cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.cbubk3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Etheostoma rufilineatum",
 "HasCoordinate is true",
 "Geometry POLYGON((-78 12, -73 12, -73 0, -78 0, -78 12))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034417-251025141854904/datasets/export for details.
DOI: 10.15468/dl.scvcy2
title: Occurrence Download

description: A dataset containing 4137 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-109.4688 23.09913, -109.3188 23.09913, -109.3188 23.24913, -109.4688 23.24913, -109.4688 23.09913))"
 ]
}

 The dataset includes 4137 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034418-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17575917
title: Data accompanying "Bootstrap Confidence Regions for Learned Feature Embeddings"

description: These data can be used to reproduce the experiments and figures from 

 

Kris Sankaran (2023): Bootstrap Confidence Regions for LearnedFeature Embeddings, Journal of Computational and Graphical Statistics, DOI:10.1080/10618600.2023.2197478

To link to this article: https://doi.org/10.1080/10618600.2023.2197478
DOI: 10.5281/zenodo.17575918
title: Data accompanying "Bootstrap Confidence Regions for Learned Feature Embeddings"

description: These data can be used to reproduce the experiments and figures from 

 

Kris Sankaran (2023): Bootstrap Confidence Regions for LearnedFeature Embeddings, Journal of Computational and Graphical Statistics, DOI:10.1080/10618600.2023.2197478

To link to this article: https://doi.org/10.1080/10618600.2023.2197478
DOI: 10.15468/dl.nwrwup
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Etheostoma simoterum",
 "HasCoordinate is true",
 "Geometry POLYGON((-78 12, -73 12, -73 0, -78 0, -78 12))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034419-251025141854904/datasets/export for details.
DOI: 10.15468/dl.t52pkj
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-109.3188 23.09913, -109.1688 23.09913, -109.1688 23.24913, -109.3188 23.24913, -109.3188 23.09913))"
 ]
}

 The dataset includes 40 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034420-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.seusj8
title: Occurrence Download

description: A dataset containing 2941 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "StateProvince is New Jersey",
 "TaxonKey is Taraxacum"
 ]
}

 The dataset includes 2941 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034421-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.frs629
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Checklist and comments on the jumping plant-lice (Hemiptera: Psylloidea) from the Indian subcontinent"
 ]
}

 The dataset includes 40 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034422-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xp2cbv
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tupaia gracilis"
 ]
}

 The dataset includes 34 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034423-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.emnveh
title: Occurrence Download

description: A dataset containing 5119 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Schinus terebinthifolia"
 ]
}

 The dataset includes 5119 records from 203 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034425-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xadsca
title: Occurrence Download

description: A dataset containing 6528 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rostellularia adscendens (R.Br.) R.Barker",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 6528 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009866-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3n5tb2rk0
title: The genetic architectures of vine and skin maturity in tetraploid potato

description: Potato vine and skin maturity, which refer to foliar senescence and
 adherence of the tuber periderm, respectively, are both important to
 production and therefore breeding. Our objective was to investigate the
 genetic architectures of these traits in a genome-wide association panel
 of 586 genotypes, and through joint linkage mapping in a half-diallel
 subset (N = 397). Skin maturity was measured by image analysis after
 mechanized harvest 120 days after planting. To correct for the influence
 of vine maturity on skin maturity under these conditions, the former was
 used as a covariate in the analysis. The genomic heritability based on a
 10K SNP array was 0.33 for skin maturity vs. 0.46 for vine maturity. Only
 minor QTL were detected for skin maturity, the largest being on chromosome
 9 and explaining 8% of the variation. As in many previous studies, S.
 tuberosum Cycling DOF Factor 1 (CDF1) had a large influence on vine
 maturity, explaining 33% of the variation in the panel as a bi-allelic SNP
 and 44% in the half-diallel as a multi-allelic QTL. From the estimated
 effects of the parental haplotypes in the half-diallel and prior knowledge
 of the allelic series for CDF1, the CDF1 allele for each haplotype was
 predicted and ultimately confirmed through whole-genome sequencing. The
 ability to connect statistical alleles from QTL models with biological
 alleles based on DNA sequencing represents a new milestone in
 genomics-assisted breeding for tetraploid species.
DOI: 10.14284/459
title: World Nemertea Database. Accessed at https://www.marinespecies.org/nemertea on yyyy-mm-dd

