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Fig. 1. Sampling sites for Idarnes wasps associated with Ficus petiolaris. Idarnes wasps were collected from host F in Community Structure and Undescribed Species Diversity in Non-Pollinating Fig Wasps Associated with the Strangler Fig Ficus petiolaris
Fig. 1. Sampling sites for Idarnes wasps associated with Ficus petiolaris. Idarnes wasps were collected from host F. petiolaris localities distributed across Sonoran Desert habitats in Baja California (1–11) and Sonora (12–16), Mexico. Locales 1–13 are from F. petiolaris subspecies palmeri and locales 14–16 are from F. petiolaris subspecies petiolaris. See Table 1 for additional details.
Figure 4 in Distinct parasitoid communities associated with host races of the leaf-mining moth Acrocercops transecta on distantly related host plants (Juglandaceae and Ericaceae)
Figure 4. Modes of parasitism of parasitoids attacking Acrocercops transecta. (A) An ovipositing female of Aneurobracon philippinensis. Before finding host larvae, females track host mines by drumming with their antennae; (B) a final instar of A. transecta that is making a cocoon; (C) a dissected cocoon of A. transecta. A prepupa of A. transecta (upper side) is fed upon by a larva of An. philippinensis (under side); (D) a pupa of An. philippinensis in the cocoon made by A. transecta; (E) a pupa of Choeras sp. in the cocoon made by A. transecta; (F) a final instar of A. transecta parasitized by Pholetesor sp. A hole is visible on the right side of the second abdominal segment from which a Pholetesor sp. larva exits the host; (G) a cocoon of Pholetesor sp. formed inside its host's mine; (H) a Eulophidae larva feeding inside its host's body; (I) a Eulophidae pupa formed inside its host's mine.
Figure 1 in Distinct parasitoid communities associated with host races of the leaf-mining moth Acrocercops transecta on distantly related host plants (Juglandaceae and Ericaceae)
Figure 1. Leaf mines of Acrocercops transecta. (A) Three mines of the Juglandaceae race on a leaflet of Juglans mandshurica; (B) a mine of the Lyonia race on Lyonia ovalifolia.
Additional information for manuscript entiteld "Host-parasitoid associations in marine planktonic time series: can metabarcoding help reveal them?" (PONE-D-20-17825R1)
<p><strong>Description:</strong></p> <p>This repository contains material to reproduce metabarcoding analyses based on the q-zip pipeline (https://github.com/PyoneerO/qzip). Raw fastq files can be downloaded from https://www.ebi.ac.uk/ena/browser/view/PRJEB37135. The used reference file can be downloaded from https://github.com/pr2database/pr2database/releases/tag/4.11.1. Please select the files created for the classifier implemented in mothur.</p> <p>The dockerfile in this repository can be used to set up the environment which inludes the installation of the needed versions of the needed tools.</p> <p>Twelve different analyses had been conducted. For each analysis one zip file had been created which contains the following files:</p> <p>- q-zip_commands.sh: the shell script to launch the pipeline</p> <p>- q-zip_parameters.txt: pipeline parameter file as input of the shell script</p> <p>- q-zip_workflow.log: log file containing stdout and sdterr</p> <p>- q-zip_seq_of_coms.txt: file containing each command executed during the pipeline run (minimal set of command to reproduce the results)</p> <p>- seq_number_stats.txt: file containing the sequence numbers at each filtering step</p> <p>- OTU tables in tsv and biom format (sequences and taxonomic annotation included)</p> <p>- Meta data map (here only including the raw file names)</p> <p>- swarm sequences in fasta format</p> <p> </p> <p><strong>The following analyses had been conducted:</strong></p> <p>- otu formation at swarm distance 1; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 2; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 3; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 5; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 10; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 1; relaxt settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 2; relaxt settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 3; relaxt settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 1; strict settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 2; strict settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 3; strict settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 1; very strict settings settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p><strong>Settings into more detail:</strong></p> <p>relaxt settings:</p> <ul> <li>trimmomatic filtering: sliding window length of 3 bp - threshold of average quality within of 5</li> <li>vsearch paired-end merging: length of minimum overlap of 25 bp - number of mismatches allowed of 5 bp</li> <li>cutadapt primer removal: percentage primer to sequence overlap of 75% - percentage mismatches allowed of 20%</li> <li>vsearch eeMax filtering: max number of errors expected per sequence of 1 bp</li> <li>minimum sequence length of 300 bp and maximum sequence length of 550 bp</li> <li>mothur classification cutoff (refers to confidence threshold of NBC) of 0.6</li> </ul> <p>default settings (used for the manuscript):</p> <ul> <li>trimmomatic filtering: sliding window length of 3 bp - threshold of average quality within of 8</li> <li>vsearch paired-end