Publications

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age-specific fitness components in hybrid females of drosophila pseudoobscura and d. persimilis.most models of hybridization assume that hybrids are less fit than their parental taxa. in contrast, some researchers have explored the possibility that hybrid individuals may actually have higher fitness and so play an important role in the generation of new species or adaptations. by estimating age-specific fitness components, we can determine not only how hybrid fitness differs from parental taxa, but also whether the fitness of hybrids relative to parental taxa changes with age. here we desc ...200911336226
early and late subjective night phases of the drosophila pseudoobscura circadian rhythm require different energies of blue light for phase shifting. 20094273696
chromosomal and allozymic diagnosis of three species of drosophila. drosophila pseudoobscura, d. persimilis, and d. miranda.techniques are presented for distinguishing the sibling species d. pseudoobscura, d. persimilis, and d. miranda in two ways: by differences in the banding sequence of salivary chromosomes, and by the frequencies of allozymes at certain diagnostic loci.2009874309
male-biased genes are overrepresented among novel drosophila pseudoobscura sex-biased genes.the origin of functional innovation is among the key questions in biology. recently, it has been shown that new genes could arise from non-coding dna and that such novel genes are often involved in male reproduction.200818577217
sexual selection and interacting phenotypes in experimental evolution: a study of drosophila pseudoobscura mating behavior.sexual selection requires social interactions, particularly between the sexes. when trait expression is influenced by social interactions, such traits are called interacting phenotypes and only recently have the evolutionary consequences of interacting phenotypes been considered. here we investigated how variation in relative fitness, or the opportunity for sexual selection, affected the evolutionary trajectories of interacting phenotypes. we used experimentally evolved populations of the natura ...200818410532
evolutionary biology: sterile saviours.sterile sperm castes are widespread, but their significance remains enigmatic. new experiments on drosophila pseudoobscura reveal that sterile sperm may promote the survival of fertilising sperm inside the spermicidal female reproductive tract.200818364233
a sterile sperm caste protects brother fertile sperm from female-mediated death in drosophila pseudoobscura.spermicide (i.e., female-mediated sperm death) is an understudied but potentially widespread phenomenon that has important ramifications for the study of sexual conflict, postcopulatory sexual selection, and fertility [1, 2]. males are predicted to evolve adaptations against spermicide, but few antispermicidal mechanisms have been definitively identified. one such adaptation may be the enigmatic infertile sperm morphs or "parasperm" produced by many species, which have been hypothesized to prote ...200818291649
selfish genetic elements promote polyandry in a fly.it is unknown why females mate with multiple males when mating is frequently costly and a single copulation often provides enough sperm to fertilize all a female's eggs. one possibility is that remating increases the fitness of offspring, because fertilization success is biased toward the sperm of high-fitness males. we show that female drosophila pseudoobscura evolved increased remating rates when exposed to the risk of mating with males carrying a deleterious sex ratio-distorting gene that als ...200819023079
selection in heterogeneous environments maintains the gene arrangement polymorphism of drosophila pseudoobscura.chromosomal rearrangements may play an important role in how populations adapt to a local environment. the gene arrangement polymorphism on the third chromosome of drosophila pseudoobscura is a model system to help determine the role that inversions play in the evolution of this species. the gene arrangements are the likely target of strong selection because they form classical clines across diverse geographic habitats, they cycle in frequency over seasons, and they form stable equilibria in pop ...200818764919
[different patterns of evolution in alternative and constitutive coding regions of drosophila alternatively spliced genes].seven hundred and ninety drosophila melanogaster genes, alternatively spliced in coding regions were considered together with their drosophila pseudoobscura orthologs. it was found that nucleotide substitutions in alternative coding regions accumulate more intensively than in constitutive regions. moreover, the evolutionary pattern of alternative regions depends on their inclusion mechanisms (use of alternative promoters, splicing sites or polyadenylation sites) significantly. the rate of synony ...200816909833
sex ratio distorter reduces sperm competitive ability in an insect.selfish genetic elements (sges) are ubiquitous in animals and often associated with low male fertility due to reduced sperm number in male carriers. in the fruit fly drosophila pseudoobscura, the meiotic driving x chromosome "sex ratio" kills y-bearing sperm in carrier males (sr males), resulting in female only broods. we competed sr males against the ejaculates of noncarrying standard males (st males), and quantified the number of sperm transferred by sr and st males to females. we show that sr ...200818373627
developmental stage and level of codon usage bias in drosophila.codon usage bias (cub) is a ubiquitous observation in molecular evolution. as a model, drosophila has been particularly well-studied and indications show that selection at least partially controls codon usage, probably through selection for translational efficiency. although many aspects of drosophila cub have been studied, this is the first study relating codon usage to development in this holometabolous insect with very different life stages. here we ask the question: what developmental stage ...200818755761
figaro: a novel statistical method for vector sequence removal.sequences produced by automated sanger sequencing machines frequently contain fragments of the cloning vector on their ends. software tools currently available for identifying and removing the vector sequence require knowledge of the vector sequence, specific splice sites and any adapter sequences used in the experiment-information often omitted from public databases. furthermore, the clipping coordinates themselves are missing or incorrectly reported. as an example, within the approximately 1.2 ...200818202027
distinguishing the forces controlling genetic variation at the xdh locus in drosophila pseudoobscura.fifty-eight isochromosomal lines sampled from two natural populations of drosophila pseudoobscura in california and one from bogota, colombia, were examined using four-cutter restriction mapping. a 4.6-kb region of the xanthine dehydrogenase locus was probed and 66 of 135 restriction sites scored were polymorphic. this predicts that on average every 12th bp would be polymorphic in this region for the genes surveyed if polymorphism occurred randomly along the coding region. in addition, there wer ...20082583480
