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539 results for “disentangling”
Data for Disentangling the influence of phylogeny and traits on climatic risk of European butterflies
<p>R code and dataset associated with Gianuca et al. 2024 "Disentangling the influence of phylogeny and traits on climatic risk of European butterflies", Global Ecology and Biogeography.</p> <p>The data includes climatic risks, traits and Phylogenetic eigenvectors.</p> <p>We provide data and metadata including traits, ecological characteristics and climatic risks for different scenarios of climate change and climate tracking scenarios</p> <p>We provide the phylogeny for 496 European species</p> <p>We provide a prunned phylogeny to facilitate the analysis of the species with available information (268 species)</p> <p>We provide the code to run the analysis as described in the main text</p> <p> </p>
Model outputs for: "Disentangling the Local Circulations over a Region with Complex Physiography in the Eastern Amazon: A Modeling Approach"
<p>This repository contains all publicly available numerical simulations related to the paper: Disentangling the Local Circulations over a Region with Complex Physiography in the Eastern Amazon: A Modeling Approach</p>
Decomposition disentangled: a test of the multiple mechanisms by which nitrogen enrichment alters litter decomposition
<ol> <li>Nitrogen (N) enrichment has direct effects on ecosystem functioning by altering soil abiotic conditions and indirect effects by reducing plant diversity and shifting plant functional composition from dominance by slow to fast growing species. Litter decomposition is a key ecosystem function and is affected by N enrichment either by a change in litter quality (the recalcitrance of the plant material) or through a change in soil quality (the abiotic and biotic components of the soil that affect decomposition). How the direct and indirect effects of N alter soil and litter quality remains poorly known.</li> <li>We designed a large grassland field experiment manipulating N enrichment, plant species richness and functional composition in a full factorial design. We used three complementary litterbag experiments, combined in a structural equation model (SEM), to quantify the effects of the treatments and various measures of functional composition and diversity on litter and soil quality and overall decomposition.</li> <li>Our results revealed multiple drivers of litter quality and showed that nutrient concentrations (N and calcium) were about twice as important as structural components (leaf dry matter content, fibres) in determining litter quality. Overall the experimental results suggest that N enrichment increases litter decomposition mostly indirectly through a shift in functional composition toward faster growing plant species, producing higher quality litter. N enrichment also altered soil quality and thereby litter decomposition, through its effects on vegetation cover.</li> <li>Our approach provides a mechanistic tool to test the drivers of litter decomposition across different ecosystems. Our results show that litter quality is determined by several nutrient and structure traits and highlight the importance of considering shifts in plant species composition when assessing the effects of N enrichment on decomposition.</li> </ol>
Disentangle the Sediment Mixing from Geochemical Proxies and Detrital Zircon Geochronology
<p>Supplementary Data of the Manuscript titled 'Disentangle the Sediment Mixing from Geochemical Proxies and Detrital Zircon Geochronology '</p>
Disentangling the roles of social and individual effects on cadmium tolerance in the ant Temnothorax nylanderi.
<p>Data from the paper 'Disentangling the roles of social and individual effects on cadmium tolerance in the ant Temnothorax nylanderi.'</p>
Do early-successional weeds facilitate or compete with seedlings in forest restoration? Disentangling abiotic vs. biotic factors
<p>Census data for seedlings part of a weed exclusion experiment at Sal del Rey, Texas within a larger field where ~100,000 seedlings were planted in October-November 2018. Records seedling height, vigor (0 - dead, > 0 - alive), branching, and animal damage for 158 individuals of eight species classified by growth habit (fast/slow) and distributed in control and exclusion (mowed) plots across seven censuses.</p>
Data from: Disentangling the factors that shape bromeliad and ant communities in the canopies of cocoa agroforestry and preserved Atlantic Forest
<p>In tropical forest canopies, host tree characteristics shape epiphyte communities, and both host tree characteristics and epiphytes determine invertebrate communities, e.g., ants. Tree height is among the factors most often mentioned as a strong predictor for both bromeliad and ant communities. However, many factors interact dynamically in shaping the tree-bromeliad-ant association. Here, we investigated the effects of the host tree and canopy structural characteristics on both bromeliads and ants. We sampled bromeliads on 180 trees and ants in 360 bromeliads living on a subset of 60 of those trees in a continuum of native forest fragments and agroforestry systems in the Atlantic Forest, a Brazilian biodiversity hotspot. We found that the host trees' crown area had a positive effect on the abundance of bromeliads. Also, the introduced tree species had higher abundance of bromeliads than native tree species. Moreover, we found that the ant species composition was different between native and introduced trees. In addition, we observed a positive effect of the size of bromeliads and tree crown height on ant species richness on both bromeliad and tree scales, but there was no effect of tree height. Taken together, our findings highlight the importance of trees with large crowns for the maintenance of bromeliads, which are also associated with richer ant communities in both Atlantic Forest and agroforestry systems. These results emphasize the importance of trees with larger crowns for biodiversity conservation in both native forest fragments and agroforestry systems.</p>
Disentangling effects of disturbance severity and frequency: does bioindication really work?
<p>Ecological disturbances are recognized as a crucial factor influencing the attributes of ecological communities. Depending on the specific adaptation or life cycle, plant species show different responses to disturbances of different magnitudes. Herben et al. (2016) proposed disturbance indicator values (DIVs) that describe the niche of each Central-European plant species along gradients of disturbance frequency and severity. Here we ask if the DIVs can be used in community ecology for bioindication of disturbance regime?</p> <p>We used a dataset of riparian forests sampled within mountain catchments (the Sudetes, SW Poland). As the regime of disturbance is driven by changes in floods from the spring towards the mouth, we calculated the position of every plot along longitudinal (upstream-downstream) gradient and used it as a proxy for the disturbance severity and frequency. We then calculated the community-weighted means (CWMs) for each of the six indices for each plot and analyzed whether these indices reflected the position of the plots along the rivers. We expected an increase in the severity indices and a decrease in the frequency indices downstream along the rivers. Moreover, we analyzed relationships between disturbance indices and species optima along longitudinal gradient.</p> <p>Surprisingly, means for all analyzed indices increased along the rivers. Severity indices showed the strongest association with the longitudinal gradient. The disturbance severity index for herbs was the only index that differed significantly among species with different responses along longitudinal gradient. On these results, we identified a strong correlation between the severity and frequency indices as the main problem.</p> <p>We conclude that the DIVs have considerable applicative potential; however, the determination of ecological niches separately for disturbance severity and frequency is difficult because different components interact to shape the realized niche of each species. All analyzed indices encompass different attributes of the disturbance regime including both severity and frequency.</p>
Disentangling the taxonomic variations within the high-Andean complex Gomphrena meyeniana (Gomphrenoideae, Amaranthaceae)
<p>Gomphrena meyeniana is an extremely variable species from the Andean highlands, which has attracted the attention of many botanists because it is the world's highest-elevation C4 eudicot and because of its wide morphological variability. It has the typical high-Andean plant morphology, with small leaves tightly clustered on a thick rootstock. The large range of morphological variation within this species, coupled with the varying opinions on the existence of several species or infra-specific taxa, and the lack of molecular information has made the clarification of the G. meyeniana complex a challenge. Our approach was to perform a broad spectrum molecular sampling to identify its phylogenetic position within Gomphrena genus and to perform a multivariate analysis to objectively differentiate taxa based on morphological characters. The ITS and trnL-F regions were analyzed individually and combined using Bayesian inference and maximum parsimony methods. To analyze the morphological characters we performed a clustering method (partitioning around medoids with the Gower's dissimilarity algorithm). The molecular analyses supported the monophyly of the G. meyeniana complex but did not support segregation into varieties. The morphological analyses gathered the infra-specific taxa into only three varieties that can be easily distinguished through three simple characters: the presence of leaves on the flowering shoot, the habit of the flowering shoot, and the pilosity of the tepals. The varieties of G. meyeniana accepted here are var. meyeniana, var. caulescens, and var. flaccida. A dichotomous key to identify the infra-specific taxa is here presented and illustrated. The varieties tucumanensis, and conwayi were synonymized with var. caulescens, and var. meyeniana respectively.</p>
Data and code - Disentangling dispersion from mean reveals true heterogeneity-diversity relationships
<p>Data and code for reproducing figures and results for the manuscript entitled "Disentangling dispersion from mean reveals true heterogeneity-diversity relationships". Published in <a href="https://doi.org/10.1038/s41467-025-64287-0">Nature Communications</a>. See references for data sources.</p> <p>Code tested with Julia version 1.11.1.</p> <p><strong>How to cite this repository</strong></p> <p>If using code or data from this repository, please cite the original publication (<a href="https://doi.org/10.1038/s41467-025-64287-0">Pellett and Valbuena, 2025</a>) and respective data source (see references and README.txt in respective data folder).</p> <p><strong>Update 2024-07-09</strong></p> <p>Minor changes to figure sizes and use of paired-sample t-tests when assessing empirical observations of heterogeneity measures.</p> <p><strong>Update 2024-08-04</strong></p> <p>Step by step instructions included in README</p> <p>Manifest.toml file included with julia and package version requirements.</p> <p><strong>Update 2024-11-18</strong></p> <p>Update following peer review feedback:</p> <p>Analysis of an additional dataset from MacArthurs' seminal paper on foliage height diversity.</p> <p>Hypothesis test of negligible trend for delta</p> <p>Modified extended data figures</p> <p><strong>Update 2025-05-16</strong></p> <p>Update following second round of peer review feedback:</p> <p>Change to equation notation for figure 2</p> <p>Additional script for simulation and review report figures </p> <p><strong>Update 2025-09-29</strong></p> <p>Figure text size adjustments after final round of peer review and editor requests.</p>
Data from: On the function of flower number: disentangling fertility from pollinator-mediated selection
<p>FLODIS is an experimental research project which aims at understanding how artificially increased flower number (i.e. enhanced floral display) impacts male and female reproductive/mating success as well as sex-specific pattern of selection on floral traits, in the dioecious insect-pollinated species <em>Silene dioica</em>.</p>
Data from: Disentangling genetic from environmental effects on phenotypic variability of Southern rock lobster (Jasus edwardsii) postlarvae
<p><span>Environmental conditions experienced during larval dispersal of marine organisms can determine size-at-settlement of recruits. It is, therefore, not uncommon that larvae undergoing different dispersal histories would exhibit phenotypic variability at recruitment. Here we investigated morphological differences in recently settled southern rock lobster (<em>Jasus</em> <em>edwardsii</em>) recruits, known as pueruli, along a latitudinal and temporal gradient on the east coast of Tasmania, Australia. We further explored whether natural selection could be driving morphological variation. We used double digest restriction-site associated DNA sequencing (ddRADseq) to assess differences in genetic structure of recently settled recruits on the east coast of Tasmania over three months of peak settlement during 2012 (August, September and October). Phenotypic differences in pueruli between sites and months of settlement were observed, with significantly smaller individuals found at the northernmost site. Also, there was a lack of overall genetic divergence; however, significant differences in pairwise FST values between settlement months were observed at the southernmost study site, located at an area of confluence of ocean currents. Specifically, individuals settling into the southernmost earlier in the season were genetically different from those settling later. The lack of overall genetic divergence in the presence of phenotypic variation indicates that larval environmental history during dispersal of <em>J</em>. <em>edwardsii</em> could be a possible driver of the resulting phenotype of settlers.</span></p>
Disentangling thermal from alternative drivers of reflectance in jewel beetles: a macroecological study
<p><span>To predict future colour-climate relationships, it is important to distinguish thermal drivers of reflectance from other evolutionary drivers. This can be achieved by comparing relationships between climate and colouration in ultraviolet-visible (UV-Vis) and near-infrared (NIR) light, separately; yet NIR properties have been measured in very few species. Here, we used jewel beetles (Coleoptera: Buprestidae) as models to identify climatic drivers of reflectance because jewel beetles have highly diverse colouration, a wide distribution, and are often active in hot conditions. Specifically, we tested the association between climate, body size and reflectance using a phylogenetic comparative analysis for three wavebands (UV-Vis, NIR, total). Results showed that reflectance of jewel beetles was more strongly predicted by body size than climate. NIR and total reflectance was not associated with climate, but larger beetles had higher NIR reflectance. For UV-Vis reflectance, small beetles were darker in warmer and more humid environments, whereas there was no association with climate for large beetles. Our study suggests that reflectance variation of jewel beetles is not driven by thermal requirements and highlights the importance of considering NIR reflectance when evaluating explanations of colour effects on thermoregulation.</span></p>
Viral reference genomes to disentangle the recombinant phylogenetic history of the potyviruses
<p>Potyviruses are a large genus of plant-infecting RNA viruses in the family Potyviridae. Due to their rapid diversification and frequent recombination, reconstructing the phylogenetic history of the potyviruses has proven difficult. Phylogenies reconstructed from different protein-coding regions of the viral genome often reveal conflicing or discordant relationships. But the extent to which discordance is due to interspecific recombination versus phylogenetic noise or errors in reconstruction is unclear. </p> <p>To explore the recombinant history of the potyviruses, we assembled a dataset containing referece genomes for 131 species of potyviruses. High-quality, full-length reference genomes for all species were obtained form NCBI GenBank. Viral genomes were carefully aligned at the codon-level and screened for recombination. The full alignment was then partitioned into several sub-alignments between each detected recombination event, such that each sub-aligment corresponds to a non-recombinant block (NRB) free of detected recombination events. Local phylogenetic trees for each NRB were then reconstructed to explore how phylogenetic relationships varied across different regions of the potyvirus genome. </p> <p>We then used our program Espalier to disentangle the phylogenetic history of the potyviruses. Espalier reconciles and removes discordances between phylogenetic trees that are likely attributable to phylogenetic error while retaining recombination events that are strongly supported by the sequence data. Applying Espalier to the potyviruses revealed that most phylogenetic discordace between local trees is likely attributable to phylogenetic noise. Removing the discordance attributable to phylogenetic error allows us to much more clearly visualize the phylogenetic history of the potyviruses.</p>
Disentangling the relative contributions of factors determining seed physical defence: a global-scale data synthesis
