cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5m6t4
title: Data from: Genes of the major histocompatibility complex highlight interactions of the innate and adaptive immune system

description: Background: A well-functioning immune defence is crucial for fitness, but
 our knowledge about the immune system and its complex interactions is
 still limited. Major histocompatibility complex (MHC) molecules are
 involved in T-cell mediated adaptive immune responses, but MHC is also
 highly upregulated during the initial innate immune response. The aim of
 our study was therefore to determine to what extent the highly polymorphic
 MHC is involved in interactions of the innate and adaptive immune defence
 and if specific functional MHC alleles (FA) or heterozygosity at the MHC
 are more important. Methods: To do this we used captive house sparrows
 (Passer domesticus) to survey MHC diversity and immune function
 controlling for several environmental factors. MHC class I alleles were
 identified using parallel amplicon sequencing and to mirror immune
 function, several immunological tests that correspond to the innate and
 adaptive immunity were conducted. Results: Our results reveal that MHC was
 linked to all immune tests, highlighting its importance for the immune
 defence. While all innate responses were associated with one single FA,
 adaptive responses (cell-mediated and humoral) were associated with
 several different alleles. Discussion: We found that repeated injections
 of an antibody in nestlings and adults were linked to different FA and
 hence might affect different areas of the immune system. Also, individuals
 with a higher number of different FA produced a smaller secondary
 response, indicating a disadvantage of having numerous MHC alleles. These
 results demonstrate the complexity of the immune system in relation to the
 MHC and lay the foundation for other studies to further investigate this
 topic.
description: 454-input -
 primersJMHC454-input - R1 -
 1.TCA.454Reads454-input - R1 -
 2.TCA.454Reads454-input - R1 -
 Primertags454-input - R2 -
 1.TCA.454Reads454-input - R2 -
 2.TCA.454Reads454-input - R2 -
 Primertags454-output - R1
 output454-output -
 R1454-output - R2
 output454-output -
 R2Genotype and phenotype
 table PeerJ 082017Microsatellite genotype
 tableSequence allignment -
 All 59 functional MHC alleles from this studySequence allignment -
 All 85 MHC alleles from this study
DOI: 10.5061/dryad.ts895r1
title: Data from: Molecular palaeontology illuminates the evolution of ecdysozoan vision

description: Colour vision is known to have arisen only twice – once in Vertebrata and
 once within the Ecdysozoa, in Arthropoda. However, the evolutionary
 history of ecdysozoan vision is unclear. At the molecular level, visual
 pigments, composed of a chromophore and a protein belonging to the opsin
 family, have different spectral sensitivities and these mediate colour
 vision. At the morphological level, ecdysozoan vision is conveyed by eyes
 of variable levels of complexity; from the simple ocelli observed in the
 velvet worms (phylum Onychophora) to the marvellously complex eyes of
 insects, spiders and crustaceans. Here we explore the evolution of
 ecdysozoan vision at both the molecular and morphological level; combining
 analysis of a large-scale opsin dataset that includes previously-unknown
 ecdysozoan opsins with morphological analyses of key Cambrian fossils with
 preserved eye structures. We found that while several non-arthropod
 ecdysozoan lineages have multiple opsins, arthropod multi-opsin vision
 evolved through a series of gene duplications were fixed in a period of 35
 to 71 Million years (Ma) along the stem-arthropod lineage. Our integrative
 study of the fossil and molecular record of vision indicates that fossils
 with more complex eyes were likely to have possessed a larger complement
 of opsin genes.
description: RevBayes
 AnalysesThis folder contains
 data scripts and results of our RevBayes analysesRevBayesAnalysis_Oct2018.zipALE analysesThis include data scripts and results of ALE analysesALE.tar.gzAnalyses of Prank Aligned SequencesThis fine include the data scripts and results of the analyses we performed on a PRANK aligned datasetPRANKPrelim.tar.gzPreliminary Analyses of MUSCLE aligned sequencesThis include the preliminary alignment generated with MUSCLE and results of analyses obtained from its phylogenetic analysesMUSCLEPrelim.tar.gzMuscle Aligned Sequences Final AnalysesThis is the final alignment we generated plus results of its analyses.MUSCLEFinalAnalysis.tar.gzOpsin Divergence timesRelaxed (CIR) Molecular clock analyses of the Opsin final MUSCLE alignmentMolecularClockPB.tar.gz
DOI: 10.5061/dryad.8m2q8
title: Data from: The arrangement of possible muscle fibres in the Ediacaran taxon Haootia quadriformis

