Biology subjects

Dunham, T. J.

Publications and source records attributed to Dunham, T. J..

5 recordsLinked to original sources

bioRxiv2026

Biparental vertical transmission of Aedes anphevirus, Guadeloupe mosquito virus, and verdadero virus in colonized Aedes aegypti

Aedes aegypti mosquitoes can be infected by arboviruses that can be transmitted to and cause disease in vertebrates. Ae. aegypti can also be infected by insect-specific viruses, which do not infect vertebrates, but may impact mosquito biology and vector competence. In this study we characterized the viromes of Ae. aegypti populations that had been maintained in laboratory colonies for 4 to 18 years. Mosquitoes were originally collected in Tapachula, Poza Rica and Merida, Mexico and New Orleans, USA. We used metagenomics to characterize the viruses present in the colonies, then quantified the vertical transmission efficiencies of the viruses by performing crosses between populations. The viruses infecting these colonies included Aedes anphevirus, Guadeloupe mosquito virus, and verdadero virus. These viruses were at high prevalence in infected populations, with over 75% of individual adult mosquitoes infected. All three viruses exhibited biparental vertical transmission: both infected mothers and infected fathers transmitted infection to their offspring, but in all cases maternal transmission was more efficient than paternal. We also identified evidence of possible horizontal transmission between adult mosquitoes that had cohabited during crosses. Efficient transgenerational transmission likely contributes to the ability of these viruses to persist in laboratory populations and nature. Because of their efficient vertical transmission and minimal apparent fitness costs, these viruses could be good candidates for gene delivery to mosquito populations, including for vector control. Author summaryAedes aegypti mosquitoes are responsible for transmission of many dangerous pathogens, including dengue virus, Zika virus, and yellow fever virus. These mosquitoes also carry viruses that do not pose a threat to public health, but might influence mosquito biology. In this study, we identified viruses that persistently infected 4 long-established Ae. aegypti colonies in our insectary. These viruses were at high prevalence in these laboratory populations, and did not appear to harm infected mosquitoes. The viruses exhibited an ability to efficiently transmit from parents to offspring, both from infected mothers and infected fathers. This provided an explanation for how these mosquitoes were able to persist so successfully in laboratory populations, and by extension in nature. Given their ability to efficiently spread and minimal apparent fitness costs, these viruses represent promising candidates for use in mosquito control or other practical applications.

microbiology↗

bioRxiv2026

Quantifying Asymmetric Coevolutionary Dynamics using Normalized Phylogenetic Costs

AO_SCPLOWBSTRACTC_SCPLOWCoevolutionary studies aim to characterize associations, such as virus-host relationships, by using phylogenetic distances to quantify the topological concordance between the phylogenies of interacting taxa. However, phylogenetic distances cannot capture asymmetrical relationships that arise from differences in sampling, evolutionary rates, or characterizations between datasets. Furthermore, a lack of accurate normalization complicates the interpretation and validation of coevolutionary analyses. To address these limitations, we employed the Asymmetric Cluster Affinity and Cluster Support costs as a general framework to quantify coevolutionary patterns across multiple biological scales. We benchmarked the precision of these costs by reanalyzing a curated dataset documenting interspecies transmission frequencies across nineteen virus-host phylogenies. Our results corroborate prior findings showing that all virus families under study can cross species boundaries; however, the asymmetric costs provide a more granular representation, demonstrating that the frequency of such events varies significantly across families. We then applied the Asymmetric Cluster Support cost to quantify preferential gene segment pairings within the Bluetongue virus genome. This analysis revealed a close phylogenetic association between the outer capsid proteins VP2 and VP5, likely reflecting shared selective pressures due to their critical roles in cell entry and exit. In contrast, gene segments encoding nonstructural proteins exhibited discordant evolutionary histories relative to other segments. Finally, we demonstrated that the Asymmetric Cluster Support cost can detect coevolutionary dynamics in swine influenza A virus, identifying novel gene pairings indicative of major viral reassortment events. Overall, our approach demonstrates that normalized asymmetric phylogenetic costs accurately capture complex biological relationships and provide a robust framework for quantifying fine-scale coevolutionary dynamics in rapidly evolving pathogens.

bioinformatics↗

bioRxiv2025

Experimental assessment of 3D-printed traps and chemical attractants for the collection of wild Drosophila melanogaster

Drosophila melanogaster, the common fruit fly, has been instrumental to our understanding of evolution, genetics and disease. There are benefits to studying these flies in the wild, including assessment of their naturally occurring microbiota. To facilitate efforts to catch wild D. melanogaster, we designed two fly traps and evaluated several candidate attractants. The first trap utilized a stable food substrate that can be used to catch live flies to establish new lab colonies. The second trap was designed to be reusable and easy to ship to enable the collection of flies over time from diverse locations. We evaluated several chemical attractants derived from banana and from marula fruit, which is the proposed ancestral food host of D. melanogaster. We found that wild flies were preferentially attracted to banana-based odorants over marula-derived ones. Overall, these traps and attractants represent an inexpensive and simple option for the collection of wild D. melanogaster and related species for sampling or colony establishment.

