cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zgmsbccf1
title: A fast, precise, in-vivo method for micron-level 3D models of corals using dental scanners

description: 1.  Several sampling and measurement strategies have been
 developed to assess biological forms in three dimensions (3D), including
 corals. However, the effectiveness (in speed and precision) of current 3D
 methods in scanning and model construction are challenging at small scales
 (μm – mm). 2.  In this paper, a practical 3D scanning and model
 construction tool using an intra-oral dental scanner was assessed to
 measure the surface area and volume of coral juveniles across multiple
 species. Intra-oral scanners using confocal imaging are fast, precise to
 the μm scale, and safe to use with live tissue, thereby eliminating the
 need to harm or kill the animals. The trial was conducted at the National
 Sea Simulator at the Australian Institute of Marine Science. 3.
  High-quality 3D scans of individual coral juveniles were
 successfully generated and integrated automatically into high-resolution
 (μm) mesh from point clouds. The attained average scanning efficiency was
 &lt; 2 min./individual, without a significant difference in
 speed given coral complexity or between live colonies or dead coral
 skeleton. 4.  Overall, this fast and precise system could become
 a promising tool for marine environmental surveys and restoration
 initiatives. This tool also removes the need to sacrifice animals for
 measurement analysis, thereby increasing conservation and animal welfare.
DOI: 10.5061/dryad.tb2rbp039
title: Data and code for: Sex-specific trait architecture in a sexually size dimorphic spider

description: Sexual dimorphism, or sex-specific trait expression, may evolve when
 selection favours different optima for the same trait between sexes, i.e.,
 under antagonistic selection. Intra-locus sexual conflict exists when the
 sexually dimorphic trait under antagonistic selection is based on genes
 shared between sexes. A common assumption is that the presence of
 sexual-size dimorphism (SSD) indicates that sexual conflict has been, at
 least partly, resolved via decoupling of the trait architecture between
 sexes. However, whether and how decoupling of the trait architecture
 between sexes has been realised often remains unknown. We tested for
 differences in architecture of adult body size between sexes in a species
 with extreme SSD, the African hermit spider (Nephilingis cruentata), where
 adult female body size greatly exceeds that of males. Specifically, we
 estimated the sex-specific importance of genetic and maternal effects on
 adult body size among individuals that we laboratory-reared for up to
 eight generations. Quantitative genetic model estimates indicated that
 size variation in females is to a larger extent explained by direct
 genetic effects than by maternal effects, but in males to a larger extent
 by maternal than by genetic effects. We conclude that this sex-specific
 body-size architecture enables body-size evolution to proceed much more
 independently than under a common architecture to both sexes.
description: Data from laboratory-reared spiders, and R analysis code as
 described in the methods part of the manuscript.
description: Text editor programmes, MS Excel or Apache OpenOffice Calc open
 data and pedigree (.csv) files, and RStudio opens the analysis code (.Rmd)
 file.
DOI: 10.5281/zenodo.15351464
title: Online high-resolution real-time monitoring techniques for anions in river water

description: High-resolution real-time monitoringwas employed and evaluated using three real-time monitoring techniques for anions at the river Rhine in Koblenz, Germany. These are a sensor for nitrate in situ and ex situ, a colorimetric device for nitrate and nitrite, and an online ion chromatography (IC) for fluoride, bromide, chloride, nitrate, nitrite, phosphate, and sulfate. 

The original data are presented in this data repository. 

Data presentation and evaluation are presented in the paper "Online high-resolution real-time monitoring techniques for anions in river water" by the authors above. The paper is published in the journal Environmental Monitoring and Assessment.
DOI: 10.5281/zenodo.15736566
title: Online high-resolution real-time monitoring techniques for anions in river water

description: High-resolution real-time monitoringwas employed and evaluated using three real-time monitoring techniques for anions at the river Rhine in Koblenz, Germany. These are a sensor for nitrate in situ and ex situ, a colorimetric device for nitrate and nitrite, and an online ion chromatography (IC) for fluoride, bromide, chloride, nitrate, nitrite, phosphate, and sulfate. 

