cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.12jm63z2g
title: Nutrient-based species selection is a prevalent driver of community assembly and functional trait space in tropical forests

description: 1. Soil nutrient availability and functional traits interact in complex
 ways during the assembly of tree communities hindering our understanding
 of the implications that this may have for their phylogenetic and
 functional diversity. 2. We combined abundance, taxonomic, phylogenetic
 and functional trait data of 222 tree species distributed along nutrient
 concentration gradients at twenty-four plots in two tropical forest study
 sites. We analysed micro and macronutrient concentration in organic and
 topsoil horizons and tested for: (1) nutrient-based species sorting due to
 contrasting trait-environment relationships; (2) whether nutrient
 filtering has consequences for phylogenetic and functional diversity, and
 functional space size and occupancy; and (3) we mapped trait distributions
 across the phylogeny of tree species to track the evolutionary signature
 of nutrient availability. 3. We found that total nitrogen (N), available
 phosphorus and total potassium in soil accounted for 68% of the variation
 in tropical tree species community composition, with strong associations
 with nutrient concentration for 89% of the tree species included in the
 analysis. This nutrient-based species selection was mediated by
 interactions between the three soil nutrient concentrations with leaf
 nitrogen, leaf thickness and wood density. Soil N concentration was
 positively associated with the functional space at the site level. At a
 plot level soil N concentration positively correlated with functional
 evenness and it was negatively associated with the functional space not
 occupied by any species in the tree community. Despite the phylogenetic
 conservatism of leaf N across tree lineages even when not considering
 legumes, many sister-species pairs show contrasting values which match
 with their habitat preferences thus indicating the evolutionary lability
 of this trait, particularly within recently diversified clades. 4.
 Synthesis. Our results demonstrate that soil nutrient-based species
 selection is a prevalent driver of community assembly in tropical forests,
 a process mediated by key functional traits within the leaf and wood
 economics spectrum. Functional space size and its filling increase with
 soil nutrient concentration, whereas niche vacancy decreases. This
 selection process has likely influenced tropical tree species
 diversification patterns via habitat specialization.
description: Data collected during fieldwork campaigns in French
 Guiana. Tree community data: Abundance, taxonomic, phylogenetic and
 functional trait data of 222 tree species distributed along nutrient
 concentration gradients at twenty-four plots in two tropical forest study
 sites in French Guiana. Soil nutrient concentration data: Micro and
 macronutrient concentration in organic and topsoil horizons from each
 study plot.
description: All the analyses where carried out with R software and the code
 is therefore provided in R programming language.
DOI: 10.5061/dryad.905qfttqc
title: Dryococelus australis genome assembly supplementary data

description: We present a chromosome-scale genome assembly for the critically
 endangered Lord Howe Island stick insect Dryococelus
 australis. Contained in this repository are the original
 unfiltered annotation .gff file, the .fasta file of repeat families
 identified by RepeatScout, and the .gff file of repetitive elements
 throughout the genome assembly.
description: Repeat families were identified de novo and classified using the
 software package RepeatModeler v2.0.1. We further filtered repeats by a
 BLAST search to the `nr` database and removed any unclassified family
 whose best hit was a known protein not originating from a transposable
 element, including mitochondrial proteins. These repeat families were then
 annotated in the genome assembly using RepeatMasker v2.0.1. Coding
 sequences from <em>Clitarchus hookeri</em>,
 <em>Medauroidea extradentata</em>, and <em>Timema
 cristinae</em> were used to train the <em>ab initio</em>
 model for <em>D. australis</em> using both AUGUSTUS software
 v2.5.5 and SNAP version 2006-07-28. We extracted RNA from tissue samples
 of both sexes of the ventral ganglion, leg muscle, gut lumen, Malpighian
 tubules, and gonads with RNEasy spin-column kits (Qiagen); libraries were
 prepared and sequenced at BGI Hong Kong on a BGISEQ-500 instrument in
 paired-end mode with 150 bp reads. Reads were mapped onto the assembly
 using STAR v2.7 and intron hints generated with the bam2hints tools within
 the AUGUSTUS software. SNAP and AUGUSTUS (with intron-exon boundary hints
 provided from RNA-Seq) were then used to predict for genes in the
 repeat-masked assembly. Only gene models that were predicted by both SNAP
 and AUGUSTUS were retained. Genes were further characterised for their
 putative function by performing a BLAST search of the peptide sequences
 against a set of protein sequences from UniProt. All raw sequence data
 have been deposited into NCBI's SRA database under BioProject
 PRJNA930028.
DOI: 10.5061/dryad.qfttdz0n9
title: Micro-CT analysis of Katian radiolarians from the Malongulli Formation, New South Wales, Australia, and implications for skeletogenesis

