophila exhibit some variation in their respective mean phototactic behaviors; however, it is not clear to what extent genetically identical individuals within each species behave idiosyncratically. such behavioral individuality has indeed been observed in laboratory arthropods; however, the neurobiological factors underlying individual-to-individual behavioral differences are unknown. we develo ...	2012	23150588
male pheromone polymorphism and reproductive isolation in populations of drosophila simulans.	the dominant cuticular hydrocarbons (hc) in drosophila simulans are 7-tricosene (7-t) and 7-pentacosene (7-p). the 7-t is the major hc in east africa and in other continents. in west africa, d. simulans is very rare and displays 7-p as the major compound. we studied three d. simulans strains from egypt (eg), sao-tome (st), and cameroon (cam), with 7-t, intermediary or 7-p phenotypes. hc profiles of st and cam female differed slightly from corresponding male profiles; females had more 7-t and les ...	2012	23145337
naturally occurring mitochondrial dna haplotypes exhibit metabolic differences: insight into functional properties of mitochondria.	linking the mitochondrial genotype and the organismal phenotype is of paramount importance in evolution of mitochondria. in this study, we determined the differences in catalytic properties of mitochondria dictated by divergences in the siii and siiii haplogroups of drosophila simulans using introgressions of siii mtdna type into the siiii nuclear background. we used a novel in situ method (permeabilized fibers) that allowed us to accurately measure the consumption of oxygen by mitochondria in c ...	2012	23025608
wolbachia gonadal density in female and male drosophila vary with laboratory adaptation and respond differently to physiological and environmental challenges.	in symbiotic associations such as those between wolbachia and insects, the within-host symbiont density plays an important role in the maintenance of the infection in natural populations, as it relates to transmission fidelity and pathogenicity of the symbiont. within-host density is speculated to be the result of complex interactions between the bacterial genotype, the host genotype and the environment, which may account for the substantial variation in wolbachia titres among wild collected ind ...	2012	22903036
an indel polymorphism in the hybrid incompatibility gene lethal hybrid rescue of drosophila is functionally relevant.	hybrid incompatibility (hi) genes are frequently observed to be rapidly evolving under selection. this observation has led to the attractive conjecture that selection-derived protein-sequence divergence is culpable for incompatibilities in hybrids. the drosophila simulans hi gene lethal hybrid rescue (lhr) is an intriguing case, because despite having experienced rapid sequence evolution, its hi properties are a shared function inherited from the ancestral state. using an unusual d. simulans lhr ...	2012	22865735
genetic dissection of nucleoporin 160 (nup160), a gene involved in multiple phenotypes of reproductive isolation in drosophila.	previous reports have suggested that the nucleoporin 160 (nup160) gene of drosophila simulans (nup160(sim)) causes the hybrid inviability, female sterility, and morphological anomalies that are observed in crosses with d. melanogaster. here we have confirmed this observation by transposon excision from the p{ep}nup160(ep372) insertion mutation of d. melanogaster. null mutations of the nup160 gene resulted in the three phenotypes caused by nup160(sim), but revertants of the gene did not. interest ...	2012	22820383
complex patterns of local adaptation in heat tolerance in drosophila simulans from eastern australia.	latitudinal clines are considered a powerful means of investigating evolutionary responses to climatic selection in nature. however, most clinal studies of climatic adaptation in drosophila have involved species that contain cosmopolitan inversion polymorphisms that show clinal patterns themselves, making it difficult to determine whether the traits or inversions are under selection. further, although climatic selection is unlikely to act on only one life stage in metamorphic organisms, a few st ...	2012	22775577
incompatibility and competitive exclusion of genomic segments between sibling drosophila species.	the extent and nature of genetic incompatibilities between incipient races and sibling species is of fundamental importance to our view of speciation. however, with the exception of hybrid inviability and sterility factors, little is known about the extent of other, more subtle genetic incompatibilities between incipient species. here we experimentally demonstrate the prevalence of such genetic incompatibilities between two young allopatric sibling species, drosophila simulans and d. sechellia. ...	2012	22761593
chemical cues influence pupation behavior of drosophila simulans and drosophila buzzatii in nature and in the laboratory.	in the wild, larvae of several species of drosophila develop in heterogeneous and rapidly changing environments sharing resources as food and space. in this scenario, sensory systems contribute to detect, localize and recognize congeners and heterospecifics, and provide information about the availability of food and chemical features of environments where animals live. we investigated the behavior of d. simulans and d. buzzatii larvae to chemicals emitted by conspecific and heterospecific larvae ...	2012	22737236
