Find research datasets worth reusing

FIGURE 14 A–C in Revision of the black fungus gnat species (Diptera: Sciaridae) described by W.A. Steffan from Micronesia

FIGURE 14 A–C. Pseudolycoriella ponapensis (Steffan, 1969). Holotype. A. Hypopygium; B. Flagellomeres 3–5; C. Apex of fore tibia (specimen strong deformed by turbidity of the medium and included air).

FIGURE 12 A–E. Phytosciara brachygaster Steffan, 1969. Paratype. A in Revision of the black fungus gnat species (Diptera: Sciaridae) described by W.A. Steffan from Micronesia

FIGURE 12 A–E. Phytosciara brachygaster Steffan, 1969. Paratype. A. Hypopygium; B. Flagellomeres 3–5; C. Wing; D. Apex of fore tibia; E. Toothed claw.

FIGURE 7 A–D in Revision of the black fungus gnat species (Diptera: Sciaridae) described by W.A. Steffan from Micronesia

FIGURE 7 A–D. Cratyna brevipalpis (Steffan, 1969). Paratype. A. Hypopygium; B. Head; C. Flagellomeres 3–5; D. Apex of fore tibia (embedding medium turbid and the structures slightly depressed).

FIGURE 8 A–B in Revision of the black fungus gnat species (Diptera: Sciaridae) described by W.A. Steffan from Micronesia

FIGURE 8 A–B. Cratyna musicola (Steffan, 1969). Holotype. A. Gonostylus; B. Head with palpus and basal flagellomeres (specimen deformed and strongly bleached).

FIGURE 3 A–D. Bradysia boninensis Steffan, 1969. Holotype. A in Revision of the black fungus gnat species (Diptera: Sciaridae) described by W.A. Steffan from Micronesia

FIGURE 3 A–D. Bradysia boninensis Steffan, 1969. Holotype. A. Hypopygium; B. Flagellomeres 1–5; C. Palpus; D. Wing.

FIGURE 6 A–E. Corynoptera heterochela Steffan, 1969. Paratype. A in Revision of the black fungus gnat species (Diptera: Sciaridae) described by W.A. Steffan from Micronesia

FIGURE 6 A–E. Corynoptera heterochela Steffan, 1969. Paratype. A. Hypopygium dorsal view; B. Head with palpus; C. Flagellomeres 3–5; D. Apex of fore tibia; E. Wing.

FIGURE 2 A–B in Revision of the black fungus gnat species (Diptera: Sciaridae) described by W.A. Steffan from Micronesia

FIGURE 2 A–B. Austrosciara multispinosa (Steffan, 1969). Holotype. A. Hypopygium; B. Apex of fore tibia.

FIGURE 5 A–B. Corynoptera heterochela Steffan, 1969. Holotype. A in Revision of the black fungus gnat species (Diptera: Sciaridae) described by W.A. Steffan from Micronesia

FIGURE 5 A–B. Corynoptera heterochela Steffan, 1969. Holotype. A. Hypopygium; B. Flagellomeres 2-4 (medium turbid and with included air).

FIGURE 4 A–C. Bradysia kraussi Steffan, 1969. Holotype. A in Revision of the black fungus gnat species (Diptera: Sciaridae) described by W.A. Steffan from Micronesia

FIGURE 4 A–C. Bradysia kraussi Steffan, 1969. Holotype. A. Hypopygium; B. Head with palpus and basal segments of flagellomeres; C. Gonostylus from Bradysia snyderi Steffan, 1969, syn. n. of B. kraussi.

FIGURE 9 A–D in Revision of the black fungus gnat species (Diptera: Sciaridae) described by W.A. Steffan from Micronesia

FIGURE 9 A–D. Epidapus jaluitensis (Steffan, 1969). Holotype. A. Hypopygium; B. Eye bridge and basal segments of antennae; C. Palpus; D. Wing.

opencc-zeroJun 2020View details →

Data from: Sustained immune activation is associated with susceptibility to the amphibian chytrid fungus

The disease chytridiomycosis caused by the fungus Bd has devastated amphibian populations worldwide. Functional genomic contributions to host susceptibility remain enigmatic and vary between species and populations. We conducted experimental Bd infections in Rana yavapaiensis, a species with intraspecific variation in chytridiomycosis susceptibility, to assess the skin and spleen transcriptomic response to infection over time. We predicted that increased immune gene expression would be associated with a positive disease outcome, but we instead found that surviving frogs had significantly reduced immune gene expression compared to susceptible frogs and to uninfected controls. MHC class II gene expression was also significantly higher in susceptible frogs compared to surviving frogs. Furthermore, susceptible frogs expressed a significantly larger number of distinct class II alleles, demonstrating a negative correlation between class II expression, functional diversity, and survival. Expression of the MHC class II locus previously associated with Bd disease outcomes was a significant predictor of Bd infection intensity at early infection stages but not at late infection stages, suggesting initial MHC-linked immune processes are important for ultimate disease outcomes. We infer through disease association and phylogenetic analysis that certain MHC variants are linked to the immune expression that was negatively associated with survival, and we hypothesize that frogs that did not express these alleles could better survive infections. Our study finds that MHC expression at early and late infection stages predicts Bd infection intensity, and suggests that generating a sustained immune response against Bd may be counterproductive for surviving chytridiomycosis in this partially susceptible species.

opencc-zeroAug 2020View details →

Allopatric instead of parapatric divergence in an ectomycorrhizal fungus (Laccaria trichodermophora) in tropical sky-islands

In tropical sky-islands, cold-affinity populations tend to become isolated at highlands during the interglacial periods, and to expand into the lowlands where they become more connected during the glacial periods. Although this has been widely studied in trees, it is poorly understood how fungal symbionts can differentiate among mountains (allopatrically), or within a single mountain (parapatrically) due to climate fluctuations. Here, we conducted population genomic analyses on the ectomycorrhizal fungus Laccaria trichodermophora in three tropical sky-islands using Genotyping by Sequencing (GBS) at low DNA concentrations. There were no significant differences between altitudes within a single mountain, but we observed significant genetic differentiation among populations from different mountains, supporting the allopatric differentiation hypothesis. Our results indicate that L. trichodermophora populations are under a sky-island population dynamics that started during the Pleistocene climate fluctuations.

opencc-by-4.0Aug 2020View details →

The invasive pathogenic fungus of ash trees alters arthropod predator – prey food webs in forest plantations

The data set contains data on: 1] Prey type and size (sheet1: prey type and size). In the cells, prey length in mm is provided for each prey item. NA is stated for a prey item that could not be measured. In this sheet, the plot ids and the spider ids are also stated, which enables connection with other sheets. Note: more prey items caught by an individual are stated in one row if they are of different type. Prey items of a same type caught by an individual are itemized in more rows. 2] Information about spider individuals (sheet2: spiders). For each spider individual, it is provided its id, so it can be connected with sheet 1, plot id where it was collected, when it was collected (month), web type, and prosoma length (mm).  3] Characteristics of sampling plots (sheet3: environmental data). It is provided plot id, age, infestation degree by Hymenoscyphus fraxineus, canopy openness, shrub coverage, and herb coverage. 4] Potential prey of spiders (sheet 4: potential prey). Standardized no. of prey per trap (20 x 15 cm, both sides were sticky) in each plot.

opencc-by-4.0Sep 2020View details →

Data sets of preference for Mucor circinelloides over edible mushrooms in the fungus gnat Bradysia impatiens

This is the raw data for the olfactory response experiments on preference for Mucor circinelloides over edible mushrooms in the fungus gnat Bradysia impatiens (Diptera: Sciaridae).

opencc-zeroAug 2021View details →

The mycorrhizal community of the epiphytic orchid Thrixspermum japonicum is strongly biased toward a single Ceratobasidiaceae fungus, despite a wide range of fungal partners