microbiology↗

bioRxiv2021

Galbut virus infection minimally influences Drosophila melanogaster fitness traits in a strain and sex-dependent manner

Galbut virus (family Partitiviridae) infects Drosophila melanogaster and can be transmitted vertically from infected mothers or infected fathers with near perfect efficiency. This form of super-Mendelian inheritance should drive infection to 100% prevalence, and indeed galbut virus is ubiquitous in wild D. melanogaster populations. But on average only about 60% of individual flies are infected. One possible explanation for this apparent paradox is that a subset of flies are resistant to infection. Although galbut virus infected flies seem healthy, infection may be sufficiently costly to drive selection for resistant hosts, thereby decreasing overall prevalence. To test this hypothesis, we quantified a variety of fitness-related traits in galbut virus infected flies from two lines from the Drosophila Genetic Reference Panel (DGRP). Galbut virus infected flies had slightly decreased average lifespan and total offspring production, but these decreases were mostly not statistically significant. Galbut virus DGRP-517 flies pupated and eclosed slightly faster than their uninfected counterparts. Some galbut virus infected flies exhibited altered sensitivity to viral, bacterial, and fungal pathogens. Galbut virus infection produced minimal changes to host mRNA levels as measured by RNA sequencing, consistent with minimal phenotypic changes. The microbiome composition of flies was not measurably perturbed by galbut virus infection. Differences in phenotype attributable to galbut virus infection varied as a function of fly sex and DGRP strain and were generally dwarfed by larger differences attributable to strain and sex. Thus, galbut virus infection does produce measurable phenotypic changes, with changes being minor, offsetting, and possibly net negative. ImportanceVirology has largely focused on viruses that cause unmistakable phenotypic changes. But metagenomic surveys are revealing that persistent virus infections are extremely common, even in apparently healthy organisms. The extent to which these persistent viruses impact host fitness and evolution remains largely unclear. Here we study fitness impacts of a partitivirus named galbut virus that is ubiquitous in wild D. melanogaster populations. Despite efficient biparental vertical transmission, galbut virus is present in only just over half of wild flies. We quantified various fitness-related traits in galbut virus infected and uninfected fly lines and found that infection produced small but measurable changes in host phenotype that in aggregate may reduce fly fitness. Further studies that take advantage of this virus that naturally infects a premier model organism that is easy to study in the wild will shed further light on the persistent virus-host dynamics that may actually represent most viral infections.

microbiology↗

bioRxiv2020

Partitiviruses infecting Drosophila melanogaster and Aedes aegypti exhibit efficient biparental vertical transmission

Partitiviruses are segmented, multipartite dsRNA viruses that until recently were only known to infect fungi, plants, and protozoans. Metagenomic surveys have revealed that partitivirus-like sequences are also commonly associated with arthropods. One arthropod-associated partitivirus, galbut virus, is extraordinarily common in wild populations of Drosophila melanogaster fruit flies. To begin to understand the processes that underlie this viruss high global prevalence, we established colonies of wild-caught infected flies. Infection remained at stably high levels over three years, with between 63-100% of individual flies infected. Galbut virus infects fly cells and replicates in tissues throughout infected adults, including reproductive tissues and the gut epithelium. We detected no evidence of horizontal transmission via ingestion but vertical transmission from either infected females or infected males was ~100% efficient. Vertical transmission of a related partitivirus, verdadero virus, that we discovered in a laboratory colony of Aedes aegypti mosquitoes was similarly efficient. This suggests that efficient biparental vertical transmission may be a feature of at least a subset of insect-infecting partitiviruses. To study the impact of galbut virus infection free from the confounding effect of other viruses, we generated an inbred line of flies with galbut virus as the only detectable virus infection. We were able to transmit infection experimentally via microinjection of homogenate from these galbut-only flies. This sets the stage for experiments to understand the biological impact and possible utility of partitiviruses infecting important model organisms and disease vectors. ImportanceGalbut virus is a recently discovered partitivirus that is extraordinarly common in wild populations of the model organism Drosophila melanogaster. Like most viruses discovered through metagenomics, most of the basic biological questions about this virus remain unanswered. We found that galbut virus, along with a closely related partitivirus found in Aedes aegypti mosquitoes, is transmitted from infected females or males to offspring with ~100% efficiency and can be maintained in laboratory colonies over years. This represents one of the most efficient means of virus transmission described, and likely underlies the successful spread of these viruses through insect populations. We created Drosophila lines that contained galbut virus as the only virus infection and showed that these flies can be used as a source for experimental infections. This provides insight into how arthropod-infecting partitiviruses may be maintained in nature and sets the stage for exploration of their biology and potential utility.

microbiology↗