merging: length of minimum overlap of 50 bp - number of mismatches allowed of 5</li> <li>cutadapt primer removal: percentage primer to sequence overlap of 90% - percentage mismatches allowed of 10%</li> <li>vsearch eeMax filtering: max number of errors expected per sequence of 0.25 bp</li> <li>minimum sequence length of 300 bp and maximum sequence length of 550 bp</li> <li>mothur classification cutoff (refers to confidence threshold of NBC) of 0.8</li> </ul> <p>strict settings:</p> <ul> <li>trimmomatic filtering: sliding window length of 1 bp - threshold of average quality within of 15</li> <li>vsearch paired-end merging: length of minimum overlap of 50 bp - number of mismatches allowed of 0</li> <li>cutadapt primer removal: percentage primer to sequence overlap of 90% - percentage mismatches allowed of 10%</li> <li>vsearch eeMax filtering: max number of errors expected per sequence of 0.1 bp</li> <li>minimum sequence length of 300 bp and maximum sequence length of 550 bp</li> <li>mothur classification cutoff (refers to confidence threshold of NBC) of 0.9</li> </ul> <ul> </ul> <p>very strict settings:</p> <ul> <li>trimmomatic filtering: sliding window length of 1 bp - threshold of average quality within of 15</li> <li>vsearch paired-end merging: length of minimum overlap of 50 bp - number of mismatches allowed of 0</li> <li>cutadapt primer removal: percentage primer to sequence overlap of 100% - percentage mismatches allowed of 0%</li> <li>vsearch eeMax filtering: max number of errors expected per sequence of 0.1 bp</li> <li>minimum sequence length of 300 bp and maximum sequence length of 550 bp</li> <li>mothur classification cutoff (refers to confidence threshold of NBC) of 0.9</li> </ul>
Asymmetric, but opposing reductions in immigrant viability and fecundity promote reproductive isolation among host-associated populations of an insect herbivore
<p>Immigrant inviability can contribute to reproductive isolation (RI) during ecological speciation by reducing the survival of immigrants in non-native environments. However, studies that assess the fitness consequence of immigrants moving from native to non-native environments typically fail to explore the potential role of concomitant reductions in immigrant fecundity despite recent evidence suggesting its prominent role during local adaptation. Here, we evaluate the directionality and magnitude of both immigrant viability and fecundity to RI in a host specific gall-forming wasp, Belonocnema treatae. Using reciprocal transplant experiments replicated across sites, we measure immigrant viability and fecundity by comparing differences in the incidence of gall formation (viability) and predicted number of eggs per female (fecundity) between residents and immigrants in each of two host-plant environments. Reduced immigrant viability was found in one environment while reduced immigrant fecundity was found in the other. Such habitat-dependent barriers resulted in asymmetric RI between populations. By surveying recent literature on local adaptation, we find that asymmetry in immigrant viability and fecundity are widespread across disparate taxa, which highlights the need to combine estimates of both common and overlooked barriers in cases of potential bi-directional gene flow to create a more comprehensive view of the evolution of RI.</p>
Association of the systemic host immune response with acute hyperglycemia in mechanically ventilated septic patients
<p>Hyperglycemia during sepsis is associated with increased organ dysfunction and higher mortality. The role of the host immune response in development of hyperglycemia during sepsis remains unclear. We performed a cross-sectional analysis of critically ill adult septic patients requiring mechanical ventilation (n=153) to study the relationship between hyperglycemia and ten markers of the host immune response measured on the first day of ICU admission (baseline). We determined associations between each biomarker and: (1) glucose, insulin, and c-peptide levels at the time of biomarker collection by Pearson correlation; (2) average glucose and glycemic variability in the first two days of ICU admission by linear regression; and (3) occurrence of hyperglycemia (blood glucose>180mg/dL) by logistic regression. Results were adjusted for age, pre-existing diabetes mellitus, severity of illness, and total insulin and glucocorticoid dose. Baseline plasma levels of ST2 and procalcitonin were positively associated with average blood glucose and glycemic variability in the first two days of ICU admission in unadjusted and adjusted analyses. Additionally, higher baseline ST2, IL-1ra, procalcitonin, and pentraxin-3 levels were associated with increased risk of hyperglycemia. Our results suggest associations between the host immune response and hyperglycemia in critically ill septic patients particularly implicating the interleukin-1 axis (IL-1ra), the interleukin-33 axis (ST2), and the host response to bacterial infections (procalcitonin, pentraxin-3).</p>
Figures 1-6 from: Li Q, Wang C, Hu H-Y (2021) Two new species of Dzhanokmenia (Hymenoptera, Eulophidae) from China, with first report on a host association for the genus. ZooKeys 1009: 67-79. https://doi.org/10.3897/zookeys.1009.57556
Figures 1-6 Dzhanokmenia stefaniolae, female (holotype): 1 habitus, dorsal 2 mesosoma, lateral 3 head, frontal 4 head, dorsal 5 wings 6 metasoma, dorsal. Scale bars: 0.2 mm.
