Find research datasets worth reusing

opencc-by-4.0Nov 2022View details →

Co-creation Decision Making Tool

Should I use co-creation? Decision-making tool

opencc-by-4.0Dec 2022View details →

Competition and co-association, but not phosphorous availability, shape the benefits of phosphate solubilising root bacteria for maize (Zea mays).

Predicting the conditions under which rhizobacteria benefit plant growth remains challenging. Here we tested the hypothesis that benefits from inoculation with phosphate-solubilising rhizobacteria will depend upon two environmental conditions: phosphate availability and competition between bacteria. Maize-associated rhizobacteria with varying phosphate solubilisation ability were used in experiments in soil, sterilised soil and gnotobiotic microcosms under conditions of varying orthophosphate availability, while  we manipulated intensity of competition by varying the number of isolates in plant inocula. Growth promotion by microbes did not depend on phosphate availability but was affected by interactions between inoculants: beneficial effects of one Serratia isolate were detectable only when plants were inoculated with a single strain and beneficial effects of a competition sensitive Rhizobium was only detectable in sterilised soil or in microcosms inoculated with single strains. Moreover, microcosm experiments suggested that facilitation of a parasitic isolate, not competitive interactions between bacteria, prevented plants from gaining benefits from a potential mutualist. Competition and facilitation affected colonization of plants in microcosms but growth promotion by Serratia was more affected by inoculation treatment than culturable densities on roots. Experimental manipulation of seed inocula can reveal whether plant growth stimulation is robust with respect to competition, as well as the ecological strategies of different rhizobacteria. From an applied perspective, phosphate solubilisation may not provide the mechanism for bacterial growth promotion but may indicate mutualistic potential due to phylogenetic associations. Importantly, benefits to plants are vulnerable to interactions between rhizobacteria and may not persist in mixed inoculations.

Data from: Two for the price of one: eDNA metabarcoding reveals temporal and spatial variability of mussel and fish co-distributions in Michigan riverine systems

Freshwater mussels (family Unionidae) are among the world's most endangered taxa, with almost 75% of North American taxa classified as a species of concern, threatened, or endangered. Despite the critical importance of comprehensive distributional data for the conservation of unionids and fishes, these data are often lacking because of the labor and resources associated with traditional survey methods. During their larval stage, unionid mussels use various fish species as obligate hosts, making native fish species vital to unionid persistence and an understanding of host distribution similarly important. Here, we utilized an eDNA metabarcoding approach to evaluate patterns of co-distribution of unionid mussels and fishes along ~362 km of the densely sampled Grand River network as well as the outlets of 19 tributaries along the eastern shore of Lake Michigan, USA. We detected a total of 21 mussel and 40 fish taxa, with distinctive composition of both mussel and fish assemblages across tributaries and differences in fish taxa between sampling periods. Notably, we detected more mussel taxa within the Grand River watershed than at the outlets of all 20 rivers combined. Within the Grand River network, two fish taxa (Pylodictus olivaris and Cyprinella) were found more frequently in areas of high mussel diversity, and three fish taxa more frequently in areas of low mussel diversity (Umbra, Leuciscidae, and Etheostoma). There was little difference between eDNA detections of mussels from samples collected in June versus August, but we detected significantly more fish taxa in August compared to June. Taken together, our findings demonstrate the value of eDNA metabarcoding for evaluating co-distribution of ecologically connected taxa. The use of eDNA as a tool for determining distributions of mussels and their obligate hosts may facilitate conservation efforts for these imperiled taxa.

Data for: Predator co-occurrence in alpine and Arctic tundra in relation to fluctuating prey

