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1,737 results for “host data”
Data from: Host conservatism, geography, and elevation in the evolution of a Neotropical moth radiation
The origins of evolutionary radiations are often traced to the colonization of novel adaptive zones, including unoccupied habitats or unutilized resources. For herbivorous insects, the predominant mechanism of diversification is typically assumed to be a shift onto a novel lineage of host plants. However, other drivers of diversification are important in shaping evolutionary history, especially for groups residing in regions with complex geological histories. We evaluated the contributions of shifts in host plant clade, bioregion, and elevation to diversification in Eois (Lepidoptera: Geometridae), a hyper-diverse genus of moths found throughout the Neotropics. Relationships among 107 taxa were reconstructed using one mitochondrial and two nuclear genes. In addition, we used a genotyping-by-sequencing approach to generate 4,641 SNPs for 137 taxa. Both data sets yielded similar phylogenetic histories, with relationships structured by host plant clade, bioregion, and elevation. While diversification of basal lineages often coincided with host clade shifts, more recent speciation events were more typically associated with shifts across bioregions or elevational gradients. Overall, patterns of diversification in Eois are consistent with the perspective that shifts across multiple adaptive zones synergistically drive diversification in hyper-diverse lineages.
wild_expression: gene expression data on wildlife hosts of emerging infectious diseases
<p>Publicly accessible data and code supporting the manuscript:</p> <p>"Host gene expression in wildlife disease: making sense of species-level responses"</p>
Data from: Predator performance and fitness Is dictated by herbivore prey type plus indirect effects of their host plant
<p>Animals, including herbivores and predators, use diet-mixing to balance their macro- and micronutrient intake. Recent work demonstrated that lady beetles fed only pea aphids from fava beans had reduced fitness caused by a deficiency of dietary sterols. However, beetles redressed this deficit by eating fava bean leaves. In the current study we used Coccinella septempunctata as a model to test the hypotheses that pea aphids are a poor sterol resource independent of their host plant, and that fava beans produce low quality prey regardless of aphid species. Additionally, we tested the reproductive rescue capacity of alfalfa and barley foliage compared to fava, and profiled the sterols of phloem exudates, foliage, and aphids reared on these different hosts. Beetle fecundity and egg viability was significantly better when provided pea aphids reared on alfalfa (compared to fava beans) and green peach aphids reared on fava plants. Alfalfa and barley leaves were not consumed by beetles and did not support beetle reproduction. The sterol profile of aphids largely reflected their host plant phloem. However, green peach aphids from fava acquired 125-times more sterol than pea aphids from fava. Our findings show how the sterol content of different host-plants can affect the third trophic level. Our results suggest that 1) prey quality varies depending on prey species, even when they occur on the same plant, 2) plant species can mediate prey quality, 3) host plant-mediated effects on prey quality partially drive omnivory, and 4) diet-mixing benefits growth and reproduction by redressing micronutrient deficits.</p>
Data from: Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida)
<p>Previous work, using morphological characters, identified a generalist copepod parasite (<i>Pharodes tortugensis</i>) at high prevalence on two common gobies (C<i>oryphopterus glaucofraenum</i> and <i>C. dicrus</i>) in the British Virgin Islands (BVI). DNA barcoding subsequently revealed <i>C. glaucofraenum</i> to be three morphologically similar species (<i>C. glaucofraenum</i>, <i>C. venezuelae</i> and <i>C. tortugae</i>), casting doubt on host identities in the BVI and the classification of the parasite as a single species. Mitochondrial cytochrome c oxidase subunit I (COI) data from 67 gobies in the BVI showed that, in addition to <i>C. dicrus</i>, host gobies were a mix of <i>C. glaucofraenum</i> and <i>C. venezuelae,</i> while <i>C. tortugae</i> was unexpectedly absent from the study area. COI data (n = 70) indicated that the copepod infecting all three hosts was a single species, almost certainly <i>P. tortugensis</i>. The pharodes–coryphopterus interaction has a strong impact on host dynamics in the BVI, and a revised understanding of these dynamics must account for any differences among the three newly confirmed hosts in transmission of, and susceptibility to, the shared parasite. No other infected hosts were discovered at our sites, but <i>P. tortugensis</i> is reportedly widespread and infects 12 additional host species elsewhere. Further DNA barcoding is thus needed to test whether <i>P. tortugensis</i> is truly a widespread generalist, or instead represents a group of more specialized cryptic species.</p>
