Find research datasets worth reusing

Vindas et al. Brain-infecting parasites leave lasting effects on behaviour even in resistant hosts

Parasites can have profound effects on intra- and inter-specific interactions at the population and community levels through their influence on host behaviour, physiology, and fitness. While host phenotypic changes are typically thought of in terms of established infections, parasite encounters may be sufficient to induce behavioural changes, even when no viable infections are established. Here, we use the Japanese rice fish medaka Oryzias latipes and the brain-infecting microsporidan parasite Pseudoloma neurophilia to understand how parasite resistance influences behaviour. Although a previous study suggested that medaka are a suitable host for P. neurophilia, an eight-week parasite exposure regime resulted in no detectable infection in our study. Both parasite-exposed and control (no parasite exposure) medaka were tested in behavioural assays that assessed boldness, activity, and sociality. We detected considerable changes in medaka behaviour following parasite exposure, with parasite-exposed fish being more active, less bold, and more social when compared to control fish. These data indicate that parasite encounters may induce behavioural alterations even in non-susceptible hosts. In addition to established infection, individual differences in parasite exposure must also be considered in studies of host responses across ecological scales.

Hosts winnow symbionts with multiple layers of absolute and conditional discrimination mechanisms

In mutualism, hosts select symbionts via partner choice and preferentially direct more resources to symbionts that provide greater benefits via sanctions. At the initiation of symbiosis, prior to resource exchange, it is not known how the presence of multiple symbiont options (i.e., the symbiont social environment) impacts partner choice outcomes. Furthermore, little research addresses whether hosts primarily discriminate among symbionts via sanctions, partner choice or a combination. We inoculated the legume, Acmispon wrangelianus, with 28 pairs of fluorescently labeled Mesorhizobium strains that vary continuously in quality as nitrogen-fixing symbionts. We find that hosts exert robust partner choice, which enhances their fitness. This partner choice is conditional such that a strain's success in initiating nodules is impacted by other strains in the social environment. This social genetic effect is as important as a strain's own genotype in determining nodulation and has both transitive (consistent) and intransitive (idiosyncratic) effects on the probability that a symbiont will form a nodule. Furthermore, both absolute and conditional partner choice act in concert with sanctions, among and within nodules. Thus, multiple forms of host discrimination act as a series of sieves that optimize host benefits and select for costly symbiont cooperation in mixed symbiont populations.

Data for: Limited host availability disrupts the genetic correlation between virulence and transmission

Virulence is expected to be linked to parasite fitness via transmission. However, it is not clear whether this relationship is genetically determined, nor if it differs when transmission occurs continuously during, or only at the end of, the infection period. Here, we used inbred lines of the macro-parasitic spider mite Tetranychus urticae to disentangle genetic vs non-genetic correlations among traits, while varying parasite density and opportunities for transmission. A positive genetic correlation between virulence and the number of transmitting stages produced was found under continuous transmission. However, if transmission occurred only at the end of the infection period, this genetic correlation disappeared. Instead, we observed a negative relationship between virulence and the number of transmitting stages, driven by density dependence. Thus, within-host density dependence caused by reduced opportunities for transmission may hamper selection for higher virulence, providing a novel explanation as to why limited host availability leads to lower virulence.

Data from: Use of an exotic host plant reduces viral burden in a native insect herbivore

Incorporation of exotic plants into the diets of native herbivores is a common phenomenon, influencing interactions with natural enemies and providing insight into the tritrophic costs and benefits of dietary expansion. We evaluated how use of an exotic plant, Plantago lanceolata, impacted immune performance, development, and susceptibility to pathogen infection in the neotropical herbivore Anartia jatrophae (Lepidoptera: Nymphalidae). Caterpillars were reared on P. lanceolata or a native plant, Bacopa monnieri, and experimentally infected with a pathogenic virus, Junonia coenia densovirus. We found that virus-challenged herbivores exhibited higher survival rates and lower viral burdens when reared on P. lanceolata compared to B. monnieri, though immune performance and development time were largely similar on the two plants. These findings reveal that use of an exotic plant can impact the vulnerability of a native herbivore to pathogen infection, suggesting diet-mediated protection against disease as a potential mechanism facilitating the incorporation of novel resources.

