| a complex suite of forces drives gene traffic from drosophila x chromosomes. | theoretical studies predict x chromosomes and autosomes should be under different selection pressures, and there should therefore be differences in sex-specific and sexually antagonistic gene content between the x and the autosomes. previous analyses have identified an excess of genes duplicated by retrotransposition from the x chromosome in drosophila melanogaster. a number of hypotheses may explain this pattern, including mutational bias, escape from x-inactivation during spermatogenesis, and ... | 2009 | 20333188 |
| 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 ... | 2008 | 18755761 |
| 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 ... | 2008 | 18373627 |
| the drosulfakinin 0 (dsk 0) peptide encoded in the conserved dsk gene affects adult drosophila melanogaster crop contractions. | we report that the drosulfakinin 0 (dsk 0; nqktmsfnh2) structure and genomic organization are conserved. the dsk 0 c-terminus, sfnh2, is widely distributed in the animal kingdom suggesting it defines a novel peptide family. we also report the first description of dsk 0 activity. dsk 0, i (dsk i, fddyghmrfnh2), and ii (dsk ii, ggddqfddyghmrfnh2) are encoded in sulfakinin (dsk). drosophila erecta, drosophila sechellia, drosophila simulans, and drosophila yakuba shared 62.5-87.5% identity to drosop ... | 2007 | 17632121 |
| 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 ... | 2006 | 17503388 |
| [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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 ... | 2004 | 14715225 |
| 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 ... | 2006 | 14691313 |
| 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 ... | 2003 | 12801649 |
| 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 ... | 2003 | 12694281 |
| high density of long dinucleotide microsatellites in drosophila subobscura. | we isolated 96 dinucleotide repeats with five or more tandemly repeated units from a subgenomic drosophila subobscura library. the mean repeat unit length of microsatellite clones in d. subobscura is 15, higher than that observed in other drosophila species. population variation was assayed in 32-40 chromosomes from barcelona, spain, using 18 randomly chosen microsatellite loci. positive correlation between measures of variation and perfect repeat length measures (mean size, most common, and lon ... | 2000 | 10908646 |
| associations between female remating behavior, oogenesis and oviposition in drosophila melanogaster and drosophila pseudoobscura. | an association between female remating behavior, oogenesis and oviposition was examined in drosophila melanogaster and drosophila pseudoobscura to investigate mechanisms that elicit remating. females receptive to remating oviposited more eggs in both species; however, the species differed in the association between remating behavior and the number and distribution of oocyte stages. we found no differences in the number of either developing eggs of different stages or mature eggs between female d ... | 2000 | 10891578 |
| conservation of read-through transcription of the drosophila serendipity genes during evolution is gratuitous. | the drosophila melanogaster serendipity (sry) genes sry alpha and sry beta, which code for unrelated proteins and functions, are transcribed both as monocistronic (sry alpha, srv beta) and dicistronic (sry beta-sry alpha) polyadenylated transcripts, the three types of transcripts being differentially expressed throughout development. we show here that, while the sry gene cluster is conserved in two other distantly related drosophila species, sry beta-sry alpha dicistronic transcription is observ ... | 1998 | 9790579 |
| sex-related genes, directional sexual selection, and speciation. | reproductive isolation and speciation can result from the establishment of either premating or postmating barriers that restrict gene flow between populations. recent studies of speciation have been dominated by a molecular approach to dissect the genetic basis of hybrid male sterility, a specific form of postmating reproductive isolation. however, relatively little attention has been paid to the evolution of genes involved in premating isolation and genes generally involved in other sex-related ... | 1998 | 9656489 |
| divergent and conserved features in the spatial expression of the drosophila pseudoobscura esterase-5b gene and the esterase-6 gene of drosophila melanogaster. | the regulatory regions of homologous genes encoding esterase 6 (est-6) of drosophila melanogaster and esterase 5b (est-5b) of drosophila pseudoobscura show very little similarity. we have undertaken a comparative study of the pattern of expression directed by the est-5b and est-6 5'-flanking dna to attempt to reveal conserved elements regulating tissue-specific expression in adults. esterase regulatory sequences were linked to a lacz reporter gene and transformed into d. melanogaster embryos. es ... | 1997 | 9223257 |
| evidence for gene conversion in the amylase multigene family of drosophila pseudoobscura. | the alpha-amylase (amy) multigene family in drosophila pseudoobscura is located on the third chromosome, which is polymorphic for more than 40 inverted gene arrangements. the number of copies in this family ranges from one to three, depending on the arrangement in question. a previous study of the three amy genes from the standard (st) arrangement suggested either that duplicated copies (amy2 and amy3) are functionally constrained or that they are undergoing gene conversion with amy1. in order t ... | 1995 | 7659012 |
| separate cis-regulatory sequences control expression of serendipity beta and janus a, two immediately adjacent drosophila genes. | the genes janus (jan) a and b, and serendipity (sry) beta and delta are two pairs of duplicated genes that are adjacent to each other on the third chromosome of drosophila melanogaster. the jan a and sry beta genes are expressed throughout development in both males and females. they are transcribed in opposite orientations from start sites separated by only 173 bp of dna. we report here the complete sequence of the jan a and b genes in drosophila pseudoobscura, a species distantly related to d. ... | 1995 | 7700229 |
