cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0zpc866v3
title: Data from: Vertical biogeography and realized niche traits of living coccolithophore community in the eastern Indian Ocean

description: Our investigations provided a broad view of annual-scale living
 coccolithophores in the quite under-sampled eastern Indian Ocean (EIO).
 The present study determined 7-year (2011-2018) living coccolithophore
 communities, as a major component in oligotrophic ecosystem, using
 polarized microscopic method. The ecologically important species
 Gephyrocapsa oceanica, Emiliania huxleyi, Algirosphaera robusta,
 Florisphaera profunda, Umbilicosphaera sibogae, and Umbellosphaera
 irregularis dominated the coccolithophore community out of 33 species.
 Annual mean coccolithophore abundance ranged 4306.1 - 11140.3 cells/L.
 Generally, coccolith detachment rates were enhanced with depth as seen
 from ratios of detached coccoliths and plated coccolithophores. We
 identified three types (upper-, middle-, lower-photic species) of vertical
 biogeography of coccolithophore taxa. To quantify the response of
 coccolithophores to environmental variables, we modeled univariate
 ecological realized niches of dominant species by applying ecological
 modelling method and acquired two niche traits: mean niche (μ) and breadth
 of niche (σ). The dataset can be further incorporated into climatic
 ecological models.
description: We conducted 7 cruises on the R/V “SHIYAN 1” or “SHIYAN 3” over
 the spring premonsoon period from Mar. 2011 to May. 2018 in the eastern
 Indian Ocean (EIO). Stations were designed along latitudinal or
 longitudinal transects (Figure 1). Seawater samples were taken from seven
 layers within the euphotic layer (0~5 m, 25 m, 50 m, 75 m, 100 m, 150 m,
 200 m) using Niskin bottles on the CTD rosette system. Temperature (°C)
 and salinity data were determined from the Seabird Conductivity
 Temperature Depth (CTD) profiler. For nutrient measurement (only from 2015
 to 2018), a total of 100 ml seawater was filtered on acid-cleaned 0.45 μm
 (diameter: 45 mm) acetate cellulose filters and then stored at -20°C. In
 the laboratory, after unfreezing samples, nutrient concentrations (NO3−,
 NO2−, PO43−, SiO32− and NH4+) (NH4+ data not shown here) were measured
 automatically using the machine (AA3, Bran+Luebbe). For chlorophyll a (chl
 <em>a</em>) collection, seawater (1000 ml) was pre-screened
 through 200 μm mesh for zooplankton removal, then filtered onto 25 mm
 Whatman GF/F filters and kept at -20°C. In 2012, 2015 and 2016,
 size-fractionated chl a (pico-chl <em>a </em>for 0.7 ~2 μm,
 nano-chl <em>a </em>for 2 ~ 20 μm, micro-chl
 <em>a</em> for 20 ~ 200 μm) samples were collected as follows:
 firstly, seawater samples were filtered through 20 μm mesh, subsequently
 filtered through 2 μm polycarbonate (PC) filter and Whatman GF/F filters
 with the same filtration. All chl <em>a </em>samples were
 measured using fluorescence method. We refer to the protocol of Parsons et
 al. (1984) to deal with chl <em>a</em> extraction and
 determination [Parsons et al., 1984].
description: The empty cell in the excel means missing value or not
 investigated data point.
DOI: 10.15468/dl.y5ajsb
title: Occurrence Download

description: A dataset containing 93213 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "Year is greater than or equal to 2010",
 "Continent is Europe",
 "TaxonKey is Trollius europaeus",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 93213 records from 339 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002210-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m37pvmczf
title: Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems

description: Loss of biodiversity from lower to upper trophic levels reduces overall
 productivity and stability of coastal ecosystems in our oceans, but rarely
 are these changes documented across both time and space. The
 characterisation of environmental DNA (eDNA) from sediment and seawater
 using metabarcoding offers a powerful molecular lens to observe marine
 biota and provides a series of ‘snapshots’ across a broad spectrum of
 eukaryotic organisms. Using these next-generation tools and downstream
 analytical innovations including machine learning sequence assignment
 algorithms and co-occurrence network analyses, we examined how
 anthropogenic pressures may have impacted marine biodiversity on
 subtropical coral reefs in Okinawa, Japan. Based on 18S ribosomal RNA, but
 not ITS2 sequence data due to inconsistent amplification across
 samples, as well as proxies for anthropogenic disturbance, we show that
 eukaryotic richness at the family level significantly increases with
 medium and high levels of disturbance. This change in richness coincides
 with compositional changes, a decrease in connectedness among taxa, an
 increase in fragmentation of taxon co-occurrence networks, and a shift in
 indicator taxa. Taken together, these findings demonstrate the ability of
 eDNA to act as a barometer of disturbance and provide an exemplar of how
 ecological functions, biotic networks, and coral reef resilience may be
 impacted by anthropogenic activities.
description: We here provide raw .fastq files for each sediment and seawater
 sample collected in this study. The naming convention for .fastq files are
 as follows: Illumina run, Primer Set, Substrate, Site, Sample ID (e.g.
 "OKIXX" or "AWFS_XX" or "SEDXX"), Forward
 Fusion Tag Number (e.g. "F123"), Reverse Fusion Tag Number (e.g.
 "R123"). Sample IDs "NCXX" indicates a negative
 extraction control. The year of sampling for each sample is indicated in
 "Supplementary Materials, Table S1, sequence read information, 18S
 and ITS2" available with the published paper.
DOI: 10.15468/dl.bdrk2w
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alexa canaracunensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 79 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002255-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bcc2fqz8f
title: Raw data on computational analysis the relationships of energy and mechanical properties with sensitivity for 1, 1-diamino-2, 2-dinitroethene based polymer bonded explosives

description: The dataset provides raw data on key properties in the text as well as raw
 data on the temperature and energy balances of the P, P1, P2, P3 and P4
 systems at room temperature. These data allow the results obtained in the
 article to be reproduced, while the reader can obtain the raw data for the
 plots not labeled with data in the article and thus quantify the exact
 magnitude of the changes shown in the plots. The main work of the article
 is: Molecular dynamics (MD) simulations have been applied to investigate
 1, 1-diamino-2, 2-dinitroethene (FOX-7) crystal and FOX-7(011)-based
 polymer-bonded explosives (PBXs) with four typical polymers, polyethylene
 glycol (PEG), fluorine-polymer (F2603), ethylene-vinyl acetate copolymer
 (EVA) and ester urethane (ESTANE5703) under COMPASS force field. Binding
 energy (Ebind), cohesive energy density (CED), initiation bond length
 distribution, radial distribution function, and isotropic mechanical
 properties of FOX-7 and its PBXs at different temperatures were reported
 for the first time, and the relationship between them and sensitivity.
 Using quantum chemistry, FOX-7 was optimized with the four polymers at the
 B3LYP/6-311++G(d,p) level, and the structure and RDG of the optimized
 composite system were analyzed.
DOI: 10.5061/dryad.d51c59zzs
title: Soil extracellular enzyme activity and stoichiometry in China’s forests

