Find research datasets worth reusing

opencc-by-4.0Dec 2023View details →

The FAIR-Device - a non-lethal and generalist semi-automatic Malaise trap for insect biodiversity monitoring: Proof of concept - Supplementary Material

<h3>Abstract</h3> Field monitoring plays a crucial role in understanding insect dynamics within ecosystems. It facilitates pest distribution assessment, control measure evaluation, and prediction of pest outbreaks. Additionally, it provides important information on bioindicators with which the state of biodiversity and ecological integrity in specific habitats and ecosystems can be accurately assessed. However, traditional monitoring systems can present various difficulties, leading to a limited temporal and spatial resolution of the obtained information. Despite recent advancements in automatic insect monitoring traps, also called e-traps, most of these systems focus exclusively on studying agricultural pests, rendering them unsuitable for monitoring diverse insect populations. To address this issue, we introduce the Field Automatic Insect Recognition (FAIR)-Device, a novel non-lethal field tool that relies on semi-automatic image capture and species identification using artificial intelligence via the iNaturalist platform. Our objective was to develop an automatic, cost-effective, and non-specific monitoring solution capable of providing high-resolution data for assessing insect diversity. During a 26-day proof-of-concept evaluation, the FAIR-Device recorded 24.8 GB of video, identifying 431 individuals from 9 orders, 50 families, and 69 genera. While improvements are possible, our device demonstrated potential as a cost-effective, non-lethal tool for monitoring insect biodiversity. Looking ahead, we envision new monitoring systems such as e-traps as valuable tools for real-time insect monitoring, offering unprecedented insights for ecological research and agricultural practices. <h3>Description of the data and file structure</h3> This repository complements the publication <a href="https://www.biorxiv.org/content/10.1101/2024.03.22.586299v2" target="_blank" rel="noopener">"The FAIR-Device - a non-lethal and generalist semi-automatic Malaise trap for insect biodiversity monitoring: Proof of concept".</a> It contains the result data from the proof of concept field test of V1.0 of the FAIR-Device, conducted between July and August 2021 at the Thünen Institute of Agricultural Technology in Braunschweig. The repository comprises three compressed files (.zip): <ul> <li>FAIR-D_captures.zip: <ul> <li>Video captures from the field tests organized by recording day.</li> <li>Filenames indicating recording time (hh-mm-ss).</li> </ul> </li> </ul> <ul> <li>FAIR-D_Tables&Code.zip: <ul> <li>Processed results from the obtained image captures, organized into:  <ul> <li>Monitoring2021_TotalPeriod.xlsx: Result table with taxonomic classifications, data analysis, and charts.</li> <li>iNat_observations.xlsx: iNaturalist reviews analysis table.</li> <li>R: code for generating article graphics.</li> </ul> </li> </ul> </li> </ul> <ul> <li>FAIR-D_V1.0_3D_Models.zip: <ul> <li>Complete 3D design of the FAIR-D V1.0 in .stl format, organized into: <ul> <li>3D_print_parts: 3D-printable parts with spatial coordinates for correct positioning in CAD software.</li> <li>other_3Dparts: Non-printable parts, also in .stl format with spatial coordinates.</li> </ul> </li> </ul> </li> </ul>   NOTE: For visualizing the videos, we recommend VLC media player - <a href="https://www.videolan.org/vlc/">https://www.videolan.org/vlc/</a>

opencc-zeroMar 2024View details →

Contrasting effects of host or local specialization: widespread haemosporidians are host generalist whereas local specialists are locally abundant

Aim: Despite the wide distribution of many parasites around the globe, the range of individual species varies significantly even among phylogenetically related taxa. Since parasites need suitable hosts to complete their development, parasite geographical and environmental ranges should be limited to communities where their hosts are found. Parasites may also suffer from a trade-off between being locally abundant or widely dispersed. We hypothesize that the geographical and environmental ranges of parasites are negatively associated to their host specificity and their local abundance. Location: Worldwide Time period: 2009 to 2021 Major taxa studied: Avian haemosporidian parasites Methods: We tested these hypotheses using a global database which comprises data on avian haemosporidian parasites from across the world. For each parasite lineage, we computed five metrics: phylogenetic host-range, environmental range, geographical range, and their mean local and total number of observations in the database. Phylogenetic generalized least squares models were ran to evaluate the influence of phylogenetic host-range and total and local abundances on geographical and environmental range. In addition, we analysed separately the two regions with the largest amount of available data: Europe and South America. Results: We evaluated 401 lineages from 757 localities and observed that generalism (i.e. phylogenetic host range) associates positively to both the parasites' geographical and environmental ranges at global and Europe scales. For South America, generalism only associates with geographical range. Finally, mean local abundance (mean local number of parasite occurrences) was negatively related to geographical and environmental range. This pattern was detected worldwide and in South America, but not in Europe. Main Conclusions: We demonstrate that parasite specificity is linked to both their geographical and environmental ranges. The fact that locally abundant parasites present restricted ranges, indicates a trade-off between these two traits. This trade-off, however, only becomes evident when sufficient heterogeneous host communities are considered.