| interspecific transgenic analysis of basal versus heat-shock-induced expression of a drosophila pseudoobscura hsp82-neo fusion gene in d. melanogaster. | drosophila melanogaster transformants containing a d. pseudoobscura hsp82-neo fusion gene were used to examine the relationship between chromosome structure and its variation to transcriptional activation and gene expression. at normal temperatures (25° c) transgenic hsp82-neo was transcribed in diffuse polytene chromosomal bands encoding antibiotic g418-resistance without intensive puff formation. substantial basal expression of the transgene was observed in all tissues examined: salivary gland ... | 1994 | 28305933 |
| components acting in localization of bicoid mrna are conserved among drosophila species. | substantial insights into basic strategies for embryonic body patterning have been obtained from genetic analyses of drosophila melanogaster. this knowledge has been used in evolutionary comparisons to ask if genes and functions are conserved. to begin to ask how highly conserved are the mechanisms of mrna localization, a process crucial to drosophila body patterning, we have focused on the localization of bcd mrna to the anterior pole of the embryo. here we consider two components involved in t ... | 1994 | 8070663 |
| synonymous codon usage in drosophila melanogaster: natural selection and translational accuracy. | i present evidence that natural selection biases synonymous codon usage to enhance the accuracy of protein synthesis in drosophila melanogaster. since the fitness cost of a translational misincorporation will depend on how the amino acid substitution affects protein function, selection for translational accuracy predicts an association between codon usage in dna and functional constraint at the protein level. the frequency of preferred codons is significantly higher at codons conserved for amino ... | 1994 | 8005445 |
| evolutionary conservation of the structure and expression of alternatively spliced ultrabithorax isoforms from drosophila. | in drosophila melanogaster, alternatively spliced mrnas from the homeotic gene ultrabithorax (ubx) encode a family of structurally distinct homeoprotein isoforms. the developmentally regulated expression patterns of these isoforms suggest that they have specialized stage- and tissue-specific functions. to evaluate the functional importance of ubx isoform diversity and gain clues to the mechanism that regulates processing of ubx rnas, we have investigated whether the ubx rnas of other insects und ... | 1994 | 7911773 |
| codon usage bias and base composition of nuclear genes in drosophila. | the nuclear genes of drosophila evolve at various rates. this variation seems to correlate with codon-usage bias. in order to elucidate the determining factors of the various evolutionary rates and codon-usage bias in the drosophila nuclear genome, we compared patterns of codon-usage bias with base compositions of exons and introns. our results clearly show the existence of selective constraints at the translational level for synonymous (silent) sites and, on the other hand, the neutrality or ne ... | 1993 | 8349115 |
| the l(2)gl homologue of drosophila pseudoobscura suppresses tumorigenicity in transgenic drosophila melanogaster. | mutations in the tumour-suppressor gene lethal(2)giant larvae (l(2)gl) of drosophila cause malignant transformation of the optic centres of the larval brain and the imaginal discs. we report the cloning and sequencing of the l(2)gl gene from drosophila pseudoobscura. comparison of this sequence with d. melanogaster reveals a significant sequence conservation within the l(2)gl protein-coding domain and a strong sequence divergence in the 5' promoter region and in the introns. the deduced amino ac ... | 1993 | 8389031 |
| adenine phosphoribosyltransferase genes in two drosophila species: dosage compensation, a nuclear matrix attachment site, and a novel intron position. | the aprt locus of drosophila encodes the structural gene for the purine salvage enzyme adenine phosphoribosyltransferase. aprt is autosomal and enzyme activity is gene-dose-dependent in drosophila melanogaster. however, aprt is x-linked and dosage compensated in drosophila pseudoobscura, as shown here. the aprt genes of both drosophila species contain a dna sequence associated with nuclear matrix attachment sites and these aprt sequences specifically bind to nuclear matrix in vitro. putative pro ... | 1993 | 8492806 |
| nucleotide divergence of the rp49 gene region between drosophila melanogaster and two species of the obscura group of drosophila. | a 2.1-kb ssti fragment including the rp49 gene and the 3' end of the delta-serendipity gene has been cloned and sequenced in drosophila pseudoobscura. rp49 maps at region 62 on the tip of chromosome ii of this species. both the coding and flanking regions have been aligned and compared with those of d. subobscura. there is no evidence for heterogeneity in the rate of silent substitution between the rp49 coding region and the rate of substitutions in flanking regions, the overall silent divergenc ... | 1993 | 8483162 |
| an evolutionary model for the duplication and divergence of esterase genes in drosophila. | the esterase 5 (est-5 = gene, est 5 = protein) enzyme in drosophila pseudoobscura is encoded by one of three paralogous genes, est-5a, est-5b, and est-5c, that are tightly clustered on the right arm of the x chromosome. the homologous est-6 locus in drosophila melanogaster has only one paralogous neighbor, est-p. comparisons of coding and flanking dna sequences among the three d. pseudoobscura and two d. melanogaster genes suggest that two paralogous genes were present before the divergence of d ... | 1992 | 1593643 |
| the urate oxidase gene of drosophila pseudoobscura and drosophila melanogaster: evolutionary changes of sequence and regulation. | the urate oxidase (uo) transcription unit of drosophila pseudoobscura was cloned, sequenced, and compared to the uo transcription unit from drosophila melanogaster. in both species the uo coding region is divided into two exons of approximately equal size. the deduced d. pseudoobscura and d. melanogaster uo peptides have 346 and 352 amino acid residues, respectively. the nucleotide sequences of the d. pseudoobscura and d. melanogaster uo protein-coding regions are 82.2% identical whereas the ded ... | 1992 | 1556745 |