description: 1. Ecoenzymatic stoichiometry links microbial decomposition with nutrient
 mineralization and improves our understanding of nutrient cycling in
 terrestrial ecosystems. Microbial C:N:P acquisition in the topsoil
 converged at a ratio of 1:1:1 in global ecosystems. However, whether the
 ratio of microbial acquisition is stable in forest soils, and is
 applicable among different soil depths remain unknown. 2. Based on
 large-scale soil sampling in China’s forests, we examined the patterns and
 environmental drivers of the eight most-widely measured enzyme activities
 and the relevant stoichiometry. 3. We found that the ratio of C:N:P
 acquisition significantly deviated from 1:1:1. The specific enzyme
 activities (g SOC-1) did not change significantly with latitude except
 those for xylosidase and acid phosphatase. Similarly, only the C:P
 acquisition ratio increased with latitude. Vertically, the specific
 activities of C-acquiring enzymes mainly increased, N-acquiring enzymes
 decreased, and P-acquiring enzymes did not change with soil depth.
 Moreover, all ratios of microbial acquisition decreased, and the
 percentage of recalcitrant C increased significantly with increasing
 depth. Our study also showed that temperature and soil C:N ratio were the
 important factors in explaining the variations in specific enzyme
 activities and microbial nutrient acquisition. 4. Our results indicated
 that no constant microbial C:N:P acquisition ratio can be widely
 recognized, and that SOC quality changed from labile to recalcitrant with
 depth. We highlight that depth-dependent enzymatic processes should be
 considered in future SOC dynamic models.
DOI: 10.5061/dryad.j6q573n9g
title: Data from: Cancer cell lines show high heritability for motility but not generation time

description: Tumour evolution depends on heritable differences between cells in traits
 affecting cell survival or replication. It is well-established that cancer
 cells are genetically and phenotypically heterogeneous; however, the
 extent to which this phenotypic variation is heritable is far less
 well-explored.  Here we estimate the broad-sense heritability
 (H2) of two cell traits related to cancer hallmarks - cell motility and
 generation time - within populations of four cancer cell lines in vitro,
 and find that motility is strongly heritable. This heritability is stable
 across multiple cell generations, with heritability values at the high end
 of those measured for a range of traits in natural populations of animals
 or plants. These findings confirm a central assumption of cancer
 evolution, provide a first quantification of the evolvability of key
 traits in cancer cells, and indicate that there is ample raw material for
 experimental evolution in cancer cell lines. Generation time, a trait
 directly affecting cell fitness, shows substantially lower values of
 heritability than cell speed, consistent with its having been under
 directional selection removing heritable variation.
description: Experiments were conducted over 7 months to record the motility
 and generation time of four cancer cell lines - HeLa, HT1080, MCF7 and
 MDA-MB-231 - in cell culture. Cell lines were cultured in vitro on a well
 plate for 24 hours before being placed into the environmental chamber of a
 Nikon TiE Timelapse Microscope. Multiple points within every well were
 chosen and videoed over a period of 72 hours. These videos were then
 analysed and cell motility and division tracked using MtrackJ and ImageJ.
 Records were kept of which cells divided and the track number assigned to
 each daughter cell. This allowed comparison between and within cell
 families so the heritability of the cell traits, motility and generation
 time, could be estimated. Broad sense heritability was estimated as the
 slope parameter of an ordinary least squares regression between related
 cells. Three cell-cell relationships were tested, mother-daughter,
 sister-sister and cousin-cousin. Our results showed that cell motility has
 high and significant heritability for all cell lines tested whereas
 generation time showed little or no significant heritability for the cell
 lines tested. This is consistent with expectations that traits closely
 linked to fitness will in general have lower heritability. These results
 are important for cancer evolution as heritability (a prerequisite for
 natural selection to be able to act) has never before been measured for
 any traits in cancer cells.
description: Measurements of broad sense heritability of generation time and
 motility in cancer cell lines
DOI: 10.5061/dryad.4j0zpc87q
title: Data from: Expected spatial patterns of alien woody plants in South Africa’s protected areas under current scenario of climate change

