Publications

synthesis of an attached autosome, c(3)rm, in drosophila pseudoobscura.	drosophila pseudoobscura has three acrocentric autosomes. in the experiments reported, homologous arms of the third chromosome were attached to the same centromere. this is a 'reversed metacentric compound' third chromosome, denoted by c(3)rm. this compound chromosome is relatively fertile in within-strain crosses (ca. 50% egg hatch) but sterile when outcrossed to a normal karyotype. when constructing translocations for this experiment, the behavior of the y-autosome translocations suggested tha ...	2008	2323568
a multispecies approach for comparing sequence evolution of x-linked and autosomal sites in drosophila.	population genetics models show that, under certain conditions, the x chromosome is expected to be under more efficient selection than the autosomes. this could lead to 'faster-x evolution', if a large proportion of mutations are fixed by positive selection, as suggested by recent studies in drosophila. we used a multispecies approach to test this: muller's element d, an autosomal arm, is fused to the ancestral x chromosome in drosophila pseudoobscura and its sister species, drosophila affinis. ...	2008	19061532
fine-scale mapping of recombination rate in drosophila refines its correlation to diversity and divergence.	regional rates of recombination often correlate with levels of nucleotide diversity, and either selective or neutral hypotheses can explain this relationship. regional recombination rates also correlate with nucleotide differences between human and chimpanzee, consistent with models where recombination is mutagenic; however, a lack of correlation is observed in the drosophila melanogaster group, consistent with models invoking natural selection. here, we revisit the relationship among recombinat ...	2008	18621713
figaro: a novel statistical method for vector sequence removal.	sequences produced by automated sanger sequencing machines frequently contain fragments of the cloning vector on their ends. software tools currently available for identifying and removing the vector sequence require knowledge of the vector sequence, specific splice sites and any adapter sequences used in the experiment-information often omitted from public databases. furthermore, the clipping coordinates themselves are missing or incorrectly reported. as an example, within the approximately 1.2 ...	2008	18202027
distinguishing the forces controlling genetic variation at the xdh locus in drosophila pseudoobscura.	fifty-eight isochromosomal lines sampled from two natural populations of drosophila pseudoobscura in california and one from bogota, colombia, were examined using four-cutter restriction mapping. a 4.6-kb region of the xanthine dehydrogenase locus was probed and 66 of 135 restriction sites scored were polymorphic. this predicts that on average every 12th bp would be polymorphic in this region for the genes surveyed if polymorphism occurred randomly along the coding region. in addition, there wer ...	2008	2583480
origin and evolution of y chromosomes: drosophila tales.	classically, y chromosomes are thought to originate from x chromosomes through a process of degeneration and gene loss. now, the availability of 12 drosophila genomes provides an opportunity to study the origin and evolution of y chromosomes in an informative phylogenetic context. surprisingly, the majority of drosophila y-linked genes are recent acquisitions from autosomes and y chromosome gene gains are more frequent than gene losses. moreover, the drosophila pseudoobscura y chromosome lacks h ...	2009	19443075
the insect snmp gene family.	snmps are membrane proteins observed to associate with chemosensory neurons in insects; in drosophila melanogaster, snmp1 has been shown to be essential for the detection of the pheromone cis-vaccenyl acetate (cva). snmps are one of three insect gene clades related to the human fatty acid transporter cd36. we previously characterized the cd36 gene family in 4 insect orders that effectively cover the holometabola, or some 80% of known insect species and the 300 million years of evolution since th ...	2009	19364529
molecular evolution of a drosophila homolog of human brca2.	the human cancer susceptibility gene, brca2, functions in double-strand break repair by homologous recombination, and it appears to function via interaction of a repetitive region ("brc repeats") with rad-51. a putatively simpler homolog, dmbrca2, was identified in drosophila melanogaster recently and also affects mitotic and meiotic double-strand break repair. in this study, we examined patterns of repeat variation both within drosophila pseudoobscura and among available drosophila genome seque ...	2009	19554456
an intron loss of dfak gene in species of the drosophila melanogaster subgroup and phylogenetic analysis.	drosophila focal adhesion kinase (dfak) gene is a single-copy nuclear gene. previous study revealed that drosophila melanogaster and drosophila simulans had lost an intron precisely within the tyrosine kinase (tyk) domain of this gene. however, this did not happen in several other drosophila species, including drosophila elegans, drosophila ficusphila, drosophila biarmipes, drosophila jambulina, drosophila prostipennis, drosophila takahashii, and drosophila pseudoobscura. in the current study, h ...	2009	18310070
