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opencc-zeroMay 2022View details →

Sharing land via keystone structure: retaining naturally regenerated trees may efficiently benefit birds in plantations

Meeting food/wood demands with increasing human population and per-capita consumption is a pressing conservation issue, and is often framed as a choice between land sparing and land sharing. Although most empirical studies comparing the efficacy of land sparing and sharing supported land sparing, land sharing may be more efficient if its performance is tested by rigorous experimental design and habitat structures providing crucial resources for various species––keystone structures––are clearly involved. We launched a manipulative experiment to retain naturally regenerated broad-leaved trees when harvesting conifer plantations in central Hokkaido, northern Japan. We surveyed birds in harvested treatments, unharvested plantation controls and natural forest references one-year before the harvest and for three consecutive post-harvest years. We developed a hierarchical community model separating abundance and space-use (territorial proportion overlapping treatment plots) subject to imperfect detection to assess population consequences of retention harvesting. Application of the model to our data showed that retaining some broad-leaved trees increased total abundance of forest birds over the harvest rotation cycle. Specifically, pre-harvest survey showed that the amount of broad-leaved trees increased forest bird abundance in a concave manner (i.e., in a form of diminishing-return). After harvesting, a small amount of retained broad-leaved trees mitigated negative harvesting impacts on abundance though retention harvesting reduced the space-use. Nevertheless, positive retention effects on the post-harvest bird density as the product of abundance and space-use exhibited a concave form. Thus, small profit reductions were shown to yield large increases in forest bird abundance. The difference in bird abundance between clear-cutting and low amounts of broad-leaved tree retention increased slightly from the first to second post-harvesting years. We conclude that retaining a small amount of broad-leaved trees may be a cost-effective on-site conservation approach for the management of conifer plantations. Retention of 20-30 broad-leaved trees per ha may be sufficient to maintain higher forest bird abundance than clear-cutting over the rotation cycle. Retention approaches can be incorporated into management systems using certification schemes and best management practices. Developing an awareness of the roles and values of naturally regenerated trees is needed to diversify plantations.

opencc-zeroMay 2022View details →

Data and original code for: A generalized approach to characterise optical properties of natural objects

To understand the diversity of ways in which natural materials interact with light, it is important to consider how their reflectance changes with the angle of illumination or viewing and to consider wavelengths beyond the visible. We chose a set of existing measurements and parameters that are generalisable to any wavelength range and spectral shape and we highlight which subsets of measures are relevant to different biological questions. As a case study, we applied these measures to 30 species of Christmas beetles. Here we provide the raw spectral data of angle integrated and angle-dependent reflection by the beetle elytra. We also provide the original code used for our analysis and figures.

opencc-by-sa-4.0Jan 2022View details →

Reconstruction of Natural Visual Scenes from Primary Visual Cortical Neural Activity Using Adversarial Learning

This data set and code goes with "Reconstruction of Natural Visual Scenes from Primary Visual Cortical Neural Activity Using Adversarial Learning"

opengpl-2.0May 2022View details →

Code: The effects of model complexity on model output uncertainty in co-evolved coupled natural–human systems

This is the code archive for the publication "The effects of model complexity on model output uncertainty in co-evolved coupled natural–human systems" in Earth's Future. Abstract: Studies have recently focused on using coupled natural–human systems (CNHS) to inform policymaking. However, model uncertainty can increase with model complexity and affect the variance of the model outcomes. Therefore, this study explores an uncertainty analysis of coupled hydrological and human decision models to better evaluate CNHS modeling properties. Five coupled models are proposed with different model complexities for human behavior settings (i.e., model structure and the number of calibrated parameters): one static, two adaptive, and two learning adaptive. Learning adaptive models (the most complex) have both a learning component (capturing long-term trends) and an adaptive component (capturing short-term variations), while adaptive models omit the learning component. The static model is the simplest, without learning or adaptive components. Applying the law of total variance, the model output uncertainty is decomposed into three sources: (1) climate change scenario uncertainty, (2) climate internal variability, and (3) different model configurations with parameter sets or model structures that are equally capable of producing similar outcomes. Our exploratory analysis demonstrated that model uncertainty would likely increase with model complexity given uncertain input data (e.g., climate forcing) and different model configurations; the inclusion of a learning mechanism in the human system can potentially offset the impact of the natural system on uncertainty through coupling natural and human systems. We also discuss other uncertainty sources, such as assumptions about model structure due to incomplete knowledge and metrics for calibration target selection for future studies.

