cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mpg4f4r33
title: Data from: An efficient method for estimating vein density of Glossopteris and its application

description: Glossopteris-type leaves are the most abundant floristic element from the
 Gondwanan continent and are recorded throughout the Permian, which was a
 period of extreme icehouse-to-hothouse climatic global change. Fossil leaf
 traits can be useful for the reconstruction of palaeoenvironments and
 identification of climatic changes throughout geological time, but the
 conservative morphology of Glossopteris leaves made them
 difficult to use for this purpose thus far. If the characters
 of Glossopteris can be better quantified then it should make them
 useful for tracking environmental changes over a wide geographic area for
 a long-time interval. Venation density is a highly variable leaf trait
 that might be useful for this purpose. This trait can be calculated,
 usually as vein length per centimetre square, but this can be a
 time-consuming procedure. In this paper, we propose a new rapid method to
 estimate venation density in a conical sector
 of Glossopteris leaf lamina through an accurate linear
 model whose predictors are three linear venation densities, measured as
 veins per centimetre. In addition to substantially reducing the data
 collection time, it is less biased and more reproducible than previous
 methods applied before with this leaf type. Using this more robust method,
 preliminary results significantly distinguish the venation densities of
 leaves produced in wet and drier ecosystems, matching a pattern similar to
 modern plants. This is the first survey using a large sample size to
 reveal that environmental stress controlled the vein architecture of
 Palaeozoic plants, in a manner similar to plants in modern ecosystems.
DOI: 10.15468/dl.cbb42r
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Artemisia unalaskensis"
 ]
}

 The dataset includes 73 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003239-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mdj2gp
title: Occurrence Download

description: A dataset containing 570 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lonicera chamissoi"
 ]
}

 The dataset includes 570 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003241-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2fqz612sb
title: A new genomic resource to enable standardized surveys of SNPs across the native range of brook trout (Salvelinus fontinalis)

description: Understanding how genetic diversity is distributed across spatiotemporal
 scales in species of conservation or management concern is critical for
 identifying large-scale mechanisms affecting local conservation status and
 implementing large-scale biodiversity monitoring programs. However,
 cross-scale surveys of genetic diversity are often impractical within
 single studies, and combining datasets to increase spatiotemporal coverage
 is frequently impeded by using different sets of molecular markers.
 Recently developed molecular tools make surveys based on standardized SNP
 panels more feasible than ever but require existing genomic information.
 Here, we demonstrate the utility of genome-wide SNPs reflective of
 range-wide genetic diversity for surveying populations across the native
 species range. These data can be leveraged to design SNP panels that allow
 datasets to be combined for large-scale analyses. We develop this resource
 for brook trout (Salvelinus fontinalis). We performed restriction
 site-associated DNA sequencing for wild brook trout from 82 locations
 spanning much of the native range and domestic brook trout from 24
 hatchery strains used in stocking efforts. We identified over 24,000 SNPs
 putatively representing neutral and adaptive regions of the brook trout
 genome. We explored the ability of these SNPs to resolve relationships
 across spatial scales, including population structure, hatchery admixture,
 and outlier loci. Our dataset captures a wide spectrum of genetic
 diversity in native brook trout, offering a valuable resource for
 developing SNP panels. We highlight potential applications of this
 resource with the goal of increasing the integration of genomic
 information into decision-making for brook trout and other species of
 conservation or management concern.
description: We performed restriction site-associated DNA sequencing (RADseq)
 on wild-caught brook trout (<em>Salvelinus fontinalis</em>)
 from 82 sites spanning much of the native species range and domestic brook
 trout representing 24 hatchery strains. RADseq libraries were prepared
 following the methods of Ali et al. (2016 <em>Genetics</em>)
 then underwent PE150 sequencing on an Illumina HiSeq 4000. We used
 resulting data to perform SNP discovery based on the <em>Salvelinus
 </em>sp. reference genome (Christensen et al. 2018, 2021<em>
 PLoS ONE</em>). We then performed quality filtering to remove loci
 and individuals missing an excessive proportion of genotypes, genotypes
 with low quality scores or read depths, genotypes with poor allele
 balance, and loci with low minor allele counts. We also removed paralogous
 loci and loci rendered monomorphic by the filtering process. The resulting
 quality filtered dataset comprises genotypes for 24,337 SNPs in 201
 wild-caught brook trout and 66 hatchery brook trout.
DOI: 10.15468/dl.k922je
title: Occurrence Download

description: A dataset containing 135 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Coelopleurum multisectum"
 ]
}