The original data are presented in this data repository. 

Data presentation and evaluation are presented in the paper "Online high-resolution real-time monitoring techniques for anions in river water" by the authors above. The paper is published in the journal Environmental Monitoring and Assessment.
DOI: 10.5061/dryad.np5hqbzwp
title: Data for: (Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions

description: Elucidating processes and mechanisms involved in rapid local adaptation to
 varied environments is a poorly understood but crucial component in
 management of invasive species. Recent studies have proposed that genetic
 and epigenetic variation could both contribute to ecological adaptation,
 yet it remains unclear on the interplay between these two components
 underpinning rapid adaptation in wild animal populations. To assess their
 respective contributions to local adaptation, we explored epigenomic and
 genomic responses to environmental heterogeneity in eight recently
 colonized ascidian (Ciona intestinalis) populations at a relatively fine
 geographical scale. Based on MethylRADseq data, we detected strong
 patterns of local environment-driven DNA methylation divergence among
 populations, significant epigenetic isolation by environment (IBE), and a
 large number of local environment-associated epigenetic loci. Meanwhile,
 multiple genetic analyses based on single nucleotide polymorphisms (SNPs)
 showed genomic footprints of divergent selection. In addition, for five
 genetically similar populations, we detected significant methylation
 divergence and local environment-driven methylation patterns, indicating
 strong effects of local environments on epigenetic variation. From a
 functional perspective, a majority of functional genes, gene ontology (GO)
 terms, and biological pathways were largely specific to one of these two
 types of variation, suggesting partial independence between epigenetic and
 genetic adaptation. The methylation quantitative trait loci (mQTL)
 analysis showed that the genetic variation explained only 18.67% of
 methylation variation, further confirming the autonomous relationship
 between these two types of variation. Altogether, we highlight the
 complementary interplay of genetic and epigenetic variation involved in
 local adaptation, which may jointly promote populations’ rapid adaptive
 capacity and successful invasions in different environments. The findings
 here provide valuable insights into interactions between invaders and
 local environments to allow invasive species to rapidly spread, thus
 contributing to better prediction of invasion success and development of
 management strategies.
DOI: 10.5061/dryad.4j0zpc8fg
title: The impact of species phylogenetic relatedness on invasion varies distinctly along resource versus nonresource environmental gradients

description: Understanding why certain plant communities are vulnerable to alien
 invasive species is essential to predicting and controlling invasion in a
 changing environment. Darwin’s naturalization hypothesis suggests that
 non-native species should be more successful in communities where their
 close relatives are absent. Empirical tests of this hypothesis, however,
 have produced mixed results. Using plot-level data from natural forests
 along elevational transects covering strong environmental gradients, we
 examined whether the invasion of the globally invasive species Ageratina
 adenophora can be explained by environmental filtering and/or competition
 from closely related species linked to environmental gradients. Abundant
 precipitation, warm temperatures, open canopies, and postfire environments
 facilitated A. adenophora invasion, whereas resident taxonomic richness
 suppressed its invasion. Importantly, we found that invader-resident
 relatedness had a strong negative effect on invader cover under resource
 scarcity conditions (e.g., low water availability), but not under
 nonresource environmental stress conditions (e.g., low temperature). Our
 findings help reconcile the varied applicability of Darwin’s
 naturalization hypothesis to biological invasions in a changing world.
DOI: 10.15159/phytop.163
title: Kaarmise

description: Phytoplankton biomass, diversity and abundance in samples collected from Lake Kaarmise during the period 1956 and 1958.
DOI: 10.15468/dl.zwwhmm
title: Occurrence Download

description: A dataset containing 305 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Mongolia)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ephedra monosperma"
 ]
}