opencc-zeroMay 2022View details →

Effects of insularity on genetic diversity within and among natural populations

We conducted a review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together "insularity"). Using populations from within the same studies, we were able to control for between-study variation in methodology, as well as demographic and life histories. Contradictory to typical expectations, insularity had relatively minor effects on GD within and among population, which points to the more important roles of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen – particularly in systems (i.e. studies) where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non-insular populations of the same system – suggesting an important role for the "scope" of influences on GD. These conclusions were more robust for within - population GD than among - population GD, although a number of biases might underlie this difference. Overall, our findings indicate that population-level genetic assumptions need to be tested rather than assumed in nature, particularly for topics highly relevant to current conservation management practices.

opencc-by-4.0Jun 2022View details →

PhytoNodes for Environmental Monitoring: Stimulus Classification based on Natural Plant Signals in an Interactive Energy-efficient Bio-hybrid System

Cities worldwide are growing, putting bigger populations at risk due to urban pollution. Environmental monitoring is essential and requires a major paradigm shift. We need green and inexpensive means of measuring at high sensor densities and with high user acceptance. We propose using phytosensing: using natural living plants as sensors. In plant experiments we gather electrophysiological data with sensor nodes. We expose the plant Zamioculcas zamiifolia to five different stimuli: wind, temperature, blue light, red light, or no stimulus. Using that data we train ten different types of artificial neural networks to classify measured time series according to the respective stimulus. We achieve good accuracy and succeed in running trained classifying artificial neural networks online on the microcontroller of our small energy-efficient sensor node. To indicate later possible use cases, we showcase the system by sending a notification to a smartphone application once our continuous signal analysis detects a given stimulus.   Data repository for our paper "PhytoNodes for Environmental Monitoring: Stimulus Classification based on Natural Plant Signals in an Interactive Energy-efficient Bio-hybrid System", submitted to the GoodIT conference. Please refer to the paper for more information.   Contents of this repository <ul> <li>mu_interface: Code for our data collection plant experiments, based on Raspberry Pis and the <a href="http://cybertronica.co/?q=products/phytosensor">Cybertronica phytosensing and phytoactuating system</a>.</li> <li>raw_data: The datasets from our plant experiments for the stimuli wind, temperature, red light, blue light, and no stimulus.</li> <li>dl-4-tsc: Deep learning framework developed by <a href="https://doi.org/10.1007/s10618-019-00619-1">Fawaz et. al (Deep learning for time series classification: a review)</a> and adapted to our use case. Find the training and testing datasets in the archives folder as well as the trained classifiers in the results folder.</li> <li>classification_results.ods: Overview of the results from the deep learning framework (accuracy, precision, recall, training time).</li> <li>TFLite_Models: The trained classifiers in TensorFlow Lite Format.</li> <li>00_AI_BLE_MeasuringOnlyWind: Source code for classification on STM-based PhytoNodes (using MCDCNN two-class classifier) and Bluetooth communication. The code is written for the STM32WB55 Nucleo board and can be transferred to the dongle.</li> <li>zavrsniProjekt_iOS: Source code of the iOS app used to receive data from the STM-based PhytoNodes.</li> <li>Watchplant_application_documentation.pdf: Instructions to build and use the iOS app.</li> </ul>

opencc-by-4.0Jun 2022View details →

VisMetHack2022: Visualizing winds and surface variables from the ECMWF IFS 1-km nature run

