| nonrandom distribution of long mono- and dinucleotide repeats in drosophila chromosomes: correlations with dosage compensation, heterochromatin, and recombination. | long stretches of (dc-da)n.(dt-dg)n, abbreviated ca/tg, have a distinctive distribution on drosophila chromosomes (m.l. pardue, k. lowenhaupt, a. rich, and a. nordheim, embo j. 6:1781-1789, 1987). the distribution of ca/tg suggests a correlation with the overall transcriptional activity of chromosomal regions and with the ability to undergo meiotic recombination. these correlations are conserved among drosophila species and may indicate one or more chromosomal functions. to test the generality o ... | 2009 | 2725493 |
| the chromatin landscape of drosophila: comparisons between species, sexes, and chromosomes. | the chromatin landscape is key for gene regulation, but little is known about how it differs between sexes or between species. here, we study the sex-specific chromatin landscape of drosophila miranda, a species with young sex chromosomes, and compare it with drosophila melanogaster. we analyze six histone modifications in male and female larvae of d. miranda (h3k4me1, h3k4me3, h3k36me3, h4k16ac, h3k27me3, and h3k9me2), and define seven biologically meaningful chromatin states that show differen ... | 2014 | 24840603 |
| incomplete dosage compensation in an evolving drosophila sex chromosome. | cellular autoradiography was used to measure relative rates of chromosomal rna synthesis and to examine the regulatory phenomenon of x-linked dosage compensation in drosophila miranda, a species containing two distinct, nonhomologous x chromosomes (x1 and x2). the x1 chromosome was found to be dosage-compensated, since the rate of rna synthesis along the single x1 chromosome in males equaled that of both x1 chromosomes in females. unlike other sex chromosomes that have been studied, the more rec ... | 1979 | 273254 |
| evidence for degeneration of the y chromosome in the dioecious plant silene latifolia. | the human y--probably because of its nonrecombining nature--has lost 97% of its genes since x and y chromosomes started to diverge [1, 2]. there are clear signs of degeneration in the drosophila miranda neoy chromosome (an autosome fused to the y chromosome), with neoy genes showing faster protein evolution [3-6], accumulation of unpreferred codons [6], more insertions of transposable elements [5, 7], and lower levels of expression [8] than neox genes. in the many other taxa with sex chromosomes ... | 2008 | 18394889 |
| a 3.5-kb dna fragment contains the cis-regulatory elements for retina-specific expression and partial dosage compensation of the arrestin b (arrb) gene of drosophila miranda. | a 3.5-kb genomic dna fragment containing the x1r chromosome-linked retina-specific arrestin b gene (also called arrestin 2) of drosophila miranda (arrb-mr) was introduced into the drosophila melanogaster genome via germ-line transformation. the results showed that the arrb-mr transgene was expressed only in the retina of the transformed flies. the transgene also showed male-specific transcriptional hyperactivation or dosage compensation, but the level was found to be 71-79% of the expected value ... | 1995 | 7642093 |
| dosage compensation and dietary glucose repression of larval amylase activity in drosophila miranda. | the functional locus for alpha-amylase (amy) in drosophila miranda is in the evolutionarily new x2 chromosome. x2 evolved from an autosome in response to an ancestral autosome-y translocation that gave rise to the "neo-y" chromosome of this species. y-linked amy, if still present in the ancestrally translocated element, is unexpressed. dosage compensation for amylase activity was examined in larvae of the s 204 strain. since dietary glucose is known to repress amy expression in drosophila melano ... | 1990 | 2085311 |
| conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in drosophila. | dosage compensation has arisen in response to the evolution of distinct male (xy) and female (xx) karyotypes. in drosophila melanogaster, the msl complex increases male x transcription approximately twofold. x-specific targeting is thought to occur through sequence-dependent binding to chromatin entry sites (cess), followed by spreading in cis to active genes. we tested this model by asking how newly evolving sex chromosome arms in drosophila miranda acquired dosage compensation. we found eviden ... | 2013 | 23630075 |
| patterns of dna-sequence divergence between drosophila miranda and d. pseudoobscura. | contrary to the classical view, a large amount of non-coding dna seems to be selectively constrained in drosophila and other species. here, using drosophila miranda bac sequences and the drosophila pseudoobscura genome sequence, we aligned coding and non-coding sequences between d. pseudoobscura and d. miranda, and investigated their patterns of evolution. we found two patterns that have previously been observed in comparisons between drosophila melanogaster and its relatives. first, there is a ... | 2009 | 19859648 |
