Find research datasets worth reusing

Data from: Landscape context and substrate characteristics shape fungal communities of dead spruce in urban and semi-natural forests

Data from: Korhonen, A., Miettinen, O., Kotze, D.J., & Hamberg, L. (2022). Landscape context and substrate characteristics shape fungal communities of dead spruce in urban and semi-natural forests. Environmental Microbiology. DOI: 10.1111/1462-2920.15903 This dataset contains occurrence data of 475 fungal ITS2 sequence clusters (OTUs) across 360 sequenced samples originating from dead wood of Norway spruce (Picea abies). Wood samples were collected from 90 downed spruce trunks, at four points from each trunk. Trunks were at intermediate stages of decay and located in spruce-dominated stands in 24 urban forests (66 trunks) and in 8 rural semi-natural forests (24 trunks) in southern Finland. The data consists of an OTU table (sequence read counts in each sample) and sample metadata (locality information, trunk characteristics and environmental variables).

Fit to template of horseback shapes

The  csv file contains the polynomial coefficients of   10th order polynoms for  reconstructing the different horses profiles on templates obtained by a professional horse saddler. All the dimensions in x and y are in cm. Column 1 contains an id for each horse. Columns  2 and 3 contain the bounds of the intervals on the x axis. Columns 4 to  14 give the coefficients of the polynom for the CL curve Columns   15 and 16 contain the bounds of the intervals on the x axis. Columns 17 to  27 give the coefficients of the polynom for the CT1 curve Columns  28 and 29 contain the bounds of the intervals on the x axis. Columns 30 to  40 give the coefficients of the polynom for the CT2 curve Columns  41 and 42 contain the bounds of the intervals on the x axis. Columns 43 to  53 give the coefficients of the polynom for the CT3 curve

Data from: Can attraction to and competition for high-quality habitats shape breeding propensity?

This archive contains the data analysed in the paper 'Can attraction to and competition for high-quality habitats shape breeding propensity?' by Acker et al. The dataset is provided as a .Rdata file ('dataset.Rdata'), and full description of the content is provided in the file 'README.txt'. All additional details are available in the main text and appendices of the paper.

Bird predation and landscape context shape arthropod communities on broccoli

Birds increase crop yields via consumption of pests in some contexts but disrupt pest control via intraguild predation in others. Landscape complexity acts as an inconsistent mediator, sometimes increasing, decreasing, or not impacting pest control. Here, we examined how landscape context and seasonal variation mediate the impact of birds on arthropod pests and natural enemies, leaf damage, and yields of broccoli (Brassica oleracea) on highly diversified farms that spanned the USA West Coast. Our study had two complementary components: a bird exclusion experiment and molecular diet analysis of 357 fecal samples collected from the most commonly captured bird species that also foraged in Brassica fields (American Goldfinch, Spinus tristis; American Robin, Turdus migratorius; Savannah Sparrow, Passerculus sandwichensis; Song Sparrow, Melospiza melodia; and White-crowned Sparrow, Zonotrichia leucophrys). Bird access yielded higher, rather than lower, numbers of pest aphids and increased their parasitism, while no other arthropods examined were consistently impacted. Independent of bird presence, percent natural cover in the landscape sometimes increased and sometimes decreased densities of arthropods in the mid-growth period, with diminishing impacts in the late-growth period. Herbivore feeding damage to broccoli leaves decreased with increasing amounts of natural land cover and in the late-growth period. Molecular diet analysis revealed that Brassica pests and predatory arthropods were relatively uncommon prey for birds. Landscape context did not alter the prey items found in bird diets. Altogether, our bird-exclusion experiment and molecular diet analysis suggested that birds have relatively modest impacts on the arthropods associated with broccoli plantings. More broadly, the limited support in our study for net natural pest control services suggests that financial incentives may be required to encourage the adoption of bird friendly farming practices in certain cropping systems.

Habitat loss shapes the structure and species roles in mutualistic seed dispersal networks

This dataset has the variables used in the paper "Habitat loss shapes the structure and species roles in tropical seed dispersal networks" as well as the script to perform the analysis.

SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8 T cells

This dataset contains aggregated CellRanger output for six 10x Genomics (5'GEX+abTCR+Feature barcoding) experiments from the study by Minervina, Pogorelyy et al (<a href="https://www.medrxiv.org/content/10.1101/2021.07.12.21260227v3">medrxiv</a>).  The scripts to process it further are available at github (<a href="https://github.com/pogorely/COVID_vax_CD8">repository</a>).  Raw sequencing data is available at SRA (acc. PRJNA744851)

Thermal plasticity and evolution shape predator-prey interactions differently in clear and turbid water

Warming and eutrophication negatively affect freshwater ecosystems by modifying trophic interactions and increasing water turbidity. We need to consider their joint effects on predator-prey interactions, and how these depend on the thermal evolution of both predator and prey. We quantified how 4°C warming and algae-induced turbidity (that integrates turbidity per se and increased food for zooplankton prey) affect functional response parameters and prey population parameters in a common-garden experiment. We did so for all combinations of high- and low-latitude predator (damselfly larvae) and prey (water fleas) populations to assess the potential impact of thermal evolution of predators and/or prey at a high latitude under warming using a space-for-time substitution. We then modelled effects on the system stability (i.e. tendency to oscillate) under different warming, turbidity and evolutionary scenarios. Warming and turbidity had little effect on the functional response parameters of high-latitude predators. In contrast, warming and turbidity reduced the handling times of low-latitude predators. Moreover, warming increased the search rates of low-latitude predators in clear water but instead decreased these in turbid water. Warming increased stability (i.e. prevented oscillations) in turbid water (except for the "high-latitude predator & high-latitude prey" system), mainly by decreasing the prey's carrying capacity and partly also by decreasing search rates, while it did not affect stability in clear water. Algae-induced turbidity generally decreased stability, mainly by increasing the prey's carrying capacity and partly also by increasing search rates. This resembles findings that nutrient enrichment can reduce the stability of trophic systems. The expected stability of the high-latitude trophic system under warming was dependent on the turbidity level: our results suggest that thermal plasticity tends to destabilize the high-latitude trophic system under warming in clear water but not in turbid water, and that thermal evolution of the predator will stabilize the high-latitude system under warming in turbid water but less so in clear water. The extent to which thermal plasticity and evolution shape trophic system stability under warming may strongly differ between clear and turbid water bodies, with their contributions having a more stabilizing role in turbid water.

Code and data from: Familiarity, dominance, sex and season shape common waxbill social networks.

In gregarious animals, social network positions of individuals may influence their life-history and fitness. Although association patterns and the position of individuals in social networks can be shaped by phenotypic differences and by past interactions, few studies have quantified their relative importance. We evaluated how phenotypic differences and familiarity influence social preferences and the position of individuals within the social network. We monitored wild-caught common waxbills (Estrilda astrild) with radio-frequency identifiers in a large mesocosm during the non-breeding and breeding seasons of two consecutive years. We found that social networks were similar, and that the centrality of individuals was repeatable, across seasons and years, indicating a stable social phenotype. Nonetheless, there were seasonal changes in social structure: waxbills associated more strongly with opposite-sex individuals in breeding seasons, while in non-breeding seasons they instead assorted according to similarities in social dominance. We also observed stronger assortment between birds that were introduced to the mesocosm at the same time, indicating long-lasting bonds among familiar individuals. Waxbills that had been introduced to the mesocosm more recently occupied more central network positions, especially during breeding seasons, perhaps indicating that these birds had less socially-differentiated associations with flock members. Finally, individual differences in color ornamentation and behavioral assays of personality, inhibitory control and stress were not related to network centrality or association patterns. Together, these results suggest that, in gregarious species like the common waxbill, social networks may be more strongly shaped by long-lasting associations with familiar individuals than by phenotypic differences among group members.

Floral shape predicts bee-parasite transmission potential

The spread of parasites is one of the primary drivers of population decline of both managed and wild bees. Several bee parasites are transmitted by the shared use of flowers, turning floral resources into potential disease hotspots. However, we know little about how floral morphology and floral species identity affect different steps of the transmission process. Here, we used the gut parasite Crithidia bombi and its primary host, bumble bees (Bombus spp.), to examine whether floral traits or species identity better predict three basic steps of parasite transmission on flowers: feces deposition on flowers, survival of the parasite on flowers, and acquisition by a new host. We also identified which traits and/or species were most strongly associated with each step in the transmission process. We found that both trait- and species-based models fit the data on deposition of feces and survival of C. bombi on flowers, but that species-based models provided a better fit than trait-based ones. However, trait-based models were better at predicting the acquisition of C. bombi on flowers. While different species tended to support higher fecal deposition or parasite survival, we found that floral shape provided explanatory power for each of the transmission steps. When we assessed overall transmission potential, floral shape had the largest explanatory effect, with wider, shorter flowers promoting higher transmission. Taken together, our results highlight the importance of flower species identity and floral traits in disease transmission dynamics of bee parasites, and floral shape as an important predictor of overall transmission potential. Identifying traits associated with transmission potential may help us create seed mix that presents lower parasite transmission risk for bees for use in pollinator habitat.

