cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qfttdz0g7
title: Scale dependency of joint species distribution models challenges interpretation of biotic interactions

description: Aim: Separating the biotic and abiotic factors controlling species
 distributions has been a long-standing challenge in ecology and
 biogeography. Joint species distribution models (JSDMs) have emerged as a
 promising statistical framework towards this objective by simultaneously
 modeling the environmental responses of multiple species and approximating
 species associations based on patterns in their (co-)occurrences. However,
 the signature of biotic interactions should be most evident at fine
 spatial resolutions. Here, we test how the resolution of input data
 affects the inferences from JSDMs. Location: Switzerland Taxon: Birds
 Methods: Using standardized survey data of 43 woodland bird species and
 eight climatic, topographic and vegetation structural predictors, we fit
 JSDMs at different spatial resolutions (125m to 1000m) and sampling
 periods (1 and 5years). In addition, we calculate functional similarity
 among all species as an independent proxy of biotic interactions,
 specifically competition. We then assess how JSDM performance and
 estimates vary with the spatial resolution of the input data and test
 whether species associations are consistent across grain sizes and with
 the alternative approach based on functional similarity. Results: Our
 results show better model performance at coarser spatial resolutions and
 for longer sampling periods. Although pairwise species associations
 estimated in JSDMs were generally shifted towards positive values, we
 found a higher proportion of negative associations at fine spatial
 resolutions. Strikingly, estimates were not consistent across spatial
 scales and frequently switched between positive and negative values.
 Moreover, estimated species associations tended to be more positive for
 functionally similar species. Main conclusions: Our results show that
 species associations are more differentiated, i.e. cover a broader range
 of values, at finer spatial resolutions. Yet, their positive correlation
 with functional similarity and the general over-representation of positive
 associations suggest that shared responses to unobserved environmental
 predictors rather than biotic interactions underlie these scaling effects,
 cautioning against a naïve interpretation of species associations
 estimated by JSDMs at any spatial scale.
description: Data collection and processing is described in detail in the
 article.
DOI: 10.5061/dryad.r4xgxd2br
title: RADseq data for Atlantic Halibut in the Northwest Atlantic

description: Characterizing the nature of genetic differentiation among individuals and
 populations and its distribution across the genome is increasingly
 important to inform both conservation and management of exploited species.
 Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and
 commercially important fish species, yet knowledge of population structure
 and genomic diversity in this species remains lacking. Here, we use
 restriction-site associated DNA sequencing and a chromosome-level genome
 assembly to identify over 86,000 single nucleotide polymorphisms mapped to
 24 chromosome-sized scaffolds, genotyped in 734 individuals across the
 Northwest Atlantic. We describe subtle but significant genome-wide
 regional structuring between the Gulf of St. Lawrence and adjacent
 Atlantic continental shelf. However, the majority of genetic divergence is
 associated with a large putative chromosomal rearrangement (5.74
 megabases) displaying high differentiation and linkage disequilibrium, but
 no evidence of geographic variation. Demographic reconstructions suggest
 periods of expansion coinciding with glacial retreat, and more recent
 declines in Ne. This work highlights the utility of genomic data to
 identify multiple sources of genetic structure and genomic diversity in
 commercially exploited marine species.  
description: bestRAD libraries 768 Atlantic Halibut prepared using the sbfI
 enzyme, demultiplxed and adapter trimmed, genotyped using
 stacks2.
description: Data described in README file
DOI: 10.5524/102762
title: Supplementary files for "RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations"

description: Background<br>RNA-Seq analysis has become a routine task in numerous genomic research labs, driven by the reduced cost of bulk RNA sequencing experiments. These studies generate billions of reads that require easy-to-run, comprehensive, and reproducible analysis. However, many labs rely on in-house scripts, which can be challenging for bench scientists to use and hinder standardization and reproducibility. While existing RNA-Seq pipelines attempt to address these challenges, they often lack a complete end-to-end user interface.<br>Findings<br>To bridge this gap, we developed RNA-SeqEZPZ, an automated pipeline with a user-friendly point-and-click interface, enabling rigorous and reproducible RNA-Seq analysis without requiring programming or bioinformatics expertise. For advanced users, the pipeline can also be executed from the command line, allowing customization of steps to suit specific applications. The innovation of this pipeline lies in the combination of three key features: (1) all software is packaged within a Singularity container, eliminating installation issues, (2) it offers a point-and-click interface from raw FASTQ files through differential expression and pathway analysis, and (3) it includes a Nextflow version, enabling scalability and portability for seamless execution across various platforms including cloud and cluster computing. Additionally, RNA-SeqEZPZ generates a thorough statistical report and offers an option for batch adjustment to minimize effects of technical variations across replicates. Reports can also be reviewed by a bioinformatician to ensure the overall quality of the analysis.<br>Conclusions<br>RNA-SeqEZPZ is a robust, accessible, and scalable solution for comprehensive RNA-Seq analysis, enabling researchers to focus on biological insights rather than computational challenges.
DOI: 10.5061/dryad.2280gb5r2
title: Mother's curse is pervasive across a large mitonuclear Drosophila panel

