cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f4qrfj71d
title: Drought neutralizes positive effects of long-term grazing on grassland productivity through altering plant-soil interactions

description: Livestock grazing is among the most intensive land-use activities in
 grasslands and can affect plant communities directly or indirectly via
 grazing-induced soil legacies. Under climate change, grasslands are
 threatened globally by recurrent drought. However, the extent to which
 drought influences grazing-induced soil legacy effects on plant biomass
 production and community composition remains largely unexplored. We grew
 five naturally co-occurring plant species (three dominants and two
 subordinates) in mixed communities in a glasshouse experiment in live and
 sterilized soil that had or had not been subjected to 19 years of grazing;
 these plant communities were then exposed to a subsequent drought. We
 tested the treatment effects on plant community biomass, proportional
 aboveground biomass of individual species, arbuscular mycorrhizal (AM)
 fungal root colonization, and soil nutrient availability. Under
 drought-free conditions, soils from grazed plots produced significantly
 higher plant aboveground and total community biomass compared to soils
 from ungrazed plots. In contrast, plant aboveground and total community
 biomass were similar between grazed and ungrazed soils under drought
 conditions. Similarly, soils from grazed plots increased the proportional
 biomass of dominant species but decreased the proportion of subordinate
 species; however, the proportional biomass of dominant and subordinate
 species was similar between grazed and ungrazed soils under drought
 conditions. Soil NO3--N in grazed soil was significantly higher compared
 to ungrazed soil. Drought dramatically increased soil NO3--N in sterilized
 soil and had a more pronounced increase in grazed soil than in ungrazed
 soil. Arbuscular mycorrhizal fungal root colonization from grazed soil was
 lower compared to ungrazed soil. Drought significantly increased the soil
 available phosphorus concentration, as well as plant community AM fungal
 root colonization. Synthesis. Our study suggests that drought can
 neutralize positive grazing effects on plant community biomass production
 via altered plant-soil interactions. Also, we found that drought can
 alleviate the negative effects of grazing legacies on subordinate species
 by reducing the competitiveness of dominant species. Our study provides
 new insights for understanding the underlying mechanisms of grazing
 effects on grassland productivity under climate change.
description: Please see the README document and the accompanying published
 article: Duan, DD., Tian, Z.,  Wu, NN., Feng, XX., Hou, FJ., Nan, ZB.,  Kardol, P.,  and  Chen,
 T. 2023. Drought neutralizes positive effects of long-term
 grazing on grassland productivity through altering plant-soil
 interactions. <em>Functional Ecology</em>.
DOI: 10.5061/dryad.xd2547dnd
title: Data for: Weaker selection on genes with treatment-specific expression consistent with a limit on plasticity evolution in Arabidopsis thaliana

description: Differential gene expression between environments often underlies
 phenotypic plasticity. However, environment-specific expression patterns
 are hypothesized to relax selection on genes, and thus limit plasticity
 evolution. We collated over 27 terabases of RNA-sequencing data
 on Arabidopsis thaliana from over 300 peer-reviewed
 studies and 200 treatment conditions to investigate this hypothesis.
 Consistent with relaxed selection, genes with more treatment-specific
 expression have higher levels of nucleotide diversity and divergence at
 nonsynonymous sites but lack stronger signals of positive selection. This
 result persisted even after controlling for expression level, gene length,
 GC content, the tissue specificity of expression, and technical variation
 between studies. Overall, our investigation supports the existence of a
 hypothesized trade-off between the environment specificity of a gene’s
 expression and the strength of selection on said gene in A.
 thaliana. Future studies should leverage multiple genome-scale datasets to
 tease apart the contributions of many variables in limiting plasticity
 evolution.
description: Please see the PDF named
 arabidopsis-conditional-expression-manuscript-methods-only.pdf in the
 Zenodo supplemental material attached to this submission for the full
 methods and equations used for data processing, including citations to
 relevant publications.    
description: The two .xlsx files can be opened with Microsoft Excel or any
 excel reader. The files ending in .gz must be decompressed with the gunzip
 command on a command line before opening, or can be opened with any reader
 for gzipped files. The PDF file can be read with any PDF reader.
DOI: 10.5061/dryad.12jm63z2x
title: Deep learning models challenge the prevailing assumption that face-like effects for objects of expertise support domain-general mechanisms