description: A world checklist of Nemertea, compiled by taxonomic experts and based on peer-reviewed literature.
description: Approximately 1300 valid, described species of the phylum Nemertea, or ribbonworms, are known worldwide, inhabiting oceans, freshwaters, and land. Current field-work suggests that at least several times this number remain to be named or discovered. Nemerteans are unsegmented worms characterized by a unique and remarkable eversible proboscis. Some are colorful, while others are drab. They range from one millimeter to more than 30 meters long. Some are highly specialized predators while others are more eclectic, with diets that favor other worms, crustaceans, and mollusks. They are poorly known to non-specialists, because most nemerteans live in concealment and are difficult to collect, and because traditional taxonomy focuses significantly on internal anatomy based on histological study, while now we use genetic data extensively. However, many are common, abundant and can be key predators, while the phylum itself is important to understanding evolution of early invertebrate body plans. This site is intended to make these worms less enigmatic. The emphasis is on taxonomy, but the intent is to accommodate all aspects of nemertean biology.
DOI: 10.6086/d12h4c
title: Average annual US industrial chemical production 1919-2019

description: This paper argues that the concepts of “normal” reproductive development
 that biologists rely upon are undergirded by heterosexism, ableism, and
 white supremacism, even if implicitly. We illustrate our argument by
 critically analyzing toxicology’s use of reproductive fitness, focusing on
 the field of endocrine- disrupting chemicals (EDCs). Toxicology both
 informs and is informed by fundamental evolutionary and ecological
 questions, as well as environmental health. Throughout, biologists
 overwhelmingly assume that “abnormal” reproductive physiologies are both
 generated by EDC exposure and necessarily threaten species survival. Such
 assumptions unwittingly obscure fundamental scientific insights while
 further discriminating against queer, trans, nonbinary, and
 differently-abled human communities. We agree that scientists should be
 sounding the alarm over unavoidable, unevenly distributed, and highly
 hazardous EDC exposures—which cause metabolic dysregulation, cancer, and
 death—but not because gonads and genitals look different. Instead, we
 encourage scientists to confront directly how chemical corporations profit
 from innumerable, irreversible harms to ecological and societal wellbeing,
 harms which may very well have nothing to do with gonads or genitals. We
 close with three specific suggestions to help scientists dismantle the
 human hierarchies embedded into biological frameworks, toward better
 science and environmental justice. By refusing the oppressive social
 ideologies assumed by prior research, toxicological and biological
 scientists will offer exciting new insights into evolutionary processes
 and urgent, justice-centered findings for environmental health.
description: The raw data were downloaded from: American
 Chemistry Council. 2020. “Chemical Activity Barometer.” <i>American
 Chemistry Council</i>. (https://www.americanchemistry.com/chemistry-in-america/data-industry-statistics/chemical-activity-barometer). Board of Governors of the Federal Reserve System. 2021. “Data: Industrial Production and Capacity Utilization - G.17.” <i>Industrial Production and Capacity Utilization - G.17</i>. (https://www.federalreserve.gov/releases/g17/download.htm). First author Melina Packer aggregated the data (average annual industrial chemical production, in metric tons, 1919-2019) to create the figure in the paper.
DOI: 10.5061/dryad.jwstqjqb7
title: NGS Data from: Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage

description: We engineered gRNAs with highly stable hairpins in their constant parts
 and further enhanced their stability by chemical modifications. The
 ‘Genome-editing Optimized Locked Design’ (GOLD)-gRNA increases genome
 editing efficiency up to around 1000-fold (from 0.08% to 80.5%) with a
 mean increase across different other targets of 7.4-fold. The related NGS
 data is deposited here.
DOI: 10.5061/dryad.n2z34tmz9
title: Annotated transcriptome data from: Transcriptome annotation reveals minimal immunogenetic diversity among Wyoming toads, Anaxyrus baxteri