synthesis of an attached autosome, c(3)rm, in drosophila pseudoobscura.drosophila pseudoobscura has three acrocentric autosomes. in the experiments reported, homologous arms of the third chromosome were attached to the same centromere. this is a 'reversed metacentric compound' third chromosome, denoted by c(3)rm. this compound chromosome is relatively fertile in within-strain crosses (ca. 50% egg hatch) but sterile when outcrossed to a normal karyotype. when constructing translocations for this experiment, the behavior of the y-autosome translocations suggested tha ...20082323568
a multispecies approach for comparing sequence evolution of x-linked and autosomal sites in drosophila.population genetics models show that, under certain conditions, the x chromosome is expected to be under more efficient selection than the autosomes. this could lead to 'faster-x evolution', if a large proportion of mutations are fixed by positive selection, as suggested by recent studies in drosophila. we used a multispecies approach to test this: muller's element d, an autosomal arm, is fused to the ancestral x chromosome in drosophila pseudoobscura and its sister species, drosophila affinis. ...200819061532
fine-scale mapping of recombination rate in drosophila refines its correlation to diversity and divergence.regional rates of recombination often correlate with levels of nucleotide diversity, and either selective or neutral hypotheses can explain this relationship. regional recombination rates also correlate with nucleotide differences between human and chimpanzee, consistent with models where recombination is mutagenic; however, a lack of correlation is observed in the drosophila melanogaster group, consistent with models invoking natural selection. here, we revisit the relationship among recombinat ...200818621713
evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life.selenocysteine (sec) is a selenium-containing amino acid that is co-translationally inserted into nascent polypeptides by recoding uga codons. selenoproteins occur in both eukaryotes and prokaryotes, but the selenoprotein content of organisms (selenoproteome) is highly variable and some organisms do not utilize sec at all.200717880704
fine-scale crossover rate heterogeneity in drosophila pseudoobscura.broad-scale differences in crossover rate across the genome have been characterized in most genomes studied. fine-scale differences, however, have only been examined in a few taxa, such as arabidopsis, yeast, humans, and mice. no prior studies have directly looked for fine-scale recombination rate heterogeneity in drosophila. we produced 370 drosophila pseudoobscura containing a crossover event within the 2-megabase (mb) region between the genes yellow and white. we then examined 19 intervals wi ...200717160365
the drosulfakinin 0 (dsk 0) peptide encoded in the conserved dsk gene affects adult drosophila melanogaster crop contractions.we report that the drosulfakinin 0 (dsk 0; nqktmsfnh2) structure and genomic organization are conserved. the dsk 0 c-terminus, sfnh2, is widely distributed in the animal kingdom suggesting it defines a novel peptide family. we also report the first description of dsk 0 activity. dsk 0, i (dsk i, fddyghmrfnh2), and ii (dsk ii, ggddqfddyghmrfnh2) are encoded in sulfakinin (dsk). drosophila erecta, drosophila sechellia, drosophila simulans, and drosophila yakuba shared 62.5-87.5% identity to drosop ...200717632121
comparative genomic analysis of allatostatin-encoding (ast) genes in drosophila species and prediction of regulatory elements by phylogenetic footprinting.the role of the yxfgla family of allatostatin (ast) peptides in dipterans is not well-established. the recent completion of sequencing of genomes for multiple drosophila species provides an opportunity to study the evolutionary variation of the allatostatins and to examine regulatory elements that control gene expression. we performed comparative analyses of ast genes from seven drosophila species (drosophila melanogaster, drosophila simulans, drosophila ananassae, drosophila yakuba, drosophila ...200717175069
divergence between the drosophila pseudoobscura and d. persimilis genome sequences in relation to chromosomal inversions.as whole-genome sequence assemblies accumulate, a challenge is to determine how these can be used to address fundamental evolutionary questions, such as inferring the process of speciation. here, we use the sequence assemblies of drosophila pseudoobscura and d. persimilis to test hypotheses regarding divergence with gene flow. we observe low differentiation between the two genome sequences in pericentromeric and peritelomeric regions. we interpret this result as primarily a remnant of the correl ...200718039875
global patterns of sequence evolution in drosophila.sequencing of the genomes of several drosophila allows for the first precise analyses of how global sequence patterns change among multiple, closely related animal species. a basic question is whether there are characteristic features that differentiate chromosomes within a species or between different species.200717996078
sexual conflict does not drive reproductive isolation in experimental populations of drosophila pseudoobscura.sexual conflict has been predicted to drive reproductive isolation by generating arbitrary but rapid coevolutionary changes in reproductive traits among allopatric populations. a testable prediction of this proposal is that allopatric populations experiencing different levels of sexual conflict should exhibit different levels of reproductive isolation. we tested this prediction using experimentally evolved populations of the promiscuous drosophila pseudoobscura. we manipulated sexual conflict by ...200717714294
meiotic transmission of drosophila pseudoobscura chromosomal arrangements.drosophila pseudoobscura harbors a rich gene arrangement polymorphism on the third chromosome generated by a series of overlapping paracentric inversions. the arrangements suppress recombination in heterokaryotypic individuals, which allows for the selective maintenance of coadapted gene complexes. previous mapping experiments used to determine the degree to which recombination is suppressed in gene arrangement heterozygotes produced non-recombinant progeny in non-mendelian ratios. the deviation ...200717565383
experimental constraints on mate preferences in drosophila pseudoobscura decrease offspring viability and fitness of mated pairs.using drosophila pseudoobscura, we tested the hypothesis that social constraints on the free expression of mate preferences, by both females and males, decrease offspring viability and reproductive success of mating pairs. mate preference arenas eliminated intrasexual combat and intersexual coercion. the time female and male choosers spent in arena tests near either of two opposite-sex individuals measured the preferences of choosers. we placed choosers in breeding trials with their preferred or ...200717360550
