Gender Identification and Classification of Drosophila melanogaster Flies Using Machine Learning Techniques

Drosophila melanogaster is an important genetic model organism used extensively in medical and biological studies. About 61% of known human genes have a recognizable match with the genetic code of Drosophila flies, and 50% of fly protein sequences have mammalian analogues. Recently, several investigations have been conducted in Drosophila to study the functions of specific genes exist in the central nervous system, heart, liver, and kidney. The outcomes of the research in Drosophila are also used as a unique tool to study human-related diseases. This article presents a novel automated system to classify the gender of Drosophila flies obtained through microscopic images (ventral view). The proposed system takes an image as input and converts it into grayscale illustration to extract the texture features from the image. Then, machine learning (ML) classifiers such as support vector machines (SVM), Naive Bayes (NB), and K-nearest neighbour (KNN) are used to classify the Drosophila as male or female. The proposed model is evaluated using the real microscopic image dataset, and the results show that the accuracy of the KNN is 90%, which is higher than the accuracy of the SVM classifier.

FlyAtlas 2 in 2022: enhancements to the Drosophila melanogaster expression atlas

FlyAtlas 2 (flyatlas2.org) is a database and web application for studying the expression of the genes of Drosophila melanogaster in different tissues of adults and larvae. It is based on RNA-Seq data, and incorporates both genes encoding proteins and microRNAs. We have now completed the population of the database with 13 tissues from both male and female adults, five sex-specific tissues, and eight larval tissues. Larval garland cell nephrocytes have also been included. Major enhancements have been made to the application. First, a facility has been added for a 'Profile' search for genes with a similar pattern of tissue expression as a query gene. This may help establish the function of genes for which this is currently unknown. Second, a facility has been added dedicated to the larval midgut, where the difference in gene expression in the five regions of different pH can be explored. A variety of further improvements to the interface are described.

A phylogeny for the Drosophila montium species group: A model clade for comparative analyses

The Drosophila montium species group is a clade of 94 named species, closely related to the model species D. melanogaster. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times within the montium species group, and its relative divergence time from D. melanogaster. To assess the robustness of our phylogenetic inferences, we use 3 non-overlapping sets of 20 single-copy coding sequences and analyze all 60 genes with both Bayesian and maximum likelihood methods. Our analyses support monophyly of the group. Apart from the uncertain placement of a single species, D. baimaii, our analyses also support the monophyly of all seven subgroups proposed within the montium group. Our phylograms and relative chronograms provide a highly resolved species tree, with discordance restricted to estimates of relatively short branches deep in the tree. In contrast, age estimates for the montium crown group, relative to its divergence from D. melanogaster, depend critically on prior assumptions concerning variation in rates of molecular evolution across branches, and hence have not been reliably determined. We discuss methodological issues that limit phylogenetic resolution - even when complete genome sequences are available - as well as the utility of the current phylogeny for understanding the evolutionary and biogeographic history of this clade.

The effects of genetic background on exercise performance in Drosophila

The use of the Drosophila model for studying the broad beneficial effects of exercise training has grown over the past decade. As work using Drosophila as an exercise model becomes more widespread, the influence of genetic background on performance should be examined in order to better understand its influence on assessments used to quantitatively measure and compare exercise phenotypes. In this article, we review the various methods of exercise training Drosophila, and the performance of different wild-type Drosophila strains on various physiological assessments of exercise response. We conclude by summarizing the performance trends of commonly used strains.

Conservation of gene architecture and domains amidst sequence divergence in the hsrω lncRNA gene across the Drosophila genus: an in silico analysis

The developmentally active and cell-stress responsive hsrω locus in Drosophila melanogaster carries two exons, one omega intron, one short translatable open reading frame (ORFω), long stretch of unique tandem repeats and an overlapping mir-4951 near its 30' end. It produces multiple long noncoding RNAs (lncRNAs) using two transcription start and four termination sites. Earlier cytogenetic studies revealed functional conservation of hsrω in several Drosophila species. However, sequence analysis in three species showed poor conservation for ORFω, tandem repeat and other regions while the 16 nt at 50 and 60 nt at 30 splice junctions of the omega intron, respectively, were found to be ultra-conserved. The present bioinformatic study using the splice-junction landmarks in D. melanogaster hsrω identified orthologues in publicly available 34 Drosophila species genomes. Each orthologue carries a short ORFω, ultra-conserved splice junctions of omega intron, repeat region, conserved 30'end located at mir-4951, and syntenic neighbours. Multiple copies of conserved nonamer motifs are seen in the tandem repeat region, despite a high variability in the repeat sequences. Intriguingly, only the omega intron sequences in different species show evolutionary relationships matching the general phylogenetic history in the genus. Search in other known insect genomes did not reveal sequence homology although a locus with similar functional properties is suggested in Chironomus and Ceratitis genera. Amidst the high sequence divergence, the conserved organization of exons, ORFω and omega intron in this gene's proximal part and tandem repeats in distal part across the Drosophila genus is remarkable and possibly reflects functional importance of higher order structure of hsrω lncRNAs and the small omega peptide.

Whole genome experimental maps of DNA G-quadruplexes in multiple species

Genomic maps of DNA G-quadruplexes (G4s) can help elucidate the roles that these secondary structures play in various organisms. Herein, we employ an improved version of a G-quadruplex sequencing method (G4-seq) to generate whole genome G4 maps for 12 species that include widely studied model organisms and also pathogens of clinical relevance. We identify G4 structures that form under physiological K+ conditions and also G4s that are stabilized by the G4-targeting small molecule pyridostatin (PDS). We discuss the various structural features of the experimentally observed G-quadruplexes (OQs), highlighting differences in their prevalence and enrichment across species. Our study describes diversity in sequence composition and genomic location for the OQs in the different species and reveals that the enrichment of OQs in gene promoters is particular to mammals such as mouse and human, among the species studied. The multi-species maps have been made publicly available as a resource to the research community. The maps can serve as blueprints for biological experiments in those model organisms, where G4 structures may play a role.

An investigation of the molecular and biochemical basis underlying chlorantraniliprole-resistant Drosophila strains and their cross-resistance to other insecticides

Chlorantraniliprole is an anthranilic diamide insecticide that binds to the insect ryanodine receptor (RyR) and induces an uncontrolled release of Ca²⁺ , resulting in paralysis and ultimately death of the target insects. Recently, it was reported that chlorantraniliprole-resistant diamondback moths, Plutella xylostella Linnaeus, have mutations in their RyR. In this study, we developed two different chlorantraniliprole-resistant Drosophila melanogaster strain. The resistance ratio (RR) of the low-concentration chlorantraniliprole-treated resistant (Low-Res) strain was 2.3, while that of the high-concentration chlorantraniliprole-treated resistant (High-Res) strain was 21.3. The LC ₅₀ of the untreated control (Con) strain was 23.8~25.9 ppm, which was significantly higher than that reported for the susceptible diamondback moth (0.03~0.51 ppm). The high LC ₅₀ of the Con may be because the helix S2 amino acid sequence of D. melanogaster RyR ( DmRyR) is identical to the I4790M mutation of the chlorantraniliprole-resistant diamondback moths, resulting in a lower binding affinity of DmRyR for chlorantraniliprole. Among the tested detoxification enzymes, the activity of esterase was significantly increased in the two Res strains, but glutathione S-transferases and acetylcholinesterase were significantly decreased in the two Res strains. The cross-resistance of the High-Res strain to other insecticides with different modes of actions (MoAs) revealed that the RRs of the neuronal acetylcholine receptor allosteric and competitive modulators were significantly increased, while those of the Na ²⁺ channel modulators were significantly reduced. Our studies showed that RRs against the same insecticide vary with the treatment concentration, and that RRs against other insecticides with different MoAs can be altered.