description: Briefly considered extinct in the wild, the future of the wild population
 of the Wyoming toad (Anaxyrus baxteri) continues to rely on captive
 breeding to supplement the wild population. Given its small natural
 geographic range and history of rapid population decline at least partly
 due to fungal disease, investigation of the diversity of key receptor
 families involved in the host immune response represents an important
 conservation need. Population decline may have reduced immunogenetic
 diversity sufficiently to increase the vulnerability of the species to
 infectious diseases.  Here we use comparative transcriptomics to
 examine the diversity of toll-like receptors and major histocompatibility
 complex (MHC) sequences across three individual Wyoming toads. We find
 reduced diversity at MHC genes compared to bufonid species with a similar
 history of bottleneck events. Our data provide a foundation for future
 studies that seek to evaluate the genetic diversity of Wyoming toads,
 identify biomarkers for infectious disease outcomes, and guide breeding
 strategies to increase genomic variability and wild release successes.
description: Methods for collecting data are described in publication
 "Transcriptome annotation reveals minimal immunogenetic diversity
 among Wyoming toads, <em>Anaxyrus
 baxteri</em>."
description: Annotated transcriptome data from publication "Transcriptome
 annotation reveals minimal immunogenetic diversity among Wyoming toads,
 <em>Anaxyrus baxteri</em>" are provided in Excel
 spreadsheets (.xlsx).
DOI: 10.5061/dryad.j9kd51cf0
title: Data from: Local population collapse of Ross's and lesser snow geese driven by failing recruitment and diminished philopatry

description: We estimated survival and per capita production of young, as well as
 emigration and immigration, from 1997 to 2017 in Ross's goose Anser
 rossii and lesser snow goose Anser caerulescens
 caerulescens, which are sympatric species of migratory birds that nest in
 the central Canadian Arctic at one of the largest breeding colonies in
 North America. We formed age-structured integrated population models for
 each species that jointly analyzed live and dead encounter data as well as
 breeding adult population size and fecundity data to understand drivers of
 population dynamics. We compared the demography between species because
 both species increased during the 1990s and early 2000s yet thereafter
 snow geese declined, while Ross's geese continued to increase, then
 stabilized and similarly declined. Declines in Ross's and snow goose
 populations were caused by reduced per capita production of young, and
 juvenile survival, as well as increased adult and juvenile emigration.
 Stronger declines in juvenile survival in snow geese explain their earlier
 population decline compared to Ross's geese. Despite the divergence
 in population trends in Ross's and snow geese, we found strong
 synchrony in demographic rates which suggested substantial emigration from
 this colony and similar responses to environmental conditions. We
 provide a novel m-array implementation specific to a multi-state Burnham
 model which greatly improved computational efficiency and convergence of
 posterior estimates.
description: Please refer to ReadMe file.
DOI: 10.5061/dryad.x3ffbg7mc
title: Data associated with: Global ecomorphological restructuring of dominant marine reptiles prior to the K/Pg mass extinction

description: Mosasaurid squamates were the dominant amniote predators in marine
 ecosystems during most of the Late Cretaceous. Here, we use a suite of
 biomechanically rooted, functionally descriptive ratios in a framework
 adapted from population ecology to investigate how the morphofunctional
 disparity of mosasaurids evolved prior to the Cretaceous-Paleogene (K/Pg)
 mass extinction. Our results suggest that taxonomic turnover in mosasaurid
 community composition from Campanian to Maastrichtian is reflected by a
 notable global increase in morphofunctional disparity, especially driven
 the North American record. Ecomorphospace occupation becomes polarised
 during the Late Maastrichtian, with morphofunctional disparity plateauing
 in the Southern Hemisphere and decreasing in the Northern Hemisphere. We
 show that these changes are not strongly associated with mosasaurid size,
 but rather with the functional capacities of their skulls. Our novel
 approach indicates that mosasaurid morphofunctional disparity was in
 decline in multiple provincial communities before the K-Pg mass
 extinction, highlighting region-specific patterns of disparity evolution
 and the importance of assessing vertebrate extinctions both globally and
 locally. Ecomorphological differentiation in mosasaurid communities,
 coupled with declines in other formerly abundant marine reptile groups,
 indicates widespread restructuring of higher trophic levels in marine food
 webs was well underway when the K/Pg mass extinction took place.
description: Raw measurement data collected from: 
 3D surface scans / photogrammetry models 2D
 images from published articles 2D images taken by
 authors Raw measurement data collected
 using linear measurement tools in ImageJ, Geomagic Wrap, and MeshLab
 softwares Raw measurement data is arranged in MS Excel
 spreadsheet format (.csv) Converted trait data
 (averaged per species) is arranged in MS Excel spreadsheet format
 (.csv) R-code for processing trait data built in
 RStudio
description: Measurements were recorded from 2D images. These were recorded in
 mm. These raw data can be processed at will in a variety of
 ways. Converted trait data per species has been
 pre-analysed to produce ratios. These data should not be treated as raw
 variables. The R-code includes commands to call all
 relevant packages to run the entire code. This code should be capable of
 running the full suite of analyses in RStudio 2021.09.1 / R
 4.1.2 Check the README.txt file for full
 details
DOI: 10.5061/dryad.fttdz08v8
title: Signatures of natural selection in a foundation tree along Mediterranean climatic gradients