description: The maternal inheritance of mitochondrial genomes entails a sex-specific
 selective sieve, whereby mutations in mitochondrial DNA can only respond
 to selection acting on females. In theory, this enables male-harming
 mutations to accumulate in mitochondrial genomes as long as they are
 neutral, beneficial, or only slightly deleterious to females. Ultimately,
 this bias could drive the evolution of male-specific mitochondrial
 mutation loads, an idea known as the mother's curse. Earlier work on
 this hypothesis has mainly used small Drosophila panels, in which
 naturally sourced mitochondrial genomes were coupled to an isogenic
 nuclear background. The lack of nuclear genetic variation in these designs
 has precluded robust generalization. Here, we test the predictions of the
 mother's curse using a large Drosophila mitonuclear genetic panel,
 comprising nine isogenic nuclear genomes coupled to nine mitochondrial
 haplotypes, giving a total of 81 different mitonuclear genotypes.
 Following a predictive framework, we tested the mother's curse
 hypothesis by screening our panel for wing size. This trait is tightly
 correlated with overall body size and is sexually dimorphic in Drosophila.
 Moreover, growth is heavily reliant on metabolism and mitochondrial
 function, making wing size an ideal trait for the study of the impact of
 mitochondrial variation. We detect high levels of mitonuclear epistasis,
 and more importantly, we report that mitochondrial genetic variance is
 larger in male than female Drosophila for eight out of the nine nuclear
 genetic backgrounds used. These results demonstrate that the maternal
 inheritance of mitochondrial DNA does indeed modulate male life history
 traits in a more generalisable way than previously demonstrated.
description: # Mother’s curse is pervasive across a large mito-nuclear Drosophila panel
 [https://doi.org/10.5061/dryad.2280gb5r2](https://doi.org/10.5061/dryad.2280gb5r2) ## Description of the data and file structure For this paper, we looked at wing centroid size across several genotypes of Drosophila with different mitonuclear combinations (81 genotypes total). Genotype: [Nuclear genotype][mtDNA genotype] So there are 9 possible nuclear genomes (A, B, C, D, E, F, G, H, i) and 9 different mtDNA haplotypes (A, B, C, D, E, F, G, H, i). For example, genotype AC has the nuclear genome from the line "A" and mtDNA from line "C". ### Files and variables ### File: lorcan.xlsx **Description:**  ##### Variables * Line: genotype * sex * mm: centroid size (millimeters)
DOI: 10.5061/dryad.dfn2z350v
title: Data supporting: Food limitation and starvation independently affect predator macronutrient selection

description: Predators are often food limited in their habitat, and some are limited by
 specific macronutrients (protein, lipid or carbohydrate). It is
 unresolved, however, to what extent and in what way food and macronutrient
 limitation are connected. Using a carabid beetle (Nebria brevicollis), we
 compared macronutrient self-selection of the animals three times:
 immediately after collection in the field, after being fed to satiation
 and nutritional balance, and after a subsequent period of starvation. Both
 sexes were food and females lipid limited in the field; after 7-21 days of
 starvation both sexes increased proportional carbohydrate intake
 significantly. Thus, starvation created a nutrient deficit that was
 different from what the animals had experienced in the field. We conclude
 that while macronutrient limitation in nature may be influenced by hunger
 due to food limitation, this is not its main determinant. Nutritional
 imbalance of available food may override this effect.
description: Feeding experiments in the laboratory
DOI: 10.5061/dryad.2rbnzs7mx
title: How fitness consequences of early-life conditions vary with age in a long-lived seabird: a Bayesian multivariate analysis of age-specific reproductive values

description: Evolutionary theory suggests that individuals can benefit from deferring
 the fitness cost of developing under poor conditions to later in life.
 Although empirical evidence for delayed fitness costs of poor
 developmental conditions is abundant, individuals that die prematurely
 have not often been incorporated when estimating fitness, such that
 age-specific fitness costs, and therefore the relative importance of
 delayed fitness costs is actually unknown. We developed a Bayesian
 statistical framework to estimate age-specific reproductive values in
 relation to developmental conditions. We applied it to data obtained from
 a long-term longitudinal study of common terns (Sterna hirundo), using
 sibling rank to describe variation in developmental conditions. Common
 terns have a maximum of three chicks, and later hatching chicks acquire
 less food, grow more slowly and have a lower fledging probability than
 their earlier hatched siblings. We estimated fitness costs in adulthood to
 constitute c. 45% and 70% of the total fitness costs of hatching third and
 second, respectively, compared to hatching first. This was due to
 third-ranked hatchlings experiencing especially high pre-fledging
 mortality, while second-ranked hatchlings had lower reproductive success
 in adulthood. Both groups had slightly lower adult survival. There was,
 however, no evidence for sibling rank-specific rates of senescence. We
 additionally found years with low fledgling production to be associated
 with particularly strong pre-fledging selection on sibling rank, and with
 increased adult survival to the next breeding season. This suggests that
 adults reduce parental allocation to reproduction in poor years, which
 disproportionately impacts low-ranked offspring. Interpreting these
 results, we suggest that selection at the level of the individual
 offspring for delaying fitness costs is counteracted by selection for
 parental reduction in brood size when resources are limiting.
DOI: 10.15468/dl.k4bysh
title: Occurrence Download