 The dataset includes 305 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003162-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2ngf1vhr7
title: Raw data from: Inter- and intra-specific variation in mycotoxin tolerance: A study of four Drosophila species

description: Many mycophagous Drosophila species have adapted to tolerate high
 concentrations of mycotoxins, an ability not reported in any other
 eukaryotes. Although an association between mycophagy and mycotoxin
 tolerance has been established in many Drosophila species, the genetic
 mechanisms of the tolerance are unknown. This study presents the inter-
 and intraspecific variation in the mycotoxin tolerance trait. We studied
 the mycotoxin tolerance in four Drosophila species from four separate
 clades within the immigrans-tripunctata radiation from two distinct
 locations. The effect of mycotoxin treatment on 20 isofemale lines per
 species was studied using seven gross phenotypes: survival to pupation,
 survival to eclosion, development time to pupation and eclosion, thorax
 length, fecundity, and longevity. We observed interspecific variation
 among four species, with D. falleni being the most tolerant, followed by
 D. recens, D. neotestacea, and D. tripunctata, in that order. The results
 also revealed geographical variation and intraspecific genetic variation
 in mycotoxin tolerance. This report provides the foundation for further
 delineating the genetic mechanisms of the mycotoxin tolerance trait.
description: R version 3.6.1 (https://www.r-project.org/foundation/) Rstudio version 2021.09.2+382 (https://www.rstudio.com/).  R package 'lme4'  R package 'ggplot2'
DOI: 10.5061/dryad.0zpc86711
title: Agroforestry carbon stocks and greenhouse gas emission rates in central Alberta, Canada

description: Agroforestry systems (AFS) contribute to carbon (C) sequestration and
 reduction in greenhouse gas emissions from agricultural lands. However,
 previously understudied differences among AFS may underestimate their
 climate change mitigation potential. In this 3-year field study, we
 assessed various C stocks and greenhouse gas emissions across two common
 AFS (hedgerows and shelterbelts) and their component land uses: perennial
 vegetated areas with and without trees (woodland and grassland,
 respectively), newly planted saplings in grassland, and adjacent annual
 cropland in central Alberta, Canada. Between 2018 and 2020
 (~April–October), nitrous oxide emissions were 89% lower under perennial
 vegetation relative to the cropland (0.02 and 0.18 g N m−2 year−1,
 respectively). In 2020, heterotrophic respiration in the woodland was 53%
 lower in shelterbelts relative to hedgerows (279 and 600 g C m−2 year−1,
 respectively). Within the woodland, deadwood C stock was particularly
 important in hedgerows (35 Mg C ha−1 or 7% of ecosystem C) relative to
 shelterbelts (2 Mg C ha−1 or &lt; 1% of ecosystem C), and likely
 affected C cycling differences between the woodland types by enhancing
 soil labile C and microbial biomass in hedgerows. Deadwood C stock was
 positively correlated with annual heterotrophic respiration and total (to
 ~100 cm depth) soil organic C, water-soluble organic C, and microbial
 biomass C. Total ecosystem C was 1.90–2.55 times greater within the
 woodland than all other land uses, with 176, 234, 237, and 449 Mg C ha−1
 found in the cropland, grassland, planted saplings treatment, and
 woodland, respectively. Shelterbelt and hedgerow woodlands contained 2.09
 and 3.03 times more C, respectively, than adjacent cropland. Our findings
 emphasize the importance of AFS for fostering C sequestration and reducing
 greenhouse gas emissions and, in particular, retaining hedgerows (legacy
 woodland) and their associated deadwood across temperate agroecosystems to
 help mitigate climate change.
description: <strong>The
 current dataset replaces a previous version and has been modified for
 clarity and carefully reviewed for
 accuracy.</strong>
DOI: 10.5061/dryad.prr4xgxpn
title: Additive genetic variation, but not temperature, influences warning signal expression in Amata nigriceps moths (Lepidoptera: Arctiinae)

