Biology subjects

Kapun, M.

Publications and source records attributed to Kapun, M..

At least 19 recordsLinked to original sources

bioRxiv2026

High variability and limited host specificity characterise the microbiome of Desmophyllum pertusum across a cold-water coral reef

Cold-water corals (CWC), like their tropical counterparts, are ecosystem engineers that create complex habitats supporting high biodiversity. Despite their broad distribution and increasing exposure to climate change and anthropogenic stressors, CWC remain comparatively understudied, particularly with respect to their associated microbiomes. Unlike tropical corals, CWC lack photosynthetic algal symbionts, suggesting that microbial associates may play a particularly important role in nutrient acquisition, biogeochemical cycling, and host resilience. Here, we investigated microbial community composition across the reef ecosystem formed by the cosmopolitan CWC Desmophyllum pertusum at Tisler Reef (NE Skagerrak, Kosterfjord, Norway). Using Nanopore sequencing of the full-length 16S rRNA gene, we characterised microbial communities associated with coral, seawater, substrate, and coral rubble to (i) assess reef-scale patterns, (ii) characterise variation in microbial assemblages between coral colonies and between branch and mucus compartments, as well as according to branch position, and (iii) identify putative core microbiome members and indicator taxa associated with D. pertusum relative to its surrounding environment. At the reef scale, microbial community structure differed among habitat compartments. Within D. pertusum, both colony identity and compartment (branch vs. mucus) contributed to structuring microbial assemblages, while branch position also explained an additional but limited proportion of the variation. The coral-associated microbiome contained a set of recurrent taxa, but many of these were also widespread in the surrounding environment, and few were consistently enriched in coral samples. Together, these findings indicate that the D. pertusum microbiome at Tisler Reef comprises recurrent microbial associates embedded within a highly variable assemblage, rather than a large and abundant core microbiome exclusive to the coral habitat. These results contribute to establishing a baseline understanding of D. pertusum microbiomes and provide insights into microbial community structure across cold-water coral reef ecosystems.

microbiology↗

bioRxiv2026

pastForward: a Snakemake pipeline for ancient and historical DNA with eukaryote-wide taxonomic screening and tracking of copy-number variation

Ancient and historical DNA has the potential to resolve many open questions in biology. While pipelines for processing ancient and historical DNA exist, none combine user-friendly, configurable processing with copy number variation tracking and targeted taxonomic profiling. Therefore, we developed pastForward, a fully automated Snakemake pipeline that integrates all analysis steps from raw reads to damage-rescaled BAM files in a single reproducible workflow. It performs ancient and historical DNA processing, including adapter trimming, read merging, deduplication, damage assessment, quality rescaling, and generates interactive reports summarizing the endogenous read content, library complexity, and breadth and depth coverage statistics. These reports allow users to rapidly assess the quality of sequencing data. It handles single- and paired-end NGS libraries. Mapping to multiple reference sequences is supported, facilitating co-analysis of host and endosymbiont sequences and genotyping of marker genes such as COI. pastForward further integrates two novel tools. ECMSD (Efficient Comprehensive Mitochondrial Sequence Detector) screens each library for eukaryotic DNA by aligning reads against a mitochondrial reference database. The presence of bacteria, archaea and viruses is detected in parallel with Centrifuge. REVEAL (Read-based Estimation and visualization of Element Abundance and Loci) quantifies and visualizes copy number variation of genetic features, such as transposable elements (TEs) or gene duplications. Two case studies demonstrate the usage of the pipeline. Using pastForward on dog genomic time series, including Neolithic samples, we confirm that the copy number of AMY2B, which encodes the starch-digesting enzyme amylase, increased during domestication. From historical D. melanogaster genomes, we recover the recent invasion of the transposable element opus. It is absent in specimens from the 1800s and present from 1933 onward. By efficiently processing large numbers of samples, pastForward facilitates longitudinal tracking of genomic features in diverse species.