Large carnivores influence ecosystem dynamics in multiple ways, e.g. by suppressing meso-carnivores and providing carrions for smaller scavengers. Loss of large carnivores is suggested to cause meso-carnivore increase and expansion. Moreover, competition between meso-carnivores may be modified by the presence of larger carnivores. In tundra ecosystems, the smallest meso-carnivore, the Arctic fox, has experienced regional declines, whereas its larger and competitively superior congener, the red fox, has increased, potentially due to changes in the abundance of apex predators. We explored if variation in occurrence of wolverine and golden eagle impacted the occurrence and co-occurrence of Arctic fox and red fox in relation to varying abundances of small rodents within the Scandinavian tundra. We applied multi-species occupancy models to an extensive wildlife camera dataset from 2011-2020 covering 98 sites. Daily detection/non-detection of each species per camera trap site and study period (late winter; March-May) was stacked across years and species occupancy was related to small rodent abundance while accounting for time of year and status of simulated carcass. Arctic fox was more likely to co-occur with red fox when wolverine was present, and less likely to co-occur with red fox when golden eagles were present and wolverine absent. Red foxes increased in occupancy when co-occurring with the larger predators. Arctic fox responded more strongly to small rodent abundance than red fox and co-occurred more often with the other species at carcasses when rodent abundance was low. Our findings suggest that the interspecific interactions within this tundra predator guild appear to be surprisingly intricate, driven by facets of fear of predation, interspecific mediation and facilitation, and food resource dynamics. These dynamics of intraguild interactions may dictate where and when conservation actions targeted towards the Arctic fox should be implemented.

Data, sample sizes, and R code for analysis of: Variation in mutation (co)variances

Because of pleiotropy, mutations affect the expression and inheritance of multiple traits and, together with selection, are expected to shape standing genetic covariances between traits and eventual phenotypic divergence between populations. It is therefore important to find if the M matrix, describing mutational variances of each trait and covariances between traits, varies between genotypes. We here estimate the M matrix for six locomotion behavior traits in lines of two genotypes of the nematode Caenorhabditis elegans that accumulated mutations in a nearly-neutral manner for 250 generations. We find significant mutational variance along at least one phenotypic dimension of the M matrices, but neither their size nor their orientation had detectable differences between genotypes. The number of generations of mutation accumulation, or the number of MA lines measured, was likely insufficient to sample enough mutations and detect potentially small differences between the two M matrices. We then tested if the M matrices were similar to one G matrix describing the standing genetic (co)variances of a population derived by the hybridization of several genotypes, including the two measured for M, and domesticated to a lab-defined environment for 140 generations. We found that the M and G were different because the genetic covariances caused by mutational pleiotropy in the two genotypes are smaller than those caused by linkage disequilibrium in the lab population. We further show that M matrices differed in their alignment with the lab population G matrix. If generalized to other founder genotypes of the lab population, these observations indicate that selection does not shape the evolution of the M matrix for locomotion behavior in the short-term of a few tens to hundreds of generations and suggests that the hybridization of C. elegans genotypes allows selection on new phenotypic dimensions of locomotion behavior.

Inferring predator-prey interactions from camera traps: A Bayesian co-abundance modelling approach

Predator-prey dynamics are a fundamental part of ecology, but directly studying interactions has proven difficult. The proliferation of camera trapping has enabled the collection of large datasets on wildlife, but researchers face hurdles inferring interactions from observational data. Recent advances in hierarchical co-abundance models infer species interactions while accounting for two species' detection probabilities, shared responses to environmental covariates, and propagate uncertainty throughout the entire modelling process. However, current approaches remain unsuitable for interacting species whose natural densities differ by an order of magnitude and have contrasting detection probabilities, such as predator-prey interactions, which introduce zero-inflation and overdispersion in count histories. Here we developed a Bayesian hierarchical N-mixture co-abundance model that is suitable for inferring predator-prey interactions. We accounted for excessive zeros in count histories using an informed zero-inflated Poisson distribution in the abundance formula and accounted for overdispersion in count histories by including a random effect per sampling unit and sampling occasion in the detection probability formula. We demonstrate that models with these modifications outperform alternative approaches, improve model goodness-of-fit, and overcome parameter convergence failures. We highlight its utility using 20 camera trapping datasets from 10 tropical forest landscapes in Southeast Asia and estimate four predator-prey relationships between tigers, clouded leopards, and muntjac and sambar deer. Tigers had a negative effect on muntjac abundance, providing support for top-down regulation, while clouded leopards had a positive effect on muntjac and sambar deer, likely driven by shared responses to unmodelled covariates like hunting. This Bayesian co-abundance modelling approach to quantify predator-prey relationships is widely applicable across species, ecosystems, and sampling approaches, and may be useful in forecasting cascading impacts following widespread predator declines. Taken together, this approach facilitates a nuanced and mechanistic understanding of food-web ecology.

opencc-by-4.0Nov 2022View details →

Grey Level Co-Occurrence Matrix and Learning Algorithms to Quantify and Classify Use-Wear on Experimental Flint Tools

These are the images and the grey levels co-occurence matrix analysis results from my experimental dataset

opencc-zeroJan 2023View details →

Scaling up gas and electric cooking in low- and middle-income countries: Climate threat or mitigation strategy with co-benefits?

