Publications

sequential evolution of a symbiont inferred from the host: wolbachia and drosophila simulans.	this study aims to unravel the biogeography of a model symbiont/host system by exploiting the prediction that a symbiont will leave a signature of infection on the host. specifically, a global sample of 1,442 drosophila simulans from 33 countries and 64 sampling localities was employed to infer the phylogeography of the maternally inherited alpha-proteobacteria wolbachia. phylogenetic analyses, from three symbiont genes and 24 mtdna genomes (excluding the a + t-rich region), showed that each of ...	2004	14660690
incipient evolution of wolbachia compatibility types.	cytoplasmic incompatibility (ci) is induced in arthropods by the maternally inherited bacterium wolbachia. when infected males mate with uninfected females or with females bearing a different wolbachia variant, paternal chromosomes behave abnormally and embryos die. this pattern can be interpreted as resulting from two bacterial effects: one (usually termed mod, for modification) would affect sperm and induce embryo death, unless wolbachia is also present in the egg, which implies the existence ...	2004	15521450
[structural organization and distribution of symbiotic bacteria wolbachia in early embryos and ovaries of drosophila melanogaster and d. simulans].	electron microscopic and morphometric analyses of wolbachia distribution in early embryos of drosophila flies have demonstrated that the number of bacteria in the embryo remains constant from fertilization to blastoderm, and that afterwards the symbionts could be observed only in the polar cells. each bacterium has a three-layer envelope, makes contacts with microtubules and moves through the cytoplasm following the actively dividing nuclei. it has been found for the first time that wolbachia co ...	2004	15214166
wolbachia and cytoplasmic incompatibility in mosquitoes.	wolbachia are maternally inherited bacteria that induce cytoplasmic incompatibility in mosquitoes, and are able to use these patterns of sterility to spread themselves through populations. for this reason they have been proposed as a gene drive system for mosquito genetic replacement, as well as for the reduction of population size or for modulating population age structure in order to reduce disease transmission. here, recent progress in the study of mosquito wolbachia is reviewed. we now have ...	2004	15242714
linking phylogenetics with population genetics to reconstruct the geographic origin of a species.	reconstructing ancestral geographic origins is critical for understanding the long-term evolution of a species. bayesian methods have been proposed to test biogeographic hypotheses while accommodating uncertainty in phylogenetic reconstruction. however, the problem that certain taxa may have a disproportionate influence on conclusions has not been addressed. here, we infer the geographic origin of drosophila simulans using 2,014 bp of the period locus from 63 lines collected from 18 countries. w ...	2004	15288072
differential fitness of mitochondrial dna in perturbation cage studies correlates with global abundance and population history in drosophila simulans.	mitochondria are often referred to as the powerhouse of the cell. however, research linking intraspecific differences in organismal fitness with genotypic mitochondrial dna (mtdna) variation has been hampered by the lack of variation in experimentally tractable species. this study examines whether fly lines harbouring three distinct drosophila simulans mtdna types (sii, -ii and -iii) exhibit differential fitness in laboratory perturbation cages. comparison of the pre-perturbation and post-pertur ...	2004	15306370
nucleotide variation and recombination along the fourth chromosome in drosophila simulans.	the fourth chromosome of drosophila melanogaster and its sister species are believed to be nonrecombining and have been a model system for testing predictions of the effects of selection on linked, neutral variation. we recently examined nucleotide variation along the chromosome of d. melanogaster and revealed that a low average level of recombination could be associated with considerably high levels of nucleotide variation. in this report, we further investigate the variation along the fourth c ...	2004	15126398
wanderings of hobo: a transposon in drosophila melanogaster and its close relatives.	the transposon hobo is present in the genomes of drosophila melanogaster and drosophila simulans (and d. mauritiana and probably d. sechellia, based on southern blots) as full-size elements and internally deleted copies. the full-size melanogaster, simulans and mauritiana hobo elements are 99.9% identical at the dna sequence level, and internally deleted copies in these species essentially differ only in having deletions. in addition to these, hobo-related sequences are present and detectable wi ...	2004	15088653
transposable element dynamics in two sibling species: drosophila melanogaster and drosophila simulans.	transposable elements (tes) in the two sibling species, drosophila melanogaster and d. simulans, differ considerably in amount and dynamics, with d. simulans having a smaller amount of tes than d. melanogaster. several hypotheses have been proposed to explain these differences, based on the evolutionary history of the two species, and claim differences either in the effective size of the population or in genome characteristics. recent data suggest, however, that the higher amount of tes in d. me ...	2004	15088652
anomalies in the expression profile of interspecific hybrids of drosophila melanogaster and drosophila simulans.	when females of drosophila melanogaster and males of drosophila simulans are mated, the male progeny are inviable, whereas the female progeny display manifold malformations and are sterile. these abnormalities result from genetic incompatibilities accumulated since the time the lineages of the species diverged, and may have their origin in aberrant gene transcription. because compensatory changes within species may obscure differences at the regulatory level in conventional comparisons of the ex ...	2004	14962989
the nature of genetic variation in sex and reproduction-related genes among sibling species of the drosophila melanogaster complex.	much is known about the biology of drosophila melanogaster. as a model organism, a comprehensive understanding of its development, physiology and reproduction has been acquired. as a result, a broad variety of transferable genetic tools and information has allowed sibling species of the d. melanogaster complex to emerge as an important speciation model system. by comparing d. melanogaster with its close relative, drosophila simulans, as well as its other sibling species, we are beginning to unde ...	2004	15088662