 The dataset includes 135 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003240-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0zpc8671f
title: Larval dispersal patterns and connectivity of Acropora on Florida’s Coral Reef and its implications for restoration

description: Since the 1980s, populations of Acropora cervicornis and A. palmata have
 experienced severe declines due to disease and anthropogenic stressors;
 resulting in their listing as threatened, and their need for restoration.
 In this study, larval survival and competency data were collected and used
 to calibrate a very high-resolution hydrodynamic model (up to 100m) to
 determine the dispersal patterns of Acropora species along the Florida’s
 Coral Reef. The resulting connectivity matrices was incorporated into a
 metapopulation model to compare strategies for restoring Acropora
 populations. This study found that Florida’s Coral Reef was historically a
 well-connected system, and that spatially selective restoration may be
 able to stimulate natural recovery. Acropora larvae are predominantly
 transported northward along the Florida’s Coral Reef, however southward
 transport also occurs, driven by tides and baroclinic eddies. Local
 retention and self-recruitment processes were strong for a broadcast
 spawner with a long pelagic larval duration. Model simulations demonstrate
 that it is beneficial to spread restoration effort across more reefs,
 rather than focusing on a few reefs. Differences in population patchiness
 between the Acropora cervicornis and A. palmata drive the need for
 different approaches to their management plans. This model can be used as
 a tool to address the species-specific management to restore genotypically
 diverse Acropora populations on the Florida’s Coral Reef, and its methods
 could be expanded to other vulnerable populations.
DOI: 10.15468/dl.n45x6s
title: Occurrence Download

description: A dataset containing 909 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is ITA.16_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Aquilegia"
 ]
}

 The dataset includes 909 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003242-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25338/b85d2x
title: Data for: Local adaptation of seed and seedling traits along a natural aridity gradient may both predict and constrain adaptive responses to climate change

description: Local adaptation of seed and seedling traits along a natural aridity
 gradient may both predict and constrain adaptive responses to climate
 change (American Journal of Botany 2022) Premise of study: Variation in
 seed and seedling traits underlies how plants interact with their
 environment during establishment, a crucial life history stage. 
 We quantified genetic-based variation in seed and seedling traits in
 populations of the annual plant Plantago patagonica across a natural
 aridity gradient, leveraging natural intraspecific variation to predict
 how populations might evolve in response to increasing aridity associated
 with climate change in the Southwestern U.S. Methods: We quantified seed
 size, seed size variation, germination timing, and specific leaf area in a
 greenhouse common garden, and related these traits to the climates of
 source populations.  We then conducted a terminal drought
 experiment to determine which traits were most predictive of survival
 under early-season drought. Key Results:  All traits showed
 evidence of clinal variation – seed size decreased, germination timing
 accelerated, and specific leaf area increased with increasing
 aridity.  Populations with more variable historical precipitation
 regimes showed greater variation in seed size, suggestive of past
 selection shaping a diversified bet-hedging strategy mediated by seed
 size.  Seedling height, achieved via larger seeds or earlier
 germination, was a significant predictor of survival under drought.
 Conclusions: We documented substantial interspecific trait variation as
 well as clinal variation in several important seed and seedling traits,
 yet these slopes were often opposite to predictions for how individual
 traits might confer drought tolerance.  This work shows that
 plant populations may adapt to increasing aridity via correlated trait
 responses associated with alternative life history strategies, but that
 trade-offs might constrain adaptive responses in individual traits.
 Keywrds: climate change, drought, intraspecific trait variation, life
 history strategies, local adaptation, Plantago, precipitation variability,
 seed size, trade-offs Data files:  This upload includes all of
 the input data (.csv and .Rdata) and scripts (.R) for analysis and figure
 generation in the manuscript.  See the included README.txt file
 for details. Location: This research was conducted at the greenhouse at
 Nothern Arizona University, using seeds collected from 12 locations in
 nothern Arizona and southern Utah.
description: These data were collected in the greenhouse and lab (see Methods
 in the manuscript).
description: All analyses and figure generation were conducted in R.
DOI: 10.5061/dryad.qrfj6q5k7
title: Supporting code and data for: Proportion of forest area burned at high-severity increases with increasing forest cover and connectivity in western US watersheds

description: This is the R code and shapefiles of the coniferous HUC-12 watersheds and
 their western US boundary for the publication, "Proportion of forest
 area burned at high-severity increases with increasing forest cover and
 connectivity in western US watersheds" 
description: Please see the publication "Proportion of forest area burned
 at high‑severity increases with increasing forest cover and connectivity
 in western US watersheds" for methods. 
description: Please read the included README.md file before use.
DOI: 10.5061/dryad.51c59zwbr
title: Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects

description: Evolution can repeat itself, resulting in parallel adaptations in
 independent lineages occupying similar environments. Moreover, parallel
 evolution sometimes, but not always, uses the same genes. Two main
 hypotheses have been put forth to explain the probability and extent of
 parallel evolution. First, parallel evolution is more likely when shared
 ecologies result in similar patterns of natural selection in different
 taxa. Second, parallelism is more likely when genomes are similar, because
 of shared standing variation and similar mutational effects in closely
 related genomes. Here we combine ecological, genomic, experimental, and
 phenotypic data with Bayesian modeling and randomization tests to quantify
 the degree of parallelism and its relationship with ecology and genetics.
 Our results show that the extent to which genomic regions associated with
 climate are parallel among species of Timema stick insects is shaped
 collectively by shared ecology and genomic background. Specifically, the
 extent of genomic parallelism decays with divergence in climatic
 conditions (i.e., habitat or ecological similarity) and genomic
 similarity. Moreover, we find that climate-associated loci are likely
 subject to selection in a field experiment, overlap with genetic regions
 associated with cuticular hydrocarbon traits, and are not strongly shaped
 by introgression between species. Our findings shed light on when
 evolution is most expected to repeat itself.
description: This dataset contains files used for different analyses
 associated with this study. These are specific analysis which use various
 formats of genomic data. The data has been processed using various
 programs such as custom perl scripts and programs such as BayPass,
 Entropy, and Treemix.
description: Any basic text editor can be used to open these data files.
 Alternatively, the less, head, tail, cat commands can be used on the UNIX
 command line to look at the files.
DOI: 10.5061/dryad.2280gb5w4
title: Data from: Allometry in Late Devonian Podocopa ostracods (Crustacea) and its implications for Ostracoda ontogeny

description: Podocopa ostracods abounds in various marine and non-marine habitats since
 the early Palaeozoic and leave diversified fossil records in strata
 worldwide. They are particularly useful for stratigraphic correlation and
 paleoenvironmental and paleogeographical reconstructions. However, being
 the most numerous ostracods during the Palaeozoic, their origins,
 evolution, ontogeny and phylogeny remain poorly defined. This paper
 represents the first study of morphological variation in Devonian
 Platycopida (an order of Podocopa) ostracods using a geometric
 morphometric approach. Our results identify substantial shape variation
 for Cribroconcha honggulelengensis from the Upper Devonian Hongguleleng
 Formation of western Junggar, NW China, demonstrating a remarkable change
 to those juveniles between stages A-3 and A-2. Using linear
 regressions between Principal component scores from right lateral view and
 carapace length, we demonstrate allometric growth patterns for the species
 C. honggulelengensis.The body plan of C. honggulelengensis developed along
 with the ontological variable, i.e., from an ovate outline with rare pores
 to an oblong outline with dense and large pores. Environmental factors
 play a major role in shape determination during ontogeny of C.
 honggulelengensis.
description: SEM images of each specimen were used to digitalize landmarks,
 with digitization performed using TpsDig2 v. 2.25 (Rohlf 2016a). A
 combination of landmarks and semilandmarks or sliding landmarks were used
 for analysing homologous points' locations together with curves
 measured on a sample of organisms. Principal component analysis (PCA) was
 subsequently applied to explore the overall diversity of within-sample
 shape variation using software  PAST v.
 2.13 (Hammer et al. 2001).
description: <strong>s1:</strong> Size information (length and height) and 74
 Principal components (PC) of all the 178 specimens of
 <em>Cribroconcha</em> <em>honggulelengensis</em>
 Song & Crasquin, 2017.
DOI: 10.5061/dryad.zs7h44jcz
title: Elevated CO2 alleviates adverse effects of drought on plant water relations and photosynthesis: a global meta-analysis

