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Long-term responses to large-scale disturbances: Spatiotemporal variation in gastropod populations and communities

The Anthropocene is characterized by complex, primarily human-generated, disturbance regimes that include combinations of long-term press (e.g. climate change, pollution) and episodic pulse (e.g. cyclonic storms, floods, wildfires, land use change) disturbances. Within any regime, disturbances occur at multiple spatial and temporal scales, creating complex and varied interactions that influence spatiotemporal dynamics in the abundance, distribution, and biodiversity of organisms. Moreover, responses to disturbance are context-dependent, with the legacies of previous disturbances affecting responses to ensuing perturbations. We use three decades of annual data to evaluate the effects of repeated pulse disturbances and global warming on gastropod populations and communities in Puerto Rico at multiple spatial scales. More specifically, we quantify (1) the relative importance of large-scale and small-scale aspects of disturbance on variation in abundance, biodiversity, and species composition; and (2) the spatial scales at which populations and communities integrate information in the spatially heterogenous environments created by disturbances. Gastropods do not exhibit consistent decreases in abundance or biodiversity in association with global warming: abundance for many species has increased over time and species richness does not evince a temporal trend. Nonetheless, gastropods are sensitive to hurricane severity, spatial environmental variation, and successional trajectories of the flora. In addition, they exhibit context-dependent (i.e. legacy effects) responses that are scale-dependent. The Puerto Rican biota has evolved in a disturbance-mediated system. This historical exposure to repeated, severe hurricane-induced disturbances has imbued the biota with high resistance and resilience to the current disturbance regime, resulting in an ability to persist or thrive under current environmental conditions. Nonetheless, these ecosystems may yet be threatened by worsening direct and indirect effects of climate change. In particular, more frequent and severe hurricanes may prevent the establishment of closed-canopy forests, negatively impacting populations and communities that rely on these habitats.

Biogeographic inferences across spatial and evolutionary scales

The field of biogeography unites landscape genetics and phylogeography under a common conceptual framework. Landscape genetics traditionally focuses on recent-time, population-based, small geographic scale, spatial genetics processes, while phylogeography typically investigates deep past, lineage- and species-based processes at large geographic scales. Here, we evaluate the link between landscape genetics and phylogeographic methods using the Western Fence lizard (Sceloporus occidentalis) as a model species. First, we conducted replicated landscape genetics studies across several geographic scales to investigate how population genetics inferences change depending on the spatial extent of the study area. Then, we carried out a phylogeographic study of population structure at two evolutionary scales informed by inferences derived from landscape genetics results to identify concordance and conflict between these sets of methods. We found significant concordance in landscape genetics processes at all but the largest geographic scale. Phylogeographic results indicate major clades are restricted to distinct river drainages or distinct hydrologic regions. At a more recent timescale, we find minor clades are restricted to single river canyons in the majority of cases, while the remainder of river canyons include samples from at most two clades. Overall, the broad scale pattern implicating stream and river valleys as key features linking populations in the landscape genetics results, and high degree of clade specificity within major topographic subdivisions in the phylogeographic results, is consistent. As landscape genetics and phylogeography share many of the same objectives, synthesizing theory, models, and methods between these fields will help bring about a better understanding of ecological and evolutionary processes structuring genetic variation across space and time.

opengpl-2.0Jan 2023View details →

Scaling Behavior for Electric Vehicle Chargers and Roadmap to Addressing the Infrastructure Gap

Source code and datasets for "Scaling Behavior for Electric Vehicle Chargers and Roadmap to Addressing the Infrastructure Gap"

Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets

Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.