Figures 19-26 from: Li Q, Wang C, Hu H-Y (2021) Two new species of Dzhanokmenia (Hymenoptera, Eulophidae) from China, with first report on a host association for the genus. ZooKeys 1009: 67-79. https://doi.org/10.3897/zookeys.1009.57556
Figures 19-26 Dzhanokmenia yuxuannis, female (19–22 holotype 23–26 paratypes): 19 habitus, lateral 20 body, dorsal 21 head, frontal 22 wings 23, 25 metasoma, dorsal 24, 26 metasoma, ventral. Scale bars: 0.2 mm.
Figures 13-18 from: Li Q, Wang C, Hu H-Y (2021) Two new species of Dzhanokmenia (Hymenoptera, Eulophidae) from China, with first report on a host association for the genus. ZooKeys 1009: 67-79. https://doi.org/10.3897/zookeys.1009.57556
Figures 13-18 13–17Stefaniola sp.: 13 larva 14, 15 pupa 16, 17 adult 18 emergence hole of adult Dzhanokmenia stefaniolae. Scale bars: 1 mm.
Figures 7-12 from: Li Q, Wang C, Hu H-Y (2021) Two new species of Dzhanokmenia (Hymenoptera, Eulophidae) from China, with first report on a host association for the genus. ZooKeys 1009: 67-79. https://doi.org/10.3897/zookeys.1009.57556
Figures 7-12 Dzhanokmenia stefaniolae, female (paratypes): 7, 9, 11 metasoma, dorsal 8, 10, 12 metasoma, ventral. Scale bars: 0.2 mm.
FIGURES 11–14 in Thysanoptera host-plant associations, with an account of species living on Tamarix, and a new species of Lissothrips (Phlaeothripidae)
FIGURES 11–14. Liothrips reuteri (female), variation in antenna.
Data from: Effects of parasitic sex-ratio distorters on host genetic structure in the Armadillidium vulgare-Wolbachia association
In the pill bug Armadillidium vulgare (Crustacea, Oniscidea) Wolbachia facilitates its spread through vertical transmission via the eggs by inducing feminization of genetic males. The spread of feminizing Wolbachia within and across populations is therefore expected to influence mtDNA genetic structure by hitchhiking. To test this hypothesis, we analysed nuclear and mtDNA genetic structure, and Wolbachia prevalence in 13 populations of the pill bug host. Wolbachia prevalence (ranging from 0 to 100% of sampled females) was highly variable among populations. All three Wolbachia strains previously observed in A. vulgare were present (wVulC, wVulM and wVulP) with wVulC being the most prevalent (9 out of 13 populations). The host showed a genetic structure on five microsatellite loci that is compatible with isolation by distance. The strong genetic structure observed on host mtDNA was correlated to Wolbachia prevalence: three mitotypes were in strong linkage disequilibrium with the three strains of Wolbachia. Neutrality tests showed that the mtDNA polymorphism is not neutral and we thus suggest that this unusual pattern of mtDNA polymorphism found in A. vulgare was due to Wolbachia.