Overview This data collection was contributed to the <a href="https://events.ecmwf.int/event/305/">Visualisation Hackathon 2022</a> (#VisMetHack2022), in conjunction with the Using <a href="https://events.ecmwf.int/event/296/">ECMWF's Forecasts (UEF2022</a>) workshop. The European Center for Medium-Range Weather Forecasts (ECMWF) and the Oak Ridge National Laboratory (ORNL) are pleased to announce access to the data collection from global 1-km nature run (NR) simulations using the Integrated Forecast System (IFS) with explicit convection. We invite you to join us in exploring this precursor to a digital twin of the earth! The NR simulations reveal unprecedented detail of the earth’s atmosphere [1], and the then outgoing Editor-in-Chief of AGU JAMES commended the project as one of “stunning ambitions,” enabled by computational capacity at scale [2]. The project also won the 2020 HPCwire Readers Choice Award for Best Use of HPC in Physical Sciences.  A set of two NR seasonal simulations have been completed, one corresponding to the northern hemispheric winter months (NDJF) and the other for the North Atlantic tropical cyclone season (ASO). The project used the Summit supercomputer at the Oak Ridge Leadership Computing Facility (OLCF). The simulations were facilitated with an INCITE award from the US Department of Energy Office of Science.  For the first seasonal run of four months (NDJF), the hydrostatic IFS model was initialized at 00Z on 1 November 2018. The NR for the TC season (AS) was initialized at 00Z on 1 August 2019. The NR simulations were constrained only by sea surface temperatures (SST) at the lower boundary. The IFS output was saved every 3 hours. After feedback and interest from the scientific community, the simulations were rerun for four specific extreme events, with output every 15 minutes. The special cases include a tropical cycle and three severe storm events over the continental USA. NR Data for visualizing winds A small subset from the 1-km IFS NR collection is make available for #VisMetHack22. This subset is extracted from the tropical cyclone area in the North Atlantic from the ASO simulations. The 912 model time steps correspond to 97935 to 111600 in minutes since the NR reference time 2019-08-01 00:00:00. The time increment is 15 minutes, corresponding to the output frequency. The following variables are provided for #VisMetHack2022:   <table> <tbody> <tr> <td> Short Name </td> <td> Parameter ID </td> <td> Units </td> <td> Long Name </td> </tr> <tr> <td> 10u </td> <td> 165 </td> <td> m/s </td> <td> 10 metre U wind component </td> </tr> <tr> <td> 10v </td> <td> 166 </td> <td> m/s </td> <td> 10 metre V wind component </td> </tr> <tr> <td> 2t </td> <td> 167 </td> <td> K </td> <td> 2 metre temperature </td> </tr> <tr> <td> i10fg </td> <td> 228029 </td> <td> m/s </td> <td> Instantaneous 10 metre wind gust </td> </tr> <tr> <td> msl </td> <td> 151 </td> <td> Pa </td> <td> Mean sea level pressure </td> </tr> <tr> <td> xtprate </td> <td> 99999 </td> <td> kg m**-2 s**-1 </td> <td> Total instantaneous precipitation rate. Summation of convective and large scale rain and snowfall rates.  </td> </tr> </tbody> </table>   Data processing <ol> <li> The native model output was in the form of data objects consisting of GRIB1/2 16-bit AEC compressed messages. The messages were extracted from the FDB database instances into one or more files. </li> <li> The files containing the GRIB messages were interpolated to 0.02 x 0.02 a regular latitude-longitude grid using ECMWF Meteorological Interpolation and Regridding (MIR), and then written out to files as GRIB messages. </li> <li> The MIR output files were extracted to the area of interest (AOI) from global fields, and converted to Netcdf-4 (NC). </li> <li> The metadata in NC4 files were selectively edited or added. </li> <li> Finally, the NC4 files were compressed to reduce volume using the ncks utility from Netcdf Operators (NCO), with lossless L1 compression. </li> <li> The variable ‘xtprate’ was calculated by a summation of instantaneous and large scape rainfall and snowfall rates. </li> </ol> Contact Valentine Anantharaj <<a href="mailto:vga@ornl.gov">vga@ornl.gov</a>> or <vga1.ornl@gmail.com>  Samuel Hatfield <<a href="mailto:Samuel.Hatfield@ecmwf.int">Samuel.Hatfield@ecmwf.int</a>>   Citation and references Please cite the following manuscript as well as the DOI provided by Zenodo: [1] Wedi, N. P., Polichtchouk, I., Dueben, P., Anantharaj, V. G., Bauer, P., Boussetta, S., et al. (2020). A baseline for global weather and climate simulations at 1 km resolution. Journal of Advances in Modeling Earth Systems, 12, e2020MS002192. <a href="https://doi.org/10.1029/2020MS002192">https://doi.org/10.1029/2020MS002192</a> [2] Anantharaj, V., Hatfield, S. and Vukovic, Milana (2022). VisMetHack2022: Visualizing winds and surface variables from the ECMWF IFS 1-km nature run. https://doi.org/10.5281/zenodo.6633929 Acknowledgements This research used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725. ECMWF also  benefited from collaborations funded via ESCAPE-2 (No. 800897), MAESTRO (No. 801101), EuroEXA (No. 754337), and ESiWACE-2 (No. 823988) projects funded by the European Union's Horizon 2020 future and emerging technologies and the research and innovation programmes.

opencc-by-4.0Jun 2022View details →

Natural color composites of VENµs images over South Col Glacier

This datasets contain images of South Col Glacier obtained from VENµs platform from 27 Nov 2017 to 30 Oct 2020. The images are shown on a UTM45\WGS84 projection, and correspond to the band combination 7-4-3. The two stars show remarkable locations.

opencc-zeroJul 2022View details →

Data from: Ruderals naturalize, competitors invade: varying roles of plant adaptive strategies along the invasion continuum