patterns of evolutionary constraints in intronic and intergenic dna of drosophila.	we develop methods to infer levels of evolutionary constraints in the genome by comparing rates of nucleotide substitution in noncoding dna with rates predicted from rates of synonymous site evolution in adjacent genes or other putatively neutrally evolving sites, while accounting for differences in base composition. we apply the methods to estimate levels of constraint in noncoding dna of drosophila. in introns, constraint (the estimated fraction of mutations that are selectively eliminated) is ...	2004	14762063
strong selective sweep associated with a transposon insertion in drosophila simulans.	we know little about several important properties of beneficial mutations, including their mutational origin, their phenotypic effects (e.g., protein structure changes vs. regulatory changes), and the frequency and rapidity with which they become fixed in a population. one signature of the spread of beneficial mutations is the reduction of heterozygosity at linked sites. here, we present population genetic data from several loci across chromosome arm 2r in drosophila simulans. a 100-kb segment f ...	2004	14745026
sex-ratio distorter of drosophila simulans reduces male productivity and sperm competition ability.	the aim of the present study was to determine whether the effects of sex-ratio segregation distorters on the fertility of male drosophila simulans can explain the contrasting success of these x-linked meiotic drivers in different populations of the species. we compared the fertility of sex-ratio and wild-type males under different mating conditions. both types were found to be equally fertile when mating was allowed, with two females per male, during the whole period of egg laying. by contrast s ...	2004	15271073
molecular population genetics of male accessory gland proteins in the drosophila simulans complex.	accessory gland proteins are a major component of drosophila seminal fluid. these proteins have a variety of functions and may be subject to sexual selection and/or antagonistic evolution between the sexes. most population genetic data from these proteins are from d. melanogaster and d. simulans. here, we extend the population genetic analysis of acp genes to the other simulans complex species, d. mauritiana and d. sechellia. we sequenced population samples of seven acp's from d. mauritiana, d. ...	2004	15238524
evolutionary genetics: mobile dnas as sources of adaptive change?	mobile dnas are potent sources of mutation in wild populations, but seem only rarely to have been used in adaptive evolution. a new study has revealed a mobile dna insertion in drosophila simulans that is associated with an apparent selective sweep and an elevation in expression level of an adjacent gene which creates insecticide resistance.	2004	15120086
the sex-ratio trait and its evolution in drosophila simulans: a comparative approach.	sex-ratio x chromosomes, which prevent the production of y-bearing sperm, have been identified in a dozen drosophila species covering a wide phylogenetic range. it has not yet been established whether the same ancestral genetic system underlies this type of meiotic drive across the genus, but the biological characteristics and the evolutionary history of species undoubtedly determine the fate of x-linked drivers. the intragenomic conflict they trigger contributes to geographical variation in d. ...	2004	15088650
do quantitative trait loci (qtl) for a courtship song difference between drosophila simulans and d. sechellia coincide with candidate genes and intraspecific qtl?	the genetic architecture of traits influencing sexual isolation can give insight into the evolution of reproductive isolation and hence speciation. here we report a quantitative trait loci (qtl) analysis of the difference in mean interpulse interval (ipi), an important component of the male courtship song, between drosophila simulans and d. sechellia. using a backcross analysis, we find six qtl that explain a total of 40.7% of the phenotypic variance. three candidate genes are located in the int ...	2004	15082549
additivity and trans-acting effects on gene expression in male drosophila simulans.	understanding how genetic variation is maintained begins with a comprehensive description of what types of genetic variation exist, the extent and magnitude of the variation, and patterns discernable in that variation. however, such studies have focused primarily on dna sequence data and have ignored genetic variation at other hierarchical levels of genetic information. microarray technology permits an examination of genetic variation at the level of mrna abundance. utilizing a round-robin desig ...	2004	15579694
association of misexpression with sterility in hybrids of drosophila simulansand d. mauritiana.	recent studies have identified genes associated with hybrid sterility and other hybrid dysfunctions, but the consequences of introgressions of these "speciation genes" are often poorly understood. previously, we identified a panel of genes that are underexpressed in sterile male hybrids of drosophila simulans and d. mauritiana relative to pure species. here, we build on this reverse-genetics approach to demonstrate that the underexpression of at least five of these genes in hybrids is associated ...	2004	15486701
identification of a locus under complex positive selection in drosophila simulans by haplotype mapping and composite-likelihood estimation.	the recent action of positive selection is expected to influence patterns of intraspecific dna sequence variation in chromosomal regions linked to the selected locus. these effects include decreased polymorphism, increased linkage disequilibrium, and an increased frequency of derived variants. these effects are all expected to dissipate with distance from the selected locus due to recombination. therefore, in regions of high recombination, it should be possible to localize a target of selection ...	2004	15454542
genetic architecture of wing morphology in drosophila simulans and an analysis of temperature effects on genetic parameter estimates.	the drosophila wing has been used as a model to investigate the mechanisms responsible for size and shape changes in nature, since such changes might underlie morphological evolution. to improve the understanding of wing morphological variation and the interpretation of genetic parameters estimates, we have established 59 lines from a drosophila simulans laboratory population through single pair random matings. the offspring of each line were reared at three different temperatures, and the wing ...	2004	15305171