description: The question of whether perceptual expertise is mediated by general-expert
 or domain-specific processing mechanisms has been debated for decades.
 Because humans are experts in face recognition, face-like neural and
 cognitive effects for objects of expertise were considered to support for
 the general-expertise hypothesis. Conversely, stronger effects for faces
 than objects of expertise were considered to support the domain-specific
 hypothesis. However, the effects of domain, experience, and level of
 categorization, are confounded in human studies, which may lead to
 erroneous inferences. To overcome these limitations, we used computational
 models of perceptual expertise and tested different domains (objects,
 faces, birds) and levels of categorization (basic, sub-ordinate,
 individual) in isolation, matched for amount of experience. Like humans,
 the models generated a larger inversion effect for faces than for objects.
 Importantly, a face-like inversion effect was found for individual-based
 categorization of non-faces (birds) but only in a network specialized for
 that domain. Thus, contrary to prevalent assumptions, face-like effects in
 objects of expertise may originate from domain-specific rather than
 domain-general processing mechanisms. More generally, we show how deep
 learning algorithms can be used to isolate the effects of factors that are
 inherently confounded in the natural environment of biological organisms.
description: Creation of verification tests for upright and inverted images is
 described in the article. Each verification test is
 composed of 2 txt files: Containing pairs
 of images belonging to the same class (both either upright or inverted,
 labeled "same") Containing pairs of images
 belonging to different classes (both either upright or inverted, labeled
 "diff") To calculate the AUROC,
 calculate the distances between the image pairs in the corresponding
 "same" and "diff" files.
 Corresponding txt files are found in the same directory, with the
 prefix "same" or "diff" and the suffix
 "_{id}.txt". For example, corresponding txt files used for the
 verification tests are "same_3.txt" and
 "diff_3.txt". Distance between image
 representations according to the different models could also be found in
 appropriately named csv files (for example, "260_inanimate.csv"
 representations from the network trained on 260 classes from
 ImageNet). Trained neural networks are available as
 PyTorch weights, and trained according to the procedure described in the
 paper.
description: Model weights are given as PyTorch state_dict.
DOI: 10.15468/dl.35x6er
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Galearis wardii"
 ]
}

 The dataset's 2 records were derived from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003011-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5066/p13a6may
title: Bedrock geochemistry, Dickinson County, Michigan

description: The southern margin of the Archean Superior Province in the central Upper Peninsula of Michigan records Paleoproterozoic tectonic events involved in the ~2.1 Ga rifting of the proposed Archean supercraton Superia and the subsequent assembly of Laurentia. Within a small area of Dickinson County, Michigan, there are many distinctive geologic units with confounding structural and stratigraphic relationships that are key to understanding the geologic and tectonic evolution of the region. The samples included in this data release were collected for geochemistry to complement recent geochronological (Vallini and others, 2006; Ayuso and others, 2018) and geophysical research (Drenth and others, 2021) in the region. The geochemical data encompass the diverse geologic units that crop out mainly in Dickinson County. These eighteen samples include rocks from the Dickinson Group (Solberg schist, Six Mile amphibolite, and East Branch arkose), as well as samples of the Bell Creek gneiss, Hardwood gneiss, porphyritic red granite, gray gneiss, and several of the mafic dikes that cut through the region. Samples were analyzed by ActLabs for major and trace elements.

Ayuso, R.A., Schulz, K.J., Cannon, W.F., Woodruff, L.G., Vasquez, J.A., Foley, N.K., and Jackson, J., 2018, New U-Pb zircon ages for rocks from the granite-gneiss terrane in northern Michigan: evidence for events at ~3750, 2750, and 1850 Ma: 64th Annual Institute on Lake Superior Geology Proceedings, Part 1—Program and Abstracts, p. 7-8.