Dusona_spp_Shape of the antennal carina

Figure 2. Shape of the antennal carina. a. antennal carina narrow and flat (D. blanda). b. antennal carina narrow and flat, frons with a strong median longitudinal keel (D. carinifrons). c. antennal carina widened dorsally to a rather inconspicuous nose-like projection (D. stygia). d. antennal carina widened dorsally to a large nose-like projection with transverse striae (D. pineticola). e. antennal carina slightly raised dorsally and transverse striate (D. sobolicida). f. antennal carina raised and strongly bent upwards forming an (ear-like) crescent-shaped plate (D. infesta). Scale bars indicate 0.5 mm. Publication: Open Access in a taxonomic sense: a morphological and molecular guide to Western Palearctic Dusona (Hymenoptera, Ichneumonidae)

More than just meat: Carcass decomposition shapes trophic identities in a terrestrial vertebrate

Most food web models fail to account for the full complexity of interactions within a community, particularly where microbes are involved. Carcasses are microbe-rich resources and may represent a common nexus for the macro- and microbiome, effectively uniting autotrophs, consumers, predators, and microbiota. We evaluated the role of carcasses as multitrophic resources and explored dietary partitioning for a sexually dimorphic obligate scavenger known for its hierarchical social system. This study was set in a well-studied community of camelids (Vicugna vicugna, Lama guanicoe), pumas (Puma concolor), and Andean condors (Vultur gryphus) in the Andes. We hypothesized that condors, by feeding on trophically distinct dietary substrates within any given carcass, would have highly variable trophic position (TP) values. Further, we expected that the microbial consumers within the carcass would inflate TP values in both, the carrion and the condors. Thus, we expected that the trophic heterogeneity within a carcass could facilitate sex-based dietary partitioning in condors. We used a multifaceted approach to assess the foraging of Andean condors, using regurgitated pellet and, bulk isotopic analyses, and also quantified the TP of the entire community of graminoids, camelids, camelid carrion, pumas, and female and male condors employing compound-specific stable isotopes analysis of amino-acids. Our analysis of condor pellets and bulk isotopes revealed non-trivial plant consumption, close to 10% of condor diet. Isotope analysis of amino-acids revealed that condors had highly variable TPs (2.9±0.3) compared to pumas (3.0±0.0) and camelids (2.0±0.1), likely representing "trophic omnivory", wherein the condors consume plants (TP=1.0±0.1) and microbe-colonized carrion (2.3±0.1). Female condors exhibited a TP (2.8±0.2) lower than strict carnivory, suggesting that they consume more plant biomass in a carcass, while males (TP=3.1±0.3) are likely consuming more of the microbe-rich animal tissue. Our study highlights that carcasses represent a trophically heterogeneous resource, and that vertebrate scavengers can feed across trophic groups within the carcass, from autotrophs to secondary consumers, and from both the macro- and microbiome. Thus, integration of microbes in macroecological contexts can help to resolve trophic identity, and better characterize the importance of microbes in detritivorous and omnivorous species.

Dusona_spp_Shape of epicnemial and transverse carinae

Figure 4. Shape of epicnemial and transverse carinae. a. ventral part of the epicnemial carina merging with the pleural part, both carinae low, transverse carina indistinct (D. bicoloripes). b. ventral part of the epicnemial carina distinctly raised, merging the transverse carina, pleural part of the epicnemial carina low and dorsally obliterated (D. tenuis). c. ventral part of the epicnemial carina only slightly raised, merging with the pleural part or the transverse carina, pleural part of the epicnemial carina dorsally complete and merging with anterior edge of the mesopleuron (D. xenocampta). d. ventral part of the epicnemial carina slightly raised, merging with the transverse carina, pleural part of the epicnemial carina completely obliterated (D. juvenilis). 1 = ventral part of the epicnemial carina. 2 = pleural part of the epicnemial carina. 3 = transverse carina. 4 = hind corner of the pronotum. Scale bars indicate 0.5 mm. Publication: Open Access in a taxonomic sense: a morphological and molecular guide to Western Palearctic Dusona (Hymenoptera, Ichneumonidae)

