cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0398029
title: Data from: Shared selective pressure and local genomic landscape lead to repeatable patterns of genomic divergence in sunflowers

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The repeated evolution of traits in organisms facing similar environmental conditions is considered to be fundamental evidence for the role of natural selection in moulding phenotypes. Yet, aside from case studies of parallel evolution and its genetic basis, the repeatability of evolution at the level of the whole genome remains poorly characterized. Here, through the use of transcriptome sequencing, we examined genomic divergence for three pairs of sister species of sunflowers. Two of the pairs (Helianthus petiolaris – H. debilis and H. annuus – H. argophyllus) have diverged along a similar latitudinal gradient and presumably experienced similar selective pressure. In contrast, a third species pair (H. exilis – H. bolanderi) diverged along a longitudinal gradient. Analyses of divergence, as measured in terms of FST, indicated little repeatability across the three pairs of species for individual genetic markers (SNPs), modest repeatability at the level of individual genes and the highest repeatability when large regions of the genome were compared. As expected, higher repeatability was observed for the two species pairs that have diverged along a similar latitudinal gradient, with genes involved in flowering time among the most divergent genes. Genes showing extreme low or high differentiation were more similar than genes showing medium levels of divergence, implying that both purifying and divergent selection contributed to repeatable patterns of divergence. The location of a gene along the chromosome also predicted divergence levels, presumably because of shared heterogeneity in both recombination and mutation rates. In conclusion, repeated genome evolution appeared to result from both similar selective pressures and shared local genomic landscapes.
DOI: 10.15468/dl.h9ncyu
title: Occurrence Download

description: A dataset containing 663 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((30.51153 50.39676,30.48405 50.38256,30.48405 50.35869,30.50895 50.34863,30.51399 50.35315,30.52418 50.35186,30.53244 50.35805,30.54573 50.35727,30.54624 50.35263,30.55837 50.35069,30.55824 50.35831,30.54869 50.3694,30.54637 50.36979,30.54495 50.36695,30.53592 50.36708,30.53269 50.36889,30.5274 50.36863,30.52663 50.36682,30.51992 50.36708,30.51257 50.36669,30.50779 50.36889,30.51476 50.37405,30.51811 50.37173,30.52598 50.37521,30.52908 50.38205,30.52869 50.38811,30.51153 50.39676))",
 "TaxonKey is Aves",
 "Year 2024-2025"
 ]
}

 The dataset includes 663 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000468-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14288/1.0398030
title: Data from: Nest boxes increase reproductive output for Tree Swallows in a forest grassland matrix in central British Columbia

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Secondary cavity-nesting birds depend on tree cavities for nesting and roosting, but many studies of these birds are conducted using nest boxes. Implementation of effective conservation strategies for cavity-nesting species such as nest-site supplementation requires careful comparisons of fecundity and other vital rates for birds using both natural and artificial nest site types. We compared breeding phenology, clutch and brood sizes, and fledging success of Tree Swallows (Tachycineta bicolor) nesting in tree cavities and nest boxes during 2001–2003 in British Columbia, Canada. Swallows using nest boxes initiated egg-laying and hatched young at approximately the same time as those in tree cavities (2 June, 23 June, respectively). Female Tree Swallows in boxes laid larger clutches (5.9 ± 0.9 eggs, N = 76) than those in tree cavities (4.2 ± 1.6 eggs, N = 67). The mean number of nestlings hatched was greater in nest boxes (5.2 ± 1.1 nestlings, N = 67) than in tree cavities (2.6 ± 2.0 nestlings, N = 58). Pairs in boxes were over twice as successful in producing fledglings (93.4%; 57 of 61 pairs fledged &gt; 1 young) than those in tree cavities (35.8%; 19 of 53 pairs). Of those successful nests, pairs nesting in boxes fledged 5.1 ± 1.1 young (N = 57), whereas those in tree cavities fledged 3.5 ± 1.2 young (N = 18). Because cavities in nest boxes averaged 60% larger in volume and 1.8 cm wider internally than tree cavities, we suggest that increased reproductive output was correlated with boxes enabling a larger clutch size. In previous research, we found that Tree Swallows were a poor competitor with other cavity-nesting passerines for tree cavities. The addition of nest boxes may serve as an effective way to supplement local reproduction for secondary cavity-nesting bird populations by reducing competition for limited nest sites. This is especially true in regions where the availability of natural nesting sites is highly variable, and where species compete with many other cavity-nesting passerines using a similar ecological niche and nesting cavities.
DOI: 10.14288/1.0398031
title: Data from: Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H+-pyrophosphatase. Phylogenetic analysis of concatenated SSU and LSU rRNA gene sequences provided strong support for the paraphyly of MALV lineages. Dinoflagellate viral nucleoproteins were found only in MALV groups that branched as sister to dinokaryotes. Our findings indicate that multiple independent origins of several characteristics early in dinoflagellate evolution, such as a parasitic life style, underlie the environmental diversity of MALVs, and suggest they have more varied trophic modes than previously thought.
DOI: 10.14288/1.0398033
title: Data from: Nonlinear averaging of thermal experience predicts population growth rates in a thermally variable environment