epistasis modifies the dominance of loci causing hybrid male sterility in the drosophila pseudoobscura species group.	speciation, the evolution of reproductive isolation between populations, serves as the driving force for generating biodiversity. postzygotic barriers to gene flow, such as f(1) hybrid sterility and inviability, play important roles in the establishment and maintenance of biological species. f(1) hybrid incompatibilities in taxa that obey haldane's rule, the observation that the heterogametic sex suffers greater hybrid fitness problems than the homogametic sex, are thought to often result from i ...	2009	19686263
the "plant drosophila": e.b. babcock, the genus "crepis," and the evolution of a genetics research program at berkeley, 1915-1947.	this paper explores the research and administrative efforts of ernest brown babcock, head of the division of genetics in the college of agriculture at the university of california, berkeley, the first academic unit so named in the united states. it explores the rationale for his choice of "model organism," the development--and transformation--of his ambitious genetics research program centering on the weedy plant genus named "crepis" (commonly known as the hawkbeard), along with examining in det ...	2009	20077617
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
the genomics of speciation in drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing.	in nature, closely related species may hybridize while still retaining their distinctive identities. chromosomal regions that experience reduced recombination in hybrids, such as within inversions, have been hypothesized to contribute to the maintenance of species integrity. here, we examine genomic sequences from closely related fruit fly taxa of the drosophila pseudoobscura subgroup to reconstruct their evolutionary histories and past patterns of genic exchange. partial genomic assemblies were ...	2009	19578407
a toolkit for high-throughput, cross-species gene engineering in drosophila.	we generated two complementary genomic fosmid libraries for drosophila melanogaster and drosophila pseudoobscura that permit seamless modification of large genomic clones by high-throughput recombineering and direct transgenesis. the fosmid transgenes recapitulated endogenous gene expression patterns. these libraries, in combination with recombineering technology, will be useful to rescue mutant phenotypes, allow imaging of gene products in living flies and enable systematic analysis and manipul ...	2009	19465918
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
age-specific fitness components in hybrid females of drosophila pseudoobscura and d. persimilis.	most models of hybridization assume that hybrids are less fit than their parental taxa. in contrast, some researchers have explored the possibility that hybrid individuals may actually have higher fitness and so play an important role in the generation of new species or adaptations. by estimating age-specific fitness components, we can determine not only how hybrid fitness differs from parental taxa, but also whether the fitness of hybrids relative to parental taxa changes with age. here we desc ...	2009	11336226
evolution of sex-dependent gene expression in three recently diverged species of drosophila.	sexual dimorphism in morphological, physiological, and behavioral traits is pervasive in animals, as is the observation of strong sexual dimorphism in genomewide patterns of gene expression in the few species where this has been studied. studies of transcriptome divergence show that most interspecific transcriptional divergence is highly sex dependent, an observation consistent with the action of sex-dependent natural selection during species divergence. however, few transcriptome evolution stud ...	2009	19720861
evolutionary dynamics of recently duplicated genes: selective constraints on diverging paralogs in the drosophila pseudoobscura genome.	duplicated genes produce genetic variation that can influence the evolution of genomes and phenotypes. in most cases, for a duplicated gene to contribute to evolutionary novelty it must survive the early stages of divergence from its paralog without becoming a pseudogene. i examined the evolutionary dynamics of recently duplicated genes in the drosophila pseudoobscura genome to understand the factors affecting these early stages of evolution. paralogs located in closer proximity have higher sequ ...	2009	19536449
a test and review of the role of effective population size on experimental sexual selection patterns.	experimental evolution, particularly experimental sexual selection in which sexual selection strength is manipulated by altering the mating system, is an increasingly popular method for testing evolutionary theory. concerns have arisen regarding genetic diversity variation across experimental treatments: differences in the number and sex ratio of breeders (effective population size; n(e)) and the potential for genetic hitchhiking, both of which may cause different levels of genetic variation bet ...	2009	19473403
repeat mediated gene duplication in the drosophila pseudoobscura genome.	genetic mutations can occur on a wide variety of scales, including those that change single nucleotides, those that add or remove content to/from a genome, and those that change the organization of a genome. gene duplications are a specific class of mutations that add content to a genome, and they can arise via a wide variety of mechanisms. i examined the mechanisms responsible for recently duplicated genes in the d. pseudoobscura genome, and i observed both retroposed and dna duplications. many ...	2009	19272434
