cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h0h8d
title: Data from: Genome-wide analysis highlights genetic dilution in Algerian sheep

description: Algeria represents a reservoir of genetic diversity with local sheep
 breeds adapted to a large range of environments and showing specific
 features necessary to deal with harsh conditions. This remarkable
 diversity results from the traditional management of dryland by
 pastoralists over centuries. Most of these breeds are poorly productive,
 and the economic pressure leads farmers to realize anarchic cross-breeding
 (that is, not carried out in the framework of selection plans) with the
 hope to increase animal’s conformation. In this study, eight of the nine
 local Algerian sheep breeds (D’men, Hamra, Ouled-Djellal, Rembi, Sidaoun,
 Tazegzawt, Berber and Barbarine) were investigated for the first time by
 genome-wide single-nucleotide polymorphism genotyping. At an international
 scale, Algerian sheep occupied an original position shaped by relations
 with African and European (particularly Italian) breeds. The strong
 genetic proximity with Caribbean and Brazilian breeds confirmed that the
 genetic make-up of these American breeds was largely influenced by the
 Atlantic slave trade. At a national scale, an alarming genetic dilution of
 the Berber (a primitive breed) and the Rembi was observed, as a
 consequence of uncontrolled mating practices with Ouled-Djellal. A
 similar, though less pronounced, phenomenon was also detected for the
 Barbarine, another ancestral breed. Genetic originality appeared to be
 better preserved in Tazegzawt, Hamra, D’men and Sidaoun. These breeds
 should be given high priority in the establishment of conservation plans
 to halt their progressive loss. For Berber and Barbarine that also occur
 in the bordering neighbor countries, urgent concerted transnational
 actions are needed.
description: Algerian sheep genotypes
 (.ped file)Genotypes obtained with
 the Illumina OvineSNP50K Genotyping BeadChip (genotype files) for eight
 Algerian sheep breeds in a Plink format.AlgerianSheep.pedAlgerian sheep genotypes (.map file)Genotypes obtained with the Illumina OvineSNP50K Genotyping BeadChip (markers files by chromosomes) for eight Algerian sheep breeds in a Plink format.AlgerianSheep.map
DOI: 10.5061/dryad.4k0q0
title: Data from: Continental-scale patterns reveal potential for warming-induced shifts in cattle diet

description: In North America, it has been shown that cattle in warmer, drier
 grasslands have lower quality diets than those cattle grazing cooler,
 wetter grasslands, which suggests warming will increase nutritional stress
 and reduce weight gain. Yet, little is known about how the plant species
 that comprise cattle diets change across these gradients and whether these
 shifts in dietary quality coincide with shifts in dietary composition,
 i.e. the relative abundance of different plant species consumed by cattle.
 To quantify geographic patterns in dietary composition, we analyzed the
 dietary composition and dietary quality of unsupplemented cattle from 289
 sites across the central US by sequence-based analyses of plant DNA
 isolated from cattle fecal samples. Overall, assuming that the percentage
 of reads for a species in a sample corresponds to the percentage of
 protein derived from the species, only 45% of the protein intake for
 cattle was derived from grasses. Within the Great Plains, northern cattle
 relied more on grasses than southern cattle, which derived a greater
 proportion of their protein from herbaceous and woody eudicots. Eastern
 cattle were also more likely to consume a unique assemblage of plant
 species than western cattle. High dietary protein was not strongly tied to
 consumption of any specific plant species, which suggests that efforts to
 promote individual plant species may not easily remedy protein
 deficiencies. A few plant species were consistently associated with lower
 quality diets. For example, the diets of cattle with high amounts of
 Elymus or Hesperostipa were more likely to have lower crude protein
 concentrations than diets with less of these grasses. Overall, our
 analyses suggest that climatic warming will increase the reliance of
 cattle on eudicots as protein concentrations of grasses decline.
 Monitoring cattle diet with this DNA-based sequencing approach can be an
 effective tool for quantifying cattle diet to better increase animal
 performance and guide mitigation strategies to changing climates.
description: DietModelPlotR code for statistical analyses and production of figuresFASTAfasta file for consensus sequences for each OTULatLongAxesInput data, latitude, longitude, and PCA scores for each sample. PCA scores generated in JMPMatrix50input data, relative read abundance for top 50 OTUs. Used in PERMANOVARRAinput data, relative read abundance for samples. All OTUs.OTULatinput data, data for graphs of relationships between read abundance and independent factorsTaxonomyNCBI taxonomy of each OTU including the % identity of the sequence and the % coverage.Treatinput data, day of year, crude protein, and digestible organic matter associated with each sample
DOI: 10.15468/dl.mn4hua
title: Occurrence Download