evolution of sex chromosomes: dosage compensation of the lcp1-4 gene cluster on the evolving neo-x chromosome in drosophila miranda.in drosophila miranda the small multigene family of the larval cuticle protein (lcp1-4) genes resides on the evolving neo-x and neo-y sex chromosome pair while in the sibling species drosophila pseudoobscura and drosophila persimilis the gene cluster is inherited autosomally. the neo-y chromosomal lcp1, lcp2 and lcp4 genes are, as previously shown by us, not expressed and only lcp3 is expressed at a strongly reduced level. as a first step in understanding the evolutionary mechanism(s) transformi ...200717352708
a short note on short dispersal events.we study how the speed of spread for an integrodifference equation depends on the dispersal pattern of individuals. when the dispersal kernel has finite variance, the central limit theorem states that convolutions of the kernel with itself will approach a suitably chosen gaussian distribution. despite this fact, the speed of spread cannot be obtained from the gaussian approximation. we give several examples and explanations for this fact. we then use the kurtosis of the kernel to derive an impro ...200717318675
evaluation of the genomic extent of effects of fixed inversion differences on intraspecific variation and interspecific gene flow in drosophila pseudoobscura and d. persimilis.there is increasing evidence that chromosomal inversions may facilitate the formation or persistence of new species by allowing genetic factors conferring species-specific adaptations or reproductive isolation to be inherited together and by reducing or eliminating introgression. however, the genomic domain of influence of the inverted regions on introgression has not been carefully studied. here, we present a detailed study on the consequences that distance from inversion breakpoints has had on ...200717179068
recombination, statistical power, and genetic studies of sexual isolation in drosophila.genetic studies of sexual isolation in drosophila have generally failed to fully evaluate the effects of their sample size and recombination between markers on their conclusions. in this study we evaluate recombinational distances between markers in drosophila pseudoobscura and d. persimilis, a species pair in which numerous genetic mapping studies have been performed. we conclude that, contrary to assertions, the inversions that distinguish these two species still allow for much recombination w ...200710768121
desiccation resistance in two species of drosophila.three populations of drosophila pseudoobscura, each one represented by 12 isofemale lines, and one laboratory strain of d. melanogaster were tested for desiccation resistance at two time periods. except in the case of one population of d. pseudoobscura, the ability to withstand drying was significantly greater in females than in the corresponding males. the males of the three populations of d. pseudoobscura differed significantly among themselves in their resistance to desiccation, as did the fe ...20073772067
no accelerated rate of protein evolution in male-biased drosophila pseudoobscura genes.sexually dimorphic traits are often subject to diversifying selection. genes with a male-biased gene expression also are probably affected by sexual selection and have a high rate of protein evolution. we used sage to measure sex-biased gene expression in drosophila pseudoobscura. consistent with previous results from d. melanogaster, a larger number of genes were male biased (402 genes) than female biased (138 genes). about 34% of the genes changed the sex-related expression pattern between d. ...200616816428
rates and patterns of chromosomal evolution in drosophila pseudoobscura and d. miranda.comparisons of gene orders between species permit estimation of the rate of chromosomal evolution since their divergence from a common ancestor. we have compared gene orders on three chromosomes of drosophila pseudoobscura with its close relative, d. miranda, and the distant outgroup species, d. melanogaster, by using the public genome sequences of d. pseudoobscura and d. melanogaster and approximately 50 in situ hybridizations of gene probes in d. miranda. we find no evidence for extensive tran ...200616547107
a recombinational portrait of the drosophila pseudoobscura genome.drosophila pseudoobscura has been intensively studied by evolutionary biologists for over 70 years. the recent publication of the genome sequence not only permits studies of comparative genomics with other dipterans but also opens the door to identifying genes associated with adaptive traits or speciation or testing for the signature of natural selection across the genome. information on regional rates of recombination, localization of inversion breakpoints distinguishing it from its sibling spe ...200616545148
simulating natural conditions in the laboratory: a re-examination of sexual isolation between sympatric and allopatric populations of drosophila pseudoobscura and d. persimilis.simulating natural conditions in the laboratory poses one of the most significant challenges to behavioral studies. some authors have argued that laboratory "choice" experiments reflect mate choice in nature more accurately than "no-choice" experiments. a recent choice experiment study questioned the conclusions of several earlier studies by failing to detect a published difference in sexual isolation between populations of drosophila pseudoobscura, and suggested their result was more robust bec ...200616502138
a further analysis of sexual isolation between sympatric and allopatric populations of drosophila pseudoobscura and d. persimilis : rejoinder to noor and ortíz-barrientos. 200616477520
no evidence for learned mating discrimination in male drosophila pseudoobscura.since females often pay a higher cost for heterospecific matings, mate discrimination and species recognition are driven primarily by female choice. in contrast, frequent indiscriminate matings are hypothesized to maximize male fitness. however, recent studies show that previously indiscriminate males (e.g., drosophila melanogaster and poecilia reticulata) can learn to avoid heterospecific courtship. this ability of males to discriminate against heterospecific courtship may be advantageous in po ...200616824212
parametric alignment of drosophila genomes.the classic algorithms of needleman-wunsch and smith-waterman find a maximum a posteriori probability alignment for a pair hidden markov model (phmm). to process large genomes that have undergone complex genome rearrangements, almost all existing whole genome alignment methods apply fast heuristics to divide genomes into small pieces that are suitable for needleman-wunsch alignment. in these alignment methods, it is standard practice to fix the parameters and to produce a single alignment for su ...200616789815
positive selection on nucleotide substitutions and indels in accessory gland proteins of the drosophila pseudoobscura subgroup.genes encoding reproductive proteins often diverge rapidly due to positive selection on nucleotide substitutions. while this general pattern is well established, the extent to which specific reproductive genes experience similar selection in different clades has been little explored, nor have possible targets of positive selection other than nucleotide substitutions, such as indels, received much attention. here, we inspect for the signature of positive selection in the genes encoding five acces ...200616752217
a genomic comparison of faster-sex, faster-x, and faster-male evolution between drosophila melanogaster and drosophila pseudoobscura.a genomic comparison of drosophila melanogaster and drosophila pseudoobscura provides a unique opportunity to investigate factors involved in sequence divergence. the chromosomal arrangements of these species include an autosomal segment in d. melanogaster which is homologous to part of the x chromosome in d. pseudoobscura. using orthologues to calculate rates of nonsynonymous (d(n)) substitutions, we found genes on the x chromosome to be significantly more diverged than those on the autosomes, ...200616612543
x chromosomes and autosomes evolve at similar rates in drosophila: no evidence for faster-x protein evolution.recent data from drosophila suggest that a substantial fraction of amino acid substitutions observed between species are beneficial. if these beneficial mutations are on average partially recessive, then the rate of protein evolution is predicted to be faster for x-linked genes compared to autosomal genes (the "faster-x" hypothesis). we test this prediction by comparing rates of protein substitutions between orthologous genes, taking advantage of variations in chromosome fusions within the genus ...200616520459
evolutionary rearrangement of the amylase genomic regions between drosophila melanogaster and drosophila pseudoobscura.two drosophila pseudoobscura genomic clones have sequence similarity to the drosophila melanogaster amylase region that maps to the 53cd region on the d. melanogaster cytogenetic map. the two clones with similarity to amylase map to sections 73a and 78c of the d. pseudoobscura third chromosome cytogenetic map. the complete sequences of both the 73a and 78c regions were compared to the d. melanogaster genome to determine if the coding region for amylase is present in both regions and to determine ...200614691313
techniques for multi-genome synteny analysis to overcome assembly limitations.genome scale synteny analysis, the analysis of relative gene-order conservation between species, can provide key insights into evolutionary chromosomal dynamics, rearrangement rates between species, and speciation analysis. with the rapid availability of multiple genomes, there is a need for efficient solutions to aid in comparative syntenic analysis. current methods rely on homology assessment and multiple alignment based solutions to determine homologs of genetic markers between species and to ...200617503388
short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression.genomic sequences are highly redundant and contain many types of repetitive dna. fuzzy tandem repeats (ftrs) are of particular interest. they are found in regulatory regions of eukaryotic genes and are reported to interact with transcription factors. however, accurate assessment of ftr occurrences in different genome segments requires specific algorithm for efficient ftr identification and classification.200616403795
evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes.comparative analysis of alternative splicing of orthologous genes from fruit flies (drosophila melanogaster and drosophila pseudoobscura) and mosquito (anopheles gambiae) demonstrated that both in the fruit fly genes and in fruit fly-mosquito comparisons, constitutive exons and splicing sites are more conserved than alternative ones. while >97% of constitutive d. melanogaster exons are conserved in d. pseudoobscura, only approximately 80% of alternative exons are conserved. similarly, 77% of con ...200616520458
the structural role of high molecular weight tropomyosins in dipteran indirect flight muscle and the effect of phosphorylation.in drosophila melanogaster two high molecular weight tropomyosin isoforms, historically named heavy troponins (tnh-33 and tnh-34), are encoded by the tm1 tropomyosin gene. they are specifically expressed in the indirect flight muscles (ifm). their n-termini are conventional and complete tropomyosin sequences, but their c-termini consist of different ifm-specific domains that are rich in proline, alanine, glycine and glutamate. the evidence indicates that in diptera these ifm-specific isoforms ar ...200616752200
periplaneta americana arginine kinase as a major cockroach allergen among thai patients with major cockroach allergies.periplaneta americana is the predominant cockroach (cr) species and a major source of indoor allergens in thailand. nevertheless, data on the nature and molecular characteristics of its allergenic components are rare. we conducted this study to identify and characterize the p. americana allergenic protein. a random heptapeptide phage display library and monoclonal antibody (mab) specific to a the p. americana component previously shown to be an allergenic molecule were used to identify the mab-b ...200616759988
the mitodrome database annotates and compares the oxphos nuclear genes of drosophila melanogaster, drosophila pseudoobscura and anopheles gambiae.the oxidative phosphorylation (oxphos) is the primary energy-producing process of all aerobic organisms and the only cellular function under the dual control of both the mitochondrial and the nuclear genomes. functional characterization and evolutionary study of the oxphos system is of great importance for the understanding of many as yet unclear aspects of nucleus-mitochondrion genomic co-evolution and co-regulation gene networks. the mitodrome database is a web-based database which provides ge ...200616982216
comparison of the oxidative phosphorylation (oxphos) nuclear genes in the genomes of drosophila melanogaster, drosophila pseudoobscura and anopheles gambiae.in eukaryotic cells, oxidative phosphorylation (oxphos) uses the products of both nuclear and mitochondrial genes to generate cellular atp. interspecies comparative analysis of these genes, which appear to be under strong functional constraints, may shed light on the evolutionary mechanisms that act on a set of genes correlated by function and subcellular localization of their products.200515693940