| dosage compensation of the drosophila pseudoobscura hsp82 gene and the drosophila melanogaster adh gene at ectopic sites in d. melanogaster. | measurements were made of the amounts of larval rna transcribed from the autosomal adh gene of drosophila melanogaster and the x chromosomal hsp82 gene of drosophila pseudoobscura carried on the same p-element transposon inserted at various sites in the d. melanogaster genome. both genes were fully compensated at sites in euchromatic regions of the x chromosome but neither was compensated at a site in the centric beta-heterochromatin of the x chromosome. no compensation of the d. pseudoobscura h ... | 1991 | 1907376 |
| species differences in the temporal pattern of drosophila urate oxidase gene expression are attributed to trans-acting regulatory changes. | the drosophila melanogaster urate oxidase (uo)-encoding gene is expressed in the third-instar larva and adult. in contrast, the drosophila pseudoobscura uo gene is only expressed in the adult, whereas the drosophila virilis uo gene is expressed only in the third-instar larva. uo activity in these three drosophila species is detected exclusively within the malpighian tubules. by using p-element mediated germ-line transformation, uo genes from d. pseudoobscura and d. virilis were integrated into t ... | 1991 | 2062830 |
| interspecific comparisons of the structure and regulation of the drosophila ecdysone-inducible gene e74. | the drosophila melanogaster e74 gene is induced directly by the steroid hormone ecdysone and is a member of a small set of "early" genes that appear to trigger the onset of metamorphosis. the gene consists of three overlapping transcription units encoding two proteins, e74a and e74b, which possess a common c terminus. according to the ashburner model for ecdysone's action, an e74 protein product potentially functions as a transcriptional activator of "late" genes as well as a repressor of early ... | 1991 | 2016053 |
| length polymorphism in the threonine-glycine-encoding repeat region of the period gene in drosophila. | single-fly polymerase chain reaction amplification and direct dna sequencing revealed high levels of length polymorphism in the threonine-glycine encoding repeat region of the period (per) gene in natural populations of drosophila melanogaster. dna comparison of two alleles of identical lengths gave a high number of synonymous substitutions suggesting an ancient time of separation. however detailed examination of the sequences of different thr-gly length variants indicated that this divergence c ... | 1991 | 1904500 |
| molecular analysis of evolutionary changes in the expression of drosophila esterases. | drosophila melanogaster transformed with the esterase 5 (est-5) gene from drosophila pseudoobscura were used to assess the evolutionary basis for differences in the sex- and tissue-specific expression of the esterase 5 (est 5) enzyme in d. pseudoobscura relative to its homologue in d. melanogaster, est 6. est 5 is expressed in the eyes and hemolymph of transformed d. melanogaster just as it is in d. pseudoobscura, but it is not detectable in the ejaculatory duct, where the homologous enzyme, est ... | 1990 | 1700427 |
| dna sequence evolution of the amylase multigene family in drosophila pseudoobscura. | the alpha-amylase locus in drosophila pseudoobscura is a multigene family of one, two or three copies on the third chromosome. the nucleotide sequences of the three amylase genes from a single chromosome of d. pseudoobscura are presented. the three amylase genes differ at about 0.5% of their nucleotides. each gene has a putative intron of 71 (amy1) or 81 (amy2 and amy3) bp. in contrast, drosophila melanogaster amylase genes do not have an intron. the functional amy1 gene of d. pseudoobscura diff ... | 1990 | 1699840 |
| mitochondrial dna evolution in the obscura species subgroup of drosophila. | mitochondrial dna (mtdna) restriction site maps for nine species of the drosophila obscura subgroup and for drosophila melanogaster were established. taking into account all restriction enzymes (12) and strains (45) analyzed, a total of 105 different sites were detected, which corresponds to a sample of 3.49% of the mtdna genome. based on nucleotide divergences, two phylogenetic trees were constructed assuming either constant or variable rates of evolution. both methods led to the same relations ... | 1990 | 2120450 |
| amylase gene expression in intraspecific and interspecific somatic transformants of drosophila. | the amylase locus in drosophila melanogaster normally contains two copies of the structural gene for alpha-amylase, a centromere-proximal copy, amy-p, and a distal copy, amy-d. products of the two genes may display discrete electrophoretic mobilities, but many strains known to carry the amy duplication are characterized by a single amylase electromorph, e.g., oregon-r, which produces the mobility variant amy-1. a transient expression assay was used in somatic transformation experiments to test t ... | 1990 | 1699842 |
| p-transposable vectors expressing a constitutive and thermoinducible hsp82-neo fusion gene for drosophila germline transformation and tissue-culture transfection. | three p-transposable vectors (approx. 16, 12, and 9 kb) were constructed containing a hsp82-neo fusion gene encoding a truncated heat-shock protein 82 of drosophila pseudoobscura and the bacterial neomycin phosphotransferase (npt). in transgenic drosophila melanogaster, hsp82-neo exhibits high levels of housekeeping gene promoter and npt activities in all cells in the absence of heat-shock and is further induced (fivefold) by elevated temperatures (35 degrees-36 degrees c). the hsp82-neo selecti ... | 1990 | 2165019 |