PREMISE: Orchids depend primarily on mycorrhizal fungi to obtain nutrients throughout their life cycle. Epiphytic orchids account for 69% of orchid diversity. The unstable availability of water and nutrients in their arboreal habitats often results in severe water and nutrient stresses. Consequently, mycorrhizal associations may be important for the survival of epiphytic orchids, but our understanding thereof remains limited. Here, we investigated the mycorrhizal community in a single epiphytic orchid species, using more samples than in any previous study. METHODS: We assessed the mycorrhizal communities of Thrixspermum japonicum, one of the most common epiphytic orchids in the temperate region of Japan. In total, 144 individuals were collected from 28 host tree species at 20 sites across 1300 km. The mycorrhizal fungi were identified based on nuclear ribosomal DNA internal transcribed spacer sequences and assigned operational taxonomic units (OTUs) based on 97% sequence similarity. RESULTS: We obtained 24 OTUs, of which 9 and 15 belonged to the Ceratobasidiaceae and Tulasnellaceae, respectively. These OTUs are widely distributed throughout the phylogenetic trees of the two fungal families. However, a single Ceratobasidiaceae OTU accounted for 49.7% of all fungal sequences and was predominant in samples from 15 host tree species and 12 sites. CONCLUSIONS: Our results imply that despite having a broad range of mycorrhizal partners, T. japonicum was predominantly associated with a single fungal taxon at most of the sites among the host-tree species investigated. These findings contribute to elucidating mycorrhizal symbiosis in epiphytic ha

opencc-zeroDec 2016View details →

Data from: Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis

One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures has advanced our understanding of Bd phylogenetics, genomic architecture, and mechanisms of virulence. However pure cultures are laborious to obtain and whole genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus we still know little about the genetic diversity of Bd in natural systems. The most common non-invasive method of sampling Bd from natural populations is to swab amphibian skin. Hundreds of thousands of swabs have been collected from amphibians around the world, but Bd DNA collected via swabs is often low in quality and/or quantity. In this study, we developed a custom Bd genotyping assay using the Fluidigm Access Array platform to amplify 192 carefully-selected regions of the Bd genome. We obtained robust sequence data for pure Bd cultures and field-collected skin swabs. This new assay has the power to accurately discriminate among the major Bd clades, recovering the basic tree topology previously revealed using whole genome data. Additionally, we established a critical value for initial Bd load for swab samples (150 Bd genomic equivalents) above which our assay performs well. By leveraging advances in microfluidic multiplex PCR technology and the globally distributed resource of amphibian swab samples, non-invasive skin swabs can now be used to address critical spatial and temporal questions about Bd and its effects on declining amphibian populations.

opencc-zeroDec 2017View details →

Data from: Phylogenomics clarifies repeated evolutionary origins of inbreeding and fungus farming in bark beetles (Curculionidae, Scolytinae)