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;As thermal regimes change worldwide, projections of future population and species persistence often require estimates of how population growth rates depend on temperature. These projections rarely account for how temporal variation in temperature can systematically modify growth rates relative to projections based on constant temperatures. Here,we tested the hypothesis that time-averaged population growth rates in fluctuating thermal environments differ from growth rates in constant conditions as a consequence of Jensen’s inequality, and that the thermal performance curves (TPCs) describing population growth in fluctuating environments can be predicted quantitatively based on TPCs generated in constant lab conditions. With experimental populations of the green alga Tetraselmis tetrahele, we show that nonlinear averaging techniques accurately predicted increased as well as decreased population growth rates influctuating thermal regimes relative to constant thermal regimes. We extrapolate from these results to project critical temperatures for population growth and persistence of 89 phytoplankton species in naturally variable thermal environments. These results advance our ability to predict population dynamics in the context of global change.
DOI: 10.14288/1.0398035
title: Data from: Scale and direction of adaptive introgression between black cottonwood (Populus trichocarpa) and balsam poplar (P. balsamifera)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Introgression can introduce novel genetic variation at a faster rate than mutation alone, and result in adaptive introgression when adaptive alleles are maintained in the recipient genome over time by natural selection. A previous study from our group demonstrated adaptive introgression from Populus balsamifera into P. trichocarpa in a target genomic region. Here we expanded our local ancestry analysis to the whole genome of both parents to provide a comprehensive, unbiased view of introgression patterns and to identify additional candidate regions for adaptive introgression genome-wide. Populus trichocarpa is a large, fast-growing tree of mild coastal regions of the Pacific northwest, whereas P. balsamifera is a smaller stature tree of continental and boreal regions with intense winter-cold. The species are parapatric with extensive hybridization. Here, using local ancestry analysis, we detected asymmetric patterns of introgression across the whole genome of these two species of poplar trees adapted to contrasting environments, with stronger introgression from P. balsamifera to P. trichocarpa than vice versa. Admixed P. trichocarpa individuals showed more genomic regions with unusually high levels of introgression (19 regions) compared with admixed P. balsamifera (9 regions) but also the largest introgressed peak (1.02 Mb). Our analysis also revealed numerous candidate regions for adaptive introgression with strong signals of selection, notably related to disease resistance, and enriched for genes that may play crucial roles for survival and adaptation. Furthermore, we revealed overrepresentation of subtelomeric regions in P. balsamifera introgression into P. trichocarpa and possible protection of the sex-determining regions from interspecific gene flow.
DOI: 10.5281/zenodo.14284407
title: Analysis of associations between cancer driver mutations and PPI neighbours
title: When neighbours play a role: a systems-level analysis of protein interactions conditioning cancer driver mutation effects

description: Data files necessary to reproduce the analysis of associations between cancer driver mutation status and its protein physical interactors. Original research article available at: https://www.biorxiv.org/content/10.1101/2025.01.18.633728v1

Code for the analysis is available at: https://github.com/GamaPintoLab/driver_neighbours. Clone the code repository and extract the data folder to the directory's root.