Nearly three billion people in low- and middle-income countries (LMICs) rely on polluting fuels, resulting in millions of avoidable deaths annually. Polluting fuels also emit short-lived climate forcers and greenhouse gases (GHGs). Liquefied petroleum gas (LPG) and grid-based electricity are scalable alternatives to polluting fuels but have raised climate and health concerns. Here, we compare emissions and climate impacts of a business-as-usual household cooking fuel trajectory to four large-scale transitions to gas and/or grid electricity in 77 LMICs. We account for upstream and end-use emissions from gas and electric cooking, assuming electrical grids evolve according to the 2022 World Energy Outlook's "Stated Policies" Scenario. We input the emissions into a reduced-complexity climate model to estimate radiative forcing and temperature changes associated with each scenario. We find full transitions to LPG and/or electricity decrease emissions from both well-mixed GHG and short-lived climate forcers, resulting in a roughly 5 millikelvin global temperature reduction by 2040. Transitions to LPG and/or electricity also reduce annual emissions of PM2.5 by over 6 Mt (99%) by 2040, which would substantially lower health risks from Household Air Pollution.

Pollen limitation and context-dependent alleviating mechanisms in a co-flowering alpine grassland community

1. The consequences of community metrics (e.g., co-flowering diversity and floral density) and plant traits (e.g., pollinator dependency and trait similarity) on pollen limitation may depend on pollinator-mediated competitive or facilitative interactions among plants in co-flowering communities, which could vary with community contexts (i.e. different altitude communities) and under human disturbances (e.g., livestock grazing). However, the mechanisms to alleviate pollen limitation under the different contexts, considering pollinator-mediated interactions among neighbor plants are unclear. 2. We investigated pollen limitation under grazing versus ungrazing conditions in low versus high altitude alpine meadows on the Tibetan Plateau to uncover the underlying mechanisms mediating pollen limitation associated with livestock grazing. 3. Pollen limitation is prevalent in alpine grasslands, irrespective of community contexts. Grazing exclusion decreased pollen limitation in the two sites but in different ways. In the high-altitude site, pollen limitation was reduced by the exclusion of grazers through increased trait similarity (suggesting facilitation). While pollen limitation was reduced by decreased trait similarity (suggesting competition avoidance) under grazing exclusion in the low-altitude site. 4. Synthesis and Applications: This study suggests that flower trait distribution patterns (i.e. trait similarity) influence pollen limitation through reducing competition in the low-altitude site or enhancing facilitation in the high-altitude site under grazing exclusion in alpine grasslands. Our results provide a mechanistic understanding of pollen limitation in co-flowering alpine grassland communities under distinct human disturbances at different altitudes, emphasizing the role of pollinator-mediated interactions among plants on plant reproductive success.

opencc-by-4.0Sep 2023View details →

Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina, Gelidium) and red (Grateloupia) macroalgae

We collected specimens of Ulva sp. (green algae), Saccharina sp. (brown algae), Grateloupia sp., and Gelidium sp. (both red algae) during all four seasons from a coastal reef in Weihai, China, and analyzed their surface-colonizing bacteria in comparison to surrounding seawater and sediment controls. 16S rRNA amplicon sequencing, extensive plate cultivation, sequencing of selected strains, and sequencing of 23 metagenomes were performed in this study. Besides composition, we analyzed the potential of phycosphere bacteria to degrade algal polysaccharides and to produce bioactive secondary metabolites. This comprehensive dataset represents a significant stepping stone towards a better understanding of macroalgal phycosphere bacteria and paves the way to functional studies on representative strains.

opencc-zeroJan 2023View details →

Underwater light attenuation inhibits native submerged plants and facilitates the invasive co-occurring plant Cabomba caroliniana

