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opencc-zeroApr 2023View details →

Management intensity affects insect pests and natural pest control on Arabica coffee in its native range

Agroforestry systems provide opportunities to reduce the trade-off between agricultural production and biodiversity, for example by enhancing a diverse community of species potentially acting as natural pest control agents. While management of agroforestry systems is intensifying across the globe, we lack insights into the impact of management intensity on pest levels and natural pest control, especially along broad management gradients and as compared with natural forests. We assessed the impact of management intensity on major insect pests (the coffee blotch miner, the serpentine leaf miner, the coffee leaf skeletonizer, and damage by other free-feeding herbivores) and natural pest control by parasitoid wasps across sixty sites in the center of origin of Arabica coffee in southwestern Ethiopia. Within this region, coffee is growing along a broad management gradient ranging from little or no management in the natural forest to intensively managed commercial plantations. In the wet season, pest levels were largely similar in the natural forest, semi-forest, and semi-plantation systems, whereas pests reached outbreak densities in the most intensively managed plantation system. In contrast, management intensity did not significantly affect pest levels in the dry season. The insect pests differed in their seasonal dynamics, consistently declined with elevation, and were largely unaffected by shade levels. Parasitism rate of the coffee blotch miner was lower, and the parasitoid community was distinct, in the most intensively managed plantation system. Synthesis and applications: Our findings support the hypothesis that the weaker top-down control by parasitoids in the intensively managed plantation sites leads to higher pest levels, and that – at least for some pest species – there is a threshold in the effect of management intensity on pest levels and natural pest control. It is important to consider such non-linear relationships to maintain or enhance the sustainability of agroforestry systems during management intensification. Overall, our findings highlight that ecological knowledge of natural pest control can be used to intensify production to improve the livelihood of smallholders without jeopardizing natural pest control, at least up to a certain point.

opencc-by-4.0Nov 2022View details →

A comprehensive open-access database of electron backscattering coefficients for energies ranging from 0.1 KeV to 15 MeV

The database provides measured values of electron backscattering coefficient for 50 elements and 19 compounds at electron energies from 0.1keV to 15MeV.

opencc-by-4.0Mar 2023View details →

Fig. 1 in Current and future suitable habitats of a range-restricted species group (Cyrtodactylus chauquangensis) in Vietnam

Fig. 1. The occurrence localities of the C. chauquangensis species group.

Apache Point Observatory Lunar Laser-ranging Operation (APOLLO) normal point data: 2006 through 2020

Normal point data from the Apache Point Observatory Lunar Laser-ranging Operation (APOLLO) covering the 15-year span from April 2006 through the end of 2020. APOLLO measures the earth-moon separation by recording the round-trip travel time of photons from the Apache Point Observatory to five retro-reflector arrays on the moon. The APOLLO data set, combined with the 50-year archive of measurements from other lunar laser ranging (LLR) stations, can be used to probe fundamental physics such as gravity and Lorentz symmetry, as well as properties of the moon itself. These normal points have a median nightly accuracy of 1.7mm, which is an order of magnitude better than other LLR stations. Data is provided in both the "JPL" format (.np) and the Consolidated Laser Ranging Data Format (.crd)

'Chaotic micro-comb based parallel ranging' dataset and code

Available data and code for manuscript: "Chaotic micro-comb based parallel ranging" Arxiv version: https://arxiv.org/abs/2112.10241 Execution tested with Matlab 2020b or newer on Windows. Unzip folder to access files. Matlab figures are stored in matlab_figures folder. Raw data are stored in raw_data folder. To obtain plots from figure 2 (arXiv manuscript) execute Hilbert_freq_noise_analysis.m file. To process raw dat for figures 3,4 utilize sequential_analysis.m script. To plot point clouds of the processed data (\raw_data\fig3\analyzed_data) utilize plot_point_cloud_rmcw.m script. Comment/uncomment to change parameters for velocity/distance measurements (chess/wheel). Contact anton.lukashchuk@epfl.ch if problems with matlab code arise.  All matlab code remains under copyright by the authors: Anton Lukashchuk, Johann Riemensberger. The code is provided solely to be used to reproduce the figures of the aforementioned paper.

