Find research datasets worth reusing

opencc-zeroJun 2022View details →

Transient amplification enhances the persistence of tropicalising coral assemblages in marginal high latitude environments

Predicting the viability of species exposed to increasing climatic stress requires an appreciation for the mechanisms underpinning the success or failure of marginal populations. Rather than traditional metrics of long-term population performance, here we illustrate that short-term (i.e., transient) demographic characteristics, including measures of resistance, recovery, and compensation, are fundamental in the poleward range expansion of hard corals, facilitating the establishment of coral populations at higher latitudes. Through the annual census of tropical and subtropical Acropora spp. colonies in Japan between 2017-2019, we show how enhanced transient amplification (i.e., short-term increases in population growth following disturbance) supports the persistence of coral assemblages within more variable high-latitude environments. The transient dynamics of both the tropical and subtropical assemblages were strongly influenced by their corresponding recruitment patterns. However, we demonstrate that variation in colony survival and fragmentation patterns between the two assemblages determines their relative capacities for transient amplification. This latitudinal variation in the transient dynamics of Acropora spp. assemblages emphasises that coral populations can possess the demographic plasticity necessary for exploiting more variable, marginal conditions.

opencc-zeroJun 2022View details →

Data from: Bighorn sheep show similar in-host responses to the same pathogen strain in two contrasting environments

Ecological context – the biotic and abiotic environment, along with its influence on population mixing dynamics and individual susceptibility – are thought to have major bearing on epidemic outcomes. However, direct comparisons of disease events in contrasting ecological contexts in wildlife systems are often confounded by concurrent differences in host genetics, exposure histories, or pathogen strains. Here, we compare disease dynamics of a Mycoplasma ovipneumoniae spillover event that affected bighorn sheep populations in two contrasting ecological contexts. One event occurred on the herd's home range near the Rio Grande Gorge in New Mexico, while the other occurred in a captive facility at Hardware Ranch in Utah. While data collection regimens varied between the two sites, general patterns of antibody signal strength and symptom emergence were consistent. Symptoms appeared in the captive setting an average of 12.9 days post-exposure, average time to seroconversion was 24.9 days, and clinical signs peaked at approximately 36 days post-infection. These patterns were consistent with serological testing and subsequent declines in symptom intensity in the free-ranging herd. At the captive site, older animals exhibited more severe declines in body condition and loin thickness, higher symptom burdens, and slower antibody response to the pathogen than younger animals. Younger animals were more likely than older animals to clear infection by the time of sampling at both sites. The patterns presented here suggest that environment may not be a major determinant of epidemiological outcomes in the bighorn sheep - M. ovipneumoniae system, elevating the possibility that host- or pathogen-factors may be responsible for observed variation.

opencc-zeroJul 2022View details →

Urban environments have species-specific associations with invasive insect herbivores

Urban areas are expanding rapidly, with the majority of the global and US population inhabiting them. Urban forests are critically important for providing ecosystem services to the growing urban populace, but their health is threatened by invasive insects. Insect density and damage are highly variable in different sites across urban landscapes, such that trees in some sites experience outbreaks and are severely damaged while others are relatively unaffected. To protect urban forests against damage from invasive insects and support future delivery of ecosystem services, we must first understand the factors that affect insect density and damage to their hosts across urban landscapes. This study explores how a variety of environmental factors that vary across urban habitats influence density of invasive insects. Specifically, we evaluate how vegetational complexity, distance to buildings, impervious surface, canopy temperature, host availability, and density of co-occurring herbivores impact three invasive pests of elm trees: the elm leaf beetle (Xanthogaleruca luteola), the elm flea weevil (Orchestes steppensis), and the elm leafminer (Fenusa ulmi). Except for building distance, all environmental factors were associated with density of at least one pest species. Furthermore, insect responses to these factors were species-specific, with direction and strength of associations influenced by insect life history. These findings can be used to inform future urban pest management and tree care efforts, making urban forests more resilient in an era where globalization and climate change make them particularly vulnerable to attack. Keywords: urban forest, invasive species, impervious surface, temperature, species interactions.

opencc-by-4.0Aug 2022View details →

Results of Secondary aerosol formation in marine Arctic environments: a model measurement comparison at Ny-Ålesund

These files contain the figures and modelled dataset used in the article "Secondary aerosol formation in marine Arctic environments: a model measurement comparison at Ny-Ålesund".