bioinformatics↗

bioRxiv2026

The fate of a dynasty: Population genomics uncovers the demographic history of Ardea insignis, one of the rarest bird species in the world

The White-bellied Heron (Ardea insignis) is one of the worlds rarest birds, with fewer than 60 known individuals remaining in the wild. Whether this extreme rarity reflects a recent anthropogenic collapse or a long history of persistently small population size has remained unknown, limiting our understanding of the species evolutionary resilience and conservation needs. Here, we present the first high-quality reference genome for A. insignis, generated using Oxford Nanopore long-read sequencing and complemented with Illumina whole-genome data. Comparative mitochondrial and nuclear phylogenomic analyses consistently recover A. insignis as the sister species of Purple Heron (A. purpurea), while revealing moderate mitonuclear discordance among deeper ardeid lineages. Genome-wide analyses demonstrate exceptionally low heterozygosity and extensive runs of homozygosity relative to the widespread and closely related Great Blue Heron (A. herodias), indicating pronounced genomic erosion and long-term inbreeding. However, the predominance of short and intermediate-length homozygous tracts, together with robust Pairwise Sequentially Markovian Coalescent (PSMC) reconstructions across alternative parameterizations, indicates that A. insignis has persisted with comparatively small effective population sizes over much of its evolutionary history rather than experiencing only a recent demographic collapse. The two sampled individuals nevertheless differ in the abundance of longer homozygous tracts, indicating that inbreeding accumulated over the past few generations has not been uniform among the surviving birds, despite their shared history of chronic rarity. Our results indicate that the White-bellied Heron represents a lineage that has survived prolonged demographic adversity and that its greatest genetic challenge may be limited adaptive potential rather than recent genomic deterioration alone. Beyond providing the first genomic resource for this critically endangered species, our study establishes an evolutionary baseline for future monitoring and highlights the importance of integrating genomic and ecological data to guide conservation strategies for species persisting at the edge of extinction.

evolutionary biology↗

bioRxiv2026

Environmental filtering across seasons and host-associated selection shape the gut microbiome of sympatric European Sepsis dung flies

Animal microbiomes are shaped by both environmental exposure and host-associated filtering, but the relative importance of these processes remains poorly understood. Dung-associated insects provide an ideal model because they develop and feed in highly dynamic microbial environments. We investigated the gut microbiomes of six sympatric dung fly species of the genus Sepsis (Diptera: Sepsidae) and compared them with microbial communities in cow dung throughout a growing season in Switzerland. Using full-length 16S rRNA gene sequencing (PacBio), we characterized bacterial communities from 74 fly and 15 dung samples. Seasonal variation was the strongest predictor of microbiome composition, whereas host species exerted weaker effects that persisted after removing dung-associated taxa, indicating that gut communities are not merely passive reflections of environmental exposure. Only few gut microbiome reads were attributable to dung-associated taxa, and environmental overlap differed among fly species rather than season. A highly non-random core microbiome persisted across all six species: 36 bacterial genera (of 469) were shared by all hosts at [~]119-fold enrichment above random expectation and remained after removing dung-associated taxa. These findings support a two-layer model of microbiome assembly, in which seasonal environmental variation determines microbial availability while host-specific processes selectively retain a subset of taxa.

ecology↗

bioRxiv2026

Natural Variation in Clock polyQ Length Is Associated with Circadian Function to Climatic Gradients in Drosophila melanogaster