Data from: Endophytes shape the legacy left by the above- and below ground litter of the host affecting the establishment of a legume
<p>Plant litter is a key component of plant-soil feedback (PSF), given its strong potential impacts on plant establishment and growth, through chemical and physical pathways. Although PSF of the layer of dead plant material on the soil surface (aboveground litter) has been widely studied little is known about the role of dead roots (belowground litter) and the impact of plant symbionts on host litter legacy. Here, we examined whether the fungal endophyte Epichloë occultans changed the effects of above and belowground litter of Lolium multiflorum plants on the establishment of Trifolium repens. We hypothesized that both types of litter deposited by the grass-endophyte symbiosis reduce the establishment of the legume due to the release of allelopathic compounds during the decomposition and leaching processes. To test this, we performed two experiments with different quantities of litter produced by plants of the same grass population, with high and low levels of endophyte infection (E+ and E-). Seeds of T. repens were exposed to the aboveground litter with or without the addition of belowground litter, or to their leachates, to separate the physical and chemical pathways. We found that the treatments with the combination of the above and belowground litter produced by E+ plants, increased the germination speed and seedling emergence of T. repens by 56% compared with both types of litter produced by E- plants. A similar effect was also observed with only the aboveground litter. However, the belowground litter of E+ plants reduced the germination speed, seedling emergence by 76% and establishment of T. repens by 73% compared with the belowground litter of E- plants. Besides, the belowground litter had positive effects on the root colonization by arbuscular mycorrhizal fungi and reduced the root nodulation of T. repens. The quantity of litter did not affect any of these responses. Our results suggest that these litter legacy effects could be due to the release of endophyte induced secondary metabolites, such as phenolic and flavonoid compounds. Changes in host plant litter inputs may have consequences for the prevalence of legume plants in grasslands and pastures, affecting their quality and dynamics.</p>
Data from: Arbuscular mycorrhizal fungi communities shaped by host-plant affect the outcome of plant-soil feedback in dryland restoration
<p><span>1. Plant inoculation with Arbuscular mycorrhizal fungi (AMF) can be a useful tool to overcome challenges in dry forest restoration. However, advances are still needed to guide choices regarding soil origin and inoculum production methods, since outcomes can vary due to plant-soil feedbacks (PSF). We evaluate how soil origin and host plant used for inoculum production affect AMF community and therefore the plant biomass accumulation and functional traits.</span></p> <p><span>2. In the conditioning phase, we investigated whether soils originating from a recovered area (Quarry) and a vegetation fragment (Caatinga) would have their AMF communities modified due to the growth of </span><span>Sorghum bicolor</span><span> (used for inoculum production) and </span><span>Senna uniflora</span><span> (used in Brazilian semiarid restoration). In the feedback phase, we compared the performance of four plants species growing on a degraded soil and inoculated or not by a mixture of AMF isolates in comparison to soil inoculum prepared from the conditioning phase.</span></p> <p><span>3. The inoculum from Caatinga presented seven times more AMF species compared to that from the Quarry, which presented ruderal and stress tolerant species. The soil inoculum conditioned by </span><span>S. uniflora</span><span>, regardless of origin, presented greater evenness compared to the soil inoculum produced with </span><span>S. bicolor</span><span> and promoted 33% more plant biomass compared to the control without inoculation. Root colonization by AMF increased PSF and decreased plant investment in functional traits such as specific root length (SRL) and specific leaf area (SLA).</span></p> <p><span>4. Our results demonstrate the importance of adopting strategies that preserve local adaptation of inoculants produced. The use of native plant for propagation of native AMF in the conditioning phase provided more positive responses for </span><span>Mesosphaerum suaveolens</span><span> and </span><span>Rhaphiodon echinus</span><span> than inoculated with introduced AMF isolates. This is probably due to the interaction of inoculated plants with responsive AMF present in the soil.</span></p> <p><span>5. Synthesis and applications</span><span>:</span><span> Our study shows that conditioning field-collected soil with </span><span>S. uniflora</span><span> and using it for inoculation can be a simple technique to promote biomass accumulation for other native herbaceous species. This preserves the compatibility between the soil inoculum produced with native AMF and native plants, representing an important tool for restoration programs</span><span>. </span></p>