Decreasing in the diversity and distribution of native submerged plants have been widely observed in recent decades. Global underwater darkening, which is mainly caused by radiation dimming and a decrease in transparency due to e.g. eutrophication, has emerged as a general trend that strongly hampers the growth of submerged plants in lakes by decreasing the light available for photosynthesis. However, few studies have attempted to compare the responses of native and invasive submerged plants to underwater darkening. In this study, we aimed to compare the effects of light attenuation on the growth and photosynthesis traits of native and invasive submerged plants.

opencc-zeroJan 2023View details →

Data and code from: Thermal niche and habitat use by co-occurring lake trout (Salvelinus namaycush) and brook trout (S. fontinalis) in stratified lakes

Realized thermal niche and habitat use are two conceptualizations of fish habitat based on organismal performance or lake-specific ecology, respectively. Both habitat types were compared for lake trout (Salvelinus namaycush) and brook trout (S. fontinalis) co-occurring in four large (> 500 ha) oligotrophic lakes. Lakes were partitioned into two morphological categories based on possession of a central or non-central deep basin with corresponding differences in adjoining shelf areas. Lake asymmetry in basin location has been shown to strongly influence food web connections based on isolation of basins from shelf areas. Generally, overlap between both habitat types occurred in several comparisons with lake trout, suggesting that thermal habitat is a reasonable proxy for habitat use boundaries though not a full replacement for insights gained from habitat use models. For brook trout, overlap was not as consistent, especially for lakes with non-central basins. In central basin lakes, there were closer proximity between the two species and overlap in both thermal niche and habitat use models. There was very limited overlap of either habitat type in lakes with non-central basins. Further, there were no shared areas of interspecific overlap between thermal niche and habitat use in non-central basins pointing to additional complexity governing habitat partitioning between lake trout and brook trout in these types of lakes. The shelf area effect on spatial structure of habitat, and likely food web connections, can occur in lakes regardless of basin centrality so long as shelf areas are large. In this lake set, lakes were sufficiently large to observe this phenomenon.

opencc-by-4.0Dec 2022View details →

Controlled crossed Andreev reflection and elastic co-tunneling mediated by Andreev bound states

This repository contains measured data related to the "Controlled crossed Andreev reflection and elastic co-tunneling mediated by Andreev bound states" publication. Code reproducing all paper plots is included as well. Tu run the Jupyter notebook, install Anaconda and the package QCoDeS.

opencc-by-4.0Jan 2023View details →

Temporal iCLIP captures co-transcriptional RNA-protein interactions

Minimum datasets required to perform analysis using code from github.

opencc-zeroDec 2021View details →

Identification of microbial taxa present in Ctenocephalides felis (cat flea) reveals widespread co-infection and associations with vector phylogeny

Background Ctenocephalides felis, the cat flea, is the most common ectoparasite of cats and dogs worldwide. As a cause of flea allergy dermatitis and a vector for two genera of zoonotic pathogens (Bartonella and Rickettsia spp.), the effect of the C. felis microbiome on pathogen transmission and vector survival is of substantial medical importance to both human and veterinary medicine. The aim of this study was to assay the pathogenic and commensal eubacterial microbial communities of individual C. felis from multiple geographic locations and analyze these findings by location, qPCR pathogen prevalence, and flea genetic diversity. Methods 16S Next Generation Sequencing (NGS) was utilized to sequence the microbiome of fleas collected from free-roaming cats, and the cox1 gene was used for flea phylogenetic analysis. NGS data were analyzed for 168 individual fleas from seven locations within the US and UK. Given inconsistency in the genera historically reported to constitute the C. felis microbiome, we utilized the decontam prevalence method followed by literature review to separate contaminants from true microbiome members. Results NGS identified a single dominant and cosmopolitan amplicon sequence variant (ASV) from Rickettsia and Wolbachia while identifying one dominant Bartonella clarridgeiae and one dominant Bartonella henselae/Bartonella koehlerae ASV. Multiple less common ASVs from these genera were detected within restricted geographical ranges. Co-detection of two or more genera (Bartonella, Rickettsia, and/or Wolbachia) or multiple ASVs from a single genus in a single flea was common. Achromobacter, Peptoniphilus, and Rhodococcus were identified as additional candidate members of the C. felis microbiome on the basis of decontam analysis and literature review. Ctenocephalides felis phylogenetic diversity as assessed by the cox1 gene fell within currently characterized clades while identifying seven novel haplotypes. NGS sensitivity and specificity for Bartonella and Rickettsia spp. DNA detection was compared to targeted qPCR. Conclusions Our findings confirm the widespread coinfection of fleas with multiple bacterial genera and strains, proposing three additional microbiome members. The presence of minor Bartonella, Rickettsia, and Wolbachia ASVs was found to vary by location and flea haplotype. These findings have important implications for flea-borne pathogen transmission and control.