Chaotic microcomb inertia-free parallel ranging dataset and code

Available data and code for manuscript: "Chaotic microcomb inertia-free parallel ranging" Arxiv version: https://arxiv.org/abs/2212.14275 Execution tested with Matlab 2020b or newer on Windows. Unzip folder to access files. Matlab figures are stored in matlab_figures folder. For figure 2 execute feed_forward_tuning_analysis.m file Change tuning rate (row 23) for appropriate values (25, 50, 100 Hz). For figure 3 execute sequential_analysis_findpeaks.m and vipa_point_cloud.m files. Raw data are stored in raw_data folder. Contact anton.lukashchuk@epfl.ch if problems with matlab code arise.  All matlab code remains under copyright by the authors: Anton Lukashchuk. The code is provided solely to be used to reproduce the figures of the aforementioned paper.

Dataset: Long Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires

The ability to redirect electron transport to new reactions in living systems opens possibilities to store energy, generate new products, or probe physiological processes. Recent work by Huang et al. showed that 3D crystals of small tetraheme cytochromes (STC) could transport electrons over nanoscopic to mesoscopic distances by an electron hopping mechanism. Such protein-based structures with multiple localized electron carriers are promising materials for nanowires. A potential barrier to protein nanowire adoption for handling long-range electron transport is that fluctuations at room temperature may distort the nanostructure, hindering efficient electron transport. To study these fluctuations at the nano- and mesoscopic scales, we carry out classical molecular dynamics simulations for a small fragment of a STC nanowire and measure the effective distance distribution for electron tunneling. From distance distributions, we develop a graph network representation for electron transport along nanowires with varying dimensions, and through stochastic methods determine the maximum electron flow that can be driven through these STC wires. Longer nanowires were capable of carrying less electron flow than shorter nanowires with the same diameter, as long electron transfer distances that occasionally arise reduce the efficiency for electron transport. Thicker nanowires permit more alternative transport pathways, increasing electron transport beyond the increase in cross-section. Thus, this model implies that the design of protein-based nanowires that depend on electron hopping between charge carriers must consider control of the inherent protein flexibility, as more flexible protein-protein interfaces impose a limit on the required minimum diameter to carry currents commensurate with conventional electronics.

Photoluminescence of Dy3+:Y2SiO5 and luminescence thermometry in the 300-900 K temperature range

Data from Dy3+:Y2SiO5 photoluminescence and luminescence thermometry measurements in the 300-900 K temperature range. All data are in Origin files.

ALIMA range-corrected photon count profiles and spectral analysis output

The dataset includes a .nc file of range-corrected and background-corrected photon counts measured by ALIMA (Airborne Lidar for Middle Atmosphere research) from six research flights (ST08, ST09, ST10, ST11, ST12, ST14) during the SouthTRAC-GW campaign in September 2019. These corrected photons counts are proportional to the atmospheric density. The data resolution (t, z) is (10s, 100m) but not yet vertically smoothed nor temporally integrated. A vertical smoothing of 900 m and a temporal integration of 1 min is recommended to obtain a sufficient signal-to-noise-ratio. Furthermore, .nc files containing spectral power density (PSD) for selected legs of each research flight averaged over 10 km altitude ranges based on vertically smoothed and temporally integrated range- and background-corrected photon counts by ALIMA are included.

opencc-zeroApr 2023View details →

Stand biomass decreases towards the edge of a range expanding invasive plant, Mikania micrantha, but only on thick soil layers

During range expansion, invasive plants may evolve distinctive traits that make them rapidly occupy the suitable sites at the invasion front, but it is unknown how stand biomass (i.e., biomass production of dense monocultural stands, which may predict invasion speed and impacts) changes during range expansion, and if stand biomass is related to competitive ability. In this study, we examined how competitive ability against common intraspecific competitors and stand biomass when six plants from the same population were grown together change during range expansion, using 27 populations of the invasive Mikania micrantha on Hainan island of China. Competitive ability did not decrease towards the range edge. Stand biomass decreased towards the range edge in 11 L pots with a thick soil layer, but not in 3 L pots with a thin soil layer. Stand biomass was negatively correlated with root-to-shoot ratio in 3 L pots but not in 11 L pots. Stand biomass was unrelated to competitive ability. Our results indicate that edge populations of invasive M. micrantha may have reduced stand-level performance in habitats with thick soil layers. In habitats with shallow soil layers, populations may evolve greater allocation to roots and reduced stand-level performance.

opencc-by-4.0Dec 2004View details →

Fig. 24 in Four new narrow-range endemic species of Gulella from Eastern Cape, South Africa (Mollusca: Pulmonata: Streptaxidae)

Fig. 24. Map of northern Eastern Cape showing distribution of new species.