Data for: Polymorphism at the nestling stage and host-specific mimicry in an Australasian cuckoo-host arms race
<p>Decades of research have shown that the coevolutionary arms race between avian brood parasites and their hosts can promote phenotypic diversification in hosts and brood parasites. However, relatively little is known about the role of brood parasitism in promoting phenotypic diversification of nestlings. We review field data collected over four decades in Australia, New Caledonia and New Zealand to assess potential for coevolutionary interactions between the shining bronze-cuckoo (<em>Chalcites lucidus</em>) and its hosts, and how diversification at the nestling stage may be generating different subspecies. The shining bronze-cuckoo is a specialist parasite of a few hosts in the family Acanthizidae. It has diversified into subspecies, of which the nestlings closely mimic the respective host nestlings in each region. Additionally, some cuckoo subspecies have polymorphic nestlings. The Acanthizidae hosts have similar breeding and nesting habits and only moderately effective frontline defences against parasitism at cuckoo egg laying or at the egg stages. However, some hosts have developed highly effective defences at the nestling stage by recognising and ejecting cuckoo nestlings from the nest. As with the cuckoo nestlings, some hosts have polymorphic nestlings. The coevolutionary interactions in each region suggest different evolutionary stages of the arms race in which either the parasite or the host is currently in the lead. The presence of moderately effective defences at the egg laying and egg stages might explain why some hosts do not have defences at the nestling stage. The south-Pacific cuckoo – host systems are excellent models to explore the evolutionary mechanisms driving the diversification at the nestling stage in the coevolutionary arms race between avian brood parasites and their hosts.</p>
Data for: Ectoparasite population dynamics affected by host body size but not host density or water temperature in a 32-year long time series
<p>Host density, host body size, and ambient temperature have all been positively associated with increases in parasite infection. However, the relative importance of these factors in shaping long-term parasite population dynamics in wild host populations is unknown due to the absence of long-term studies. Here, we examine long-term drivers of gill lice (Copepoda) infections in Arctic charr (Salmonidae) over 32 years. We predicted that host density and body size and water temperature would all positively affect parasite population size and population growth rate. Our results show that fish size was the main driver of gill lice infections in Arctic charr. In addition, Arctic charr became infected at smaller sizes and with more parasites in years of higher brown trout population size. Negative intraguild interactions between brown trout and Arctic charr appear to drive smaller Arctic charr to seek refuge in deeper areas of the lake, thus increasing infection risk. There was no effect of host density on the force of infection, and the relationship between Arctic charr density and parasite mean abundance was negative, possibly due to an encounter-dilution effect. The population densities of host and parasite fluctuated independently of one another. Water temperature had negligible effects on the temporal dynamics of the gill lice population. Understanding long-term drivers of parasite population dynamics is key for research and management. In fish farms, artificially high densities of hosts lead to vast increases in the transmission of parasitic copepods. However, in wild fish populations fluctuating at natural densities, the surface area available for copepodid attachment might be more important than the density of available hosts.</p>
[Data S2] Microbiota dictate T cell clonal selection to augment graft-vs-host disease after stem cell transplantation
<p><strong>Data</strong> <strong>S2. GLIPH2 hits for all recipient pairs amongst B6 to B6D2F1 transplants with or without antibiotic exposure and 900cGy vs. 1300cGy TBI conditioning. </strong>For all TCRs within each recipient pair (12 mice total, 66 pairs for spleen; 15 pairs for SILP analysis), GLIPH2 specificity groups are generated as described in methods.</p>
[Data S1] Microbiota dictate T cell clonal selection to augment graft-vs-host disease after stem cell transplantation
<p><strong>Data S1. ALICE hits for all recipient pairs amongst B6 to B6D2F1 transplants with or without antibiotic exposure and 900cGy vs. 1300cGy TBI conditioning. </strong>For each recipient pair (12 mice total, 66 pairs for spleen; 15 pairs for SILP analysis), all ALICE hits generated as described in methods.</p>
Data for: Limited host availability disrupts the genetic correlation between virulence and transmission
