cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.16n10
title: Data from: Predicting the outcome of competition when fitness inequality is variable

description: Traditional niche theory predicts that when species compete for one
 limiting resource in simple ecological settings the more fit competitor
 should exclude the less fit competitor. Since the advent of neutral theory
 ecologists have increasingly become interested both in how the magnitude
 of fitness inequality between competitors and stochasticity may affect
 this prediction. We used numerical simulations to investigate the outcome
 of two-species resource competition along gradients of fitness inequality
 (inequality in R*) and initial population size in the presence of
 demographic stochasticity. We found that the deterministic prediction of
 more fit competitors excluding less fit competitors was often unobserved
 when fitness inequalities were low or stochasticity was strong, and
 unexpected outcomes such as dominance by the less fit competitor,
 long-term co-persistence of both competitors or the extinction of both
 competitors could be common. By examining the interaction between fitness
 inequality and stochasticity our results mark the range of parameter space
 in which the predictions of niche theory break down most severely, and
 suggest that questions about whether competitive dynamics are driven by
 neutral or niche processes may be locally contingent.
description: RSOS Submission Code and
 DataData files used in
 analysis of Pedruski et al. "Predicting the outcome of competition
 when fitness inequality is variable", and script files (code)
 necessary to produce these data files and associated
 figures.
DOI: 10.5061/dryad.5090r
title: Data from: Editor and reviewer gender influence the peer review process but not peer review outcomes at an ecology journal

description: Lack of diversity on editorial boards might generate disparities in
 editorial and peer review that contribute to gender and geographic
 disparities in scholarly publishing. We use a comprehensive data set of
 the peer review process for all papers submitted to the journal Functional
 Ecology from January 2004 to June 2014 to examine how gender, seniority
 and geographic location of editors and reviewers influence reviewer
 recruitment and scores given to papers by reviewers. The gender ratio of
 editors for Functional Ecology was majority male, but the proportion of
 female editors increased over time. The gender ratio of selected reviewers
 was also highly majority male, but the proportion of women selected as
 reviewers increased over the 10 years largely because the number of women
 on the editorial board increased and female editors invited more female
 reviewers than did male editors. Male editors selected &lt;25% female
 reviewers even in the year they selected the most women, but female
 editors consistently selected ˜30–35% female reviewers. Editors also
 over-selected reviewers from their own geographic locality. Women invited
 to review were less likely to respond to review invitations, but more
 likely to accept if they responded. Women invited to review responded to
 the invitation similarly regardless of whether the editor inviting them
 was male or female, but men invited to review were both less likely to
 respond and more likely to decline if the editor was female. Review scores
 given to papers did not differ between male and female reviewers, and
 final decisions (proportion of papers rejected) did not differ between
 male and female editors. The proportion of women among selected reviewers
 decreased with editor seniority when the editor was male but increased
 with editor seniority when the editor was female. Thus, the gender ratio
 of selected reviewers differed little between early-career male and female
 editors but differed a lot between late-career (more senior) male and
 female editors. Individuals invited to review were less likely to agree to
 review if the editor was more senior. Editor gender, seniority and
 geographic location affect who is invited to review for Functional
 Ecology, and how invitees respond to review invitations, but not the final
 outcome of the peer review process. To increase diversity of reviewer
 populations, journals should increase gender, age and geographic diversity
 of their editorial boards.
description: Fox et al_Reviewer and
 editor gender influence the peer review processFox et al_reviewers and
 editors.xlsx
DOI: 10.7910/dvn/lii9wh
title: Comparative Cues, Not Uniform Distrust: Foreign Media and Tiered Political Trust in China (Replication Package)

description: This dataset provides a replication package for: "Comparative Cues, Not Uniform Distrust: Foreign Media and Tiered Political Trust in China" (Zhao & Liu).
It includes (i) a de-identified replication dataset derived from the publicly released 2021 Internet Users' Social Awareness Survey (analytic N = 3,693), (ii) reproducible analysis scripts, and (iii) documentation (survey instruments and codebook).