Avifaunal diversity study of Garhwal-Himalayan Range

The Avifaunal diversity study of Garhwal-Himalayan Range was conducted by Lina Chatterjee and the identification and data analysis was by Nature Mates-Nature Club team in May month of year 2022. <pre>  </pre>

Identifying the environmental drivers of corridors and predicting connectivity between seasonal ranges in multiple populations of Alpine ibex (Capra ibex) as tools for conserving migration

# GPS locations of Alpine ibex This dataset contains migratory tracks of Alpine ibex identified using the application Migration Mapper (https://migrationinitiative.org/content/migration-mapper) and used in the work Identifying the environmental drivers of corridors and predicting connectivity between seasonal ranges in multiple populations of Alpine ibex (Capra ibex) as tools for conserving migration # Dataset structure Each row of the dataset represents a GPS location with its coordinates contained in the x (longitude) and y(latitude) columns. Coordinates are given in wgs84 (epsg 4326). The column t1_ informs on the date and time the location was recorded. The id and pop columns provide information about the identity of the animal and the population to which it belongs.

Snakes on a plain: Complex biotic and abiotic factors determine venom variation in North America's widest-ranging rattlesnake

Background. Snake venoms are trophic adaptations that represent an ideal model to examine the evolutionary factors that shape polymorphic traits under strong natural selection. Venom compositional variation is substantial within and among venomous snake species. However, the forces shaping this phenotypic complexity, as well as the potential integrated roles of biotic and abiotic factors, have received little attention. Here, we investigate geographic variation in venom composition in a wide-ranging rattlesnake (Crotalus viridis viridis) and contextualize this variation by investigating dietary, phylogenetic, and environmental variables that covary with venom. Results. Using shotgun proteomics, venom biochemical profiling, and lethality assays, we identify 2 distinct divergent phenotypes that characterize major axes of venom variation in this species: a myotoxin-rich phenotype and a snake venom metalloprotease (SVMP)-rich phenotype. We find that dietary availability and temperature-related abiotic factors are correlated with geographic trends in venom composition. Conclusions. Our findings highlight the potential for snake venoms to vary extensively within species, for this variation to be driven by biotic and abiotic factors, and for the importance of integrating biotic and abiotic variation for understanding complex trait evolution. Links between venom variation and variation in biotic and abiotic factors indicate that venom variation likely results from substantial geographic variation in selection regimes that determine the efficacy of venom phenotypes across populations and snake species. Our results highlight the <a>implicit </a>influence of abiotic factors on biotic factors that ultimately shape venom phenotype, providing evidence for a central role of local selection as a key driver of venom variation.

Wide range of Brachyceran fly taxa attracted to synthetic and semi-synthetic generic noctuid lures and the description of new attractants for Sciomyzidae and Heleomyzidae families - RAW Data

Wide range of Brachyceran fly taxa attracted to synthetic and semi-synthetic generic noctuid lures and the description of new attractants for Sciomyzidae and Heleomyzidae families - RAW Data

Quantifying the age-structure of free-ranging delphinid populations: testing the accuracy of Unoccupied Aerial System-photogrammetry