opencc-by-4.0Jun 2022View details →

Dataset collection from a SubT environment

This article presents a dataset collected from the subterranean (SubT) environment with a current state-of-the-art sensors required for <a href="https://www.sciencedirect.com/topics/computer-science/autonomous-navigation">autonomous navigation</a>. The dataset includes sensor measurements collected with RGB, RGB-D, event-based and thermal cameras, 2D and 3D lidars, inertial <a href="https://www.sciencedirect.com/topics/engineering/units-of-measurement">measurement unit</a> (IMU), and <a href="https://www.sciencedirect.com/topics/engineering/ultra-wideband">ultra wideband</a> (UWB) positioning systems which are mounted on the mobile robot. The overall sensor setup will be referred further in the article as a data collection platform. The dataset contains synchronized raw data measurements from all the sensors in the robot operating system (ROS) message format and video feeds collected with action and 360 cameras. A detailed description of the sensors embedded into the data collection platform and a data collection process are introduced. The collected dataset is aimed for evaluating navigation, <a href="https://www.sciencedirect.com/topics/engineering/localisation">localization</a> and <a href="https://www.sciencedirect.com/topics/computer-science/mapping-algorithm">mapping algorithms</a> in SubT environments. This article is accompanied with the public release of all collected datasets from the SubT environment.

opencc-by-4.0Aug 2022View details →

Videos of nests of Harpagoxenus sublaevis and Leptothorax acervorum containing Leptothorax acervorum workers transferred as pupae into different social environments i.e. colonies

Ant collection and colony maintenance Colonies of the hosts Leptothorax acervorum and L. muscorum and the dulotic ant Harpagoxenus sublaevis were collected in July 2020 close to Nuremberg, Germany (49.345592, 11.258971 and 49.413857, 11.026181). At the University of Mainz, ants were transferred to plastered nest boxes containing artificial nest sites consisting of a Plexiglas cavity sandwiched between two microscope slides (7.5 cm x 2.5 cm x 0.5 cm) covered with a red foil and kept at 18°C with a 12:12 light: dark cycle. Ants were fed with crickets and honey every fourth day and provided with water ad libitum. Experimental manipulation For our experiment, we selected ten colonies of L. acervorum and five colonies each of L. muscorum and H. sublaevis. Colonies were assigned to one of five replicates, each replicate containing one colony for each of the four treatments. We prepared experimental colonies by standardizing colony size to one queen, 15 small larvae and 30 adult workers (15 inside + 15 outside workers). Adult workers were marked with a thin metal wire between thorax and abdomen (0.02 mm diameter, Elektrisola, red) to allow distinguishing them from our focal newly emerged workers. We removed 24 pupae from each L. acervorum colony, of which six were returned to the natal colony (referred to as “original” treatment), and six each were transferred into another L. acervorum colony (“conspecific” treatment), into an L. muscorum colony (“heterospecific” treatment) and a colony of H. sublaevis (“parasitic” treatment). For the parasitic treatment, we standardized the number of host workers to 60 as described above, but additionally added all H. sublaevis ants (18.4 ± 13.56 adult female individuals). Workers of these obligate social parasites do not take over worker chores, such as brood care and foraging, which are outsourced to host workers. Unfortunately, worker pupae from two of our replicates did not develop into adult workers in sufficient numbers, so that we focused our transcriptomic analyses on workers from the remaining three replicates. Moreover, all L. acervorum pupae transferred into L. muscorum colonies (“heterospecific” treatment) were either killed or expelled from the colony or did not emerge into workers (Survival: Kruskal-Wallis p = 0.05; Rejection (pupae outside the nest over the first three days): Kruskal-Wallis p < 0.001, Wilcoxon Heterospecific-Parasitic p = 0.016, Wilcoxon Heterospecific-Conspecific p = 0.012, Wilcoxon Heterospecific-Original p = 0.004) indicating that L. muscorum not only recognise L. acervorum pupae, but also eliminate them from their colonies. While we were unable to include this heterospecific treatment thus in our analyses, the number of transferred individuals still alive at the end of the experiment did not differ between the remaining treatments (Kruskal-Wallis: p = 0.34). Rejection was calculated as the number of pupae outside the nest over the first three days. Behavioural observations About 10 weeks (63-69 days) after the emergence of the first worker, colonies were transferred to 22°C and the red foil from their glass nest was removed to allow workers to adapt to light. The next day, the slide nest was transferred to a fluon-treated arena (3 cm x 7.5 cm) and each colony was filmed for 100 min in 4k using a SONY FDR-AX33 camera under a Leica KL1500 LED light.