For Dataverse-safe sharing, the public replication dataset includes only variables required to reproduce the reported results and excludes survey administration metadata, device/platform strings, and open-ended text fields.

File: replication_package_updated.zip
DOI: 10.15468/dl.97u2pt
title: Occurrence Download

description: A dataset containing 1676 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Boechera stricta (Graham) Al-Shehbaz"
 ]
}

 The dataset includes 1676 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192213-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18390407
title: VSL_BRAND1_200F_1_23C_0k_EDLC_single

description: Part of the Variable Temperature DataBase: Temp: 23°C
DOI: 10.5281/zenodo.18390406
title: VSL_BRAND1_200F_1_23C_0k_EDLC_single

description: Part of the Variable Temperature DataBase: Temp: 23°C
DOI: 10.5061/dryad.2j48p
title: Data from: Seasonal variation in life history traits in two Drosophila species

description: Seasonal environmental heterogeneity is cyclic, persistent and
 geographically widespread. In species that reproduce multiple times
 annually, environmental changes across seasonal time may create different
 selection regimes that may shape the population ecology and life history
 adaptation in these species. Here, we investigate how two closely related
 species of Drosophila in a temperate orchard respond to environmental
 changes across seasonal time. Natural populations of Drosophila
 melanogaster and D. simulans were sampled at four timepoints from June
 through November to assess seasonal change in fundamental aspects of
 population dynamics as well as life history traits. D. melanogaster
 exhibit pronounced change across seasonal time: early in the season, the
 population is inferred to be uniformly young and potentially represents
 the early generation following overwintering survivorship. D. melanogaster
 isofemale lines derived from the early population and reared in a common
 garden are characterized by high tolerance to a variety of stressors as
 well as a fast rate of development in the laboratory environment that
 declines across seasonal time. In contrast, wild D. simulans populations
 were inferred to be consistently heterogeneous in age distribution across
 seasonal collections; only starvation tolerance changed predictably over
 seasonal time in a parallel manner as in D. melanogaster. These results
 suggest fundamental differences in population and evolutionary dynamics
 between these two taxa associated with seasonal heterogeneity in
 environmental parameters and associated selection pressures.
description: StarvationData documenting hours of survival when flies are in starvation conditions for wild-derived isofemale lines collected across seasonal time.AgingData documenting post-capture survival in days for wild flies caught across seasonal time and full lifespan of their F1 offspring.Chill Coma RecoveryData documenting minutes to recovery after an ice bath for wild-derived isofemale lines collected across seasonal time.Development TimeData documenting development time of wild-derived isofemale lines collected across seasonal time.FecundityData documenting post-capture fecundity of wild female Drosophila across seasonal time.Heat KnockdownData documenting knockdown time when Drosophila are exposed to 37C for wild-derived isofemale lines collected across seasonal time.metadataDescription of the data collected and the variable names.
DOI: 10.15468/dl.wnauvg
title: Occurrence Download

description: A dataset containing 4994 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((2.6792 48.39082,2.67784 48.38823,2.68837 48.38678,2.68952 48.38987,2.6792 48.39082))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 4994 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001646-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bv3gm
title: Data from: Genes mirror geography in Daphnia magna