Natural variation in circadian clock genes provides a powerful framework for understanding how organisms respond to environmental heterogeneity. The Clock (Clk) gene encodes a core transcriptional regulator of circadian rhythms and contains a polymorphic polyglutamine (polyQ) tract whose evolutionary significance remains unclear. Here, we integrate population genomic, behavioral, and molecular analyses to investigate the functional and geographic patterns of Clk polyQ variation in Drosophila melanogaster. Using data from 127 European populations, we identify 11 Clk polyQ alleles and find that their frequencies are geographically structured, most consistently along an east-west gradient: the Q25 and Q27 alleles show robust clines in longitude and in a bioclimatic axis of continentality, whereas latitudinal and altitudinal trends are weaker. Behavioral assays of near-isogenic lines revealed that polyQ length modulates circadian function under thermal challenge: most alleles maintained stable free-running periods across temperatures, whereas the intermediate-length Q25 allele showed the strongest, though modest, temperature sensitivity. Circadian phase showed pronounced allele-specific sensitivity to elevated temperature in laboratory assays, although phase variation did not display a consistent relationship with geographic variables. At the molecular level, luciferase reporter assays showed that longer polyQ alleles exhibited higher transcriptional activity, linking polyQ length to CLK-mediated gene expression. Together, these results demonstrate that natural variation in Clk polyQ length has measurable functional consequences for circadian regulation and is geographically structured in patterns consistent with underlying climatic variation, highlighting the potential for low-complexity regions to modulate clock function in a context-dependent manner across environmental gradients.

evolutionary biology↗

bioRxiv2025

How to catch flies in the city (fast): Citizen Science on Drosophila ecology helps to raise awareness for biodiversity in urban environments

To efficiently mitigate biodiversity loss both robust ecological data and broader societal engagement are needed. Citizen science offers a pathway to address these dual challenges by combining data collection with public involvement. Here, we introduce the citizen science project Vienna City Fly, conducted at the Natural History Museum Vienna (NHMW), which used fruit flies (Drosophila) as a model organism group for urban biodiversity research and public engagement. Participants deployed standardized traps across Vienna, enabling systematic sampling and active participation in research, which resulted in hundreds of fly collections, thousands of sampled fly specimens and new insights into the biodiversity and ecology of the collected fly species, demonstrating the feasibility of large-scale ecological research through public collaboration. To assess motivational drivers and perceived impacts of participation, we conducted an online survey (N=59) using the validated psychometric MORFEN-CS scale. Survey results revealed that nature conservation values and the intention to contribute to biodiversity conservation emerged as the strongest drivers of engagement, complemented by sociopolitical responsibility and citizen science-based motivations. Reported outcomes include knowledge gain (61%), more positive attitude toward study organisms (50%), and increased awareness of biodiversity (30%). Satisfaction was very high, with 85% rating their experience at the top of the scale and all participants expressing willingness to join future citizen science projects. Recruitment occurred mainly via social networks, and the sample of participants was highly educated, indicating limits to inclusivity and reach. Our findings demonstrate that citizen science can contribute to robust ecological data collection while gaining knowledge and awareness. Natural history museums, as trusted institutions, play a key role in facilitating such initiatives. Overall, Drosophila research proves to be a suitable field for citizen science, combining accessibility with strong potential for advancing ecological and biodiversity research as well as public engagement in urban biodiversity research.

scientific communication and education↗

bioRxiv2025

Ecology and temporal dynamics of urban Drosophila species communities as potential indicators of biodiversity decline

Understanding the impact of ecological factors on biodiversity is central in the context of accelerating climate change and biodiversity loss. Urban areas, as landscapes under particularly strong anthropogenic influence, are undergoing rapid ecological change, yet the consequences for urban biodiversity and ecosystem functioning remain poorly understood. In this study, we focused on fruit flies of the genus Drosophila - a diverse group of dipterans with variable ecological niches and degrees of synanthropy - to investigate species composition and community ecology in the metropolitan area of Vienna, Austria. With the help of numerous citizen scientists, we have collected approximately 18,000 specimens through dense spatio-temporal sampling both indoors and outdoors of human dwellings. A total of 13 Drosophila species were identified, with communities dominated by widespread cosmopolitan synanthropic species. Among these, D. mercatorum and D. virilis represent novel records for Austria. Comparisons to a previous study from more than 30 years ago revealed that the species richness in Vienna was more than 50% lower than before and showed that formerly common species were potentially replaced by neobiots. We further assessed ecological niches by intersecting species abundance data with high-dimensional, high-resolution earth observation datasets, which revealed distinct ecological preferences among species. In particular, the neozoan D. mercatorum emerged as a highly synanthropic species, tightly confined to urban areas with high levels of imperviousness. In summary, our study underpins the versatility of the Drosophila system as indicators of biodiversity loss in a rapidly changing world.

