Publications

genetics of natural populations ix. temporal changes in the composition of populations of drosophila pseudoobscura.		1943	17247077
genetics of natural populations. viii. concealed variability in the second and the fourth chromosomes of drosophila pseudoobscura and its bearing on the problem of heterosis.		1942	17247053
genetics of natural populations. vii. the allelism of lethals in the third chromosome of drosophila pseudoobscura.		1942	17247048
genetics of natural populations. v. relations between mutation rate and accumulation of lethals in populations of drosophila pseudoobscura.		1941	17246997
a comparison of x-ray induced and naturally occurring chromosomal variations in drosophila pseudoobscura.		1941	17246993
genetics of natural populations. iv. mexican and guatemalan populations of drosophila pseudoobscura.		1939	17246930
dominance modifiers of scute in drosophila pseudoobscura.		1939	17246923
genetics of natural populations. iii gene arrangements in populations of drosophila pseudoobscura from contiguous localities.		1939	17246909
genetics of natural populations. ii. genic variation in populations of drosophila pseudoobscura inhabiting isolated mountain ranges.		1938	17246895
genetics of natural populations. i. chromosome variation in populations of drosophila pseudoobscura inhabiting isolated mountain ranges.		1938	17246883
the homology of the eye color genes in drosophila melanogaster and drosophila pseudoobscura as determined by transplantation. ii.		1938	17246882
inversions in the chromosomes of drosophila pseudoobscura.		1938	17246876
linkage groups in drosophila pseudoobscura, race b.		1937	17246865
further data on the variation of the y chromosome in drosophila pseudoobscura.		1937	17246845
crossing over in the sex chromosome of racial hybrids of drosophila pseudoobscura.		1937	17246837
studies on hybrid sterility iv. transplanted testes in drosophila pseudoobscura.		1936	17246823
genetic maps of the autosomes in drosophila pseudoobscura.		1936	17246820
geographical distribution and cytology of "sex ratio" in drosophila pseudoobscura and related species.		1936	17246805
studies on hybrid sterility. ii. localization of sterility factors in drosophila pseudoobscura hybrids.		1936	17246786
salivary gland chromosomes in the two races of drosophila pseudoobscura.		1935	17246768
the y chromosome of drosophila pseudoobscura.		1935	17246766
modifier genes of the sex ratio trait in drosophila pseudoobscura.	the msr trait of drosophila pseudoobscura occurs when "sex-ratio" males produce a very high frequency of null-x sperm which give rise to sterile male (x/o) progeny. the trait involves dramatically lowered fecundity due to spermiogenic failure. the msr trait is multigenic and the genes are located on autosomes ii, iii and iv of the l116 laboratory stock. this stock also carries genes on the y chromosome that lower the level of msr. when the genes on the l116 autosomes are present together or with ...	1987	17246384
a comprehensive study of genic variation in natural populations of drosophila melanogaster. i. estimates of gene flow from rare alleles.	in order to assess the evolutionary significance of molecular variation in natural populations of drosophila melanogaster, we have started a comprehensive genetic variation study program employing a relatively large number of gene-protein loci and an array of populations obtained from various geographic locations throughout the world. in this first report we provide estimates of gene flow based on the spatial distributions of rare alleles at 117 gene loci in 15 worldwide populations of d. melano ...	1987	17246368
an investigation of the genetics of "male sex-ratio" phenotype in drosophila pseudoobscura.	a laboratory strain of drosophila pseudoobscura (l116) is studied that, when crossed to sex-ratio homozygous females, produces sons that exhibit varying levels of the male sex-ratio (msr) phenotype. the msr phenotype occurs only in sex-ratio males and is due to the production of a high frequency of nullo-xy sperm. the level of the msr phenotype is variable, and new variability is generated in one father-son transmission. pedigree studies indicate the genes for msr reside on the y chromosome or t ...	1986	17246330
genetic variation for dispersal by drosophila pseudoobscura and drosophila persimilis.	release-recapture experiments using drosophila pseudoobscura and d. persimilis strains of different karyotypes were performed in a heterogeneous environment. the heterogeneity was due to both spatial variation and the species of yeast used to attract the released flies. no karyotypic-specific habitat preferences were detected. however, in all releases, different strains did behave differently with respect to one or both of the heterogeneous factors. these results indicate there is variation for ...	1986	17246313