description: A diverse and well-preserved radiolarian assemblage from the Malongulli
 Formation, New South Wales, Australia contains 13 species representing ten
 genera and six families. One new genus: Wiradjuri n.
 gen. is introduced to accommodate pre-Devonian single-shelled entactiniid
 taxa and one new species: Secuicollacta
 malongulliensis n. sp. is recorded together with some previously
 described forms. The micro-structure of the ‘rotasphaerid
 structure/primary unit’ and the ‘ectopic spicule’ are investigated to
 validate their roles as fundamental units in the Secuicollactidae together
 with comprehensive documentation of the previously
 enigmatic Pseudorotasphaera internal skeleton. The
 results of this investigation suggest that, among all radiolarian genera
 that survived the Late Ordovician Mass Extinction event
 (LOME) and transitioned into the Silurian, Secuicollacta, Haplotaeniatum,
 and Palaeoephippium maintained stable body plans during the
 transition and were more successfully established. The selective
 advantages these lineages had during the LOME, were most likely
 spontaneous outcomes of the mode of structural development involving
 sequential skeletogenesis and a tendency to evolve towards simpler body
 plans. 
description: MicroCT reconstructions of
 radiolarians collected from the Upper Ordovician
 (Katian) Malongulli Formation, NSW, Australia
  (33°34'57.58"S, 148°52'54.06"E). 
 Fossil specimens were scanned
 using a Zeiss Xradia Versa XRM-500 high-resolution micro-CT scanner at the
 Julius Kruttschnitt Mineral Research Centre, The University of
 Queensland. 3D models were
 generated using Avizo® 9.7 (2020.2 version) volume rendering
 software.
description: Datafiles can be viewed using any software that will open and run
 mpg files.
DOI: 10.5061/dryad.3ffbg79nw
title: Data for: Properties of wing scales on butterflies with different distribution patterns

description: Butterflies play a crucial role in understanding the spread of life due to
 their complex thermal adaptations. The cooling capacity provided by wing
 scales is a dominant factor associated with the ambient temperature of
 their habitats. However, it remains unclear how the wing scale structure
 of butterflies varies to regulate cooling capacity and participate in
 shaping distribution patterns. Based on data acquired from quantitative
 measurements, rank sum and ANOVA tests were used to test whether the
 structure and cooling capacity of wing scales responded to butterfly
 distribution. Virtual simulations and Spearman tests were used to confirm
 the correlation between the structure and cooling capacity of wing scales.
 The response was first resolved using three representative species with
 gradient differences in distribution, and then macroscopically validated
 using 99 species within their phylogenetic framework, with a presampling
 control to exclude potential effects of taxonomic position, body size, and
 migratory behaviour. Both optical and thermal properties were used to
 measure the cooling capacity. Thermal data generated from specimens in
 different states were used to exclude the effects of other
 thermoregulatory pathways. The results show that the cooling capacity of
 butterfly wings decreases and becomes more homogeneous as the temperature
 of their habitat decreases. The decrease in cooling capacity is due to the
 decrease in maximum emissivity, while the homogenisation is due to both
 the decrease in maximum emissivity and the increase in minimum emissivity.
 Variation in cooling capacity is due to changes in the structure of wing
 scale, which homogenises as the habitat becomes colder. As butterflies
 generally spread from the tropics to temperate zones, it is inferred that
 the generation of a low overall cooling capacity through structural
 homogenisation of wing scales has supported the dispersal of butterflies.
 For the first time, we provide cascading evidence for the links between
 butterfly distribution, thermal adaptation, and functional morphology. We
 also highlight the role of structural homogenisation on the poikilothermic
 body surface in the adaptive process for dispersal. Further investigation
 using genetic information would be beneficial to resolve the mechanism
 behind thermal adaptation at a deeper level.
DOI: 10.5061/dryad.np5hqbzz5
title: Data for: Host shift promotes divergent evolution between closely related holoparasitic species