Vegetation cover and biodiversity reduce parasite infection in wild hosts across ecological levels and scales

Land use changes and biodiversity loss critically disrupt ecosystem functioning and are major drivers of infectious disease outbreaks. Trypanosoma cruzi, the agent of Chagas disease, is a multi-host parasite whose epidemiology has changed due to the expansion of anthropogenic activities over natural areas. We aimed to understand the ecological processes increasing parasite prevalence at the individual, the community and the landscape levels using the largest database on small mammal infection by T. cruzi in Brazil. We applied machine learning techniques and structural equation models to show that allometric traits and the relative abundance of rodents in the community were important predictors of infection risk, followed by variables associated with the landscape environmental quality. Natural vegetation cover change and the taxonomic and functional dimensions of biodiversity indirectly reduced infection through its effect on the abundance distribution and composition of host communities. According to our findings, approaches to biodiversity conservation and restoration based on the integration of social inclusion and human welfare would contribute to regulating the prevalence of T. cruzi in wild hosts, which may reduce overall transmission risk.

Data from: Scale-dependent effects of landscape structure on pollinator traits, species interactions and pollination success

Data: Plant-pollinator interactions, pollinator body size (inter-tegular distance, ITD) and plant reproductive success (number of seeds produced). Data collected by Christie J. Webber. Data collected in 14 experimental flowering plant patches during December 2012–February 2013. Patches were located in a 105 hectare sheep farm pasture in Oxford, North Canterbury, New Zealand (43°19'21"S 172°12'25"E). Files: <ul> <li>Data_S1: contains plant-pollinator interactions sampled and pollinator inter-tegular distance (ITD). Data_S1 columns: patch ID where the interaction was recorded, plant species, pollinator ITD (mm), and pollinator family, genus and species.</li> <li>Data_S2: contains the number of seeds produced by each of the five flowers of each plant individual from each plant species on each patch. Data_S2 columns: patch ID where the measurement was taken, plant species, plant number (individual sampled), number of seeds.</li> </ul> Dataset used in "Scale-dependent effects of landscape structure on pollinator traits, species interactions and pollination success" by G. Peralta, C.J. Webber, G.L.W. Perry, D.B. Stouffer, D.P. Vázquez and J.M. Tylianakis.

The geological map of Italy 1:100,000 scale INSPIRE harmonised

The INSPIRE Directive institute a European infrastructure for spatial information to support the environmental policies of the European Union. In the mainframe of the Directive, 34 different themes that represents different environmental information has been identified. One of this is the Geology theme; it is split into three subthemes and represent a "reference data theme” because it provides basic knowledge on the physical properties and composition of rocks and sediments, their structure and their age as represented in geological maps, as well as geomorphological features. In the feature catalogue of the INSPIRE application schema Geology has been defined the term lists for the information types. Some of these are fully compliant with the features defined in the 1:100.000 scale geological map database and are used in the semantic harmonization procedure. The Geological Map of Italy at 1:100,000 scale is, at present, the most detailed complete geological map of Italy. It consists of a collage of 277 sheets, and it was produced over a period of more than 100 years, with some sheets in two editions. In the late 1990s, it was transformed into a vector database by digitising from raster format. The dataset was revised, integrated, and corrected between 2005-2009 by the Geological Survey of Italy. In 2021-22 the dataset was harmonised according to the INSPIRE and GeoSciML data models. The whole area has been subdivided into three different .gml format dataset on geographic base: Northern, Central and Southern Italy.

Interview Transcriptions related to PhD Thesis "Degrowth at a Global Scale? Geographies of Chile's Fruit Production and Export between Extractivism and Socio-Ecological Transformation"

The material is composed of transcriptions of interviews conducted for the empirical work of this PhD Thesis. Not all conducted interviews are included (which can be seen from the accompanying table); those not included are not available mostly due to lack of consent of interviewees or because certain interviews were not registered and only hand-written notes were taken.

opencc-by-nc-4.0Jan 2023View details →

A multi-system comparison of forecast flooding extent using a scale-selective approach [data]

