Drosophila polymorphism database (DPDB): a portal for nucleotide polymorphism in Drosophila

As a growing number of haplotypic sequences from resequencing studies are now accumulating for Drosophila in the main primary sequence databases, collectively they can now be used to describe the general pattern of nucleotide variation across species and genes of this genus. The Drosophila Polymorphism Database (DPDB) is a secondary database that provides a collection of all well-annotated polymorphic sequences in Drosophila together with their associated diversity measures and options for reanalysis of the data that greatly facilitate both multi-locus and multi-species diversity studies in one of the most important groups of model organisms. Here we describe the state-of-the-art of the DPDB database and provide a step-by-step guide to all its searching and analytic capabilities. Finally, we illustrate its usefulness through selected examples. DPDB is freely available at http://dpdb.uab.cat.     

Two Modes of Balancing Selection in Drosophila Melanogaster: Overcompensation and Overdominance

Overdominance is often invoked to account for the extensive polymorphisms found in natural populations of organisms; overcompensation, however, may be equally or more important. Overcompensation occurs when limiting resources are better exploited by a genetically mixed than by a uniform population, and is often causally related to frequency-dependent selection. We have designed experiments to test whether overcompensation occurs in Drosophila melanogaster, using the Sod locus as a marker. Tests are made at each of two densities and two temperatures for cultures with desired genetic compositions. Both temperature and density have statistically significant effects on the per-female productivity of the cultures. More important, there are strong effects due to overcompensation. Cultures that are more polymorphic are also more productive than less polymorphic ones even when the level of individual heterozygosity is the same in all. There is also overdominance for the Sod locus: the heterozygotes are more productive than either homozygote at every temperature and density, and the differences are statistically significant in several cases. These results corroborate previous studies showing that overdominance may contribute to the maintenance of the Sod polymorphisms. Moreover, our results indicate that the significance of overcompensation as a mechanism to account for polymorphism in natural populations deserves further investigation.     

Modeling gynodioecy: novel scenarios for maintaining polymorphism

Nuclear-cytoplasmic gynodioecy is a breeding system of plants in which females and hermaphrodites co-occur in populations, and gender is jointly determined by cytoplasmic male sterility (CMS) genes and nuclear restorers of male fertility. Persistent polymorphism at both CMS and nuclear-restorer loci is necessary to maintain this breeding system. Theoretical models have explained how nuclear-cytoplasmic gynodioecy can be stable for certain assumptions. However, recent advances in our understanding of the genetics, population biology, and molecular mechanisms of sex determination in nuclear-cytoplasmic gynodioecious species suggest the utility of new models with different underlying assumptions. In this article, we examine different negative pleiotropic fitness effects of nuclear restorers (costs of restoration) using genetic and population assumptions based on recent literature. Specifically, we model populations with two CMS types and separate nuclear restorer loci for each CMS type. Under these assumptions, both overdominance for fitness and frequency-dependent selection at nuclear-restorer loci can support nuclear-cytoplasmic gynodioecy. Costs of restoration can be either dependent or independent of the cytoplasmic background. Seed fitness costs are more vulnerable to fixation of CMS types than pollen costs. Survivorship costs are effective at maintaining polymorphism even when total reproductive effects are low. Overall, our models display differences in the stability of nuclear-cytoplasmic gynodioecy and predicted population sex ratios that should be informative to researchers studying gynodioecy in the wild.     

Seed storage: maintaining seed viability and vigor for restoration use

Effective seed storage after sourcing (harvesting or purchasing) is critical to restoration practitioners and native seed producers, as it is key to maintaining seed viability. Inadequate seed storage can lead to a waste of both natural and economic resources when seeds of poor quality are sown. When working with native species with unknown storage behavior, general assumptions can be made based on studies on related species, and standard practices may be applied with caution; however, an investigation should be conducted to understand if specific storage requirements are needed and for how long seeds can be stored before they lose significant viability. In this paper of the Special Issue Standards for Native Seeds in Ecological Restoration, we provide an overview of the key concepts in seed storage and the steps to take for effective storage of native seeds for restoration use.     

Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila

Previous studies of repetitive elements (REs) have implicated a mechanistic role in generating new chimerical genes. Such examples are consistent with the classic model for exon shuffling, which relies on non-homologous recombination. However, recent data for chromosomal aberrations in model organisms suggest that ectopic homology-dependent recombination may also be important. Lack of a dataset comprising experimentally verified young duplicates has hampered an effective examination of these models as well as an investigation of sequence features that mediate the rearrangements. Here we use approximately 7,000 cDNA probes (approximately 112,000 primary images) to screen eight species within the Drosophila melanogaster subgroup and identify 17 duplicates that were generated through ectopic recombination within the last 12 mys. Most of these are functional and have evolved divergent expression patterns and novel chimeric structures. Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes. Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species.     