Drenth, B.J., Cannon, W.F., Schulz, K.J., and Ayuso, R.A., 2021, Geophysical insights into Paleoproterozoic tectonics along the southern margin of the Superior Province, central Upper Peninsula, Michigan, USA: Precambrian Research, v. 359, 106205.

Vallini, D.A., Cannon, W.F., and Schulz, K.J., 2006, Age constraints for Paleoproterozoic glaciation in the Lake Superior region: detrital zircon and hydrothermal xenotime ages for the Chocolay Group, Marquette Range Supergroup: Canadian Journal of Earth Science, v. 43, p. 571-591.
DOI: 10.5061/dryad.qz612jmm8
title: Data from: Fast visual adaptation to dim light in a cavity-nesting bird

description: Many birds move fast into dark nest cavities forcing the visual system to
 adapt to low light intensities. Their visual system takes between 15 and
 60 minutes for complete dark adaptation, but little is known about the
 visual performance of birds during the first seconds in low light
 intensities.  In a forced two-choice behavioural experiment we
 studied how well budgerigars can discriminate stimuli of different
 luminance directly after entering a darker environment. The birds made
 their choices within about one second and did not wait to adapt their
 visual system to the low light intensities. When moving from a bright
 facility into an environment with 0.5 log unit lower illuminance, the
 budgerigars detected targets with a luminance of 0.825 cd/m2 on a black
 background. When moving into an environment with 1.7 or 3.5 log units
 lower illuminance, they detected targets with luminances between 0.106 and
 0.136 cd/m2. In tests with two simultaneously displayed targets, the birds
 discriminated similar luminance differences between the targets (Weber
 fraction of 0.41-0.54) in all light levels. Our results support the notion
 that partial adaptation of bird eyes to the lower illumination occurring
 within one second allows them to safely detect and feed their chicks.
description: The threshold data were collected in a forced 2-choice behaviour
 experiment. Stimulus strength was varied according to a 1-up/2-down
 staircase proceedure, and a threshold for each session was calculated by
 averaging the "turning points" for the 20 last
 choices.  Time recordings and calculations were created
 by a simple script in MATLAB. "Timestamps" were noted as a bird
 passively triggered a breakbeam motion detector or the experimenter
 actively pressed a key to indicate a specific behaviour of the
 bird.
description: The data files were created in Microsoft Excel but can in
 addition be opened in LibreOffice calc and similar open source
 programs.
DOI: 10.15468/dl.uw4r7t
title: Occurrence Download

description: A dataset containing 62338 records in GBIF matching the query:
SELECT
 '468' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 46.479780028101516
 AND decimalLatitude &lt;= 51.21395264452012
 AND decimalLongitude &gt;= -73.49581818030033
 AND decimalLongitude &lt;= -62.94398091796209
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 62338 records were derived from 167 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003009-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kkwh70s8f
title: Data from: Evaluating growth in Macrospondylus bollensis (Crocodylomorpha: Teleosauroidea) in the Toarcian Posidonia Shale, Germany

description: The dataset includes raw data (S1 - S3), .txt files (S3) and R codes (S3).
 Raw data is comprised of bone element measurements. S3 is a compressed
 .zip folder which includes all data (code, raw and additional) that
 pertains to our (1) ANCOVA and (2) evolutionary allometry analyses. We
 have decided to keep all these files together in one folder for better
 access and to not mix them with our ontogenetic data.
DOI: 10.5061/dryad.tht76hf41
title: Persistent gene flow suggests an absence of reproductive isolation in an African antelope speciation model