experimental manipulation of sexual selection promotes greater male mating capacity but does not alter sperm investment.	sexual selection theory makes clear predictions regarding male spermatogenic investment. to test these predictions we used experimental sexual selection in drosophila pseudoobscura, a sperm heteromorphic species in which males produce both fertile and sterile sperm, the latter of which may function in postmating competition. specifically, we determined whether the number and size of both sperm types, as well as relative testis mass and accessory gland size, increased with increased sperm competi ...	2009	19236477
a single gene causes both male sterility and segregation distortion in drosophila hybrids.	a central goal of evolutionary biology is to identify the genes and evolutionary forces that cause speciation, the emergence of reproductive isolation between populations. despite the identification of several genes that cause hybrid sterility or inviability-many of which have evolved rapidly under positive darwinian selection-little is known about the ecological or genomic forces that drive the evolution of postzygotic isolation. here, we show that the same gene, overdrive, causes both male ste ...	2009	19074311
early and late subjective night phases of the drosophila pseudoobscura circadian rhythm require different energies of blue light for phase shifting.		2009	4273696
chromosomal and allozymic diagnosis of three species of drosophila. drosophila pseudoobscura, d. persimilis, and d. miranda.	techniques are presented for distinguishing the sibling species d. pseudoobscura, d. persimilis, and d. miranda in two ways: by differences in the banding sequence of salivary chromosomes, and by the frequencies of allozymes at certain diagnostic loci.	2009	874309
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
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
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
adaptive evolution of genes duplicated from the drosophila pseudoobscura neo-x chromosome.	drosophila x chromosomes are disproportionate sources of duplicated genes, and these duplications are usually the result of retrotransposition of x-linked genes to the autosomes. the excess duplication is thought to be driven by natural selection for two reasons: x chromosomes are inactivated during spermatogenesis, and the derived copies of retroposed duplications tend to be testis expressed. therefore, autosomal derived copies of retroposed genes provide a mechanism for their x-linked paralogs ...	2010	20351054
translocation of y-linked genes to the dot chromosome in drosophila pseudoobscura.	one of the most striking cases of sex chromosome reorganization in drosophila occurred in the lineage ancestral to drosophila pseudoobscura, where there was a translocation of y-linked genes to an autosome. these genes went from being present only in males, never recombining, and having an effective population size of 0.5n to a state of autosomal linkage, where they are passed through both sexes, may recombine, and their effective population size has quadrupled. these genes appear to be function ...	2010	20147437
the quantitative genetics and coevolution of male and female reproductive traits.	studies of experimental sexual selection have tested the effect of variation in the intensity of sexual selection on male investment in reproduction, particularly sperm. however, in several species, including drosophila pseudoobscura, no sperm response to experimental evolution has occurred. here, we take a quantitative genetics approach to examine whether genetic constraints explain the limited evolutionary response. we quantified direct and indirect genetic variation, and genetic correlations ...	2010	20100215
increased opportunity for sexual conflict promotes harmful males with elevated courtship frequencies.	mating systems have a profound influence on the probability of conflict occurring between the sexes. promiscuity is predicted to generate sexual conflict, thereby driving the evolution of male traits that harm females, whereas monogamy is expected to foster reproductive cooperation, thus rendering such traits redundant. we tested these predictions using experimentally evolved drosophila pseudoobscura subject to different mating systems. female survival was not influenced by the mating system tre ...	2010	20039999
coadaptation revisited.	during the four decades or more since dobzhansky introduced the term "coadaptation" to refer to the commonly observed selective superiority of inversion heterozygotes in populations of drosophila pseudoobscura, the definition of the term has evolved, as have views concerning the rapidity with which coadaptation might occur. indeed, the paucity of demonstrated instances of linkage disequilibrium in natural populations has led many to dismiss coadaptation as a factor in evolutionary change. the pr ...	2010	1901579
odorant receptor (or) genes: polymorphism and divergence in the d. melanogaster and d. pseudoobscura lineages.	in insects, like in most invertebrates, olfaction is the principal sensory modality, which provides animals with essential information for survival and reproduction. odorant receptors are involved in this response, mediating interactions between an individual and its environment, as well as between individuals of the same or different species. the adaptive importance of odorant receptors renders them good candidates for having their variation shaped by natural selection.	2010	20967126
spermatogenic cyst and organ culture in drosophila pseudoobscura.	spermatogenesis is a complex series of processes that involves (1) the maintenance of a renewable pool of diploid stem cells within a niche, (2) the mitotic expansion of a subpopulation of stem cells committed to the spermatogenic pathway, and (3) the differentiation of diploid cells into highly specialized, haploid spermatozoa through meiotic and post-meiotic cellular transformations. drosophila melanogaster is a desirable model for studying spermatogenesis, as similarities exist between mammal ...	2010	20694478