A new A-P compartment boundary and organizer in holometabolous insect wings

Decades of research on the highly modified wings of Drosophila melanogaster has suggested that insect wings are divided into two Anterior-Posterior (A-P) compartments separated by an axis of symmetry. This axis of symmetry is created by a developmental organizer that establishes symmetrical patterns of gene expression that in turn pattern the A-P axis of the wing. Butterflies possess more typical insect wings and butterfly wing colour patterns provide many landmarks for studies of wing structure and development. Using eyespot colour pattern variation in Vanessa butterflies, here we show an additional A-P axis of symmetry running between wing sectors 3 and 4. Boundaries of Drosophila mitotic clones suggest the existence of a previously undetected Far-Posterior (F-P) compartment boundary that coincides with this additional A-P axis. A similar compartment boundary is evident in butterfly mosaic gynandromorphs. We suggest that this additional compartment boundary and its associated developmental organizer create an axis of wing colour pattern symmetry and a gene expression-based combinatorial code, permitting each insect wing compartment to acquire a unique identity and allowing for the individuation of butterfly eyespots.

Measuring thermal behavior in smaller insects: A case study in Drosophila melanogaster demonstrates effects of sex, geographic origin, and rearing temperature on adult behavior

Measuring thermal behavior in smaller insects is particularly challenging. In this study, we describe a new horizontal thermal gradient apparatus designed to study adult thermal behavior in small insects and apply it using D. melanogaster as a model and case study. Specifically, we used this apparatus and associated methodology to examine the effects of sex, geographic origin, and developmental rearing temperature on temperature preferences exhibited by adults in a controlled laboratory environment. The thermal gradient established by the apparatus was stable over diurnal and calendar time. Furthermore, the distribution of adult flies across thermal habitats within the apparatus remained stable following the period of acclimation, as evidenced by the high degree of repeatability across both biological and technical replicates. Our data demonstrate significant and predictable variation in temperature preference for all 3 assayed variables. Behaviorally, females were more sensitive than males to higher temperatures. Flies originating from high latitude, temperate populations exhibited a greater preference for cooler temperatures; conversely, flies originating from low latitude, tropical habitats demonstrated a relative preference for higher temperatures. Similarly, larval rearing temperature was positively associated with adult thermal behavior: low culture temperatures increased the relative adult preference for cooler temperatures, and this response was distinct between the sexes and for flies from the temperate and subtropical geographic regions. Together, these results demonstrate that the temperature chamber apparatus elicits robust, predictable, and quantifiable thermal preference behavior that could readily be applied to other taxa to examine the role of temperature-mediated behavior in a variety of contexts.

Weak Polygenic Selection Drives the Rapid Adaptation of the Chemosensory System: Lessons from the Upstream Regions of the Major Gene Families

The animal chemosensory system is involved in essential biological processes, most of them mediated by proteins encoded in multigene families. These multigene families have been fundamental for the adaptation to new environments, significantly contributing to phenotypic variation. This adaptive potential contrasts, however, with the lack of studies at their upstream regions, especially taking into account the evidence linking their transcriptional changes to certain phenotypic effects. Here, we explicitly characterize the contribution of the upstream sequences of the major chemosensory gene families to rapid adaptive processes. For that, we analyze the genome sequences of 158 lines from a population of Drosophila melanogaster that recently colonized North America, and integrate functional and transcriptional data available for this species. We find that both, strong negative and strong positive selection, shape transcriptional evolution at the genome-wide level. The chemosensory upstream regions, however, exhibit a distinctive adaptive landscape, including multiple mutations of small beneficial effect and a reduced number of cis-regulatory elements. Together, our results suggest that the promiscuous and partially redundant transcription and function of the chemosensory genes provide evolutionarily opportunities for rapid adaptive episodes through weak polygenic selection.

Selfish drive can trump function when animal mitochondrial genomes compete

Mitochondrial genomes compete for transmission from mother to progeny. We explored this competition by introducing a second genome into Drosophila melanogaster to follow transmission. Competitions between closely related genomes favored those functional in electron transport, resulting in a host-beneficial purifying selection. In contrast, matchups between distantly related genomes often favored those with negligible, negative or lethal consequences, indicating selfish selection. Exhibiting powerful selfish selection, a genome carrying a detrimental mutation displaced a complementing genome, leading to population death after several generations. In a different pairing, opposing selfish and purifying selection counterbalanced to give stable transmission of two genomes. Sequencing of recombinant mitochondrial genomes showed that the noncoding region, containing origins of replication, governs selfish transmission. Uniparental inheritance prevents encounters between distantly related genomes. Nonetheless, in each maternal lineage, constant competition among sibling genomes selects for super-replicators. We suggest that this relentless competition drives positive selection, promoting change in the sequences influencing transmission.

Dynamic BMP signaling polarized by Toll patterns the dorsoventral axis in a hemimetabolous insect

Toll-dependent patterning of the dorsoventral axis in Drosophila represents one of the best understood gene regulatory networks. However, its evolutionary origin has remained elusive. Outside the insects Toll is not known for a patterning function, but rather for a role in pathogen defense. Here, we show that in the milkweed bug Oncopeltus fasciatus, whose lineage split from Drosophila's more than 350 million years ago, Toll is only required to polarize a dynamic BMP signaling network. A theoretical model reveals that this network has self-regulatory properties and that shallow Toll signaling gradients are sufficient to initiate axis formation. Such gradients can account for the experimentally observed twinning of insect embryos upon egg fragmentation and might have evolved from a state of uniform Toll activity associated with protecting insect eggs against pathogens.

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans

Gene expression variation within species is relatively common, however, the role of natural selection in the maintenance of this variation is poorly understood. Here we investigate low and high latitude populations of Drosophila melanogaster and its sister species, D. simulans, to determine whether the two species show similar patterns of population differentiation, consistent with a role for spatially varying selection in maintaining gene expression variation. We compared at two temperatures the whole male transcriptome of D. melanogaster and D. simulans sampled from Panama City (Panama) and Maine (USA). We observed a significant excess of genes exhibiting differential expression in both species, consistent with parallel adaptation to heterogeneous environments. Moreover, the majority of genes showing parallel expression differentiation showed the same direction of differential expression in the two species and the magnitudes of expression differences between high and low latitude populations were correlated across species, further bolstering the conclusion that parallelism for expression phenotypes results from spatially varying selection. However, the species also exhibited important differences in expression phenotypes. For example, the genomic extent of genotype × environment interaction was much more common in D. melanogaster. Highly differentiated SNPs between low and high latitudes were enriched in the 3’ UTRs and CDS of the geographically differently expressed genes in both species, consistent with an important role for cis-acting variants in driving local adaptation for expression-related phenotypes.

