cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k4v262p
title: Data from: Shifts in plant functional composition following long-term drought in grasslands

description: 1. Plant traits can provide unique insights into plant performance at the
 community scale. Functional composition, defined by both functional
 diversity and community-weighted trait means (CWMs), can affect the
 stability of aboveground net primary production (ANPP) in response to
 climate extremes. Further complexity arises, however, when functional
 composition itself responds to environmental change. The duration of
 climate extremes, such as drought, is expected to increase with rising
 global temperatures; thus, understanding the impacts of long-term drought
 on functional composition and the corresponding effect that has on
 ecosystem function could improve predictions of ecosystem sensitivity to
 climate change. 2. We experimentally reduced growing season precipitation
 by 66% across six temperate grasslands for four years and measured changes
 in three indices of functional diversity (functional dispersion, richness,
 and evenness), community-weighted trait means, and phylogenetic diversity
 (PD). Specific leaf area (SLA), leaf nitrogen content (LNC) and (at most
 sites) leaf turgor loss point (πTLP) were measured for species
 cumulatively representing ~90% plant cover at each site. 3. Long-term
 drought led to increased community functional dispersion in three sites,
 with negligible effects on the remaining sites. Species re-ordering
 following the mortality/senescence of dominant species was the main driver
 of increased functional dispersion. The response of functional diversity
 was not consistently matched by changes in phylogenetic diversity.
 Community-level drought strategies (assessed as CWMs) largely shifted from
 drought tolerance to drought avoidance and/or escape strategies, as
 evidenced by higher community-weighted πTLP, SLA, and LNC. Lastly,
 ecosystem drought sensitivity (i.e. relative reduction in ANPP) was
 positively correlated with community-weighted SLA and negatively
 correlated with functional diversity. 4. Synthesis: Increased functional
 diversity following long-term drought may stabilize ecosystem functioning
 in response to future drought. However, shifts in community-scale drought
 strategies may increase ecosystem drought sensitivity, depending on the
 nature and timing of drought. Thus, our results highlight the importance
 of considering both functional diversity and abundance-weighted traits
 means of plant communities as their collective effect may either stabilize
 or enhance ecosystem sensitivity to drought.
description: community weighted means
 per plotCommunity weighted trait
 values for each plot within the EDGE experiment (see main text for
 description)SES_diversity_allFunctional diversity data per plotSBK traitsMean traits for species at the Sevilleta black grama site.SBL traitsMean trait data for species at the Sevilleta blue grama sitecommunity weighted means metadataDescribes abbreviations in the community-weighted means datafileSES_diversity_all_metadataDescribes abbreviations in the "SES" functional diversity datafile
DOI: 10.5061/dryad.mb7664h
title: Data from: Efficiency of genomic prediction of nonassessed testcrosses

description: In plant breeding, genomic selection has been mainly used to predict
 untested single crosses and testcrosses. The objectives of this study were
 to assess the efficiency of prediction of untested testcrosses and the
 significance of the factors affecting the prediction. We simulated 20,000
 testcrosses from two groups of 5000 related doubled haploid lines (DHs)
 and two unrelated elite inbred lines. The DHs were genotyped for 20,000
 single nucleotide polymorphisms (SNPs) and the testcrosses were phenotyped
 for grain yield. The average SNP density was 0.1 cM. We assumed genetic
 control by 400 quantitative trait loci (QTLs) and heritability of 25, 50,
 and 75% for the assessed testcrosses. The training set sizes were 10 and
 30% of the available DHs. The process of random sampling of the field
 assessed and predicted testcrosses were replicated 50 times. We computed
 the prediction accuracy and the coincidence index, a measure of the
 selection efficacy of the nonassessed testcrosses. The results evidenced
 that genomic selection is an efficient process for selecting superior
 nonassessed testcrosses, if there is sufficient relatedness between the
 available DHs, linkage disequilibrium in the DHs and genotypic variance
 between testcrosses, a training set size of at least 10% of the available
 DHs, and a SNP density of at least 1 cM. The efficacy of selecting the
 superior nonassessed testcrosses ranged between 0.1 and 0.9, proportional
 to the heritability of the assessed testcrosses (0.25–1.00). It is
 important to highlight that the parametric coincidence ranged from 0.1 to
 0.8. Furthermore, genomic prediction is much more efficient than
 pedigree-based best linear unbiased prediction.
description: DHs and
 testcrossesGenotypic and phenotypic
 data for DHs and testcrosses.
DOI: 10.5061/dryad.30501q7
title: Data from: A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity

description: In the Caenorhabditis elegans germline, fem-3 Binding Factor (FBF)
 partners with LST-1 to maintain stem cells. A crystal structure of an
 FBF-2/LST-1/RNA complex revealed that FBF-2 recognizes a short RNA motif
 different from the characteristic 9-nt FBF binding element, and compact
 motif recognition coincided with curvature changes in the FBF-2 scaffold.
 Previously, we engineered FBF-2 to favor recognition of shorter RNA motifs
 without curvature change (Bhat et al., 2019). In vitro selection of RNAs
 bound by FBF-2 suggested sequence specificity in the central region of the
 compact element. This bias, reflected in the crystal structure, was
 validated in RNA-binding assays. FBF-2 has the intrinsic ability to bind
 to this shorter motif. LST-1 weakens FBF-2 binding affinity for short and
 long motifs, which may increase target selectivity. Our findings highlight
 the role of FBF scaffold flexibility in RNA recognition and suggest a new
 mechanism by which protein partners refine target site selection.
description: Seqrs data for the LST-1
 FBF-2 complexLST1rd5.txtSEQRS data for FBF-2FBFrd5.txt
DOI: 10.5067/asdc_daac/scar_a/0001
title: Sulfates, Clouds and Radiation America NASA ER-2 Moderate Resolution Imaging Spectrometer (MODIS) Airborne Simulator (MAS) Data
DOI: 10.5061/dryad.k67cg66
title: Data from: Shining new light on mammalian diving physiology using wearable near-infrared spectroscopy

description: Investigation of marine mammal dive-by-dive blood distribution and
 oxygenation has been limited by a lack of non-invasive technology for use
 in freely diving animals. Here, we developed a non-invasive near-infrared
 spectroscopy (NIRS) device to measure relative changes in blood volume and
 haemoglobin oxygenation continuously in the brain and blubber of
 voluntarily diving harbour seals. Our results show that seals routinely
 exhibit preparatory peripheral vasoconstriction accompanied by increased
 cerebral blood volume approximately 15 s before submersion. These
 anticipatory adjustments confirm that blood redistribution in seals is
 under some degree of cognitive control that precedes the mammalian dive
 response. Seals also routinely increase cerebral oxygenation at a
 consistent time during each dive, despite a lack of access to ambient air.
 We suggest that this frequent and reproducible reoxygenation pattern,
 without access to ambient air, is underpinned by previously unrecognised
 changes in cerebral drainage. The ability to track blood volume and
 oxygenation in different tissues using NIRS will facilitate a more
 accurate understanding of physiological plasticity in diving animals in an
 increasingly disturbed and exploited environment.
description: MetadataFigures 2 and 3Ulf 7th March 2017; where R1 is the shortest emitter-receiver channel and R3 is the longestFigures 4 and 5Ulf 9th February 2017. Where R1 is the shortest emitter-receiver channel and R3 is the longest.Figure 6A VebjornFigure 6A UlfFigure 6B VebjornFigure 6B UlfFigure S1 AFigure S1 BFigure S2
DOI: 10.5061/dryad.p6m4340
title: Data from: A migration-associated supergene reveals loss of biocomplexity in Atlantic cod