description: Identifying the presence and magnitude of population genetic structure
 remains a major consideration in evolutionary biology as doing so allows
 one to understand the demographic history of a species as well as make
 predictions of how the evolutionary process will proceed. Next-generation
 sequencing methods allow us to reconsider previous ideas and conclusions
 concerning the distribution of genetic variation, and what this
 distribution implies about a given species evolutionary history. A
 previous phylogeographic study of the crustacean Daphnia magna suggested
 that, despite strong genetic differentiation among populations at a local
 scale, the species shows only moderate genetic structure across its
 European range, with a spatially patchy occurrence of individual lineages.
 We apply RAD sequencing to a sample of D. magna collected across a wide
 swath of the species' Eurasian range and analyse the data using
 principle component analysis (PCA) of genetic variation and Procrustes
 analytical approaches, to quantify spatial genetic structure. We find
 remarkable consistency between the first two PCA axes and the geographic
 coordinates of individual sampling points, suggesting that, on a
 continent-wide scale, genetic differentiation is driven to a large extent
 by geographic distance. The observed pattern is consistent with unimpeded
 (i.e. no barriers, landscape or otherwise) migration at large spatial
 scales, despite the fragmented and patchy nature of favourable habitats at
 local scales. With high-resolution genetic data similar patterns may be
 uncovered for other species with wide geographic distributions, allowing
 an increased understanding of how genetic drift and selection have shaped
 their evolutionary history.
description: D_magna_RADseq.vcfPolymorphism data derived from 24 Daphnia magna clones, generated using the GATK v.3 pipeline.variant_calling.txtDescription of the GATK pipeline used for generating .vcf file for 24 D. magna individuals.smartpca_run.txtDescriptions of the creation and commands to use SmartPCA to generate PCA eigenvectors and eigenvalues.Procrustes_test.txtR commands to run Procrustes rotation and significance test.relatedness_analysis.txtScripts for using VCFtools and R to assess relationship between pair-wise relatedness and distance.Geographic_distance_matrix.txtPair-wise genetic distance between sampled clones, in kilometers.Pairwise_relatedness_full_dataset.txtEstimates of pairwise relatedness derived from a full dataset of all clones, using VCFtools.Pairwise_relatedness_full_MNremoved.txtEstimates of pairwise relatedness derived from a reduced dataset of clones, with the Mongolian clone removed, using VCFtools.Pairwise_relatedness_full_MNandILremoved.txtEstimates of pairwise relatedness derived from a reduced dataset of clones, with the Mongolian and Israel clone removed, using VCFtools.
DOI: 10.5061/dryad.877n3
title: Data from: Mutations in different pigmentation genes are associated with parallel melanism in island flycatchers

description: The independent evolution of similar traits across multiple taxa provides
 some of the most compelling evidence of natural selection. Little is
 known, however, about the genetic basis of these convergent or parallel
 traits: are they mediated by identical or different mutations in the same
 genes, or unique mutations in different genes? Using a combination of
 candidate gene and reduced representation genomic sequencing approaches,
 we explore the genetic basis of and the evolutionary processes that
 mediate similar plumage colour shared by isolated populations of the
 Monarcha castaneiventris flycatcher of the Solomon Islands. A genome-wide
 association study (GWAS) that explicitly controlled for population
 structure revealed that mutations in known pigmentation genes are the best
 predictors of parallel plumage colour. That is, entirely black or melanic
 birds from one small island share an amino acid substitution in the
 melanocortin-1 receptor (MC1R), whereas similarly melanic birds from
 another small island over 100 km away share an amino acid substitution in
 a predicted binding site of agouti signalling protein (ASIP). A third
 larger island, which separates the two melanic populations, is inhabited
 by birds with chestnut bellies that lack the melanic MC1R and ASIP allelic
 variants. Formal FST outlier tests corroborated the results of the GWAS
 and suggested that strong, directional selection drives the near fixation
 of the MC1R and ASIP variants across islands. Our results, therefore,
 suggest that selection acting on different mutations with large phenotypic
 effects can drive the evolution of parallel melanism, despite the
 relatively small population size on islands.
description: MClade_MC1R_ASIP.hmpA hapmap (text) file containing all of the SNPs and their genotypes in each individual that were used in the genome-wide association analysis. (See TASSEL documentation for more info. on the hapmap format).Mon_filter10X.hmpA hapmap file containing SNPs for the same data set, but in this case reads were filtered with a depth minimum of 10X (versus 5X) before SNP calling.
DOI: 10.5061/dryad.g3jc1
title: Data from: Higher genetic diversity in recolonized areas than in refugia of Alnus glutinosa triggered by continent-wide lineage admixture