| dosage compensation of a retina-specific gene in drosophila miranda. | the x1r chromosome of drosophila miranda and the 3l autosome of drosophila melanogaster are thought to have originated from the ancestral d chromosomal element and therefore may contain the same set of genes. it is expected that these genes will be dosage compensated in d. miranda because of their x linkage. to test these possibilities and to study evolution of the dosage compensation mechanism, we used the 3l-linked autosomal head-specific gene 507 ml of d. melanogaster to isolate the homologou ... | 1991 | 1706975 |
| 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 |
| preferential y chromosomal location of trim, a novel transposable element of drosophila miranda, obscura group. | we have isolated a novel transposable element from the y chromosome of drosophila miranda (obscura group) which shows an organization intermediate between that of typical retroviruses and the i factor of drosophila melanogaster. the site of integration of this element, trim, is an inverted repeat. on the 5' side the central region of trim is bordered by a sequence homologous to the trna primer binding site (pbs) and on the 3' side by a sequence homologous to the polypurine tract (ppt). the 5' lt ... | 1991 | 1665124 |
| 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 |
| ancestral polymorphisms in drosophila pseudoobscura and drosophila miranda. | ancestral polymorphisms are defined as variants that arose by mutation prior to the speciation event that generated the species in which they segregate. their presence may complicate the interpretation of molecular data and lead to incorrect phylogenetic inferences. they may also be used to identify regions of the genome that are under balancing selection. it is thus important to take into account the contribution of ancestral polymorphisms to variability within species and divergence between sp ... | 2011 | 21767458 |
| evidence for male-driven evolution in drosophila. | in several vertebrate taxa studied to date, mutation rates are higher in males than females (male-driven evolution). the male-to-female mutation rate (alpha) can be estimated by contrasting dna divergence data at x-linked, y-linked, and autosomal loci. previous studies in drosophila, comparing x-linked and autosomal divergence, have found no evidence for male-driven evolution in this genus. here, i compare levels of nucleotide divergence between homologous x- and y-linked loci in drosophila mira ... | 2008 | 18234707 |
| sex-specific adaptation drives early sex chromosome evolution in drosophila. | most species' sex chromosomes are derived from ancient autosomes and show few signatures of their origins. we studied the sex chromosomes of drosophila miranda, where a neo-y chromosome originated only approximately 1 million years ago. whole-genome and transcriptome analysis reveals massive degeneration of the neo-y, that male-beneficial genes on the neo-y are more likely to undergo accelerated protein evolution, and that neo-y genes evolve biased expression toward male-specific tissues--the sh ... | 2012 | 22822149 |
| muller's ratchet and the degeneration of the drosophila miranda neo-y chromosome. | since its formation about 1.75 million years ago, the drosophila miranda neo-y chromosome has undergone a rapid process of degeneration, having lost approximately half of the genes that it originally contained. using estimates of mutation rates and selection coefficients for loss-of-function mutations, we show that the high rate of accumulation of these mutations can largely be explained by muller's ratchet, the process of stochastic loss of the least-loaded mutational class from a finite, nonre ... | 2010 | 20215466 |
| evolution of amino-acid sequences and codon usage on the drosophila miranda neo-sex chromosomes. | we have studied patterns of dna sequence variation and evolution for 22 genes located on the neo-x and neo-y chromosomes of drosophila miranda. as found previously, nucleotide site diversity is greatly reduced on the neo-y chromosome, with a severely distorted frequency spectrum. there is also an accelerated rate of amino-acid sequence evolution on the neo-y chromosome. comparisons of nonsynonymous and silent variation and divergence suggest that amino-acid sequences on the neo-x chromosome are ... | 2006 | 17028318 |
| expression profile of a degenerating neo-y chromosome in drosophila. | gene-poor, degenerate y chromosomes have evolved repeatedly from ordinary autosomes, but little is known about the processes that silence most genes on an evolving y. | 2006 | 16950105 |
| 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 |
| 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 |
| estimating the parameters of selection on nonsynonymous mutations in drosophila pseudoobscura and d. miranda. | we present the results of surveys of diversity in sets of >40 x-linked and autosomal loci in samples from natural populations of drosophila miranda and d. pseudoobscura, together with their sequence divergence from d. affinis. mean silent site diversity in d. miranda is approximately one-quarter of that in d. pseudoobscura; mean x-linked silent diversity is about three-quarters of that for the autosomes in both species. estimates of the distribution of selection coefficients against heterozygous ... | 2010 | 20516497 |
| unusual pattern of single nucleotide polymorphism at the exuperantia2 locus of drosophila pseudoobscura. | we have investigated the pattern of dna sequence variation at the exuperantia2 locus in drosophila pseudoobscura. this adds to the increasing dataset of genetic variation in d. pseudoobscura, a useful model species for evolutionary genetic studies. the level of silent site nucleotide diversity and the divergence from an outgroup drosophila miranda are comparable with those for other x-linked loci. one peculiar pattern at the exu2 locus of d. pseudoobscura is a complete linkage disequilibrium bet ... | 2003 | 14768894 |
| non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements. | transposable elements (tes) allow rewiring of regulatory networks, and the recent amplification of the isx element dispersed 77 functional but suboptimal binding sites for the dosage compensation complex to a newly formed x chromosome in drosophila. here we identify two linked refining mutations within isx that interact epistatically to increase binding affinity to the dosage compensation complex. selection has increased the frequency of this derived haplotype in the population, which is fixed a ... | 2015 | 25688566 |
| de novo transcriptome assembly reveals sex-specific selection acting on evolving neo-sex chromosomes in drosophila miranda. | the drosophila miranda neo-sex chromosome system is a useful resource for studying recently evolved sex chromosomes. however, the neo-y genomic assembly is fragmented due to the accumulation of repetitive sequence. furthermore, the separate assembly of the neo-x and neo-y chromosomes into genomic scaffolds has proven to be difficult, due to their low level of sequence divergence, which in coding regions is about 1.5%. here, we de novo assemble the transcriptome of d. miranda using rna-seq data f ... | 2014 | 24673816 |
| the epigenome of evolving drosophila neo-sex chromosomes: dosage compensation and heterochromatin formation. | sex chromosomes originated from autosomes but have evolved a highly specialized chromatin structure. drosophila y chromosomes are composed entirely of silent heterochromatin, while male x chromosomes have highly accessible chromatin and are hypertranscribed as a result of dosage compensation. here, we dissect the molecular mechanisms and functional pressures driving heterochromatin formation and dosage compensation of the recently formed neo-sex chromosomes of drosophila miranda. we show that th ... | 2013 | 24265597 |
| evolution of sex chromosomes: dosage compensation of the lcp1-4 gene cluster on the evolving neo-x chromosome in drosophila miranda. | in drosophila miranda the small multigene family of the larval cuticle protein (lcp1-4) genes resides on the evolving neo-x and neo-y sex chromosome pair while in the sibling species drosophila pseudoobscura and drosophila persimilis the gene cluster is inherited autosomally. the neo-y chromosomal lcp1, lcp2 and lcp4 genes are, as previously shown by us, not expressed and only lcp3 is expressed at a strongly reduced level. as a first step in understanding the evolutionary mechanism(s) transformi ... | 2007 | 17352708 |
| adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in drosophila. | what advantage might sexual recombination confer? population genetics theory predicts that asexual genomes are less efficient at eliminating deleterious mutations and incorporating beneficial alleles. here, i compare patterns of genome evolution in a 40-kb gene-rich region on homologous neo-sex chromosomes of drosophila miranda. genes on the non-recombining neo-y show various signs of degeneration, including transposable-element insertions, frameshift mutations and a higher rate of amino-acid su ... | 2003 | 12754509 |
| gene loss on y chromosomes: a consequence of purifying selection? | recombination restriction between evolving sex chromosomes leads to the degeneration of the chromosome that is present only in the heterogametic sex (the y chromosome in xy species). the evolutionary forces driving y chromosome degeneration, however, are still under debate and include positive and negative selection models. in a recent study, we showed that the rate of accumulation of loss-of-function mutations on the neo-y chromosome of drosophila miranda is compatible with the process of mulle ... | 2013 | 20657178 |
| 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 |
| 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 |
| characterizing the influence of effective population size on the rate of adaptation: gillespie's darwin domain. | characterizing the role of effective population size in dictating the rate of adaptive evolution remains a major challenge in evolutionary biology. depending on the underlying distribution of fitness effects of new mutations, populations of different sizes may differ vastly in their rate of adaptation. here, we collect polymorphism data at over 100 loci for two closely related drosophila species with different current effective population sizes (n(e)), drosophila miranda and d. pseudoobscura, to ... | 2011 | 21705473 |
| structural organization of the alpha-amylase gene locus in drosophila melanogaster and drosophila miranda. | chromosomal sites belonging to the alpha-amylase gene family have been identified in d. melanogaster and d. miranda and in the sibling species of miranda, pseudoobscura, and persimilis. two sites occur in chromosome 2 of melanogaster; one contains the amy gene locus (54a) and the other an amylase "pseudogene" (53cd). two sites of homology exist at 73a and 78c and perhaps another at 81bc in chromosome 3 of pseudoobscura and persimilis and in the homologous regions of the x2 chromosome in miranda. ... | 1987 | 3110097 |
| a duplication including the y allele of lcp2 and the trim retrotransposon at the lcp locus on the degenerating neo-y chromosome of drosophila miranda: molecular structure and mechanisms by which it may have arisen. | evolutionary changes during the process of sex chromosome differentiation in drosophila miranda are associated with massive dna rearrangements. comparing the dna structure of the larval cuticle protein (lcp) region from the x2 and neo-y chromosome pair, we observed insertions, deletions and a large duplication at the neo-y chromosomal locus. the duplication encompasses a complete copy of the neo-y allele of lcp2, and the isy3 and the isy4 insertion sequences. the latter was identified as a retro ... | 1993 | 8392013 |
| the dosage compensation system of drosophila is co-opted by newly evolved x chromosomes. | in species where males and females differ in number of sex chromosomes, the expression of sex-linked genes is equalized by a process known as dosage compensation. in drosophila melanogaster, dosage compensation is mediated by the binding of the products of the male-specific lethal (msl) genes to the single male x chromosome. here we report that the sex- and chromosome-specific binding of three of the msl proteins (msls) occurs in other drosophilid species, spanning four genera. moreover, we show ... | 1996 | 8774878 |
| molecular evolution of inversions in drosophila pseudoobscura: the amylase gene region. | the amylase region of the third chromosome of drosophila pseudoobscura has been cloned and localized to cytological band 73a. it is contained within a series of highly polymorphic inversions and serves as a convenient tool for a molecular evolutionary analysis of the inverted gene arrangements. amylase in d. pseudoobscura is a family of three genes, and some chromosomes have deletions for one or two of them. two overlapping clones covering 26 kilobases were isolated and used as probes to survey ... | 1991 | 1702542 |
| extremely low nucleotide diversity in the x-linked region of papaya caused by a strong selective sweep. | the papaya y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. the same populations were used to study nucleotide diversity and population structure in the x-linked region. | 2016 | 27890017 |
| spreading good news. | | 2015 | 25838131 |
| similar rates of protein adaptation in drosophila miranda and d. melanogaster, two species with different current effective population sizes. | adaptive protein evolution is common in several drosophila species investigated. some studies point to very weak selection operating on amino-acid mutations, with average selection intensities on the order of nes approximately in d. melanogaster and d. simulans. species with lower effective population sizes should undergo less adaptation since they generate fewer mutations and selection is ineffective on a greater proportion of beneficial mutations. | 2008 | 19091130 |
| genomic degradation of a young y chromosome in drosophila miranda. | y chromosomes are derived from ordinary autosomes and degenerate because of a lack of recombination. well-studied y chromosomes only have few of their original genes left and contain little information about their evolutionary origin. here, we take advantage of the recently formed neo-y chromosome of drosophila miranda to study the processes involved in y degeneration on a genomic scale. | 2008 | 18269752 |
| reduced selection for codon usage bias in drosophila miranda. | biased codon usage in many species results from a balance among mutation, weak selection, and genetic drift. here i show that selection to maintain biased codon usage is reduced in drosophila miranda relative to its ancestor. analyses of mutation patterns in noncoding dna suggest that the extent of this reduction cannot be explained by changes in mutation bias or by biased gene conversion. low levels of variability in d. miranda relative to its sibling species, d. pseudoobscura, suggest that it ... | 2007 | 17457633 |
| selection, recombination and demographic history in drosophila miranda. | selection, recombination, and the demographic history of a species can all have profound effects on genomewide patterns of variability. to assess the impact of these forces in the genome of drosophila miranda, we examine polymorphism and divergence patterns at 62 loci scattered across the genome. in accordance with recent findings in d. melanogaster, we find that noncoding dna generally evolves more slowly than synonymous sites, that the distribution of polymorphism frequencies in noncoding dna ... | 2006 | 17028331 |
| molecular evolution of the sex-ratio inversion complex in drosophila pseudoobscura: analysis of the esterase-5 gene region. | the sex-ratio chromosome in drosophila pseudoobscura is subject to meiotic drive. it is associated with a series of three nonoverlapping paracentric inversions on the right arm of the x chromosome. the esterase-5 gene region has been localized to section 23 within the subbasal inversion of the sex-ratio inversion complex, making esterase-5 a convenient locus for molecular evolutionary analyses of the sex-ratio inversion complex and the associated drive system. a 504-bp fragment of noncoding, int ... | 1996 | 8587496 |
| an experimental investigation of the unit charge model of protein polymorphism and its relation to the esterase-5 locus of drosophila pseudoobscura, drosophila persimilis, and drosophila miranda. | the relationship between charge changes and electrophoretic mobility changes is investigated experimentally. the charge of several proteins is altered by reaction with small molecules of known structure and the change in electrophoretic mobility is measured. the method of ferguson plots is used to separate charge and shape components of mobility differences. the average effect of an amino acid charge change on the mobility of the esterase-5( 1.00) allele of drosophila pseudoobscura is estimated ... | 1977 | 17248784 |
| estimating selection on nonsynonymous mutations. | the distribution of mutational effects on fitness is of fundamental importance for many aspects of evolution. we develop two methods for characterizing the fitness effects of deleterious, nonsynonymous mutations, using polymorphism data from two related species. these methods also provide estimates of the proportion of amino acid substitutions that are selectively favorable, when combined with data on between-species sequence divergence. the methods are applicable to species with different effec ... | 2006 | 16299397 |
| sex chromosome evolution: molecular aspects of y-chromosome degeneration in drosophila. | ancient y-chromosomes of various organisms contain few active genes and an abundance of repetitive dna. the neo-y chromosome of drosophila miranda is in transition from an ordinary autosome to a genetically inert y-chromosome, while its homolog, the neo-x chromosome, is evolving partial dosage compensation. here, i compare four large genomic regions located on the neo-sex chromosomes that contain a total of 12 homologous genes. in addition, i investigate the partial coding sequence for 56 more h ... | 2005 | 16169921 |
| retroelements: tools for sex chromosome evolution. | many eukaryotic taxa inherit a heteromorphic sex chromosome pair. it is a generally accepted hypothesis that the sex chromosome pair is derived from a pair of homologous autosomes that has developed after the occurrence of a sex differentiator in an evolutionary process into two structurally and functionally different partners. in most of the analyzed systems the occurrence of the dominant sex differentiator is paralleled by the suppression of recombination within and close by that region. the r ... | 2005 | 16093665 |
| the sex-determining mechanism of drosophila miranda. | | 1939 | 17246918 |
| drosophila miranda, a new species. | | 1935 | 17246767 |
| patterns of selection on synonymous and nonsynonymous variants in drosophila miranda. | we have investigated patterns of within-species polymorphism and between-species divergence for synonymous and nonsynonymous variants at a set of autosomal and x-linked loci of drosophila miranda. d. pseudoobscura and d. affinis were used for the between-species comparisons. the results suggest the action of purifying selection on nonsynonymous, polymorphic variants. among synonymous polymorphisms, there is a significant excess of synonymous mutations from preferred to unpreferred codons and of ... | 2005 | 15545653 |
| evidence that positive selection drives y-chromosome degeneration in drosophila miranda. | why does the y chromosome harbor so few functional loci? evolutionary theory predicts that y chromosomes degenerate because they lack genetic recombination. both positive and negative selection models have been invoked to explain this degeneration, as both can result in the recurrent fixation of linked deleterious mutations on a nonrecombining y chromosome. to distinguish between these models, i investigated patterns of nucleotide variability along 37 kb of the recently formed neo-y chromosome i ... | 2004 | 15107853 |
| protein evolution and codon usage bias on the neo-sex chromosomes of drosophila miranda. | the neo-sex chromosomes of drosophila miranda constitute an ideal system to study the effects of recombination on patterns of genome evolution. due to a fusion of an autosome with the y chromosome, one homolog is transmitted clonally. here, i compare patterns of molecular evolution of 18 protein-coding genes located on the recombining neo-x and their homologs on the nonrecombining neo-y chromosome. the rate of protein evolution has significantly increased on the neo-y lineage since its formation ... | 2003 | 14668377 |
| a survey of chromosomal and nucleotide sequence variation in drosophila miranda. | there have recently been several studies of the evolution of y chromosome degeneration and dosage compensation using the neo-sex chromosomes of drosophila miranda as a model system. to understand these evolutionary processes more fully, it is necessary to document the general pattern of genetic variation in this species. here we report a survey of chromosomal variation, as well as polymorphism and divergence data, for 12 nuclear genes of d. miranda. these genes exhibit varying levels of dna sequ ... | 2003 | 12930746 |
| on the genomic location of the exuperantia1 gene in drosophila miranda: the limits of in situ hybridization experiments. | in situ hybridization to drosophila polytene chromosomes is a powerful tool for determining the chromosomal location of genes. using in situ hybridization experiments, yi and charlesworth recently reported the transposition of the exuperantia1 gene (exu1) from a neo-sex chromosome to the ancestral x chromosome of drosophila miranda, close to exuperantia2 (exu2). by characterizing sequences flanking exu1, however, we found the position of exu1 to be conserved on the neo-sex chromosome. further, t ... | 2003 | 12871928 |
| accumulation of spock and worf, two novel non-ltr retrotransposons, on the neo-y chromosome of drosophila miranda. | transposable elements constitute a major fraction of eukaryotic genomes. here, i characterize two novel non-ltr retrotransposons, cloned from the neo-y chromosome of drosophila miranda. worf is 4.1 kb in size and shows homology to the t1-2 non-ltr transposon characterized in anopheles. spock is 4.9 kb in size and shows similarity to the doc element of d. melanogaster. southern blot analysis of both elements yielded stronger signals for male dna. in situ hybridization to polytene chromosomes reve ... | 2003 | 12598683 |
| reduced adaptation of a non-recombining neo-y chromosome. | sex chromosomes are generally believed to have descended from a pair of homologous autosomes. suppression of recombination between the ancestral sex chromosomes led to the genetic degeneration of the y chromosome. in response, the x chromosome may become dosage-compensated. most proposed mechanisms for the degeneration of y chromosomes involve the rapid fixation of deleterious mutations on the y. alternatively, y-chromosome degeneration might be a response to a slower rate of adaptive evolution, ... | 2002 | 11907578 |
| biased distribution of repetitive elements: a landmark for neo-y chromosome evolution in drosophila miranda. | it is generally assumed that the sex chromosomes developed from a pair of homologs. over evolution, the proto-y chromosome, with a very short differential segment, matured in its final stage into a heterochromatic and, for the most part, genetically eroded y chromosome. the constraints on the evolution of the proto-y chromosome have been speculated upon since the sex chromosomes were discovered. several models have been suggested. drosophila miranda has proved to be a unique and potent model sys ... | 2001 | 11528116 |
| common mechanisms of y chromosome evolution. | y chromosome evolution is characterized by the expansion of genetic inertness along the y chromosome and changes in the chromosome structure, especially the tendency of becoming heterochromatic. it is generally assumed that the sex chromosome pair has developed from a pair of homologues. in an evolutionary process the proto-y-chromosome, with a very short differential segment, develops in its final stage into a completely heterochromatic and to a great extends genetically eroded y chromosome. th ... | 2000 | 11293785 |
| a selective sweep associated with a recent gene transposition in drosophila miranda. | in drosophila miranda, a chromosome fusion between the y chromosome and the autosome corresponding to muller's element c has created a new sex chromosome system. the chromosome attached to the ancestral y chromosome is transmitted paternally and hence is not exposed to crossing over. this chromosome, conventionally called the neo-y, and the homologous neo-x chromosome display many properties of evolving sex chromosomes. we report here the transposition of the exuperantia1 (exu1) locus from a neo ... | 2000 | 11102371 |
| reduced levels of microsatellite variability on the neo-y chromosome of drosophila miranda. | in many species, sex is determined by a system involving x and y chromosomes, the latter having lost much of their genetic activity. sex chromosomes have evolved independently many times, and several different mechanisms responsible for the degeneration of the y chromosome have been proposed. here, we have taken advantage of the secondary sex chromosome pair in drosophila miranda to test for the effects of evolutionary forces involved in the early stages of y-chromosome degeneration. because of ... | 2000 | 10996069 |
| contrasting patterns of molecular evolution of the genes on the new and old sex chromosomes of drosophila miranda. | in organisms with chromosomal sex determination, sex is determined by a set of dimorphic sex chromosomes that are thought to have evolved from a set of originally homologous chromosomes. the chromosome inherited only through the heterogametic sex (the y chromosome in the case of male heterogamety) often exhibits loss of genetic activity for most of the genes carried on its homolog and is hence referred to as degenerate. the process by which the proto-y chromosome loses its genetic activity has l ... | 2000 | 10779531 |
| the amylase gene cluster on the evolving sex chromosomes of drosophila miranda. | on the basis of chromosomal homology, the amylase gene cluster in drosophila miranda must be located on the secondary sex chromosome pair, neo-x (x2) and neo-y, but is autosomally inherited in all other drosophila species. genetic evidence indicates no active amylase on the neo-y chromosome and the x2-chromosomal locus already shows dosage compensation. several lines of evidence strongly suggest that the amy gene cluster has been lost already from the evolving neo-y chromosome. this finding show ... | 1999 | 9872956 |
| accelerated adaptive evolution on a newly formed x chromosome. | sex chromosomes originated from ordinary autosomes, and their evolution is characterized by continuous gene loss from the ancestral y chromosome. here, we document a new feature of sex chromosome evolution: bursts of adaptive fixations on a newly formed x chromosome. taking advantage of the recently formed neo-x chromosome of drosophila miranda, we compare patterns of dna sequence variation at genes located on the neo-x to genes on the ancestral x chromosome. this contrast allows us to draw infe ... | 2009 | 19402745 |
| accelerated pseudogenization on the neo-x chromosome in drosophila miranda. | y chromosomes often degenerate via the accumulation of pseudogenes and transposable elements. by contrast, little is known about x-chromosome degeneration. here we compare the pseudogenization process between genes on the neo-sex chromosomes in drosophila miranda and their autosomal orthologues in closely related species. the pseudogenization rate on the neo-x is much lower than the rate on the neo-y, but appears to be higher than the rate on the orthologous autosome in d. pseudoobscura. genes u ... | 2016 | 27897175 |
| degenerating y chromosome of drosophila miranda: a trap for retrotransposons. | in drosophila miranda, the larval cuticle protein (lcp) genes are located on the x2 and y chromosomes, while in other drosophila species the lcp genes are inherited on the autosomes. we chose the d. miranda species as a model system to analyze the molecular bases of y chromosome degeneration, a phenomenon observed in many species. dna sequence analysis of the y chromosomal lcp gene locus reveals dense clustering of trapped retrotransposons. once inserted at the y chromosomal location they cannot ... | 1992 | 1323846 |
| dosage compensation for a chromosome that comprises an x chromosome and an autosome as its two homologs in interspecific hybrids of drosophila miranda and d. persimilis. | a chromosomal element (c) of an interspecific hybrid of d. miranda (females) and d. persimilis (males) represented a unique situation, where between its two homologous, one derived from an x chromosome (x2 of miranda) and the other from an autosome (3rd chromosome of persimilis). in cytological preparations of polytene nuclei, the x chromosomal homolog in hybrid males exhibited the male-x like inflated structure, known as prerequisite for hypertranscription; whereas the autosomal homolog existed ... | 1992 | 1506023 |
| evolution of the larval cuticle proteins coded by the secondary sex chromosome pair: x2 and neo-y of drosophila miranda: ii. comparison at the amino acid sequence level. | the larval cuticle proteins (lcps) are encoded by a multigene family, lcp1-4, located at the right arm of the metacentric autosome 2 (2r) in drosophila melanogaster. due to a chromosome fusion the lcp locus of drosophila miranda is situated on a pair of secondary sex chromosomes, the x2 and neo-y chromosomes. comparing the deduced amino acid sequences of the autosomal d. melanogaster loci with the sex-chromosomal loci of d. miranda, we were able to trace the evolution of the lcp loci with respec ... | 1996 | 8798346 |