description: Chromosome structural variation may underpin ecologically-important
 intraspecific diversity by reducing recombination within supergenes
 containing linked, co-adapted alleles. Here, we confirm that an ancient
 chromosomal rearrangement is strongly associated with migratory phenotype
 and individual genetic structure in Atlantic cod (Gadus morhua) across the
 Northwest Atlantic. We reconstruct trends in effective population size
 over the last century, and for the first time reveal declines in effective
 population size matching onset of industrialized harvest (post 1950). We
 find different demographic trajectories between individuals homozygous for
 the chromosomal rearrangement relative to heterozygous or homozygous
 individuals for the non-inverted haplotype, suggesting different selective
 histories across the last 150 years. These results illustrate how
 chromosomal structural diversity can mediate fine-scale genetic,
 phenotypic and demographic variation in a highly connected marine species,
 and show how overfishing may have led to loss of biocomplexity within
 Northern cod.
description: Kess et al 2019 Northern
 Cod Collapse Dryad dataAtlantic cod SNP chip
 genotypes at 6669 SNP loci, in plink (.ped, .map) and genepop (.gen)
 format. Lists of SNPs from the chip found within rearranged genomic
 regions on LG1 and LG12. Complete table of inversion genotype assignments
 and migratory phenotype assignments.
DOI: 10.5061/dryad.v7d0350
title: Data from: A general approach for predicting protein epitopes targeted by antibody repertoires using whole proteomes

description: Antibodies are essential to functional immunity, yet the epitopes targeted
 by antibody repertoires remain largely uncharacterized. To aid in
 characterization, we developed a generalizable strategy to identify
 antibody-binding epitopes within individual proteins and entire proteomes.
 Specifically, we selected antibody-binding peptides for 273 distinct sera
 out of a random library and identified the peptides using next-generation
 sequencing. To identify antibody-binding epitopes and the antigens from
 which these epitopes were derived, we tiled the sequences of candidate
 antigens into short overlapping subsequences of length k (k-mers). We used
 the enrichment over background of these k-mers in the antibody-binding
 peptide dataset to identify antibody-binding epitopes. As a positive
 control, we used this approach, termed K-mer Tiling of Protein Epitopes
 (K-TOPE), to identify epitopes targeted by monoclonal and polyclonal
 antibodies of well-characterized specificity, accurately recovering their
 known epitopes. K-TOPE characterized a commonly targeted antigen from
 Rhinovirus A, identifying three epitopes recognized by antibodies present
 in 83% of sera (n = 250). An analysis of 2,908 proteins from 400 viral
 taxa that infect humans revealed seven enterovirus epitopes and five
 Epstein-Barr virus epitopes recognized by &gt;30% of specimens.
 Analysis of Staphylococcus and Streptococcus proteomes similarly revealed
 six epitopes recognized by &gt;40% of specimens. These common viral
 and bacterial epitopes exhibited excellent agreement with previously
 mapped epitopes. Additionally, we identified 30 HSV2-specific epitopes
 that were 100% specific against HSV1 in novel and previously reported
 antigens. The K-TOPE approach thus provides a powerful new tool to
 elucidate the organisms, antigens, and epitopes targeted by human antibody
 repertoires.
description: KTOPE_SequencesContains 278 files which have a single line of metadata with PROJECT CLASSIFICATION NAME for each specimen followed by a peptide sequence on each line. These files contain the antibody-binding peptides for each specimen. These peptide lists were used as inputs for this study. There are 250 specimens which have “Specimen” in their name and were used for general population studies. Also, there are 22 HSV specimen peptide lists. Finally, there are 6 specimens which represent a single serum specimen spiked with monoclonal or polyclonal antibodies.
DOI: 10.5061/dryad.6mg5g10
title: Data from: Gender and language use in scientific grant writing

description: Women in STEM are not equally represented across tenure-track career
 stages, and this extends to grant funding, where women applicants often
 have lower success rates compared to men. While gender bias in reviewers
 has been documented, it is currently unknown whether written language in
 grant applications varies predictably with gender to elicit bias against
 women. Here we analyse the text of ~2000 public research summaries from
 the 2016 Natural Sciences and Engineering Research Council (NSERC)
 individual Discovery Grant (DG) program. We explore the relationship
 between language variables, inferred gender and career stage, and funding
 levels. We also analyse aggregated data from the 2012-2018 NSERC DG
 competitions to determine whether gender impacted the probability of
 receiving a grant for early-career researchers. We document a marginally
 significant gender difference in funding levels for successful grants,
 with women receiving $1756 less than men, and a large and significant
 difference in rejection rates among early-career applicants (women: 40.4%
 rejection; men: 33.0% rejection rate). Language variables had little
 ability to predict gender or funding level using predictive modelling. Our
 results indicate that NSERC funding levels and success rates differ
 between men and women, but we find no evidence that gendered language use
 affected funding outcomes.
description: GenderedWording_projectThis zip directory contains the R Studio Project, custom scripts, and datasets required to reproduce analyses reported in Urquhart-Cronish, M. and Otto, S.P. 2019ms Gender and language use in scientific grant writing.
DOI: 10.5061/dryad.t9v70p3
title: Data from: From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon

description: The use of genetic information is crucial in conservation programs for the
 establishment of breeding plans and for the evaluation of restocking
 success. Short tandem repeats (STRs) have been the most widely used
 molecular markers in such programs, but next-generation sequencing
 approaches have prompted the transition to genome-wide markers such as
 single-nucleotide polymorphisms (SNPs). Until now, most sturgeon species
 have been monitored using STRs. The low diversity found in the critically
 endangered European sturgeon (Acipenser sturio), however, makes its future
 genetic monitoring challenging and the current resolution needs to be
 increased. Here, we describe the discovery of a highly informative set of
 79 SNPs using Double Digest Restriction Associated DNA (ddRAD) sequencing
 and its validation by genotyping using the MassArray system. Comparing
 with STRs, the SNP panel proved to be highly efficient and reproducible,
 allowing for more accurate parentage and kinship assignments’ on 195
 juveniles of known pedigree and 40 wild-born adults. We explore the
 effectiveness of both markers to estimated relatedness and inbreeding,
 using simulated and empirical datasets. Interestingly, we found
 significant correlations between STRs and SNPs at individual
 heterozygosity and inbreeding that give support to a reasonable
 representation of whole genome diversity for both markers. These results
 are useful for the conservation program of A. sturio in building a
 comprehensive studbook, which will optimize conservation strategies. This
 approach also proves suitable for other case studies in which highly
 discriminatory genetic markers are needed to assess parentage and kinship.
description: GENOYPES 40 SAMPLES
 LIBRARY SNPSThis dataset describes
 the genotypes of the 40 samples that were selected for the ddRADseq
 library for SNPs detection40 COMPAR SNP
 STRThis dataset describes
 the genotypes of n=40 European sturgeon (Acipenser sturio) analysed by
 both SNP and STR markers. This dataset has been analysed for comparison of
 parentage assignment using both markers.Genotype of 192
 JUVENILES analysed by SNPsThis dataset describes
 the genotypes of n=192 F1 European sturgeon juveniles kept in captivity at
 the St Seurin experimental station (France)192 JUVENILES SNPs DRYAD
 OK.xlsx
DOI: 10.5061/dryad.2df87g2
title: Data from: Phylogeography of Dendrolimus punctatus (Lepidoptera: Lasiocampidae): population differentiation and last glacial maximum survival

description: Although the Masson pine moth, Dendrolimus punctatus, is one of the most
 destructive forest pest insects and is an endemic condition in China, we
 still do not fully understand the patterns of how its distribution range
 varies in response to Quaternary climatic oscillations. Here we sequenced
 one maternally inherited mitochondrial gene (COI) and biparentally
 inherited nuclear data (ITS1 and ITS2 ) among 23 natural populations
 across the entire range of the species in China. A total of 51 mitotypes
 and 38 ribotypes were separately obtained using mtDNA and ITS1 data.
 Furthermore, significant phylogeographical structure (NST &gt; GST, P
 &lt; 0.01) were detected. The spatial distribution of mitotypes
 implied that two distinct groups existed in the species: one in the
 southwest distribution, including 10 locations, and the other located in
 the northeast region of China. It is suggested, therefore that each group
 was derived from ancestors that occupied different isolated refugia during
 previous periods, possibly Last Glacial Maximum (LGM). Mismatch
 distribution and Bayesian population dynamics analysis suggested the
 population size underwent sudden expansion, which is consistent with the
 results of ecological niche modelling (ENM). As a typical phytophagous
 insect, the history of population expansion was in accordance with the
 host plants, providing abundant food resources and habitat. Intraspecific
 success rate of barcoding identification was lower than interspecific
 ones, indicating a level of difficulty in barcoding individuals from
 different populations. However, it still provides an early insight into
 the pattern of genetic diversity within a species.
description: Genetic diversity of
 Dendrolimus punctatusLocations of populations
 of Dendrolimus punctatus sampled, including the sample sizes (N),
 frequencies of COI and Ribotypes per population (Nh), and estimates of
 haplotype diversity (h) and nucleotide diversity (π) for each
 populations.Table
 S1-4.docx
DOI: 10.5061/dryad.57q7865
title: Data from: Distance-dependent seed‒seedling transition in the tree Castanopsis sclerophylla is altered by fragment size