description: Genetic admixture is supposed to be an important trigger of species
 expansions because it can create the potential for selection of genotypes
 suitable for new climatic conditions. Up until now, however, no
 continent-wide population genetic study has performed a detailed
 reconstruction of admixture events during natural species expansions. To
 fill this gap, we analysed the postglacial history of Alnus glutinosa, a
 keystone species of European swamp habitats, across its entire
 distribution range using two molecular markers, cpDNA and nuclear
 microsatellites. CpDNA revealed multiple southern refugia located in the
 Iberian, Apennine, Balkan and Anatolian Peninsulas, Corsica and North
 Africa. Analysis of microsatellites variation revealed three main
 directions of postglacial expansion: (i) from the northern part of the
 Iberian Peninsula to Western and Central Europe and subsequently to the
 British Isles, (ii) from the Apennine Peninsula to the Alps and (iii) from
 the eastern part of the Balkan Peninsula to the Carpathians followed by
 expansion towards the Northern European plains. This challenges the
 classical paradigm that most European populations originated from refugial
 areas in the Carpathians. It has been shown that colonizing lineages have
 met several times and formed secondary contact zones with unexpectedly
 high population genetic diversity in Central Europe and Scandinavia. On
 the contrary, limited genetic admixture in southern refugial areas of A.
 glutinosa renders rear-edge populations in the Mediterranean region more
 vulnerable to extinction due to climate change.
description: A_glutinosa_haplotypes_alignmentA_glutinosa_haplotypes_TreeMBA_glutinosa_haplotypes_TreeMPmicrosatellite_genotypesStructure_input_file
DOI: 10.5061/dryad.k8hr0
title: Data from: A multi-breed genome-wide association analysis for canine hypothyroidism identifies a shared major risk locus on CFA12

description: [No abstract entered]
description: Bianchi, Dahlgren et
 al., Canine Hypothyroidism data
DOI: 10.5061/dryad.8f230
title: Data from: Auxotrophy and intra-population complementary in the 'interactome' of a cultivated freshwater model community

description: Microorganisms are usually studied either in highly complex natural
 communities or in isolation as monoclonal model populations that we manage
 to grow in the laboratory. Here, we uncover the biology of some of the
 most common and yet-uncultured bacteria in freshwater environments using a
 mixed culture from Lake Grosse Fuchskuhle. From a single shotgun
 metagenome of a freshwater mixed culture of low complexity, we recovered
 four high-quality metagenome-assembled genomes (MAGs) for metabolic
 reconstruction. This analysis revealed the metabolic interconnectedness
 and niche partitioning of these naturally dominant bacteria. In
 particular, vitamin- and amino acid biosynthetic pathways were distributed
 unequally with a member of Crenarchaeota most likely being the sole
 producer of vitamin B12 in the mixed culture. Using coverage-based
 partitioning of the genes recovered from a single MAG intrapopulation
 metabolic complementarity was revealed pointing to ‘social’ interactions
 for the common good of populations dominating freshwater plankton. As
 such, our MAGs highlight the power of mixed cultures to extract naturally
 occurring ‘interactomes’ and to overcome our inability to isolate and grow
 the microbes dominating in nature.
description: 16SrRNA+PhyloPhlAnThis is a zip file that contains three folders. One folder includes all raw data from the 16S amplicons used to create figure 1. Another folder includes the aligned 16S for creating figure S2. The last folder includes the whole tree data, protein alignments and taxa code for creating figure 2.
DOI: 10.5061/dryad.7gr39
title: Data from: An empirical review: characteristics of plant microsatellite markers that confer higher levels of genetic variation