description: African antelope diversity is a globally unique vestige of a much richer
 world-wide Pleistocene megafauna. Despite this, the evolutionary processes
 leading to the prolific radiation of African antelopes are not well
 understood. Here, we sequenced 145 whole genomes from both subspecies of
 the waterbuck, an African antelope believed to be in the process of
 speciation. We investigated genetic structure and population divergence
 and found evidence of a mid-Pleistocene separation on either side of the
 eastern Great Rift Valley, consistent with vicariance caused by a rain
 shadow along the so-called ‘Kingdon’s Line’. However, we also found
 pervasive evidence of not only isolated and recent, but also widespread
 historical gene flow across the Rift Valley barrier. By inferring the
 genome-wide landscape of variation among subspecies, we found 14 genomic
 regions of elevated differentiation, including a locus that may be related
 to each subspecies’ distinctive coat pigmentation pattern. We investigated
 these regions as candidate speciation islands. However, we observed no
 significant reduction in gene flow in these regions, nor any indications
 of selection against hybrids. Altogether, these results suggest a pattern
 whereby climatically driven vicariance is the most important process
 driving the African antelope radiation, and suggest that reproductive
 isolation may not set in until very late in the divergence process.
description: # Persistent gene flow suggests an absence of reproductive isolation in an
 African antelope speciation model --- ## Description of data
 SB.waterbuck.MinorR2.SupplementaryFile.pdf ---Supplementary information of
 methods details and Supplementary Figures/Tables SupplementaryTable2.xlsx
 (on Dryad) ---Samples inclusion after different steps of sample filtering.
 SupplementaryFigure16.pdf---Plot of Fst between two subspecies and
 variation in local topological relationships between two subspecies using
 TWISST, pairwise diversity, Tajimas D, and the pattern of localized
 linkage disequilibrium (LD) for defassa waterbuck (orange) and common
 waterbuck (light purple) of all 11 chromosomes where differentiation
 islands were found. SupplementaryFigure18.pdf---Plot of F st within all 14
 outlying F st windows and its surrounding genomic region, together with
 its annotated protein coding genes. SupplementaryFigure20.pdf---No
 signatures for reduced gene flow in 14 differentiation islands.
 SupplementaryFigure22.pdf---No signatures for reduced gene flow in 14
 differentiation islands when adding 11 recently admixed samples.
 SupplementaryFigure23.pdf---Highlighting D-statistics values of 10
 disparate samples identified in Supplementary Figure 20. All supplementary
 PDFs are in the linked Zenodo repository.  ## Sharing/Access information
 Raw data-FastQ format in SRA with BioProject accession code PRJNA985556 in
 NCBI
DOI: 10.5061/dryad.vt4b8gtxd
title: The genomics of adaptation to climate in European great tit (Parus major) populations

description: The recognition that climate change is occurring at an unprecedented rate
 means that there is increased urgency in understanding how organisms can
 adapt to a changing environment. Wild great tit (Parus major) populations
 represent an attractive ecological model system to understand the genomics
 of climate adaptation. They are widely distributed across Eurasia and they
 have been documented to respond to climate change. We performed a Bayesian
 genome-environment analysis, by combining local climate data with SNP
 genotype data from 20 European populations (broadly spanning the species’
 continental range). We found 36 unique putative climate adaptation genes
 that were associated with variation in climate. Following an enrichment
 analysis of biological process Gene Ontology (GO) terms, we identified
 over-represented terms and pathways among the genes putatively under
 selection for climate adaptation. Because many different genes and GO
 terms are associated with climate variables, it seems likely that climate
 adaptation is polygenic and genetically complex. Our findings also suggest
 that geographical climate adaptation has been occurring since great tits
 left their Southern European refugia at the end of the last ice age.
 Finally, we show that substantial climate-associated genetic variation
 remains, which will be essential for adaptation to future changes.
description: R, RStudio, text editor.
DOI: 10.5061/dryad.rjdfn2zhd
title: Scaling of biological rates with body size as a backbone in the assembly of metacommunity biodiversity