Bark and ambrosia beetles (Curculionidae, Scolytinae) display a conspicuous diversity of unusual genetic and ecological attributes and behaviors. Reconstructing the evolution of Scolytinae, particularly the large and ecologically significant tribe Cryphalini (pygmy borers), has long been problematic. These challenges have not adequately been addressed using morphological characters, and previous research has used only DNA sequence data from small numbers of genes. Through a combination of anchored hybrid enrichment, low-coverage draft genomes, and transcriptomes, we addressed these challenges by amassing a large molecular phylogenetic dataset for bark and ambrosia beetles. The resulting DNA sequence data from 251 protein coding genes (114,276 bp of nucleotide sequence data) support inference of the first robust phylogeny of Scolytinae, with a special focus on the species rich tribe Cryphalini and its close relatives. Key strategies, including inbreeding mating systems and fungus farming, evolved repeatedly across Scolytinae. We confirm 12 of 16 hypothesized origins of fungus farming, 6 of 8 origins of inbreeding polygyny and at least 11 independent origins of a super-generalist host range. These three innovations are statistically correlated, but their appearance within lineages was not necessarily simultaneous. Additionally, the evolution of extreme host plant generalism often preceded, rather than succeeded, fungus farming. Of the high-diversity tribes of Scolytinae, only Xyleborini is monophyletic, Corthylini is paraphyletic and Cryphalini is highly polyphyletic. Cryphalini sensu stricto is part of a clade containing the genera Hypothenemus, Cryphalus and Trypophloeus, and the tribe Xyloterini. Stegomerus and Cryptocarenus (Cryphalini) are part of a clade otherwise containing all Corthylini. Several other genera, including Ernoporus and Scolytogenes (Cryphalini), make up a distantly related clade. Several of the genera of Cryphalini are also intermixed. For example, Cryphalus and Hypocryphalus are intermingled, as well as Ernoporicus, Ptilopodius and Scolytogenes. Our data are consistent with widespread polyphyly and paraphyly across Scolytinae and within Cryphalini, and provides new insights into the evolution of inbreeding mating systems and fungus farming in the species rich and ecologically significant weevil subfamily Scolytinae.

opencc-zeroDec 2011View details →

Data from: Genetic structure of the poplar rust fungus Melampsora larici-populina: Evidence for isolation by distance in Europe and recent founder effects overseas

Dispersal has a great impact on the genetic structure of populations, but remains difficult to estimate by direct measures. In particular, gradual and stochastic dispersal are often difficult to assess and to distinguish, although they have different evolutionary consequences. Plant pathogens, especially rust fungi, are suspected to display both dispersal modes, though on different spatial scales. In this study, we inferred dispersal capacities of the poplar rust fungus Melampsora larici-populina by examining the genetic diversity and structure of 13 populations from eight European and two overseas countries in the Northern hemisphere. M. larici-populina was sampled from both cultivated hybrid poplars and on the wild host, Populus nigra. The populations were analyzed with 11 microsatellite and 8 virulence markers. Although isolates displayed different virulence profiles according to the host plant, neutral markers revealed little population differentiation with respect to the type of host. This suggests an absence of reproductive isolation between populations sampled from cultivated and wild poplars. Conversely, studying the relationship between geographic and genetic structure allowed us to distinguish between isolation by distance (IBD) patterns and long distance dispersal (LDD) events. The European populations exhibited a significant IBD pattern, suggesting a regular and gradual dispersal of the pathogen over this spatial scale. Nonetheless, the genetic differentiation between these populations was low, suggesting an important gene flow on a continental scale. The two overseas populations from Iceland and Canada were shown to result from rare LDD events, and exhibited signatures of strong founder effects. Furthermore, the high genetic differentiation between both populations suggested that these two recent introductions were independent. This study illustrated how the proper use of population genetics methods can enable contrasted dispersal modes to be revealed.

opencc-zeroDec 2012View details →

Data from: The "Dr Jekyll and Mr Hyde fungus": noble rot versus gray mold symptoms of Botrytis cinerea on grapes

Many cryptic species have recently been discovered in fungi, especially in fungal plant pathogens. Cryptic fungal species co-occurring in sympatry may occupy slightly different ecological niches, for example infecting the same crop plant but specialized on different organs or having different phenologies. Identifying cryptic species in fungal pathogens of crops and determining their ecological specialization is therefore crucial for disease management. Here we addressed this question in the ascomycete Botrytis cinerea, the agent of grey mold on a wide range of plants. On grape, B. cinerea causes severe damages but is also responsible for noble rot used for processing sweet wines. We used microsatellite genotyping and clustering methods to elucidate whether isolates sampled on grey mold vs. noble rot symptoms in three French regions belong to genetically differentiated populations. The inferred population structure matched geography rather than the type of symptom. Noble rot symptoms therefore do not seem caused by a specific B. cinerea population but instead seem to depend essentially on microclimatic conditions, which has applied consequences for the production of sweet wines.