Bioturbation as a mechanism for setting and maintaining levels of diversity in subtidal macrobenthic communities

Over 2 years, experiments were conducted tocompare the effects of sediment disturbance by different bioturbating, macrofaunal organisms on the diversity and structure of the associated infaunal community. The four species investigated were the bivalves Nuculoma tenuis (Montagu, 1808) and Abra alba (Wood, 1802), the heart urchin Brissopsis lyrifera (Forbes, 1841), and the burrowing decapod Calocaris macandreae (Bell, 1846). These organisms were chosen to allow assessment of the effects of contrasting feeding activities and body sizes of the bioturbating species on the diversity of the macrobenthic communities. Bioturbation by the sub-surface deposit feeders N. tenuis and B. lyrifera promoted higher levels of and diversity in treatments exposed to intermediate levels of disturbance. Whilst no such intermediate response was demonstrated for A. alba or C. macandreae, it was evident that changes in the associated fauna were influenced by the feeding type of the bioturbating organism responsible. It was also shown that different elements of the associated community responded differently to biotic disturbance. The results indicate that the variability in density and distribution of such bioturbators are important factors in structuring infaunal communities, and in setting and maintaining levels of diversity in apparently homogeneous areas.     

Hyperplasia as a mechanism for rapid resealing urothelial injuries and maintaining high transepithelial resistance

When the urothelial barrier, i.e., the blood−urine barrier, is injured, rapid resealing of the injury is crucial for the normal functioning of the organism. In order to investigate the mechanisms required for rapid resealing of the barrier, we established in vitro models of hyperplastic and normoplastic urothelia. We found that hyperplastic urothelia achieve significantly higher transepithelial resistance (TER) than normoplastic urothelia. However, the expression of cell junctional (claudin-8, occludin, E-cadherin) and differentiation-related proteins (cytokeratin 20 and uroplakins) is weaker in hyperplastic urothelia. Further investigation of cell differentiation status at the ultrastructural level confirmed that superficial urothelial cells (UCs) in hyperplastic urothelial models achieve a lower differentiation stage than superficial UCs in normoplastic urothelial models. With the establishment of such in vitro models and the aid of TER measurements, flow cytometry, molecular and ultrastructural analysis, we here provide unequivocal evidence that the specific cell-cycle distribution and, consequently, the number of cell layers have a significant influence on the barrier function of urothelia. We demonstrate the importance of hyperplasia for the rapid restoration of the urothelial barrier and the maintenance of high TER until the UCs reach a highly differentiated stage and restoration of the urothelial barrier after injury is complete. The information that this approach provides is unique and we expect that further exploitation of hyperplastic and normoplastic urothelial models in future studies may advance our understanding of blood−urine barrier development and functionality.     

Good genes and sexual selection in dung beetles (Onthophagus taurus): genetic variance in egg-to-adult and adult viability

Whether species exhibit significant heritable variation in fitness is central for sexual selection. According to good genes models there must be genetic variation in males leading to variation in offspring fitness if females are to obtain genetic benefits from exercising mate preferences, or by mating multiply. However, sexual selection based on genetic benefits is controversial, and there is limited unambiguous support for the notion that choosy or polyandrous females can increase the chances of producing offspring with high viability. Here we examine the levels of additive genetic variance in two fitness components in the dung beetle Onthophagus taurus. We found significant sire effects on egg-to-adult viability and on son, but not daughter, survival to sexual maturity, as well as moderate coefficients of additive variance in these traits. Moreover, we do not find evidence for sexual antagonism influencing genetic variation for fitness. Our results are consistent with good genes sexual selection, and suggest that both pre- and postcopulatory mate choice, and male competition could provide indirect benefits to females.     

Genetic variation for preadult viability in Drosophila melanogaster

The extent of genetic variation in fitness and its components and genetic variation's dependence on environmental conditions remain key issues in evolutionary biology. We present measurements of genetic variation in preadult viability in a laboratory-adapted population of Drosophila melanogaster, made at four different densities. By crossing flies heterozygous for a wild-type chromosome and one of two different balancers (TM1, TM2), we measure both heterozygous (TM1/+, TM2/+) and homozygous (+/+) viability relative to a standard genotype (TM1/TM2). Forty wild-type chromosomes were tested, of which 10 were chosen to be homozygous viable. The mean numbers produced varied significantly between chromosome lines, with an estimated between-line variance in log(e) numbers of 0.013. Relative viabilities also varied significantly across chromosome lines, with a variance in log(e) homozygous viability of 1.76 and of log(e) heterozygous viability of 0.165. The between-line variance for numbers emerging increased with density, from 0.009 at lowest density to 0.079 at highest. The genetic variance in relative viability increases with density, but not significantly. Overall, the effects of different chromosomes on relative viability were remarkably consistent across densities and across the two heterozygous genotypes (TM1, TM2). The 10 lines that carried homozygous viable wild-type chromosomes produced significantly more adults than the 30 lethal lines at low density and significantly fewer adults at the highest density. Similarly, there was a positive correlation between heterozygous viability and mean numbers at low density, but a negative correlation at high density.     

A new role for Drosophila Aurora-A in maintaining chromosome integrity

Chromosoma - Aurora-A is a conserved mitotic kinase overexpressed in many types of cancer. Growing evidence shows that Aurora-A plays a crucial role in DNA damage response (DDR) although this...     