evolution of expression patterns of two odorant-binding protein genes, obp57d and obp57e, in drosophila.	odorant-binding proteins (obps) function in the perception of chemical signals together with odorant and taste receptors. genes encoding obps form a large family in insect genomes. in drosophila, the evolution of obp gene repertoire has been well studied by comparisons of the whole genome sequences from 12 closely related species. in contrast, their expression patterns are known only in drosophila melanogaster. two obp genes, obp57d and obp57e, arose by gene duplication at the early stage of d. ...	2010	20637846
adverse interactions between micro-rnas and target genes from different species.	it is commonly assumed but not proven that micrornas (mirnas) and their targets coevolve. under this assumption, mirnas and targets from different species may interact adversely, resulting in reduced fitness. however, the strength of the adverse interactions may not be detectable because even outright deletions of mirnas often manifest only subtle fitness effects. we tested and measured the strength of heterospecific interactions by carrying out transgenic experiments across drosophila species b ...	2010	20615957
fish mapping of microsatellite loci from drosophila subobscura and its comparison to related species.	microsatellites are highly polymorphic markers that are distributed through all the genome being more abundant in non-coding regions. whether they are neutral or under selection, these markers if localized can be used as co-dominant molecular markers to explore the dynamics of the evolutionary processes. their cytological localization can allow identifying genes under selection, inferring recombination from a genomic point of view, or screening for the genomic reorganizations occurring during th ...	2010	20198419
polyandry prevents extinction.	females of most animal species are polyandrous, with individual females usually mating with more than one male. however, the ubiquity of polyandry remains enigmatic because of the potentially high costs to females of multiple mating. current theory to account for the high prevalence of polyandry largely focuses on its benefits to individual females. there are also higher-level explanations for the high incidence of polyandry-polyandrous clades may speciate more rapidly. here we test the hypothes ...	2010	20188561
in vivo rnai rescue in drosophila melanogaster with genomic transgenes from drosophila pseudoobscura.	systematic, large-scale rna interference (rnai) approaches are very valuable to systematically investigate biological processes in cell culture or in tissues of organisms such as drosophila. a notorious pitfall of all rnai technologies are potential false positives caused by unspecific knock-down of genes other than the intended target gene. the ultimate proof for rnai specificity is a rescue by a construct immune to rnai, typically originating from a related species.	2010	20126626
sex ratio drive promotes sexual conflict and sexual coevolution in the fly drosophila pseudoobscura.	selfish genetic elements occur in all living organisms and often cause reduced fertility and sperm competitive ability in males. in the fruit fly drosophila pseudoobscura, the presence of a sex-ratio distorting x-chromosome meiotic driver sex ratio (sr) has been shown to promote the evolution of increased female remating rates in laboratory populations. this is favored because it promotes sperm competition, which decreases the risk to females of producing highly female-biased broods and to their ...	2010	19922445
enrichment of mrna-like noncoding rnas in the divergence of drosophila males.	with the advent of transcriptome data, it has become clear that mrna-like noncoding rnas (mlncrnas) are widespread in eukaryotes. although their functions are poorly understood, these transcripts may play an important role in development and could thus be involved in determining developmental complexity and phenotypic diversification. however, few studies have assessed their potential roles in the divergence of closely related species. here, we identify and study patterns of sequence and express ...	2010	21041796
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
hundreds of putatively functional small open reading frames in drosophila.	the relationship between dna sequence and encoded information is still an unsolved puzzle. the number of protein-coding genes in higher eukaryotes identified by genome projects is lower than was expected, while a considerable amount of putatively non-coding transcription has been detected. functional small open reading frames (smorfs) are known to exist in several organisms. however, coding sequence detection methods are biased against detecting such very short open reading frames. thus, a subst ...	2011	22118156
a conserved developmental patterning network produces quantitatively different output in multiple species of drosophila.	differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between closely related species. to assess the scope of such changes, we used high-resolution imaging methods to measure mrna expression in blastoderm embryos of drosophila yakuba and drosophi ...	2011	22046143
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
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
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