Dusona_spp_Shape and sculpture of the propodeum

Figure 6. Shape and sculpture of the propodeum. a. propodeum hardly depressed with irregular wrinkles (D. bicoloripes). b. propodeum broadly and shallowly depressed, irregularly wrinkled anteriorly and with transverse wrinkles medially and posteriorly (D. stygia). c. propodeum broadly and shallowly depressed, rugose or irregularly wrinkled with some short transverse wrinkles posteriorly and a rather complete carination (D. terebrator). D. propodeum narrowly and deeply depressed with short transverse wrinkles in the sulcus (D. angustifrons). E. propodeum narrowly and deeply depressed with long transverse wrinkles in the sulcus (D. Flagellator). F. propodeum rather broadly and deeply depressed with distinct transverse wrinkles posteriorly and medially (D. stragifex). Scale bars indicate 0.5 mm. Publication: Open Access in a taxonomic sense: a morphological and molecular guide to Western Palearctic Dusona (Hymenoptera, Ichneumonidae)

Research compendium for 'Bringing shape into focus: Assessing differences between blades and bladelets and their technological significance in 3D form'

Abstract: Laminar technologies were adopted by Paleolithic foragers to produce a variable range of stone implements. Archaeologists have reconstructed the different reduction procedures involved in the production of laminar stone tools, often underlying a separation between the bigger blanks (i.e., blades) and smaller bladelets. However, these two blank types are in most cases poorly defined, as their classification typically relies on arbitrary size thresholds that do not consider blank shape, which is a fundamental component of tool production and function. In this study, we investigate whether traditional classifications of blades and bladelets are morphologically and technologically meaningful. For this purpose, we employ a three-dimensional geometric morphometric approach on a large sample of complete blanks retrieved from one of the earliest laminar industries assigned to modern humans in southern Europe: the Protoaurignacian from Fumane Cave. We rely on a cutting-edge protocol for acquiring virtual 3D meshes of stone tools using micro-computed tomography. This novel approach allows us to scan large quantities of small lithics in a short period of time and without the typical technical problems associated with scanning small objects. After calculating the principal components of shape variation, we explore differences and similarities across the dataset using linear discriminant analysis and analysis of variance. Our multivariate study highlights distinct morphological tendencies across blades and bladelets that are however better framed when the technological organization of Protoaurignacian stone knapping is taken into consideration. Overall, our results demonstrate that virtual analysis of stone tool shape can help elucidate aspects of lithic technology and its implications for past human behavior. Overview of contents: 1. Raw landmark data. All landmark coordinates for each blank analyzed in this study and digitized in AGMT3-D; 2. R project with all steps performed to import the Cartesian coordinates of each artifact to R and run GPA, PCA, and Shape ANOVA in geomorph. Furthermore, we include the steps to visualize the shape changes in both geomorph and Morpho (after performing a GPA and PCA in that package too); 3. PC scores of the PCA performed in geomorph and .csv dataset with all attributes used in this study; 4. Datasets in .sav and .dat formats used to run statistical analyses in SPSS and Past; 5. Results of the LDA analyses conducted in the study; 6. R script used to design the bivariate plot of the PCA; Extra: All 3D meshes of blades and bladelets are available on Zenodo following this link: https://doi.org/10.5281/zenodo.6362150

Archived data for: Balancing selection, genetic drift, and human mediated-introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout

The extraordinary polymorphism of Major Histocompatibility Complex (MHC) genes is considered a paradigm of pathogen-mediated balancing selection, although empirical evidence is still scarce. Furthermore, the relative contribution of balancing selection to shape MHC population structure and diversity, compared to that of neutral forces, as well as its interaction with other evolutionary processes such as hybridization, remains largely unclear. To investigate these issues, we analysed adaptive (MHC-DAB gene) and neutral (11 microsatellite loci) variation in 156 brown trout (Salmo trutta complex) from six wild populations in central Italy exposed to introgression from domestic hatchery lineages (assessed with the LDH gene). MHC diversity and structuring correlated with those at microsatellites, indicating the substantial role of neutral forces. However, individuals carrying locally rare MHC alleles/supertypes (regardless of the zygosity status and degree of sequence dissimilarity of MHC) were in better body condition (a proxy of individual fitness/parasite load), hence supporting balancing selection under rare allele advantage, but not heterozygote advantage or divergent allele advantage. The association between specific MHC supertypes and body condition confirmed in part this finding. Across populations, MHC allelic richness increased with increasing admixture between native and domestic lineages, indicating introgression as a source of MHC variation. Furthermore, introgression across populations appeared more pronounced for MHC than microsatellites, possibly because initially-rare MHC variants are expected to introgress more readily under rare allele advantage. Providing evidence for the complex interplay among neutral evolutionary forces, balancing selection and human-mediated introgression in shaping the pattern of MHC (functional) variation, our findings contribute to a deeper understanding of the evolution of MHC genes in wild populations exposed to anthropogenic disturbance.

