Find research datasets worth reusing

16S rRNA sequences from Siganidae (S. rivulatus and S. luridus) gut microbiome in their native (Red Sea) and invaded (Mediterranean Sea) ranges

The microbiome of invasive species is increasingly seen as a potential key factor of their ecological success, and this appears particularly true in herbivorous invaders whose digestive abilities rely on the microbes hosted in their gut. We characterized the gut microbiome of two invasive herbivorous fishes (Siganus rivulatus and Siganus luridus) in their native (Red Sea) and invaded (Levantine Sea and Northern Crete) ranges. We found that gut bacterial communities contain a higher taxonomic and phylogenetic diversity while becoming increasingly different from the native microbiome as the fishes move away from the native zone. This shift resulted in the homogenization of the microbiomes between individuals from the same species as well as between the two species. Firmicutes and Tenericutes reduced drastically in abundance while Proteobacteria and Bacteroidetes became more dominant in both species. This led to a modification of the functional potential of the gut microbiome associated with the metabolism of short-chanin fatty acids that also became more homogeneous in the invaded range. Altogether, our results suggest that the plasticity of the gut microbiome in Siganidae could be a key factor underlying their ecological success in Mediterranean ecosystems.

Data from: Heat stress conditions affect the social network structure of free‐ranging sheep

Extreme weather conditions, like heatwave events, are becoming more frequent with climate change. Animals often modify their behaviour to cope with environmental changes and extremes. During heat stress conditions, individuals change their spatial behaviour and increase the use of shaded areas to assist with thermoregulation. Here, we suggest that for social species, these behavioural changes and ambient conditions have the potential to influence an individual's position in its social network, and the social network structure as a whole. We investigated whether heat stress conditions (quantified through the temperature humidity index) and the resulting use of shaded areas, influence the social network structure and an individual's connectivity in it. We studied this in free‐ranging sheep in the arid zone of Australia, GPS‐tracking all 48 individuals in a flock. When heat stress conditions worsened, individuals spent more time in the shade and the network was more connected (higher density) and less structured (lower modularity). Furthermore, we then identified the behavioural change that drove the altered network structure and showed that an individual's shade use behaviour affected its social connectivity. Interestingly, individuals with intermediate shade use were most strongly connected (degree, strength, betweenness), indicating their importance for the connectivity of the social network during heat stress conditions. Heat stress conditions, which are predicted to increase in severity and frequency due to climate change, influence resource use within the ecological environment. Importantly, our study shows that these heat stress conditions also affect the animal's social environment through the changed social network structure. Ultimately, this could have further flow on effects for social foraging and individual health since social structure drives information and disease transmission.

Data for: Increasing planting density increases fruit mass and reduces the dispersal ability of a range-expanding invasive plant, Mikania micrantha

Aim: Invasive plants may evolve a suite of distinctive traits during spread in the new range. Among these traits, dispersal ability is an important trait determining the invasion speed of exotic plants. There is evidence that higher dispersal ability is favored at the invasion front, where population density may be low. However, no study has explicitly tested how planting density in a common garden affects the dispersal ability of invasive plants. Location: Hainan island of China. Methods: In this study, using 27 populations of an invasive plant, Mikania micrantha, which is expanding its range on Hainan island of China, we examine how three dispersal-related traits (i.e., dispersal ability, fruit mass, and pappus radius) change with distance from invasion centre and field population density, and how planting density in a common garden affects dispersal traits. Results: Dispersal traits did not change with distance from the invasion centre and field population cover either in the natural environment or in the common garden. In the common garden, increasing planting density from one to five plants per pot increased fruit mass and decreased dispersal ability, indicating that the effect of density on dispersal traits could not be detected in the field. The relationship between dispersal ability in the natural environment and that in the common garden was positive but significant only under the five plants per pot treatment, possibly because dispersal traits in natural conditions were selected under high density growth conditions. Main conclusions: Our results indicate that increasing population density may increase fruit mass and reduce the dispersal ability of range-expanding invasive plants. We suggest that further studies exploring the patterns of dispersal traits in range-expanding invasive plants in a common garden should consider intraspecific competition.

DNA metabarcoding reveals a broad dietary range for Tasmanian devils introduced to a naïve ecosystem

Top carnivores are essential for maintaining ecosystem stability and biodiversity. Yet, carnivores are declining globally and current in situ threat mitigations cannot halt population declines. As such, translocations of carnivores to historic sites or those outside the species' native range are becoming increasingly common. As carnivores are likely to impact herbivore and small predator populations, understanding how carnivores interact within an ecosystem following translocation is necessary to inform potential remedial management and future translocations. Dietary analyses provide a preliminary assessment of the direct influence of translocated carnivores on a recipient ecosystem. We used a metabarcoding approach to quantify the diet of Tasmanian devils introduced to Maria Island, Tasmania, a site outside the species' native range. We extracted DNA from 96 scats and used a universal primer set targeting the vertebrate 12S rRNA gene to identify diet items. Tasmanian devils on Maria Island had an eclectic diet, with 63 consumed taxa identified. Cat DNA was detected in 14% of scats, providing the first instance of cats appearing as part of Tasmanian devil diets either via predation or scavenging. Short-tail shearwaters and little penguins were commonly consumed, corresponding with previous surveys showing sharp population declines in these species since the introduction of Tasmanian devils. Our results indicate that the introduction of carnivores to novel ecosystems can be very successful for the focal species, but that commonly consumed species should be closely monitored to identify any vulnerable species in need of remedial management.

opencc-by-4.0Nov 2023View details →

Effect of Long-Range Transported Fire Aerosols on Cloud Condensation Nuclei Concentrations and Cloud Properties at High Latitudes

The tab-delimited files contain Aerosol chemical composition data, size distribution data measured by AMS, ACSM, MAAP, and SMPS, and DMPS at the SMEAR IV station (Puijo) and the Zepplein observatory (Zep) . Please read the file named 'Information.txt' for more details about the files.

opencc-zeroMar 2024View details →

Defensive spines are associated with large geographic range but not diversification in spiny ants (Hymenoptera: Formicidae: Polyrhachis)

Several prominent evolutionary theories propose mechanisms whereby the evolution of a defensive trait or suite of traits causes significant shifts in species diversification rate and niche evolution. We investigate the role of cuticular spines, a highly variable morphological defensive trait in the hyperdiverse ant genus Polyrhachis, on species diversification and geographic range size. Informed by key innovation theory and the escape-and-radiate hypothesis, we predicted that clades with longer spines would exhibit elevated rates of diversification and larger range sizes compared to clades with shorter spines. To address these predictions, we estimated phylogenetic relationships with a phylogenomic approach utilizing ultra-conserved elements (UCEs) and compiled morphological and biogeographic trait databases. In contrast to the first prediction, we found no association between diversification rate and any trait (spine length, body size, and range size). However, we recovered a positive correlation between spine length and geographic range size, suggesting that spines promote expanded geographic range. Notably, these results were consistent across analyses using different phylogenetic inference approaches and spine trait measurement schemes. This study provides a rare investigation of the role of a defensive trait on geographic range size, and ultimately supports the hypothesis that defensive spines are a factor in increased range size in Polyrhachis ants. Furthermore, the lack of support for an association between spines and diversification, which contrasts with previous work demonstrating a positive association between spines and diversification rate, is intriguing and warrants further study.

opencc-by-4.0Mar 2024View details →

Frequency-comb-linearized, widely tunable lasers for coherent ranging

This data contains the raw data of the experiment and the code and corresponding data of the figures in the artical.

opencc-by-4.0Mar 2024View details →

Antipsychotic drugs selectively decorrelate long-range interactions in deep cortical layers

All raw data and Matlab code necessary to produce the figures of https://elifesciences.org/reviewed-preprints/86805

opencc-zeroMar 2024View details →

Data from: Plant-soil interactions during the native and exotic range expansion of an annual plant

Range expansions, whether they are biological invasions or climate change-mediated range shifts, may have profound ecological and evolutionary consequences for plant-soil interactions. Range-expanding plants encounter soil biota with which they have a limited coevolutionary history, especially when introduced to a new continent. Past studies have found mixed results on whether plants experience positive or negative soil feedback interactions in their novel range, and these effects often change over time. One important theoretical explanation is that plants locally adapt to the soil pathogens and mutualists in their novel range. We tested this hypothesis in Dittrichia graveolens, an annual plant that is both expanding its European native range, initially coinciding with climate warming, and rapidly invading California, after human introduction. In parallel greenhouse experiments on both continents, we used plant genotypes and soils from five locations at the core and edge of each range to compare plant growth in soil from D. graveolens populations and nearby control microsites as a measure of plant-soil feedback. Plant-soil interactions were highly idiosyncratic across sites in each range. On average, plant-soil feedbacks were more positive in the native range than in the exotic range. In line with the strongly heterogeneous pattern of soil responses along our biogeographic gradients, we found no evidence for evolutionary differentiation between plant genotypes from the core to the edge of either range. Our results suggest that the evolution of plant-soil interactions during range expansion may be more strongly driven by local evolutionary dynamics varying across the range than by large-scale biogeographic shifts.