The timings of host diapause and epidemic progression mediate host genetic diversity and future epidemic size in Daphnia-parasite populations

Epidemics commonly exert parasite-mediated selection and cause declines in host population genetic diversity. This could lead to evolution of resistance in the long-term and smaller subsequent epidemics. Alternatively, the loss of genetic diversity could increase host vulnerability to future disease spread and larger future epidemics. Matters are made more complex by the fact that a great many host organisms produce diapausing life stages in response to environmental change (often as a result of sexual reproduction) e.g., plant seeds and invertebrate resting eggs. These diapausing stages can disrupt the relationship between past epidemics, host genetic diversity and future epidemics because they allow host dispersal through time. Specifically, temporally dispersing hosts avoid infection and thus selection from contemporary parasites, and also archive genetic variation for the future. We studied 80 epidemics in 20 semi-natural populations of the temporally dispersing crustacean Daphnia magna and its sterilising bacterial parasite Pasteuria ramosa, and half of these populations experienced a simulated environmental disturbance treatment. We found that early initiation of diapause relative to the timing of the epidemic led to greater host genetic diversity and reduced epidemic size in the subsequent year, but this was unaffected by environmental disturbance.

Vegetation cover and biodiversity reduce parasite infection in wild hosts across ecological levels and scales

Land use changes and biodiversity loss critically disrupt ecosystem functioning and are major drivers of infectious disease outbreaks. Trypanosoma cruzi, the agent of Chagas disease, is a multi-host parasite whose epidemiology has changed due to the expansion of anthropogenic activities over natural areas. We aimed to understand the ecological processes increasing parasite prevalence at the individual, the community and the landscape levels using the largest database on small mammal infection by T. cruzi in Brazil. We applied machine learning techniques and structural equation models to show that allometric traits and the relative abundance of rodents in the community were important predictors of infection risk, followed by variables associated with the landscape environmental quality. Natural vegetation cover change and the taxonomic and functional dimensions of biodiversity indirectly reduced infection through its effect on the abundance distribution and composition of host communities. According to our findings, approaches to biodiversity conservation and restoration based on the integration of social inclusion and human welfare would contribute to regulating the prevalence of T. cruzi in wild hosts, which may reduce overall transmission risk.

Data from: Viral transmission and infection prevalence in a cannibalistic host–pathogen system

<div> <div> <div> <div> Cannibalism, while prevalent in the natural world, is often viewed as detrimental to a cannibal's health, especially when they consume pathogen-infected conspecifics. The argument stems from the idea that cannibalizing infected individuals increases the chance of coming into contact with a pathogen and subsequently becoming infected. Using an insect pest, the fall armyworm (Spodoptera frugiperda), that readily cannibalizes at the larval stage and its lethal pathogen, we experimentally examined how cannibalism affects viral transmission at both an individual and population level. Prior to death, the pathogen in the system stops the larval host from growing, resulting in infected individuals being smaller than healthy individuals. This leads to size-structured cannibalism of infected individuals with the larger healthy larvae consuming the smaller infected larvae, which is commonly observed. At the individual level, we show that the probability of cannibalism is relatively high for both infected and uninfected individuals especially when the cannibal is larger than the victim. However, the probability of the cannibal becoming infected given that a pathogen-infected individual has been cannibalized is relatively low. On a population level, when cannibalism is allowed to occur transmission rates decline. Additionally, by cannibalizing infected larvae, cannibals lower the infection risk for non-cannibals. Thus, cannibalism can decrease infection prevalence and, therefore, may not be as deleterious as once thought. Under certain circumstances, cannibalizing infected individuals, from the uninfected host's perspective, may even be advantageous, as one obtains a meal and decreases competition for resources with little chance of becoming infected. </div> </div> </div> </div>

Thicker eggshells are not predicted by host egg ejection behaviour in four species of Australian cuckoo

Defences of hosts against brood parasitic cuckoos include detection and ejection of cuckoo eggs from the nest. Ejection behaviour often involves puncturing the cuckoo egg, which is predicted to drive the evolution of thicker eggshells in cuckoos that parasitise such hosts. Here we test this prediction in four Australian cuckoo species and their hosts, using Hall-effect magnetic-inference to directly estimate eggshell thickness in parasitised clutches. In Australia, hosts that build cup-shaped nests are generally adept at ejecting cuckoo eggs, whereas hosts that build dome-shaped nests mostly accept foreign eggs. We analysed two datasets: a small sample of hosts with known egg ejection rates and a broader sample of hosts where egg ejection behaviour was inferred based on nest type (dome or cup). Contrary to predictions, cuckoos that exploit dome-nesting hosts (acceptor hosts) had significantly thicker eggshells relative to their hosts than cuckoos that exploit cup-nesting hosts (ejector hosts). No difference in eggshell thicknesses was observed in the smaller sample of hosts with known egg ejection rates, probably due to lack of power. Overall cuckoo eggshell thickness did not deviate from the expected avian relationship between eggshell thickness and egg length estimated from 74 bird species. Our results do not support the hypothesis that thicker eggshells have evolved in response to host ejection behaviour in Australian cuckoos, but are consistent with the hypothesis that thicker eggshells have evolved to reduce the risk of breakage when eggs are dropped into dome nests.