description: Distinct hosts have been hypothesized to possess the potential for
 affecting species differentiation and genome evolution of parasitic
 organisms. However, what host shift history is experienced by the closely
 related parasites and whether disparate evolution of their genomes occur
 remain largely unknown. Here, we screened horizontal gene transfer (HGT)
 events in a pair of sister species of holoparasitic Boschniakia
 (Orobanchaceae) having obligate hosts from distinct families to recall the
 former host-parasite associations and performed a comparative analysis to
 investigate the difference of their organelle genomes. Except these from
 present hosts (Ericaceae and Betulaceae), a number of HGTs from Rosaceae
 were identified to support the occurrence of unexpected ancient host
 shifts. Different hosts transfer functional genes which changed nuclear
 genomes of the sister species. Similarly, different donors transfer
 sequences to their mitogenomes which size varies due to foreign and
 repetitive elements rather than other factors found in other parasites.
 The plastomes are both severely reduced, but the extent of differences in
 reduction syndrome is near to the genus level. Our findings provide new
 insights into the genome evolution of parasites adapting different hosts
 and extend the mechanism of host shift promoting species differentiation
 to parasitic plant lineages.
DOI: 10.5061/dryad.mkkwh714m
title: Vessel noise exposures of harbour seals from the Wadden Sea

description: The North Sea faces intense ship traffic owing to increasing human
 activities at sea. As harbour seals (Phoca vitulina) are abundant top
 predators in the North Sea, it is hypothesised that they experience
 repeated, high-amplitude vessel exposures. Here, we test this hypothesis
 by quantifying vessel noise exposures from deployments of long-term sound
 and movement tags (DTAGs) on nine harbour seals from the Wadden Sea. An
 automated tool was developed to detect intervals of elevated noise in the
 sound recordings. An assessment by multiple raters was performed to
 classify the source as either vessels or other sounds. A total of 133
 vessel passes were identified with received levels &gt;97 dB re 1µPa
 RMS in the 2 kHz decidecade band and with ambient noise &gt;6 dB below
 this detection threshold. Tagged seals spent most of their time within
 Marine Protected Areas (89 ± 13%, mean ± SD) and were exposed to
 high-amplitude vessel passes 4.3 ± 1.6 times per day. Only 32% of vessel
 passes were plausibly associated with an AIS-registered vessel. We
 conclude that seals in industrialized waters are exposed repeatedly to
 vessel noise, even in areas designated as protected, and that exposures
 are poorly predicted by AIS data.
DOI: 10.5061/dryad.mw6m9061s
title: Data for: Steal the rain: Interception loses and rainfall partitioning by a broad-leaf and a fine-leaf woody encroaching species in a southern African semi-arid savanna

description: Woody plant encroachment (WPE) has been found to alter ecosystem
 functioning and services in savannas. In rain-limited savannas, increasing
 woody cover can reduce streamflow and groundwater by altering
 evapotranspiration rates and rainfall partitioning, but the ecological
 relevance of this impact is not well known. This study quantified the
 altered partitioning of rainfall by two woody plant structural types
 (fine- and broad-leaved trees) across a gradient of encroachment in a
 semi-arid savanna in South Africa. Averaged across both plant functional
 types, loss of rainfall through canopy interception and subsequent
 evaporation roughly doubled (from 20.5 to 43.6% of total rainfall) with a
 roughly 13-fold increase in woody cover (from 2.4 to 31.4 m2/ha tree basal
 cover). Spatial partitioning changes comprised fourfold increases in
 stemflow (from 0.8 to 3.9% of total rainfall) and a decline in throughfall
 proportion of about two-fifths (from 80.2% to 47.3% of total rainfall).
 Changes in partitioning were dependent on plant functional type; rainfall
 interception by the fine-leaved multi-stemmed shrub Dichrostachys cinerea
 was almost double that of the broad-leaved tree Terminalia sericea at the
 highest levels of woody encroachment (i.e., 49.7% vs 29.1% of total
 rainfall intercepted at tree basal area of 31.4 m2/ha). Partitioning was
 also dependent on rainfall characteristics, with the proportion of
 rainfall intercepted inversely related to rainfall event size and
 intensity. Therefore, increasing tree cover in African grassy ecosystems
 reduces the amount of canopy throughfall, especially beneath canopies of
 fine-leaved species in smaller rainfall events. Rainfall interception
 traits may thus confer a selective advantage, especially for fine-leaved
 woody plant species in semi-arid savannas.
DOI: 10.6078/d19t4v
title: Minimal impact of chronic proprioceptive loss on implicit sensorimotor adaptation and perceived movement outcome