fine-scale genetic analysis of species-specific female preference in drosophila simulans.	behavioural differences are thought to be the first components to contribute to species isolation, yet the precise genetic basis of behavioural isolation remains poorly understood. here, we used a combination of behaviour assays and genetic mapping to provide the first refined map locating candidate genes for interspecific female preference isolating drosophila simulans from d. melanogaster. first, we tested whether two genes identified as affecting d. melanogaster female intraspecific mate choi ...	2012	22694106
genome sequencing reveals complex speciation in the drosophila simulans clade.	the three species of the drosophila simulans clade--the cosmopolitan species, d. simulans, and the two island endemic species, d. mauritiana and d. sechellia--are important models in speciation genetics, but some details of their phylogenetic and speciation history remain unresolved. the order and timing of speciation are disputed, and the existence, magnitude, and timing of gene flow among the three species remain unclear. here we report on the analysis of a whole-genome four-species sequence a ...	2012	22534282
local dynamics of a fast-evolving sex-ratio system in drosophila simulans.	by distorting mendelian transmission to their own advantage, x-linked meiotic drive elements can rapidly spread in natural populations, generating a sex-ratio bias. one expected consequence is the triggering of a co-evolutionary arms race between the sex chromosome that carries the distorter and suppressors counteracting its effect. such an arms race has been theoretically and experimentally established and can have many evolutionary consequences. however, its dynamics in contemporary population ...	2013	24118375
postcopulatory sexual selection generates speciation phenotypes in drosophila.	identifying traits that reproductively isolate species, and the selective forces underlying their divergence, is a central goal of evolutionary biology and speciation research. there is growing recognition that postcopulatory sexual selection, which can drive rapid diversification of interacting ejaculate and female reproductive tract traits that mediate sperm competition, may be an engine of speciation. conspecific sperm precedence (csp) is a taxonomically widespread form of reproductive isolat ...	2013	24076241
stress-induced plastic responses in drosophila simulans following exposure to combinations of temperature and humidity levels.	plastic responses to heat and desiccation stress in insects have been studied in many laboratory experiments on drosophila. however, in these studies the possible interaction between the corresponding stress factors in natural environments has not been taken into consideration. we investigated changes in heat and desiccation resistance of adult drosophila simulans after short-term exposures to different temperatures (35, 31 and 18°c) in combination with high and low relative humidity (ca. 90 and ...	2013	24072792
a novel approach identifying hybrid sterility qtl on the autosomes of drosophila simulans and d. mauritiana.	when species interbreed, the hybrid offspring that are produced are often sterile. if only one hybrid sex is sterile, it is almost always the heterogametic (xy or zw) sex. taking this trend into account, the predominant model used to explain the genetic basis of f1 sterility involves a deleterious interaction between recessive sex-linked loci from one species and dominant autosomal loci from the other species. this model is difficult to evaluate, however, as only a handful of loci influencing in ...	2013	24039910
elimination of y chromosome-bearing spermatids during spermiogenesis in an autosomal sex-ratio mutant of drosophila simulans.	sex ratio distortion, which is commonly abbreviated as sex-ratio, has been studied in many drosophila species, but the mechanism remains largely unknown. here, we report on the sex-ratio mutant of d. simulans named excess of females (exf). the third chromosomal recessive mutation results in a sex ratio of approximately 0.2 or less (males/total). cytological observation demonstrated that meiosis appeared to be completed normally, but that most y chromosome-bearing nuclei failed to elongate during ...	2013	23832303
genotype-by-environment interactions for female mate choice of male cuticular hydrocarbons in drosophila simulans.	recent research has highlighted the potential importance of environmental and genotype-by-environment (g×e) variation in sexual selection, but most studies have focussed on the expression of male sexual traits. consequently, our understanding of genetic variation for plasticity in female mate choice is extremely poor. in this study we examine the genetics of female mate choice in drosophila simulans using isolines reared across two post-eclosion temperatures. there was evidence for g×es in femal ...	2013	23825675
