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data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in 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.

A rapid change in P-element-induced hybrid dysgenesis status in Ukrainian populations of Drosophila melanogaster

The Drosophila melanogaster P-transposable element is an example of mobile DNA transferred horizontally and known to have spread globally over the last 50-60 years. In Drosophila, the P-element causes a syndrome known as 'P-M hybrid dysgenesis' that obstructs normal ovary development in the female progeny of susceptible populations. Despite extensive research, the stability and global population dynamics of P-M dysgenic phenotypes remain poorly understood. Here, we report a recent and rapid transition in the P-M status of D. melanogaster populations from Ukraine. We demonstrate that these populations are currently dominated by the P'-cytotype characterized by active genomic P-elements and unknown from Ukraine just two decades ago. Our results suggest a recent invasion of the P-element in Ukraine, a pattern that matches recent discoveries from Turkey.

A HIGH FREQUENCY OF HERITABLE CHANGES IN NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER IN UKRAINE

Spontaneous mutations are thought to have a stable rate for a given species. If non-adaptive, they appear at low frequencies and are governed by drift. However, environmental factors have been reported to cause spread of non-adaptive mutations in populations, governed by mechanisms, such as genetic assimilation. In the present study, we report a simultaneous appearance of a mutant and apparently non-adaptive C2 vein in Drosophila melanogaster at higher than expected frequencies in several distant populations, which excludes the role of drift or selection as the cause of the reported mutation frequencies. We discuss explanations of the phenomenon, including the role of externalfactors, such as temperature, in the possible genetic assimilation of the trait.

TP53 codon 72 polymorphic variants (Rs1042522) frequency in the Ukrainian population

OBJECTIVE

To estimate frequencies of polymorphic variants of TP53 codon 72 in the Ukrainian population.

MATERIALS AND METHODS

We determined the allele frequencies for 148 healthy people. Genotyping was performed by allele specific polymerase chain reaction.

RESULTS

We identified 31 individuals (20.9 %) with Arg/Arg genotype, Arg/Pro genotype was identified for 116 indi viduals (78.4 %), whereas genotype Pro/Pro was rare and was found in one person only (0.7 %). Genotype distribu tions were not within Hardy Weinberg equilibrium (χ2 = 59,7, p < 0.0001).

CONCLUSIONS

Arg and Pro allele frequencies in the population of Ukraine are 60 and 40 % respectively, which is sig nificantly differ from the frequencies described in the literature for Poland, the Czech Republic, the USA and Brazil.

Colonization of a temperate-zone region by the fruit fly Drosophila simulans (Diptera: Drosophilidae)

The fruit flies Drosophila simulans Sturtevant, 1919 and Drosophila melanogaster Meigen, 1830 are sibling species that occupy similar niches. However, unlike D. simulans, D. melanogaster has spread far beyond tropical and subtropical regions deep into temperate climate zones. A number of invasion events by D. simulans into temperate climate zones have been reported; however, its ability to overwinter and establish local populations in these areas is disputed. Here, we report the wide dispersal of D. simulans in mixed populations with D. melanogaster in Ukraine. Drosophila simulans flies found in Ukraine belong to the siII mtDNA haplogroup and are infected with maternally inherited intracellular symbiotic bacteria of the genus Wolbachia Hertig, 1936 of the strain wRi. These genetic markers indicate a common origin of the Ukrainian D. simulans flies from a subgroup of the species found to invade other temperate climate areas worldwide. Here, we report for the first time detection of D. simulans flies early in the breeding season in a temperate climate area with severe winter conditions. We also report a moderate negative relationship between relative abundance of D. simulans and mean temperature in the month of sampling reflecting this species’ known lower tolerance of high temperatures.

[The puzzle of Wolbachia spreading out through natural populations of Drosophila melanogaster]

The endosymbiotic bacteria Wolbachia are widely spread in natural populations of arthropods all over the world. This phenomenon, according to the current views, may be due either to so called reproductive parasitism (modification of sexual reproduction) or to mutualistic interrelationships with the host organism, since the bacteria are transmitted transovarially. Wolbachia are extremely widespread in natural populations and laboratory lineages of Drosophila melanogaster though they do not cause any known modifications of this insect sexual reproduction that could influence the bacteria frequency in the populations. It is found out that Wolbachia effects on drosophila reproductive processes can only consist in low-level of cytoplasmic incompatibility within laboratory lineages; in natural drosophila populations even such an effect has not been detected. The attempts to explain the wide spread of Wolbachia among representatives of D. melanogaster through fitness increasing of infected individuals were not successful either. Data obtained thereupon are contradictive and the results are not versatile. Meanwhile, there are some incomplete data on the bacteria affecting drosophila sexual behavior, expression of certain genes, ferrum metabolism. It is shown that the bacteria enhance individual resistance to RNA-viruses that, under natural conditions, infect fruit flies rather frequently, but the mechanisms of the phenomenon remain uncertain as well as the commonness of the phenomenon itself. Thus, at the one hand, it can be stated that infection by Wolbachia leads to a rather complex effect on D. melanogaster while, at the other hand, the reasons behind the wide spread of Wolbachia in natural populations of D. melanogaster still remain unclear.

[Infection with Wolbachia does not influence crossing over in Drosophila melanogaster]

The influence of infection with endosymbiotic bacteria Wolbachia on crossingover in Drosophila melanogaster between the white and cut genes in the X chromosome was studied. Reciprocal crosses have been conducted between infected and non-infected fruit fly strains. The results showed no significant effect of Wolbachia infection on the crossingover rates in D. melanogaster between the white and cut genes in X-chromosome.