description: Implicit sensorimotor adaptation keeps our movements well-calibrated amid
 changes in the body and environment. We have recently postulated that
 implicit adaptation is driven by a perceptual error: the difference
 between the desired and perceived movement outcome. According to this
 perceptual re-alignment model, implicit adaptation ceases when the
 perceived movement outcome – a multimodal percept determined by a prior
 belief conveying the intended action, the motor command, and feedback from
 proprioception and vision – is aligned with the desired movement outcome.
 Here, we examined the role of proprioception in implicit motor adaptation
 and perceived movement outcome by examining individuals who experience
 deafferentation (i.e., individuals with impaired proprioception and
 touch). We used a modified visuomotor rotation task designed to isolate
 implicit adaptation and probe perceived movement outcome throughout the
 experiment. Surprisingly, both implicit adaptation and perceived movement
 outcome were minimally impacted by chronic deafferentation, posing a
 challenge to the perceptual re-alignment model of implicit adaptation.
DOI: 10.5061/dryad.69p8cz95z
title: Hepatotoxicity in immune checkpoint inhibitors: A pharmacovigilance study from 2014–2021

description: Adverse events(AEs) related to hepatotoxicity have been reported in
 patients treated with immune checkpoint inhibitors (ICIs). As the number
 of adverse events increases, it is necessary to assess the differences in
 each immune checkpoint inhibitor regimen. The purpose of this study was to
 examine the relationship between ICIs and hepatotoxicity in a scientific
 and systematic manner. Data were obtained from the FDA Adverse Event
 Reporting System database (FAERS) and included data from the first quarter
 of 2014 to the fourth quarter of 2021. Disproportionality analysis
 assessed the association between drugs and adverse reactions based on the
 reporting odds ratio (ROR) and information components (IC). 9,806 liver
 adverse events were reported in the FAERS database. A strong signal was
 detected in older patients (≥65 years) associated with ICIs. Hepatic
 adverse events were most frequently reported with Nivolumab (36.17%).
 Abnormal liver function, hepatitis, and autoimmune hepatitis were most
 frequently reported, and hepatitis and immune-mediated hepatitis signals
 were generated in all regimens. In clinical use, patients should be alert
 to these adverse effects, especially in elderly patients, who may be
 aggravated by the use of ICI.
description: Please see the README document
 ("README.txt") and the accompanying article:Hepatotoxicity in
 immune checkpoint inhibitors: A pharmacovigilance study from
 2014–2021. Data for the retrospective pharmacovigilance
 study were obtained from the FAERS database. All data
 downloaded  were processed by SAS 9.4 and further analyzed using R
 software. 
description: Please see the README document
 ("README.txt") and the accompanying article:Hepatotoxicity in
 immune checkpoint inhibitors: A pharmacovigilance study from
 2014–2021. Data for the retrospective pharmacovigilance
 study were obtained from the FAERS database. All data
 downloaded  were processed by SAS 9.4 and further analyzed using R
 software.
DOI: 10.25338/b8k05n
title: Molecular dynamics simulation primer for: Introduction to atomistic modeling and simulation of biomolecular systems