description: Many aposematic species show variation in their colour patterns even
 though selection by predators is expected to stabilise warning signals
 towards a common phenotype. Warning signal variability can be explained by
 trade-offs with other functions of colouration, such as thermoregulation,
 that may constrain warning signal expression by favouring darker
 individuals. Here, we investigated the effect of temperature on warning
 signal expression in aposematic Amata nigriceps moths that vary in their
 black and orange wing patterns. We sampled moths from two flight seasons
 that differed in the environmental temperatures and also reared different
 families under controlled conditions at three different temperatures.
 Against our prediction that lower developmental temperatures would reduce
 the warning signal size of the adult moths, we found no effect of
 temperature on warning signal expression in either wild or
 laboratory-reared moths. Instead, we found sex- and population-level
 differences in wing patterns. Our rearing experiment indicated that ~70%
 of the variability in the trait is genetic but understanding what
 signalling and non-signalling functions of wing colouration maintain the
 genetic variation requires further work. Our results emphasise the
 importance of considering both genetic and plastic components of warning
 signal expression when studying intraspecific variation in aposematic
 species.
description: We collected data from a) wild Amata nigriceps moths that were
 captured from Macquarie Park (Sydney, Australia) during years 2017-2020,
 and from b) Amata nigriceps moths that were reared in the laboratory in
 three different temperatures (20C, 24C and 28C) during summer 2020-2021.
 We photographed the moths and quantified the proportion of orange in the
 wings using <em>pavo </em>package in R to investigate
 within-species variation in warning signal expression. We also measured
 wing length from the photographs using ImageJ. We recorded collection
 site, collection date and sex of the wild-caught individuals. In the
 rearing experiment, we also recorded larval survival, length of the larval
 period, pupal weight, time from pupa to eclosion and eclosion
 success.
description: The first datasheet contains data from wild-caught individuals
 collected between years 2017 and 2020, which was used to analyse seasonal
 differences in warning signal expression in the wild population. The
 second datasheet contains individual data from the rearing experiment,
 which was used to analyse the effect of temperature on life-history traits
 and warning signal expression. The third datasheet contains records of
 larval survival in the rearing experiment (to analyse the effect of
 temperature on survival), and the fourth datasheet contains data to create
 a figure of larval survival in the rearing experiment (Fig. 3 in the
 published article). In addition, we have provided an R script for the
 analyses.
DOI: 10.5061/dryad.jsxksn0cr
title: Riparian buffers provide refugia during secondary forest succession

description: Aim Secondary forests regenerating from human disturbance are increasingly
 becoming a predominant forest type in many regions, and they play a
 significant role in forest community dynamics. Understanding the factors
 that underlie the variation in species responses during secondary
 succession is important for understanding community assembly and
 biodiversity monitoring and management. Because species vary in ecology
 and behavior, responses to ecosystem change should vary among species.
 Here, we show that habitat type (riparian, upland), phylogeny, and species
 traits mediate anuran and lizard probability of occurrence and species
 richness in pasture and secondary forest. Location Sarapiquí and Osa
 Peninsula, Costa Rica. Methods We used phylogenetic occupancy models to
 estimate assemblage-level and species-specific responses to forest
 succession in 30 chronosequence sites that include pasture, secondary
 forest regenerating from pasture, and mature forest sites. Results For the
 majority of species, we found increasing probability of occurrence in
 upland habitats as forest regenerated from pasture to secondary forest and
 similar probability of occurrence in riparian habitats across pasture,
 secondary forest, and mature forest sites. Species’ responses to forest
 stage were phylogenetically correlated, and the trend was especially
 strong for anuran response to pasture sites. Anurans with lotic larval
 habitat had a positive occupancy response to pasture upland habitat and
 anurans with lentic larval habitat had a variable response to different
 forest stages compared to mature forest.
DOI: 10.5061/dryad.6djh9w13w
title: Population models used in: Method to assess potential magnitude of terrestrial European avian population reductions from ingestion of lead ammunition