1. It is increasingly recognized that the factors facilitating plant invasions depend on the stage along the introduction-naturalization-invasion continuum. Adaptative strategies, i.e., combinations of functional traits that represent overall fitness in the face of one or more selection pressures, have shown promise in explaining plant invasions. However, whether adaptive strategy patterns change with the stages of plant invasion is not yet known. 2. Using the Pladias Database of the Czech Flora and Vegetation, we explored how Grime's adaptive strategies (competitors, stress-tolerators, ruderals; CSR) and introduction pathways (deliberate vs. accidental) relate to plant invasion along the introduction-naturalization-invasion continuum. 3. Phylogenetically corrected ANOVAs showed that naturalized species (referring to non-invasive naturalized species in this study) were mostly R-selected, whereas invasive species tended to be C-selected. The results of phylogenetic regression analysis further confirmed that across the deliberately and accidentally introduced species, R- and C-selection were positively related to naturalization and invasion success, respectively. We also found that deliberate introduction was negatively related to naturalization success and grid-cell occupancy of naturalized species, likely due to the different CSR strategies possessed by deliberately and accidentally introduced aliens. 4. Our study provides empirical evidence that different adaptive strategies are associated with species that have reached different invasion stages and confirms the usefulness of the CSR strategy framework for understanding plant invasion. It has implications for predicting and preventing potential high-impact invaders. For example, our results show that naturalized C-selected species have a higher probability of becoming invasive than naturalized R-selected species. Therefore, management actions are essential to prevent further introductions and spread of competitors.

opencc-by-4.0Jul 2022View details →

Fig. 16. Lycosa piochardi Simon, 1876, natural history. A in Lycosa Latreille, 1804 (Araneae, Lycosidae) of Israel, with a note on Geolycosa Montgomery, 1904

Fig. 16. Lycosa piochardi Simon, 1876, natural history. A. Feeding on Pyrrhocoris apterus (Linnaeus, 1758), Mt. Gilboa. B. At the opening of a turretless burrow, central Negev. C. Female with egg sac, Midreshet Ben-Gurion. D. Turreted burrow sealed with silk, Midreshet Ben-Gurion. Photos by I. Armiach Steinpress.

opencc-zeroJul 2022View details →

Data from: What ecological factors favor parthenogenesis over sexual reproduction? A study on the facultatively parthenogenetic mayfly Alainites muticus in natural populations

Different reproductive modes are characterized by costs and benefits which depend on ecological contexts. For example, sex can provide benefits under complex biotic interactions, while its costs increase under mate limitation. Furthermore, ecological contexts often vary along abiotic gradients. Here, we study how these factors simultaneously influence the frequency of sex in the facultatively parthenogenetic mayfly Alainites muticus . We first verified that parthenogenesis translates into female-biased population sex ratios. We then measured the density of individuals (a proxy for mate limitation) and community diversity (biotic interaction complexity) for 159 A. muticus populations covering a broad altitudinal gradient and used structural equation modeling to investigate their direct and indirect influences on sex ratios. We found no effect of community diversity or altitude on sex ratios. Furthermore, even when females can reproduce parthenogenetically, they generally reproduce sexually, indicating that the benefits of sex exceed its costs in most situations. Sex ratios only become female-biased under low population densities, as expected if mate limitation was the main factor selecting for parthenogenesis. Mate limitation might be widespread in mayflies because of their short adult lifespan and limited dispersal, which can generate strong selection for reproductive assurance and may provide a stepping-stone towards obligate parthenogenesis.

opencc-by-3.0Aug 2022View details →

Field margins and cropping system influence natural enemies of bean aphids

The data presents beneficial effects of field margin vegetation on natural enemies with reduced aphid infestation in lablab field plots and higher grain yield. The data further shows that cropping system have some influence on natural enemy diversity and abundance.

opencc-by-4.0Oct 2020View details →

The cost of self-promotion: Ecological and demographic implications of the mentor effect in natural Taraxacum populations

This data accompanies the pending publication "The cost of self-promotion: Ecological and demographic implications of the mentor effect in natural Taraxacum populations" by Lynn et al. The work is also published under Austin Lynn's PhD Dissertation, which is under embargo until 2022.

opencc-zeroSep 2015View details →

IODP Expedition 352 Natural gamma radiation

Natural gamma radiation (NGR) data in the ~0.1 to 3.0 MeV range were measured using eight custom-designed sodium iodide (thallium) [NaI(Tl)] detectors arranged along the core measurement axis at 20 cm intervals. The NGR system uses layers of passive shielding (lead) and active shielding (plastic scintillators and coincidence electronics) to reduce the cosmic-ray signal for low-count analysis of sediment core sections and to obtain the maximum signal-to-noise ratio. Data are reported on a total counts per second basis and the raw spectral files are available as compressed files for later analysis.