description: Temperature and precipitation regimes are rapidly changing, resulting in
 forest dieback and extinction events, particularly in Mediterranean-type
 climates (MTC). Forest management that enhance forests’ resilience is
 urgently required, however adaptation to climates in heterogeneous
 landscapes with multiple selection pressures is complex.  For
 widespread trees in MTC we hypothesized that: patterns of local adaptation
 are associated with climate; precipitation is a stronger factor of
 adaptation than temperature; functionally related genes show similar
 signatures of adaptation; and adaptive variants are independently sorting
 across the landscape. We sampled 28 populations across the geographic
 distribution of Eucalyptus marginata (jarrah), in South-west Western
 Australia, and obtained 13,534 independent single nucleotide polymorphic
 (SNP) markers across the genome. Three genotype-association analyses that
 employ different ways of correcting  population structure were
 used to identify putatively adapted SNPs associated with independent
 climate variables. While overall levels of population differentiation were
 low (FST = 0.04), environmental association analyses found a total of
 2,336 unique SNPs associated with temperature and precipitation variables,
 with 1,440 SNPs annotated to genic regions. Considerable allelic turnover
 was identified for SNPs associated with temperature seasonality and mean
 precipitation of the warmest quarter, suggesting that both temperature and
 precipitation are important factors in adaptation. SNPs with similar gene
 functions had analogous allelic turnover along climate gradients, while
 SNPs among temperature and precipitation variables had uncorrelated
 patterns of adaptation. These contrasting patterns provide evidence that
 there may be standing genomic variation adapted to current climate
 gradients, providing the basis for adaptive management strategies to
 bolster forest resilience in the future.
description: We used over ten thousand polymorphic markers (SNPs) to disclose patterns of population structure, genetic diversity, and identify putative adaptive variants associated with climate gradients. We also used available genomic resources to annotate functional genes found to be significantly associated with climate, as well as novel ways to elucidate broader adaptive patterns by grouping genes with similar functions to describe the strongest adaptive signals.
description: See README file for all details regarding each folder and
 file.
DOI: 10.5061/dryad.ht76hdrhp
title: Cestode infection facilitates co-infection by other parasites in a metapopulation of threespine stickleback

description: Parasitic infections are a global occurrence and impact the health of many
 species. Co-infections, where two or more species of parasite are present
 in a host, are a common phenomenon across species. Co-infecting parasites
 can interact directly or indirectly via their manipulation of (and
 susceptibility to) the immune system of their shared host. Helminths, such
 as the cestode Schistocephalus solidus, are well known to
 suppress immunity of their host (threespine stickleback), potentially
 facilitating other parasite species. Yet, hosts can evolve a more robust
 immune response (as seen in some stickleback populations), potentially
 turning facilitation into inhibition. Using wild-caught stickleback from
 21 populations with non-zero S. solidus prevalence, we
 show there is an overall tendency towards facilitation: individuals
 with S. solidus infections have 28% higher diversity of
 other parasites, compared to S. solidus-uninfected individuals
 from the corresponding lakes. This facilitation effect, however, is
 stronger in lakes where S. solidus is particularly
 successful but tends towards inhibition in lakes with sparse and smaller
 cestodes (indicative of stronger host immune response). These results
 illustrate how even a single parasite species can vary geographically in
 their capacity for facilitation or inhibition of co-infections.
description: Wild-caught fish were dissected to identify and enumerate
 macroparasites.