phylogenetic and structural analysis of the drosophila melanogaster p21-activated kinase dmpak3.p21-activated kinases (paks) are a family of serine/threonine kinases whose diverse cellular functions in cytoskeletal reorganisation, cell motility, transformation and cell death are regulated both by the binding of the small rhogtpases rac and cdc42 and by rhogtpase independent mechanisms. the genome of drosophila melanogaster encodes three different pak proteins: dmpak1, dmmbt (dmpak2) and dmpak3. although structurally related, dmpak and dmmbt control different developmental processes and als ...200515777717
ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mrna splicing.recently, we identified a large number of ultraconserved (uc) sequences in noncoding regions of human, mouse, and rat genomes that appear to be essential for vertebrate and amniote ontogeny. here, we used similar methods to identify ultraconserved genomic regions between the insect species drosophila melanogaster and drosophila pseudoobscura, as well as the more distantly related anopheles gambiae. as with vertebrates, ultraconserved sequences in insects appear to occur primarily in intergenic a ...200515899965
conserved genomic organisation of group b sox genes in insects.sox domain containing genes are important metazoan transcriptional regulators implicated in a wide rage of developmental processes. the vertebrate b subgroup contains the sox1, sox2 and sox3 genes that have early functions in neural development. previous studies show that drosophila group b genes have been functionally conserved since they play essential roles in early neural specification and mutations in the drosophila dichaete and soxn genes can be rescued with mammalian sox genes. despite th ...200515943880
a cellular drosophila melanogaster protein with similarity to baculovirus f envelope fusion proteins.baculovirus f (fusion) proteins are found in the envelopes of budded virions. recently a drosophila melanogaster gene (cg4715) that encodes a protein with sequence similarity to baculovirus f proteins was discovered. to examine similarities and differences with baculovirus f proteins, we cloned the d. melanogaster cellular f (dm-cf) protein gene and analyzed dm-cf expression and localization. the predicted dm-cf protein sequence lacks a furin cleavage site, and transiently expressed dm-cf showed ...200515956544
the coevolution of insect muscle tpnt and tpni gene isoforms.in bilaterians, the main regulator of muscle contraction is the troponin (tpn) complex, comprising three closely interacting subunits (c, t, and i). to understand how evolutionary forces drive molecular change in protein complexes, we have compared the gene structures and expression patterns of tpn genes in insects. in this class, while tpnc is encoded by multiple genes, tpnt and tpni are encoded by single genes. their isoform expression pattern is highly conserved within the drosophilidae, and ...200516049195
variable rates of evolution among drosophila opsin genes.dna sequences and chromosomal locations of four drosophila pseudoobscura opsin genes were compared with those from drosophila melanogaster, to determine factors that influence the evolution of multigene families. although the opsin proteins perform the same primary functions, the comparisons reveal a wide range of evolutionary rates. amino acid identities for the opsins range from 90% for rh2 to more than 95% for rh1 and rh4. variation in the rate of synonymous site substitution is especially st ...20051398053
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 ...200515851675
whole-genome analysis reveals a strong positional bias of conserved dmyc-dependent e-boxes.myc is a transcription factor with diverse biological effects ranging from the control of cellular proliferation and growth to the induction of apoptosis. here we present a comprehensive analysis of the transcriptional targets of the sole myc ortholog in drosophila melanogaster, dmyc. we show that the genes that are down-regulated in response to dmyc inhibition are largely identical to those that are up-regulated after dmyc overexpression and that many of them play a role in growth control. the ...200515831447
subdivision of large introns in drosophila by recursive splicing at nonexonic elements.many genes with important roles in development and disease contain exceptionally long introns, but special mechanisms for their expression have not been investigated. we present bioinformatic, phylogenetic, and experimental evidence in drosophila for a mechanism that subdivides many large introns by recursive splicing at nonexonic elements and alternative exons. recursive splice sites predicted with highly stringent criteria are found at much higher frequency than expected in the sense strands o ...200515802507
sequence turnover and tandem repeats in cis-regulatory modules in drosophila.the path by which regulatory sequence can change, yet preserve function, is an important open question for both evolution and bioinformatics. the recent sequencing of two additional species of drosophila plus the wealth of data on gene regulation in the fruit fly provides new means for addressing this question. for regulatory sequences, indels account for more base pairs (bp) of change than substitutions (between drosophila melanogaster and drosophila yakuba), though they are fewer in number. us ...200515659554
the latest buzz in comparative genomics.a second species of fruit fly has just been added to the growing list of organisms with complete and annotated genome sequences. the publication of the drosophila pseudoobscura sequence provides a snapshot of how genomes have changed over tens of millions of years and sets the stage for the analysis of more fly genomes.200515642105
experimental removal and elevation of sexual selection: does sexual selection generate manipulative males and resistant females?sexual conflict over reproduction can occur between males and females. in several naturally promiscuous insect species, experimental evolution studies that have enforced monogamy found evidence for sexual conflict. here, we subjected the naturally promiscuous, sperm-heteromorphic fruit fly drosophila pseudoobscura to enforced monogamy, standard levels of promiscuity, and elevated opportunities for promiscuity in four replicate lines. we examined the effect of male and female selection history an ...200515795864
the detection of shared and ancestral polymorphisms.there is increasing evidence that closely related species contain many polymorphisms that were present in their common ancestral species. use of a more distant relative as an outgroup increases the ability to detect such ancestral polymorphisms. we describe a method for further improving estimates of the fraction of polymorphisms that are ancestral, and illustrate this with reference to data on drosophila pseudoobscura and d. miranda. we also derive formulae for the proportion of fixations arisi ...200516207392