description: A dataset containing 170458 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Indonesia",
 "GadmGid is one of (IDN.7_1, IDN.9.5_1)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 170458 records from 275 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002770-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2m3zwm
title: CCDC 2416911: Experimental Crystal Structure Determination

description: Related Article: Zhiwei Yao, Ting Gao, Pengfei Yan, Yanyan Zhou, Hongfeng Li|2025|Dalton Trans.|54|5731|doi:10.1039/D5DT00219B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lrpjl
title: CCDC 2406050: Experimental Crystal Structure Determination

description: Related Article: Y.-J. Wang, Y. Zhang, Y.-Y. Tang, X.-G. Chen|2025|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|81|224|doi:10.1107/S2053229625001986
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lrpln
title: CCDC 2406052: Experimental Crystal Structure Determination

description: Related Article: Y.-J. Wang, Y. Zhang, Y.-Y. Tang, X.-G. Chen|2025|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|81|224|doi:10.1107/S2053229625001986
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lrphk
title: CCDC 2406049: Experimental Crystal Structure Determination

description: Related Article: Y.-J. Wang, Y. Zhang, Y.-Y. Tang, X.-G. Chen|2025|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|81|224|doi:10.1107/S2053229625001986
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lrpkm
title: CCDC 2406051: Experimental Crystal Structure Determination

description: Related Article: Y.-J. Wang, Y. Zhang, Y.-Y. Tang, X.-G. Chen|2025|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|81|224|doi:10.1107/S2053229625001986
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ly793
title: CCDC 2411375: Experimental Crystal Structure Determination

description: Related Article: D. Kondhare, S. Budow-Busse, C.G. Daniliuc, P. Leonard|2025|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|81|230|doi:10.1107/S2053229625001998
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.dcjzwc
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Austrinoecia isocheira (G.W.Müller, 1906)"
 ]
}

 The dataset includes 23 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001614-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17617/3.oxrl59
title: Data for "Disorder-induced suppression of superconductivity in infinite-layer nickelates"

description: Electronic transport data for samples included in "Disorder-induced suppression of superconductivity in infinite-layer nickelates" by A. Ranna, R. Grasset, M. Gonzalez, K. Lee, B. Y. Wang, E. Abarca Morales, F. Theuss, Z. H. Filipiak, M. Moravec, M. Konczykowski, H. Y. Hwang, A. P. Mackenzie, and B. H. Goodge
DOI: 10.15468/dl.fkzxzj
title: Occurrence Download

description: A dataset containing 1309 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Macaca nemestrina (Linnaeus, 1766))",
 "Country is one of (Afghanistan, Armenia, Azerbaijan, Bahrain, Bangladesh, Bhutan, Brunei Darussalam, Cambodia, China, Cyprus, Georgia, Hong Kong, India, Indonesia, Iran (Islamic Republic of), Iraq, Israel, Japan, Jordan, Kazakhstan, Korea (Democratic People’s Republic of), Korea, Republic of, Kuwait, Kyrgyzstan, Lao People’s Democratic Republic, Lebanon, Macao, Malaysia, Maldives, Mongolia, Myanmar, Nepal, Oman, Pakistan, Palestine, State of, Philippines, Qatar, Saudi Arabia, Singapore, Sri Lanka, Syrian Arab Republic, Tajikistan, Thailand, Timor-Leste, Türkiye, Turkmenistan, United Arab Emirates, Uzbekistan, Viet Nam, Yemen)"
 ]
}

 The dataset includes 1309 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016185-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kpxjve
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Macaca nemestrina (Linnaeus, 1766))",
 "Country is one of (Bermuda, Canada, Greenland, Saint Pierre and Miquelon, United States of America)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016186-250525065834625/datasets/export for details.
DOI: 10.15468/dl.ag3yu9
title: Occurrence Download

description: A dataset containing 1710916 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CollectionCode is vannmiljo",
 "DatasetKey is Norwegian Biodiversity Information Centre - Other datasets"
 ]
}

 The dataset includes 1710916 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016166-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.anhaae
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "DatasetKey is one of (iNaturalist Research-grade Observations, Plant Resources Center, Digitalización y sistematización de las colecciones biológicas del INECOL (Herbario))",
 "TaxonKey is Rubus adenotrichos",
 "Year 2000-2025"
 ]
}

 The dataset includes 52 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024832-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r9fzuh
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cromeria occidentalis)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024833-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.grpfs5
title: Occurrence Download

description: A dataset containing 7201 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Bidens pilosa L.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 7201 records from 348 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011042-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.