cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8931zcrrt
title: Thallium(I) exposure perturbs the gut microbiota and metabolic profile as well as the regional immune function of C57BL/6 J mice

description: Intestinal microbes regulate the development of diseases induced by
 environmental exposure. Thallium (Tl) is a highly toxic heavy metal, and
 its toxicity is rarely discussed in relation to gut microbes. Herein, we
 showed that Tl(I) exposure (10 ppm for two weeks) affected the alpha
 diversity of bacteria in the ileum, colon, and feces, but had little
 effect on the beta diversity of bacteria through 16S rRNA sequencing.
 LEfSe analysis revealed that Tl(I) exposure changed the abundance of
 intestinal microbiota along the digestive tract. Cecum metabolomic
 detection and analysis showed that Tl(I) exposure altered the abundance
 and composition of metabolites. In addition, the Kyoto Encyclopedia of
 Genes and Genomes (KEGG) enrichment analysis revealed that Tl(I) exposure
 impaired amino acid, lipid, purine metabolism, and G protein-coupled
 receptor signalling pathways. A consistency test revealed a strong
 correlation, and a Pearson’s correlation analysis showed an extensive
 interaction, between microorganisms and metabolites. Analysis of the
 intestinal immunity revealed that Tl(I) exposure suppressed the immune
 responses, which also had regional differences. These results identify the
 perturbation of the intestinal microenvironment by Tl exposure and provide
 a new explanation for Tl toxicity.
description: Mice in the experimental group
 were exposed to 10 ppm TINO<sub>3 </sub>for two weeks. Cecum
 content (50 mg) metabolite extract was used to perform metabolomics
 analysis using UHPLC-QTOF-MS/MS (Waters, USA). Waters Acquity UPLC HSS T3
 (1.8 µm, 2.1 mm × 100 mm) was used to separate the components of the
 metabolite extract. One microliter of metabolites solution was injected
 and eluted with a mobile phase comprising solvent A (0.1% formic acid) and
 B (0.1% formic acid-acetonitrile) at a flow rate of 400 μL/min according
 to the following process: solvent B was maintained at 2% for 0.25 min;
 subsequently, the concentration of solvent B was linearly increased from
 2% to 98% over 10 min and maintained for 3 min; finally, the concentration
 of solvent B was decreased to 2% within 0.1 min, and maintained for 1.9
 min. The mass spectrometry conditions were as follows: capillary voltage,
 2000 V (positive ion mode) or -1500V (negative ion mode); cone voltage, 30
 V; ion source temperature, 150 °C; desolventizing gas temperature, 500 °C;
 cone gas flow rate, 50 L/h; and desolventizing gas flow rate, 800 L/h.
 Full scans were acquired in a scan range of 50–1200 m/z with a scan
 frequency of 0.2 s, and data were collected via MassLynx (v. 4.2, Waters)
 and processed by Progenesis QI software such as peak extraction and peak
 alignment, and identification based on the METLIN database. At the same
 time, theoretical fragment identification was performed. The mass
 deviations were all within 100 ppm.
DOI: 10.15468/dl.4fc6wm
title: Occurrence Download

description: A dataset containing 978 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thecamoeba",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 978 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002980-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ksn02v759
title: Predicted alteration of vertebrate communities in response to climate-induced elevational shifts

description: Aim Climate change is driving species to migrate to novel areas as current
 environments become unsuitable. As a result, species distributions have
 shifted uphill in montane ecosystems globally, leading to projections of
 severe impacts on upland specialist species. Heterogenous dispersal rate
 among shifting species could result in complex changes to community
 assemblages. For example, interspecific differences in dispersal ability
 could lead to the disruption, or creation, of species interactions and
 processes within communities, likely amplifying the impact of climate
 change on ecosystems. Here, we provide a comprehensive assessment of the
 impacts of climate change on communities and ecosystems by developing a
 novel spatially explicit approach focussing on changes in local
 populations. Location The Australian Wet Tropics. Method We used a
 spatially explicit approach to simulate the elevational shift of 7,613
 community assemblages (defined at the patch level) along the elevational
 gradient, using empirical information about the distribution of 202
 vertebrate species. We analysed changes in community structures and
 species co-occurrence derived from the elevational shift as a proxy for
 potential changes in species interactions. Results Our results showed a
 consistent pattern of increasing temporal β-dissimilarity between
 community assemblages along the elevational gradient resulting from local
 species extinctions. The local extinction rate was especially remarkable
 at high elevations, suggesting potential mass local extinctions of upland
 species unable to shift to the isolated mountaintops. Furthermore, the
 increasing local extinction rate with elevation resulted in a marked
 decline in species co-occurrence towards mountaintops. Main conclusions
 Our study highlights the escalating impact of climate change on community
 assemblages in response to climate-induced elevational shifts in
 species' ranges, providing a classic example of the "escalator
 to extinction". Future predictions of the impacts of climate change
 on ecosystems will benefit from improvements in understanding species
 interactions and species potential to adapt to a changing environment.
description: Data collection and processing can be found at https://doi.org/10.1890/09-1069.1
DOI: 10.25338/b8m62w
title: Directed movement changes coexistence outcomes in heterogeneous environments

