Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

The discovery, distribution, and diversity of DNA viruses associated with Drosophila melanogaster in Europe

Drosophila melanogaster is an important model for antiviral immunity in arthropods, but very few DNA viruses have been described from the family Drosophilidae. This deficiency limits our opportunity to use natural host-pathogen combinations in experimental studies, and may bias our understanding of the Drosophila virome. Here, we report fourteen DNA viruses detected in a metagenomic analysis of 6668 pool-sequenced Drosophila, sampled from forty-seven European locations between 2014 and 2016. These include three new nudiviruses, a new and divergent entomopoxvirus, a virus related to Leptopilina boulardi filamentous virus, and a virus related to Musca domestica salivary gland hypertrophy virus. We also find an endogenous genomic copy of galbut virus, a double-stranded RNA partitivirus, segregating at very low frequency. Remarkably, we find that Drosophila Vesanto virus, a small DNA virus previously described as a bidnavirus, may be composed of up to twelve segments and thus represent a new lineage of segmented DNA viruses. Two of the DNA viruses, Drosophila Kallithea nudivirus and Drosophila Vesanto virus are relatively common, found in 2 per cent or more of wild flies. The others are rare, with many likely to be represented by a single infected fly. We find that virus prevalence in Europe reflects the prevalence seen in publicly available datasets, with Drosophila Kallithea nudivirus and Drosophila Vesanto virus the only ones commonly detectable in public data from wild-caught flies and large population cages, and the other viruses being rare or absent. These analyses suggest that DNA viruses are at lower prevalence than RNA viruses in D.melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redressing an earlier bias toward RNA virus studies in Drosophila, and lay the foundation needed to harness the power of Drosophila as a model system for the study of DNA viruses.

Mating behavior as an indicator of quality of Drosophila subobscura males?

According to current theoretical predictions, any deleterious mutations that reduce nonsexual fitness may have a negative influence on mating success. This means that sexual selection may remove deleterious mutations from the populations. Males of good genetic quality should be more successful in mating, compared to the males of lower genetic quality. As mating success is a condition dependent trait, large fractions of the genome may be a target of sexual selection and many behavioral traits are likely to be condition dependent. We manipulated the genetic quality of Drosophila subobscura males by inducing mutations with ionizing radiation and observed the effects of the obtained heterozygous mutations on male mating behavior: courtship occurrence, courtship latency, mating occurrence, latency to mating and duration of mating. We found possible effects of mutations. Females mated more frequently with male progeny of nonirradiated males and that these males courted females faster compared to the male progeny of irradiated males. Our findings indicate a possible important role of sexual selection in purging deleterious mutations.

Heterozygosity maintains developmental stability of sternopleural bristles in Drosophila subobscura interpopulation hybrids

Interpopulation hybridization can lead to outbreeding depression within affected populations due to breakdown of coadapted gene complexes or heterosis in hybrid populations. One of the principal methods commonly used to estimate the level of developmental instability (DI) is fluctuating asymmetry (FA). We used three genetically differentiated Drosophila subobscura populations according to inversion polymorphism analysis and measured the variability of sternopleural bristle number and change in FA across generations P, F1, and F2 between intra- and interpopulation hybrids of D. subobscura. The mean variability of sternopleural bristle number in intra- and interpopulation hybrids of D. subobscura across generations cannot determine whether the changes at the level of developmental homeostasis are due exclusively to genomic coadaptation or to heterozygosity. Phenotypic variance (V(p)) and FA of sternopleural bristle number was higher in interpopulation than in intrapopulation hybrids across generations. F1 hybrids were more developmentally stable compared to each parental population in both intra- and interpopulation hybrids. The most probable mechanism providing developmental homeostasis is heterozygote or hybrid superiority, also called overdominace. However, V(p) was higher and FA lower in the F2 generation when compared to F1, due mainly to crossing-over in the formation of F2.

Antimutagenic effect of sage tea in the wing spot test of Drosophila melanogaster

The present study assayed the antimutagenic potential of Salvia officinalis (sage) in the form of tea infusion, by the somatic mutation and recombination test (SMART) on Drosophila melanogaster. The use of herbal infusions is much common in the human diet, so the aim of the present study was to estimate the antimutagenic effects of the S. officinalis tea rather than essential oils. Methyl methanesulphonate (MMS) was used as the mutagen and positive control. Several types of treatment were performed: short acute treatment with sage infusion or MMS, longer (chronic) treatment with sage solution or MMS, and two combined treatments, i.e. short treatment with sage followed by a longer treatment with MMS and vice versa. Sage infusion used in our experiments showed a clear antimutagenic effect, reducing the frequency of mutations induced by MMS. The inhibition effect of sage tea is obtained and confirmed when pre- or post-treatments with mutagen were used. The results indicate that although sage in this regime decreases the number of mutation events, it is not efficient enough in case of the 2 h sage pre-treatment. Antioxidant activity, suppression of metabolic activation, could be mechanisms through which sage or some of its components act as desmutagen.