opencc-zeroMar 2024View details →

Data from: Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance

Declines in bumblebee species ranges and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumblebee (Bombus affinis) is the first federally-listed bumblebee species in North America. We conducted a range-wide population genetics study of B. affinis from across all extant conservation units to inform conservation efforts. To understand the species' vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range wide male diploidy rate of ~15%. Our results suggest the Appalachians represents a genetically distinct cluster with high levels of private alleles and substantial differentiation from the rest of the extant range. Site-level analyses suggest low colony abundance estimates for B. affinis compared to similar datasets of stable, co-occurring species. These results lend genetic support to trends from observational studies suggesting B. affinis has undergone a recent decline and exhibits substantial spatial structure. The low colony abundances observed here suggest caution in overinterpreting the stability of populations even where B. affinis is reliably detected interannually. These results help delineate informed management units, provide context for the potential risks of translocation programs, and can help set clear recovery targets for this and other threatened bumblebee species.

openapache2.0Mar 2024View details →

Replication package for article 'Parallel Program Analysis on Path Ranges'

This Replication package contains all the results for the article "Parallel Program Analysis on Path Ranges" Abstract. Symbolic execution is a software verification technique symbolically running programs and thereby checking for bugs.   Ranged symbolic execution   performs symbolic execution on program parts, so called {\em path ranges}, in parallel. Due to the parallelism, verification is accelerated and hence scales to larger programs. In this paper, we discuss a generalization of ranged symbolic execution to arbitrary program analyses. More specifically, we present a verification approach that splits programs into path ranges and then runs arbitrary analyses on the ranges in parallel. Our approach in particular allows to run {\em different} analyses on different program parts. We have implemented this generalization on top of  the tool \textsc{CPAchecker} and evaluated it on programs from the SV-COMP benchmark. Our evaluation shows that verification can benefit from the parallelisation of the verification task, but also needs a form of work stealing (between analysis) as to become efficient.

opencc-by-4.0Apr 2024View details →

The potential range of Agrilus planipennis according to current and future climate conditions

This dataset is associated to the following reference: Jean-Pierre Rossi, Raphaëlle Mouttet, Pascal Rousse and Jean-Claude Streito (2024) Modelling the potential range of Agrilus planipennis in Europe according to current and future climate conditions. In press. Trees, Forests and People. https://doi.org/10.1016/j.tfp.2024.100559 The files correspond to rasters saved as geotiff files. They can be used in geographical information systems. Current climate conditions: 2001-2018. The maps correspond to the whole world. CS_2001-2018_Bart.tif Climate suitability for Agrilus planipennis modelled using the BART algorithm and the reference conditions (2001-2018). The climate suitability ranges from 0 (unsuitable) to 1 (suitable). CS_2001-2018_Brt.tif Climate suitability for Agrilus planipennis modelled using the BRT algorithm and the reference conditions (2001-2018). The climate suitability ranges from 0 (unsuitable) to 1 (suitable). CS_2001-2018_Rf.tif Climate suitability for Agrilus planipennis modelled using the RF algorithm and the reference conditions (2001-2018). The climate suitability ranges from 0 (unsuitable) to 1 (suitable). CS_2001-2018_Bart_pres_abs.tif Reclassified climate suitability maps for Agrilus planipennis modelled using the algorithm BART and the reference conditions (2001-2018). The raster contains 2 classes: suitable conditions (raster value = 1) and unsuitable conditions (raster value = 0). CS_2001-2018_Brt_pres_abs.tif Reclassified climate suitability maps for Agrilus planipennis modelled using the algorithm BRT and the reference conditions (2001-2018). The raster contains 2 classes: suitable conditions (raster value = 1) and unsuitable conditions (raster value = 0). CS_2001-2018_Rf_pres_abs.tif Reclassified climate suitability maps for Agrilus planipennis modelled using the algorithm RF and the reference conditions (2001-2018). The raster contains 2 classes: suitable conditions (raster value = 1) and unsuitable conditions (raster value = 0). CS_2001-2018_committee.tif Map showing the percentage of algorithms indicating suitable climate conditions for Agrilus planipennis. The algorithms (BART, BRT and RF) are projected using the current climate conditions (2001-2018). Future climate conditions: 2041-2060. The maps correspond to Europe.  CS_2041-2060_SSP1-2.6_committee.tif Map showing the percentage of algorithms indicating suitable climate conditions for Agrilus planipennis. The algorithms (BART, BRT and RF) are projected using the climate data associated with 11 GCMs for the period 2041-2060 and the SSP1-2.6.  CS_2041-2060_SSP2-4.5_committee.tif Map showing the percentage of algorithms indicating suitable climate conditions for Agrilus planipennis. The algorithms (BART, BRT and RF) are projected using the climate data associated with 11 GCMs for the period 2041-2060 and the SSP2-4.5.  CS_2041-2060_SSP3-7.0_committee.tif Map showing the percentage of algorithms indicating suitable climate conditions for Agrilus planipennis. The algorithms (BART, BRT and RF) are projected using the climate data associated with 11 GCMs for the period 2041-2060 and the SSP3-7.0.  CS_2041-2060_SSP5-8.5_committee.tif Map showing the percentage of algorithms indicating suitable climate conditions for Agrilus planipennis. The algorithms (BART, BRT and RF) are projected using the climate data associated with 11 GCMs for the period 2041-2060 and the SSP5-8.5.   BART: Bayesian Additive Regression Trees BRT: Boosted Regression Trees RF: Random Forest