A multi-system comparison of forecast flooding extent using a scale-selective approach, data. Creator: Helen Hooker[1] Publication Year: 2023 Organisation(s): 1. Department of Meteorology, University of Reading, U.K Description: This dataset contains: - SAR-derived observed flood maps used in the study. - CSM validation maps for forecast flood maps from Food Foresight (FF), GloFAS Rapid Flood Mapping (RFM) and FFWC Super Model (FFWC) predicting flooding extent on 25 July 2020 for the Jamuna River, Bangladesh compared against Sentinel-1 SAR-derived flooding extent. File format is e.g. CSM_FF_forecastdate_rundate.tif. CSM maps for Flood Foresight following system improvement are labelled with ..._reas.tif. Helen Hooker. (2023). A multi-system comparison of forecast flooding extent using a scale-selective approach (v1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7509980 Related publications: A multi-system comparison of forecast flooding extent using a scale-selective approach; 2023; Hydrology Research (in preparation) Helen Hooker[1], Sarah L. Dance[1,2,3], David C. Mason[4], John Bevington[5], and Kay Shelton[5] <ol> <li>Department of Meteorology, University of Reading, UK.</li> <li>Department of Mathematics and Statistics, University of Reading, UK.</li> <li>NCEO, University of Reading, UK.</li> <li>Department of Geography and Environmental Science, University of Reading, UK.</li> <li>JBA Consulting, UK.</li> </ol> Correspondence: Helen Hooker (<a href="mailto:h.hooker@pgr.reading.ac.uk">h.hooker@pgr.reading.ac.uk</a>)

Fijian sea krait behavior relates to fine‐scale environmental heterogeneity in old‐growth coastal forest: The importance of integrated land–sea management for protecting amphibious animals

Here the data for "Fijian sea krait behaviour relates to fine-scale environmental heterogeneity in old growth forest: the importance of integrated land-sea management for protecting amphibious animals" by Lowe, C., Keppel, G., Waqa, K., Peters, S., Fisher, R.N., Scanlon, A., Osborne-Naikatini, T, and Thomas-Moko, N is provided. This article investigates the habitat of Yellow Lipped Sea Kraits, Laticauda colubrina, in the terrestrial realm on Leluvia Island, a small, topographically flat atoll in Fiji with coastal forest. The investigation uses concurrent microclimate measurements and behaviour surveys, as well as vegetation surveys, and the data collected for these analyses are provided here. Microclimates were significantly related to canopy cover, leaf litter depth, and distance from the high-water mark (HWM). Sea kraits were almost exclusively observed in coastal forest within 30 m of the HWM. Sloughing of skins only occurred within crevices of mature or dying trees. Resting L. colubrina were significantly more likely to occur at locations with higher mean diurnal temperatures, lower leaf litter depths, and shorter distances from the HWM. On Leleuvia, behaviour of L. colubrina therefore relates to environmental heterogeneity created by old-growth coastal forests, particularly canopy cover and crevices in mature and dead tree trunks. The importance of healthy coastal habitats, both terrestrial and marine, for L. colubrina suggests it could be a good flagship species for advocating integrated land-sea management. Furthermore, our study highlights the importance of coastal forests and topographically flat atolls for biodiversity conservation. Effective conservation management of amphibious species that utilise land- and seascapes is therefore likely to require a holistic approach that incorporates connectivity among ecosystems and environmental heterogeneity at all relevant scales.

opencc-by-4.0Apr 2007View details →

Fig. 3. Isolated type A coprolites viewed using transmitted-light microscopy. Scale bars 100 in The ecological role of immature phantom midges (Diptera: Chaoboridae) in the Eocene Lake Messel, Germany

Fig. 3. Isolated type A coprolites viewed using transmitted-light microscopy. Scale bars 100 µm.

Data from: Navigating the scales of diversity in subtropical and coastal fish assemblages ascertained by eDNA and visual surveys