description: Although protected areas (PAs) are declared to provide sanctuaries for
 biodiversity, they are increasingly threatened by the synergistic effects
 of invasive alien species and climate change. Consequently, interventions
 are required to minimize the impacts of these threats on PAs’ integrity.
 To inform these interventions in the South African context and under the
 current climate change scenario, we tested for geographic patterns of
 alien woody species distribution across the network of 1453 PAs using
 three alien invasion indices – alien species abundance, invaded area ratio
 and alien species richness. Our analysis shows that, under current climate
 change scenario, none of the PAs would be effective in shielding against
 alien plants and PAs that are geographically close tend to share similar
 invasion patterns. In addition, PAs that are hotspots of alien species are
 too geographically clustered but these findings are biome-dependent. Our
 outlier analysis reveals not only an island of disproportionately-rich PAs
 in alien species, but also identifies some alien-poor PAs. We suggest that
 PAs that are hotspots of alien species as well as outliers of
 disproportionately-rich PAs in alien species should be priority in
 monitoring and invasion control programmes in the face of climate change.
description: This dataset was collected as explained below: "To maximize
 sampling of occurrence data, we combined the SAPIA database and PRECIS
 database of the National Herbarium in Pretoria (Germishuizen and
 Meyer 2003; which contains records for more than 900,000 specimens of native and non‐native species distributed across 24,500 taxa from southern Africa). We additionally supplemented these data with sampling locations from the African Centre for DNA Barcoding, through the Toyota Enviro Outreach program (http://toyotaoutreach2012.blogspot.co.za/) and the national invasive DNA barcoding project of the WfW program" (Bezeng et al. 2017). How was the data processed? "Point data were cleaned to remove records with doubtful or imprecise localities. The maximum number of point records was 5336, for the woolly nightshade (<i>Solanum mauritianum</i>), and the minimum was eight, for the stinging tree (<i>Wigandia urens</i>)" (Bezeng et al. 2017).  References: Bezeng, S.B., Van der Bank, M.,<sup> </sup>Yessoufou, K., Daru, B.H. & Davies, T.J. Climate change may reduce the spread of invasive and invading species in South Africa. <i>Ecosphere</i> <b>8</b>, e01694. Germishuizen, G., and N. L. Meyer. 2003. Plants of southern Africa: an annotated checklist. Strelitzia 14:1–1231
description: This paper was also used in Bezeng, S.B., Van der Bank,
 M.,<sup> </sup>Yessoufou, K., Daru, B.H. & Davies,
 T.J. Climate change may reduce the spread of invasive and invading species
 in South Africa. <i>Ecosphere</i> <b>8</b>,
 e01694.
DOI: 10.5061/dryad.0gb5mkkxr
title: How does increasing mast seeding frequency affect population dynamics of seed consumers? Wild boar as a case study

description: Mast seeding in temperate oak populations shapes the dynamics of seed
 consumers and numerous communities. Mast seeding responds positively to
 warm spring temperatures and is therefore expected to increase under
 global warming. We investigated the potential effects of changes in oak
 mast seeding on wild boar population dynamics, a widespread and abundant
 consumer species. Using long-term monitoring data, we showed that abundant
 acorn production enhances the proportion of breeding females. With a body
 mass-structured population model and a fixed hunting rate of 0.424, we
 showed that high acorn production over time would lead to an average wild
 boar population growth rate of 1.197 whereas non-acorn production would
 lead to a stable population. Finally, using climate projections and a
 mechanistic model linking weather data to oak reproduction, we predicted
 that mast seeding frequency might increase over the next century, which
 would lead to increase in both wild boar population size and the magnitude
 of its temporal variation. Our study provides rare evidence that some
 species could greatly benefit from global warming thanks to higher food
 availability and therefore highlights the importance of investigating the
 cascading effects of changing weather conditions on the dynamics of wild
 animal populations to reliably assess the effects of climate change.
description: Using climate projections defined at the spatial scale of our
 study site and a resource budget model that mecanisticly linked weather
 data to oak reproduction, we projected scenario of acorn production
 dynamics over the next century (Scenario 1 to 10). Additonnaly, we
 projected reference scenarios of acorn production dynamics based on
 climate data that assumed no increase in spring temperatures in coming
 decades.  Lastly, we used a body mass-structured
 population model to project the response of our wild boar population to
 the different scenarios of acorn production we simulated.
DOI: 10.5061/dryad.2z34tmphm
title: Data from: Soil solution in Swiss forest stands: a 20 year's time series

description: Soil solution chemistry is influenced by atmospheric deposition of air
 pollutants, exchange processes with the soil matrix and
 soil-rhizosphere-plant interactions. In this study we present the results
 of the long-term Intercantonal Forest Observation Program in Switzerland
 with soil solution measurements since 1998 on a current total of 47 plots.
 The forest sites comprise two major forest types of Switzerland including
 a wide range of ecological gradients such as different nitrogen (N)
 deposition and soil conditions. The long-term data set of 20 years of soil
 solution measurements revealed an ongoing, but site-specific soil
 acidification. In strongly acidified soils (soil pH below 4.2),
 acidification indicators changed only slowly over the measured period,
 possibly due to high buffering capacity of the aluminum buffer (pH 4.2 –
 3.8). In contrast, in less acidified sites we observed an increasing
 acidification rate over time, reflected, for example, by the continuous
 decrease in the ratio of base cations to aluminum (BC/Al ratio). Nowadays,
 the main driver of soil acidification is the high rate of N deposition,
 causing cation losses and hampering sustainable nutrient balances for tree
 nutrition. Mean nitrate leaching rates for the years 2005-2017 were 9.4 kg
 N ha‑1 yr‑1, ranging from 0.04 to 53 kg N ha‑1 yr‑1. Three plots with high
 N input had a remarkable low nitrate leaching. Both N deposition and
 nitrate leaching have decreased since 2000. However, the latter trend may
 be partly explained due to increased drought in recent years. Nonetheless,
 those high N depositions are still affecting the majority of the forest
 sites. Taken together, this study gives evidence of anthropogenic soil
 acidification in Swiss forest stands. The underlying long-term
 measurements of soil solution provides important information on nutrient
 leaching losses and the impact climate change effects such as droughts..
 Furthermore, this study improves the understanding of forest management
 and tree mortality regarding varying nitrate leaching rates.
description: Please check material and methods section of the full paper
 published in PLOS ONE.
description: Please consider the corresponding ReadMe file of the data sets.
 All R-codes of the data manipulation and analysis of the various models
 are given in the RMarkdown file in the R-Project folder.
DOI: 10.5061/dryad.1vhhmgqpv
title: Eighty-four per cent of all Amazonian arboreal plant individuals are useful to humans

description: Plants have been used in Amazonian forests for millennia and some of these
 plants are disproportionally abundant (hyperdominant). At local scales,
 people generally use the most abundant plants, which may be abundant as
 the result of management of indigenous peoples and local communities.
 However, it is unknown whether plant use is also associated with abundance
 at larger scales. We used the population sizes of 4,454 arboreal species
 (trees and palms) estimated from 1946 forest plots and compiled
 information about uses from 29 Amazonian ethnobotany books and articles
 published between 1926 and 2013 to investigate the relationship between
 species usefulness and their population sizes, and how this relationship
 is influenced by the degree of domestication of arboreal species across
 Amazonia. We found that half of the arboreal species (2,253) are useful to
 humans, which represents 84% of the estimated individuals in Amazonian
 forests. Useful species have mean populations sizes six times larger than
 non-useful species, and their abundance is related with the probability of
 usefulness. Incipiently domesticated species are the most abundant.
 Population size was weakly related to specific uses, but strongly related
 with the multiplicity of uses. This study highlights the enormous
 usefulness of Amazonian arboreal species for local peoples. Our
 findings support the hypothesis that the most abundant plant species have
 a greater chance to be useful at both local and larger
 scales, and suggest that although people use the most abundant
 plants, indigenous people and local communities have
 contributed to plant abundance through long-term
 management.
description: <b>Trees and palms uses</b> This dataset contains information about the uses of tree and palm species in Amazonian forests. See Metadata file for explanation of the data contained in each column.