Raw data files were retrieved from the TCGA Pan Cancer cohort through the UCSC Xena online tool (https://pancanatlas.xenahubs.net):



gene expression RNAseq—Batch effects normalized mRNA data: EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena

phenotype—Curated clinical data: Survival_SupplementalTable_S1_20171025_xena_sp

phenotype—sample type and primary disease: TCGA_phenotype_denseDataOnlyDownload.tsv

somatic mutation (SNP and INDEL): mc3.v0.2.8.PUBLIC.xena

somatic mutation (SNP and INDEL)—Gene level non-silent mutation: mc3.v0.2.8.PUBLIC.nonsilentGene.xena


Protein-protein interaction data:



HuRI (Version HI-III-22): http://www.interactome-atlas.org/

APID (August 2024): http://apid.dep.usal.es:8080/APID/init.action

STRING (Version 12.0): https://string-db.org/

BioGRID (Release 4.4.225): https://thebiogrid.org/


Cancer driver genes from the Network of Cancer Genes and Heathy Drivers (NCG7.0): http://network-cancer-genes.org/

Consensus RNA data from The Human Protein Atlas (version 24.0): https://www.proteinatlas.org/humanproteome/tissue/data#consensus_tissues_rna

The opentargets folder contains files from the Open Targets Platform (Version 24.09): (https://platform.opentargets.org/)

Additionally, we also include a processed folder, which includes all generated files required to reproduce the figures in the mentioned article, without needing to run all the provided code.
DOI: 10.5281/zenodo.16933542
title: Analysis of associations between cancer driver mutations and PPI neighbours
title: When neighbours play a role: a systems-level analysis of protein interactions conditioning cancer driver mutation effects

description: Data files necessary to reproduce the analysis of associations between cancer driver mutation status and its protein physical interactors. Original research article available at: https://www.biorxiv.org/content/10.1101/2025.01.18.633728v1

Code for the analysis is available at: https://github.com/GamaPintoLab/driver_neighbours. Clone the code repository and extract the data folder to the directory's root.

Raw data files were retrieved from the TCGA Pan Cancer cohort through the UCSC Xena online tool (https://pancanatlas.xenahubs.net):



gene expression RNAseq—Batch effects normalized mRNA data: EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena

phenotype—Curated clinical data: Survival_SupplementalTable_S1_20171025_xena_sp

phenotype—sample type and primary disease: TCGA_phenotype_denseDataOnlyDownload.tsv

somatic mutation (SNP and INDEL): mc3.v0.2.8.PUBLIC.xena

somatic mutation (SNP and INDEL)—Gene level non-silent mutation: mc3.v0.2.8.PUBLIC.nonsilentGene.xena


Protein-protein interaction data:



HuRI (Version HI-III-22): http://www.interactome-atlas.org/

APID (August 2024): http://apid.dep.usal.es:8080/APID/init.action

STRING (Version 12.0): https://string-db.org/

BioGRID (Release 4.4.225): https://thebiogrid.org/


Cancer driver genes from the Network of Cancer Genes and Heathy Drivers (NCG7.0): http://network-cancer-genes.org/

Consensus RNA data from The Human Protein Atlas (version 24.0): https://www.proteinatlas.org/humanproteome/tissue/data#consensus_tissues_rna

The opentargets folder contains files from the Open Targets Platform (Version 24.09): (https://platform.opentargets.org/)