While gene expression variation in natural populations is common, the population genetic processes responsible for the maintenance of this variation remain obscure. Here we study geographic differences in gene expression in recently established low and high latitude populations of two closely related species of Drosophila. We observe substantial parallelism in expression differences and expression plasticity between populations, which supports the idea that spatially varying selection correlated with latitude contributes to the maintenance of gene expression variation in these species. Comparison of inter-population sequence differentiation and expression differentiation suggests that cis-acting variants play a role in geographic expression differentiation.

Specific activation of an I-like element in Drosophila interspecific hybrids

The non-long terminal repeat (LTR) retrotransposon I, which belongs to the I superfamily of non-LTR retrotransposons, is well known in Drosophila because it transposes at a high frequency in the female germline cells in I-R hybrid dysgenic crosses of Drosophila melanogaster. Here, we report the occurrence and the upregulation of an I-like element in the hybrids of two sister species belonging to the repleta group of the genus Drosophila, D. mojavensis, and D. arizonae. These two species display variable degrees of pre- and postzygotic isolation, depending on the geographic origin of the strains. We took advantage of these features to explore the transposable element (TE) dynamics in interspecific crosses. We fully characterized the copies of this TE family in the D. mojavensis genome and identified at least one complete copy. We showed that this element is transcriptionally active in the ovaries and testes of both species and in their hybrids. Moreover, we showed that this element is upregulated in hybrid males, which could be associated with the male-sterile phenotype.

FB-NOF is a non-autonomous transposable element, expressed in Drosophila melanogaster and present only in the melanogaster group

Most foldback elements are defective due to the lack of coding sequences but some are associated with coding sequences and may represent the entire element. This is the case of the NOF sequences found in the FB of Drosophila melanogaster, formerly considered as an autonomous TE and currently proposed as part of the so-called FB-NOF element, the transposon that would be complete and fully functional. NOF is always associated with FB and never seen apart from the FB inverted repeats (IR). This is the reason why the FB-NOF composite element can be considered the complete element. At least one of its ORFs encodes a protein that has always been considered its transposase, but no detailed studies have been carried out to verify this. In this work we test the hypothesis that FB-NOF is an active transposon nowadays. We search for its expression product, obtaining its cDNA, and propose the ORF and the sequence of its potential protein. We found that the NOF protein is not a transposase as it lacks any of the motifs of known transposases and also shows structural homology with hydrolases, therefore FB-NOF cannot belong to the superfamily MuDR/foldback, as up to now it has been classified, and can be considered as a non-autonomous transposable element. The alignment with the published genomes of 12 Drosophila species shows that NOF presence is restricted only to the 6 Drosophila species belonging to the melanogaster group.

Widespread polymorphism in the positions of stop codons in Drosophila melanogaster

The mechanisms underlying evolutionary changes in protein length are poorly understood. Protein domains are lost and gained between species and must have arisen first as within-species polymorphisms. Here, we use Drosophila melanogaster population genomic data combined with between species divergence information to understand the evolutionary forces that generate and maintain polymorphisms causing changes in protein length in D. melanogaster. Specifically, we looked for protein length variations resulting from premature termination codons (PTCs) and stop codon losses (SCLs). We discovered that 438 genes contained polymorphisms resulting in truncation of the translated region (PTCs) and 119 genes contained polymorphisms predicted to lengthen the translated region (SCLs). Stop codon polymorphisms (SCPs) (especially PTCs) appear to be more deleterious than other polymorphisms, including protein amino acid changes. Genes harboring SCPs are in general less selectively constrained, more narrowly expressed, and enriched for dispensable biological functions. However, we also observed exceptional cases such as genes that have multiple independent SCPs, alleles that are shared between D. melanogaster and Drosophila simulans, and high-frequency alleles that cause extreme changes in gene length. SCPs likely have an important role in the evolution of these genes.

Observations of cardiac beating behaviors of wild-type and mutant Drosophilae with optical coherence tomography

Time-resolved optical coherence tomography (OCT) scanning images of wild-type and mutant fruit flies (Drosophila melanogaster), illustrating the heartbeat patterns for evaluating their cardiac functions, are demonstrated. Based on the heartbeat patterns, the beat rate and the relative phase between the first two heart segments can be evaluated. The OCT scanning results of mutant flies with impaired proteasome function in cardiac muscles show irregular heartbeat patterns and systematically decreased average beat rates, when compared with the regular patterns of ~4.97 beats/s in average beat rate of the wild-type. In both wild-type and proteasome mutant flies, the beatings at different locations in the same heart segment are essentially synchronized. However, between different heart segments, although the beating in the second segment shows a lag in phase behind that of the first segment in a wild-type, in a proteasome mutant, the beating in the second segment becomes significantly leading that of the first segment. Besides the comparison between the wild-type and proteasomal mutant flies, the influences of using different methods for immobilizing flies during OCT scanning on the heart functions are demonstrated.

Variation in the male pheromones and mating success of wild caught Drosophila melanogaster

Drosophila melanogaster males express two primary cuticular hydrocarbons (male-predominant hydrocarbons). These act as sex pheromones by influencing female receptivity to mating. The relative quantities of these hydrocarbons vary widely among natural populations and can contribute to variation in mating success. We tested four isofemale lines collected from a wild population to assess the effect of intrapopulation variation in male-predominant hydrocarbons on mating success. The receptivity of laboratory females to males of the four wild-caught lines varied significantly, but not consistently in the direction predicted by variation in male-predominant hydrocarbons. Receptivity of the wild-caught females to laboratory males also varied significantly, but females from lines with male-predominant hydrocarbon profiles closer to a more cosmopolitan one did not show a correspondingly strong mating bias toward a cosmopolitan male. Among wild-caught lines, the male-specific ejaculatory bulb lipid, cis-vaccenyl acetate, varied more than two-fold, but was not associated with variation in male mating success. We observed a strong inverse relationship between the receptivity of wild-caught females and the mating success of males from their own lines, when tested with laboratory flies of the opposite sex.

The evolution of dorsal-ventral patterning mechanisms in insects

The gene regulatory network (GRN) underpinning dorsal-ventral (DV) patterning of the Drosophila embryo is among the most thoroughly understood GRNs, making it an ideal system for comparative studies seeking to understand the evolution of development. With the emergence of widely applicable techniques for testing gene function, species with sequenced genomes, and multiple tractable species with diverse developmental modes, a phylogenetically broad and molecularly deep understanding of the evolution of DV axis formation in insects is feasible. Here, we review recent progress made in this field, compare our emerging molecular understanding to classical embryological experiments, and suggest future directions of inquiry.