| conservatism of sites of trna loci among the linkage groups of several drosophila species. | the sites of seven trna genes (arg-2, lys-2, ser-2b, ser-7, thr-3, thr-4, val-3b) were studied by in situ hybridization. 125i-labeled trna probes from drosophila melanogaster were hybridized to spreads of polytene chromosomes prepared from four drosophila species representing different evolutionary lineages (d. melanogaster, drosophila hydei, drosophila pseudoobscura, and drosophila virilis). most trna loci occurred on homologous chromosomal elements of all four species. in some cases the number ... | 1990 | 2107332 |
| conserved arrangement of nested genes at the drosophila gart locus. | the drosophila melanogaster gart gene encodes three enzymatic activities in the pathway for purine de novo synthesis. alternative processing of the primary transcript leads to the synthesis of two overlapping polypeptides. the coding sequence for both polypeptides is interrupted by an intron that contains a functional cuticle protein gene encoded on the opposite dna strand. here we show that this nested organization also exists at the homologous locus of a distantly related species, drosophila p ... | 1987 | 3123310 |
| 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 |
| historical effective size and the level of genetic diversity in drosophila melanogaster and drosophila pseudoobscura. | we report the results of a sequential gel electrophoretic study of protein variation in drosophila melanogaster and its comparison with d. pseudoobscura. the number of alleles and mean heterozygosity were lower in d. melanogaster than in d. pseudoobscura. on the other hand, geographical populations of drosophila melanogaster have been shown to be much more differentiated than those of d. pseudoobscura. the results suggest that in d. melanogaster low-frequency alleles have been lost during the co ... | 1987 | 3107543 |
| the isolation of biological rhythm mutations on the autosomes of drosophila melanogaster. | a selection for autosomal circadian rhythm variants in drosophila melanogaster resulted in the isolation of 3 new mutants, all of which display an abnormal synchronization of daily rhythms to entraining environmental cycles. in populations of phase-angle-2 (psi-2) and phase-angle-3 (psi-3) mutants, daily peaks of adult emergence are hours earlier than normal when the strains are entrained to cycles of either light and dark or high and low temperature. like an early-emerging strain previously iso ... | 1983 | 6443122 |
| genic variation in abundant soluble proteins of drosophila melanogaster and drosophila pseudoobscura. | genic variation was surveyed for 20 proteins of drosophila melanogaster and 18 proteins of d. pseudoobscura. analysis was by extraction and one-dimensional polyacrylamide gel electrophoresis under nondenaturing conditions, followed by staining with coomassie brilliant blue to detect soluble proteins present in relatively large amounts ("abundant soluble proteins"). d. melanogaster was polymorphic for 65% of its protein loci and an individual was heterozygous for 10% of its loci. the respective f ... | 1982 | 7173605 |
| protein synthesis inhibition alters drosophila mating behavior. | fruit fly drosophila pseudoobscura virgin ar females mate preferentially with ar males given a choice between ar and or males. however, ar females which mated with or males when young show a significant change in sexual selection in favor of or over ar males in subsequent simultaneous choice tests. ingestion of food moistened with 4 ml cycloheximide (400 microng/ml) produces 75% protein synthesis inhibition in the female flies. females exposed to cycloheximide (cxm) immediately after their initi ... | 1977 | 857258 |
| the homology of the eye color genes in drosophila melanogaster and drosophila pseudoobscura as determined by transplantation. ii. | | 1938 | 17246882 |
| functional nonequivalence of sperm in drosophila pseudoobscura. | we report on a form of sperm polymorphism, termed polymegaly, that occurs in species of the drosophila obscura group. individual males of species in this group characteristically produce more than one discrete length of nucleated, motile sperm. hypotheses suggested to explain the evolutionary significance of sperm polymorphism have been either nonadaptive or adaptive, with the latter focusing on sperm competition or nutrient provisioning. these hypotheses assume all sperm types fertilize eggs; h ... | 1994 | 7972038 |
| genomic changes following the reversal of a y chromosome to an autosome in drosophila pseudoobscura. | robertsonian translocations resulting in fusions between sex chromosomes and autosomes shape karyotype evolution by creating new sex chromosomes from autosomes. these translocations can also reverse sex chromosomes back into autosomes, which is especially intriguing given the dramatic differences between autosomes and sex chromosomes. to study the genomic events following a y chromosome reversal, we investigated an autosome-y translocation in drosophila pseudoobscura. the ancestral y chromosome ... | 2017 | 28322435 |
| remating responses are consistent with male postcopulatory manipulation but not reinforcement in d. pseudoobscura. | reinforcement occurs when hybridization between closely related lineages produces low-fitness offspring, prompting selection for elevated reproductive isolation specifically in areas of sympatry. both premating and postmating prezygotic behaviors have been shown to be the target of reinforcing selection, but it remains unclear whether remating behaviors experience reinforcement, although they can also influence offspring identity and limit formation of hybrids. here, we evaluated evidence for re ... | 2017 | 28116047 |
| we also canfly! the 2nd mexfly drosophila research conference. | the 2nd mexican drosophila research conference (mexfly) took place on june 30th and july 1st, 2016 in mexico city, at the center for research and advanced studies of the national polytechnic institute (cinvestav). principal investigators, postdocs, students, and technicians from drosophila labs across mexico attended. the guest speaker was chris rushlow from new york university, who presented work on zelda, a key transcriptional activator of the early zygotic genome. here we provide a brief repo ... | 2016 | 27960619 |