opencc-by-4.0Jan 2023View details →

Utilizing traditional and remote sensing techniques to assess Colorado potato beetle host preference in the Columbia Basin -- Derived data 2020 & 2021

This is derived data from a remote sensing experiment performed in 2020 and 2021. This repository contains .csv and .R files that can be used to replicate the analysis presented here: <a href="https://zenodo.org/record/6859791#.Y-K6ky-B1z8">https://zenodo.org/record/6859791#.Y-K6ky-B1z8</a> If you have any questions or comments regarding this dataset please contact Dr. Max Feldman via email: max.feldman@usda.gov

opencc-by-4.0Jan 2023View details →

Utilizing traditional and remote sensing techniques to assess Colorado potato beetle host preference in the Columbia Basin -- 2020 Data

This is a remote sensing dataset collected in 2020 that contains orthomosaic images, shape files, analysis scripts, and derived numerical data from each plot. Data was collected using the protocol described here: <a href="https://www.protocols.io/view/usda-ars-potato-genetics-lab-drone-data-collection-bp2l6148dvqe/v1">https://www.protocols.io/view/usda-ars-potato-genetics-lab-drone-data-collection-bp2l6148dvqe/v1</a> Provided are "field map" files that denote the location and contents of each plot, a folder from each date that contains the 5 band orthomosiac, surface model image, a cropped and rotated image, shape files indicating the location of each plot, and derived data. The analysis can be replicated by following along with workflow listed in file named: rondon_cpb_2020.R. Derived data from this experiment can be found it the file named: "Rondon_CPB_data_2020_UAS_all.csv" If you have any questions or comments regarding this dataset please contact Dr. Max Feldman via email: max.feldman@usda.gov

Genomic evidence for contrasting patterns of host‐associated genetic differentiation across shared host‐plant species in leaf‐ and bud‐galling sawflies

Resource specialization and host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous examples of HAD in insect herbivores, the general rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary time scales. We applied genome-wide SNP data obtained through low-coverage genome resequencing to define species limits and to compare host-plant use in population samples of leaf- and bud-galling sawflies collected from seven shared willow (Salix) host species. To infer the repeatability of long-term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their Salix hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species than are most bud gallers. In contrast to bud gallers, leaf gallers also exhibit statistically significant cophylogenetic signal with their Salix hosts. The observed discordant patterns of resource specialization and long-term host use in two related galler groups that have radiated in parallel across a shared resource base indicate a general lack of evolutionary repeatability and suggest that short- and long-term host use and ecological diversification in plant-feeding insects are dominated by stochasticity and/or lineage-specific effects.

Data for: Host shift promotes divergent evolution between closely related holoparasitic species

Distinct hosts have been hypothesized to possess the potential for affecting species differentiation and genome evolution of parasitic organisms. However, what host shift history is experienced by the closely related parasites and whether disparate evolution of their genomes occur remain largely unknown. Here, we screened horizontal gene transfer (HGT) events in a pair of sister species of holoparasitic Boschniakia (Orobanchaceae) having obligate hosts from distinct families to recall the former host-parasite associations and performed a comparative analysis to investigate the difference of their organelle genomes. Except these from present hosts (Ericaceae and Betulaceae), a number of HGTs from Rosaceae were identified to support the occurrence of unexpected ancient host shifts. Different hosts transfer functional genes which changed nuclear genomes of the sister species. Similarly, different donors transfer sequences to their mitogenomes which size varies due to foreign and repetitive elements rather than other factors found in other parasites. The plastomes are both severely reduced, but the extent of differences in reduction syndrome is near to the genus level. Our findings provide new insights into the genome evolution of parasites adapting different hosts and extend the mechanism of host shift promoting species differentiation to parasitic plant lineages.

opencc-by-4.0Feb 2023View details →

Datasets and R script to replicate the theoretical modeling from the article entitled Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission

Datasets and R script to replicate the theoretical modeling from the article entitled " Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission" by Vantaux A., Moiroux N., Dabire K. R., Cohuet A., Lefevre T. 2023

Spatial structure and benefits to hosts allow plasmids with and without post-segregational killing (PSK) systems to coexist

To persist a plasmid relies on being passed on to a daughter cell, but this does not always occur. Plasmids with post-segregational killing (PSK) systems kill a daughter cell if it has not been passed on. By killing the host, it also kills competing plasmids in the same host, something competing plasmids without a similar system cannot do. Accordingly, plasmids with PSK systems can displace other plasmids. In nature, plasmids with and without PSK systems coexist and prior theory has suggested this is expected to be very rare or unstable, such that one or the other type of plasmid eventually takes over. Here, we show that if there is spatial structure and plasmids confer benefits to hosts, coexistence of plasmids occurs broadly. Often plasmids confer benefits (even ones with a PSK system) and bacteria are often spatially structured. So, our results may be generally applicable.