description: A dataset containing 5612 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Biodiversity of ants (Formicidae) in some regions of European Russia",
 "Geometry POLYGON((22.75954 43.51472,65.24046 43.51472,65.24046 60.48528,22.75954 60.48528,22.75954 43.51472))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 5612 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001469-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.187b3
title: Data from: Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

description: Variation in the presence or absence of transposable elements (TEs) is a
 major source of genetic variation between individuals. Here, we identified
 23,095 TE presence/absence variants between 216 Arabidopsis accessions.
 Most TE variants were rare, and we find these rare variants associated
 with local extremes of gene expression and DNA methylation levels within
 the population. Of the common alleles identified, two thirds were not in
 linkage disequilibrium with nearby SNPs, implicating these variants as a
 source of novel genetic diversity. Many common TE variants were associated
 with significantly altered expression of nearby genes, and a major
 fraction of inter-accession DNA methylation differences were associated
 with nearby TE insertions. Overall, this demonstrates that TE variants are
 a rich source of genetic diversity that likely plays an important role in
 facilitating epigenomic and transcriptional differences between
 individuals, and indicates a strong genetic basis for epigenetic
 variation.
description: Figure 2 - source data
 3Arabidopsis TE variants,
 including final classifications for each variant as a TE insertion,
 deletion, or NA.TEPID_TEPAV.tsv.gzFigure 1 - source data 1TE insertions in Lerinsertions_ler.bed.gzFigure 1 - source data 2TE absences in Lerdeletions_ler.bed.gzFigure 2 - source data 1TE insertions in all 216 Arabidopsis accessionsinsertions.tsv.gzFigure 2 - source data 2TE absences in all 216 Arabidopsis accessionsabsences.tsv.gzFigure 2 - source data 4TE family enrichments for TE insertion and TE deletion variantsfamily_enrichments.tsvFigure 4 - source data 1Significantly differentially expressed genes dependent on TE presence/absencesig_genes.tsv
DOI: 10.6084/m9.figshare.31157585
title: Supplementary Material from DNA methylation reflects tissue and caste identity but not parasitism-induced changes in a social insect

description: Supplementary_Files.zip
DOI: 10.6084/m9.figshare.31157585.v1
title: Supplementary Material from DNA methylation reflects tissue and caste identity but not parasitism-induced changes in a social insect

description: Supplementary_Files.zip
DOI: 10.5061/dryad.04tq4
title: Data from: Genetic signatures of ecological diversity along an urbanization gradient