Intron retention in the Drosophila melanogaster Rieske Iron Sulphur Protein gene generated a new protein

Genomes can encode a variety of proteins with unrelated architectures and activities. It is known that protein-coding genes of de novo origin have significantly contributed to this diversity. However, the molecular mechanisms and evolutionary processes behind these originations are still poorly understood. Here we show that the last 102 codons of a novel gene, Noble, assembled directly from non-coding DNA following an intronic deletion that induced alternative intron retention at the Drosophila melanogaster Rieske Iron Sulphur Protein (RFeSP) locus. A systematic analysis of the evolutionary processes behind the origin of Noble showed that its emergence was strongly biased by natural selection on and around the RFeSP locus. Noble mRNA is shown to encode a bona fide protein that lacks an iron sulphur domain and localizes to mitochondria. Together, these results demonstrate the generation of a novel protein at a naturally selected site.

Mitochondrial-nuclear epistasis affects fitness within species but does not contribute to fixed incompatibilities between species of Drosophila

Efficient mitochondrial function requires physical interactions between the proteins encoded by the mitochondrial and nuclear genomes. Coevolution between these genomes may result in the accumulation of incompatibilities between divergent lineages. We test whether mitochondrial-nuclear incompatibilities have accumulated within the Drosophila melanogaster species subgroup by combining divergent mitochondrial and nuclear lineages and quantifying the effects on relative fitness. Precise placement of nine mtDNAs from D. melanogaster, D. simulans, and D. mauritiana into two D. melanogaster nuclear genetic backgrounds reveals significant mitochondrial-nuclear epistasis affecting fitness in females. Combining the mitochondrial genomes with three different D. melanogaster X chromosomes reveals significant epistasis for male fitness between X-linked and mitochondrial variation. However, we find no evidence that the more than 500 fixed differences between the mitochondrial genomes of D. melanogaster and the D. simulans species complex are incompatible with the D. melanogaster nuclear genome. Rather, the interactions of largest effect occur between mitochondrial and nuclear polymorphisms that segregate within species of the D. melanogaster species subgroup. We propose that a low mitochondrial substitution rate, resulting from a low mutation rate and/or efficient purifying selection, precludes the accumulation of mitochondrial-nuclear incompatibilities among these Drosophila species.

Research on the karyotype and evolution of Drosophila melanogaster species group

Mitotic metaphase chromosomes of 34 species of Drosophila melanogaster species group were examined. Certain new karyotypes were described for the first time, and their evolutionary and interspecific genetic relationships among 8 subgroups of D. melanogaster species group were analyzed systematically. The results were as follows. The basic karyotype of elegans subgroup was type A. The karyotypes of eugracilis subgroup, melanogaster subgroup, and ficusphila subgroup were all type C. The karyotypes of takahashii subgroup and suzukii subgroup were both type C and type D. The montium subgroup had six kinds of karyotypes: types B, C, C', D, D', and E. The ananassae subgroup had three kinds of karyotypes: types F, G, and H. Thus, the melanogaster species group was classified into five pedigrees based on the diversity of these karyotypes: 1) elegans; 2) eugracilis-melanogaster-ficusphila; 3) takkahashii-suzukii; 4) montium; 5) ananassae. The above-mentioned results in karyotypic evolution were consistent with those of DNA sequence analysis reported by Yang except for the elegans subgroup and this subgroup was considered as the ancestral subgroup. Karyotype analysis of the same drosophila from different isofemale lines indicated that the same Drosophila from different places showed karyotypic variation which might be due to different geographical environment and evolutionary degree or interaction between the two factors.

Evolutionary origin of the tumor suppressor hyperplastic discs protein

Previous evolutionary study of the tumor suppressor Merlin revealed that this protein family was produced by very early metazoans with the exception of some or all flatworm lineages [Golovnina et al., 2005]. We ask whether other tumor-suppressor proteins had also been in existence in these times and focus our attention on hyperplastic discs (Hyd) protein, a classic tumor suppressor in Drosophila melanogaster which, when mutated, may cause over-proliferation and malignancy. Phylogenetic analysis of the Hyd protein indicates that it was present among metazoa by the time Trichoplax adhaerens had emerged from the common unicellular ancestor of the Animalia.

Duplication and gene conversion in the Drosophila melanogaster genome

Using the genomic sequences of Drosophila melanogaster subgroup, the pattern of gene duplications was investigated with special attention to interlocus gene conversion. Our fine-scale analysis with careful visual inspections enabled accurate identification of a number of duplicated blocks (genomic regions). The orthologous parts of those duplicated blocks were also identified in the D. simulans and D. sechellia genomes, by which we were able to clearly classify the duplicated blocks into post- and pre-speciation blocks. We found 31 post-speciation duplicated genes, from which the rate of gene duplication (from one copy to two copies) is estimated to be 1.0 x 10(-9) per single-copy gene per year. The role of interlocus gene conversion was observed in several respects in our data: (1) synonymous divergence between a duplicated pair is overall very low. Consequently, the gene duplication rate would be seriously overestimated by counting duplicated genes with low divergence; (2) the sizes of young duplicated blocks are generally large. We postulate that the degeneration of gene conversion around the edges could explain the shrinkage of "identifiable" duplicated regions; and (3) elevated paralogous divergence is observed around the edges in many duplicated blocks, supporting our gene conversion-degeneration model. Our analysis demonstrated that gene conversion between duplicated regions is a common and genome-wide phenomenon in the Drosophila genomes, and that its role should be especially significant in the early stages of duplicated genes. Based on a population genetic prediction, we applied a new genome-scan method to test for signatures of selection for neofunctionalization and found a strong signature in a pair of transporter genes.

Genetic variability and robustness of host odor preference in Drosophila melanogaster

Chemosensory stimuli play a crucial role for host selection in insects, including the fruit fly Drosophila melanogaster. Drosophila has been instrumental in unraveling the neurological basis of olfactory processing in insects. Basic knowledge regarding chemical ecology and thorough studies of olfactory preferences are still lacking to a great extent in D. melanogaster, however. We have characterized repeatable variation in olfactory preference between five classical D. melanogaster wild-type strains toward a large array of natural host odors and synthetic compounds. By recording the rate of attraction over up to 24 hr, we could compare stimuli varying in attractiveness and characterize phenotypic parameters on the basis of individual stimuli and the whole stimulus array. Behavioral differences between strains were predominantly due to variation in a single phenotypic parameter: their overall responsiveness toward optimal and suboptimal olfactory stimuli. These differences were not explained by variation in olfactory sensitivity, locomotory activity, or general vigor monitored by survival. Comparisons with three recently established wild-type strains indicated that a high behavioral threshold against accepting suboptimal olfactory stimuli is the characteristic phenotype of wild D. melanogaster.

Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster

We describe here the Drosophila gene hydra that appears to have originated de novo in the melanogaster subgroup and subsequently evolved in both structure and expression level in Drosophila melanogaster and its sibling species. D. melanogaster hydra encodes a predicted protein of ~300 amino acids with no apparent similarity to any previously known proteins. The syntenic region flanking hydra on both sides is found in both D. ananassae and D. pseudoobscura, but hydra is found only in melanogaster subgroup species, suggesting that it originated less than ~13 million y ago. Exon 1 of hydra has undergone recurrent duplications, leading to the formation of nine tandem alternative exon 1s in D. melanogaster. Seven of these alternative exons are flanked on their 3′ side by the transposon DINE-1 (Drosophila interspersed element-1). We demonstrate that at least four of the nine duplicated exon 1s can function as alternative transcription start sites. The entire hydra locus has also duplicated in D. simulans and D. sechellia. D. melanogaster hydra is expressed most intensely in the proximal testis, suggesting a role in late-stage spermatogenesis. The coding region of hydra has a relatively high Ka/Ks ratio between species, but the ratio is less than 1 in all comparisons, suggesting that hydra is subject to functional constraint. Analysis of sequence polymorphism and divergence of hydra shows that it has evolved under positive selection in the lineage leading to D. melanogaster. The dramatic structural changes surrounding the first exons do not affect the tissue specificity of gene expression: hydra is expressed predominantly in the testes in D. melanogaster, D. simulans, and D. yakuba. However, we have found that expression level changed dramatically (~ >20-fold) between D. melanogaster and D. simulans. While hydra initially evolved in the absence of nearby transposable element insertions, we suggest that the subsequent accumulation of repetitive sequences in the hydra region may have contributed to structural and expression-level evolution by inducing rearrangements and causing local heterochromatinization. Our analysis further shows that recurrent evolution of both gene structure and expression level may be characteristics of newly evolved genes. We also suggest that late-stage spermatogenesis is the functional target for newly evolved and rapidly evolving male-specific genes.

Similar groups of animals have similar numbers of genes, but not all of these genes are the same. While some genes are highly conserved and can be easily and uniquely identified in species ranging from yeast to plants to humans, other genes are sometimes found in only a small number or even in a single species. Such newly evolved genes may help produce traits that make species unique. We describe here a newly evolved gene called hydra that occurs only in a small subgroup of Drosophila species. hydra is expressed in the testes, suggesting that it may have a function in male fertility. hydra has evolved significantly in its structure and protein-coding sequence among species. The authors named the gene hydra after the nine-headed monster slain by Hercules because in one species, Drosophila melanogaster, hydra has nine potential alternative first exons. Perhaps because of this or other structural changes, the level of RNA made by hydra differs significantly between one pair of species. This analysis reveals that newly created genes may evolve rapidly in sequence, structure, and expression level.

[Molecular-cytogenetic analysis of pericentromeric heterochromatin in ovarian nurse cells of Drosophila melanogaster subgroup species]

Evolutionary rearrangements of pericentromeric heterochromatin among Drosophila melanogaster subgroup species have been investigated. Region-specific DNA library from Drosophila orena ovarian nurse cell chromocenter has been obtained by microdissection of polytene chromosomes. The probe was localized on ovarian nurse cells chromosomes of D. melanogaster subgroup species using fluorescent in situ hybridization. Sequences homologous to the sequences of the DNA-probe were found in chromocenter and pericentromeric regions of D. orena polytene chromosomes; and in all pericentromeric regions of other species with several exceptions. So, there was no labeling on one of the arms of D. simulans chromosome 2 but such sequences were present on telomere of D. erecta chromosome 3 and in regions adjacent to the brightly DAPI-stained heterochromatic blocks of D. yakuba, D. santomea and D. teissieri chromosomes 2 and 3. At S6 stage (secondary reticulate nucleus), the labeled chromatin in D. orena could be found mostly within a restricted area and no such chromatin could be detected throughout the rest of the nucleus. On the contrary, the labeled DNA was spread diffusely in the nuclei of other species at this stage.

Evolution of gene sequence in response to chromosomal location

Evolutionary forces acting on the repetitive DNA of heterochromatin are not constrained by the same considerations that apply to protein-coding genes. Consequently, such sequences are subject to rapid evolutionary change. By examining the Troponin C gene family of Drosophila melanogaster, which has euchromatic and heterochromatic members, we find that protein-coding genes also evolve in response to their chromosomal location. The heterochromatic members of the family show a reduced CG content and increased variation in DNA sequence. We show that the CG reduction applies broadly to the protein-coding sequences of genes located at the heterochromatin:euchromatin interface, with a very strong correlation between CG content and the distance from centric heterochromatin. We also observe a similar trend in the transition from telomeric heterochromatin to euchromatin. We propose that the methylation of DNA is one of the forces driving this sequence evolution.

Can artificially selected phenotypes influence a component of field fitness? Thermal selection and fly performance under thermal extremes

Artificially selected lines are widely used to investigate the genetic basis of quantitative traits and make inferences about evolutionary trajectories. Yet, the relevance of selected traits to field fitness is rarely tested. Here, we assess the relevance of thermal stress resistance artificially selected in the laboratory to one component of field fitness by investigating the likelihood of adult Drosophila melanogaster reaching food bait under different temperatures. Lines resistant to heat reached the bait more often than controls under hot and cold conditions, but less often at intermediate temperatures, suggesting a fitness cost of increased heat resistance but not at temperature extremes. Cold-resistant lines were more common at baits than controls under cold as well as hot field conditions, and there was no cost at intermediate temperatures. One of the replicate heat-resistant lines was caught less often than the others under hot conditions. Direct and correlated patterns of responses in laboratory tests did not fully predict the low performance of the heat selected lines at intermediate temperatures, nor the high performance of the cold selected lines under hot conditions. Therefore, lines selected artificially not only behaved partly as expected based on laboratory assays but also evolved patterns only evident in the field releases.

Evolutionary pathways of the tirant LTR retrotransposon in the Drosophila melanogaster subgroup of species

Tirant, a LTR retrotransposon with copies scattered over the chromosome arms of Drosophila melanogaster, is in the process of being lost from the chromosome arms of most natural populations of the sister species D. simulans. In an attempt to clarify the dynamics and evolution of tirant, we have studied the regulatory and reverse transcriptase regions in copies of the nine closely related species of the D. melanogaster subgroup. We show that tirant is mainly vertically transmitted in these species, with the exception of a horizontal transfer event from an ancestor of D. melanogaster to D. teissieri. We propose that, in four of the species (D. melanogaster, D. simulans, D. sechellia, and D. mauritiana), the observed patterns of evolution of the regulatory region vary with genome constraints and with the history and biogeography of the species.