Figure 5 in Variations in trophic niches of generalist predators with plant community composition as indicated by stable isotopes and fatty acids

Figure 5. Principal components analysis of the relative abundance (mol %, logit- transformed) of individual NLFAs of Trochosa ruricola using body size (small, large), flooding index (FI), plant species richness (SR), plant functional group richness (FG), presence of grasses (Gr), legumes (Leg), small herbs (SH) and tall herbs (TH) as supplementary variables.

Figure 4 in Variations in trophic niches of generalist predators with plant community composition as indicated by stable isotopes and fatty acids

Figure 4. Variations in δ15N signatures of Trochosa ruricola as affected by flooding index (P = 0.04, R2 = 0.12) and body size (small, large; P <0.01).

Figure 1 in Variations in trophic niches of generalist predators with plant community composition as indicated by stable isotopes and fatty acids

Figure 1. Variations in δ15N and δ13C signatures of Harpalus rufipes (black) and Trochosa ruricola (pink) across the study site of the Jena Experiment.

Figure 3 in Variations in trophic niches of generalist predators with plant community composition as indicated by stable isotopes and fatty acids

Figure 3. Principal components analysis of the relative abundance (mol %, logit-transformed) of individual NLFAs of Harpalus rufipes using flooding index (FI), plant species richness (SR), plant functional group richness (FG), presence of grasses (Gr), legumes (Leg), small herbs (SH) and tall herbs (TH) as supplementary variables.

Figure 6 in Variations in trophic niches of generalist predators with plant community composition as indicated by stable isotopes and fatty acids

Figure 6. Principal components analysis of the relative abundance (mol%, logit- transformed) of individual PLFAs of soil microorganisms using flooding index (FI), plant species richness (SR), plant functional group richness (FG), presence of grasses (Gr), legumes (Leg), small herbs (SH) and tall herbs (TH) as supplementary variables.

Figure 2 in Variations in trophic niches of generalist predators with plant community composition as indicated by stable isotopes and fatty acids

Figure 2. Variations in δ15N signatures of Harpalus rufipes (P <0.01, R2 = 0.11) as affected by plant species richness (log-transformed).

opencc-by-4.0Apr 2024View details →

From Generalist to Specialist: Incorporating Domain-Knowledge into Flamingo for Chest X-Ray Report Generation

This subset of the MIMIC-CXR split file contains the study identifiers and paths to the chest X-ray images used for training, validation and testing of all models presented in the paper: "From Generalist to Specialist: Incorporating Domain-Knowledge into Flamingo for Chest X-Ray Report Generation".

opencc-by-4.0Nov 2021View details →

Geographical variation of floral scents in generalist entomophilous species with variable pollinator communities

This is the dataset used for the article: "Geographical variation of floral scents in generalist entomophilous species with variable pollinator communities" by de Manincor N. et al., 2021 published in Functional Ecology (https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2435.13984) In this study we investigated the floral scent (Volatile Organic Compounds, VOCs) variation of four perennial plant species, with generalist pollination, in two different environments: under natural condition (field) and controlled condition (greenhouse). The focal plant species are: Anthyllis vulneraria (AV), Globularia vulgaris (GV), Pilosella officinarum (PO) and Ranunculus bulbosus (RB). The dataset is composed by different files that have been used to investigate (1) variation of VOCs under natural condition (files "field"), (2) variation of VOCs under controlled condition (files "greenhouse"), (3) the effect of the reared condition and the role of phenotypic plasticity (field vs greenhouse, files "FvsGH") and (4) variation of the pollinator community associated with the four focal species (files "poll_" and (5) whether changes in floral scents in the field were associated to some variation in the pollinator communities (at the species level, using an RDA analysis, files "Pollinators-2017", "VOC-2017"). We also provided two scripts: the script with an example to calculate VOCs variation, and the script for the RDA analysis.

opencc-by-4.0Jan 2022View details →

Data for Ecology Letters paper: Jack-of-all-trades paradigm meets long-term data: generalist herbivores are more widespread and locally less abundant.