Ability of the ash dieback pathogen to reproduce and to induce damage on its host are controlled by different environmental parameters

Ash dieback, induced by an invasive ascomycete, Hymenoscyphus fraxineus, has emerged in the late 1990s as a severe disease threatening ash populations in Europe. Future prospects for ash are improved by the existence of individuals with natural genetic resistance or tolerance to the disease and by limited disease impact in many environmental conditions where ash is common. Nevertheless, it was suggested that, even in those conditions, ash trees are infected and enable pathogen transmission. We studied the influence of climate and local environment on the ability of H. fraxineus to infect, be transmitted and cause damage on its host. We showed that healthy carriers, i.e. individuals showing no dieback but carrying H. fraxineus, exist and may play a significant role in ash dieback epidemiology. The environment strongly influenced H. fraxineus with different parameters being important depending on the life cycle stage. The ability of H. fraxineus to establish on ash leaves and to reproduce on the leaf debris in the litter (rachises) mainly depended on total precipitation in July-August and was not influenced by local tree cover. By contrast, damage to the host, and in particular shoot mortality was significantly reduced by high summer temperature in July-August and by high autumn average temperature. As a consequence, in many situations, ash trees are infected and enable H. fraxineus transmission while showing limited or even no damage. We also observed a decreasing trend of severity (leaf necrosis and shoot mortality probability) with the time of disease presence in a plot that could be significant for the future of ash dieback.

The association of host and vector characteristics with Ctenocephalides felis pathogen and endosymbiont infection

Surveillance of the flea species and flea-borne pathogens infecting cats is important for both human and animal health. Multiple zoonotic Bartonella and Rickettsia species are known to infect the most common flea-infesting cats and dogs worldwide: Ctenocephalides felis, the cat flea. The ability of other flea species to transmit pathogens is relatively unexplored. We aimed to determine cat host and flea factors independently associated with flea infection with Bartonella and Rickettsia species. We also compared the presence and prevalence of cat host and flea pathogen infection by geographic location. To accomplish these aims, we performed qPCR for the detection of Bartonella, hemotropic Mycoplasma, Rickettsia, and Wolbachia DNA using paired cat and flea samples obtained from free-roaming cats presenting for spay or neuter across multiple geographic locations in the United States. A logistic regression model was employed to identify the effect of cat (sex, body weight, geographic location, and Bartonella, hemotropic Mycoplasma, and Rickettsia spp. infection) and flea (clade, pathogen infection, and Wolbachia infection) factors on C. felis Bartonella clarridgeiae infection. From 189 free-roaming cats, we collected 84 fleas from four flea species: Ctenocephalides felis (78/84, 92%), Cediopsylla simplex (4/84, 5%), Orchopeas howardi (1/84), and Nosopsyllus fasciatus (1/84). Ctenocephalides felis were phylogenetically assigned to Clades 1, 4, and 6 by cox1 gene amplification. Rickettsia asembonensis (52/84, 62%) and B. clarridgeiae (16/84, 19%) were the most common pathogenic bacteria detected in fleas. Our model identified host cat sex and body weight as independently associated with B. clarridgeiae infection in fleas. When controlling for cat sex, body weight, and number of fleas collected from each cat, flea infection with B. clarridgeiae was not associated with geographic location, flea infection with Rickettsia spp. or Wolbachia spp., or cat infection with B. clarridgeiae. Rickettsia asembonensis, Rickettsia felis (7/84, 8%), and Bartonella henselae (7/84, 8%) were only found in fleas from specific clades: R. felis was detected only in Clades 1 and 6, while B. henselae and R. asembonensis were detected only in Clade 4. Wolbachia spp. also displayed clade specificity with strains other than Wolbachia wCfeT only infecting fleas from Clade 6. There was poor flea and host agreement for Bartonella spp. infection; however, there was agreement in the Bartonella species detected in cats and fleas by geographic location. These findings reinforce the importance of considering reservoir host attributes and vector phylogenetic diversity in epidemiological studies of flea-borne pathogens. Furthermore, while flea pathogen infection was not indicative of infection in a specific host cat, it may provide insight into the pathogens present in specific geographic areas. Widespread sampling from across the United States is necessary to identify the geographic, host, and vector factors driving flea-borne pathogen presence and transmission.