| mistaken identity: another bias in the use of relative genetic divergence measures for detecting interspecies introgression. | measures of genetic divergence have long been used to identify evolutionary processes operating within and between species. however, recent reviews have described a bias in the use of relative divergence measures towards incorrectly identifying genomic regions that are seemingly immune to introgression. here, we present a novel and opposite bias of relative divergence measures: misidentifying regions of introgression between sister species. we examine two distinct haplotypes of intermediate freq ... | 2016 | 27760228 |
| hubby and lewontin on protein variation in natural populations: when molecular genetics came to the rescue of population genetics. | the 1966 genetics papers by john hubby and richard lewontin were a landmark in the study of genome-wide levels of variability. they used the technique of gel electrophoresis of enzymes and proteins to study variation in natural populations of drosophila pseudoobscura, at a set of loci that had been chosen purely for technical convenience, without prior knowledge of their levels of variability. together with the independent study of human populations by harry harris, this seminal study provided t ... | 2016 | 27516612 |
| union of phylogeography and landscape genetics. | phylogeography and landscape genetics have arisen within the past 30 y. phylogeography is said to be the bridge between population genetics and systematics, and landscape genetics the bridge between landscape ecology and population genetics. both fields can be considered as simply the amalgamation of classic biogeography with genetics and genomics; however, they differ in the temporal, spatial, and organismal scales addressed and the methodology used. i begin by briefly summarizing the history a ... | 2016 | 27432989 |
| genomics of natural populations: how differentially expressed genes shape the evolution of chromosomal inversions in drosophila pseudoobscura. | chromosomal rearrangements can shape the structure of genetic variation in the genome directly through alteration of genes at breakpoints or indirectly by holding combinations of genetic variants together due to reduced recombination. the third chromosome of drosophila pseudoobscura is a model system to test hypotheses about how rearrangements are established in populations because its third chromosome is polymorphic for >30 gene arrangements that were generated by a series of overlapping invers ... | 2016 | 27401754 |
| temperature can shape a cline in polyandry, but only genetic variation can sustain it over time. | multiple mating by females (polyandry) is a widespread behavior occurring in diverse taxa, species, and populations. polyandry can also vary widely within species, and individual populations, so that both monandrous and polyandrous females occur together. genetic differences can explain some of this intraspecific variation in polyandry, but environmental factors are also likely to play a role. one environmental factor that influences many fundamental biological processes is temperature. higher t ... | 2017 | 27004012 |
| sexual selection and assortative mating: an experimental test. | mate choice and mate competition can both influence the evolution of sexual isolation between populations. assortative mating may arise if traits and preferences diverge in step, and, alternatively, mate competition may counteract mating preferences and decrease assortative mating. here, we examine potential assortative mating between populations of drosophila pseudoobscura that have experimentally evolved under either increased ('polyandry') or decreased ('monogamy') sexual selection intensity ... | 2016 | 26970522 |
| recombining without hotspots: a comprehensive evolutionary portrait of recombination in two closely related species of drosophila. | meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. in almost every species, this variation takes the form of discrete recombination hotspots, determined in some mammals by a protein called prdm9. hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. drosophila, in contrast, are anomalous in their absence of hotspots, p ... | 2015 | 26430062 |
| temporal stability of molecular diversity measures in natural populations of drosophila pseudoobscura and drosophila persimilis. | many molecular ecological and evolutionary studies sample wild populations at a single point in time, but that data represents genetic variation from a potentially unrepresentative snapshot in time. variation across time in genetic parameters may occur quickly in species that produce multiple generations of offspring per year. here, we compare genetic diversity in wild caught populations of drosophila persimilis and drosophila pseudoobscura collected 16 years apart at the same time of year and s ... | 2017 | 25969560 |
| opposite environmental and genetic influences on body size in north american drosophila pseudoobscura. | populations of a species often differ in key traits. however, it is rarely known whether these differences are associated with genetic variation and evolved differences between populations, or are instead simply a plastic response to environmental differences experienced by the populations. here we examine the interplay of plasticity and direct genetic control by investigating temperature-size relationships in populations of drosophila pseudoobscura from north america. we used 27 isolines from t ... | 2015 | 25887658 |
| mating system variation drives rapid evolution of the female transcriptome in drosophila pseudoobscura. | interactions between the sexes are believed to be a potent source of selection on sex-specific evolution. the way in which sexual interactions influence male investment is much studied, but effects on females are more poorly understood. to address this deficiency, we examined gene expression in virgin female drosophila pseudoobscura following 100 generations of mating system manipulations in which we either elevated polyandry or enforced monandry. gene expression evolution following mating syste ... | 2014 | 25360260 |
| can patterns of chromosome inversions in drosophila pseudoobscura predict polyandry across a geographical cline? | female multiple mating, known as polyandry, is ubiquitous and occurs in a wide variety of taxa. polyandry varies greatly from species in which females mate with one or two males in their lifetime to species in which females may mate with several different males on the same day. as multiple mating by females is associated with costs, numerous hypotheses attempt to explain this phenomenon. one hypothesis not extensively explored is the possibility that polyandrous behavior is captured and "fixed" ... | 2014 | 25247064 |
| evolution of divergent female mating preference in response to experimental sexual selection. | sexual selection is predicted to drive the coevolution of mating signals and preferences (mating traits) within populations, and could play a role in speciation if sexual isolation arises due to mating trait divergence between populations. however, few studies have demonstrated that differences in mating traits between populations result from sexual selection alone. experimental evolution is a promising approach to directly examine the action of sexual selection on mating trait divergence among ... | 2014 | 24931497 |
| does polyandry control population sex ratio via regulation of a selfish gene? | the extent of female multiple mating (polyandry) can strongly impact on the intensity of sexual selection, sexual conflict, and the evolution of cooperation and sociality. more subtly, polyandry may protect populations against intragenomic conflicts that result from the invasion of deleterious selfish genetic elements (sges). sges commonly impair sperm production, and so are likely to be unsuccessful in sperm competition, potentially reducing their transmission in polyandrous populations. here, ... | 2014 | 24695427 |
| age-dependent male mating investment in drosophila pseudoobscura. | male mating investment can strongly influence fitness gained from a mating. yet, male mating investment often changes with age. life history theory predicts that mating investment should increase with age, and males should become less discriminatory about their mate as they age. understanding age-dependent changes in male behavior and their effects on fitness is important for understanding how selection acts in age-structured populations. although the independent effects of male or female age ha ... | 2014 | 24586373 |
| evidence that natural selection on codon usage in drosophila pseudoobscura varies across codons. | like other species of drosophila, drosophila pseudoobscura has a distinct bias toward the usage of c- and g-ending codons. previous studies have indicated that this bias is due, at least in part, to natural selection. codon bias clearly differs among amino acids (and other codon classes) in drosophila, which may reflect differences in the intensity of selection on codon usage. ongoing natural selection on synonymous codon usage should be reflected in the shapes of the site frequency spectra of d ... | 2014 | 24531731 |
| recent selection on the y-to-dot translocation in drosophila pseudoobscura. | the drosophila pseudoobscura dot chromosome acquired genes from the ancestral drosophila y chromosome in a y-to-dot translocation event that occurred between 12.7 and 20.8 ma. the formerly y-linked genes mostly retained their testis-specific expression but shrank drastically in size, mostly through intron reduction, since becoming part of the dot chromosome in this species. we investigated the impact of this translocation on the evolution of the both the y-to-dot translocated region and the orig ... | 2014 | 24390701 |
| intra-specific regulatory variation in drosophila pseudoobscura. | it is generally accepted that gene regulation serves an important role in determining the phenotype. to shed light on the evolutionary forces operating on gene regulation, previous studies mainly focused on the expression differences between species and their inter-specific hybrids. here, we use rna-seq to study the intra-specific distribution of cis- and trans-regulatory variation in drosophila pseudoobscura. consistent with previous results, we find almost twice as many genes (26%) with signif ... | 2013 | 24386226 |
| tissue- and stage-dependent dosage compensation on the neo-x chromosome in drosophila pseudoobscura. | sex chromosome dosage compensation (dc) is widely accepted in various organisms. this concept is mostly supported by comparisons of gene expression between chromosomes and between sexes. however, genes on the x chromosome and autosomes are mostly not homologous, and the average gene expression level on these chromosomes may not be the same even under dc, which complicates comparisons between chromosomes. many genes with sex-biased expression also make comparisons between sexes difficult. to over ... | 2014 | 24307686 |
| multifaceted, cross-generational costs of hybridization in sibling drosophila species. | maladaptive hybridization, as determined by the pattern and intensity of selection against hybrid individuals, is an important factor contributing to the evolution of prezygotic reproductive isolation. to identify the consequences of hybridization between drosophila pseudoobscura and d. persimilis, we estimated multiple fitness components for f1 hybrids and backcross progeny and used these to compare the relative fitness of parental species and their hybrids across two generations. we document m ... | 2013 | 24265807 |
| integrated and independent evolution of heteromorphic sperm types. | sperm are a simple cell type with few components, yet they exhibit tremendous between-species morphological variation in those components thought to reflect selection in different fertilization environments. however, within a species, sperm components are expected to be selected to be functionally integrated for optimal fertilization of eggs. here, we take advantage of within-species variation in sperm form and function to test whether sperm components are functionally and genetically integrated ... | 2013 | 24004938 |