opencc-by-4.0Apr 2023View details →

Earthworm migration improves soil quality and modifies tri-trophic interactions with rice-fish co-culture

Earthworm migration improves soil quality and modifies tri-trophic interactions with rice-fish co-culture

opencc-by-4.0Mar 2023View details →

Dataset for proceedings paper: How international is co-authorship outside of Web of Science? The case of social sciences and humanities in Flanders, Belgium

This is an anonymized dataset containing data on international collaboration in the social sciences and humanities (SSH) in Flanders, Belgium. It is based on all peer-reviewed publications in <a href="https://www.ecoom.be/en/data-collections/vabb-shw">VABB-SHW</a>, regardless of their indexation in WoS or other databases. The dataset accompanies the conference paper 'How international is co-authorship outside of Web of Science? The case of social sciences and humanities in Flanders, Belgium,' which was submitted to <a href="https://cns-iu.github.io/workshops/2023-07-02_issi/index.html">ISSI 2023</a>.

opencc-zeroMar 2023View details →

Data from: The Competitive exclusion – tolerance rule explains habitat partitioning among co-occurring species of burying beetles

Habitat partitioning among co-occurring, ecologically similar species is widespread in nature and thought to be an important mechanism for coexistence. The factors that cause habitat partitioning, however, are unknown for most species. We experimentally tested among three alternative hypotheses to explain habitat partitioning among two species of co-occurring burying beetle (Nicrophorus) that occupy forest (N. orbicollis) and wetland (N. hebes) habitats. Captive experiments revealed that the larger N. orbicollis (forest) was consistently dominant to N. hebes (wetland) in competitive interactions for carcasses that they require for reproduction. Transplant enclosure experiments in nature revealed that N. hebes had poor reproductive success whenever the dominant N. orbicollis was present. In the absence of N. orbicollis, N. hebes performed as well, or better, in forest versus its typical wetland habitat. In contrast, N. orbicollis performed poorly in wetlands regardless of the presence of N. hebes. These results support the Competitive exclusion – tolerance rule where the competitively dominant N. orbicollis excludes the subordinate N. hebes from otherwise suitable or preferable forest habitat, while the subordinate N. hebes is uniquely able to tolerate the challenges of breeding in wetlands. Transplant experiments further showed that carcass burial depth – an important trait thought to enhance the competitive ability of the dominant N. orbicollis – is costly in wetland habitats. When in the presence of N. hebes, N. orbicollis buried carcasses deeper; deeper burial is thought to provide a competitive advantage in forests, but further compromised the reproductive success of N. orbicollis in wetlands. Overall, results provide evidence that the Competitive exclusion – tolerance rule underlies habitat partitioning among ecologically similar species, and that the traits important for competitive dominance in relatively benign environments are costly in more challenging environments, consistent with a trade-off.

opencc-by-4.0Mar 2023View details →

Output data: China's energy-water-land system co-evolution under carbon neutrality goal and climate impacts

Outputs for Wang, J., Duan, Y., Wang, C., 2023. China’s energy-water-land system co-evolution under carbon neutrality goal and climate impacts. (In progress) Folder demeter contains the spatially downscaled land use/land cover datasets. Folder tethys contains the spatially downscaled water withdrawal datasets. The sub-folder names correspond to the scenarios described in the paper. For landcover datasets, land type ratios in each grid are presented. Land types include water, forest, shrub, grass, urban, snow, sparse and crops. For water withdrawal datasets, “wd” = “water withdrawal spatially downscaled”, “twd” = “water withdrawal spatially and temporally downscaled”, “dom”=”domestic/municipal sector”, “elec”=”electricity sector”, ”irr”=”irrigation sector”, “liv”=”livestock sector”, “mfg”=”manufacturing/industry sector”, “min”=”mining/primary energy sector”, “nonag”=”non-agricultural sector”, “total”=”all sectors”.