ecology↗

bioRxiv2024

AmpliPiper: A versatile amplicon-seq analysis tool for multilocus DNA barcoding

The advent of third generation sequencing technology has revolutionized parallelized sequencing of DNA fragments of varying lengths, such as PCR amplicons, which provides unprecedented new opportunities for large-scale and diverse DNA barcoding projects that, for example, aim to quantify the accelerating biodiversity crisis. However, the broad-scale application of these new technologies for biodiversity research is often hindered by the demand for advanced bioinformatics skills to carry out quantitative analyses. To facilitate the application of multilocus amplicon sequencing (amplicon-seq) data for biodiversity and integrative taxonomic research questions, we present AmpliPiper, an automated and user-friendly software pipeline which carries out bioinformatics analyses of multilocus amplicon-seq data generated with Oxford Nanopore (ONT) sequencing. AmpliPiper combines analysis methods for DNA barcoding data that include demultiplexing of pooled amplicon-seq data, haplotype-specific consensus sequence reconstruction, species identification based on comparison to the BOLD and GenBank databases, phylogenetic analyses and species delimitation. We demonstrate the applicability and workflow of our approach based on a newly generated dataset of 14 hoverfly (Syrphidae) samples that were amplified and sequenced at four marker genes. We further benchmark our approach with Sanger sequencing and simulated amplicon-seq data which show that DNA barcoding with ONT is both accurate and sensitive to detect even subtle genetic variation.

bioinformatics↗

bioRxiv2024

Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource

Large scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009-2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species demographic history and identify novel signs of adaptation across spatial and temporal dimensions. We showed that patterns of secondary contact, originally characterized in North America, are replicated in South America and Australia. We also found that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatio-temporal patterns of genetic variation in this classic model system.

evolutionary biology↗

bioRxiv2023

Wolbachia effects on thermal preference of natural Drosophila melanogaster are influenced by host genetic background, Wolbachia type and bacterial titer.

Temperature plays a fundamental role for the fitness of all organisms. In particular, it strongly affects metabolism and reproduction in ectotherms that have limited physiological capabilities to regulate their body temperature. Ectotherms thus have to maintain thermal homeostasis by behavioral adjustments. The influence of temperature variation on the physiology and behavior of ectotherms is well studied but we still know little about the influence of symbiotic interactions on thermal preference (Tp) of the host. The Wolbachia-Drosophila host-symbiont system represents an ideal model for addressing these questions. A growing number of studies demonstrated that different Wolbachia types can influence Tp in different Drosophila species, but these results may be confounded by the use of long-term Drosophila lab-strains that may not be representative for natural fly populations. To account for this, we investigated the effect of Wolbachia on Tp in wild-type D. melanogaster flies recently collected from nature. Consistent with previous data, we found reduced Tp compared to an uninfected control in one of two fly strains infected with the wMelCS Wolbachia type. Additionally, we, for the first time, found that Wolbachia titer variation influences thermal preference of the host fly. These data indicate that the interaction of Wolbachia and Drosophila resulting in behavioral variation is complex and strongly influenced by the genetic background of host and symbiont. Our results further emphasize the necessity for more in-depth studies to better understand the evolutionary significance of Tp variation influenced by Wolbachia in natural Drosophila populations.

ecology↗

bioRxiv2023

Historic museum samples provide evidence for a recent replacement of Wolbachia types in European Drosophila melanogaster.