likelihoods from summary statistics: recent divergence between species.we describe an importance-sampling method for approximating likelihoods of population parameters based on multiple summary statistics. in this first application, we address the demographic history of closely related members of the drosophila pseudoobscura group. we base the maximum-likelihood estimation of the time since speciation and the effective population sizes of the extant and ancestral populations on the pattern of nucleotide variation at dps2002, a noncoding region tightly linked to a p ...200516143628
mechanisms of genetic exchange within the chromosomal inversions of drosophila pseudoobscura.we have used the inversion system of drosophila pseudoobscura to investigate how genetic flux occurs among the gene arrangements. the patterns of nucleotide polymorphism at seven loci were used to infer gene conversion events between pairs of different gene arrangements. we estimate that the average gene conversion tract length is 205 bp and that the average conversion rate is 3.4 x 10(-6), which is 2 orders of magnitude greater than the mutation rate. we did not detect gene conversion events be ...200516143625
postmating-prezygotic isolation is not an important source of selection for reinforcement within and between species in drosophila pseudoobscura and d. persimilis.most work on adaptive speciation to date has focused on the role of low hybrid fitness as the force driving reinforcement (the evolution of premating isolation after secondary contact that reduces the likelihood of matings between populations). however, recent theoretical work has shown that postmating, prezygotic incompatibilities may also be important in driving premating isolation. we quantified premating, postmating-prezygotic, and early postzygotic fitness effects in crosses among three pop ...200516136803
sexual isolation between sympatric and allopatric populations of drosophila pseudoobscura and d. persimilis.according to reinforcement theory, sexual isolation between species in sympatry is strengthened by natural selection against maladaptive hybrids. drosophila pseudoobscura and d. persimilis from four locations where these species are sympatric, and from three locations where only d. pseudoobscura has been found, were utilized in studies of sexual isolation. multiple-choice observation chambers were used to record matings between sympatric and allopatric strains of the two species. there was a wid ...200515864445
experimental manipulation of sexual selection and the evolution of courtship song in drosophila pseudoobscura.courtship song serves as a sexual signal and may contribute to reproductive isolation between closely related species. using lines of drosophila pseudoobscura experimentally selected under different sexual selection regimes, we tested whether increased promiscuity and enforced monogamy led to evolutionary changes in courtship song elements. in d. pseudoobscura, males produce both a low and high rate repetition song. we found that both song types diverged after selection and that the direction of ...200515864440
the genetic basis of reproductive isolation: insights from drosophila.recent studies of the genetics of speciation in drosophila have focused on two problems: (i) identifying and characterizing the genes that cause reproductive isolation, and (ii) determining the evolutionary forces that drove the divergence of these "speciation genes." here, i review this work. i conclude that speciation genes correspond to ordinary loci having normal functions within species. these genes fall into several functional classes, although a role in transcriptional regulation could pr ...200515851676
sex chromosomes: evolution of the weird and wonderful.new findings in the platypus and drosophila pseudoobscura illustrate, yet again, that the sex chromosomes seem never to stop evolving. degeneration processes lead to a continual loss of genes and gene activity on the y chromosome, and complete loss of y-linked genes is possible if autosomal genes take over control of male fertility - though addition of new material to the sex chromosomes may start the process anew.200515723783
segregation distortion in hybrids between the bogota and usa subspecies of drosophila pseudoobscura.we show that, contrary to claims in the literature, "sterile" males resulting from the cross of the bogota and usa subspecies of drosophila pseudoobscura are weakly fertile. surprisingly, these hybrid males produce almost all daughters when crossed to females of any genotype (pure bogota, pure usa, hybrid f1). several lines of evidence suggest that this sex ratio distortion is caused by sex chromosome segregation distortion in hybrid males. we genetically analyze this normally cryptic segregatio ...200515654115
y chromosome of d. pseudoobscura is not homologous to the ancestral drosophila y.we report a genome-wide search of y-linked genes in drosophila pseudoobscura. all six identifiable orthologs of the d. melanogaster y-linked genes have autosomal inheritance in d. pseudoobscura. four orthologs were investigated in detail and proved to be y-linked in d. guanche and d. bifasciata, which shows that less than 18 million years ago the ancestral drosophila y chromosome was translocated to an autosome in the d. pseudoobscura lineage. we found 15 genes and pseudogenes in the current y o ...200515528405
evidence for a one-allele assortative mating locus.theoretical models have shown that speciation with gene flow can occur readily via a "one-allele mechanism," where the spread of the same allele within both of two diverging species reduces their subsequent hybridization. here we present direct genetic evidence for such an allele in drosophila pseudoobscura. alleles conferring high or low assortative mating in d. pseudoobscura produce the same effects when inserted into d. persimilis. this observation suggests that the type of genetic variation ...200516322450
a test of the chromosomal rearrangement model of speciation in drosophila pseudoobscura.recent studies suggest that chromosomal rearrangements play a significant role in speciation by preventing recombination and maintaining species persistence despite interspecies gene flow. factors conferring adaptation or reproductive isolation are maintained in rearranged regions in the face of hybridization, while such factors are eliminated from collinear regions. as a direct test of this rearrangement model, we evaluated the genetic basis of hybrid male sterility in a sympatric species pair, ...200415446438
multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of drosophila pseudoobscura and d. persimilis.the genetic study of diverging, closely related populations is required for basic questions on demography and speciation, as well as for biodiversity and conservation research. however, it is often unclear whether divergence is due simply to separation or whether populations have also experienced gene flow. these questions can be addressed with a full model of population separation with gene flow, by applying a markov chain monte carlo method for estimating the posterior probability distribution ...200415238526
phylogenetic relationships of drosophila melanogaster species group deduced from spacer regions of histone gene h2a-h2b.nucleotide sequences of the spacer region of the histone gene h2a-h2b from 36 species of drosophila melanogaster species group were determined. the phylogenetic trees were reconstructed with maximum parsimony, maximum likelihood, and bayesian methods by using drosophila pseudoobscura as the out group. our results show that the melanogaster species group clustered in three main lineages: (1). montium subgroup; (2). ananassae subgroup; and (3). the seven oriental subgroups, among which the montium ...200414715225
inbreeding and mating patterns in drosophila pseudoobscura. 2004539969
the drosophila gene start1: a putative cholesterol transporter and key regulator of ecdysteroid synthesis.human metastatic lymph node 64 (mln64) is a transmembrane protein that shares homology with the cholesterol-binding vertebrate steroid acute regulatory protein (star)-related lipid transfer domain (start) and is involved in cholesterol traffic and steroid synthesis. we identified a drosophila melanogaster gene whose putative protein product shows extensive homology with mln64 and that we name start1 (flybase cg3522). the putative start1 protein, derived from start1 cdna sequences, contains an ad ...200414745013
"plus-c" odorant-binding protein genes in two drosophila species and the malaria mosquito anopheles gambiae.olfaction plays a crucial role in many aspects of insect behaviour, including host selection by agricultural pests and vectors of human disease. insect odorant-binding proteins (obps) are thought to function as the first step in molecular recognition and the transport of semiochemicals. the whole genome sequence of the fruit fly drosophila melanogaster has been completed and a large number of genes have been annotated as obps, based on the presence of six conserved cysteine residues and a conser ...200414960367
computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in drosophila melanogaster and drosophila pseudoobscura.the identification of sequences that control transcription in metazoans is a major goal of genome analysis. in a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. nine of these clusters overlapped known ...200415345045
transcription of drosophila troponin i gene is regulated by two conserved, functionally identical, synergistic elements.the drosophila wings-up a gene encodes troponin i. two regions, located upstream of the transcription initiation site (upstream regulatory element) and in the first intron (intron regulatory element), regulate gene expression in specific developmental and muscle type domains. based on lacz reporter expression in transgenic lines, upstream regulatory element and intron regulatory element yield identical expression patterns. both elements are required for full expression levels in vivo as indicate ...200414718563
computational identification of microrna targets.recent experiments have shown that the genomes of organisms such as worm, fly, human, and mouse encode hundreds of microrna genes. many of these micrornas are thought to regulate the translational expression of other genes by binding to partially complementary sites in messenger rnas. phenotypic and expression analysis suggests an important role of micrornas during development. therefore, it is of fundamental importance to identify microrna targets. however, no experimental or computational high ...200415013811
conservation of dna methylation in dipteran insects.dna methylation is a central mechanism of epigenetic regulation. whereas vertebrate dna methylation requires at least four different dna methyltransferases, drosophila melanogaster only utilizes a single, dnmt2-like enzyme. this profound difference has raised the question of the evolutionary significance of the drosophila methylation system. we have now identified dnmt2-like open reading frames in the genome sequences of drosophila pseudoobscura and anopheles gambiae. these genes represent the o ...200415056358
molecular evolution of x-linked accessory gland proteins in drosophila pseudoobscura.in drosophila melanogaster and drosophila simulans, positive darwinian selection drives high rates of evolution of male reproductive genes, and accessory gland proteins (acps) in particular. here, we tested whether 13 x-linked male-specific genes, 4 acps and 9 non-acps, are under selective forces in the drosophila pseudoobscura species group, much as those in the d. melanogaster group. we observed a statistically significant correlation in relative rates of nonsynonymous evolution between the tw ...200415073226
evolution of the trans-splicing drosophila locus mod(mdg4) in several species of diptera and lepidoptera.the modifier of mdg4 (mod[mdg4]) locus of drosophila melanogaster (dme) encodes chromatin proteins which are involved in position effect variegation, establishment of chromatin boundaries, nerve pathfinding, meiotic chromosome pairing and apoptosis. it was recently shown that mrna trans-splicing is involved in the generation of at least 26 different mod(mdg4) transcripts. here, we show that a similar complex mod(mdg4) locus exists in drosophila pseudoobscura (dps), drosophila virilis (dvi), anop ...200415094203
analysis of the insect os-d-like gene family.insect os-d-like proteins, also known as chemosensory (csp) or sensory appendage proteins (sap), are broadly expressed in various insect tissues, where they are thought to bind short to medium chain length fatty acids and their derivatives. although their specific function remains uncertain, os-d-like members have been isolated from sensory organs (including the sensillum lymph in some cases), and a role in olfaction similar to that of the insect odorant binding proteins (obp) has been suggested ...200415274438
evolutionary genomics of inversions in drosophila pseudoobscura: evidence for epistasis.drosophila pseudoobscura harbors a rich polymorphism for paracentric inversions on the third chromosome, and the clines in the inversion frequencies across the southwestern united states indicate that strong natural selection operates on them. isogenic inversion strains were made from isofemale lines collected from four localities, and eight molecular markers were mapped on the third chromosome. nucleotide diversity was measured for these loci and formed the basis of an evolutionary genomic anal ...200312824467
microrna targets in drosophila.the recent discoveries of microrna (mirna) genes and characterization of the first few target genes regulated by mirnas in caenorhabditis elegans and drosophila melanogaster have set the stage for elucidation of a novel network of regulatory control. we present a computational method for whole-genome prediction of mirna target genes. the method is validated using known examples. for each mirna, target genes are selected on the basis of three properties: sequence complementarity using a position- ...200314709173
turnover of binding sites for transcription factors involved in early drosophila development.despite the importance of cis-regulatory regions in evolution, little is know about their evolutionary dynamics. in this report, we analyze the process of evolution of binding sites for transcription factors using as a model a well characterized system, the drosophila early developmental enhancers. we compare the sequences of eight enhancer regions for early developmental genes between drosophila melanogaster and other two species, drosophila virilis and drosophila pseudoobscura, searching for t ...200312801649
the evolution of conspecific sperm precedence in drosophila.conspecific sperm precedence takes place when females inseminated by both conspecific and heterospecific sperm preferentially produce conspecific rather than hybrid offspring. although many studies have documented conspecific sperm precedence, most have only identified it between taxa that are already considered to be good species. here, we test for sperm precedence between two drosophila pseudoobscura subspecies and between two drosophila melanogaster races to evaluate how early in evolutionary ...200312694281
unusual pattern of single nucleotide polymorphism at the exuperantia2 locus of drosophila pseudoobscura.we have investigated the pattern of dna sequence variation at the exuperantia2 locus in drosophila pseudoobscura. this adds to the increasing dataset of genetic variation in d. pseudoobscura, a useful model species for evolutionary genetic studies. the level of silent site nucleotide diversity and the divergence from an outgroup drosophila miranda are comparable with those for other x-linked loci. one peculiar pattern at the exu2 locus of d. pseudoobscura is a complete linkage disequilibrium bet ...200314768894
characterization of a male-predominant antisense transcript underexpressed in hybrids of drosophila pseudoobscura and d. persimilis.characterizing genes that are misregulated in hybrids may elucidate the genetic basis of hybrid sterility or other hybrid dysfunctions that contribute to speciation. previously, a small segment of a male-predominant transcript that is underexpressed in adult male hybrids of drosophila pseudoobscura and d. persimilis relative to pure species was identified in a differential display screen. here, we obtained the full sequence of this 1330-bp transcript and determined that it is an antisense messag ...200314704168
divergent environments and population bottlenecks fail to generate premating isolation in drosophila pseudoobscura.while the feasibility of bottleneck-induced speciation is in doubt, population bottlenecks may still affect the speciation process by interacting with divergent selection. to explore this possibility, i conducted a laboratory speciation experiment using drosophila pseudoobscura involving 78 replicate populations assigned in a two-way factorial design to both bottleneck (present vs. absent) and environment (ancestral vs. novel) treatments. populations independently evolved under these treatments ...200314686531
indiscriminate females and choosy males: within- and between-species variation in drosophila.the classic view of choosy, passive females and indiscriminate, competitive males gained theoretical foundations with parental investment theory. when females invest more in offspring than males, parental investment theory says that selection operates so that females discriminate among males for mates (i.e., females are choosy and passive) and males are indiscriminate (i.e., males are profligate and competitive). here we report tests of predictions using drosophila pseudoobscura and d. melanogas ...200314575325
drosophila lola encodes a family of btb-transcription regulators with highly variable c-terminal domains containing zinc finger motifs.alternative splicing is an important mechanism contributing to the increased proteome diversity in higher eukaryotes. we have explored the alternative splicing events in the drosophila longitudinals lacking (lola) gene by means of 5' race, 3' race, genome sequence searches, and est sequencing. we demonstrated that the lola locus is comprised of 32 exons spanning over 60 kb, and encodes a total of 80 alternatively spliced variants consisting of 5' and 3' variable sequences and constitutive common ...200312853139
evolution of gab family adaptor proteins.the gab/dos/soc-1 proteins form a family of multi-adaptor/scaffolding proteins involved in receptor tyrosine kinase signaling. to further understanding of the gab family and the drosophila dos protein in particular, we isolated a dos homolog from both drosophila pseudoobscura and drosophila virilis and compared their gene structures and protein sequences with the rest of the gab family. the presence of two conserved introns confirmed that the dos and gab genes are orthologous, but the caenorhabd ...200312853137
the causes of phylogenetic conflict in a classic drosophila species group.bifurcating phylogenies are frequently used to describe the evolutionary history of groups of related species. however, simple bifurcating models may poorly represent the evolutionary history of species that have been exchanging genes. here, we show that the history of three well-known closely related species, drosophila pseudoobscura, d. persimilis and d. p. bogotana, is not well represented by a bifurcating phylogenetic tree. the phylogenetic relationships among these species vary widely betwe ...200312816659
phospholipase c-gamma contains introns shared by src homology 2 domains in many unrelated proteins.many proteins with novel functions were created by exon shuffling around the time of the metazoan radiation. phospholipase c-gamma (plc-gamma) is typical of proteins that appeared at this time, containing several different modules that probably originated elsewhere. to gain insight into both plc-gamma evolution and structure-function relationships within the drosophila plc-gamma encoded by small wing (sl), we cloned and sequenced the plc-gamma homologs from drosophila pseudoobscura and d. virili ...200312807765
sex chromosome loss induced by the "sex-ratio" trait in drosophila pseudoobscura males.frequencies of sex chromosome aneuploid sperm were measured for standard and "sex-ratio" drosophila pseudoobscura males with identical genetic backgrounds. the "sex-ratio" males produced a 15.6-fold higher frequency of nullo-xy sperm than the standard males produced, but diplo-xy sperm were produced at the same rate in the two types of males. "sex-ratio" males with the same sr chromosome but with different chromosome backgrounds were found to produce different frequencies of sterile sons. these ...20031578108
gene arrangements in the third chromosome of drosophila pseudoobscura. ii. all possible configurations. 20036055325
a new gene arrangement in the third chromosome of drosophila pseudoobscura. 20036031680
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