Short-finned pilot whales exhibit behavioral plasticity in foraging strategies mediated by their environment

Predators adapt their foraging behavior to exploit a variety of prey in a range of environments. Short-finned pilot whales are wide-ranging predators in tropical and sub-tropical oceans, but most previous studies of their foraging ecology have been conducted near oceanic islands. We deployed sound and movement recording tags on 43 short-finned pilot whales off Cape Hatteras, North Carolina, USA, to measure their foraging behavior in a continental shelf-break ecosystem and investigate how variation in the environment shapes their behavior. Overall, the foraging behavior of pilot whales off Cape Hatteras was similar to that of their counterparts from island-associated habitats. Off Cape Hatteras, pilot whales made foraging dives as deep as 1077 m (mean: 445 m), lasting up to 23 min (mean: 12.8 min), with sprints (pursuit at speeds over 3 m/s and up to 6.9 m/s) in more than half of foraging dives. However, tagged whales off Cape Hatteras produced higher buzz rates (11.3 buzzes/dive), foraged more extensively in daytime hours, and engaged in more frequent benthic foraging than island-associated ecotypes. By parsing the echoic scene generated by the animal's own echolocation clicks, we show that pilot whales off Cape Hatteras frequently exploit bathymetric features for foraging, with benthic dives resulting in higher prey capture attempts than pelagic dives. The ability of these predators to strategically adapt foraging strategies to local habitat features likely contributes to their ecological success and may allow them to adjust to shifts in prey distributions in a rapidly changing Anthropocene ocean.

Data from: Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges

The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid-origin lineages to occupy unique environmental space relative to one (or both) parents. We document such a case of hybridization between two sedge species, Carex nova and Carex nelsonii (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (C. nelsonii) is at the edge of its environmental tolerance. Hybrid-origin individuals display mixed ancestry between the parental taxa – of nearly 7,000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage – approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid-origin lineage, we conducted genotype-environment association analyses on different combinations of loci – with and without excess ancestry – and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (C. nelsonii), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent.

opencc-by-4.0Aug 2022View details →

Schematic and adapted figures from IPBES Sustainable Use of Wild Species Assessment - Chapter 3. Status of and trends in the use of wild species and its implications for wild species, the environment and people

Schematic and adapted figures from Chapter 3 of the thematic assessment of the sustainable use of wild species of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services.

opencc-by-4.0Mar 2022View details →

Dataset- Barking up the right tree: Using tree bark to track airborne particles in school environment and link science to society

Experimental data regarding magnetic properties measured in bio-sensors and air filters. Bio-sensors include tree bark samples, either collected in situ (courtyard tree bark) and exposed indoors-outdoors (bio-sensors) in the schools. Bio-sensors had their magnetic properties measured.  PM1, EC and OC concentrations and SIRM measured on air filters.

FIG. 3. — A in An emic understanding of honey bees and their environment: attracting bee swarms to nest on rafters in Belitung, Indonesia

FIG. 3. — A "stowed" rafter (unggat type) with two colonies. Credit: C. Vuillier.

FIG. 2 in An emic understanding of honey bees and their environment: attracting bee swarms to nest on rafters in Belitung, Indonesia

FIG. 2. — Two models of rafters: A, sunggau muke; B, sunggau bantai. Credits: C. Vuillier.

FIG. 7 in An emic understanding of honey bees and their environment: attracting bee swarms to nest on rafters in Belitung, Indonesia

FIG. 7. — Two rafters taking advantage of the same access path. Credit: N. Césard.

FIG. 4. — A in An emic understanding of honey bees and their environment: attracting bee swarms to nest on rafters in Belitung, Indonesia

FIG. 4. — A rafter (tingku) in Central Sulawesi. Credits: N. Césard (A), C. Vuillier (B).

Airborne spectral reflectance dataset of submerged plastic targets in a coastal environment (SUPPLEMENTARY DATA FILES)

SUPPLEMENTARY DATA FILES for the paper entitled: "Airborne spectral reflectance dataset of submerged plastic targets in a coastal environment." Data are organized in three categories: - orthophoto maps (date in YYYY,MM,DD e.g. 20210615_SPOTS_Ortho_UTM_35N) - Hyper Cubes UTM_35N NO Normalized (date in YYYY,MM,DD_Flight number_Height_UTM zone e.g. 20210615_F47_H25_UTM_35N) Hyper Cubes UTM_35N Normalized (date in YYYY,MM,DD_Flight number_Height_UTM zone_NORM e.g. 20210615_F47_H25_UTM_35N_NORM)

Genetic response to human‐induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway

Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a self-recruiting population in barely few decades. Landvikvannet sprat proved to be genetically isolated from the three main populations described for this species; i.e. Norwegian fjords, Baltic Sea, and the combination of North Sea, Kattegat and Skagerrak. This distinctness was depicted by an accuracy self-assignment of 89% and a highly significant FST between the lake sprat and each of the remaining samples (average of ≈0.105). The correlation between genetic and environmental variation indicated that salinity could be an important environmental driver of selection (3.3% of the 91 SNPs showed strong associations). Likewise, Isolation by Environment was detected for salinity, although not for temperature, in samples not adhering to an Isolation by Distance pattern. Neighbour-joining tree analysis suggested that the source of the lake sprat is in the Norwegian fjords, rather than in the Baltic Sea despite a similar salinity profile. Strongly drifted allele frequencies and lower genetic diversity in Landvikvannet compared with the Norwegian fjords concur with a founder effect potentially associated with local adaptation to low salinity. Genetic differentiation (FST) between marine and brackish sprat is larger in the comparison Norway- Landvikvannet than in Norway-Baltic, which suggests that the observed divergence was achieved in Landvikvannet in some 65 generations, i.e., 132 years, rather than gradually over thousands of years (the age of the Baltic Sea), thus highlighting the pace at which human-driven evolution can happen.

The effect of migration and variation on populations of Escherichia coli adapting to complex fluctuating environments

Migration, a critical evolutionary force, can have contrasting effects on adaptation. It can aid as well as impede adaptation. The effects of migration on microbial adaptation have been studied primarily in simple constant environments. Very little is known about the effects of migration on adaptation to complex, fluctuating environments. In our study, we subjected replicate populations of Escherichia coli, adapting to complex and unpredictably fluctuating environments to different proportions of clonal ancestral immigrants. Contrary to the results from simple/constant environments, the presence of clonal immigrants reduced all measured proxies of fitness. However, migration from a source population with a greater variance in fitness resulted in no change in fitness w.r.t the no-migration control, except at the highest level of migration. Thus, the presence of variation in the immigrants could counter the adverse effects of migration in complex and unpredictably fluctuating environments. Our study demonstrates that the effects of migration are strongly dependent on the nature of the destination environment and the genetic makeup of immigrants. These results enhance our understanding of the influences of migrating populations, which could help better predict the consequences of migration.

opencc-zeroSep 2022View details →

Co-occurrence of antimicrobials and metals in swine manure as potential drivers of antimicrobial resistance in the environment

In many regions of the United States (US) and other countries, animal manures are often agronomically applied to cropland to recycle nutrients. However, aggregated manure wastes commonly contain contaminants including veterinary antimicrobials, heavy metals, and antimicrobial resistance genes (ARGs) that can stimulate the development and proliferation of antimicrobial resistance (AMR). While the presence of antimicrobials in manure is well-documented, very little has been reported on the co-occurrence of other chemical stressors in swine manure that may stimulate AMR spread in exposed bacteria. This study quantifies and analyzes correlations between antimicrobials, metals, and certain ARGs present in manure samples from swine farms in Iowa, US. Relationships between contaminants and different stages of swine production or feed composition are also investigated. Results revealed notable levels of tetracyclines (up to 1,260 µg g-1 dry weight (d.w.) of manure for oxytetracycline) detected in all samples. Tiamulin, two ionophores (monensin and lasalocid), and one macrolide (tilmicosin) were detected at maximum class concentrations of 9.4, 0.547, and 0.472 µg g-1 d.w., respectively. The median relative abundances of ErmB and TetM were 0.13 and 0.17 copies g-1 wet weight (w.w.) manure (normalized to 16S gene), respectively. Additionally, high levels of copper (Cu), iron (Fe), and zinc (Zn) were detected in all samples, with maximum concentrations of 887, 1,900, and 2,100 µg g-1 d.w., respectively. Notably, uranium was detected in 11 samples, at concentrations up to 0.77 µg g-1. A global analysis of AMR-stressor relationships using Spearman's rank correlation indicates Cu, and Ba are the most positively and significantly correlated with anhydrotetracycline (ATC) and/or anhydrochlortetracycline (ACTC) concentrations in all tested facilities (Cu-ATC: ρ = 0.67, p = 0.0093; Cu-ACTC: ρ = 0.75, p = 0.0022; Ba-ATC: ρ = 0.84, p = 0.0002). Interestingly, ermB and tetM genes were strongly, positively correlated to each other (ρ=0.92, p= 0.000), suggesting possible co-selection, despite the absence of correlation between ARGs and tetracycline concentrations. This study demonstrates the complexity of interactions between antimicrobials, metals, and ARGs in multiple manure storage pits prior to cropland application.

Scaling protein-water interactions in the Martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments

This dataset contains molecular dynamics (MD) trajectories used for preparation of the following manuscript:  "Scaling protein-water interactions in the Martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments".