cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0vt4b8h01
title: SNP dataset for the threatened plant species Dinizia jueirana-facao (Fabaceae)

description: By performing sensitivity analyses, we empirically investigated how
 decisions about the percentage of missing data (MD) and the minor allele
 frequency (MAF) set in bioinformatic processing of genomic data affect
 direct (i.e., parentage analysis) and indirect (i.e., fine-scale spatial
 genetic structure - SGS) gene flow estimates. We focus specification on
 these manifestations in small plant populations, and specifically, in the
 rare tropical plant species Dinizia jueirana-facao, where assumptions
 implicit to analytical procedures for accurate estimates of gene flow may
 not hold. Avoiding biases in dispersal estimates are essential given this
 species is facing extinction risks due to habitat loss, and so we also
 investigate the effects of forest fragmentation on the accuracy of
 dispersal estimates under different filtering criteria by testing for
 recent decrease in the scale of gene flow. Our sensitivity analyses
 demonstrate that gene flow estimates are robust to different setting of
 MAF (0.05 to 0.35) and MD (0 to 20%). Comparing the direct and indirect
 estimates of dispersal, we find that contemporary estimates of gene
 dispersal distance (σrt = 41.8 m) was ~ fourfold smaller than the
 historical estimates, supporting the hypothesis of a temporal shift in the
 scale of gene flow in D. jueirana-facao, which is consistent with
 predictions based on recent, dramatic forest fragmentation process. While
 we identified settings for filtering genomic data to avoid biases in gene
 flow estimates, we stress that there is no ‘rule of thumb’ for
 bioinformatic filtering or that relying on default program settings is
 advisable. Instead, we suggest that the approach implemented here be
 applied independently in each separate empirical study to confirm
 appropriate settings to obtain unbiased population genetics estimates.
description: We created one genomic library using a double-digest restriction
 site-associated DNA sequencing (i.e., ddRADseq) protocol (Peterson et al.
 2012), with modifications to minimize the risk of high variance in the
 number of reads per individual (see Nazareno et al. 2017 for more
 details). Files containing the raw sequence reads were
 analyzed in Stacks 2.41 (Catchen et al. 2011, Catchen et al. 2013,
 Rochette et al. 2019) using <i>de novo</i> assembly. We used
 the process_radtags program in Stacks to initially assign reads to
 individuals and eliminate poor quality reads and reads missing the
 expected <i>EcoRI</i> cut site (options –barcode_dist 2 -q -e
 ecoRI). All sequences were processed in ustacks to produce consensus
 sequences of RAD tags, applying a maximum-likelihood framework to estimate
 the diploid genotype for each individual at each nucleotide position
 (Hohenlohe et al. 2011).
description: The csv.file contains the genotypes for all the 50 samples (rows
 2 to 51) for each of the 256 loci (columns D to IY). The geographic
 coordinates (X and Y) for each sample are presented at the columns B and
 C.
DOI: 10.5061/dryad.ncjsxksv8
title: Data from: Environmental context determines pollution impacts on ecosystem functioning

description: Global change assessments have typically ignored synthetic chemical
 pollution, despite the rapid increase of pharmaceuticals, pesticides, and
 industrial chemicals in the environment. Part of the problem reflects the
 multifarious origins of these micropollutants, which can derive from urban
 and agricultural sources. Understanding how micropollutants harm
 ecosystems is a major scientific challenge due to asymmetries of stress
 across trophic levels and ecological surprises generated by multiple
 drivers interacting in human-impacted landscapes. We used field assays
 above and below municipal wastewater treatment plants (WWTPs) in 60
 sampling locations across 20 Swiss streams to test how micropollutants and
 nutrients originating from WWTPs affect two trophic levels (microbes and
 detritivores) and their role in leaf litter processing. Wastewater impacts
 were asymmetric across trophic levels, with the detritivore contribution
 declining relative to microbial-driven decomposition. The strength of
 negative impacts was context-dependent, peaking at sites with the highest
 upstream abundances of detritivorous invertebrates. Diffuse pollution from
 intensive agriculture and wastewater-born micropollutants contributed to
 reduced litter processing rates, including indirect effects apparently
 mediated through negative influences of insecticides on detritivores.
 Asymmetries in stress responses across trophic levels can introduce
 quantitative changes in consumer-resource dynamics and leaf litter
 processing. This means functional redundancies at different trophic levels
 are insufficient to compensate for biodiversity losses, causing
 environmental stressors such as chemical pollutants to have pervasive
 ecosystem-level impacts. 
description: Please see the README document
 ("README_EnvironmentContextPollution_v.1.0.txt") and the
 accompanying published article: Burdon, F. J., Reyes, M., Schönenberger,
 U., Räsänen, K., Tiegs, S. D., Eggen, R.I.L., & Stamm, C. (2022)
 Environmental context determines pollution impacts on ecosystem
 functioning. Oikos. DOI:10.1111/oik.09131 
description: Please see the README document
 ("README_EnvironmentContextPollution_v.1.0.txt") and the
 accompanying published article: Burdon, F. J., Reyes, M., Schönenberger,
 U., Räsänen, K., Tiegs, S. D., Eggen, R.I.L., & Stamm, C. (2022)
 Environmental context determines pollution impacts on ecosystem
 functioning. Oikos. DOI:10.1111/oik.09131
DOI: 10.5061/dryad.dr7sqv9zb
title: Discrete-space continuous-time models of marine mammal exposure to Navy sonar

description: Assessing the patterns of wildlife attendance to specific areas is
 relevant across many fundamental and applied ecological studies,
 particularly when animals are at risk of being exposed to stressors within
 or outside the boundaries of those areas. Marine mammals are increasingly
 being exposed to human activities that may cause behavioural and
 physiological changes, including military exercises using active sonars.
 Assessment of the population-level consequences of anthropogenic
 disturbance requires robust and efficient tools to quantify the levels of
 aggregate exposure for individuals in a population over biologically
 relevant time frames. We propose a discrete-space, continuous-time
 approach to estimate individual transition rates across the boundaries of
 an area of interest, informed by telemetry data collected with
 uncertainty. The approach allows inferring the effect of stressors on
 transition rates, the progressive return to baseline movement patterns,
 and any difference among individuals. We apply the modelling framework to
 telemetry data from Blainville's beaked whale (Mesoplodon
 densirostris) tagged in the Bahamas at the Atlantic Undersea Test and
 Evaluation Center (AUTEC), an area used by the US Navy for fleet readiness
 training. We show that transition rates changed as a result of exposure to
 sonar exercises in the area, reflecting an avoidance response. Our
 approach will support the assessment of the aggregate exposure of
 individuals to sonar and the resulting population-level consequences. The
 approach has potential applications across many applied and fundamental
 problems where telemetry data are used to characterise animal occurrence
 within specific areas.
description: Data are satellite telemetry data from seven Blainville's
 beaked whales (<em>Mesoplodon densirostris</em>) tagged
 between 2009 and 2015 within or near the Atlantic Undersea Test and
 Evaluation Center (AUTEC), in the Bahamas. This region is regularly used
 by the U.S. Navy to carry out military exercises with active sonar.
 Tagging was carried out in advance of large-scale exercises (Submarine
 Command Courses) to monitor resulting changes in the animals'
 movement behavior. Animals were fitted with Wildlife
 Computers SPLASH transmitters (<em>n</em> = 2, Mk-10; Wildlife
 Computers Inc., Redmond, WA, USA) and SPOT model tags
 (<em>n</em> = 5, AM‐S240A‐C; Wildlife Computers Inc.) in the
 Low Impact Minimally Percutaneous External-electronics Transmitter
 (LIMPET) configuration. Tags were attached on or near the dorsal fin from
 distances of 5-25 m using a crossbow or black powder gun. Location
 estimates of tagged whales were provided by the Argos system based on the
 Kalman filtering method.  See manuscript for further
 details.
DOI: 10.5061/dryad.rxwdbrv8k
title: Diet and temperature modify the relationship between energy use and ATP production to influence behaviour in zebrafish (Danio rerio)

description: Food availability and temperature influence energetics of animals, and can
 alter behavioural responses such as foraging and spontaneous activity.
 Food availability, however, is not necessarily a good indictator of energy
 (ATP) available for cellular processes. The efficiency of energy
 transduction from food-derived substrate to ATP in mitochondria can change
 with environmental context. Our aim was to determine whether the
 interaction between food availability and temperature affects
 mitochondrial efficiency and behaviour in zebrafish (Danio rerio). We
 conducted a fully factorial experiment to test the effects of feeding
 frequency, acclimation temperature (three weeks to 18 or 28°C), and acute
 test temperature (18 and 28°C) on whole-animal oxygen consumption,
 mitochondrial bioenergetics and efficiency (ADP consumed per oxygen atom;
 P:O ratio), and behaviour (boldness and exploration). We show that
 infrequently fed (once per day on four days per week) zebrafish have
 greater mitochondrial efficiency than frequently fed (three times per day
 on five days er week) animals, particularly when warm-acclimated. The
 interaction between temperature and feeding frequency influenced
 exploration of a novel environment, but not boldness. Both resting rate of
 producing ATP and scope for increasing it were positively correlated with
 time spent exploring and distance moved in standardised trials. In
 contrast, behaviour was not associated with whole-animal aerobic (oxygen
 consumption) scope, but exploration was positively correlated with resting
 oxygen consumption rates. We highlight the importance of variation in both
 metabolic (oxygen consumption) rate and efficiency of producing ATP in
 determining animal performance and behaviour. Oxygen consumption
 represents energy use, and P:O ratio is a variable that determines how
 much of that energy is allocated to ATP production. Our results emphasise
 the need to integrate whole-animal responses with subcellular traits to
 evaluate the impact of environmental conditions on behaviour and movement.
 --
DOI: 10.5061/dryad.dfn2z3521
title: Plant functional traits in 42 paramo species in Colombia

description: Páramos are exceptionally species-rich tropical alpine ecosystems that
 provide several important ecosystem services, including carbon storage and
 water provision. The responses of páramo plant species
 to climatic change are largely unknown, but classifying
 species by functional type and ecological strategy can help reduce
 complexity for modeling and conservation efforts. We measured 22 traits in
 42 plant species with various growth forms in the Colombian Andes. We
 classified plant ecological strategies using CSR (C: competitor, S: stress
 tolerator, R: ruderal) analysis and identified plant functional types
 (PFTs) using hierarchical clustering of principal components.
 Additionally, we calculated the functional originality of each species to
 identify species with unique trait combinations. We identified a high
 degree of convergence among traits and strategies, with most species
 characterized by the S and SC strategies. Considering the full
 set of traits, only three PFTs were identified: one composed of forbs and
 shrubs with tender leaves (PFT1), another composed only of species with
 rosettes form (PFT2), and a third composed of shrubs with tough leaves
 (PFT3). Values of functional originality were generally low, suggesting
 high redundancy in plant traits. PFT2 species, mostly
 rosettes, exhibited the highest functional originality of all the
 groups. Our results imply the existence of a limited set
 of ecophysiological strategies in the páramos,
 likely driven by the extremely stressful conditions in these systems. This
 functional redundancy may indicate heightened vulnerability to
 environmental changes; however, the presence of multiple species with
 shared functional traits could provide some resilience to
 disturbance.
DOI: 10.5061/dryad.ht76hdrg1
title: Data from: Functional diversity and redundancy of tropical forests shift with elevation and forest-use intensity

description: 1. Change and intensification of forest use alter tropical ecosystems,
 influencing biodiversity and, subsequently, ecosystem functioning. The
 implications of eroding biodiversity may go beyond decreases in species
 diversity, resulting in changes of functional diversity, i.e. the
 diversity of ecological strategies present in the community, and
 functional redundancy, i.e. how redundant these strategies are to
 biodiversity loss. However, how environmental conditions and anthropogenic
 influences shape functional diversity and redundancy in tropical forests
 remains poorly understood. 2. Here, we examine how tropical forests
 respond to forest-use intensity along an extensive elevational gradient in
 Mexico from the tropical lowlands to high-elevational mountain forests (0
 to 3500 m), in terms of functional diversity and functional redundancy,
 and how these biodiversity facets are related to forest structure. In our
 study, elevation was crossed with three levels of forest-use intensity:
 old-growth, degraded, and secondary forests. At eight elevational sites,
 five replicate plots were inventoried for each level of forest-use
 intensity (total n = 120 plots). Functional diversity and redundancy were
 calculated using leaf and wood traits of 144 tree species for Hill numbers
 zero, one, and two. 3. Interactive effects between elevation and
 forest-use intensity significantly affected biodiversity facets. However,
 interactive effects resulted from forest-use intensity influencing
 biodiversity facets at only a few elevations, and not from a consistent,
 negative impact of forest-use intensity. Forest structure, specifically
 stem density and the Gini coefficient, explained variation across
 biodiversity facets when these facets gave equal weight to common and rare
 species.  4. Synthesis and applications. High functional
 diversity and functional redundancy from lowland to mid-elevation tropical
 forests suggest that these ecosystems can be resilient to future
 disturbances. Our results indicate that the ability of high-elevation
 forests may be particularly susceptible to climate change and increasing
 forest-use intensity. For these high-elevation forests, we recommend that
 forest managers implement enrichment plantings with native species that
 can tolerate future environmental conditions. Finally, our study shows
 that efforts to conserve structurally heterogeneous forests and actively
 managing forests to increase structural heterogeneity will enhance the
 resilience of tropical forests while conserving their biodiversity.
DOI: 10.5061/dryad.41ns1rndk
title: Resveratrol loaded chitosan-pectin core-shell nanoparticles as novel drug delivery vehicle for sustained release and improved antioxidant activities

description: Resveratrol, chemically known as 3, 5, 4'-trihydroxy-trans-stilbene,
 is a natural polyphenol with promising multi-targeted health benefits. The
 optimal therapeutic uses of resveratrol are limited due to its poor
 solubility, rapid metabolism and low bioavailability. To address the
 issues, we have encapsulated resveratrol inside the nanosized core made of
 chitosan and coated this core with pectin - shell in order to fabricate a
 drug delivery vehicle which can entrap resveratrol for a longer period of
 time. The core - shell nanoparticles fabricated in this way were
 characterized with the help of Fourier Transform Infrared Spectrometer
 (FTIR), Field Emission Scanning Electron Microscope (FESEM), Field
 Emission Transmission electron microscopy/Selected Area Electron
 Diffraction (FETEM/SAED), High-Resolution Transmission Electron
 Microscope (HRTEM)), Dynamic Light Scattering (DLS) and Zeta Potential
 measurements. In vitro drug release study showed the ability of the
 core-shell nanoparticles to provide sustained release of resveratrol for
 almost 30 hours. The release efficiency of the drug was found to be pH
 dependent and a sequential control over drug release can be obtained
 varying the shell thickness. The resveratrol encapsulated in a nanocarrier
 was found to have a better in vitro antioxidant activity than free
 resveratrol as determined by DPPH radical scavenging method. This work
 finally offers a novel nano-based drug delivery system.
description: The dataset in supplementary file was collected by recording (i)
 HRTEM images of the synthesized samples (ii) UV Vis spectra of the samples
 (iii) FT- IR spectrum of the sample.
description: One should have the knowledge of analysing Transmission Electron
 Microscopic images and FTIR spectra. For statistical significance,
 knowledge of ANOVA two way is required.
DOI: 10.5061/dryad.2v6wwpznc
title: Non-invasive surveys of mammalian viruses using environmental DNA

description: This dataset provides supplemental information to interpret the data
 published in Alfano & Dayaram et al. 2021. The study investigates
 how environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) can be
 used to characterize the yet largely unknown virome present in mammalian
 wildlife. Environmental DNA and iDNA are used to survey biodiversity
 non-invasively to mitigate difficulties in obtaining wildlife samples,
 particularly in remote areas or for rare species. Recently, eDNA/iDNA were
 used to monitor known wildlife pathogens, however, most wildlife pathogens
 are unknown and often evolutionarily divergent. To detect and
 identify known and novel mammalian viruses from eDNA/iDNA, we used a
 curated set of RNA oligonucleotides as viral baits in a hybridization
 capture system coupled with high throughput sequencing. We detected
 multiple known and novel mammalian RNA and DNA viruses from multiple viral
 families from both waterhole eDNA and leech derived iDNA. Congruence was
 found between detected hosts and viruses identified in leeches and
 waterholes. Our results demonstrate that eDNA/iDNA samples
 represent an effective non-invasive resource for studying wildlife viral
 diversity and for detecting novel potentially zoonotic viruses prior to
 their emergence.
description: This dataset contains several supplementary files that support
 the findings of Alfano N, Dayaram A, et al. 2021
 (https://doi.org/10.1111/2041-210X.13661). It contains phylogenetic trees
 of the different virus families, assembly plots of the viral sequencing
 reads and other supportive information. The readme file
 contains an explanation of each of the variables in the supplemental
 tables (Suppl._Tab._1 - Suppl._Tab._5). NA denotes not available
 information. For detailed information on how data was processed please see
 the method section in the above publication (Alfano, N. & Dayaram,
 A., et al. (2021)). 
 <strong>Supplemental_material_Info.pdf:</strong><br> It
 contains additional information on the check for potentail suid DNA
 contaminations, phylogenetic trees of the different virus families and
 assembly plots of the viral sequencing reads. 
 <strong>Suppl._Tab._1_noSRA.xlsx:</strong><br> Read
 counts for leech and waterhole samples. 
 <strong>Suppl._Tab._2.xlsx:</strong><br> Primers used
 and amplification results obtained for the leech viral contigs
 confirmation PCRs. 
 <strong>Suppl._Tab._3.xlsx:</strong><br> Leech and
 vertebrate species genomes used in BLAST searches to identify potential
 endogenous viral elements among the viral sequences generated in this
 study. <strong>Suppl._Tab._4.xlsx:
 </strong><br> Best BLAST hit for each viral contig identified
 in leech and waterhole samples. 
 <strong>Suppl._Tab._5.xlsx:</strong><br> Viral
 enrichment achieved by capture for each sample.
DOI: 10.5061/dryad.866t1g1qx
title: Mycorrhizal symbiosis and phosphorus supply determine interactions among plants with contrasting nutrient-acquisition strategies

description: Highly diverse plant communities growing on nutrient-impoverished soils
 are test beds for theories on species coexistence. Here, neighbouring
 mycorrhizal and non-mycorrhizal plants compete for limited phosphorus. The
 impact of belowground interactions on community dynamics is underexplored.
 We used an experimental approach to investigate effects of inoculation
 with arbuscular mycorrhizal (AM) fungi and a phosphorus supply gradient on
 competitive and facilitative interactions among mixed assemblages of woody
 plants in microcosms. The plant species, one cluster-root forming (CR)
 species and four AM species, are native to jarrah forest that grows on
 nutrient-impoverished soils in south-western Australia. We measured plant
 growth in microcosms, with and without inoculation with the AM fungus
 Rhizophagus irregularis, and across a gradient of P supply: 0, 9, 27, and
 243 mg P per kg of soil. Our data show evidence of plant-plant
 facilitation at low P supply and competition at high P supply. Growth of
 the CR species, Hakea undulata, was highest in microcosms with 0P and
 without AM inoculation. One AM species, Bossiaea aquifolium, also
 performed better at lower P levels, possibly benefitting from P mobilised
 by H. undulata. The other three AM species, one strongly obligate,
 performed better at higher P levels. Data for Acacia celastrifolia
 suggested it was facultatively mycotropic, and because there was no
 correlation between AM colonisation and the relative inoculum effect, we
 suggest positive effects of AM inoculation at 9P might be due to benefits
 other than P-acquisition, such as pathogen defence. Benefit of AM
 inoculation diminished for three of four mycorrhizal species at the
 highest P-level as we had predicted. The fourth species, Eucalyptus
 marginata (jarrah), had higher growth in microcosms that were not
 inoculated with AM, perhaps because the species benefits more from
 ectomycorrhizas. Synthesis. Our experimental data suggests spatial
 heterogeneity of soil P, coupled with a diversity of nutrient acquisition
 strategies, and plasticity among plant-plant and plant-AM fungi
 interactions, contributes to plant species coexistence in the
 nutrient-impoverished jarrah forest. Our research highlights the
 importance of belowground mechanisms for understanding factors determining
 community structure including a potential role of AM fungi in plant
 pathogen defence.
description: The data were collected following execution of a microcosm
 experiment. The raw data are presented.
description: Please refer to README file.