Cyclical environmental changes as a factor maintaining genetic polymorphism. 1. Two-locus haploid selection

To classify different types of cyclic selection, a measure of fitness disequilibrium was used, and a class of systems were considered where this measure has the same sign in all states (sign-concordant environments). The necessary conditions for existence of a fixed point (considering any moment within the period as a referring one) are obtained for sign-concordant systems. However, analytical study of such systems, in the case of selection for equal additive genes, and numerical testing of more general situations, allowed us to conclude that no polymorphism is possible. In the alternative class of sign-concordant systems, polymorphism is possible. However, we found that global stability is an exception rather than a rule for sign-nonconcordant systems. Massive numerical simulations of selection in a four-state environment were made for cycle lengths in the range 8–28 and with evenly distributed selection coefficients. The proportion of polymorphic regimes ranged up to about 1.5%, and was dependent on the recombination rate between the loci. It should be stressed, that polymorphism maintenance in the haploid systems, when it is possible, can not be considered as an effect derived from constant selection, or be a result of any hidden form of heterozygous advantage. In other words, polymorphism stability is causally connected with environmental fluctuations. Equally important is that this effect of fluctuations is only possible because of recombination: in single locus systems haploid cyclical selection is unable to produce protected polymorphism.     

A UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase is essential for viability in Drosophila melanogaster

We report the first demonstration that the activity of a member of the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase gene family is necessary for viability in Drosophila melanogaster. Expression of the wild-type recombinant pgant35A gene in COS7 cells resulted in in vitro activity against peptide and glycopeptide substrates, demonstrating that this gene encodes a biochemically active transferase. Previous mutagenesis studies identified recessive lethal mutations that were rescued by a genomic fragment containing the pgant35A gene; however, the presence of additional open reading frames within this fragment left open the possibility that another gene was responsible for rescue of the observed lethality. Here, we have determined the molecular nature of the mutations in three independent mutant alleles. Two of the mutant alleles contain premature stop codons within the coding region of pgant35A. The third mutant contains an arginine to tryptophan amino acid change, which, when expressed in COS7 cells, resulted in a dramatic reduction of transferase activity in vitro. PCR amplification of this gene from Drosophila cDNA panels and Northern analysis revealed that it is expressed throughout embryonic, larval, and pupal stages as well as in adult males and females. This study provides the first direct evidence for the involvement of a member of this conserved multigene family in eukaryotic development and viability.     

Larval competition in Drosophila melanogaster: frequency-dependence of viability

Summary The application of the overfeeding technique (interruption of the competition during larval development) to the study of larval competition in two-strain cultures of Drosophila melanogaster demonstrates the following points: (1) viability is a function of competition time; (2) viability becomes more frequency-dependent as competition time increases; (3) the dynamics of the inner subpopulation (adults that have passed all their development in a crowded condition) and outer subpopulation (adults coming from larvae recovered by interruption of competition) vary with time as regards frequency-dependence; and (4) the wild type strain Oregon is the active agent in competition with the strain cardinal.     

Maintenance mechanism of polymorphism at the α-Gpdh locus in Drosophila melanogaster

Polymorphism at the alpha-Gpdh locus was studied in Drosophila melanogaster. Using two different lines, one marked by the F allele (FF line) another by the S allele (SS line), four populations were initiated, two in which the initial frequency of F was 0.1 and two in which it was 0.9. They have been observed for 34 generations. From the fifth generation on, the equilibrium frequency in the four cages was about 0.60. Viability has been measured during the evolution of te populations while F frequencies changed and recombinations between the FF and SS lines occurred. It has been evaluated in synthetic populations built with different frequencies: (1) from the original FF and SS lines and (2) from FF and SS lines extracted after 34 generations of joint evolution. In all three cases, the FF viability depended on the frequency of the F allele. The similarity of the three linear regressions implies that alpha-Gpdh locus or other closely linked loci is the target of the selection in the populations analyzed here.     

Bicoid mRNA diffusion as a mechanism of morphogenesis in Drosophila early development

We show that mRNA diffusion is the main morphogenesis mechanism that consistently explains the establishment of Bicoid protein gradients in the embryo of Drosophila, contradicting the current view of protein diffusion. Moreover, we show that if diffusion for both bicoid mRNA and Bicoid protein were assumed, a steady distribution of Bicoid protein with a constant concentration along the embryo would result, contradicting observations.     

Translocations and a balanced polymorphism in a Drosophila population

A Drosophila population cage initiated with equal numbers of two viable II–III translocation homozygotes rapidly evolved into a balanced polymorphism with the two translocations maintained throughout 25 generations at which time the experiment was terminated. The fertility of this population averaged 26%; a control population averaged 90%. The establishment of the polymorphism was interpreted with reference to the reduced viability of the two homozygotes such that their net fitness was considerably less than that of partially sterile double heterozygote. By the incorporation of specific values for the relative fitness of the three genotypes in a computer programme it was possible to simulate the polymorphism.