description: During microsatellite marker development, researchers must choose from a
 pool of possible primer pairs to further test in their species of
 interest. In many cases, the goal is maximizing detectable levels of
 genetic variation. To guide researchers and determine which markers are
 associated with higher levels of genetic variation, we conducted a
 literature review based on 6782 genomic microsatellite markers published
 from 1997–2012. We examined relationships between heterozygosity (He or
 Ho) or allele number (A) with the following marker characteristics: repeat
 type, motif length, motif region, repeat frequency, and microsatellite
 size. Variation across taxonomic groups was also analyzed. There were
 significant differences between imperfect and perfect repeat types in A
 and He. Dinucleotide motifs exhibited significantly higher A, He, and Ho
 than most other motifs. Repeat frequency and motif region were positively
 correlated with A, He, and Ho, but correlations with microsatellite size
 were minimal. Higher taxonomic groups were disproportionately represented
 in the literature and showed little consistency. In conclusion,
 researchers should carefully consider marker characteristics so they can
 be tailored to the desired application. If researchers aim to target high
 genetic variation, dinucleotide motif lengths with large repeat
 frequencies may be best.
description: Plant Microsatellite
 DatabaseThis database contains
 plant microsatellite markers (Simple Sequence Repeats; SSRs) for the
 larger part of the last two decades. The dataset was compiled in an Excel
 2007 spreadsheet from the Molecular Ecology Resources online database
 (where authors are required to submit primer information as a condition of
 publication) at http://tomato.bio.trinity.edu or were manually compiled
 from published articles in Molecular Ecology, Molecular Ecology Notes,
 Molecular Ecology Resources, and American Journal of Botany (AJB),
 spanning in total from 1997 to 2012. The articles were found by screening
 the Scopus (Elsevier) search engine. Please see the publication for more
 specifics on how the dataset was compiled and analyzed. Null values are
 represented with a period (‘.’). We have included a ReadMe file to
 describe column headings.Microsatellite_Database.csvExcluded entriesThis file contains entries that were purposefully removed from our analyzed dataset. Please see the publication for more details. The ReadMe file is the same as that associated with the Plant Microsatellite Database file and contains column heading descriptions.Excluded_entries.csv
DOI: 10.5066/p13mls8b
title: Vegetation and land use/land cover of the Altar Valley, AZ mapped from Sentinel-2 data (2024)

description: This data release provides 10-meter vegetation and land-use/land-cover (LULC) maps for the Santa Margarita Ranch and the surrounding Altar Valley and Brawley Wash region of southern Arizona. Maps were generated for 2024 using two complementary Random Forest classification approaches implemented in Google Earth Engine (GEE): (1) a seasonal Sentinel-2 (S2) spectral–topographic model based on early- and late-season (ESLS) composites, and an additional model (2) based on Google’s Satellite Embedding V1 dataset. Both approaches incorporate 21 LULC classes derived from the USGS GAP CONUS 2011 land cover classification scheme available in GEE. Developed and agricultural classes were adapted directly from the 2021 National Land Cover Database (NLCD) to ensure consistent representation of human-modified land. Across the two models, predictor variables include Sentinel-2 surface reflectance bands, vegetation and moisture indices, seasonal differences, Google embedding bands, and 10-m terrain derivatives from the USGS 3D Elevation Program (3DEP). Each classification product is provided as a 10-m GeoTIFF accompanied by an ArcGIS auxiliary metadata file (.tif.aux.xml) that stores the raster’s virtual attribute table (VAT). The VAT contains the GAP land-cover codes, class descriptions, and color scheme used for visualization, along with the corresponding NLCD 2021 class codes, descriptions, and colors. NLCD attributes are included to document pixels where developed and agricultural classes were burned into the final map and to provide a built-in crosswalk, allowing users to reclassify the dataset into the NLCD scheme if needed. Accuracy assessment results are provided as CSV files and include overall accuracy, Kappa, per-class producer’s and user’s accuracy, and the confusion matrix.