description: Despite decades of work in environmental science and ecology, estimating
 human influences on ecosystems remains challenging. This is partly due to
 complex chains of causation among ecosystem elements, exacerbated by the
 difficulty of collecting biological data at sufficient spatial, temporal,
 and taxonomic scales. Here, we demonstrate the utility of environmental
 DNA (eDNA) for quantifying associations between human land use and changes
 in an adjacent ecosystem. We analyze metazoan eDNA sequences from water
 sampled in nearshore marine eelgrass communities and assess the
 relationship between these ecological communities and the degree of
 urbanization in the surrounding watershed. Counter to conventional wisdom,
 we find strongly increasing richness and decreasing beta diversity with
 greater urbanization, and similar trends in the diversity of life
 histories with urbanization. We also find evidence that urbanization
 influences nearshore communities at local (hundreds of meters) rather than
 regional (tens of km) scales. Given that different survey methods sample
 different components of an ecosystem, we then discuss the advantages of
 eDNA—which we use here to detect hundreds of taxa simultaneously—as a
 complement to traditional ecological sampling, particularly in the context
 of broad ecological assessments where exhaustive manual sampling is
 impractical. Genetic data are a powerful means of uncovering
 human-ecosystem interactions that might otherwise remain hidden;
 nevertheless, no sampling method reveals the whole of a biological
 community.
description: R data
 fileR
 data file containing metadata, OTU table, and other R objects used for
 publication.PS_urban_eDNA_data.rDataR analysis scriptR script used for analyses resulting in the publication. Calls data from associated Rdata file.PS_urban_eDNA_Analysis_20160707.RBanzai parametersParameters for bioinformatics pipeline used for dataset.analysis_parameters.txtBanzai scriptAnalytical script for bioinformatics (Banzai Pipeline, O'Donnell, available at: https://github.com/jimmyodonnell/banzai/) used in publication.analysis_script.txtmetadata_PugetSound_eDNAMetadata for DNA sequences accessioned in Genbank Bioproject 408172.BioSampleObjectsContains more specific Genbank accession information relevant to the project.
DOI: 10.5061/dryad.85b2m
title: Data from: Who let the CAT out of the bag? accurately dealing with substitutional heterogeneity in phylogenomic analyses

description: As phylogenetic datasets have increased in size, site-heterogeneous
 substitution models such as CAT-F81 and CAT-GTR have been advocated in
 favor of other models because they purportedly suppress long-branch
 attraction (LBA). These models are two of the most commonly used models in
 phylogenomics, and they have been applied to a variety of taxa ranging
 from Drosophila to land plants. However, many arguments in favor of CAT
 models have been based on tenuous assumptions about the true phylogeny
 rather than rigorous testing with known trees via simulation. Moreover,
 CAT models have not been compared to other approaches for handling
 substitutional heterogeneity such as data partitioning with
 site-homogeneous substitution models. We simulated amino acid sequence
 datasets with substitutional heterogeneity on a variety of tree shapes
 including those susceptible to LBA. Data were analyzed with both CAT
 models and partitioning to explore model performance; in total over
 670,000 CPU hours were used, of which over 97% was spent running analyses
 with CAT models. In many cases, all models recovered branching patterns
 that were identical to the known tree. However, CAT-F81 consistently
 performed worse than other models in inferring the correct branching
 patterns, and both CAT models often overestimated substitutional
 heterogeneity. Additionally, reanalysis of two empirical metazoan datasets
 supports the notion that CAT-F81 tends to recover less accurate trees than
 data partitioning and CAT-GTR. Given these results, we conclude that
 partitioning and CAT-GTR perform similarly in recovering accurate
 branching patterns. However, computation time can be orders of magnitude
 less for data partitioning, with commonly used implementations of CAT-GTR
 often failing to reach completion in a reasonable time frame (i.e., for
 Bayesian analyses to converge). Practices such as removing constant sites
 and parsimony uninformative characters, or using CAT-F81 when CAT-GTR is
 deemed too computationally expensive, cannot be logically justified. Given
 clear problems with CAT-F81, phylogenies previously inferred with this
 model should be reassessed.
description: Supplementary_Text_and_TablesSupplementary text and supplementary tablesNexusFiles_PartitionFiles_ProgramCommandsData files used for this studySupplementary_FiguresZip file of all supplementary figures
DOI: 10.5061/dryad.f68th
title: Data from: Seed set variation in wild Clarkia populations: teasing apart the effects of seasonal resource depletion, pollen quality, and pollen quantity