<p>Physical defence investment in seeds varies greatly among plant species and is affected by many potential factors. However, the relative importance of influential factors has not yet been systematically evaluated. Here, we compiled a global database of the seed coat ratio (SCR), a proxy of seed physical defence, for 1,357 species. Using partial R<sup>2</sup> calculation that can estimate the reduction in explained variance of a given factor after removing it from a full model containing all the other factors, we disentangled the relative contributions of seven factors commonly used to explain variation in the SCR. Seed desiccation response and phylogeny explained a large amount of SCR variation among species, with a partial R<sup>2</sup><sub>lik</sub> value of 13.31% and 10.62%, respectively. Seed dormancy, plant growth form, seed mass, climate region, and fruit type showed little power to explain SCR variation, although they are often cited in the literature as potential factors. Our results highlight the important roles of seed desiccation response and phylogeny in shaping interspecific variation in the SCR. These findings provide a detailed interpretation of both evolutionary and ecological patterns underlying the physical defence mechanisms and allocation strategies of plant seeds.</p>
When is warmer better? Disentangling within- and between-generation effects of thermal history on early survival
<ol> <li>Understanding the fitness consequences of thermal history is necessary to predict organismal responses to global warming. This is especially challenging for ectotherms with complex life cycles, where distinct life stages can differ in thermal sensitivity, acclimate to different thermal environments, and accrue responses to acclimation within and between generations.</li> <li>Although acclimation is often hypothesized to benefit organisms by helping them (or their offspring) to compensate for negative impacts of environmental change, mixed support for this hypothesis highlights the need to assess alternatives. Assessments that explicitly dissect responses across life stages and generations, however, remain limited. </li> <li>We assess alternative hypotheses of acclimation (none, beneficial, colder-is-better, and warmer-is-better) within and between generations of a marine tubeworm whose vulnerability to warming rests on survival at early planktonic stages (gametes, embryos, and larvae). First, we acclimate parents, gametes, and embryos to ambient and projected warmer temperatures (17°C and 22°C) factorially by life stage. Next, we rear offspring with differing acclimation histories to the end of larval development at test temperatures from 10°C to 28°C (lower and upper survival limits, respectively). Last, we estimate thermal survival curves for development and compare them among thermal histories. </li> <li>We show that survival curves are most responsive to parental acclimation followed by acclimation at embryogenesis, but are buffered against acclimation at fertilization. Moreover, curves respond independently to acclimation within and between generations and respond largely as predicted by the warmer-is-better hypothesis, despite the semblance of beneficial acclimation after successive doses of warmer temperature. </li> <li>Our study demonstrates the varied nature of thermal acclimation and the importance of considering how responses aggregate across complex life cycles when predicting vulnerability to warming.</li> </ol>
Scripts and Data for "Disentangling the Hydrological and Hydraulic Controls on Streamflow Variability in E3SM V2 – A Case Study in the Pantanal Region"
<p>Matlab scripts for processing and showing the coupled ELM-MOSART coupled simulations for Pantanal region.</p> <p>domain_lnd_Pantanal_default.nc, MOSART_Pantanal_default_c211116.nc, and surfdata_Pantanal_default_c220520.nc are the domain file, MOSART input file, and ELM surface dataset, respectively. </p> <p><a href="https://zenodo.org/api/files/6be468b6-cbfa-4ef4-bb10-0f15812be9bd/Pantanal_half_calibration_CLMCRUNCEPv7.sh">Pantanal_half_calibration_CLMCRUNCEPv7.sh</a> is the bash script to run E3SM with coupled ELM-MOSART configuration. ANd detailed instruction of running E3SMV2 can be found at: https://e3sm.org/model/running-e3sm/e3sm-quick-start/ (last access: Aug 2023).</p> <p>Pantanal_GSIM.zip contains the observed streamflow that used in this study, which is downloaded from <a href="https://doi.pangaea.de/10.1594/PANGAEA.887470">https://doi.pangaea.de/10.1594/PANGAEA.887470</a> (last access: Aug 2023). The reference is Gudmundsson, Lukas; Do, Hong Xuan; Leonard, Michael; Westra, Seth (2018): The Global Streamflow Indices and Metadata Archive (GSIM) – Part 2: Quality control, time-series indices and homogeneity assessment. Earth System Science Data, 10(2), 787-804, https://doi.org/10.5194/essd-10-787-2018.