sexual and natural selection both influence male genital evolution.	rapid and divergent evolution of male genital morphology is a conspicuous and general pattern across internally fertilizing animals. rapid genital evolution is thought to be the result of sexual selection, and the role of natural selection in genital evolution remains controversial. however, natural and sexual selection are believed to act antagonistically on male genital form. we conducted an experimental evolution study to investigate the combined effects of natural and sexual selection on the ...	2013	23717488
natural variation of the y chromosome suppresses sex ratio distortion and modulates testis-specific gene expression in drosophila simulans.	x-linked sex-ratio distorters that disrupt spermatogenesis can cause a deficiency in functional y-bearing sperm and a female-biased sex ratio. y-linked modifiers that restore a normal sex ratio might be abundant and favored when a x-linked distorter is present. here we investigated natural variation of y-linked suppressors of sex-ratio in the winters systems and the ability of these chromosomes to modulate gene expression in drosophila simulans. seventy-eight y chromosomes of worldwide origin we ...	2013	23591516
edge-interior differences in the species richness and abundance of drosophilids in a semideciduous forest fragment.	habitat fragmentation is the main cause of biodiversity loss, as remnant fragments are exposed to negative influences that include edge effects, prevention of migration, declines in effective population sizes, loss of genetic variability and invasion of exotic species. the drosophilidae (diptera), especially species of the genus drosophila, which are highly sensitive to environmental variation, have been used as bioindicators. a twelve-month field study was conducted to evaluate the abundance an ...	2013	23556146
multivariate analysis of adaptive capacity for upper thermal limits in drosophila simulans.	thermal tolerance is an important factor influencing the distribution of ectotherms, but our understanding of the ability of species to evolve different thermal limits is limited. based on univariate measures of adaptive capacity, it has recently been suggested that species may have limited evolutionary potential to extend their upper thermal limits under ramping temperature conditions that better reflect heat stress in nature. to test these findings more broadly, we used a paternal half-sibling ...	2013	23517493
mapping wolbachia distributions in the adult drosophila brain.	the maternally inherited bacterium wolbachia infects the germline of most arthropod species. using drosophila simulans and d. melanogaster, we demonstrate that localization of wolbachia to the fat bodies and adult brain is likely also a conserved feature of wolbachia infection. examination of three wolbachia strains (wmel , wriv , wpop ) revealed that the bacteria preferentially concentrate in the central brain with low titres in the optic lobes. distribution within regions of the central brain ...	2013	23490256
optimal temperature range of a plastic species, drosophila simulans.	1. when a species experiences a new climate, it can adapt in two main ways: become genetically adapted to the new temperature, or adopt a plastic approach that allows it to survive at a range of temperatures. 2. the constraint on fitness for genetically adapted populations that are exposed to a new temperature has been well studied, but the range of optimal temperatures and their effect on fitness has never been examined across the worldwide distribution of a plastic species. 3. here, we determi ...	2013	23360477
a population genetic model for the maintenance of r2 retrotransposons in rrna gene loci.	r2 retrotransposable elements exclusively insert into the tandemly repeated rrna genes, the rdna loci, of their animal hosts. r2 elements form stable long-term associations with their host, in which all individuals in a population contain many potentially active copies, but only a fraction of these individuals show active r2 retrotransposition. previous studies have found that r2 rna transcripts are processed from a 28s co-transcript and that the likelihood of r2-inserted units being transcribed ...	2013	23326244
heritability of male attractiveness persists despite evidence for unreliable sexual signals in drosophila simulans.	sexual signals can be used to attract mates, but to be honest indicators of signaller quality they need to convey information reliably. however, environmental variation and genotype-by-environment (g × e) interactions have the potential to compromise the reliability of sexual signals. here, we test the reliability of cuticular hydrocarbons (chcs) as signals of heritable aspects of male attractiveness in drosophila simulans. we examined the heritability of male attractiveness and a measure of the ...	2013	23206188
genotype-by-environment interactions for cuticular hydrocarbon expression in drosophila simulans.	genotype-by-environment interactions (g × es) describe genetic variation for phenotypic plasticity. recent interest in the role of these interactions in sexual selection has identified g × es across a diverse range of species and sexual traits. additionally, theoretical work predicts that g × es in sexual traits could help to maintain genetic variation, but could also disrupt the reliability of these traits as signals of mate quality. however, empirical tests of these theoretical predictions are ...	2013	23163514