a test for rare male mating advantage with drosophila pseudoobscura karyotypes.	recent work has called into question the reality of the rare male mating advantage, pointing out that it could be a statistical artifact of marking flies for behavioral observation or of experimental bias in collecting males. we designed an experiment to test for rare male mating advantage that avoids these sources of bias. large numbers of males of three drosophila pseudoobscura karyotypes were allowed to mate with females of one karyotype in population cages. the females were then isolated bef ...	1984	17246224
population genetics of drosophila amylase. v. genetic background and selection on different carbohydrates.	frequency changes in amylase allozymes and patterns of tissue-specific expression of amylase have been monitored in laboratory populations of drosophila pseudoobscura maintained on media in which the only carbohydrate source was maltose or starch. nonrandom changes occurred in patterns of expression, whereas no patterns in allozyme frequency changes were discernible. the nature of the pattern changes was similar to an identical study done on populations derived from a natural population several ...	1984	17246202
virility deficiency and the sex-ratio trait in drosophila pseudoobscura. ii. multiple mating and overall virility selection.	previous studies on fitness components of drosophila have shown the over-whelming importance of virility selection. in this study, virility selection is further partitioned into two components-one with respect to virgin females and the other with respect to nonvirgin females. the relative importance of the two components to the overall virility selection depends on the remating tendency of females which is investigated here. a theoretical model is then proposed to estimate virility selection und ...	1983	17246171
virility deficiency and the sex-ratio trait in drosophila pseudoobscura. i. sperm displacement and sexual selection.	the sex-ratio (sr) phenomenon is associated with the x chromosome of many species of drosophila. males carrying sr transmit predominantly sperm bearing the x chromosome. sr, therefore, has a very significant advantage in segregation. this paper provides an experimental analysis of the role of virility selection in preventing the fixation of sr. sr males are found to suffer substantial virility reduction when mated with nonvirgin females but not with virgin females. the reduced virility arises be ...	1983	17246170
evidence for extensive genetic differentiation between the sex-ratio and the standard arrangement of drosophila pseudoobscura and d. persimilis and identification of hybrid sterility factors.	this study deals with sex-ratio genes tightly linked within the sex-ratio inversion. by taking advantage of the fact that the sex-ratio chromosome of drosophila persimilis [sr(b)] is homosequential to the standard chromosome of d. pseudoobscura [st(a)], we carried out two reciprocal introgression experiments. individual segments of sr(b) or st(a) were introgressed into the genome of d. pseudoobscura or d. persimilis, respectively. males possessing a hybrid sr(b)-st(a) x chromosome and a genetic ...	1983	17246158
frequency distribution of esterase-5 alleles in two populations of drosophila pseudoobscura.	statistical tests comparing allele frequencies in natural populations with those predicted by various theories of genic variation depend critically on the accurate enumeration of alleles. this study used a series of five sequential electrophoretic conditions to characterize the allele frequency distributions of esterase-5 in two large population samples of drosophila pseudoobscura from california. in standard chromosome lines 12 electromorphs were discriminated using a single electrophoretic con ...	1983	17246152
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 ...	2007	17179068
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
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 ...	2007	17160365
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 ...	2006	16982216
[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 ...	2008	16909833
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 ...	2006	16824212
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. ...	2006	16816428
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 ...	2006	16789815
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 ...	2006	16759988
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 ...	2006	16752217
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 ...	2006	16752200
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, ...	2006	16612543
selection for geotaxis in monomorphic and polymorphic populations of drosophila pseudoobscura.		1962	16591004
frequencies of inversion combinations in the third chromosome of wild males of drosophila pseudoobscura.		1955	16589771
environmental modification of heterosis in drosophila pseudoobscura.		1954	16589496
viability of hybrids between local populations of drosophila pseudoobscura.		1953	16589231
experiments on sexual isolation in drosophila: x. reproductive isolation between drosophila pseudoobscura and drosophila persimilis under natural and under laboratory conditions.		1951	16589029
the suppression of crossing over in inversion heterozygotes of drosophila pseudoobscura.		1948	16588794
influence of humidity on the survival of different chromosomal types in drosophila pseudoobscura.		1947	16588745
experiments on sexual isolation in drosophila: vii. the nature of the isolating mechanisms between drosophila pseudoobscura and drosophila persimilis.		1946	16588725
experiments on sexual isolation in drosophila: iv. modification of the degree of isolation between drosophila pseudoobscura and drosophila persimilis and sexual preferences in drosophila prosoltans.		1945	16588688
high mutation frequency in drosophila pseudoöbscura, race b.		1943	16588609
temperature and "sex-ratio" in drosophila pseudoöbscura.		1942	16588521
intersexes in drosophila pseudoöbscura.		1941	16588503
an effect of the y-chromosome on the sex-ratio of interracial hybrids of drosophila pseudoöbscura.		1937	16588164
compressed deficiency and the location of the spindle attachment in the x-chromosome of drosophila pseudoöbscura.		1937	16588162
maternal effect as a cause of the difference between the reciprocal crosses in drosophila pseudoöbscura.		1935	16587996
identification of the salivary gland chromosomes in drosophila pseudoobscura.		1935	16587958
experiments on sexual isolation in drosophila: viii. influence of light on the mating behavior of drosophila subobscura, drosophila persimilis and drosophila pseudoobscura.		1946	16578209
experiments on sexual isolation in drosophila: vi. isolation between drosophila pseudoobscura and drosophila persimilis and their hybrids.		1946	16578193
experiments on sexual isolation in drosophila: v. the effect of varying proportions of drosophila pseudoobscura and drosophilia persimilis on the frequency of insemination in mixed populations.		1945	16578166
female sterility in interracial hybrids of drosophila pseudoöbscura.		1941	16578014
two x-ray induced mosaics in drosophila pseudoöbscura.		1940	16577959
microgeographic variation in drosophila pseudoöbscura.		1939	16577905
inversions in the third chromosome of wild races of drosophila pseudoobscura, and their use in the study of the history of the species.		1936	16577723
further data on material effects in drosophila pseudoöbscura hybrids.		1935	16577691
rôle of the autosomes in the drosophila pseudoobscura hybrids.		1933	16577590
on the sterility of the interracial hybrids in drosophila pseudoobscura.		1933	16577530
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 ...	2006	16547107
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 ...	2006	16545148
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 ...	2006	16520459
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 ...	2006	16520458
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 ...	2006	16502138
a further analysis of sexual isolation between sympatric and allopatric populations of drosophila pseudoobscura and d. persimilis : rejoinder to noor and ortíz-barrientos.		2006	16477520
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.	2006	16403795
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 ...	2005	16322450
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 ...	2005	16207392
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 ...	2005	16143628
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 ...	2005	16143625
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 ...	2005	16136803
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 ...	2005	16049195
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 ...	2005	15956544
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 ...	2005	15943880
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 ...	2005	15899965
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 ...	2005	15864445
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 ...	2005	15864440
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 ...	2005	15851676
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
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 ...	2005	15831447
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 ...	2005	15802507
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 ...	2005	15795864
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 ...	2005	15777717
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.	2005	15723783
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.	2005	15693940
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 ...	2005	15659554
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 ...	2005	15654115
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.	2005	15642105
comparative genome sequencing of drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.	we have sequenced the genome of a second drosophila species, drosophila pseudoobscura, and compared this to the genome sequence of drosophila melanogaster, a primary model organism. throughout evolution the vast majority of drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. a repetitive sequence is found in the d. pseudoobscura genome at many junctions b ...	0	15632085
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 ...	2005	15528405