quantitative trait loci for sexual isolation between drosophila simulans and d. mauritiana.	sexual isolating mechanisms that act before fertilization are often considered the most important genetic barriers leading to speciation in animals. while recent progress has been made toward understanding the genetic basis of the postzygotic isolating mechanisms of hybrid sterility and inviability, little is known about the genetic basis of prezygotic sexual isolation. here, we map quantitative trait loci (qtl) contributing to prezygotic reproductive isolation between the sibling species drosop ...	2004	15280240
new regulatory regions of drosophila 412 retrotransposable element generated by recombination.	there are no doubts that transposable elements (tes) have greatly influenced genomes evolution. they have, however, evolved in different ways throughout mammals, plants, and invertebrates. in mammals they have been shown to be widely present but with low transposition activity; in plants they are responsible for large increases in genome size. in drosophila, despite their low amount, transposition seems to be higher. therefore, to understand how these elements have evolved in different genomes a ...	2005	15574808
quantitative trait loci and interaction effects responsible for variation in female postmating mortality in drosophila simulans and d. sechellia introgression lines.	mating appears to inflict a cost to drosophila females, resulting in a reduction of their lifespan shortly after mating. males from different chromosome extracted lines differ significantly in their detrimental effects on postmating female survival, and seminal fluid proteins produced in the male accessory glands are at least partially responsible for the effect. this suggests that there is a genetic basis underlying the male inflicted effect on female's postmating mortality. however, the genes ...	2005	15354189
identification of co-regulated transcripts affecting male body size in drosophila.	factor analysis is an analytic approach that describes the covariation among a set of genes through the estimation of 'factors', which may be, for example, transcription factors, micrornas (mirnas), and so on, by which the genes are co-regulated. factor analysis gives a direct mechanism by which to relate gene networks to complex traits. using simulated data, we found that factor analysis clearly identifies the number and structure of factors and outperforms hierarchical cluster analysis. noise ...	2005	15960805
characterization of active r2 retrotransposition in the rdna locus of drosophila simulans.	the rrna gene (rdna) loci of all arthropod lineages contain non-ltr retrotransposable elements that have evolved to specifically insert into the 28s rrna genes. extensive in vitro experiments have been conducted to investigate the mechanism of r2 retrotransposition but little is known of the insertion frequency or cellular factors that might regulate r2 activity. in this article, isofemale lines obtained from a population of drosophila simulans were surveyed for recent r2 insertions. within most ...	2005	15781697
resistance to fipronil in drosophila simulans: influence of two point mutations in the rdl gaba receptor subunit.	the eyguieres 42 strain of drosophila simulans, obtained by laboratory selection, displayed approximately 20,000-fold resistance to the insecticide fipronil. molecular cloning of the cdna encoding the rdl gaba receptor subunit of this strain revealed the presence of two mutations: the rdl mutation (a301g) and an additional mutation in the third transmembrane domain (t350m). in order to assess the individual and combined roles of the two mutations in fipronil resistance, the functional properties ...	2005	15748149
linkage disequilibrium and recent selection at three immunity receptor loci in drosophila simulans.	immune system genes in a california population sample of drosophila simulans were shown to bear several hallmarks of the effects of past directional selection. one potential effect of directional selection is an increase in linkage disequilibrium among the polymorphic sites that are linked to the site under selection. in this study, we focus on three d. simulans immunity loci, hmu, sr-ci/sr-ciii, and tehao, for which the polymorphic sites are in nearly perfect linkage disequilibrium, an unusual ...	2005	15654108
a rapid decrease in number of the complete ninja element and concomitant increase of the defective element in a strain of drosophila simulans.	the ninja element, originally isolated from an unstable white mutant strain white-milky (w(mky)) of drosophila simulans, is a member of the retrotransposon family with long terminal repeats (ltrs). we show that ninja is present in high copy numbers in the w(mky)-derivative sublines white-chocolate (w(cho)) and white-persimmonl (w(psm1)), in a low copy number in another derivative subline white-milky 3 (w(mky3)), and in only a few copies in a wild type strain. we have cloned the ninja elements fr ...	2005	16011008
the evolution of antifungal peptides in drosophila.	an essential component of the immune system of animals is the production of antimicrobial peptides (amps). in vertebrates and termites the protein sequence of some amps evolves rapidly under positive selection, suggesting that they may be coevolving with pathogens. however, antibacterial peptides in drosophila tend to be highly conserved. we have inferred the selection pressures acting on drosophila antifungal peptides (drosomycins) from both the divergence of drosomycin genes within and between ...	2005	16157672
the sinbad retrotransposon from the genome of the human blood fluke, schistosoma mansoni, and the distribution of related pao-like elements.	of the major families of long terminal repeat (ltr) retrotransposons, the pao/bel family is probably the least well studied. it is becoming apparent that numerous ltr retrotransposons and other mobile genetic elements have colonized the genome of the human blood fluke, schistosoma mansoni.	2005	15725362
filarial susceptibility and effects of wolbachia in aedes pseudoscutellaris mosquitoes.	the mosquito aedes pseudoscutellaris (theobald), a member of the aedes (stegomyia) scutellaris complex (diptera: culicidae), is an important vector of subperiodic wuchereria bancrofti (cobbold) (spirurida: onchocercidae), causing human lymphatic filariasis, on south pacific islands. maternal inheritance of filarial susceptibility in the complex has previously been asserted, and larval tetracycline treatment reduced susceptibility; the maternally inherited wolbachia in these mosquitoes were sugge ...	2005	15752178