| molecular population genetics of inversion breakpoint regions in drosophila pseudoobscura. | paracentric inversions in populations can have a profound effect on the pattern and organization of nucleotide variability along a chromosome. regions near inversion breakpoints are expected to have greater levels of differentiation because of reduced genetic exchange between different gene arrangements whereas central regions in the inverted segments are predicted to have lower levels of nucleotide differentiation due to greater levels of genetic flux among different karyotypes. we used the inv ... | 2013 | 23665879 |
| effects of premature termination codon polymorphisms in the drosophila pseudoobscura subclade. | premature termination codon (ptc) mutations can have dramatic effects--both adaptive and deleterious--on gene expression and function. here, we examine the number and selective effects of ptc mutations within the drosophila pseudoobscura subclade using 18 resequenced genomes aligned to the reference genome. we located and characterized 1,679 ptc mutations in 605 genes across each of these genomes relative to the d. pseudoobscura reference genome, and use rt-pcr to confirm transcription of a subs ... | 2012 | 23132097 |
| experience of mating rivals causes males to modulate sperm transfer in the fly drosophila pseudoobscura. | male responses to risk of sperm competition play an important role in sexual selection, sexual conflict, and the evolution of mating systems. such responses can combine behavioural and physiological processes, and can be mediated through different components of the ejaculate such as sperm numbers and seminal proteins. an additional level of ejaculate complexity is sperm heteromorphism, with the inclusion of non-fertilising parasperm in the ejaculate. we now test the response to rivals in a sperm ... | 2012 | 23085556 |
| evaluation of different reference based annotation strategies using rna-seq - a case study in drososphila pseudoobscura. | rna-seq is a powerful tool for the annotation of genomes, in particular for the identification of isoforms and utrs. nevertheless, several software tools exist and no standard strategy to obtain a reliable annotation is yet established. we tested different combinations of the most commonly used reference-based alignment tools (tophat, gsnap) in combination with two frequently used reference-based assemblers (cufflinks, scripture) and evaluated the potential of rna-seq to improve the annotation o ... | 2012 | 23056304 |
| zinc finger binding motifs do not explain recombination rate variation within or between species of drosophila. | in humans and mice, the cys(2)his(2) zinc finger protein prdm9 binds to a dna sequence motif enriched in hotspots of recombination, possibly modifying nucleosomes, and recruiting recombination machinery to initiate double strand breaks (dsbs). however, since its discovery, some researchers have suggested that the recombinational effect of prdm9 is lineage or species specific. to test for a conserved role of prdm9-like proteins across taxa, we use the drosophila pseudoobscura species group in an ... | 2012 | 23028758 |
| sexual selection and experimental evolution of chemical signals in drosophila pseudoobscura. | our expectations for the evolution of chemical signals in response to sexual selection are uncertain. how are chemical signals elaborated? does sexual selection result in complexity of the composition or in altered quantities of expression? we addressed this in drosophila pseudoobscura by examining male and female cuticular hydrocarbons (chs) after 82 generations of elevated (e) sexual selection or relaxed sexual selection through monogamy (m). the ch profile consisted of 18 different components ... | 2012 | 22984915 |
| time in a bottle: the evolutionary fate of species discrimination in sibling drosophila species. | disadvantageous hybridization favors the evolution of prezygotic isolating behaviors, generating a geographic pattern of interspecific mate discrimination where members of different species drawn from sympatric populations exhibit stronger preference for members of their own species than do individuals drawn from allopatric populations. geographic shifts in species' boundaries can relax local selection against hybridization; under such scenarios the fate of enhanced species preference is unknown ... | 2012 | 22384069 |
| geographic selection in the small heat shock gene complex differentiating populations of drosophila pseudoobscura. | environmental temperature plays a crucial role in determining a species distribution and abundance by affecting individual physiological processes, metabolic activities, and developmental rates. many studies have identified clinal variation in phenotypes associated with response to environmental stresses, but variation in traits associated with climatic adaptation directly attributed to sequence variation within candidate gene regions has been difficult to identify. insect heat shock genes are p ... | 2017 | 22345645 |
| the evolution of multiple mating: costs and benefits of polyandry to females and of polygyny to males. | polyandry is a paradox: why do females mate multiple times when a single ejaculate often provides enough sperm for lifetime egg production? gowaty et al. addressed explanations for polyandry in drosophila pseudoobscura from the perspective of hypotheses based on sex differences in costs of reproduction (cor). contrary to cor, gowaty et al. showed that (1) a single ejaculate was inadequate for lifetime egg production; (2) polyandry provided fitness benefits to females beyond provision of adequate ... | 2017 | 22223093 |
| genomic impacts of chromosomal inversions in parapatric drosophila species. | chromosomal inversions impact genetic variation and facilitate speciation in part by reducing recombination in heterokaryotypes. we generated multiple whole-genome shotgun sequences of the parapatric species pair drosophila pseudoobscura and drosophila persimilis and their sympatric outgroup (drosophila miranda) and compared the average pairwise differences for neutral sites within, just outside and far outside of the three large inversions. divergence between d. pseudoobscura and d. persimilis ... | 2012 | 22201171 |