description: 1. The elevated CO2 concentration (eCO2) is expected to improve plant
 water relations and carbon (C) uptakes, with a potential to mitigate
 drought stress. However, the interactive effects of eCO2 and drought on
 plant physiology and growth are not clear. 2. We performed a meta-analysis
 on the interactive effects of eCO2 and drought on plant water relations,
 photosynthesis, biomass production and allocation. 3. We found that eCO2
 did not lead to conservation of soil water, but improved leaf water status
 under drought conditions as evidenced by a higher leaf relative water
 content and a less negative midday leaf water potential, resulting from
 reduced stomatal conductance (gs) and increased root to shoot ratio.
 Elevated CO2 retarded gs response to drought, which may be mediated by
 decreases in leaf abscisic acid concentration under eCO2 and drought.
 Drought imposed stomatal limitations on photosynthesis (A), which was
 alleviated by eCO2 via increasing intercellular CO2 concentration (Ci).
 This led to a stronger A response to eCO2 under drought, supporting the
 “low Ci effect”. However, no interaction of eCO2 and drought was detected
 on plant biomass production. Intrinsic water use efficiency (iWUE)
 increased proportionally with eCO2, while plant-scale WUE was less
 responsive to eCO2 regardless of water availability. The advantages of
 eCO2 on C3 plants over C4 plants under well-watered conditions diminished
 under drought conditions. Within C3 plants, drought caused a greater
 reduction in biomass for woody plants than for herbs. Biomass declined
 progressively as drought prolonged for plants growing in both ambient CO2
 and eCO2. The physiology and biomass of plants growing in pots showed more
 negative responses to drought than those growing in field. Biomass
 increase in free-air carbon dioxide enrichment experiments was
 significantly less than those in growth chamber and open top chamber
 experiments. 4. Synthesis. These findings suggest that eCO2 can alleviate
 the adverse impacts of drought on plant water relations and C
 sequestration, and are of significance in the prediction of plant growth
 and ecosystem productivity under global changes.
DOI: 10.5061/dryad.z34tmpghh
title: Data from: Protection status, human disturbance, snow cover and trapping drive density of a declining wolverine population in the Canadian Rocky Mountains

description: Protected areas are important in species conservation, but high rates of
 human-caused mortality outside their borders and increasing popularity for
 recreation can negatively affect wildlife populations. We quantified
 wolverine (Gulo gulo) population trends from 2011 to 2020 in &gt;14
 000 km2 protected and non-protected habitat in southwestern Canada. We
 conducted wolverine and multi-species surveys using non-invasive DNA and
 remote camera-based methods. We developed Bayesian integrated models
 combining spatial capture-recapture data of marked and unmarked
 individuals with occupancy data. Wolverine density and occupancy declined
 by 39 percent, with an annual population growth rate of 0.925. Density
 within protected areas was 3 times higher than outside and declined
 between 2011 (3.6 wolverines/1000 km2) and 2020 (2.1 wolverines/1000 km2).
 Wolverine density and detection probability increased with snow cover and
 decreased near development. Detection probability also decreased with
 human recreational activity. The annual harvest rate of 13% was above the
 maximum sustainable rate. We conclude that humans negatively affected the
 population through direct mortality, sub-lethal effects and habitat
 impacts. Our study exemplifies the need to monitor population trends for
 species at risk – within and between protected areas - as steep declines
 can occur unnoticed if key conservation concerns are not identified and
 addressed.
DOI: 10.5061/dryad.6wwpzgn2c
title: CZ Software Mentions: A large dataset of software mentions in the biomedical literature

description: We describe the CZ Software Mentions dataset, a new dataset of software
 mentions in biomedical papers. Plain-text software mentions are extracted
 with a trained SciBERT model from several sources: the NIH PubMed Central
 collection and from papers provided by various publishers to the Chan
 Zuckerberg Initiative. The dataset provides sources, context and metadata,
 and, for a number of mentions, the disambiguated software entities and
 links. We extract 1.12 million unique string software mentions from 2.4
 million papers in the NIH PMC-OA Commercial subset, 481k unique mentions
 from the NIH PMC-OA Non-Commercial subset (both gathered in October 2021)
 and 934k unique mentions from 4 million papers in the Publishers’
 collection. There is variation in how software is mentioned in papers and
 extracted by the NER algorithm. We propose a clustering-based
 disambiguation algorithm to map plain-text software mentions into distinct
 software entities and apply it on the NIH PubMed Central Commercial
 collection. Through this methodology, we disambiguate 1.12 million unique
 strings extracted by the NER model into ~97000 unique software entities,
 covering 78% of all links. We link 185 000 of the mentions to a
 repository, covering about 55% of all software-paper links. We make all
 data and code publicly available as a new resource to help assess the
 impact of software (in particular scientific open source projects) on
 science.
description: We describe our methodology in detail in our preprint and on the
 Github Repository.
description: Examples of notebooks showing how to interact with the dataset
 are available on the Github Repository, under sample_notebooks.