description: The dispersal-body mass association has been highlighted as a main
 determinant of biodiversity patterns in metacommunities. However, less
 attention has been devoted to other well recognized determinants of
 metacommunity diversity: the scaling in density and regional richness with
 body size. Among active dispersers, the increase in movement with body
 size may enhance local richness and decrease beta diversity. Nevertheless,
 the reduction of population size and regional richness with body mass may
 determine a negative diversity-body size association. Consequently,
 metacommunity assembly probably emerges from a balance between the effect
 of these scalings. We formalize this hypothesis relating the exponents of
 size-scaling rules with simulated trends in alpha, beta, and gamma
 diversity with body size. Our results highlight that the diversity-body
 size relationship in metacommunities may be driven by the combined effect
 of different scaling rules. Given their ubiquity in most terrestrial and
 aquatic biotas, these scaling rules may represent the basic
 determinants—backbone—of biodiversity, over which other mechanisms operate
 determining metacommunity assembly. Further studies are needed, aimed at
 explaining biodiversity patterns from functional relationships between
 biological rates and body size, as well as their association with
 environmental conditions and species interactions.
description: Scripts include the lottery-based metacommunity model with which
 the simulations were performed, and the code lines used to generate all
 the statistical results and figures.
description: Scripts are written in R language. R software is required to
 access the file.
DOI: 10.5061/dryad.kwh70rz8n
title: Diberyllocene: xyz-coordinates of optimized structures

description: The complex diberyllocene, CpBeBeCp (Cp = cyclopentadienyl anion), has
 been the subject of numerous chemical investigations over the past five
 decades, yet has eluded experimental characterization. Here we report
 preparation and isolation of the compound by the reduction of beryllocene
 (BeCp2) with a dimeric magnesium(I) complex and determination of its
 structure in the solid state by x-ray crystallography. Diberyllocene acts
 as a reductant in reactions that form beryllium bonds to aluminum or zinc.
 Quantum chemical calculations indicate parallels between the electronic
 structure of diberyllocene and the simple homodiatomic species diberyllium
 (Be2).
description: Structures of known compounds were optimised from
 crystallographic data. Hypothetical compounds were generated in Avogadro.
 The geometry optimizations (B3LYP D3BJ def2-TZVP def2/J) were performed
 with the ORCA (Revision 5.0.3) programme. D3BJ dispersion corrections were
 used. Full analytical frequency calculations were performed for the
 optimized structures to ensure the nature of the stationary points found
 (minima, no imaginary frequencies).
DOI: 10.5061/dryad.mw6m90621
title: Nanoelectrochemistry reveals how soluble Aβ42 oligomers alter vesicular storage and release of glutamate

description: Glutamate (Glu) is the major excitatory transmitter in the nervous system.
 Impairment of its vesicular release by β-amyloid (Aβ) oligomers is thought
 to participate in pathological processes leading to Alzheimer's
 disease (AD). However, it remains unclear
 whether soluble Aβ42 oligomers affect intravesicular
 amounts of Glu or their release in the brain, or both. Measurements made
 in this work on single Glu varicosities with an amperometric nanowire Glu
 biosensor revealed that soluble Aβ42 oligomers first caused a dramatic
 increase in vesicular Glu storage and stimulation-induced release,
 accompanied by a high level of parallel spontaneous exocytosis, ultimately
 resulting in depletion of intravesicular Glu content and greatly reduced
 release. Molecular biology tools and mouse models of Aβ
 amyloidosis have further established that the transient hyperexcitation
 observed during the primary pathological stage is mediated by an altered
 behavior of vesicular glutamate transporter 1 (VGLUT1) responsible for
 transporting Glu into synaptic vesicles. Thereafter, an overexpression of
 Vti1a, a protein that maintains spontaneous release of neurotransmitters
 by selective interaction with t-SNAREs, resulted in a depletion of
 intravesicular Glu content, triggering advanced-stage neuronal
 malfunction. These findings are expected to open new perspectives for
 remediating Aβ42-induced neuronal hyperactivity and neuronal degeneration.
description: The
 amperometric spikes were recorded by a patchclamp amplifier at a constant
 potential of +700 mV with Ag/AgCl as reference. Signals were sampled at 10
 kHz, and Bessel-filtered at 2.9 kHz. Raw amperometric data were collected
 using the “Pulse” software and analyzed by Igor Pro software kindly
 provided by Dr. E. V. Mosharov from Columbia University.