Adaptive significance of amylase polymorphism in Drosophila: XIV. Effect of substrates with different carbohydrate composition on some life-history traits of Drosophila subobscura

The Amy-locus polymorphism of Drosophila subobscura is used as a model-system for an experimental population genetic study of adaptive significance of alpha-amylase activity on substrates of different carbohydrate compositions. So far, fitness components have not commonly been included in ecological-genetic studies of alpha-amylase polymorphism in this species. In the present paper fitness components are analyzed in relation to different amylase activities in D. subobscura individuals homozygous for "slow" and "fast" Amy allele, associated with substrates of different carbohydrate compositions. The results indicate a significant effect of substrate carbohydrate composition on fitness components of the genotypes homozygous for S or F Amy allele in D. subobscura through their enzyme activity.

The effect of lead on fitness components and developmental stability in Drosophila subobscura

We analyzed the developmental time, egg-to-adult viability, and developmental stability (fluctuating wing size asymmetry) in Drosophila subobscura, maintained for six generations on different concentrations of lead. Development time is significantly affected by generation and lead concentration, but interaction of these factors is not a significant source of variability for this fitness component. Generation and the interaction generation x concentration of lead significantly affect egg-to-adult viability. Levene's test of heterogeneity of variance showed that variability of FA is not significant in any of the samples. Within both lead concentrations females showed significantly higher FA indices for the wing width than males. Within sexes, a significantly higher FA was found only in females for wing width FA between the control and the lower concentration of lead. The results show that if strong relationship between FA and the studied fitness components exists, it results in a stronger selection of unstable genotypes under lead as a stress factor and, consequently, FA needs to be used with caution as a biomarker in natural populations under environmental stress.

Monitoring of the genetic structure of natural populations: change of the effective population size and inversion polymorphism in Drosophila subobscura

We analyzed changes in the genetic structure and effective population size of two ecologically distinct populations of Drosophila subobscura over several years. Population sizes of D. subobscura in beech and oak wood habitats for a period of 6 years were estimated by the capture-mark-release-recapture method. Inversion polymorphism parameters were also assessed in the same populations for a period of 3 years. Significant differences in the numbers of individuals were observed between sexes. This affected the effective population sizes between particular years. The ratio of the effective size over the cenzus dropped significantly in beech wood in 2 years. Although overall heterozygosity remained unchanged during the years in both habitats, frequencies of gene arrangements on five chromosomes show variability. After the bottleneck, some complex chromosomal arrangements appeared for the first time in both populations. Standard gene arrangements of chromosome A increased in frequency over the years in each habitat, while the complex arrangements remain rather stable and specific for each population. The results obtained indicate that the population structure may significantly change if the effective size of D. subobscura population is reduced, which is mostly related to microclimatic changes in habitats. Based on the results to date, monitoring of microevolutionary changes by using D. subobscura and its relatives seems a promising way to study the effects of global climate changes.

The effect of different concentrations of lead on inversion polymorphism in Drosophilasubobscura

Drosophila subobscura is a wild Drosophila species that is spread over almost all of Europe. It possesses an uniquely rich inversion polymorphism on all five long chromosomes. This polymorphism is to a certain degree associated with the variation and dynamics of ecological factors in space and time. We analyzed the changes of inversion polymorphism components of Drosophila subobscura flies maintained on media with different concentrations of lead in laboratory conditions. The effects of lead on inversion polymorphism were observed by cytological analysis of gene arrangements on all of the five acrocentric chromosomes, as well as by cytological analysis of karyotypes on all of the four autosomes. The frequencies of particular gene arrangements on the four autosomes changed significantly in the samples maintained on medium not supplemented with lead. The frequencies of some gene arrangements on all of the five acrocentric chromosomes changed significantly in the flies maintained on media supplemented with lead. The length of exposure to different lead concentrations results in a significant change in the frequency of a few gene arrangements on two autosomes. However, the results show that different concentrations of lead, as well as the length of exposure, do not affect major parameters of inversion polymorphism. The results suggest that some gene arrangements could be linked with adaptive processes in evolving heavy metal resistance.

Adaptive significance of amylase polymorphism in Drosophila XIII. Old World obscura species subgroup divergence according to biochemical properties of alpha-amylase

Biochemical properties of enzyme alpha-amylase were surveyed in Drosophila obscura Old world group of species (D. subobscura, D. ambigua, D. obscura and D. tristis) sampled in the same habitat, with the aim to reveal some ecological and evolutionary aspects of amylase polymorphism, which has been studied extensively in D. subobscura, but not compared with other species in the group. The data obtained show that D. subobscura is distinct from the other three species regarding all biochemical amylase properties. Such a divergence also correlates with the niche breadth and relative abundance of these species in the same habitat.