Understanding the population health status of long-lived and slow-reproducing species is critical for their management. However, it can take decades with traditional monitoring techniques to detect population-level changes in demographic parameters. Early detection of the effects of environmental and anthropogenic stressors on vital rates would aid in forecasting changes in population dynamics and therefore inform management efforts. Changes in vital rates strongly correlate with deviations in population growth, highlighting the need for novel approaches that can provide early warning signs of population decline (e.g., changes in age-structure). We tested a novel and frequentist approach, using Unoccupied Aerial System- (UAS) photogrammetry, to assess the population age-structure of small delphinids. First, we measured the precision and accuracy of UAS-photogrammetry in estimating total body length (TL) of trained bottlenose dolphins (Tursiops truncatus). Using a log-transformed linear model, we estimated TL using the blowhole-to-dorsal-fin-distance (BHDF) for surfacing animals. To test the performance of UAS-photogrammetry to age-classify individuals, we then used length measurements from a 35-year dataset from a free-ranging bottlenose dolphin community to simulate UAS-estimates of BHDF and TL. We tested five age-classifiers and determined where young individuals (<10 years) were assigned when misclassified. Finally, we tested whether UAS-simulated BHDF only or the associated TL estimates provided better classifications. TL of surfacing dolphins was overestimated by 3.3% ±3.1% based on UAS-estimated BHDF. Our age-classifiers performed best in predicting age-class when using broader and fewer (two and three) age-class bins with ~80% and ~72% assignment performance, respectively. Overall, 72.5-93% of the individuals were correctly classified within two years of their actual age-class bin. Similar classification performances were obtained using both proxies. UAS-photogrammetry is a non-invasive, inexpensive, and effective method to estimate TL and age-class of free-swimming dolphins. UAS-photogrammetry can facilitate the detection of early signs of population changes, which can provide important insights for timely management decisions.

modeled and measured diffuse and diffuse fraction of PAR range

Csv file with the diffuse fraction of PAR (modeled and measured), diffuse component of PAR (modeled and measured), and clearness index in the PAR and Total ranges.

Data from: Genomic data clarify Aquarana systematics and reveal isolation-by-distance dominates phylogeography of the wide-ranging frog Rana clamitans

Wide-ranging species are often polytypic, span geographic dispersal barriers, and experience opportunities for divergence via genetic drift or natural selection. Such conditions can be favorable for speciation and wide-ranging taxa are frequently subdivided into multiple species by modern molecular studies. However, with wide-ranging species, it is important to explicitly test for isolation-by-distance (IBD) which can produce continuous genetic variation that may be misinterpreted as discrete population structure or even distinct species. Here we examine the Green Frog (Rana clamitans), a wide-ranging species of the Aquarana clade distributed across much of North America. Although Rana clamitans is phenotypically variable enough to previously merit description of two subspecies, patterns of genetic diversity remain unclear. Additionally, the broader phylogenetic context for R. clamitans is poorly understood, particularly its relationship with the closely related and IUCN Vulnerable Bog Frog (Rana okaloosae). Using genome-wide ddRAD markers, we largely resolve relationships within Aquarana and unambiguously identify R. okaloosae as the sister lineage to R. clamitans. Within R. clamitans we find two well-supported and geographically divided clades which are identified as distinct species by a widely used genetic species delimitation method, BPP. However, the two clades exhibit low genealogical divergence and population genetic analyses reveal that genetic variation within R. clamitans is best described by a pattern of IBD rather than independently evolving lineages. We conclude that R. clamitans is indeed a single species and the subspecies concept is of limited use. Our analysis emphasizes how existing approaches can erroneously split species characterized by continuous genetic variation and highlights the power of combining population genetic and phylogenetic perspectives to better understand diversity within wide-ranging taxa.

Data from: Glucocorticoids negatively relate to body mass on the short-term in a free-ranging ungulate

Environmental fluctuations force animals to adjust glucocorticoids (GCs) secretion and release to current conditions. GCs are a widely used proxy of an individual stress level. While short-term elevation in GCs is arguably beneficial for fitness components, previous studies have documented that the relationship between long-term baseline GCs elevation and fitness components can vary according to ecological and individual factors and according to the life-history of the species studied. Using longitudinal data on roe deer (Capreolus capreolus) from two populations facing markedly different environmental contexts, we tested whether baseline GC levels negatively correlate with body mass – a trait positively associated with demographic individual performance – on the short- to long-term. In support, higher baseline GC concentrations were associated to lighter body mass, both measured during the same capture event, in adults of both populations. Overall, we showed that despite the marked environmental and demographic differences between populations and despite the between-sex differences in life history (i.e. reproductive tactics), the relationship between body mass and GCs is consistent across environmental contexts, but might differ according to the life history stage of an individual. This work opens promising perspectives to further explore the relationship between GC and fitness-related traits according to life history stages in free-ranging mammals across seasonal and environmental contexts. The timing and context-dependence of GC levels highlight the complexity of studying stress responses in the wild.

Environmental DNA detection range for Hydrilla

Dataset associated with publication of the same name including qPCR results, measured variables, and other supplemental data.