Testing chromosomal phylogenies and inversion breakpoint reuse in Drosophila

A combination of cytogenetic and bioinformatic procedures was used to test the chromosomal phylogeny relating Drosophila buzzatii with D. repleta. Chromosomes X and 2, harboring most of the inversions fixed between these two species, were analyzed. First, chromosomal segments conserved during the divergence of the two species were identified by comparative in situ hybridization to the D. repleta chromosomes of 180 BAC clones from a BAC-based physical map of the D. buzzatii genome. These conserved segments were precisely delimited with the aid of clones containing inversion breakpoints. Then GRIMM software was used to estimate the minimum number of rearrangements necessary to transform one genome into the other and identify all possible rearrangement scenarios. Finally, the most plausible inversion trajectory was tested by hybridizing 12 breakpoint-bearing BAC clones to the chromosomes of seven other species in the repleta group. The results show that chromosomes X and 2 of D. buzzatii and D. repleta differ by 12 paracentric inversions. Nine of them are fixed in chromosome 2 and entail two breakpoint reuses. Our results also show that the cytological relationship between D. repleta and D. mercatorum is closer than that between D. repleta and D. peninsularis, and we propose that the phylogenetic relationships in this lineage of the repleta group be reconsidered. We also estimated the rate of rearrangement between D. repleta and D. buzzatii and conclude that rates within the genus Drosophila vary substantially between lineages, even within a single species group.

History and structure of sub-Saharan populations of Drosophila melanogaster

Drosophila melanogaster is an important model organism in evolutionary genetics, yet little is known about the population structure and the demographic history of this species within sub-Saharan Africa, which is thought to contain its ancestral range. We surveyed nucleotide variation at four 1-kb fragments in 240 individual lines representing 21 sub-Saharan and 4 Palearctic population samples of D. melanogaster. In agreement with recent studies, we find a small but significant level of genetic differentiation within sub-Saharan Africa. A clear geographic pattern is observed, with eastern and western African populations composing two genetically distinct groups. This pattern may have resulted from a relatively recent establishment of D. melanogaster in western Africa. Eastern populations show greater evidence for long-term stability, consistent with the hypothesis that eastern Africa contains the ancestral range of the species. Three sub-Saharan populations show evidence for cosmopolitan introgression. Apart from those cases, the closest relationships between Palearctic and sub-Saharan populations involve a sample from the rift zone (Uganda), suggesting that the progenitors of Palearctic D. melanogaster might have come from this region. Finally, we find a large excess of singleton polymorphisms in the full data set, which is best explained by a combination of population growth and purifying selection.

Does lack of recombination enhance asymmetric evolution among duplicate genes? Insights from the Drosophila melanogaster genome

Gene duplication has different outcomes: pseudogenization (death of one of the two copies), gene amplification (both copies remain the same), sub-functionalization (both copies are required to perform the ancestral function) and neo-functionalization (one copy acquires a new function). Asymmetric evolution (one copy evolves faster than the other) is usually seen as a signature of neo-functionalization. However, it has been proposed that sub-functionalization could also generate asymmetric evolution among duplicate genes when they experience different local recombination rates. Indeed, the low recombination copy is expected to evolve faster because of Hill-Robertson effects. Here we tested this idea with about 100 pairs of young duplicates from the Drosophila melanogaster genome. Looking only at young duplicates allowed us to compare recombination rates and evolutionary rates on a similar time-scale contrary to previous work. We found that dispersed pairs tend to evolve more asymmetrically than tandem ones. Among dispersed copies, the low recombination copy tends to be the fast-evolving one. We also tested the possibility that all this was explained by a confounding factor (expression level) but found no evidence for it. In conclusion, our results do support the idea that asymmetric evolution among duplicates is enhanced by restricted recombination. However, further work is needed to clearly distinguish between sub-functionalization and neo-functionalization for the asymmetrically-evolving duplicate pairs that we found.

Evolutionary pattern of the gtwin retrotransposon in the Drosophila melanogaster subgroup

The gtwin retrotransposon was recently discovered in the Drosophila melanogaster genome and it is evolutionarily closer to gypsy endogenous retrovirus. This study has identified gtwin homologous sequences in the genome of D. simulans, D. sechellia, D. erecta and D. yakuba by performing homology searches against the public genome database of Drosophila species. The phylogenetic analyses of the gtwin env gene sequences of these species have shown some incongruities with the host species phylogeny, suggesting some horizontal transfer events for this retroelement. Moreover, we reported the existence of DNA sequences putatively encoding full-length Env proteins in the genomes of Drosophila species other than D. melanogaster. The results suggest that the gtwin element may be an infectious retrovirus able to invade the genome of new species, supporting the gtwin evolutionary picture shown in this work.

Altitudinal patterns for latitudinally varying traits and polymorphic markers in Drosophila melanogaster from eastern Australia

Altitudinal changes in traits and genetic markers can complement the studies on latitudinal patterns and provide evidence of natural selection because of climatic factors. In Drosophila melanogaster, latitudinal variation is well known but altitudinal patterns have rarely been investigated. Here, we examine five traits and five genetic markers on chromosome 3R in D. melanogaster collected at high and low altitudes from five latitudes along the eastern coast of Australia. Significant altitudinal differentiation was observed for cold tolerance, development time, ovariole number in unmated females, and the microsatellite marker DMU25686. Differences tended to match latitudinal patterns, in that trait values at high altitudes were also found at high latitudes, suggesting that factors linked to temperature are likely selective agents. Cold tolerance was closely associated with average temperature and other climatic factors, but no significant associations were detected for the other traits. Genes around DMU25686 represent good candidates for climatic adaptation.

BLISS: binding site level identification of shared signal-modules in DNA regulatory sequences

Background

Regulatory modules are segments of the DNA that control particular aspects of gene expression. Their identification is therefore of great importance to the field of molecular genetics. Each module is composed of a distinct set of binding sites for specific transcription factors. Since experimental identification of regulatory modules is an arduous process, accurate computational techniques that supplement this process can be very beneficial. Functional modules are under selective pressure to be evolutionarily conserved. Most current approaches therefore attempt to detect conserved regulatory modules through similarity comparisons at the DNA sequence level. However, some regulatory modules, despite the conservation of their responsible binding sites, are embedded in sequences that have little overall similarity.

Results

In this study, we present a novel approach that detects conserved regulatory modules via comparisons at the binding site level. The technique compares the binding site profiles of orthologs and identifies those segments that have similar (not necessarily identical) profiles. The similarity measure is based on the inner product of transformed profiles, which takes into consideration the p values of binding sites as well as the potential shift of binding site positions. We tested this approach on simulated sequence pairs as well as real world examples. In both cases our technique was able to identify regulatory modules which could not to be identified using sequence-similarity based approaches such as rVista 2.0 and Blast.

Conclusion

The results of our experiments demonstrate that, for sequences with little overall similarity at the DNA sequence level, it is still possible to identify conserved regulatory modules based solely on binding site profiles.

Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison

Non-coding DNA comprises approximately 80% of the euchromatic portion of the Drosophila melanogaster genome. Non-coding sequences are known to contain functionally important elements controlling gene expression, but the proportion of sites that are selectively constrained is still largely unknown. We have compared the complete D. melanogaster and Drosophila simulans genome sequences to estimate mean selective constraint (the fraction of mutations that are eliminated by selection) in coding and non-coding DNA by standardizing to substitution rates in putatively unconstrained sequences. We show that constraint is positively correlated with intronic and intergenic sequence length and is generally remarkably strong in non-coding DNA, implying that more than half of all point mutations in the Drosophila genome are deleterious. This fraction is also likely to be an underestimate if many substitutions in non-coding DNA are adaptively driven to fixation. We also show that substitutions in long introns and intergenic sequences are clustered, such that there is an excess of substitutions <8 bp apart and a deficit farther apart. These results suggest that there are blocks of constrained nucleotides, presumably involved in gene expression control, that are concentrated in long non-coding sequences. Furthermore, we infer that there is more than three times as much functional non-coding DNA as protein-coding DNA in the Drosophila genome. Most deleterious mutations therefore occur in non-coding DNA, and these may make an important contribution to a wide variety of evolutionary processes.

The phylogeny of the subgroups within the melanogaster species group: likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny

The relationships among the majority of the subgroups in the Drosophila melanogaster species group remain unresolved. We present a 2223basepair dataset for mitochondrial cytochrome oxidase I and cytochrome oxidase II for 43 species (including new data from 11 species), sampled to include the major subgroups. After a brief review of competing hypotheses for the ananassae, montium, suzukii, and takahashii subgroups, we combine the two genes based on a new use of the SH test and present KH and SH likelihood comparisons (Kishino and Hasegawa, 1989. J. Mol. Evol. 29, 170-179; Shimodaira and Hasegawa, 1999) to test the monophyly and placement of these subgroups within the larger species group. Although we find insignificant differences between the two suggested placements for the ananassae subgroup, the ananassae is sister to the rest of the subgroups in the melanogaster species group in every investigation. For the takahashii subgroup, although we cannot reject monophyly, the species are so closely related to the suzukii subgroup for these data that the two subgroups often form one clade. Finally, we present a Bayesian estimate of the phylogeny for both genes combined, utilizing a recently published method that allows for different models of evolution for different sites.

Identification of one intron loss and phylogenetic evolution of Dfak gene in the Drosophila melanogaster species group

Intron loss and its evolutionary significance have been noted in Drosophila. The current study provides another example of intron loss within a single-copy Dfak gene in Drosophila. By using polymerase chain reaction (PCR), we amplified about 1.3 kb fragment spanning intron 5-10, located in the position of Tyr kinase (TyK) domain of Dfak gene from Drosophila melanogaster species group, and observed size difference among the amplified DNA fragments from different species. Further sequencing analysis revealed that D. melanogaster and D. simulans deleted an about 60 bp of DNA fragment relative to other 7 Drosophila species, such as D. elegans, D. ficusphila, D. biarmipes, D. takahashii, D. jambulina, D. prostipennis and D. pseudoobscura, and the deleted fragment located precisely in the position of one intron. The data suggested that intron loss might have occurred in the Dfak gene evolutionary process of D. melanogaster and D. simulans of Drosophila melanogaster species group. In addition, the constructed phylogenetic tree based on the Dfak TyK domains clearly revealed the evolutionary relationships between subgroups of Drosophila melanogaster species group, and the intron loss identified from D. melanogaster and D. simulans provides a unique diagnostic tool for taxonomic classification of the melanogaster subgroup from other group of genus Drosophila.

Systematic analysis of the visual projection neurons ofDrosophila melanogaster. I. Lobula-specific pathways

In insects, visual information is processed in the optic lobe and conveyed to the central brain. Although neural circuits within the optic lobe have been studied extensively, relatively little is known about the connection between the optic lobe and the central brain. To understand how visual information is read by the neurons of the central brain, and what kind of centrifugal neurons send the control signal from the central brain to the optic lobe, we performed a systematic analysis of the visual projection neurons that connect the optic lobe and the central brain of Drosophila melanogaster. By screening approximately 4,000 GAL4 enhancer-trap strains we identified 44 pathways. The overall morphology and the direction of information of each pathway were investigated by expressing cytoplasmic and presynapsis-targeted fluorescent reporters. A canonical nomenclature system was introduced to describe the area of projection in the central brain. As the first part of a series of articles, we here describe 14 visual projection neurons arising specifically from the lobula. Eight pathways form columnar arborization in the lobula, whereas the remaining six form tangential or tree-like arborization. Eleven are centripetal pathways, among which nine terminate in the ventrolateral protocerebrum. Terminals of each columnar pathway form glomerulus-like structures in different areas of the ventrolateral protocerebrum. The posterior lateral protocerebrum and the optic tubercle were each contributed by a single centripetal pathway. Another pathway connects the lobula on each side of the brain. Two centrifugal pathways convey signals from the posterior lateral protocerebrum to the lobula.

Fruitless specifies sexually dimorphic neural circuitry in the Drosophila brain

The Drosophila fruitless (fru) gene product Fru has been postulated to be a neural sex determination factor that directs development of the central nervous system (CNS), thereby producing male-typical courtship behaviour and inducing male-specific muscle. Male-specific Fru protein is expressed in small groups of neurons scattered throughout the CNS of male, but not female, Drosophila. Collectively, these observations suggest that Fru 'masculinizes' certain neurons, thereby establishing neural substrates for male-typical behaviour. However, specific differences between neurons resulting from the presence or absence of Fru are unknown. Previous studies have suggested that Fru might result in sexual differences in the CNS at the functional level, as no overt sexual dimorphism in CNS structure was discernible. Here we identify a subset of fru-expressing interneurons in the brain that show marked sexual dimorphism in their number and projection pattern. We also demonstrate that Fru supports the development of neurons with male-specific dendritic fields, which are programmed to die during female development as a result of the absence of Fru. Thus, Fru expression can produce a male-specific neural circuit, probably used during heterosexual courtship, by preventing cell death in identifiable neurons.

I element distribution in mitotic heterochromatin of Drosophila melanogaster reactive strains: identification of a specific site which is correlated with the reactivity levels

The I factor is a Drosophila melanogaster LINE-like element that efficiently transposes in the genetic system of I-R hybrid dysgenesis. It has been suggested that some of the I-related sequences located in the heterochromatin of D. melanogaster are involved in the regulation of I factor activity. In this work we have performed fluorescent in situ hybridization (FISH) mapping of I element sequences in mitotic heterochromatin of nine differentially reactive D. melanogaster strains. The results of our analysis showed that a single hybridization site mapping to region h28 of the distal heterochromatin of the X chromosome is present in three strains with low or intermediate levels of reactivity, while it is undetectable in six highly reactive strains. Together, these observations suggest a negative correlation between I sequences located at h28 and the level of reactivity. To this regard, it is intriguing that flamenco and COM, two loci that regulate the activity of D. melanogaster endogenous retroviruses also map to the distal heterochromatin of the X chromosome. Our data represent the first experimental evidence in favour of a silencing effect exerted by naturally occurring I element sequences located in pericentromeric heterochromatin.