description: Haootia quadriformis from Newfoundland, Canada, is one of the most unusual
 impressions of a soft-bodied macro-organism yet described from the late
 Ediacaran Period. Interpreted as a metazoan of cnidarian grade, the body
 impression of H. quadriformis possesses features interpreted as fibrous
 structures that represent possible evidence for muscular tissue. Evidence
 both in support of and against a relationship between H. quadriformis and
 the Staurozoa, one of the cnidarian groups to which Haootia was compared
 in Liu et al., is outlined by Miranda et al.. Our intention in our
 original paper was to illustrate the staurozoan body plan for comparative
 purposes, rather than suggest homology or direct ancestry. Nevertheless,
 fresh insights from workers with expertise in the biology of extant
 cnidarians are welcomed.
description: haootia02Image of the Haootia quadriformis holotype specimen, taken under low lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, Canada, by Duncan McIlroy.haootia03Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.haootia04Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.haootia05Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.haootia07Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.haootia09Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.haootia10Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.haootia11Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.haootia13Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.haootia14Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.haootia15 labelImage of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.haootia106Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.
DOI: 10.5281/zenodo.18378484
title: Hurricanes along the Southeast Atlantic Coast build marsh resiliency through mineral sedimentation (Dataset)

description: The current online repository contains the datasets used to produce the figures and the analyses presented in the paper “Hurricanes along the Southeast Atlantic Coast build marsh resiliency through mineral sedimentation”. In this study we quantify the depositional impact of Hurricane Irma (September 2017) on four salt marshes in the southeastern United States.In addition to the datasets, this repository contains a readme file (Hurricane_irma_metadata.docx) to serve as a guide as it outlines the file names, explanation for each variable and parameter included, and example of usage. The Version v2 of this repository (26-01-2026) also contains photos and X-Ray of the cores used for the study, as well as an updated calculation of bulk density for some of the Hilton Head cores.
DOI: 10.15468/dl.zw8ag3
title: Occurrence Download

description: A dataset containing 27636 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Puma concolor"
 ]
}

 The dataset includes 27636 records from 460 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000359-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16655535
title: Hurricanes along the Southeast Atlantic Coast build marsh resiliency through mineral sedimentation (Dataset)

description: The current online repository contains the datasets used to produce the figures and the analyses presented in the paper “Hurricanes along the Southeast Atlantic Coast build marsh resiliency through mineral sedimentation”. In this study we quantify the depositional impact of Hurricane Irma (September 2017) on four salt marshes in the southeastern United States.In addition to the datasets, this repository contains a readme file (Hurricane_irma_metadata.docx) to serve as a guide as it outlines the file names, explanation for each variable and parameter included, and example of usage. The Version v2 of this repository (26-01-2026) also contains photos and X-Ray of the cores used for the study, as well as an updated calculation of bulk density for some of the Hilton Head cores.
DOI: 10.5061/dryad.m8g90
title: Data from: Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus

description: The bacterial communities inhabiting arthropods are generally dominated by
 a few endosymbionts that play an important role in the ecology of their
 hosts. Rather than comparing bacterial species richness across samples,
 ecological studies on arthropod endosymbionts often seek to identify the
 main bacterial strains associated with each specimen studied. The
 filtering out of contaminants from the results and the accurate taxonomic
 assignment of sequences are therefore crucial in arthropod microbiome
 studies. We aimed here to validate an Illumina 16S rRNA gene sequencing
 protocol and analytical pipeline for investigating endosymbiotic bacteria
 associated with aphids. Using replicate DNA samples from 12 species
 (Aphididae: Lachninae, Cinara) and several controls, we removed individual
 sequences not meeting a minimum threshold number of reads in each sample
 and carried out taxonomic assignment for the remaining sequences. With
 this approach, we show that: i) contaminants accounted for a negligible
 proportion of the bacteria identified in our samples; ii) the taxonomic
 composition of our samples and the relative abundance of reads assigned to
 a taxon were very similar across PCR and DNA replicates for each aphid
 sample; in particular, bacterial DNA concentration had no impact on the
 results. Furthermore, by analysing the distribution of unique sequences
 across samples rather than aggregating them into operational taxonomic
 units (OTUs), we gained insight into the specificity of endosymbionts for
 their hosts. Our results confirm that Serratia symbiotica is often present
 in Cinara species, in addition to the primary symbiont, Buchnera
 aphidicola. Furthermore, our findings reveal new symbiotic associations
 with Erwinia and Sodalis-related bacteria. We conclude with suggestions
 for generating and analysing 16S rRNA gene sequences for arthropod
 endosymbiont studies.
description: Illumina_16SCinaraThis is an archive containing results of the sequencing of 16S rRNA gene for all samples of the publication (the results have been demultiplexed : each file corresponds to the sequecining of a PCR product).final.aln.count_tablethis compiles the distribution of sequences across samples (this file can be uploaded to run the R script)final.aln.fastaFinal alignment of all unique sequences: output from the Galaxy pipeline, input of the R scriptAppendix1_RR script described in the paper to analyse output from Galaxy -produce summary tables (number of sequences per sample before and after applying various thresholds, distribution of sequences across samples , -scripto to conduct diversity analyses described in the paper
DOI: 10.5061/dryad.7k4c1
title: Data from: Selection and sex-biased dispersal in a coastal shark: the influence of philopatry on adaptive variation