Additionally, we also include a processed folder, which includes all generated files required to reproduce the figures in the mentioned article, without needing to run all the provided code.
DOI: 10.15468/dl.zmshzx
title: Occurrence Download

description: A dataset listing the 1477 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "GadmGid is USA.13.21_1",
 "TaxonKey is Animalia"
 ]
}

 The dataset's 1477 records were derived from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035587-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2ursme
title: Occurrence Download

description: A dataset containing 12358 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Agrostis perennans"
 ]
}

 The dataset includes 12358 records from 310 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035605-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zxeh9p
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parapholis incurva",
 "Country is Mexico",
 "HasCoordinate is true"
 ]
}

 The dataset includes 48 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035607-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h29btm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parapholis incurva",
 "Country is Kuwait",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035606-250811113504898/datasets/export for details.
DOI: 10.15468/dl.5w29by
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parapholis incurva",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035608-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f3x2mu
title: Occurrence Download

description: A dataset containing 1935 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Bidens pilosa"
 ]
}

 The dataset includes 1935 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035609-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fyrv7y
title: Occurrence Download

description: A dataset containing 206 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Puccinellia walkeri"
 ]
}

 The dataset includes 206 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035610-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hhjemn
title: Occurrence Download

description: A dataset containing 1338 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cymbopogon pospischilii"
 ]
}

 The dataset includes 1338 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035611-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4r9cee
title: Occurrence Download

description: A dataset containing 2599 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cymbopogon caesius"
 ]
}

 The dataset includes 2599 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035612-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/qletgg
title: Mach Number, Relative Thickness, Sweep and Lift Coefficient of the Wing – An Empirical Investigation of Parameters and Equations
title: Links to all related documents:

description: 12 equations were investigated to calculate the relative thickness t/c of the wing of an aircraft. The calculated relative thickness was taken as the average relative thickness of the wing. The data obtained from these 12 equations was checked against the given average relative thickness of 29 carefully selected aircraft, spanning a space of the parameters Mach number, lift coefficient, sweep, and type of airfoil. Some equations selected are empirical in their nature (partly based on aerodynamic derivation) other equations are purely statistical. Whenever equations had free parameters, these were optimized against the aircraft data. The best equation turned out to be an equation based on nonlinear regression. It achieved a Standard Error of Estimate of only 0.75% for the average relative thickness of the wing. Torenbeek’s equation will probably be preferred by those who like to see an equation that is based on aerodynamic considerations. It achieved a Standard Error of Estimate of 0.80% when all its free parameters were considered for optimization. The worst equation produced a Standard Error of Estimate of 8%. For an airfoil with 10% relative thickness this would give an unacceptable 10% ± 8% band of values for t/c which renders equations like this quite useless.
description: Excel
description: Digital Library - Projects and Theses - Prof. Dr. Scholz
DOI: 10.15468/dl.5agygc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parapholis incurva",
 "Country is Romania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035614-250811113504898/datasets/export for details.
DOI: 10.15468/dl.p6jw4z
title: Occurrence Download

description: A dataset containing 237 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ajania fastigiata"
 ]
}

 The dataset includes 237 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035613-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vu9d4w
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parapholis incurva",
 "Country is South Africa",
 "HasCoordinate is true"
 ]
}

 The dataset includes 56 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035615-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rmqbjx
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cygnus atratus",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035616-250811113504898/datasets/export for details.
DOI: 10.15468/dl.3uu2md
title: Occurrence Download

description: A dataset containing 246 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cygnus atratus",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 246 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035617-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vddnwy
title: Occurrence Download

description: A dataset containing 13413 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cygnus atratus",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 13413 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035618-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kzsz3m
title: Occurrence Download

description: A dataset containing 706 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parapholis incurva",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 706 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035621-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2j6xwy
title: Occurrence Download

description: A dataset containing 562 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pultenaea densifolia"
 ]
}

 The dataset includes 562 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035620-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.