[structural organization and distribution of the symbiotic bacteria wolbachia during spermatogenesis of drosophila simulans].	electron microscopy and morphometric analysis have shown that the symbiotic bacteria wolbachia occur the testis cells during spermatogenesis and are absent in mature spermatids. bacteria did not affect the structural organization of testis cells, which have a typical morphology during morphogenesis. bacteria were distributed along the meiotic spindle microtubules near the mitochondria. they increased in number in spermatids at the stage of elongation. endosymbionts aggregated at the spermatid di ...	2005	15807436
efficient procedure for purification of obligate intracellular wolbachia pipientis and representative amplification of its genome by multiple-displacement amplification.	bacteria belonging to the genus wolbachia are obligatory microendocytobionts that infect a variety of arthropods and a majority of filarial nematode species, where they induce reproductive alterations or establish a mutualistic symbiosis. although two whole genome sequences of wolbachia pipientis, for strain wmel from drosophila melanogaster and strain wbm from brugia malayi, have been fully completed and six other genome sequencing projects are ongoing (http://www.genomesonline.org/index.cgi?wa ...	2005	16269725
high divergence among drosophila simulans mitochondrial haplogroups arose in midst of long term purifying selection.	we characterize the type of selection acting within and among mitochondrial lineages in five closely related drosophila species. we focus on d. simulans, where three genetically distinct mitochondrial haplogroups show high interhaplogroup divergence and low intrahaplogroup polymorphism. using maximum likelihood models we find that the branches leading to these three distinct mitochondrial groups show a significantly reduced rate of nonsynonymous relative to synonymous substitution. this interhap ...	2005	15955513
drosophila simulans as a novel model for studying mitochondrial metabolism and aging.	mitochondria generate much of the cellular energy through the process of oxidative phosphorylation (oxphos). oxphos function may be affected by a mutation in any of the mitochondrial (mt) dna encoded genes and/or nuclear encoded genes that produce proteins imported into the mitochondrion that form (or assemble) the five complexes located on the inner mitochondrial membrane. decreasing mitochondrial oxphos efficiency, defined as the amount of inorganic phosphate incorporated into atp per mole of ...	2005	16169180
is genome size influenced by colonization of new environments in dipteran species?	genome size differences are usually attributed to the amplification and deletion of various repeated dna sequences, including transposable elements (tes). because environmental changes may promote modifications in the amount of these repeated sequences, it has been postulated that when a species colonizes new environments this could be followed by an increase in its genome size. we tested this hypothesis by estimating the genome size of geographically distinct populations of drosophila ananassae ...	2005	15723678
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
patterns of evolution of genes disrupted in expression in drosophila species hybrids.	divergence between species in regulatory pathways may contribute to hybrid incompatibilities such as sterility. consistent with this idea, genes involved in male fertility often evolve faster than most other genes both in amino acid sequence and in expression. previously, we identified a panel of male-specific genes under-expressed in sterile male hybrids of drosophila simulans and d. mauritiana relative to pure species, and we showed that this under-expression is associated with infertility. in ...	2005	16174330
inheritance mode of drosophila simulans female mating propensity with d. melanogaster males.	the genetic factors involved in the sexual isolation between drosophila simulans females and d. melanogaster males are hardly known. we present a study of female mating propensity of d. simulans from different geographic origins with d. melanogaster males. our results reveal the existence of genetic variability in d. simulans for this trait. female discrimination is dominant against high female interspecific mating, which differs from that detected in other drosophila species crosses.	2006	9487683
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
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
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
rapid evolution and gene-specific patterns of selection for three genes of spermatogenesis in drosophila.	hybrid males resulting from crosses between closely related species of drosophila are sterile. the f1 hybrid sterility phenotype is mainly due to defects occurring during late stages of development that relate to sperm individualization, and so genes controlling sperm development may have been subjected to selective diversification between species. it is also possible that genes of spermatogenesis experience selective constraints given their role in a developmental pathway. we analyzed the molec ...	2006	16357040
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
fast protein evolution and germ line expression of a drosophila parental gene and its young retroposed paralog.	this is the first detailed study of the evolution, phylogenetic distribution, and transcription of one young retroposed gene, cg13732, and its parental gene cg15645, whose functions are unknown. cg13732 is a recognizable retroposed copy of cg15645 retaining the signals of this process. we name the parental gene cervantes and the retrogene quijote. to determine when this duplication occurred and the phylogenetic distribution of quijote, we employed polymerase chain reaction, southern blotting, an ...	2006	16916943
origination of an x-linked testes chimeric gene by illegitimate recombination in drosophila.	the formation of chimeric gene structures provides important routes by which novel proteins and functions are introduced into genomes. signatures of these events have been identified in organisms from wide phylogenic distributions. however, the ability to characterize the early phases of these evolutionary processes has been difficult due to the ancient age of the genes or to the limitations of strictly computational approaches. while examples involving retrotransposition exist, our understandin ...	2006	16715176
wolbachia infection influences the development of culex pipiens embryo in incompatible crosses.	wolbachia are maternally inherited endosymbiotic bacteria that infect many arthropod species and have evolved several different ways for manipulating their host, the most frequent being cytoplasmic incompatibility (ci). ci leads to embryo death in crosses between infected males and uninfected females, as well as in crosses between individuals infected by incompatible wolbachia strains. in the mosquito culex pipiens, previous studies suggested developmental variation in embryos stemming from diff ...	2006	16639421
interspecific transfer of wolbachia into the mosquito disease vector aedes albopictus.	intracellular wolbachia bacteria are obligate, maternally inherited endosymbionts found frequently in insects and other invertebrates. the evolutionary success of wolbachia is due in part to an ability to manipulate reproduction. in mosquitoes and many other insects, wolbachia causes a form of sterility known as cytoplasmic incompatibility (ci). wolbachia-induced ci has attracted interest as a potential agent for affecting medically important disease vectors. however, application of the approach ...	2006	16777718
a wolbachia-associated fitness benefit depends on genetic background in drosophila simulans.	the alpha-proteobacteria wolbachia infect a number of insect species and influence host reproduction to favour the spread of infected females through a population. the fitness effect of this infection is important in understanding the spread and maintenance of wolbachia within and among host populations. however, a full elucidation of fitness effect requires careful control of host genetic background. here, i transferred a single clone of wolbachia (the wha strain) into three genetically distinc ...	2006	16777731
induced paternal effects mimic cytoplasmic incompatibility in drosophila.	wolbachia is an intracellular microbe found in a wide diversity of arthropod and filarial nematode hosts. in arthropods these common bacteria are reproductive parasites that manipulate central elements of their host's reproduction to increase their own maternal transmission in one of several ways. cytoplasmic incompatibility (ci) is one such manipulation where sperm are somehow modified in infected males and this modification must be rescued by the presence of the same bacterial strain in the eg ...	2006	16489228
evolutionary dynamics of wau-like wolbachia variants in neotropical drosophila spp.	wolbachia bacteria are common intracellular symbionts of arthropods and have been extensively studied in drosophila. most research focuses on two old word hosts, drosophila melanogaster and drosophila simulans, and does not take into account that some of the wolbachia associations in these species may have evolved only after their fast global expansion and after the exposure to wolbachia of previously isolated habitats. here we looked at wolbachia of neotropical drosophila species. seventy-one l ...	2006	16391124
nuclear-mitochondrial epistasis and drosophila aging: introgression of drosophila simulans mtdna modifies longevity in d. melanogaster nuclear backgrounds.	under the mitochondrial theory of aging, physiological decline with age results from the accumulated cellular damage produced by reactive oxygen species generated during electron transport in the mitochondrion. a large body of literature has documented age-specific declines in mitochondrial function that are consistent with this theory, but relatively few studies have been able to distinguish cause from consequence in the association between mitochondrial function and aging. since mitochondrial ...	2006	16219776
sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression.	we describe sebida, a database of genes with sex-biased expression. the database integrates results from multiple, independent microarray studies comparing male and female gene expression in drosophila melanogaster, drosophila simulans and anopheles gambiae. sebida uses standard nomenclature, which allows individual genes to be compared across different microarray platforms and to be queried by gene name, symbol, or annotation number. in addition to ratios of male/female expression for each gene ...	2006	16882652
incomplete maternal transmission of mitochondrial dna in drosophila.	the possibility of incomplete maternal transmission of mitochondrial dna (mtdna) in drosophila, previously suggested by the presence of heteroplasmy, was examined by intra- and interspecific backcrosses of drosophila simulans and its closest relative, drosophila mauritiana. mtdnas of offspring in these crosses were characterized by southern hybridization with two alpha-32p-labeled probes that are specific to paternal mtdnas. this method could detect as little as 0.03% paternal mtdna, if present, ...	2006	2249764
wolbachia infection suppresses both host defence and parasitoid counter-defence.	endosymbiotic bacteria in the genus wolbachia have been linked to several types of reproductive parasitism, which enhance their own transmission, while their direct effects on the host vary from beneficial to neutral or detrimental. here, we report negative effects of infection on immunity-related traits of drosophila simulans and the parasitoid wasp leptopilina heterotoma. infected d. simulans showed a reduced ability to encapsulate parasitoid eggs, compared to a tetracycline-treated, bacterium ...	2006	16618671
wolbachia infection reduces sperm competitive ability in an insect.	the maternally inherited bacterium wolbachia pipientis imposes significant fitness costs on its hosts. one such cost is decreased sperm production resulting in reduced fertility of male drosophila simulans infected with cytoplasmic incompatibility (ci) inducing wolbachia. we tested the hypothesis that wolbachia infection affects sperm competitive ability and found that wolbachia infection is indeed associated with reduced success in sperm competition in non-virgin males. in the second male role, ...	2006	16777737
nora virus, a persistent virus in drosophila, defines a new picorna-like virus family.	several viruses, including picornaviruses, are known to establish persistent infections, but the mechanisms involved are poorly understood. here, a novel picorna-like virus, nora virus, which causes a persistent infection in drosophila melanogaster, is described. it has a single-stranded, positive-sense genomic rna of 11879 nt, followed by a poly(a) tail. unlike other picorna-like viruses, the genome has four open reading frames (orfs). one orf encodes a picornavirus-like cassette of proteins fo ...	2006	16963764
historical biogeography of drosophila simulans based on y-chromosomal sequences.	y-chromosomal sequences have been used for phylogeographic studies in humans and other mammals, but so far have been ignored as a source of historical information in drosophila and other insects with x/y sex determination. here, we present the first phylogeographic study of drosophila simulans based on the y chromosome. geographic distribution of y-chromosomal haplotypes suggests a high degree of population subdivision within africa, as well as between the african and cosmopolitan groups of popu ...	2006	16051503