opencc-by-4.0Apr 2024View details →

Dataset: diamagnetic susceptibility of nitrogen molecule within temperature range 50-2000K

Please see the attached PDF for a brief description of the data included in the dataset.

Vegetation changes with climate change in the Grandes Rousses mountain range

Questions: We assessed interactions between climate change, bedrock types and snow cover duration on the trajectories of taxonomic and functional composition of subalpine plant communities. We predict (i) an increase in species richness on siliceous bedrock due to a reduced competition and a decrease in richness on calcareous bedrock due to increasing drought stress, (ii) decreasing snow cover duration should induce a higher shrub encroachment in hollows as compared to ridges (iii) increasing growing season temperature should induce taller sizes and more conservative growth traits, in particular in hollows. Location: Subalpine belt of the Grandes Rousses mountain range, south western Alps (France). Methods: 189 vegetation plots were sampled in 1997 and 2017-2018. The duration of snow cover was assessed during two years in 1995-1997 and five functional traits were measured on 108 species in 2021. We performed multivariate analyses, quantified community weighted-means (CWM) of traits and used ANOVAs to detect responses to local-scale factors and changes in snow cover, temperature and precipitation since 1997 according to a nearby meteorological station. Results: Overall, taxonomic composition weakly changed and changes were more dependent on the position of communities along the snow cover duration gradient than on their bedrock type. The abundance of drought-tolerant species increased at the border of hollows and there was, over all communities, a slight increase in the abundance of dwarf shrubs and tall herbaceous species, a strong decrease in short herbaceous species and, thus, an overall decrease in species richness. There were important overall changes in CWM of size traits, in particular leaf area which increased the most in hollows irrespective of bedrock types. Conclusion: In this subalpine site the effects of decreasing snow cover duration overwhelmed the effects of bedrocks, which may explain the overall increase in competitive species and decrease in species richness.

opencc-by-4.0Mar 2024View details →

Supplementary data: Bayesian multi-exposure image fusion for robust high dynamic range ptychography

Accompanying supplementary data for the paper. To download this data automatically and use the software, please refer to the details in the README of the linked github repository.  Github URL: <a href="https://github.com/microscopic-image-analysis/bayes-mef">https://github.com/microscopic-image-analysis/bayes-mef</a>

Vocal range and ultraviolet-induced photoluminescence in gliding mammals and their relatives

Gliding is only present in six extant groups of mammals – interestingly, despite divergent evolutionary histories, all mammalian gliders are strictly nocturnal. Gliding mammals also seem to have relatively high rates of ultrasound use and ultraviolet-induced photoluminescence (UVP) in contrast with their close relatives. Therefore, we hypothesized that, despite diverging lineages, gliding mammals use similar modes of cryptic communication compared to their non-gliding counterparts. We developed two datasets containing the vocal range (minimum-maximum of the dominant harmonic; kHz) and UVP of 73 and 82 species, respectively; we report five novel vocal repertoires and 57 novel observations of the presence or absence of UVP. We complemented these datasets with information about body size, diel activity patterns, habitat openness, and sociality to explore possible covariates related to vocal production and UVP. We found that the maximum of the dominant harmonic was significant higher in gliding mammals when vocalizing than their non-gliding relatives. Additionally, we found that nocturnality was the only significant predictor of UVP, consistent with the previous hypothesis that luminophores primarily drive UVP in mammal fur. In contrast, however, we did not find UVP ubiquitous in nocturnal mammals, suggesting that some unknown process may contribute to variation in this trait.