Environmental DNA (eDNA) metabarcoding emerges as a powerful method, allowing a more exhaustive investigation of fish fauna than any other methods. Yet, the general use of eDNA as a replacement of traditional methods such as visual surveys or physical sampling remains debatable. Therefore, a prior understanding of eDNA's spatial resolution is necessary. This study aimed to compare the assessments of fish diversity at three spatial scales by eDNA, underwater visual census (UVC), and diver-operated video (DOV) surveys across 21 reef sites in northern Taiwan. The specific objectives were to explore the regional species pool (γ-diversity), reveal spatial patterns of fish assemblages (β-diversity), and disentangle the relationships between fish assemblages and benthic composition (α-diversity). At the γ-diversity level, a total of 438 marine fish species were detected across methods. eDNA exhibits an extraordinary power to explore the regional species pool given sufficient replication, a power which is unachievable by DOV and UVC. At the β-diversity level, all the methods successfully revealed the same spatial patterns of beta diversity and the distance decay of similarity in fish assemblages. At the α-diversity level, none of the methods is capable of investigating the entire resident fish fauna, but visual surveys are more suitable for scrutinizing interactions between fish and benthos. Instead of undiscriminatingly recommending a combination of eDNA with traditional survey methods, we suggest implementing specific surveys in accordance with the ecological questions of interest.

A Dataset for Lateral Load Capacities of Large Scale Monopiles

The dataset is used for training a hybrid neural network and is generated using Finite Element Modeling. The presented dataset contains the lateral response (kN) of the monopile at 0.5 and 1 degree of rotation along with the monopile's length (m), the moment of inertia (m4), and load eccentricity (m). The dataset also contains the values of depth (m) and its corresponding cone resistance (qc: kPa) obtained from the CPT test.

Data for: Sex-biased infections scale to population impacts for an emerging wildlife disease

Demographic factors are fundamental in shaping infectious disease dynamics. Aspects of populations that create structure, like age and sex, can affect patterns of transmission, infection intensity and population outcomes. However, studies rarely link these processes from individual to population-scale effects. Moreover, the mechanisms underlying demographic differences in disease are frequently unclear. Here, we explore sex-biased infections for a multi-host fungal disease of bats, white-nose syndrome, and link disease-associated mortality between sexes, the distortion of sex ratios, and the potential mechanisms underlying sex differences in infection. We collected data on host traits, infection intensity, and survival of five bat species at 42 sites across seven years. We found females were more infected than males for all five species. Females also had lower apparent survival over winter and accounted for a smaller proportion of populations over time. Notably, female-biased infections were evident by early hibernation and likely driven by sex-based differences in autumn mating behavior. Male bats were more active during autumn which likely reduced replication of the cool-growing fungus. Higher disease impacts in female bats may have cascading effects on bat populations beyond the hibernation season by limiting recruitment and increasing the risk of Allee effects.

supplementary to "SnowPappus v1.0, a blowing-snow model for large-scale applications of Crocus snow scheme" , 2D wind forcing

This is a supplementary material to article "SnowPappus v1.0, a blowing-snow model for large-scale applications of Crocus snow scheme" ( unpublished at the publication date of this dataset) It contains the 2D wind forcing for Crocus-SnowPappus simulations on the Grandes Rousses test zone. It was generated using DEVINE wind downscaling method ( Le Toumelin et al., 2022 )

Stability of the next-to-tribimaximal mixings under radiative corrections with the variation of SUSY breaking scale

<pre>We analyse the stability of the next-to-tribimaximal mixings ($NTBM$) under radiative corrections with the variation of SUSY breaking scale ($m_s$) for both normal and inverted hierarchical cases at the fixed value of seesaw scale $M_R = 10^{15}$ GeV and $\tan \beta = 30$. All the neutrino oscillation parameters receive varying radiative corrections irrespective of the $m_s$ values at the electroweak scale, which are all within $3\sigma$ range of the latest global fit data. NH case is found to be more stable than IH case for all four cases.</pre>

Scaled RNA sequencing counts accompaining the publication Singh and Gollapalli 2023