</p> <p>BFI3.mat is the baseflow index from GSCD and processed to the study domain. The GSCD dataset was download from <a href="http://www.gloh2o.org/gscd/">http://www.gloh2o.org/gscd/</a> (last access: Aug 2023). The reference is Beck, H. E., van Dijk, A. I. J. M., Miralles, D. G., de Jeu, R. A. M., Bruijnzeel, L. A., McVicar, T. R., and Schellekens, J.: Global patterns in base flow index and recession based on streamflow observations from 3394 catchments, Water Resour Res, 49, 7843-7863, <a href="https://doi.org/10.1002/2013WR013918">https://doi.org/10.1002/2013WR013918</a>, 2013.</p> <p>runoff_uncertianty.mat contains the annual runoff time series from GRUN, LORA, and GFRF that processed to the study domain. The GRUN runoff dataset was downloaded from <a href="https://doi.org/10.6084/m9.figshare.9228176">https://doi.org/10.6084/m9.figshare.9228176</a> (last access: Aug 2023). The LORA runoff dataset was downloaded from <a href="https://dap.nci.org.au/thredds/remoteCatalogService?catalog=http://dapds00.nci.org.au/thredds/catalog/ks32/ARCCSS_Data/LORA/v1-0/catalog.xml">https://dap.nci.org.au/thredds/remoteCatalogService?catalog=http://dapds00.nci.org.au/thredds/catalog/ks32/ARCCSS_Data/LORA/v1-0/catalog.xml</a> (last access: Aug 2023). The reference is Hobeichi, S., Abramowitz, G., Evans, J., and Beck, H. E.: Linear Optimal Runoff Aggregate (LORA): a global gridded synthesis runoff product, Hydrol. Earth Syst. Sci., 23, 851-870, 10.5194/hess-23-851-2019, 2019. The GRFR runoff was downloaded from <a href="http://hydrology.princeton.edu/data/mpan/GRFR/runoff/monthly_1deg/">http://hydrology.princeton.edu/data/mpan/GRFR/runoff/monthly_1deg/</a> (last access: Aug 2023). The reference is Yang, Y., Pan, M., Lin, P., Beck, H. E., Zeng, Z., Yamazaki, D., David, C. d. H., Lu, H., Yang, K., Hong, Y., and Wood, E. F.: Global Reach-level 3-hourly River Flood Reanalysis (1980-2019), B Am Meteorol Soc, 1-49, 10.1175/BAMS-D-20-0057.1, 2021.</p> <p>GLAD_Pantanal_half.mat, GLAD_Pantanal_8th.mat are the processed surface water fraction from GLAD at half and 8th spatial resoution. Specifically, The GLAD surface water dynamics was downloaded from <a href="https://console.cloud.google.com/storage/browser/earthenginepartners-hansen/water;tab=objects">https://console.cloud.google.com/storage/browser/earthenginepartners-hansen/water;tab=objects</a> (last access: Aug 2023). The reference is Pickens, A. H., Hansen, M. C., Hancher, M., Stehman, S. V., Tyukavina, A., Potapov, P., Marroquin, B., and Sherani, Z.: Mapping and sampling to characterize global inland water dynamics from 1999 to 2018 with full Landsat time-series, Remote Sens Environ, 243, 111792, <a href="https://doi.org/10.1016/j.rse.2020.111792">https://doi.org/10.1016/j.rse.2020.111792</a>, 2020.</p>
Dataset for "Disentangling mechanisms responsible for wind energy effects on European bats"
<p>Data used in the study "Disentangling mechanisms responsible for wind energy effects on European bats".</p> <p><strong>site </strong>= ID attributed to the studied site ; <strong>ID_Parc</strong> = ID attributed to the studied wind farm ; <strong>night </strong>= date of the sampling ; <strong>SM4 </strong>= ID attributed to the recorder ; <strong>NbWT_1500m</strong> = number of wind turbines in a 1500m buffer ; <strong>Dist_WT</strong> = distance to the nearest wind turbine ; <strong>Dist_water</strong> = distance to the nearest water body or water course ; <strong>Dist_forest</strong> = distance to the nearest forest ; <strong>avg_temp</strong> = average temperature of the night ; <strong>Prev_wind_mod1</strong> = prevailing wind direction of the night ; <strong>count_prev_wind22.5</strong> = number of hours during which the wind direction was close (± 22.5°) to the prevailing wind direction (mode) of the night ; <strong>angle </strong>= angle between the axis wind-turbine - detector and the north direction ; <strong>MES_year</strong> = year of commissioning of the nearest wind turbines ; <strong>Model </strong>= model of the nearest wind turbine ; <strong>Rotor_diameter</strong> = diameter of the rotor of the nearest wind turbine ; <strong>Hub_height</strong> = height of the hub of the nearest wind turbine ; <strong>ID_WT</strong> = ID attributed to the nearest wind turbine</p>
Population links between an insectivorous bird and moths disentangled through national scale monitoring data
<p>Code in support of "Population links between an insectivorous bird and moths disentangled through national scale monitoring data"</p> <p>Luke Christopher Evans, Malcolm D. Burgess, Simon G. Potts, William E. Kunin, Tom H. Oliver</p>
Data from: Disentangling the relative contributions of factors determining seed physical defence: a global-scale data synthesis
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Allen Brain Atlas
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OpenNeuro
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