| evolution of the larval cuticle proteins coded by the secondary sex chromosome pair: x2 and neo-y of drosophila miranda: i. comparison at the dna sequence level. | the larval cuticle protein genes (lcps) represent a multigene family located at the right arm of the metacentric autosome 2 (2r) in drosophila melanogaster. due to a chromosome fusion the lcp locus of drosophila miranda is situated on a pair of secondary sex chromosomes, the x2 and neo-y chromosome. comparing the dna sequences from d. miranda and d. melanogaster organization and the gene arrangement of lcp1-lcp4 are similar, although the intergene distances vary considerably. the greatest differ ... | 1996 | 8798345 |
| a bamhi repeat element is predominantly associated with the degenerating neo-y chromosome of drosophila miranda but absent in the drosophila melanogaster genome. | in drosophila miranda, females have two x1 and two evolving x2 chromosomes, and males have one of each of these two x chromosomes and a y chromosome. in males, the homologue of the x2 chromosome, the neo-y chromosome, is attached to the y chromosome and is under the process of degenerative evolution. we have examined a developmentally regulated x2/neo-y chromosome-linked gene, 549mr, of d. miranda and found that the neo-y chromosome-linked copy of this gene (549mr-ny) contains an insertional dna ... | 1992 | 1311096 |
| nucleotide sequence of the arrestin-like 49 kd protein gene of drosophila miranda. | | 1990 | 2216789 |
| genetic divergence in closely related sibling species drosophila pseudoobscura, drosophila persimilis and drosophila miranda. | | 1977 | 28567734 |
| the mechanism of non-random segregation of sex chromosomes in male drosophila miranda. | | 1946 | 21021046 |
| the synapsis of the sex chromosomes of drosophila miranda in relation to their directed segregation. | | 1944 | 16588671 |
| enigma of y chromosome degeneration: neo-y and neo-x chromosomes of drosophila miranda a model for sex chromosome evolution. | y chromosome degeneration is characterized by structural changes in the chromosome architecture and expansion of genetic inertness along the y chromosome. it is generally assumed that the heteromorphic sex chromosome pair has developed from a pair of homologues. several models have been suggested. we use the unique situation of the secondary sex chromosome pair, neo-y and neo-x (x2), in drosophila miranda to analyze molecular mechanisms involved in the evolutionary processes of y chromosome dege ... | 1998 | 9720292 |
| the enigma of y chromosome degeneration: tram, a novel retrotransposon is preferentially located on the neo-y chromosome of drosophila miranda. | we have cloned a novel transposable element from the neo-y chromosome of drosophila miranda. the size of the element, designated as tram, is 3.452 bp, including on both sides long terminal direct repeats (ltrs) of 372 bp, respectively. the element is flanked by a 5-bp target site duplication, atatg. the putative primer binding site (pbs) for minus-strand priming is complementary to 18 nucleotides of the 3'-end of trna(trp). data base screens for dna sequence identities were negative, apart from ... | 1997 | 9071582 |
| how y chromosomes become genetically inert. | we have investigated the mechanistic aspects of inactivation of the major larval cuticle protein genes (lcp1-4) in drosophila miranda during y chromosome evolution. the lcp genes are located on the x2 and neo-y chromosomes in d. miranda but are autosomally inherited in all other drosophila species investigated so far. in the neo-y chromosome all four lcp loci are embedded within a dense cluster of transposable elements. the x2 lcp1-4 loci are expressed, while the y chromosomal lcp3 locus shows o ... | 1993 | 8390679 |
| morphology and replication of a degenerating chromosome in drosophila miranda. | | 1988 | 3198149 |
| multiple sex chromosomes in drosophila miranda: a system to study the degeneration of a chromosome. | drosophila miranda possesses an intriguing sex chromosome constitution. while female metaphase plates have 10 chromosomes (diploid set), in males only 9 chromosomes can be identified. the missing homologue has been translocated to the y, forming a neo-y chromosome which is polytenized in the salivary gland cells. this report presents a detailed characterization of dna, isolated from d. miranda flies. in situ hybridizations, using crna transcribed from unfractionated d. miranda dna, reveal hybrid ... | 1982 | 7172863 |
| ancient male recombination shaped genetic diversity of neo-y chromosome in drosophila albomicans. | researchers studying y chromosome evolution have drawn attention to neo-y chromosomes in drosophila species due to their resembling the initial stage of y chromosome evolution. in the studies of neo-y chromosome of drosophila miranda, the extremely low genetic diversity observed suggested various modes of natural selection acting on the nonrecombining genome. however, alternative possibility may come from its peculiar origin from a single chromosomal fusion event with male achiasmy, which potent ... | 2016 | 26494844 |