Data from: Prevalence, diversity, and host associations of Bartonella strains in bats from Georgia (Caucasus)
Bartonella infections were investigated in seven species of bats from four regions of the Republic of Georgia. Of the 236 bats that were captured, 212 (90%) specimens were tested for Bartonella infection. Colonies identified as Bartonella were isolated from 105 (49.5%) of 212 bats Phylogenetic analysis based on sequence variation of the gltA gene differentiated 22 unique Bartonella genogroups. Genetic distances between these diverse genogroups were at the level of those observed between different Bartonella species described previously. Twenty-one reference strains from 19 representative genogroups were characterized using four additional genetic markers. Host specificity to bat genera or families was reported for several Bartonella genogroups. Some Bartonella genotypes found in bats clustered with those identified in dogs from Thailand and humans from Poland.
Data from: Host and tissue variation overshadow the response of boreal moss-associated fungal communities to increased nitrogen load
Human activity has more than doubled the amount of nitrogen entering the global nitrogen cycle, and the boreal forest biome is a nitrogen-limited ecosystem sensitive to nitrogen load perturbation. Although bryophyte-associated microbes contribute significantly to boreal forest ecosystem function, particularly in carbon and nitrogen cycling, little is known about their responses to anthropogenic global change. Amplicon pyrosequencing of the ITS2 region of rDNA was used to investigate how fungal communities associated with three bryophyte species responded to increased nitrogen loads in a long-term fertilization experiment in a boreal Picea abies forest in southern Norway. Overall, OTU richness, community composition, and the relative abundance of specific ecological guilds were primarily influenced by host species identity and tissue-type. Although not the primary factor affecting fungal communities, nitrogen addition did impact the abundance of specific guilds of fungi and the resulting overall community composition. Increased nitrogen loads decreased ectomycorrhizal abundance, with Amphinema, Cortinarius, Russula, and Tylospora OTUs responding negatively to fertilization. Pathogen abundance increased with fertilization, particularly in the moss pathogen Eocronartium. Saprophytic fungi were both positively and negatively impacted by the nitrogen addition, indicating a complex community level response. The overshadowing of the effects of increased nitrogen loads by variation related to host and tissue-type highlights the complexity of bryophyte-associated microbial communities and the intricate nature of their responses to anthropogenic global change.
Data from: Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter
Genome-wide association studies have the potential to identify causal genetic factors underlying important phenotypes but have rarely been performed in bacteria. We present an association mapping method that takes into account the clonal population structure of bacteria and is applicable to both core and accessory genome variation. Campylobacter is a common cause of human gastroenteritis as a consequence of its proliferation in multiple farm animal species and its transmission via contaminated meat and poultry. We applied our association mapping method to identify the factors responsible for adaptation to cattle and chickens among 192 Campylobacter isolates from these and other host sources. Phylogenetic analysis implied frequent host switching but also showed that some lineages were strongly associated with particular hosts. A seven-gene region with a host association signal was found. Genes in this region were almost universally present in cattle but were frequently absent in isolates from chickens and wild birds. Three of the seven genes encoded vitamin B5 biosynthesis. We found that isolates from cattle were better able to grow in vitamin B5-depleted media and propose that this difference may be an adaptation to host diet.
Data from: Host plant phylogeny and abundance predict root-associated fungal community composition and diversity of mutualists and pathogens
• Interactions between plants and their root-associated fungi (RAF) may influence the relative abundance of tree species and determine forest community diversity. Such plant-soil feedbacks in turn depend on the degree to which spatial distance and phylogenetic relatedness of host trees structure pathogen and mutualist communities, but research detailing these aspects of RAF communities is lacking. Here, we characterize plant-RAF associations across a diverse plant community, focusing on the degree to which RAF communities are structured by spatial distance, host phylogenetic relatedness, and host abundance. We compare results for different functional groups, including both putative mutualists and pathogens, an aspect poorly examined hitherto. • We collected roots at regular intervals along ten 50 m by 2 m transects, then used DNA barcoding to identify host plants, and characterize the associated fungal community. Variance partitioning was used to measure the relative contributions of host phylogenetic relatedness and spatial distance to explaining RAF community composition. A weighted linear regression was used to measure the correlation between host abundance and RAF diversity. • Phylogenetic distance among hosts was a better predictor of RAF community composition than spatial distance, but this relationship was stronger for putative pathogens than for mutualists, suggesting that pathogens show stronger host preference than mutualists. Across all functional groups, RAF showed similar levels of spatial structure. Additionally, RAF communities of locally abundant plants were less diverse than RAF communities of rare plants. • Synthesis: We found that RAF communities are structured by the phylogenetic relatedness of hosts and, to a lesser extent, by spatial distance, with pathogens showing stronger host preference than mutualists. Abundant hosts had less diverse RAF communities than rare hosts, which is notable because abundant plants tend to experience weaker negative plant-soil feedback. Going forward, mechanisms underlying the host abundance-RAF diversity relationship warrant further investigation. Additionally, the survey approach presented here could be paired with experiments linking RAF community composition to plant recruitment.
Data from: Finding flies in the mushroom soup: host specificity of fungus-associated communities revisited with a novel molecular method
Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour-intensive methods involving cultivation and morphology-based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (1) initial salt-isopropanol extraction of all nucleic acids in the sample is followed by (2) an extra clean-up step using solid-phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples — regardless of biomass or other properties — being successfully PCR amplified using metabarcoding primers and subsequently sequenced. As a proof-of-concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus-associated communities, i.e., do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing ten species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology-based identifications, we find a species-rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus-associated interaction webs and communities.
Data from: Evolutionary associations between host traits and parasite load: insights from Lake Tanganyika cichlids
Parasite diversity and abundance (parasite load) vary greatly among host species. However, the influence of host traits on variation in parasitism remains poorly understood. Comparative studies of parasite load have largely examined measures of parasite species richness and are predominantly based on records obtained from published data. Consequently, little is known about the relationships between host traits and other aspects of parasite load, such as parasite abundance, prevalence and aggregation. Meanwhile, understanding of parasite species richness may be clouded by limitations associated with data collation from multiple independent sources. We conducted a field study of Lake Tanganyika cichlid fishes and their helminth parasites. Using a Bayesian phylogenetic comparative framework, we tested evolutionary associations between five key host traits (body size, gut length, diet breadth, habitat complexity and number of sympatric hosts) predicted to influence parasitism, together with multiple measures of parasite load. We find that the number of host species that a particular host may encounter due to its habitat preferences emerges as a factor of general importance for parasite diversity, abundance and prevalence, but not parasite aggregation. In contrast, body size and gut size are positively related to aspects of parasite load within, but not between species. The influence of host phylogeny varies considerably among measures of parasite load, with the greatest influence exerted on parasite diversity. These results reveal that both host morphology and biotic interactions are key determinants of host–parasite associations and that consideration of multiple aspects of parasite load is required to fully understand patterns in parasitism.
Data from: You are where you live: parasitic nematode mitochondrial genome size is associated with the thermal environment generated by hosts
There exists remarkable interspecific variation in mitochondrial sequence evolution rates and in mitochondrial genome sizes. A number of hypotheses based on the forces of mutation and selection have been proposed to explain this variation. Among such hypotheses, we test three: 1) the 'longevity-dependent selection', 2) the 'functional constraints' and 3) the 'race for replication' hypotheses, using published mtDNA genomic sequences of 47 Nematoda species. We did not find any relationship between body size (used as a proxy for longevity) and genome size or the substitution rate of protein sequences, providing little evidence for the first hypothesis. Parasitic species from different thermal habitats, as determined by their definitive host type (ectothermal vs. endothermal), did not differ in their rates of protein evolution. Therefore, little support was obtained for the second hypothesis. However, we revealed that mitogenomes of parasites of endotherms were significantly smaller than those of parasites of ectotherms, supporting the race for replication hypothesis. As mitochondrial genomes of endothermal animals are usually more compact than those of ectothermal animals, intriguingly, nematode parasites of endotherms and ectotherms exhibit similar patterns of mtDNA length variation to their hosts.
Data from: Greater host breadth still not associated with increased diversification rate in the Nymphalidae – a response to Janz et al
In their technical comment, Janz et al. take issue with our recent study examining the association between host breadth and diversification rates in the brush footed butterflies (Lepidoptera: Nymphalidae) (Hamm and Fordyce 2015). Specifically, they are concerned that we misrepresent their "oscillation hypothesis" (OH) (Janz et al. 2016; Janz and Nylin 2008) and that one of our models was inadequate to test hypotheses regarding host breadth and diversification rate. Given our mutual interests in the macroevolutionary patterns of herbivorous insects, we appreciate the opportunity to respond to their concerns.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.