description: Current estimates of terrestrial bird losses across Europe from ingestion
 of lead ammunition are based on uncertain or generic assumptions. A method
 is needed to develop defensible European-specific estimates compatible
 with available data that does not require long-term field studies. We
 propose a 2-step method using carcass data and population models. The
 method estimates percentage of deaths diagnosed as directly caused by lead
 poisoning as a lower bound and, as an upper bound, the percentage of
 possible deaths from sublethal lead poisoning that weakens birds, making
 them susceptible to death by other causes. We use these estimates to
 modify known population-level annual mortality. Our method also allows for
 potential reductions in reproduction from lead shot ingestion because
 reductions in survival and reproduction are entered into population models
 of species with life histories representative of the most groups of
 susceptible species. The models estimate the sustainability and potential
 population decreases from lead poisoning in Europe. Using the best
 available data, we demonstrate the method on two taxonomic groups of
 birds: gallinaceous birds and diurnal raptors. The direction of the
 population trends affects the estimate, and we incorporated such trends
 into the method. Our midpoint estimates of the reduction in population
 size of the European gallinaceous bird (&lt; 2%) group and raptor
 group  (2.9 – 7.7%) depend on the species life history, maximum
 growth rate,  population trend, and if reproduction is assumed to
 be reduced. Our estimates can be refined as more information becomes
 available in countries with data gaps. We advocate use of this method to
 improve upon or supplement approaches currently being used. As we
 demonstrate, the method also can be applied to individual species of
 concern if enough data across countries are available.
description: These population models were used to evaluate effect of lead
 ammunition on terrestrial avian populations in Europe. The models were
 calibrated on a red kite population in Wales, a common buzzard population
 in Germany, a bearded vulture population in the French/Spanish Pyrenees,
 and grey partridge in continental Europe. They are used to evaluate
 effects of lead ammunition ingestion using exposure to the four individual
 species and exposure to all susceptible raptor species (using 3 raptor
 models) or gallinaceous species (using partridge model) that have similar
 population trends (stable or decreasing, increasing). Bearded vulture
 model represents large-bodied raptors such as eagles and vultures, other
 raptor models are for small-bodied raptors.These models are constructed in
 R programming language (R core team). The data used in them are in the
 manuscript and supplementary files.
description: R (R core team 2021)
DOI: 10.5061/dryad.mkkwh7132
title: Data underlying the publication: Callisto's atmosphere: First evidence for H2 and constraints on H2O

description: We explore the parameter space for the contribution to Callisto's H
 corona observed by the Hubble Space Telescope (Roth et al. 2017a) from
 sublimated H2O and radiolytically produced H2 using the Direct Simulation
 Monte Carlo (DSMC) method. The spatial morphology of this corona produced
 via photo- and magnetospheric electron impact-induced dissociation is
 described by tracking the motion of and simulating collisions between the
 hot H atoms and thermal molecules including a near-surface O2 component.
 Our results indicate that sublimated H2O produced from the surface ice,
 whether assumed to be intimately mixed with or distinctly segregated from
 the dark non-ice or ice-poor regolith, cannot explain the observed
 structure of the H corona. On the other hand, a global H2 component can
 reproduce the observation, and is also consistent with enhanced electron
 densities observed at high altitudes by Galileo's plasma-wave
 instrument (Gurnett et al. 1997, 2000), providing the first evidence of H2
 in Callisto's atmosphere. The range of H2 surface densities explored,
 under a variety of conditions, that are consistent with these observations
 is ∼(0.4-1)×108 cm-3. The simulated H2 escape rates and estimated
 lifetimes suggest that Callisto has a neutral H2 torus. We also place a
 rough upper limit on the peak H2O number density (&lt;∼108 cm-3),
 column density (&lt;∼1015 cm-2), and sublimation flux (&lt;∼1012
 cm-2 s-1), all of which are 1-2 orders of magnitude less than that assumed
 in previous models. Finally, we discuss the implications of these results,
 as well as how they compare to Europa and Ganymede.
description: The figures were produced using Python, but any software that is
 able to read .txt files should suffice.