| sexual isolation between north american and bogota strains of drosophila pseudoobscura. | sexual isolation, the reduced ability of organisms of different species to successfully mate, is one of the reproductive barriers that prevent gene flow between different taxa. various species-specific signals during courtship are attributed to the sexual isolation between them. drosophila pseudoobscura has been widely used to study the behavioral and genetic mechanisms underlying selection for sexual isolation, as a model system for speciation. d. pseudoobscura and its sibling species, d. persm ... | 2012 | 22065259 |
| nonrandom gene loss from the drosophila miranda neo-y chromosome. | a lack of recombination leads to the degeneration of an evolving y chromosome. however, it is not known whether gene loss is largely a random process and primarily driven by the order in which mutations occur or whether certain categories of genes are lost less quickly than others; the latter would imply that selection counteracts the degeneration of y chromosomes to some extent. in this study, we investigate the relationship between putative ancestral expression levels of neo-y-linked genes in ... | 2011 | 21987387 |
| genetic architecture of male sterility and segregation distortion in drosophila pseudoobscura bogota-usa hybrids. | understanding the genetic basis of reproductive isolation between recently diverged species is a central problem in evolutionary genetics. here, i present analyses of the genetic architecture underlying hybrid male sterility and segregation distortion between the bogota and usa subspecies of drosophila pseudoobscura. previously, a single gene, overdrive (ovd), was shown to be necessary but not sufficient for both male sterility and segregation distortion in f(1) hybrids between these subspecies, ... | 2011 | 21900263 |
| effects of inversions on within- and between-species recombination and divergence. | chromosomal inversions disrupt recombination in heterozygotes by both reducing crossing-over within inverted regions and increasing it elsewhere in the genome. the reduction of recombination in inverted regions facilitates the maintenance of hybridizing species, as outlined by various models of chromosomal speciation. we present a comprehensive comparison of the effects of inversions on recombination rates and on nucleotide divergence. within an inversion differentiating drosophila pseudoobscura ... | 2011 | 21828374 |
| genetics of hybrid male sterility among strains and species in the drosophila pseudoobscura species group. | taxa in the early stages of speciation may bear intraspecific allelic variation at loci conferring barrier traits in hybrids such as hybrid sterility. additionally, hybridization may spread alleles that confer barrier traits to other taxa. historically, few studies examine within- and between-species variation at loci conferring reproductive isolation. here, we test for allelic variation within drosophila persimilis and within the bogota subspecies of d. pseudoobscura at regions previously shown ... | 2011 | 21729052 |
| preference status does not indicate intrinsic quality differences in drosophila pseudoobscura. | the good genes hypothesis states that choosers prefer individuals of high intrinsic quality to individuals of lower intrinsic quality. variation in longevity is thought to reflect, in part, intrinsic quality differences of individuals in addition to the costs of mating and reproduction. here we report longevity variation of drosophila pseudoobscura, a species in which previous experiments have demonstrated that individual mate preferences (pre-touching mate assessments) of females and males are ... | 2010 | 21392338 |
| evolutionary history of the third chromosome gene arrangements of drosophila pseudoobscura inferred from inversion breakpoints. | the third chromosome of drosophila pseudoobscura is polymorphic for numerous gene arrangements that form classical clines in north america. the polytene salivary chromosomes isolated from natural populations revealed changes in gene order that allowed the different gene arrangements to be linked together by paracentric inversions representing one of the first cases where genetic data were used to construct a phylogeny. although the inversion phylogeny can be used to determine the relationships a ... | 2011 | 21339510 |
| determinants of synonymous and nonsynonymous variability in three species of drosophila. | we estimated the intensity of selection on preferred codons in drosophila pseudoobscura and d. miranda at x-linked and autosomal loci, using a published data set on sequence variability at 67 loci, by means of an improved method that takes account of demographic effects. we found evidence for stronger selection at x-linked loci, consistent with their higher levels of codon usage bias. the estimates of the strength of selection and mutational bias in favor of unpreferred codons were similar to th ... | 2011 | 21191087 |
| polyandry increases offspring viability and mother productivity but does not decrease mother survival in drosophila pseudoobscura. | polyandrous mating is common, but the benefits for females of polyandry remain controversial. to test whether mating with multiple males affects female fitness, we compared lifetime components of fitness of three experimental sets of drosophila pseudoobscura females: monogamous females allowed to copulate one time (moc); monogamous females held with a male over her entire life and experiencing many copulations (mmc); and polyandrous females with a different male over each day of their lives and ... | 2010 | 20643932 |
| characterizing recurrent positive selection at fast-evolving genes in drosophila miranda and drosophila pseudoobscura. | characterizing the distribution of selection coefficients in natural populations remains a central challenge in evolutionary biology. we resequenced a subset of 19 fast-evolving protein-coding genes in the sister species drosophila miranda and d. pseudoobscura and their flanking regions to characterize the spatial footprint left by recurrent and recent selection. consistent with previous findings, fast-evolving genes and their flanking regions show reduced levels of neutral diversity compared wi ... | 2010 | 20624741 |