description: Molecular dynamics (MD) and related techniques have been used for computer
 simulations of biomolecular systems for over 40 years, but only recently
 due to advances in computer hardware, simulation software and
 methodologies, as well as breakthroughs in structural biology, have they
 become a widely-used tool for studying the molecular mechanisms of
 biological function and its modulation. This dataset represents a primer
 for learning basic MD simulation setup and analysis using a prototypical
 K+ channel KcsA embedded in a hydrated lipid bilayer. The dataset includes
 files necessary for setup of MD simulations using CHARMM-GUI web toolkit,
 running them using nanoscale MD (NAMD) and analysing using visual MD (VMD)
 sofware. Detailed explanations are provided in the book chapter
 "Introduction to Atomistic Modeling and Simulation of Biomolecular
 Systems" to be published soon.
description: The dataset was generated using CHARMM-GUI online toolkit to
 build a system for molecular dynamics (MD) simulations using
 K<sup>+</sup> channel KcsA PDB ID: 1K4C crystal structure as
 an input. The protein was embedded in a POPC lipid bilayer solvated by
 aqueous 0.15 M KCl solution. Molecular system coordinate, topology and
 force field parameter files were generated along with input files for
 several popular MD simulation packages such as NAMD, Amber, Gromacs
 OpenMM, etc. CHARMM36m protein, C36 lipid force fields and TIP3P water
 model were used for MD simulations. NAMD software was used to run ~102 ns
 long MD simulation with the first 2 ns used as a restrained equilibration
 and subsequent 100 ns as a restraint-free production MD run. VMD software
 Tcl scripts were used to combine original NAMD binary trajectories and
 save them using 1 ns frequency and also fix issues with periodic boundary
 condition (PBC) protein image centering. VMD software was also used to
 perform multiple MD simulation analyses such as inter-residue distances,
 root-mean-square deviations (RMSD) and fluctuations (RMSF) of protein
 atoms. Analysis scripts, data files, plotting scripts and images are
 provided in the dataset as well. 
description: CHARMM-GUI membrane builder (https://www.charmm-gui.org/?doc=input/membrane.bilayer ) was used for simulation system setup. Nanoscale molecular dynamics (NAMD) is needed to run MD simulations with other options (Gromacs, Amber, etc.) possible as well. Visual molecular dynamics (VMD) software is needed to perform MD simulation analysis. Both NAMD (http://www.ks.uiuc.edu/Research/namd/) and VMD (https://www.ks.uiuc.edu/Research/vmd/) are available free of charge for academic users.
DOI: 10.5061/dryad.98sf7m0nv
title: Modeling wetland functions: Is space-to-time substitution of perimeter-area relation appropriate?

description: Wetlands’ morphometric or shape properties such as their area and
 perimeter impact a multitude of ecosystem functions and services. However,
 current models used to quantify these functions often only use area as an
 independent variable, as the static area and perimeter of different
 wetlands have been found to be closely related. The study uses monthly
 satellite-based inundation maps to assess the temporal covariation of
 geographically isolated wetlands' perimeter and surface area. The
 results show that using static representations of wetlands to evaluate
 temporal dynamic perimeter-area relations can introduce significant
 discrepancies and that these discrepancies can be reduced if evaluations
 using static data are performed separately for each wetlandscape. The
 study concludes that current models that use implicit area-perimeter
 relations based on static wetland representations should be used with
 caution and that incorporating perimeter-area relations from temporally
 dynamic data can improve wetland function estimates.
description: Please see the README document ("README.md") and the
 accompanying published article: Park, J., Kumar, M., Jones, C.N.
 2023. Modeling wetland functions: Is space-to-time substitution of
 perimeter-area relation appropriate? Limnology and Oceanography Letters.
 Under review.
DOI: 10.5061/dryad.3n5tb2rnb
title: Data from: Social disappointment and partner presence affect long-tailed macaque refusal behaviour in an "inequity aversion" experiment

description: Protest in response to unequal reward distribution is thought to have
 played a central role in the evolution of human cooperation. Some animals
 refuse food and become demotivated when rewarded more poorly than a
 conspecific, and this has been taken as evidence that non-human animals,
 like humans, protest in the face of inequity. An alternative explanation -
 social disappointment – shifts the cause of this discontent away from the
 unequal reward, to the human experimenter who could – but elects not to –
 treat the subject well. This study investigates whether social
 disappointment could explain frustration behaviour in long-tailed
 macaques, Macaca fascicularis. We tested 12 monkeys in a novel `inequity
 aversion’ paradigm. Subjects had to pull a lever and were rewarded with
 low-value food; in half of the trials, a partner worked alongside the
 subjects receiving high-value food. Rewards were distributed either by a
 human or a machine. In line with the social disappointment hypothesis,
 monkeys rewarded by the human refused food more often than monkeys
 rewarded by the machine. Our study extends previous findings in
 chimpanzees and suggests that social disappointment plus social
 facilitation or food competition effects drive food refusal patterns.
DOI: 10.15468/dl.8edqj3
title: Occurrence Download

description: A dataset containing 67395 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Parkinsonia aculeata"
 ]
}

 The dataset includes 67395 records from 547 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002852-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.