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
mind the gap: upgrading genomes with pacific biosciences rs long-read sequencing technology.	many genomes have been sequenced to high-quality draft status using sanger capillary electrophoresis and/or newer short-read sequence data and whole genome assembly techniques. however, even the best draft genomes contain gaps and other imperfections due to limitations in the input data and the techniques used to build draft assemblies. sequencing biases, repetitive genomic features, genomic polymorphism, and other complicating factors all come together to make some regions difficult or impossib ...	2012	23185243
cytogenetic mapping of marker genes on the chromosome elements c and e of drosophila pseudoobscura and d. subobscura.	enzyme loci, visible marker genes and lambda-cloned dna-sequences from a d. miranda library were mapped cytologically on the chromosome elements c and e of d. pseudoobscura and d. subobscura. new data are incorporated into the linkage maps of the two species. homologous segments can now be localized in the polytene chromosomes with these markers. a comparison of the chromosome elements e of d. melanogaster and d. subobscura shows 12 conserved subsections which have been rearranged by paracentric ...	2012	3504805
genetics of male and female sterility in hybrids of drosophila pseudoobscura and d. persimilis.	the genetic basis of male and female sterility in hybrids of drosophila pseudoobscura-drosophila persimilis was studied using backcross analysis. previous studies indirectly assessed male fertility by measuring testis size; these studies concluded that male sterility results from an x chromosome-autosome imbalance. by directly scoring for the production of motile sperm, male sterility is shown to be largely due to an incompatibility between genes on the x and y chromosomes of these two species. ...	2013	3623079
nucleotide sequence of the adh gene region of drosophila pseudoobscura: evolutionary change and evidence for an ancient gene duplication.	the alcohol dehydrogenase (adh) locus (adh; alcohol: nad+ oxidoreductase, ec 1.1.1.1) of drosophila pseudoobscura was cloned and sequenced. forty-five percent of the "effectively silent sites" have changed between adh in d. pseudoobscura of the obscura species group and the homologous dna sequence in d. mauritiana, the latter representing the melanogaster species group. the untranslated leader sequence of the adult transcript of d. pseudoobscura has two deletions relative to the d. mauritiana me ...	2013	3666441
macromolecular interaction and the electrophoretic mobility of esterase-5 from drosophila pseudoobscura.	esterase-5 is one of the most polymorphic loci in drosophila pseudoobscura. some variants reportedly produce a dimeric enzyme, while a few produce a monomeric form. this paper reports the finding that during electrophoresis esterase-5 exists in a dynamic equilibrium between monomers and dimers, an equilibrium that is dependent on the running temperature of the gels. this is shown by a series of analytical electrophoresis experiments in which the apparent molecular weights of several variants are ...	2013	3606564
how hot are drosophila hotspots? examining recombination rate variation and associations with nucleotide diversity, divergence, and maternal age in drosophila pseudoobscura.	fine scale meiotic recombination maps have uncovered a large amount of variation in crossover rate across the genomes of many species, and such variation in mammalian and yeast genomes is concentrated to <5kb regions of highly elevated recombination rates (10-100x the background rate) called "hotspots." drosophila exhibit substantial recombination rate heterogeneity across their genome, but evidence for these highly-localized hotspots is lacking. we assayed recombination across a 40kb region of ...	2013	23967224
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
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
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
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
a novel dataset for identifying sex-biased genes in drosophila.	phenotypic differences between males and females of sexually dimorphic species are caused in large part by differences in gene expression between the sexes, most of which occurs in the gonads. to accurately identify genes differentially expressed between males and females in drosophila, we sequenced the testis and ovary transcriptomes of d. yakuba, d. pseudoobscura, and d. ananassae and used them to identify sex-biased genes in the latter two species. we highlight the increased sensitivity and i ...	2014	25031657
comparative gene expression analysis of dtg, a novel target gene of dpp signaling pathway in the early drosophila melanogaster embryo.	in the early drosophila melanogaster embryo, dpp, a secreted molecule that belongs to the tgf-β superfamily of growth factors, activates a set of downstream genes to subdivide the dorsal region into amnioserosa and dorsal epidermis. here, we examined the expression pattern and transcriptional regulation of dtg, a new target gene of dpp signaling pathway that is required for proper amnioserosa differentiation. we showed that the expression of dtg was controlled by dpp and characterized a 524-bp e ...	2014	24321690