paternal transmission of mitochondrial dna as an integral part of mitochondrial inheritance in metapopulations of drosophila simulans.	maternal inheritance is one of the hallmarks of animal mitochondrial dna (mtdna) and central to its success as a molecular marker. this mode of inheritance and subsequent lack of heterologous recombination allows us to retrace evolutionary relationships unambiguously down the matriline and without the confounding effects of recombinant genetic information. accumulating evidence of biparental inheritance of mtdna (paternal leakage), however, challenges our current understanding of how this molecu ...	2013	23010820
divergence of water balance mechanisms in two sibling species (drosophila simulans and d. melanogaster): effects of growth temperatures.	drosophila simulans is more abundant under colder and drier montane habitats in the western himalayas as compared to its sibling d. melanogaster but the mechanistic bases of such climatic adaptations are largely unknown. previous studies have described d. simulans as a desiccation sensitive species which is inconsistent with its occurrence in temperate regions. we tested the hypothesis whether developmental plasticity of cuticular traits confers adaptive changes in water balance-related traits i ...	2013	23080219
pupariation site preference within and between drosophila sibling species.	holometabolous insects pass through a sedentary pupal stage and often choose a location for pupation that is different from the site of larval feeding. we have characterized a difference in pupariation site choice within and between sibling species of drosophila. we found that, in nature, drosophila sechellia pupariate within their host fruit, morinda citrifolia, and that they perform this behavior in laboratory assays. in contrast, in the laboratory, geographically diverse strains of drosophila ...	2013	24033178
genetic analysis of mate discrimination in drosophila simulans.	courtship is an elaborate behavior that conveys information about the identity of animal species and suitability of individual males as mates. in drosophila, there is extensive evidence that females are capable of evaluating and comparing male courtships, and accepting or rejecting males as mates. these relatively simple responses minimize random sexual encounters involving subpar conspecific males and heterospecific males, and over generations can potentially select novel physical and behaviora ...	2013	23888855
a selective sweep across species boundaries in drosophila.	adaptive mutations that accumulate during species divergence are likely to contribute to reproductive incompatibilities and hinder gene flow; however, there may also be a class of mutations that are generally advantageous and can spread across species boundaries. in this study, we characterize a 15 kb region on chromosome 3r that has introgressed from the cosmopolitan generalist species drosophila simulans into the island endemic d. sechellia, which is an ecological specialist. the introgressed ...	2013	23827876
variation in response to co2 in drosophila melanogaster and d. simulans.	a type of slow-recovery from high temperature co2 exposure is a wild-type characteristic of drosophila simulans. species hybrids of wild-type d. melanogaster and d. simulans have intermediate recovery times. the response to nitrogen exposure at both high and low temperatures is the same for the two species suggesting that the observed co2 response is more than just anoxia. since there is no female bias in hybrids, and since injections of d. simulans extract into d. melanogaster produced no incre ...	2013	6408161
uncovering wolbachia diversity upon artificial host transfer.	the common endosymbiotic wolbachia bacteria influence arthropod hosts in multiple ways. they are mostly recognized for their manipulations of host reproduction, yet, more recent studies demonstrate that wolbachia also impact host behavior, metabolic pathways and immunity. besides their biological and evolutionary roles, wolbachia are new potential biological control agents for pest and vector management. importantly, wolbachia-based control strategies require controlled symbiont transfer between ...	2013	24376534
rapid sequential spread of two wolbachia variants in drosophila simulans.	the maternally inherited intracellular bacteria wolbachia can manipulate host reproduction in various ways that foster frequency increases within and among host populations. manipulations involving cytoplasmic incompatibility (ci), where matings between infected males and uninfected females produce non-viable embryos, are common in arthropods and produce a reproductive advantage for infected females. ci was associated with the spread of wolbachia variant wri in californian populations of drosoph ...	2013	24068927
comparative genomics of wolbachia and the bacterial species concept.	the importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. however, whether divergent strains of highly recombining intracellular bacteria, such as wolbachia, can maintain their genetic distinctness when infecting the same host is not known. we first developed a protocol for the genome sequencing of uncultivable endosymbionts. using this method, we have se ...	2013	23593012
variation of gene expression associated with colonisation of an anthropized environment: comparison between african and european populations of drosophila simulans.	the comparison of transcriptome profiles among populations is a powerful tool for investigating the role of gene expression change in adaptation to new environments. in this study, we use massively parallel sequencing of 3' cdnas obtained from large samples of adult males, to compare a population of drosophila simulans from a natural reserve within its ancestral range (eastern africa) with a derived population collected in the strongly anthropized rhône valley (france). the goal was to scan for ...	2013	24260296
modelling a wolbachia invasion using a slow-fast dispersal reaction-diffusion approach.	this paper uses a reaction-diffusion approach to examine the dynamics in the spread of a wolbachia infection within a population of mosquitoes in a homogeneous environment. the formulated model builds upon an earlier model by skalski and gilliam (am. nat. 161(3):441-458, 2003), which incorporates a slow and fast dispersal mode. this generates a faster wavespeed than previous reaction-diffusion approaches, which have been found to produce wavespeeds that are unrealistically slow when compared wit ...	2013	23756849
infection, growth and maintenance of wolbachia pipientis in clonal and non-clonal aedes albopictus cell cultures.	insect cell lines provide useful in vitro models for studying biological systems, including interactions between mosquitoes and obligate intracellular endosymbionts such as wolbachia pipientis. the aedes albopictus aa23 cell line was the first cell line developed to allow examination of wolbachia infections. however, wolbachia studies using aa23 can be complicated by the presence of different cell types in the cell line and the substantial temporal variation in infection level. two approaches we ...	2013	23113940
genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in drosophila mauritiana.	although it is well understood that selection shapes the polymorphism pattern in drosophila, signatures of classic selective sweeps are scarce. here, we focus on drosophila mauritiana, an island endemic, which is closely related to drosophila melanogaster. based on a new, annotated genome sequence, we characterized the genome-wide polymorphism by sequencing pooled individuals (pool-seq). we show that the interplay between selection and recombination results in a genome-wide polymorphism pattern ...	2013	23051690
rapid diversification of sperm precedence traits and processes among three sibling drosophila species.	postcopulatory sexual selection is credited with driving rapid evolutionary diversification of reproductive traits and the formation of reproductive isolating barriers between species. this judgment, however, has largely been inferred rather than demonstrated due to general lack of knowledge about processes and traits underlying variation in competitive fertilization success. here, we resolved processes determining sperm fate in twice-mated females, using transgenic drosophila simulans and droso ...	2013	23888856
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
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
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
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
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
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
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
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
genome diversity and divergence in drosophila mauritiana: multiple signatures of faster x evolution.	drosophila mauritiana is an indian ocean island endemic species that diverged from its two sister species, drosophila simulans and drosophila sechellia, approximately 240,000 years ago. multiple forms of incomplete reproductive isolation have evolved among these species, including sexual, gametic, ecological, and intrinsic postzygotic barriers, with crosses among all three species conforming to haldane's rule: f(1) hybrid males are sterile and f(1) hybrid females are fertile. extensive genetic r ...	2014	25193308
the roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression.	evolutionary changes in gene expression underlie many aspects of phenotypic diversity within and among species. understanding the genetic basis for evolved changes in gene expression is therefore an important component of a comprehensive understanding of the genetic basis of phenotypic evolution. using interspecific introgression hybrids, we examined the genetic basis for divergence in genome-wide patterns of gene expression between drosophila simulans and drosophila mauritiana. we find that cis ...	2014	24043293
evolutionary changes in gene expression, coding sequence and copy-number at the cyp6g1 locus contribute to resistance to multiple insecticides in drosophila.	widespread use of insecticides has led to insecticide resistance in many populations of insects. in some populations, resistance has evolved to multiple pesticides. in drosophila melanogaster, resistance to multiple classes of insecticide is due to the overexpression of a single cytochrome p450 gene, cyp6g1. overexpression of cyp6g1 appears to have evolved in parallel in drosophila simulans, a sibling species of d. melanogaster, where it is also associated with insecticide resistance. however, i ...	2014	24416303