Feeding on a Bartonella henselae infected host triggers temporary changes in the Ctenocephalides felis microbiome

The effect of Bartonella henselae on the microbiome of its vector, Ctenocephalides felis (the cat flea) is largely unknown, as a majority of C. felis microbiome studies have utilized wild-caught pooled fleas. Therefore, we surveyed the microbiome of laboratory-origin C. felis fed on B. henselae-infected cats to identify changes to microbiome diversity and microbe prevalence compared to unfed fleas, and fleas fed on uninfected cats. To evaluate changes over time, fleas were fed on cats for 24 hours or 9 days. Utilizing Next Generation Sequencing (NGS) on the Illumina platform, we documented an increase in microbial diversity, richness, and evenness in C. felis fed on Bartonella-infected cats for 24 hours, changes that returned to baseline (unfed fleas or fleas fed on uninfected cats) after 9 days on the host. The increased diversity in the C. felis microbiome when fed on B. henselae-infected cats may be related to the mammalian, flea, or endosymbiont response, factors that remain to be explored and potentially exploited for pathogen control. In addition, poor B. henselae acquisition was documented in these laboratory-maintained C. felis. Potential hypotheses to account for this finding include poor acquisition by adult fleas, the influence of flea genetic variation on B. henselae acquisition, and lack of co-feeding with B. henselae-infected C. felis. This study provides an investigation of the C. felis microbiome response to blood feeding and blood-feeding on B. henselae-infected cats; however, future studies are necessary to fully characterize the effect of endosymbionts and C. felis diversity on B. henselae acquisition.

opencc-by-4.0Feb 2023View details →

Datasets related to identification of invasive weeds S. elaeagnifolium, S. rostratum and S. nigrum as potential ToBRFV hosts

These datasets highlight the invasive weeds S. elaeagnifolium, S. rostratum and S. nigrum as potential ToBRFV hosts, and support the data provided directly in the scientific publication titled "Solanum elaeagnifolium and S. rostratum as potential hosts of the tomato brown rugose fruit virus", published in the <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0282441#ack">PLOS journal</a>.  The data was obtained through a series of viral inoculations and bioassays, serological tests for viral infections (i.e. ELISA), viral RNA extraction and reverse transcription (RT)-PCR, as well as quantitative RT-PCR (RT-qPCR). The methods are described directly in the scientific publication with indicators allowing for interoperability and reusability by fellow researchers.   The provided datasets are discussed and interpreted in detail, as well as their subsequent results, in the scientific publication. This research was conducted within the VIRTIGATION project, which is part of the EU Open Research Data pilot. This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 101000570.

opencc-zeroMar 2023View details →

Dating the origin and spread of specialization on human hosts in Aedes aegypti mosquitoes

The globally invasive mosquito subspecies Aedes aegypti aegypti is a highly effective vector of human arboviruses because it specializes in biting humans and breeding in human habitats. Recent work suggests that specialization first arose as an adaptation to long, hot dry seasons in the West African Sahel, where Ae. aegypti is forced to rely on human-stored water for breeding. However, rainfall patterns in this region have changed dramatically over the past 10–20 thousand years, and we do not yet know exactly when specialization occurred. Here we use whole-genome cross-coalescent analysis to date the emergence of human specialist populations in the Sahel and thus further probe the climate hypothesis. Importantly, we take advantage of the known migration of human-specialist populations out of Africa during the Atlantic Slave Trade to calibrate the coalescent clock and thus obtain a more precise estimate of the older evolutionary event than would otherwise be possible. We find that human-specialist mosquitoes diverged rapidly from ecological generalists approximately 5,000 years ago, which corresponds to the end of the African Humid Period—a time when the Sahara dried and water stored by humans became a uniquely stable, aquatic niche in the Sahel. We also use population genomic analyses to date a previously observed influx of human-specialist alleles into major West African cities, where mosquitoes tend to be more attracted to humans than in nearby rural populations regardless of climate. In this case, the characteristic length of tracts of human-specialist ancestry present on a generalist genetic background in Kumasi, Ghana and Ouagadougou, Burkina Faso suggests the change in behavior occurred during rapid urbanization over the last 20–40 years. Taken together, we show that the timing and ecological context of two previously observed shifts toward human biting in Ae. aegypti differ; climate was likely the original driver, but urbanization has become increasingly important in recent decades. Understanding the changing relationship between mosquitoes and humans over time is critical for predicting and managing the burdens of mosquito-borne disease.