description: In habitats where resource availability declines during the growing
 season, selection may favor early-flowering individuals. Under such
 ephemerally favorable conditions, late-blooming species (and individuals)
 may be particularly vulnerable to resource limitation of seed production.
 In California, a region prone to seasonal drought, members of the annual
 genus Clarkia are among the last to flower in the spring. We compared
 pollen limitation (PL) of seed set and outcrossing rates between early-
 and late-flowering individuals in two mixed-mating Clarkia taxa to detect
 whether flowering time is associated with changes in seed set due to
 resource depletion, PL, or increased selfing. In 2008–2010, we
 hand-pollinated one flower on a total of 1855 individual plants either
 Early (near the onset of flowering) or Late (near the end of flowering) in
 the flowering season and compared seed set to adjacent, open-pollinated
 flowers on the same stem. To assess the contribution of pollen quality to
 reproduction, we first (2008) used allozymes to estimate outcrossing rates
 of seeds produced by Early and Late open-pollinated flowers. Second
 (2009), we conducted an anther-removal experiment to estimate self-pollen
 deposition. Seed set in Clarkia unguiculata was not pollen-limited.
 Clarkia xantiana ssp. xantiana was pollen-limited in 2008 and 2010, but
 not 2009. PL did not differ between Early and Late treatments. In both
 taxa, seed set of Early flowers was greater than Late flowers, but not due
 to PL in the latter. Reproduction was generally pollinator-dependent. Most
 pollen deposition was xenogamous, and outcrossing rates were &gt;0.7 –
 and similar between Early and Late periods. These results suggest that
 pollen receipt and pollen quality remain seasonally consistent. By
 contrast, the resources necessary to provision seeds decline, reducing the
 fitness benefits associated with resource allocation to ovules.
description: Hove et al. Seed Set
 Data 2008-2010This Excel file contains
 data on seed set in Clarkia unguiculata and Clarkia xantiana ssp. xantiana
 from 2008-2010.Hove et al. Pollen
 Deposition DataThis Excel file contains
 data on pollen deposition for the plants used in a floral emasculation
 study that estimated the relative contribution of outcrossing,
 geitonogamous selfing, and autogamous selfing to seed set in Clarkia
 unguiculata and Clarkia xantiana ssp. xantiana.Hove et al. Allozyme
 DataThis Excel file contains
 data reporting the allozyme genotypes used to estimate outcrossing rates
 in Clarkia unguiculata and Clarkia xantiana ssp. xantiana populations in
 2008.
DOI: 10.11583/dtu.31134109
title: DATA for publication: Electrochemical operando TEM analysis of single gadolinia-doped ceria nanofiber

description: Data for the publication:W.L. Dacayan, C. Chatzichristodoulou, Z. Ma, W. Zhang, J.-C. Grivel, K.S. Mølhave, S.B. Simonsen<b>:</b><b> </b>“Electrochemical operando TEM analysis of single gadolinia-doped ceria nanofiber” Electrochimica Acta 529 (2025) 146349, DOI: 10.1016/j.electacta.2025.146349
DOI: 10.11583/dtu.31134109.v1
title: DATA for publication: Electrochemical operando TEM analysis of single gadolinia-doped ceria nanofiber

description: Data for the publication:W.L. Dacayan, C. Chatzichristodoulou, Z. Ma, W. Zhang, J.-C. Grivel, K.S. Mølhave, S.B. Simonsen<b>:</b><b> </b>“Electrochemical operando TEM analysis of single gadolinia-doped ceria nanofiber” Electrochimica Acta 529 (2025) 146349, DOI: 10.1016/j.electacta.2025.146349
DOI: 10.15468/dl.w46fxg
title: Occurrence Download

description: A dataset containing 465 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Venezuela (Bolivarian Republic of)",
 "OccurrenceStatus is Present",
 "TaxonKey is Culex quinquefasciatus"
 ]
}

 The dataset includes 465 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001470-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7kb45
title: Data from: Multiple dispersal vectors drive range expansion in an invasive marine species