evidence for stabilizing selection on codon usage in chromosomal rearrangements of drosophila pseudoobscura.	there has been a renewed interest in investigating the role of stabilizing selection acting on genome-wide traits such as codon usage bias. codon bias, when synonymous codons are used at unequal frequencies, occurs in a wide variety of taxa. standard evolutionary models explain the maintenance of codon bias through a balance of genetic drift, mutation and weak purifying selection. the efficacy of selection is expected to be reduced in regions of suppressed recombination. contrary to observations ...	2014	25326424
faster-x effects in two drosophila lineages.	under certain circumstances, x-linked loci are expected to experience more adaptive substitutions than similar autosomal loci. to look for evidence of faster-x evolution, we analyzed the evolutionary rates of coding sequences in two sets of drosophila species, the melanogaster and pseudoobscura clades, using whole-genome sequences. one of these, the pseudoobscura clade, contains a centric fusion between the ancestral x chromosome and the autosomal arm homologous to 3l in d. melanogaster. this of ...	2014	25323954
the heritability of mating behaviour in a fly and its plasticity in response to the threat of sperm competition.	phenotypic plasticity is a key mechanism by which animals can cope with rapidly changeable environments, but the evolutionary lability of such plasticity remains unclear. the socio-sexual environment can fluctuate very rapidly, affecting both the frequency of mating opportunities and the level of competition males may face. males of many species show plastic behavioural responses to changes in social environment, in particular the presence of rival males. for example, drosophila pseudoobscura ma ...	2014	24587294
krüppel expression levels are maintained through compensatory evolution of shadow enhancers.	many developmental genes are controlled by shadow enhancers—pairs of enhancers that drive overlapping expression patterns. we hypothesized that compensatory evolution can maintain the total expression of a gene, while individual shadow enhancers diverge between species. to test this hypothesis, we analyzed expression driven by orthologous pairs of shadow enhancers from drosophila melanogaster, drosophila yakuba, and drosophila pseudoobscura that control expression of krüppel, a transcription fac ...	2015	26344774
assessment of rival males through the use of multiple sensory cues in the fruitfly drosophila pseudoobscura.	environments vary stochastically, and animals need to behave in ways that best fit the conditions in which they find themselves. the social environment is particularly variable, and responding appropriately to it can be vital for an animal's success. however, cues of social environment are not always reliable, and animals may need to balance accuracy against the risk of failing to respond if local conditions or interfering signals prevent them detecting a cue. recent work has shown that many mal ...	2015	25849643
molecular heterosis for heat-sensitive enzyme alleles.	heat denaturation studies were carried out and revealed hidden genic variants with the same net charge at the octanol dehydrogenase-1 locus in drosophila pseudoobscura. studies of several genetic crosses between strains with different heat-sensitivity alleles showed that the f(1) retained more in vitro enzyme activity after being heat-treated for a specified amount of time at a given temperature than the heat-resistant parent. we call this phenomenon "heterosis for heat-stability of enzyme activ ...	2015	4525464
behavior in different environments of populations of drosophila, pseudoobscura selected for phototaxis and geotaxis.	when tested in hirsch-hadler mazes, drosophila pseudoobscura descended from natural populations is phototactically and geotactically neutral on the average. decidedly positive and negative populations have been obtained by artificial selection. the behavior is independent of temperature (15-27 degrees ) and age (2-17 days). the flies perceive light as weak as 0.2 lux; from 7 to 3000 lux the behavior difference between positive and negative strains increases little, and perhaps decreases at 8000 ...	2015	4525308
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
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
effectiveness of intraspecific and interspecific matings in drosophila pseudoobscura and drosophila persimilis.		2015	20286615
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
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
comparative expression dynamics of intergenic long noncoding rnas in the genus drosophila.	thousands of long noncoding rnas (lncrnas) have been annotated in eukaryotic genomes, but comparative transcriptomic approaches are necessary to understand their biological impact and evolution. to facilitate such comparative studies in drosophila, we identified and characterized lncrnas in a second drosophilid-the evolutionary model drosophila pseudoobscura using rna-seq and computational filtering of protein-coding potential, we identified 1,589 intergenic lncrna loci in d. pseudoobscura we su ...	2016	27189981
winter is coming: hibernation reverses the outcome of sperm competition in a fly.	sperm commonly compete within females to fertilize ova, but research has focused on short-term sperm storage: sperm that are maintained in a female for only a few days or weeks before use. in nature, females of many species store sperm for months or years, often during periods of environmental stress, such as cold winters. here we examine the outcome of sperm competition in the fruit fly drosophila pseudoobscura, simulating the conditions in which females survive winter. we mated females to two ...	2016	26565889
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
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