description: Understanding mechanisms of coexistence is a central topic in ecology.
 Mathematical analysis of models of competition between two identical
 species moving at different rates of symmetric diffusion in heterogeneous
 environments show that the slower mover excludes the faster one. The
 models have not been tested empirically and lack inclusions of a component
 of directed movement toward favorable areas. To address these gaps, we
 extended previous theory by explicitly including exploitable resource
 dynamics and directed movement. We tested the mathematical results
 experimentally using laboratory populations of the nematode worm,
 Caenorhabditis elegans. Our results not only support the previous theory
 that the species diffusing at a slower rate prevails in heterogeneous
 environments but also reveal that moderate levels of a directed movement
 component on top of the diffusive movement allow species to coexist. Our
 results broaden the theory of species coexistence in heterogeneous space
 and provide empirical confirmation of the mathematical predictions.
description: The experimental data were collected in the laboratory system of
 the free-living soil nematode worm, <i>Caenorhabditis
 elegans.</i> The difference in final proportion
 of the slow mover was assessed using ANOVA across initial proportions in
 both heterogeneous and homogeneous environments. Assumptions of equal
 variance and normality were examined by the residual plots along the
 fitted values and the normal quantile plot, respectively.
DOI: 10.5061/dryad.b5mkkwhf4
title: Is species richness mediated by functional and genetic divergence? A global analysis in birds

description: Unravelling why species richness varies shows such dramatic spatial
 variation is an ongoing challenge. Common to many theories is that
 increasing species richness requires a compensatory trade-off on an axis
 of species’ ecology. Spatial variation in species richness may also affect
 genetic diversity if large numbers of coexisting, related species result
 in smaller population sizes. Here, we test whether increasing species
 richness results in differential occupation of morphospace by the
 constituent species, or decreases species’ genetic diversity. We test for
 two potential mechanisms of morphological accommodation: denser packing in
 ecomorphological space, and expansion of the space. We then test whether
 species differ in their nucleotide diversity depending on allopatry or
 sympatry with relatives, indicative of potential genetic consequences of
 coexistence that would reduce genetic diversity in sympatry. We ask these
 questions in a spatially explicit framework, using a global database of
 avian functional trait measurements in combination with &gt;120,000
 sequences downloaded from GenBank. We find that higher species richness
 within families is not systematically correlated with either packing in
 morphological space or overdispersion but, at the Class level, we find a
 general positive relationship between packing and species richness, but
 that packing is comparatively greater in tropical points relative to their
 species richness. We find limited evidence that geographical co-occurrence
 with closely related species or tropical distributions decreases
 nucleotide diversity of nuclear genes; however, this requires further
 analysis. Our results suggest that avian families can accumulate species
 regionally with minimal tradeoffs or cost, implying that external biotic
 factors do not limit species richness.
DOI: 10.5061/dryad.g79cnp5qv
title: Genetic and species-level biodiversity patterns are linked by demography and ecological opportunity

description: The processes that give rise to species richness gradients are not well
 understood, but may be linked to resource-based limits on the number of
 species a region can support. Ecological limits placed on regional species
 richness should also affect population demography, suggesting that these
 processes could also generate genetic diversity gradients. If true, we
 might better understand how broad-scale biodiversity patterns are formed
 by identifying the common causes of genetic diversity and species
 richness. We develop a hypothetical framework based on the consequences of
 regional variation in ecological limits set by resource availability and
 heterogeneity to simultaneously explain spatial patterns of species
 richness and neutral genetic diversity. Repurposing raw genotypic data
 spanning 38 mammal species sampled across 801 sites in North America, we
 show that estimates of genome-wide genetic diversity and species richness
 share spatial structure. Notably, species richness hotspots tend to harbor
 lower levels of within-species genetic variation. A structural equation
 model encompassing eco-evolutionary processes related to resource
 availability, habitat heterogeneity, and contemporary human disturbance
 supports the spatial patterns we detect. These results suggest broad-scale
 patterns of species richness and genetic diversity could both partly be
 caused by intraspecific demographic and evolutionary processes acting
 simultaneously across species.
description: Associated code is available on github:
 https://github.com/chloewsch/genetic_species_biodiversity
DOI: 10.5061/dryad.73n5tb2z0
title: Postcranial osteometric data from human and 27 North American faunal species