description: The establishment and subsequent spread of invasive species is widely
 recognized as one of the most threatening processes contributing to global
 biodiversity loss. This is especially true for marine and estuarine
 ecosystems, which have experienced significant increases in the number of
 invasive species with the increase in global maritime trade. Understanding
 the rate and mechanisms of range expansion is therefore of significant
 interest to ecologists and conservation managers alike. Using a
 combination of population genetic surveys, environmental DNA (eDNA)
 plankton sampling and hydrodynamic modelling, we examined the patterns of
 introduction of the predatory Northern Pacific seastar (Asterias
 amurensis) and pathways of secondary spread within southeast Australia.
 Genetic surveys across the invasive range reveal some genetic divergence
 between the two main invasive regions and no evidence of ongoing gene
 flow, a pattern that is consistent with the establishment of the second
 invasive region via a human-mediated translocation event. In contrast,
 hydrodynamic modelling combined with eDNA plankton sampling demonstrated
 that the establishment of range expansion populations within a region is
 consistent with natural larval dispersal and recruitment. Our results
 suggest that both anthropogenic and natural dispersal vectors have played
 an important role in the range expansion of this species in Australia. The
 multiple modes of spread combined with high levels of fecundity and a long
 larval duration in A. amurensis suggests it is likely to continue its
 range expansion and significantly impact Australian marine ecosystems.
description: Microsatellite_genotypes_genepopThe Microsatellite genotypes used in the genepop formatAustralian_data_genepop.txtmicrosatellite_genotypes_structureThe micorsatellite genotype input file for STRUCTURE analysisAustralian_data_Structure_in.txtSTRUCTURE_config_fileThe main parameters file required to rerun our STRUCTURE analysismainparams1Popgen_analysis_RscriptThe R code to rerun our population genetic analysis - the best way to use it is to copy and paste into your R terminalPopgen_analysis.Rmicrosatellite_genotypes_VIC_subsetSubset of the microsatellite genotypes for just Victorian populations - needed by the R scriptAustralian_data_VIC.genmicrosatellite_genotypes_TAS_subsetSubset of the microsatellite genotypes for just Tasmanian populations - needed by the R scriptAustralian_data_Tas.txtdispersal_modelling_dataOutput of the dispersal modelling run on the Connie2 interface - data is represented and Long and Lat for model cells and the probability of particles dispersing through those cellsVic_popgen_locationsLong and Lat of the Victorian sites - used to test for IBD in Victorian - needed by the R scriptVic_popgen_loc4dist.txtCoDiDi_REInput file for the CoDiDi program
DOI: 10.5061/dryad.3dp50
title: Data from: Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin

description: Understanding how natural selection generates and maintains adaptive
 genetic diversity in heterogeneous environments is key to predicting the
 evolutionary response of populations to rapid environmental change.
 Detecting selection in complex spatial environments remains challenging,
 especially for threatened species where the effects of strong genetic
 drift may overwhelm signatures of selection. We carried out a basinwide
 riverscape genomic analysis in the threatened southern pygmy perch
 (Nannoperca australis), an ecological specialist with low dispersal
 potential. High-resolution environmental data and 5162 high-quality
 filtered SNPs were used to clarify spatial population structure and to
 assess footprints of selection associated with a steep hydroclimatic
 gradient and with human disturbance across the naturally and
 anthropogenically fragmented Murray–Darling Basin (Australia). Our
 approach included FST outlier tests to define neutral loci, and a
 combination of spatially explicit genotype–environment association
 analyses to identify candidate adaptive loci while controlling for the
 effects of landscape structure and shared population history. We found low
 levels of genetic diversity and strong neutral population structure
 consistent with expectations based on spatial stream hierarchy and life
 history. In contrast, variables related to precipitation and temperature
 appeared as the most important environmental surrogates for putatively
 adaptive genetic variation at both regional and local scales. Human
 disturbance also influenced the variation in candidate loci for
 adaptation, but only at a local scale. Our study contributes to
 understanding of adaptive evolution along naturally and anthropogenically
 fragmented ecosystems. It also offers a tangible example of the potential
 contributions of landscape genomics for informing in situ and ex situ
 conservation management of biodiversity.
description: Reference sequences for
 5162 lociFasta file of the
 reference sequences used for calling 5162 SNPs for Nannoperca
 australis.SPP5162_reference.fastaSPPLG_263_5162.struData in STRUCTURE input format for 263 individuals and 5162 SNP lociEnvironmental dataEnvironmental data for 40 variables at 25 Nannoperca australis sampling locations.SPPLG_Env.txtTable_S8-S11Supplementary tables S8-S11 describing the BLAST and annotation results.