Evolutionary forces generating sequence homogeneity and heterogeneity within retrotransposon families

Genome projects allow us to sample copies of a retrotransposon sequence family residing in a host genome. The variation in DNA sequence between these individual copies will reflect the evolutionary process that has spread the sequences through the genome. Here I review quantitatively the expected diversity of elements belonging to a transposable genetic element family. I use a simple neutral model for replicative mobile DNAs such as retrotransposons to predict the extent of sequence variability between members of a single family of transposable elements, both within and between species. The effects of horizontal transfer are also explored. I also consider the impact on these distributions of an increase in transposition rate arising from a mutational change in copy of the sequence. In addition, I consider the question of the interaction between retrotransposons and their hosts, and the causes of the abundance of transposable elements in the genomes that they occupy.

Fixed and unstable I-related transposable elements in heterochromatin of Drosophila melanogaster

Transposable elements are disproportionately abundant in the heterochromatin of Drosophila melanogaster. Among the forces contributing to this bias in genomic distribution, fixation due to positive selection has been put forward. We have studied I-related elements which are located in pericentromeric heterochromatin and are believed to have a role in the control of active I elements. Flies straight from the wild have been studied where fixed elements are expected to emerge clearly over the highly polymorphic background in the genomic distribution of transposable elements. The results show that some restriction fragments due to I-related elements are conserved in size and are present in all individuals tested, consistent with a selective pressure for a role. Other fragments are polymorphic in presence/absence and intensity in individuals from the wild but appear homogeneous in laboratory stocks. Although the significance of this type of instability is unclear, the finding that these polymorphic bands are recurrent in populations from distant geographical locations is also suggestive of a selective pressure for a role.

Evolution of heterochromatic genes of Drosophila

Heterochromatin is generally associated with gene silencing, yet in Drosophila melanogaster, heterochromatin harbors hundreds of functional protein-encoding genes, some of which depend on heterochromatin for expression. Here we document a recent evolutionary transition of a gene cluster from euchromatin to heterochromatin, which occurred <20 million years ago in the drosophilid lineage. This finding reveals evolutionary fluidity between these two genomic compartments and provides a powerful approach to identifying differences between euchromatic and heterochromatic genes. Promoter mapping of orthologous gene pairs led to the discovery of the "slippery promoter," characterized by multiple transcriptional start sites predominantly at adenines, as a common promoter type found in both heterochromatic and euchromatic genes of Drosophila. Promoter type is diverse within the gene cluster but largely conserved between heterochromatic and euchromatic genes, eliminating the hypothesis that adaptation to heterochromatin required major alterations in promoter structure. Transition to heterochromatin is consistently associated with gene expansion due to the accumulation of transposable elements and increased A-T content. We conclude that heterochromatin-dependent regulation requires specialized enhancers or higher-order interactions and propose a facilitating role for transposable elements.

Rapid evolution of genomic Acp complement in the melanogaster subgroup of Drosophila

Unusual properties of molecular evolution in reproduction-related Drosophila genes, including atypically rapid rates of protein evolution, support the idea that natural selection plays an important role in divergence of reproductive function in Drosophila. We used subtractive hybridization to investigate another potential side of evolution of the male reproductive transcriptome. We carried out a screen for genes with much greater transcript abundance in Drosophila simulans reproductive tracts than in Drosophila melanogaster reproductive tracts. Such genes could be present in both species but diverged dramatically in transcript abundance or could be present in D. simulans but absent from D. melanogaster. Here we report data from melanogaster subgroup species for three previously unknown accessory gland protein genes (Acps) identified in this screen. We found multiple Acps that were present in some lineages yet absent from other closely related melanogaster subgroup lineages, representing several losses of genes. An Acp that may have been lost in D. melanogaster and Drosophila erecta is segregating a null allele in Drosophila yakuba, yet shows evidence of adaptive protein evolution in contrasts of polymorphism and divergence within and between D. yakuba and its close relative, Drosophila teissieri. These data suggest that turnover of Acps occurs rapidly in Drosophila, consistent with rapid evolution of seminal fluid function.

Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation

Identifying regions of the Drosophila melanogaster genome that have been recent targets of positive Darwinian selection will provide evidence for adaptations that have helped this species to colonize temperate habitats. We have begun a search for such genomic regions by analyzing multiple loci (about 250) dispersed across the X chromosome in a putatively ancestral population from East Africa and a derived European population. For both populations we found evidence for past changes in population size. We estimated that a major bottleneck associated with the colonization of Europe occurred about 3,500-16,000 years ago. We also found that while this bottleneck can account for most of the reduction in variation observed in the European sample, there is a deficit of polymorphism in some genomic regions that cannot be explained by demography alone.

Entropy and GC Content in the beta-esterase gene cluster of the Drosophila melanogaster subgroup

We perform spectral entropy and GC content analyses in the beta-esterase gene cluster, including the Est-6 gene and the psiEst-6 putative pseudogene, in seven species of the Drosophila melanogaster species subgroup. psiEst-6 combines features of functional and nonfunctional genes. The spectral entropies show distinctly lower structural ordering for psiEst-6 than for Est-6 in all species studied. Our observations agree with previous results for D. melanogaster and provide additional support to our hypothesis that after the duplication event Est-6 retained the esterase-coding function and its role during copulation, while psiEst-6 lost that function but now operates in conjunction with Est-6 as an intergene. Entropy accumulation is not a completely random process for either gene. Structural entropy is nucleotide dependent. The relative normalized deviations for structural entropy are higher for G than for C nucleotides. The entropy values are similar for Est-6 and psiEst-6 in the case of A and T but are lower for Est-6 in the case of G and C. The GC content in synonymous positions is uniformly higher in Est-6 than in psiEst-6, which agrees with the reduced GC content generally observed in pseudogenes and nonfunctional sequences. The observed differences in entropy and GC content reflect an evolutionary shift associated with the process of pseudogenization and subsequent functional divergence of psiEst-6 and Est-6 after the duplication event.

Methoxy-resorufin ether as an electrochemically active biological probe for cytochrome P450 O-demethylation

This paper describes the utilisation of methoxy-resorufin ether as an electrochemical probe for studying cytochrome P450 CYP6G1. Methoxy-resorufin ether is well established as a versatile substrate for cytochrome P450, as its demethylated product, resorufin, is a fluorophore. We show that in addition to these established properties, methoxy-resorufin ether also exhibits reversible two electron transfer on glassy carbon and edge plane graphite electrodes. Cyclic voltammetry measurements and differential pulse voltammetry measurements show that methoxy-resorufin ether can be easily detected at low concentrations (down to 200 nM) in a conventional three electrode electrochemical cell. These properties of methoxy-resorufin ether mean that it could be used as an electrochemical probe, to follow the rate of its demethylation by CYP6G1. We show that electrochemical measurements could discriminate between the enzyme activity of protein microsomes taken from two strains of Drosophila melanogaster (fruit fly).