Data, R-code, and meta-data document for a 2022 paper in Ecology Letters that examines assumptions about associations between local abundance and dietary specialization using an 18-year dataset of caterpillar-plant interactions in Ecuador.

opencc-zeroMar 2022View details →

Native generalist natural enemies and an introduced specialist parasitoid together control an invasive forest insect

Specialized natural enemies have long been considered a major force driving the population dynamics of outbreaking forest insects. While research has traditionally focused on the role of specialist parasitoids, recent studies and reviews reflect an appreciation of complex interactions among many regulatory factors. The sources suggest that specialist parasitoids and generalist predators can each inflict strong top‐down effects and that specialists and generalists can interact to regulate insect herbivore populations. Here we use the model study organism winter moth (Operophtera brumata) in its invasive range in the northeast United States to investigate interactions between the introduced, host-specific tachinid parasitoid Cyzenis albicans and native, generalist pupal predators. Prior research in Canada showed that predation of winter moth pupae increased after C. albicans establishment. To explain this phenomenon, the following hypotheses have been suggested: (1) parasitoids suppress the winter moth population to a density that can be maintained by generalist predators, (2) unparasitized pupae are preferred by predators and thus experience higher mortality rates, or (3) C. albicans sustain higher predator populations throughout the year more effectively than winter moth alone. We tested these hypotheses by deploying winter moth pupae over six years spanning 2005 to 2017 and by modeling pupal predation rates as a function of winter moth density and C. albicans establishment. We also compared predation rates of unparasitized and parasitized pupae and considered additional mortality by a native pupal parasitoid. We found support for the first hypothesis; we detected both temporal and spatial density dependence, but only in the latter years of the study when winter moth densities were lower. We found no evidence for the latter two hypotheses. Our findings suggest that pupal predators have a regulatory effect on winter moth populations only after populations have been reduced, presumably by the introduction of the host-specific parasitoid C. albicans.

opencc-zeroDec 2021View details →

Individual dietary specialization in a generalist bee varies across populations but has no effect on the richness of associated microbial communities

Despite the increasingly documented occurrence of individual specialization, the relationship between individual consumer interactions and diet-related microbial communities in wild populations is still unclear. Using data from nests of the bee Ceratina australensis from three different wild populations, we combine metabarcoding and network approaches to explore the existence of individual variation in resource use within and across populations, and whether dietary specialization affects the richness of pollen-associated microbes. We reveal the existence of marked dietary specialization. In the most specialized population, we also show that individuals' diet breadth was positively related to the richness of fungi, but not bacteria. Overall, individual specialization appeared to have a weak or negligible effect on the microbial richness of nests, suggesting that different mechanisms beyond environmental transmission may be at play regarding microbial acquisition in wild bees.

opencc-zeroSep 2022View details →

Environmental stochasticity increases extinction risk to a greater degree in pollination specialists than in generalists

Pollination sustains terrestrial food webs and agricultural systems and links the dynamics of interacting plant and pollinator species. Although environmental stochasticity is ubiquitous and can propagate through communities via species interactions in a way that increases extinction risk, it is unknown whether stochasticity affects species uniformly across pollination networks. In this paper, we introduce a stochastic dynamic model that makes novel use of the birth function and apply it to pollination networks of increasing size. We start with two- and four-species networks, in order to first illustrate the effects of stochasticity per se and then how those effects combine with specialization. We then describe the relationship between partner number and stochastic extinction risk in empirical networks with >20 species. In the 2-species network, increasing the variance of the stochastic term of the model increased the size of the region in parameter space where extinctions occur. In networks with 4 or more species, specialists were more vulnerable to extinction than generalists over a broad range of variances. Extinction risk in networks with >20 species declined nonlinearly with increasing mutualist partner number. Our results demonstrate the importance of including species interactions and stochasticity when using population-dynamic models to compare species' extinction risk. While models that omit either of these factors are likely to underestimate extinction risk, they disproportionately underestimate the vulnerability of specialists.

opencc-by-4.0Jan 2021View details →

FIGURE 6 in Evaluating the ecology of Spinosaurus: Shoreline generalist or aquatic pursuit specialist?

FIGURE 6. Suggested head positions of Spinosaurus relative to water. A) when dipping the snout in the water to forage while leaving the naris above the waterline as per the wading model. Head angle of 45 degrees based on Schade et al. (2020) for Irritator. B) while lying submerged, keep the naris and orbit clear of the water while minimising the amount of head that is exposed as per Arden et al. (2019), C) fully submerged as if coming up for air and trying to expose only the nares to breathe. Scale bar equals 1 m.