Wolbachia is one of the most common bacterial endosymbionts, which is frequently found in numerous arthropods and nematode taxa. Wolbachia infections can have a strong influence on the evolutionary dynamics of their hosts since these bacteria are reproductive manipulators that affect the fitness and life history of their host species for their own benefit. Host-symbiont interactions with Wolbachia are perhaps best studied in the model organism Drosophila melanogaster, which is naturally infected with five different types among which wMel and wMelCS are the most frequent ones. Comparisons of infection types between natural flies and long-term lab stocks have previously indicated that wMelCS represents the ancestral type, which was only very recently replaced by the nowadays dominant wMel in most natural populations. In this study, we took advantage of recently sequenced museum specimens of D. melanogaster that have been collected 90-200 years ago in Northern Europe to test this hypothesis. Our comparison to contemporary Wolbachia samples provides compelling support for the replacement hypothesis and identifies potential infections with yet unknown Wolbachia types of supergroup B. Our analyses show that sequencing data from historic museum specimens and their bycatch are an emerging and unprecedented resource to address fundamental questions about evolutionary dynamics in host-symbiont interactions.

evolutionary biology↗

bioRxiv2023

Wolbachia has no effect on thermal preference at different life-stages in highly inbred Drosophila melanogaster

Temperature fluctuations are challenging for ectotherms which are not able to regulate body temperature by physiological means and thus have to adjust their thermal environment via behavior. However, little is yet known about whether microbial symbionts influence thermal preference (Tp) in ectotherms by modulating their physiology. Several recent studies have demonstrated substantial effects of Wolbachia infections on host Tp in different Drosophila species. These data indicate that the direction and strength of thermal preference variation is strongly dependent on host and symbiont genotypes and highly variable among studies. By employing highly controlled experiments, we investigated the impact of several environmental factors including humidity, food quality, light exposure, and experimental setup that may influence Tp measurements in adult Drosophila melanogaster flies. Additionally, we assessed the effects of Wolbachia infection on Tp of Drosophila at different developmental stages, which has not been done before. We find only subtle effects of Wolbachia on host Tp which are strongly affected by experimental variation in adult, but not during juvenile life stages. Our in-depth analyses show that environmental variation has a substantial influence on Tp which demonstrates the necessity of careful experimental design and cautious interpretations of Tp measurements together with a thorough description of the methods and equipment used to conduct behavioral studies.

animal behavior and cognition↗

bioRxiv2023

An Ancestral Balanced Inversion Polymorphism Confers Global Adaptation

Since the pioneering work of Dobzhansky in the 1930s and 1940s, many chromosomal inversions have been identified but how they contribute to adaptation remains poorly understood. In Drosophila melanogaster, the widespread inversion polymorphism In(3R)Payne underpins latitudinal clines in fitness traits on multiple continents. Here, we use single-individual whole-genome sequencing, transcriptomics and published sequencing data to study the population genomics of this inversion on four continents: in its ancestral African range and in derived populations in Europe, North America, and Australia. Our results confirm that this inversion originated in sub-Saharan Africa and subsequently became cosmopolitan; we observe marked monophyletic divergence of inverted and non-inverted karyotypes, with some substructure among inverted chromosomes between continents. Despite divergent evolution of this inversion since its out-of-Africa migration, derived non-African populations exhibit similar patterns of long-range linkage disequilibrium between the inversion breakpoints and major peaks of divergence in its center, consistent with balancing selection and suggesting that the inversion harbors alleles that are maintained by selection on several continents. Using RNA-seq we identify overlap between inversion-linked SNPs and loci that are differentially expressed between inverted and non-inverted chromosomes. Expression levels are higher for inverted chromosomes at low temperature, suggesting loss of buffering or compensatory plasticity and consistent with higher inversion frequency in warm climates. Our results suggest that this ancestrally tropical balanced polymorphism spread around the world and became latitudinally assorted along similar but independent climatic gradients, always being frequent in subtropical/tropical areas but rare or absent in temperate climates.

evolutionary biology↗

bioRxiv2021

Restriction of Wolbachia bacteria in early embryogenesis of neotropical Drosophila species via ER-mediated autophagy

Wolbachia bacteria are maternally transmitted intracellular microbes that are not only restricted to the reproductive organs but also found in various somatic tissues of their native hosts. The abundance of the endosymbiont in somatic tissues, usually a dead end for vertically transmitted bacteria, causes a multitude of effects on life history traits of their hosts, which are still not well understood. Thus, deciphering the host-symbiont interactions on a cellular level throughout a hosts lifecycle is of great importance to understand their homeostatic nature, persistence and spreading success. Using fluorescent and transmission electron microscopy, we conducted a comprehensive analysis of Wolbachia tropism in somatic and reproductive tissues of six Drosophila species at the intracellular level during host development. Our data uncovered diagnostic patterns of infections to embryonic primordial germ cells and to particular cells of somatic tissues in three different neotropical Drosophila species of the willistoni and saltans groups that have apparently evolved in both independently. We further found that restricted patterns of Wolbachia tropism are already determined in early fly embryogenesis. This is achieved via selective autophagy, and the restriction of infection is preserved through larval hatching and metamorphosis. We further uncovered tight interactions of Wolbachia with membranes of the endoplasmic reticulum, which might play a scaffolding role for autophagosome formation and subsequent elimination of the endosymbiont. Finally, by analyzing D. simulans lines transinfected with non-native Wolbachia, we uncovered that the host genetic background regulates tissue tropism of infection. Our data demonstrate a peculiar and novel mechanism to limit and spatially restrict bacterial infection in somatic tissues during a very early stage of host development.

developmental biology↗

bioRxiv2021

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 datasets from natural populations of this species have been published over the last 20 years. A major challenge is the integration of these disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution and population structure 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 population samples from over 100 locations in >20 countries on four continents based on a combination of 121 unpublished and 150 previously published genomic datasets. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. 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 dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

genomics↗

bioRxiv2021

Note: Updating the metadata of four misidentified samples in the DrosRTEC dataset

This note details the consortiums rationale behind its decision to modify the metadata for putatively misidentified European samples in the DrosRTEC dataset. In brief, we use PCA on published datasets from North America and Europe to generate phylogeographic clusters reflective of worldwide D. melanogaster demography. We used this PCA to train a DAPC model in order the predict the group membership. Our results indicate that 4 out of 73 samples were misclassified and the metadata was updated accordingly. These samples are a spring-fall pair from Spain and Austria.

genomics↗

bioRxiv2020

The genomic architecture of adaptation to larval malnutrition points to a trade-off with adult starvation resistance in Drosophila

Periods of nutrient shortage impose strong selection on animal populations. Experimental studies of genetic adaptation to nutrient shortage largely focus on resistance to acute starvation at adult stage; it is not clear how conclusions drawn from these studies extrapolate to other forms of nutritional stress. We studied the genomic signature of adaptation to chronic juvenile malnutrition in six populations of Drosophila melanogaster evolved for 150 generations on an extremely nutrient-poor larval diet. Comparison with control populations evolved on standard food revealed repeatable genomic differentiation between the two set of population, involving >3,000 candidate SNPs forming >100 independently evolving clusters. The candidate genomic regions were enriched in genes implicated in hormone, carbohydrate, and lipid metabolism, including some with known effects on fitness-related life-history traits. Rather than being close to fixation, a substantial fraction of candidate SNPs segregated at intermediate allele frequencies in all malnutrition-adapted populations. This, together with patterns of among-population variation in allele frequencies and estimates of Tajimas D, suggests that the poor diet results in balancing selection on some genomic regions. Our candidate genes for tolerance to larval malnutrition showed a high overlap with genes previously implicated in acute starvation resistance. However, adaptation to larval malnutrition in our study was associated with reduced tolerance to acute adult starvation. Thus, rather than reflecting synergy, the shared genomic architecture appears to mediate an evolutionary trade-off between tolerances to these two forms of nutritional stress.

evolutionary biology↗

bioRxiv2020

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 approximately 6500 pool-sequenced Drosophila, sampled from 47 European locations between 2014 and 2016. These include three new Nudiviruses, a new and divergent Entomopox virus, 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 dsRNA 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 12 segments and 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% 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.

microbiology↗