description: Sex-biased dispersal is expected to homogenize nuclear genetic variation
 relative to variation in genetic material inherited through the
 philopatric sex. When site fidelity occurs across a heterogeneous
 environment, local selective regimes may alter this pattern. We assessed
 spatial patterns of variation in nuclear-encoded, single nucleotide
 polymorphisms (SNPs) and sequences of the mitochondrial control region in
 bonnethead sharks (Sphyrna tiburo), a species thought to exhibit female
 philopatry, collected from summer habitats used for gestation. Geographic
 patterns of mtDNA haplotypes and putatively neutral SNPs confirmed female
 philopatry and male-mediated gene flow along the northeastern coast of the
 Gulf of Mexico. A total of 30 outlier SNP loci were identified; alleles at
 over half of these loci exhibited signatures of latitude-associated
 selection. Our results indicate that in species with sex-biased dispersal,
 philopatry can facilitate sorting of locally adaptive variation, with the
 dispersing sex facilitating movement of potentially adaptive variation
 among locations and environments.
description: Filtered SNP
 VCFFinal set of filtered
 SNPsSNP.FINAL.recode.vcfSNP filtering stepsThis file outlines the exact steps to filter variant calls into a final SNP data set. Lines are commented and file is executable.Filter_Script.shTotalRawVariants.vcfCompressed VCF of all raw variant calls. Gunzip this file to follow the filtering protocol.List of loci visually identified as artifacts.These loci were visually inspected and determined to be artifactual. They were removed from all analyses.visualistFB_filters_BheadBash script used to automate part of the SNP filtering process.Population Map for IndividualsThis file lists the putative population of each individual based on collection locality.pop_map.sharkSampleCollectionInfoSpreadsheet with Sample_Name, Collection Date, Location Code, Locality, Sex, Weight (kg), and Total Length (cm) for each individual used in the study.OutlierHapsOutlier haplotype genotypes in Genepop format.NeutralHapsNeutral haplotype-based genotypes in Genepop format.HaplotypeListAligned haplotype list for mtDNA sequences.HaplistNov21.hapSample Collection information with mtDNA haplotypesSpreadsheet with Sample_Name, Collection Date, Location Code, Locality, Sex, Weight (kg), Total Length (cm), and mtDNA haplotype for each individual used in the study.SampleCollectionInfo.xlsxReference fasta fileSet of reference sequences generated by the custom dDocent codereference.fasta
DOI: 10.5061/dryad.4vd70
title: Data from: Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity.

description: How standing genetic variation within a pathogen contributes to diversity
 in host/pathogen interactions is poorly understood, partly because most
 studied pathogens are host-specific, clonally reproducing organisms which
 complicates genetic analysis. In contrast, Botrytis cinerea is a sexually
 reproducing, true haploid ascomycete that can infect a wide range of
 diverse plant hosts. While previous work had shown significant genomic
 variation between two isolates, we proceeded to assess the level and
 frequency of standing variation in a population of B. cinerea. To begin
 measuring standing genetic variation in B. cinerea, we re-sequenced the
 genomes of 13 different isolates and aligned them to the previously
 sequenced T4 reference genome. In addition one of these isolates was
 resequenced from 4 independently repeated cultures. A high level of
 genetic diversity was found within the 13 isolates. Within this variation,
 we could identify clusters of genes with major effect polymorphisms, i.e.
 polymorphisms that lead to a predicted functional knockout, that
 surrounded genes involved in controlling vegetative incompatibility. The
 genotype at these loci was able to partially predict the interaction of
 these isolates in vegetative mating assays showing that these loci control
 vegetative incompatibility. This suggests that the vegetative mating loci
 within B. cinerea are associated with regions of increased genetic
 diversity. The genome re-sequencing of four clones from the one isolate
 (Grape) that had been independently propagated over ten years showed no
 detectable spontaneous mutation. This suggests that B. cinerea does not
 display an elevated spontaneous mutation rate. Future work will allow us
 to test if, and how, this diversity may be contributing to the pathogen’s
 broad host range.
description: Botrytis_isolates_ploidy1Sequence polymorphism information for : Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity
DOI: 10.5061/dryad.246qg
title: Data from: Transformation of stimulus correlations by the retina