Infrequent oceanic long-range dispersal and evolution of a top terrestrial arthropod predator in the sub-Antarctic

The UNESCO world heritage sub-Antarctic terrestrial ecosystems are unique. They have been isolated for over 30 million years by constant circum-polar currents and winds, and shaped by climatic cycles that surpass the tolerance limits of many species. Despite this recognition, surprisingly little is known about how these ecosystems acquired their native terrestrial fauna and how it changed over deep time scales. Here the patterns and timing of colonization and speciation in the largest and dominant arthropod predators in the Eastern sub-Antarctic – spiders of the genus Myro – are demonstrated for the first time. Our results indicate that this lineage originated from Australia before the Plio-Pleistocenic glacial cycles and underwent an adaptive radiation on the Crozet archipelago. We discuss the gain and loss of pre-adaptations acting as filter that enabled only one of four Myro species native to the Crozet islands to repeatedly disperse via the Antarctic circum-polar current, resulting in an outstanding distribution range over 9000 kilometres. The results highlight the outstanding role of the volcanic Crozet archipelago for the evolution of arthropod life in the sub-Antarctic, and the potential of terrestrial macro-invertebrates to achieve rare but ecologically influential trans-oceanic dispersal events over thousands of kilometres under hostile conditions.

Data rom: Stiffness anisotropy coordinates supracellular contractility driving long-range myotube-ECM alignment

The ability of cells to organize into tissues with proper structure and function requires the effective coordination of proliferation, migration, polarization, and differentiation across length scales. Skeletal muscle is innately anisotropic; however, few biomaterials can emulate mechanical anisotropy to determine its influence on tissue patterning without introducing confounding topography. Here, we demonstrate that substrate stiffness anisotropy coordinates contractility-driven collective cellular dynamics resulting in C2C12 myotube alignment over millimeter-scale distances. When cultured on mechanically anisotropic liquid crystalline polymer networks (LCNs) lacking topography, C2C12 myoblasts collectively polarize in the stiffest direction. Cellular coordination is amplified through reciprocal cell-ECM dynamics that emerge during fusion, driving global myotube-ECM ordering. Conversely, myotube alignment was restricted to small local domains with no directional preference on mechanically isotropic LCNs of the same chemical formulation. These findings provide valuable insights for designing biomaterials that mimic anisotropic microenvironments and underscore the significance of stiffness anisotropy in orchestrating tissue morphogenesis.

GPS tracking data for: Male mating season range expansion results from an increase in scale of daily movements for a polygynous-promiscuous bird

Males of species with promiscuous mating systems are commonly observed to use larger ranges during the mating season relative to non-mating seasons, which is often attributed to a change in movements related to reproductive activities. However, few studies link seasonal range sizes to variations in daily space use patterns to provide insight into the behavioral mechanisms underlying mating season range expansion. We studied 20 GPS-tagged male wild turkeys (Meleagris gallopavo), a large upland gamebird, during the mating and summer non-mating seasons to test the hypothesis that larger mating season ranges resulted from male wild turkeys expanding the scale of daily movement activities to locate and court females. We delineated mating and non-mating seasons based on the intensity of gobbling, a vocalization tied to courtship behavior, recorded by autonomous recording units distributed across the study area. Mating season ranges were significantly larger than non-mating season ranges. Daily ranges were larger in the mating season, as were distances between roost sites used on consecutive nights. Variance in daily range size was greater in the mating season, but low temporal autocorrelation suggested considerable daily variability in both seasons. We found no evidence that male wild turkeys changed how they distributed daily movements within seasonal ranges, or differences in habitat use, suggesting larger mating season ranges result from male wild turkeys increasing the scale of their daily movements, rather than a systematic shift to a nomadic movement strategy. Likely, the distribution of females is more dynamic and ephemeral compared to other resources, prompting males to traverse larger daily ranges during the mating season to locate and court females. Our work illustrates the utility of using daily movement to understand the behavioral process underlying larger space use patterns.