description: Negative distance-dependence of conspecific seedling mortality (NDisDM) is
 a crucial stabilizing force that regulates plant diversity, but it remains
 unclear whether and how fragment size shifts the strength of NDisDM. Here,
 we surveyed the seed‒seedling transition process for a total of 25,500
 seeds of a local dominant tree species on islands of various sizes in a
 reservoir and on the nearby mainland. We found significant NDisDM on the
 mainland and large and medium islands, with significantly stronger NDisDM
 on medium islands. However, positive distance-dependent mortality was
 detected on small islands. Changes in distance-dependence were critically
 driven by both rodent attack and pathogen infestation, which were
 significantly affected by fragment size. Our results emphasized the
 necessity of incorporating the effects of fragment size on
 distance-dependent regeneration of dominant plant species into the
 existing frameworks for better predicting the consequences of habitat
 fragmentation.
description: Data for
 distance-dependent seed‒seedling transition in the tree Castanopsis
 sclerophylla is altered by fragment sizeData are divided into
 three sheets matching different parts of data analysis in the manuscript,
 i.e. DTNCTs, DTNISs and rodent density. In the sheets of DTNCTs and
 DTNISs, each row represents a seed and a column indicates a status or
 character of seeds. In the sheet of rodent density, each row represents an
 experimental site.data_19_06_27.xlsx
DOI: 10.5061/dryad.n41d2dv
title: Data from: Leaf trait variability between and within subalpine grassland species differs depending on site conditions and herbivory

description: Plant traits are commonly used to predict ecosystem-level processes, but
 the validity of such predictions is dependent on the assumption that trait
 variability between species is greater than trait variability within a
 speciesthe robustness assumption. Here, we compare leaf trait
 intraspecific and interspecific variability depending on: geographical
 differences between sites, and five years of experimental herbivore
 exclusion in two vegetation types of subalpine grasslands in Switzerland.
 Four-leaf traits were measured from eight herbaceous species common to all
 18 sites. Intraspecific trait variability differed significantly depending
 on site and herbivory. However, the amount and structure of variability
 depended on the trait measured and whether considering leaf traits
 separately or multiple leaf traits simultaneously. Leaf phosphorus (P)
 concentration showed the highest intraspecific variability, while specific
 leaf area (SLA) showed the highest interspecific variability and displayed
 intraspecific variability only in response to herbivore exclusion. Species
 identity based on multiple traits was not predictable. We find
 intraspecific variability is an essential consideration when using plant
 functional traits as a common currency not just species mean traits. This
 is particularly true for leaf nutrient concentrations, which showed high
 intraspecific variability in response to site differences and herbivore
 exclusion; a finding which suggests that the robustness assumption does
 not always hold.
description: Full_data_Swiss_intraspecificMeta data 1.Grassland Grassland site where the exclosure was set up; overall there were 6 grassland sites 2.Vegetation Vegetation type; either short-grass or tall-grass 3.Treatment Type of exclosure: 1Control 2Deer 3Marmot 4Mouse 5Insect 4.Taxa species identity-8 species Trifolium repens Lotus corniculatus Festuca rubra Galium pumilum Carex sempervirens Crepis aurea Briza media Carex caryophyllea 5.Life form function of species: grasses, sedges, forbs and legumes 6.SLA specific leaf area; leaf size divded by dry weight tissue; mm2/g 7. P leaf P; 8. C leaf C concentration (%) 9. N leaf N concentration (%)