description: Redundancies and correlations in the responses of sensory neurons may seem
 to waste neural resources, but they can also carry cues about structured
 stimuli and may help the brain to correct for response errors. To
 investigate the effect of stimulus structure on redundancy in retina, we
 measured simultaneous responses from populations of retinal ganglion cells
 presented with natural and artificial stimuli that varied greatly in
 correlation structure; these stimuli and recordings are publicly available
 online. Responding to spatio-temporally structured stimuli such as natural
 movies, pairs of ganglion cells were modestly more correlated than in
 response to white noise checkerboards, but they were much less correlated
 than predicted by a non-adapting functional model of retinal response.
 Meanwhile, responding to stimuli with purely spatial correlations, pairs
 of ganglion cells showed increased correlations consistent with a static,
 non-adapting receptive field and nonlinearity. We found that in response
 to spatio-temporally correlated stimuli, ganglion cells had faster
 temporal kernels and tended to have stronger surrounds. These properties
 of individual cells, along with gain changes that opposed changes in
 effective contrast at the ganglion cell input, largely explained the
 pattern of pairwise correlations across stimuli where receptive field
 measurements were possible.
description: Spike and Stimulus
 Timing DataData.zipFullFieldFlickerFull-field flicker stimuli used in experiments. See README.txt associated with Data.zip.LowContrastStimuliLow-contrast white noise and multiscale stimuli used in experiments. See README.txt associated with Data.zip.MultiscaleCorrNoiseMultiscale correlated (scale-invariant) stimuli used in experiments. See README.txt associated with Data.zip.ExponentialCorrNoiseExponentially correlated stimuli used in experiments. See README.txt associated with Data.zip.NaturalStimuliNatural movie and scrambled natural movie stimuli used in experiments. See README.txt associated with Data.zip.WhiteNoiseWhite noise checkerboard stimuli used in experiments. See README.txt associated with Data.zip.
DOI: 10.5061/dryad.2c47d
title: Data from: Asymmetric visual input and route recapitulation in homing pigeons

description: Pigeons (Columba livia) display reliable homing behaviour, but their
 homing routes from familiar release points are individually idiosyncratic
 and tightly recapitulated, suggesting that learning plays a role in route
 establishment. In light of the fact that routes are learned, and that both
 ascending and descending visual pathways share visual inputs from each eye
 asymmetrically to the brain hemispheres, we investigated how information
 from each eye contributes to route establishment, and how information
 input is shared between left and right neural systems. Using on-board
 global positioning system loggers, we tested 12 pigeons' route
 fidelity when switching from learning a route with one eye to homing with
 the other, and back, in an A-B-A design. Two groups of birds, trained
 first with the left or first with the right eye, formed new idiosyncratic
 routes after switching eyes, but those that flew first with the left eye
 formed these routes nearer to their original routes. This confirms that
 vision plays a major role in homing from familiar sites and exposes a
 behavioural consequence of neuroanatomical asymmetry whose ontogeny is
 better understood than its functional significance.
description: Ex2controlsgpx and csv files of all control flights in experiment. B number is subject identifier, number following indicates flight. L and R indicate open eye in flight. B indicates flight is binocularEx2expgpx and csv files of all experimental flights in experiment. B number is subject identifier, number following indicates flight. L and R indicate open eye in flight. B indicates flight is binocularEx2all50.zip
DOI: 10.5061/dryad.8ks16
title: Data from: Phage display peptide libraries: deviations from randomness and correctives

description: Peptide-expressing phage display libraries are widely used for the
 interrogation of antibodies. Affinity selected peptides are then analyzed
 to discover epitope mimetics, or are subjected to computational algorithms
 for epitope prediction. A critical assumption for these applications is
 the random representation of amino acids in the initial naïve peptide
 library. In a previous study we implemented Next Generation Sequencing to
 evaluate a naïve library and discovered severe deviations from randomness
 in UAG codon overrepresentation as well as in high G phosphoramidite
 abundance causing amino acid distribution biases. In this study we
 demonstrate that the UAG overrepresentation can be attributed to the
 burden imposed on the phage upon the assembly of the recombinant Protein 8
 subunits. This was corrected by constructing the libraries using
 supE44-containing bacteria which suppress the UAG driven abortive
 termination. We also demonstrate that the overabundance of G stems from
 variant synthesis-efficiency and can be corrected using compensating
 oligonucleotide-mixtures calibrated by Mass Spectroscopy. Construction of
 libraries implementing these correctives results in markedly improved
 libraries that display random distribution of amino acids, thus ensuring
 that enriched peptides obtained in biopanning represent a genuine
 selection event, a fundamental assumption for phage display applications.
description: 1st_generation_libraryThe archive includes the raw (fastq) and filtered (fasta) sequences of the 1st generation random library described in the main text.2nd_generation_libraryThe archive includes the raw (fastq) and filtered (fasta) sequences of the 2nd generation random library described in the main text.3rd_generation_libraryThe archive includes the raw (fastq) and filtered (fasta) sequences of the 3rd generation random library described in the main text.4st_generation_libraryThe archive includes the raw (fastq) and filtered (fasta) sequences of the 4st generation random library described in the main text.