description: Although nonhuman remains constitute a significant portion of forensic
 anthropological casework, the potential use of quantitative methods to
 assess human origins and classify species from gross bone morphology has
 not been thoroughly investigated. This study aimed to test the utility of
 a few basic long bone measurements to distinguish human from nonhuman
 remains and classify species. More than 50,000 measurements were compiled
 from humans and 27 nonhuman species (mostly North American). Decision
 trees developed from the long bone data differentiate human and nonhuman
 remains with more than 90% accuracy (&gt;98% accuracy for the human
 sample), even if all long bones are pooled. Stepwise discriminant function
 results were slightly lower (&gt;87.4% overall accuracy). The
 quantitative models can be used to support visual identifications or
 preliminarily assess forensic significance at scenes. For species
 classification, bone-specific discriminant functions returned accuracies
 between 77.7% and 89.1%, but classification results varied highly across
 species. A web tool, OsteoID, was developed from the study data where
 users can input basic measurements, and photographs of potential
 bones/species are returned for visual identification. Additional resources
 (e.g., 3D scans) are provided, creating an important resource for forensic
 anthropologists and others to assist in skeletal species identification
 and comparative osteology training.
description: Osteometric data (maximum lengths, proximal and distal maximum
 widths (medio-lateral) and depths (antero-posterio) and mishaft maximum
 and minimum diameters) were collected from human and nonhuman bones
 curated in museums and institutions using digital calipers. Additional
 data were compiled from previously published studies and publicly
 available skeletal databases. Citations are provided for data collected
 from these literature/database sources. The data uploaded here contains
 the raw measurements.
description: Missing values denoted by blank cells or #NULL!. READ ME file and
 "Variables Definitions" sheet of excel file provides column
 explanations and measurement definitions. Additional resources can be
 found at the OsteoID website (www.boneidentification.com). Please cite
 this dataset and either OsteoID, the associated publication (In Review
 currently), and/or the NIJ project final report
 (NIJ 2018-DU-BX-0229).
DOI: 10.5061/dryad.7h44j0zvb
title: Effects of temperature on seed dormancy and germination of the coastal dune plant Viola grayi: Germination phenology and responses to winter warming

description: PREMISE: In temperate sand dunes, rising air temperature owing to climate
 change could not only further elevate surface soil temperatures during
 summers but also drastically change the range of soil temperatures in
 other seasons. Winter warming may shift the timing of seed germination of
 dune species that require cold stratification for dormancy release.
 METHODS: We assessed the effects of temperature on dormancy and
 germination of Viola grayi seeds and evaluated whether winter warming
 could affect its germination phenology by conducting germination
 experiments and analyzing soil temperature data in cold and warm winters.
 RESULTS: Viola grayi seeds were dormant when dispersed in spring.
 One-month moist-chilling treatment (4°C) effectively released dormancy,
 while short, intermittent lower temperatures (alternating 20/5°C) did not.
 Continuous higher temperatures induced secondary dormancy in non-dormant
 seeds. During a cold, snowy winter, the surface soil temperatures of the
 sand dune remained at 0–2°C for approximately one month owing to the
 accumulated snow, while the period of such stable low soil temperatures
 was much shorter during a warm, less snowy winter, and the highest soil
 temperature class reached 20–25°C. These results suggest that dispersed
 seeds germinate in the following spring after winter chilling, but they
 may remain dormant after warm winters. CONCLUSIONS: With winter warming,
 prolonged seed dormancy and associated germination delay could occur in V.
 grayi seeds. Assessing the minimum requirements for dormancy release and
 the potential to form persistent soil seed banks is important for judging
 the necessity and urgency of conservation efforts for temperate dune
 species.
DOI: 10.5061/dryad.v15dv41wv
title: CircRNAs sequencing database of Gastric carcinoma cells (SGC-7901) and 5-fluorouracil-resistant cells (SGC-7901-5-fu)

description: The circRNAs of two different gastric cancer cell lines were sequenced in
 this database. The sequencing results were compared and annotated with the
 database as analysis background data, and the screening conditions for
 differential expression of circRNA in the two cells line were defined as
 fold changes (FC) ≥ 2 and P &lt;0.05.
DOI: 10.5061/dryad.rr4xgxd99
title: Data for: Warming temperatures limit the maximum body length of teleost fishes across a latitudinal gradient in Norwegian waters

description: As the majority of marine organisms are water-breathing ectotherms,
 temperature and dissolved oxygen are key environmental variables that
 influence their fitness and geographic distribution. In line with the
 gill-oxygen limitation theory (GOLT), the maximum asymptotic body size of
 water-breathing ectotherms is limited by an insufficient amount of oxygen
 that is supplied to meet metabolic demand once a threshold of gill surface
 area to body weight ratio is surpassed. Here we employed generalised
 additive models (GAMs) to investigate the relative influence of
 temperature, regional variation in dissolved oxygen, and geographic
 location (that encompasses multiple latent variables) on the maximum body
 length of ten teleost fish species, as well to predict their maximum body
 length, across a large temperature, depth and latitudinal gradient
 throughout Norwegian waters. As dissolved oxygen levels were near
 saturation across the study area, we conclude that the predicted maximum
 lengths of our study species were not limited by oxygen availability.
 Conversely, the majority of study species display a clear relationship in
 that their predicted maximum length is either decreasing, asymptotic or
 parabolic across their observed temperature range. We also observed
 smaller maximum body lengths for multiple species within the coldest
 extent of their temperature range, which may be explained by increases in
 basal metabolism via cold denaturation. Overall, our results suggest that
 the maximum lengths of our study species are influenced by temperature,
 thus supporting the tenants of the GOLT.
description: See manuscript for methods. The marine
 organism length data employed in analyses were derived from the Norwegian
 Institute of Marine Research’s long-term bottom trawl surveys between 1990
 and 2020 (Djupevåg 2020). A pre-filtered version of this dataset can be
 found in the 'length_location' zip file.
 Djupevåg O (2020) IMR bottom trawl data 1980-2020.
 https://doi.org/10.21335/NMDC-328259372 The ocean
 temperature and dissolved oxygen concentration data used in analyses were
 extracted from the online database Bio-Oracle. Assis J,
 Tyberghein L, Bosch S, et al (2018) Bio-ORACLE v2.0: Extending marine data
 layers for bioclimatic modelling. Glob Ecol Biogeogr 27:277–284.
 https://doi.org/https://doi.org/10.1111/geb.12693
DOI: 10.34740/kaggle/dsv/14647687
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.5mkkwh773
title: Drought-induced reductions in plant defenses

description: Extrafloral nectaries (EFNs) are anti-herbivory defense-related glands. We
 measured morphological and anatomical EFN traits in Pityrocarpa
 moniliformis trees along a rainfall gradient in Caatinga dry forest. We
 observed a reduction in structural EFN traits as rainfall decreased. We
 conclude that this reduction is a cost-saving strategy, probably mediated
 by ants.
DOI: 10.5061/dryad.tht76hf0w
title: Larval and metamorph traits of cane toads

description: As an invasive organism spreads into a novel environment, it may encounter
 strong selective pressures to adapt to abiotic challenges. We examined the
 effect of water temperature during larval life on rates of survival and
 growth of the early life-history stages of cane toads (Rhinella marina)
 from two geographic regions (tropical vs. temperate) in the species’
 invaded range in eastern Australia. If local adaptation at the southern
 (cool-climate) invasion front has extended the cold-tolerance of early
 life-stages, we would expect to see higher viability of
 southern-population toads under cooler conditions. Our comparisons
 revealed no such divergence: the effects of water temperature on rates of
 larval survival and growth, time to metamorphosis, size at metamorphosis
 and locomotor performance of metamorphs were similar in both sets of
 populations. In two cases where tropical and temperate-zone populations
 diverged in responses to temperature, the tropical animals performed
 better at low to medium temperatures than did conspecifics from cooler
 regions. Adaptation to low temperatures in the south might be constrained
 by behavioural shifts (e.g., in reproductive seasonality, spawning-site
 selection) that allow toads to breed in warmer water even in cool
 climates, by gene flow from warmer-climate populations, or by phylogenetic
 conservatism in these traits.
description: Adult toads were collected at sites in tropical and
 temperate-zone eastern Australia. The toads were bred in captivity and
 their progeny raised at a series of controlled temperatures so that we
 could evaluate effects of larval temperatures on life-history
 traits.
DOI: 10.5061/dryad.zs7h44jb4
title: Decay by ectomycorrhizal fungi couples soil organic matter to nitrogen availability

description: Interactions between soil nitrogen (N) availability, fungal community
 composition, and soil organic matter (SOM) regulate soil carbon (C)
 dynamics in many forest ecosystems, but context dependency in these
 relationships has precluded general predictive theory. We found that
 ectomycorrhizal (ECM) fungi with peroxidases decreased with increasing
 inorganic N availability across a natural inorganic N gradient in northern
 temperate forests, whereas ligninolytic fungal saprotrophs exhibited no
 response. Lignin-derived SOM and soil C were negatively correlated with
 ECM fungi with peroxidases and were positively correlated with inorganic N
 availability, suggesting decay of lignin-derived SOM by these ECM fungi
 reduced soil C storage. The correlations we observed link SOM decay in
 temperate forests to tradeoffs in tree N nutrition and ECM composition,
 and we propose SOM varies along a single continuum across temperate and
 boreal ecosystems depending upon how tree allocation to functionally
 distinct ECM taxa and environmental stress covary with soil N
 availability.