<p>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 <em>Tetranychus urticae</em> 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.</p>
Data from: Use of an exotic host plant reduces viral burden in a native insect herbivore
<p>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, <em>Plantago lanceolata</em>, impacted immune performance, development, and susceptibility to pathogen infection in the neotropical herbivore<em> Anartia jatrophae</em> (Lepidoptera: Nymphalidae). Caterpillars were reared on <em>P. lanceolata</em> or a native plant, <em>Bacopa monnieri</em>, 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 <em>P. lanceolata</em> compared to <em>B. monnieri</em>, 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.</p>
Data from: Viral transmission and infection prevalence in a cannibalistic host–pathogen system
<div> <div> <div> <div> <p>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 (<em>Spodoptera frugiperda</em>), 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.</p> </div> </div> </div> </div>
Utilizing traditional and remote sensing techniques to assess Colorado potato beetle host preference in the Columbia Basin -- Derived data 2020 & 2021
<p>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:</p> <p><a href="https://zenodo.org/record/6859791#.Y-K6ky-B1z8">https://zenodo.org/record/6859791#.Y-K6ky-B1z8</a></p> <p>If you have any questions or comments regarding this dataset please contact Dr. Max Feldman via email: max.feldman@usda.gov</p>
Utilizing traditional and remote sensing techniques to assess Colorado potato beetle host preference in the Columbia Basin -- 2020 Data
<p>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:</p> <p><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></p> <p>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"<br> <br> If you have any questions or comments regarding this dataset please contact Dr. Max Feldman via email: max.feldman@usda.gov</p>
Data for: Host shift promotes divergent evolution between closely related holoparasitic species
<p>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.</p>
Figures and Data Set of "The Effelsberg survey of FU Orionis and EX Lupi objects I. - Host environments of FUors/EXors traced by NH3"
<p>This is the full version of Figure 1 and the fits files for the NH<sub>3</sub> detections for the paper "The Effelsberg survey of FU Orionis and EX Lupi objects I. - Host environments of FUors/EXors traced by NH<sub>3</sub>".</p> <p>The paper is published in Astronomy & Astrophysics, and can be found at: <a href="https://doi.org/10.1051/0004-6361/202244911">https://doi.org/10.1051/0004-6361/202244911</a></p> <p> </p>
Clownfish Hosting Anemone Location Data from GBIF
<p>This is a location dataset derived from GBIF location data for the 10 Clownfish hosting anemones. The data was downloaded, filtered, and used to create range maps in R. The species included are:</p> <ol> <li>Cryptodendrum adhaesivum</li> <li>Entacmaea quadricolor</li> <li>Heteractis aurora</li> <li>Heteractis crispa</li> <li>Heteractis magnifica</li> <li>Heteractis malu</li> <li>Macrodactyla doreensis</li> <li>Stichodactyla gigantea</li> <li>Stichodactyla haddoni</li> <li>Stichodactyla mertensii</li> </ol>
Data for: The impact of wildlife and environmental factors on hantavirus infection in host and its translation into human risk
<p><span>Identifying factors that drive infection dynamics in reservoir host populations is essential in understanding human risk from wildlife-originated zoonoses. We studied zoonotic <em>Puumala</em> <em>orthohantavirus</em> (PUUV) in the host, the bank vole (<em>Myodes</em> <em>glareolus</em>), populations in relation to the host population, rodent and predator community and environment-related factors and whether these processes are translated into human infection incidence. We used 5-year rodent trapping and bank vole PUUV serology data collected from 30 sites located in 24 municipalities in Finland. We found that PUUV seroprevalence was negatively associated with the abundance of red foxes, but this process did not translate into human disease incidence, which showed no association with PUUV seroprevalence. The abundance of weasels, the proportion of juvenile bank voles in the host populations and rodent species diversity were negatively associated with the abundance index of PUUV-positive bank voles, which, in turn, showed a positive association with human disease incidence. Our results suggest certain predators, high proportion of young bank vole individuals and a diverse rodent community, may reduce PUUV risk for humans through their negative impacts on the abundance of infected bank voles.</span></p>
Data for: Dispersal-limited symbionts exhibit unexpectedly wide variation in host specificity
<p>A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macroevolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode versus multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. Comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts.</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
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