RNA-Seq analysis of WT and taurine-deficient osteoblasts. RNA was extracted from the mouse primary calvarial osteoblasts prepared from day 3–5 neonates of WT or Slc6a6-/- genotypes using the RNeasy extraction kit (Qiagen). RNA sequencing libraries were prepared with Illumina-compatible NEBNext UltraTM II Directional RNA library kit at Genotypic Technology, Inc. The raw data were trimmed for adapter sequences and low-quality bases (<q30) using Cutadapt with default parameters [DOI:10.14806/ej.17.1.200] and checked for quality using FastQC [Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data]. Mouse raw reads were aligned to the mouse reference genome (mm9) using Hisat2(24) with default parameters. HTSeq [G Putri, S Anders, PT Pyl, JE Pimanda, F Zanini Analyzing high-throughput sequencing data with HTSeq 2.0 arXiv:2112.00939 (2021)] was used to estimate gene abundance. Downstream analyses were done using the analysis framework tidybulk (25, 26). The filterByExpr functionality of edgeR (27) was used to identify the abundant gene-transcripts included in downstream analyses using default parameters and the knock-out phenotype as the factor of interest. The algorithm trimmed mean of M valued (TMM) values identified sample-wise scaling to compensate for differences in sequencing depth across samples (28). For aiding data exploration, we reduced the data dimensionality using principal component analysis (PCA). Differential expression analyses were performed using the robust likelihood ratio implementation of edgeR, testing for differences in gene transcript abundance greater than 1 log-fold (29, 30). The ppcseq method was used to investigate the presence of outlier observation among the significant results to avoid biases in the statistics (31). The ggplot2 software produced most of the data visualizations, whereas tidyHeatmap was used for heatmap visualization (32-34). We performed gene-set enrichment analyses using the MSigDB C2 experimentally derived gene set, the clusterProfiler algorithm, and the visualization tool enrichplot (cran.r-project.org/) (https://rdrr.io/cran/msigdbr/) (35). An aging signature was composed of a union of gene sets from MSigDB and a set of genes derived from aging datasets identified in this study through gene set enrichment analysis and published literature (36). The p-values of gene set analyses were corrected for multiple testing using the Benjamini Hochberg correction (37).

dataset for "Corner-bridge flow as pore-scale flow mechanism controlling capillary pressure curve at low saturations"

dataset for "Corner-bridge flow as pore-scale flow mechanism controlling capillary pressure curve at low saturations", including raw images from drainage experiments

dataset for "GPU-enhanced DEM analysis of flow behaviour of irregularly shaped particles in a full-scale twin screw granulator"

This dataset contains the numerical simulation data describing the conveying behaviour of shaped-particle systems. Detailed study on the conveying behaviour is presented in a journal paper entitled "GPU-enhanced DEM analysis of flow behaviour of irregularly shaped particles in a full-scale twin screw granulator". We provide all the essential data in a single excel file with the description below: Dataset 1- Average particle speed (Fig. 7a) and XYZ components (Fig. 7b) for: Sphere at t = 2.1 s, Cube at t = 2.85 s, Biluna at t = 3.1 s, HexP at t = 3.45 s. (Data of Fig. 7) Dataset 2 - XYZ coordinates of a typical particle trapped in the granulator. (Data of Fig. 9) Dataset 3 - Particle retention numbers for different shaped particles. (Data of Fig. 10). Dataset 4 - Average particle speeds for different shaped particles. (Data of Fig. 11). Dataset 5 - Average axial particle speeds for different shaped particles (Data of Fig. 12). Dataset 6 - Residence time distributions for various shaped particles. (Data of Fig. 13) Dataset 7 - Normalised residence time distributions for various shaped particles. (Data of Fig. 14) Dataset 8 - Mean residence time for various shaped particles. (Data of Fig. 15) Dataset 9 - The variance of RTD for different shaped particles. (Data of Fig. 16) Dataset 10 - Cumulative exit age distribution for various shaped particles. (Data of Fig. 17) Dataset 11 - Normalised cumulative exit age distribution for various shaped particles. (Data of Fig. 18) Dataset 12 - Evolution of the cumulative power consumption for various shaped particles. (Data of Fig.19) Dataset 13 - Power consumption distribution for various shaped particles. (Data of Fig.20)

Data from "Enhanced radiative forcing from aerosol-cloud interactions due to large-scale circulation adjustments" by Guy Dagan, Netta Yeheskel and Andrew I. L. Williams.

This is the data presented in "Enhanced radiative forcing from aerosol-cloud interactions due to large-scale circulation adjustments" by Guy Dagan, Netta Yeheskel and Andrew I. L. Williams.   Please read the README file for explanations about the data.