mobilization of a hobo-related sequence in the genome of drosophila simulans.	the hobo transposable element can occur under three forms in the drosophila genome: as a complete element (also called canonical), as internally deleted copies, or as hobo-related sequences (relics). some evidence indicated that canonical elements and internally deleted copies are recent acquisitions of drosophila genomes, while the "relics" are old components, normally degenerated and immobile. here we present the characterization of a hobo-related sequence, found in the genome of a hypermutabl ...	2006	16502088
positive selection versus demography: evolutionary inferences based on an unusual haplotype structure in drosophila simulans.	coalescent simulations were used to investigate the possible role of population subdivision and history in shaping nucleotide variation in a recombining 88-kb genomic fragment of drosophila simulans displaying an unusual large-scale haplotype structure. the multilocus analysis, based on summary statistics using specific demographic null models under recombination, indicates that the observed levels of linkage disequilibrium differed significantly from the values expected under different bottlene ...	2006	16757657
inbreeding reduces power-law scaling in the distribution of fluctuating asymmetry: an explanation of the basis of developmental instability.	the study of fluctuating asymmetry has been controversial because of conflicting results found in much of the primary literature. it has been suggested that the source of this conflict is the fact that the basis of fluctuating asymmetry is poorly understood and that, as a consequence, methodology of fluctuating asymmetry studies may be flawed. a new model for the phenomenological basis of fluctuating asymmetry, that variation in fluctuating asymmetry is in large part due to the random exponentia ...	2006	16736063
organization of the sex-ratio meiotic drive region in drosophila simulans.	sex-ratio meiotic drive is the preferential transmission of the x chromosome by xy males, which occurs in several drosophila species and results in female-biased progeny. although the trait has long been known to exist, its molecular basis remains completely unknown. here we report a fine-mapping experiment designed to characterize the major drive locus on a sex-ratio x chromosome of drosophila simulans originating from the seychelles (xsr6). this primary locus was found to contain two interacti ...	2006	16387875
contrasted polymorphism patterns in a large sample of populations from the evolutionary genetics model drosophila simulans.	african populations of drosophila simulans are thought to be ancestral in this model species and are increasingly used for testing general hypotheses in evolutionary genetics. it is often assumed that african populations are more likely to be at a neutral mutation drift equilibrium than other populations. here we examine population structuring and the demographic profile in nine populations of d. simulans. we surveyed sequence variation in four x-linked genes (runt, sevenless, sex-lethal, and ve ...	2006	16510794
proceedings of the smbe tri-national young investigators' workshop 2005. accurate inference and estimation in population genomics.	both intra- and interspecific genomic comparisons have revealed local similarities in the level and frequency of mutational variation, as well as in patterns of gene expression. this autocorrelation between measurements leads to violations of assumptions of independence in many statistical methods, resulting in misleading and incorrect inferences. here i show that autocorrelation can be due to many factors and is present across the genome. using a one-dimensional spatial stochastic model, i furt ...	2006	16407459
intron length evolution in drosophila.	i present data on the evolution of intron lengths among 3 closely related drosophila species, d. melanogaster, drosophila simulans, and drosophila yakuba. using d. yakuba as an outgroup, i mapped insertion and deletion mutations in 148 introns (spanning approximately 30 kb) to the d. melanogaster and d. simulans lineages. intron length evolution in the 2 sister species has been different: in d. melanogaster, x-linked introns have increased slightly in size, whereas autosomal ones have decreased ...	2006	16923822
sex-ratio meiotic drive in drosophila simulans: cellular mechanism, candidate genes and evolution.	the sex-ratio trait, reported in a dozen drosophila species, is a type of naturally occurring meiotic drive in which the driving elements are located on the x chromosome. typically, as the result of a shortage of y-bearing spermatozoa, males carrying a sex-ratio x chromosome produce a large excess of female offspring. the presence of sex-ratio chromosomes in a species can have considerable evolutionary consequences, because they can affect individual fitness and trigger extended intragenomic con ...	2006	16856861
intraspecific variation in survival and mitochondrial oxidative phosphorylation in wild-caught drosophila simulans.	lifespans of organisms vary greatly even among individuals of the same species. under the framework of the free oxygen radical theory of aging, it is predicted that variation in individual lifespan within a species will correlate with variation in the accumulation of oxidative damage to cell components from reactive oxygen species. in this study we test the hypothesis that variation in survival of three wild-caught drosophila simulans fly lines (hw09, nc48 and md106) correlates with three key as ...	2006	16842495
body size patterns in drosophila inhabiting a mesocosm: interactive effects of spatial variation in temperature and abundance.	body size is a major component of fitness. however, the relative contributions of different factors to optimal size, and the determinants of spatial and temporal variation in size, have not been fully established empirically. here, we use a mesocosm of a drosophilidae assemblage inhabiting decaying nectarines to investigate the influence of spatial variation in temperature on adult body size in drosophila simulans sturtevant. two treatments were established; one in the sun where developing larva ...	2006	16773332
estimating the genomewide rate of adaptive protein evolution in drosophila.	when polymorphism and divergence data are available for multiple loci, extended forms of the mcdonald-kreitman test can be used to estimate the average proportion of the amino acid divergence due to adaptive evolution--a statistic denoted alpha. but such tests are subject to many biases. most serious is the possibility that high estimates of alpha reflect demographic changes rather than adaptive substitution. testing for between-locus variation in alpha is one possible way of distinguishing betw ...	2006	16582427
genetic architecture of variation in sex-comb tooth number in drosophila simulans.	the sex comb on the forelegs of drosophila males is a secondary sexual trait, and the number of teeth on these combs varies greatly within and between species. to understand the relationship between the intra- and interspecific variation, we performed quantitative trait locus (qtl) analyses of the intraspecific variation in sex-comb tooth number. we used five mapping populations derived from two inbred drosophila simulans strains that were divergent in the number of sex-comb teeth. although no q ...	2006	16709273
strong purifying selection on the odysseus gene in two clades of sibling species of the drosophila montium species subgroup.	the odysseus (odsh) gene was duplicated from its ancestral neuron-expressed gene, unc-4, and then evolved very rapidly under strong positive darwinian selection as a speciation gene causing hybrid-male sterility between closely related species of the drosophila simulans clade. has odsh also experienced similar positive selection between drosophila sibling species other than those of the simulans clade? we cloned and sequenced odsh and unc-4 from two clades of the drosophila montium species subgr ...	2006	16612548
two dobzhansky-muller genes interact to cause hybrid lethality in drosophila.	the dobzhansky-muller model proposes that hybrid incompatibilities are caused by the interaction between genes that have functionally diverged in the respective hybridizing species. here, we show that lethal hybrid rescue (lhr) has functionally diverged in drosophila simulans and interacts with hybrid male rescue (hmr), which has functionally diverged in d. melanogaster, to cause lethality in f1 hybrid males. lhr localizes to heterochromatic regions of the genome and has diverged extensively in ...	2006	17124320
microsatellite variation and differentiation in african and non-african populations of drosophila simulans.	drosophila simulans originated in sub-saharan africa or madagascar and colonized the rest of the world after the last glaciation about 10 000 years ago. consistent with this demographic history, sub-saharan african populations have been shown to harbour higher levels of microsatellite and sequence variation than cosmopolitan populations. nevertheless, only limited information is available on the population structure of d. simulans. here, we analysed x-linked and autosomal microsatellite loci in ...	2006	17054491
the effect of thermal stress on the mating behavior of three drosophila species.	selection may act on the weakest link in fitness to change how a species adapts to an environmental stress. for many species, this limitation may be reproduction. after adult drosophila melanogaster, drosophila simulans, and drosophila mojavensis males were exposed to varying levels of thermal stress well below those that endanger life, courtship and mating frequency declined. the regression coefficients of both courtship and mating success did not differ significantly between d. melanogaster an ...	2006	11731970
[development of sexual dimorphism as an expression of gene est-6 in the ontogenesis of drosophila melanogaster and drosophila simulans].		2006	4217999
comparative analysis of mitochondrial genotype and aging.	a common feature across all animals, including humans, is that mitochondrial bioenergetics is linked to oxidative stress, but the nature of these relationships with survival is yet to be properly defined. in this study we included 12 drosophila simulans isofemale lines: four of each distinct mtdna haplogroup (sii, -ii, and -iii). first, we investigated sequence variation in six mtdna and 13 nuclear encoded genes (nine nuclear-encoded subunits, and the four known isoforms, of complex iv of the el ...	2007	17934050
working harder to stay alive: metabolic rate increases with age in drosophila simulans but does not correlate with life span.	the hypothesis that metabolic rate is inversely correlated with life span has long been debated. another area of controversy has been the relationship between metabolic rate and aging. in most molecular studies key aspects of cellular metabolism have been shown to decline with age. less attention has been focused on metabolic rate as an organism ages. we studied the survival of three drosophila simulans fly lines and measured whole organism metabolic rate, mitochondrial dna copy number and walki ...	2007	17915248
sex differences in survival and mitochondrial bioenergetics during aging in drosophila.	the goal of this study is to test the role of mitochondria and of mitochondrial metabolism in determining the processes that influence aging of female and male drosophila. we observe that drosophila simulans females tended to have shorter lifespan, higher levels of hydrogen peroxide production and significantly lower levels of catalase but not superoxide dismutase compared to males. in contrast, mammalian females tend to be longer lived, have lower rates of reactive oxygen species production and ...	2007	17725690
mitochondrial dna variation is associated with measurable differences in life-history traits and mitochondrial metabolism in drosophila simulans.	recent studies have used a variety of theoretical arguments to show that mitochondrial (mt) dna rarely evolves as a strictly neutral marker and that selection operates on the mtdna of many species. however, the vast majority of researchers are not convinced by these arguments because data linking mtdna variation with phenotypic differences are limited. we investigated sequence variation in the three mtdna and nine nuclear genes (including all isoforms) that encode the 12 subunits of cytochrome c ...	2007	17598752
rampant adaptive evolution in regions of proteins with unknown function in drosophila simulans.	adaptive protein evolution is pervasive in drosophila. genomic studies, thus far, have analyzed each protein as a single entity. however, the targets of adaptive events may be localized to particular parts of proteins, such as protein domains or regions involved in protein folding. we compared the population genetic mechanisms driving sequence polymorphism and divergence in defined protein domains and non-domain regions. interestingly, we find that non-domain regions of proteins are more frequen ...	2007	17971876
adaptive gene expression divergence inferred from population genomics.	detailed studies of individual genes have shown that gene expression divergence often results from adaptive evolution of regulatory sequence. genome-wide analyses, however, have yet to unite patterns of gene expression with polymorphism and divergence to infer population genetic mechanisms underlying expression evolution. here, we combined genomic expression data--analyzed in a phylogenetic context--with whole genome light-shotgun sequence data from six drosophila simulans lines and reference se ...	2007	17967066
comparative population genetics of the immunity gene, relish: is adaptive evolution idiosyncratic?	the frequency of adaptive evolution acting on common loci in distant lineages remains an outstanding question in evolutionary biology. we asked whether the immunity factor, relish, a gene with a history of directional selection in drosophila simulans, shows evidence of a similar selective history in other drosophila species. we found only weak evidence of recurrent adaptive protein evolution at the relish locus in three sister species pairs, suggesting that this key component of the insect immun ...	2007	17505533
unusual pattern of nucleotide sequence variation at the os-e and os-f genomic regions of drosophila simulans.	nucleotide variation at the genomic region encompassing the odorant-binding protein genes os-e and os-f (os region) was surveyed in two populations of drosophila simulans, one from europe and the other from africa. we found that the european population shows an atypical and large haplotype structure, which extends throughout the approximately 5-kb surveyed genomic region. this structure is depicted by two major haplotype groups segregating at intermediate frequency in the sample, one haplogroup ...	2007	17277360
genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in drosophila.	the effect of recurrent selective sweeps is a spatially heterogeneous reduction in neutral polymorphism throughout the genome. the pattern of reduction depends on the selective advantage and recurrence rate of the sweeps. because many adaptive substitutions responsible for these sweeps also contribute to nonsynonymous divergence, the spatial distribution of nonsynonymous divergence also reflects the distribution of adaptive substitutions. thus, the spatial correspondence between neutral polymorp ...	2007	18073425
drosophila simulans lethal hybrid rescue mutation (lhr) rescues inviable hybrids by restoring x chromosomal dosage compensation and causes fluctuating asymmetry of development.	the drosophila simulans lhr rescues lethal hybrids from the cross of d. melanogaster and d. simulans. we describe here, the phenotypes of lhr dependent rescue hybrids and demonstrate the effects of lhr on functional morphology of the salivary chromosomes in the hybrids. our results reveal that the phenotypes of the 'lhr dependent rescued' hybrids were largely dependent on the genetic background and the dominance in species and hybrids, and not on lhr. cytological examination reveal that while th ...	2007	18305340
population genomics: whole-genome analysis of polymorphism and divergence in drosophila simulans.	the population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. here we present a population genetic analysis of drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, d. melanogaster and d. yakuba. we discovered previou ...	2007	17988176
a sex-ratio meiotic drive system in drosophila simulans. ii: an x-linked distorter.	the evolution of heteromorphic sex chromosomes creates a genetic condition favoring the invasion of sex-ratio meiotic drive elements, resulting in the biased transmission of one sex chromosome over the other, in violation of mendel's first law. the molecular mechanisms of sex-ratio meiotic drive may therefore help us to understand the evolutionary forces shaping the meiotic behavior of the sex chromosomes. here we characterize a sex-ratio distorter on the x chromosome (dox) in drosophila simulan ...	2007	17988173
a sex-ratio meiotic drive system in drosophila simulans. i: an autosomal suppressor.	sex ratio distortion (sex-ratio for short) has been reported in numerous species such as drosophila, where distortion can readily be detected in experimental crosses, but the molecular mechanisms remain elusive. here we characterize an autosomal sex-ratio suppressor from d. simulans that we designate as not much yang (nmy, polytene chromosome position 87f3). nmy suppresses an x-linked sex-ratio distorter, contains a pair of near-perfect inverted repeats of 345 bp, and evidently originated throug ...	2007	17988172
rapid evolution of smell and taste receptor genes during host specialization in drosophila sechellia.	our understanding of the genetic basis of host specialization in insects is limited to basic information on the number and location of genetic factors underlying changes in conspicuous phenotypes. we know nothing about general patterns of molecular evolution that may accompany host specialization but are not traceable to a single prominent phenotypic change. here, i describe changes in the entire repertoire of 136 olfactory receptor (or) and gustatory receptor (gr) genes of the recently speciali ...	2007	17360391
symbiotic bacteria in oocyte and ovarian cell mitochondria of the tick ixodes ricinus: biology and phylogenetic position.	under natural conditions, eukaryote cells may contain bacteria. arthropods such as ticks, insects or mites are a group particularly favoured by the obligate intracellular bacteria. while arthropods are vectors for some of them, other bacteria inhabit invertebrate host cells having entered mutualistic interactions. such endosymbionts dwell usually in the host cell vacuoles or cytoplasm but have been also reported from tick oocyte mitochondria. the microorganisms contribute to mitochondria degrada ...	2007	17226040
from parasite to mutualist: rapid evolution of wolbachia in natural populations of drosophila.	wolbachia are maternally inherited bacteria that commonly spread through host populations by causing cytoplasmic incompatibility, often expressed as reduced egg hatch when uninfected females mate with infected males. infected females are frequently less fecund as a consequence of wolbachia infection. however, theory predicts that because of maternal transmission, these "parasites" will tend to evolve towards a more mutualistic association with their hosts. drosophila simulans in california provi ...	2007	17439303
comparative genomic analysis of allatostatin-encoding (ast) genes in drosophila species and prediction of regulatory elements by phylogenetic footprinting.	the role of the yxfgla family of allatostatin (ast) peptides in dipterans is not well-established. the recent completion of sequencing of genomes for multiple drosophila species provides an opportunity to study the evolutionary variation of the allatostatins and to examine regulatory elements that control gene expression. we performed comparative analyses of ast genes from seven drosophila species (drosophila melanogaster, drosophila simulans, drosophila ananassae, drosophila yakuba, drosophila ...	2007	17175069