Environmental heterogeneity shapes physiological traits in tropical direct-developing frogs

1. Tropical ectotherm species tend to have narrower physiological limits than species from temperate areas. As a consequence, tropical species are considered highly vulnerable to climate change since minor temperature increases can push them beyond their physiological thermal tolerance. Differences in physiological tolerances can also be seen at finer evolutionary scales, such as among populations of ectotherm species along elevation gradients, highlighting the physiological sensitivity of such organisms. 2. Here we analyze the influence of elevation and bioclimatic domains, defined by temperature and precipitation, on thermal sensitivities of a terrestrial direct-developing frog (Craugastor loki) in a tropical gradient. We address the following questions: i) Does preferred temperature vary with elevation and among bioclimatic domains? ii) Do thermal tolerance limits, i.e. critical thermal maximum and critical thermal minimum vary with elevation and bioclimatic domains?, and iii) Are populations from high elevations more vulnerable to climate warming? 3. We found that along an elevation gradient body temperature decreases as environmental temperature increases. The preferred temperature tends to moderately increase with elevation within the sampled bioclimatic domains. Our results indicate that the ideal thermal landscape for this species is located at mid-elevations, where the thermal accuracy (db) and thermal quality of the environment (de) are suitable. The critical thermal maximum is variable across elevations and among the bioclimatic domains, decreasing as elevation increases. Conversely, the critical thermal minimum is not as variable as the critical thermal maximum. 4. Populations from the lowlands may be more vulnerable to future increases in temperature. We highlight that the critical thermal maximum is related to high temperatures exhibited across the elevation gradient and within in each bioclimatic domain, therefore, it is a response to high environmental temperatures.

Effect of density gradients on the generation of a highly energetic and strongly collimated proton beam from a laser irradiated Gaussian-shaped Hydrogen microsphere

Simulation input files and data sets of "Effect of density gradients on the generation of a highly energetic and strongly collimated proton beam from a laser irradiated Gaussian-shaped Hydrogen microsphere" by A. Bhagawati et al. Simulation code:  Picpsi3D, Version 0.1 beta 11 (c) Copyright Kartik Patel, L & PTD, BARC

Data from: Parasite-driven cascades or hydra effects: susceptibility and foraging depression shape parasite-host-resource interactions

This contains data for the manuscript listed in the title. We measured the foraging rates of individual zooplankton hosts, Daphnia dentifera, on phytoplankton resources, Ankistrodesmus falcatus, in the presence of fungal parasites of zooplankton, Metschnikowia bicuspidata. Some of these data are previously published (Genotypes12_foraging.csv by Strauss, Alexander T., et al. "Genotypic variation in parasite avoidance behaviour and other mechanistic, nonlinear components of transmission." Proceedings of the Royal Society B 286.1915 (2019): 20192164.) and some are published now for the first time (Genotype3_foraging.csv). In addition, we present novel evidence from a mesocosm experiment (Mesocosm_data1.csv-Mesocosm_data20.csv) of populations of each genotype or each pair of genotypes with phytoplankton resources and fungal parasites present or absent; our last treatment was low or high nutrient supply for the phytoplankton. With data on infection prevalence, host density, and phytoplankton density, we show how host traits and nutrients control outcomes for prevalence, host density, and phytoplankton density. These data may be reused with appropriate citation.

Dataset from: Morphometric analyses of leaf shapes in four sympatric Medi-terranean oaks and hybrids in the Algerian Kabylie fores

Data correspond to the characterization of putative hybrids and oak species coexisting in a highly diversified oak forest in Algeria with four native oak species (Quercus suber, Q. ilex, Q. canariensis, and Q. afares). Sixteen plots, including 89 trees from the four native species and their putative hybrids were sampled. Leaves were scanned and their geometric morphometry analyzed by using 11 landmarks on the right side on their abaxial surface. Related paper: Akli, A.; Lorenzo, Z.; Alia, R.; Rahbi, K.; Torres, E. Morphometric analyses of leaf shapes in four sympatric Mediterranean oaks and hybrids in the Algerian Kabylie forest. Forests 2022, 13(4), 508  <a href="https://doi.org/10.3390/f13040508">https://doi.org/10.3390/f13040508</a>