opencc-by-4.0Sep 2022View details →

Dual-band Reflectarray Antennas Using Integrated Resonant and Non-Resonant Natures of Metallic Waveguide Elements at Millimeter Wave Frequencies

Pure metallic reflectarray antennas have good power efficiency and low fabrication cost, which were limited to single band operation. A dual-band reflectarray antenna is developed for two directional beams by two feeds. The reflecting elements are metal waveguides, and have novel properties of both resonant and non-resonant modes at the two frequency bands. The low and high frequency bands can be easily separated by the cutoff frequency of waveguide modes. The phase changing mechanisms via ray optics and fundamental waveguide modes, respectively provide simple formulations for elemental structure design of directional beams. Radiation characteristics of the linear and circular polarizations are cross-examined with good performance by full-wave simulations using HFSS, FEKO and CST at 28 and 60 GHz bands for 5G front-haul network applications.

opencc-zeroAug 2015View details →

IODP Expedition 351 Natural gamma radiation

Near-shore island lizard fauna shaped by a combination of human-mediated and natural dispersal

Aim: Island biotas provide opportunities to study colonization and adaptation to novel environments. Islands, especially near-shore islands, may have a long record of human habitation such that some lineages result from human-assisted introductions. Here, we combine phylogenetic analyses with fossil data and historical specimen records to reconstruct colonization histories, characterize among-island divergence, and assess the role of humans in shaping the evolutionary history of lizards inhabiting a near-shore island archipelago. Location: Channel Islands and adjacent mainland of California, USA. Taxa: Western fence lizard ( Sceloporus occidentalis), southern alligator lizard (Elgaria multicarinata), common side-blotched lizard (Uta stansburiana). Methods: We sequenced mitochondrial DNA (ND1, cyt-b) from each of three lizard species, covering their entire island distributions plus the adjacent mainland. For each, we estimated diversity within and among each island, obtained maximum likelihood bootstrapped phylogenies, constructed haplotype networks, and tested for population expansion. We used museum specimen records and microfossil evidence to infer colonization scenarios. Results: Sceloporus occidentalis is characterized by a single island-colonization event, and exhibits the deepest divergences from mainland relatives and the highest among-island divergence. Elgaria multicarinata and Uta stansburiana each have at least three distinct colonization events, with fossil and historical data indicating that some of these occurred after humans arrived to the islands. Main Conclusions: The evolution of Channel Island lineages for two lizard taxa has been mediated by ancient and contemporary anthropogenic activity, while the evolution of the third is shaped by natural dispersal and vicariance caused by sea-level rise. Genetic divergence corroborates the treatment of S. occidentalis as an endemic island species, S. becki. The unique histories of these three taxa are synthesized with other Channel Island lineages highlighting that taxa inhabiting islands with long histories of human activity should be carefully studied to assess the role of people in facilitating colonization and subsequent gene flow.

Diet composition based on stable isotopic analysis of fecal samples revealed the preference of Black-faced Spoonbill (Platalea minor) for natural wetlands and fishponds

Background: Black-faced spoonbill (BFS) is a global endangered species, distributed only in the coastal zones of East Asia. Xinghua Bay is one of the main wintering sites and migration stopovers of BFS in mainland China. However, with the reduction and degradation of natural wetlands, it is uncertain whether the constructed wetland can provide habitat for the endangered BFS. Research on diet of BFS will help to understand their preference between natural and artificial wetlands, and also provide reference for their conservation and habitat restoration. Results: In the early winter, the proportion of Palaemonidae in BFS's food was as high as 74.4%, while that of other food was only 3.0% to 6.0%. In the late winter, the food contribution of BFS was as follow: Portunidae 39.3% > Palaemonidae 26.1% > Cyprinidae 8.8% > Mugilidae 8.5% > Gobiidae 7.3% > Crucian 5.1% > Whiteshrimp 4.8%. The proportion of Portunidae exceeded that of Palaemonidae, and together with Palaemonidae, it has become the main food of BFS in late winter. Conclusion: The diet composition of BFS between the early and late winter was significantly different, which may be due to seasonal changes in food resources. Natural wetlands are the main feeding grounds of BFS, but artificial wetlands also provide them with supplementary feeding grounds and resting places. Aquaculture ponds play an important ecological function in maintaining the overwintering population of BFS in Xinghua Bay.

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29 355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P < 1.7 × 10−6). Markers were found across 19 chromosomes, explained 1–13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa