cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.24732
title: Data from: Near absence of differential gene expression in the retina of rainbow trout after exposure to a magnetic pulse: implications for magnetoreception

description: The ability to perceive Earth’s magnetic field, or magnetoreception,
 exists in numerous animals. Although the mechanism underlying
 magnetoreception has not been clearly established in any species, in
 salmonid fish it is hypothesized to occur by means of crystals of
 magnetite associated with nervous tissue such as the brain, olfactory
 organ, or retina. In this study, rainbow trout (Oncorhynchus mykiss) were
 exposed to a brief magnetic pulse known to disrupt magnetic orientation
 behavior in several animals. Changes in gene expression induced by the
 pulse were then examined in the retina. Analyses indicated that the pulse
 elicited differential expression of only a single gene, gamma-crystallin
 M3-like (crygm3). The near-absence of an effect of the magnetic pulse on
 gene expression in the retina stands in sharp contrast to a recent study
 in which 181 genes were differentially expressed in brain tissue of O.
 mykiss after exposure to the same pulse. Overall, our results suggest
 either that magnetite-based magnetoreceptors in trout are not located in
 the retina, or else that they are unaffected by magnetic pulses that can
 disrupt magnetic orientation behavior in animals.
description: README
 fileThis file contains a
 description of all the contents of this data archiveExpression
 countsCounts of aligned reads
 to annotated genescounts.tsvMerged AssemblyMerged assembly files from 'cuffmerge'Merged.tar.gzSample SheetA spreadsheet of sample names and associated metadatasamplesheet.tsvNovel gene annotationsAnnotations of novel genes identified from Cufflinksnovel-genes.gtfNovel gene sequencesSequences of novel genes identified from Cufflinksnovel-genes.falncRNA top HitsThe top hit for each novel gene sequence to a database of known trout lncRNAs using BLASTNlncRNA-TopHit.tsvCuffdiff ResultsThis archive contains all the output files from cuffdiff characterizing differential expression for genes, transcripts, promoters, splice sites, etc.Cuffdiff_results.tar.gzTreatment EffectDifferential expression results for the treatment (magnetic pulse) effect from DESeq2Treatment-effect.DESeq2.tsvInteraction EffectDifferential expression results for the interaction effect from DESeq2Interaction-effect.DESeq2.tsv
DOI: 10.5061/dryad.12t21
title: Data from: On cross-frequency phase-phase coupling between theta and gamma oscillations in the hippocampus

description: Phase-amplitude coupling between theta and multiple gamma sub-bands is a
 hallmark of hippocampal activity and believed to take part in information
 routing. More recently, theta and gamma oscillations were also reported to
 exhibit phase-phase coupling, or n:m phase-locking, suggesting an
 important mechanism of neuronal coding that has long received theoretical
 support. However, by analyzing simulated and actual LFPs, here we question
 the existence of theta-gamma phase-phase coupling in the rat hippocampus.
 We show that the quasi-linear phase shifts introduced by filtering lead to
 spurious coupling levels in both white noise and hippocampal LFPs, which
 highly depend on epoch length, and that significant coupling may be
 falsely detected when employing improper surrogate methods. We also show
 that waveform asymmetry and frequency harmonics may generate artifactual
 n:m phase-locking. Studies investigating phase-phase coupling should rely
 on appropriate statistical controls and be aware of confounding factors;
 otherwise, they could easily fall into analysis pitfalls.
description: Multisite LFP recordings
 from the rat hippocampus during REM sleepREM_LFP_HPC.rar
DOI: 10.5061/dryad.5v8m0
title: Data from: Spatiotemporal measurement of surfactant distribution on gravity–capillary waves

description: Materials adsorbed onto the surface of a fluid – for instance, crude oil,
 biogenic slicks or industrial/medical surfactants – will move in response
 to surface waves. Owing to the difficulty of non-invasive measurement of
 the spatial distribution of a molecular monolayer, little is known about
 the dynamics that couple the surface waves and the evolving density field.
 Here, we report measurements of the spatiotemporal dynamics of the density
 field of an insoluble surfactant driven by gravity–capillary waves in a
 shallow cylindrical container. Standing Faraday waves and travelling waves
 generated by the meniscus are superimposed to create a non-trivial
 surfactant density field. We measure both the height field of the surface
 using moiré imaging, and the density field of the surfactant via the
 fluorescence of NBD-tagged phosphatidylcholine, a lipid. Through phase
 averaging stroboscopically acquired images of the density field, we
 determine that the surfactant accumulates on the leading edge of the
 travelling meniscus waves and in the troughs of the standing Faraday
 waves. We fit the spatiotemporal variations in the two fields using an
 ansatz consisting of a superposition of Bessel functions, and report
 measurements of the wavenumbers and energy damping factors associated with
 the meniscus and Faraday waves, as well as the spatial and temporal phase
 shifts between them. While these measurements are largely consistent for
 both types of waves and both fields, it is notable that the damping
 factors for height and surfactant in the meniscus waves do not agree. This
 raises the possibility that there is a contribution from longitudinal
 waves in addition to the gravity–capillary waves.
description: Spatiotemporal
 measurement of surfactant distribution on gravity–capillary
 wavesProvides two
 Matlab-formated (.mat) data files containing the surface height and
 surfactant concentration profiles, one for each of the two datasets
 presented in the paper. The README.txt file contains instructions about
 how to read the data into Matlab and visualize it in a manner similar to
 the paper figures.Strickland-2015-JFM.zip
DOI: 10.5061/dryad.fk41r
title: Data from: Genome assembly and annotation of the medicinal plant Calotropis gigantea, a producer of anticancer and antimalarial cardenolides

description: Calotropis gigantea produces specialized secondary metabolites known as
 cardenolides which have anti-cancer and anti-malarial properties. Although
 transcriptomic studies have been conducted in other cardenolide-producing
 species, no nuclear genome assembly for an Asterid cardenolide-producing
 species has been reported to date. A high quality de novo assembly was
 generated for C. gigantea, representing 157,284,427 bp with an N50
 scaffold size of 805,959 bp, for which quality assessments indicated a
 near complete representation of the genic space. Transcriptome data in the
 form of RNA-sequencing libraries from a developmental tissue series was
 generated to aid in annotation and construction of a gene expression
 atlas. Using an ab initio and evidence-driven gene annotation pipeline,
 18,197 high confidence genes were annotated. Homologous and syntenic
 relationships between C. gigantea and other species within the Apocynaceae
 family confirmed previously identified evolutionary relationships and
 suggest the emergence or loss of the specialized cardenolide metabolites
 after the divergence of the Apocynaceae subfamilies. The C. gigantea
 genome assembly, annotation, and RNA-sequencing data provide a novel
 resource to study the cardenolide biosynthesis pathway especially for
 understanding the evolutionary origin of cardenolides and engineering of
 cardenolide production in heterologous organisms for existing and novel
 pharmaceutical applications.
description: README.txtREADME.txtCAL_genome_asm_v2.2_1000_rmscaff.fastaFinal genome assembly for C. giganteaCAL_genome_asm_v2.2_1000_rmscaff_hard_masked.fastaFinal hard masked genome assembly for C. giganteaCAL_genome_asm_v2.2_1000_rmscaff_soft_masked.fastaFinal soft masked genome assembly for C. giganteashort_summary_asm_v2.2_1000.txtTable summary of the number and percentage of Embryophyta orthologs for each categoryfull_table_asm_v2.2_1000.tsvTable providing the location in the genome assembly for each Embryophyta orthologmissing_busco_list_asm_v2.2_1000.tsvList of missing Embryophyta orthologs from the genome assemblycal_hc_gene_models.rmscaff.gff3Generic feature format (gff3) of high-confidence genes in C. giganteacal_hc_gene_models.rmscaff.cdna.faTranscript sequences (cDNA) of high-confidence genes in C. giganteacal_hc_gene_models.rmscaff.cds.faCoding sequences (CDS) of high-confidence genes in C. giganteacal_hc_gene_models.rmscaff.pep.faProtein sequences of high-confidence genes in C. giganteacal_hc_repr_gene_models.rmscaff.gff3Generic feature format (gff3) of representative models for high-confidence genes in C. giganteacal_hc_gene_models.rmscaff.repr.pep.faProtein sequences of representative models for high-confidence genes in C. giganteacal_hc_func_anno.txtFunctional annotation for high-confidence genes in C. giganteacal_FPKM_matrix.txtTable with FPKM expression values for high-confidence genes in C. gigantea
DOI: 10.5061/dryad.h738s
title: Data from: Comparative transcriptome resources of eleven Primulina species, a group of “stone plants” from a biodiversity hotspot

description: The genus Primulina is an emerging model system in studying the drivers
 and mechanisms of species diversification, for its high species richness
 and endemism, together with high degree of habitat specialization. In this
 study, we sequenced transcriptomes for eleven Primulina species across the
 phylogeny of the genus using the Illumina HiSeq 2000 platform. A total of
 336 million clean reads were processed into 355 573 unigenes with a mean
 length of 1336 bp and an N50 value of 2191 bp after pooling and
 reassembling twelve individual pre-assembled unigene sets. Of these
 unigenes, 249 973 (70%) were successfully annotated and 256 601 (72%) were
 identified as coding sequences (CDSs). We identified a total of 38 279
 simple sequence repeats (SSRs) and 367 123 single nucleotide polymorphisms
 (SNPs). Marker validation assay revealed that 354 (27.3%) of the 1296 SSR
 and 795 (39.6%) of the 2008 SNP loci showed successful genotyping
 performance and exhibited expected polymorphism profiles. We screened 834
 putative single-copy nuclear genes and proved their high effectiveness in
 phylogeny construction and estimation of ancestral population parameters.
 We identified a total of 85 candidate orthologs under positive selection
 for 46 of the 66 species pairs. This study provided an efficient
 application of RNA-seq in development of genomic resources for a group of
 ‘stone plants’ from south China Karst regions, a biodiversity hot spot of
 the World. The assembled unigenes with annotations and the massive
 gene-associated molecular markers would help guide further molecular
 systematic, population genetic and ecological genomics studies in
 Primulina and its relatives.
description: Fasta files of the
 assembled unigenesUnigene.rarAnnotation of the assembled unigenesAnnotation.rarFasta files of predicted coding sequencesCDS.rarSSR listSSR Flanking sequenceGenotypes of 354 SSR lociSSR_354 loci_genotypes.xlsSNP listGenotypes of 795 SNP lociSNP_795 loci_genotypes.xlsFasta files of single copy genesSingle copy genes.rarFasta file of adaptive genesAdaptive genes.fasta
DOI: 10.5061/dryad.hn082
title: Data from: The coevolution of sexual imprinting by males and females

description: Sexual imprinting is the learning of a mate preference by direct
 observation of the phenotype of another member of the population. Sexual
 imprinting can be paternal, maternal, or oblique if individuals learn to
 prefer the phenotypes of their fathers, mothers, or other members of the
 population, respectively. Which phenotypes are learned can affect trait
 evolution and speciation rates. “Good genes” models of polygynous systems
 predict that females should evolve to imprint on their fathers, because
 paternal imprinting helps females to choose mates that will produce
 offspring that are both viable and sexy. Sexual imprinting by males has
 been observed in nature, but a theory for the evolution of sexual
 imprinting by males does not exist. We developed a good genes model to
 study the conditions under which sexual imprinting by males or by both
 sexes can evolve and to ask which sexual imprinting strategies maximize
 the fitness of the choosy sex. We found that when only males imprint,
 maternal imprinting is the most advantageous strategy. When both sexes
 imprint, it is most advantageous for both sexes to use paternal
 imprinting. Previous theory suggests that, in a given population, either
 males or females but not both will evolve choosiness in mating. We show
 how environmental change can lead to the evolution of sexual imprinting
 behavior by both sexes in the same population.
description: Vecor_fields
DOI: 10.5061/dryad.rk345
title: Data from: The (in)effectiveness of simulated blur for depth perception in naturalistic images

description: We examine depth perception in images of real scenes with naturalistic
 variation in pictorial depth cues, simulated dioptric blur and binocular
 disparity. Light field photographs of natural scenes were taken with a
 Lytro plenoptic camera that simultaneously captures images at up to 12
 focal planes. When accommodation at any given plane was simulated, the
 corresponding defocus blur at other depth planes was extracted from the
 stack of focal plane images. Depth information from pictorial cues,
 relative blur and stereoscopic disparity was separately introduced into
 the images. In 2AFC tasks, observers were required to indicate which of
 two patches extracted from these images was farther. Depth discrimination
 sensitivity was highest when geometric and stereoscopic disparity cues
 were both present. Blur cues impaired sensitivity by reducing the contrast
 of geometric information at high spatial frequencies. While simulated
 generic blur may not assist depth perception, it remains possible that
 dioptric blur from the optics of an observer’s own eyes may be used to
 recover depth information on an individual basis. The implications of our
 findings for virtual reality rendering technology are discussed.
description: Spatial_DataSetTemporal_DataSetcrosstalksdioptersMatlabAnalysisCode
DOI: 10.15468/dl.qtrrjm
title: Occurrence Download

description: A dataset containing 3523 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euphractus sexcinctus",
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 }
 ]
}

 The dataset includes 3523 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000361-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.puequ4
title: Occurrence Download

description: A dataset containing 1750 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Gentianopsis thermalis"
 ]
}

 The dataset includes 1750 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000363-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j57c0
title: Data from: Pleistocene expansion of the bipolar lichen Cetraria aculeata into the Southern hemisphere

description: Many boreal and polar lichens occupy bipolar distributional ranges that
 frequently extend into high mountains at lower latitudes. Although such
 disjunctions are more common among lichens than in other groups of
 organisms, the geographic origin of bipolar lichen taxa, and the way and
 time frame in which they colonized their ranges have not been studied in
 detail. We used the predominantly vegetative, widespread lichen Cetraria
 aculeata as a model species. We surveyed the origin and history of its
 bipolar pattern using population genetics, phylogenetic and genealogical
 reconstruction methods. Cetraria aculeata originated in the Northern
 Hemisphere and dispersed southwards during the Pleistocene. The genetic
 signal suggests a Pleistocene dispersive burst in which a population size
 expansion concurred with the acquisition of a South-American range that
 culminated in the colonization of the Antarctic.
description: 1_Complete_data_matrixFull dataset including all individuals. It includes geographic information, haplotype assignment per locus, Genebank accesions, Assignment to Mixture clusters, MLC and SLC obtained in BAPSMEC_Complete_Dataset.txt2_ITS_complete_rootedITS alignment in Nexus formatITSb.nex2_GPD_complete_rootedGPD alignment in nexus formatGPDb.nex3_mtlsu_complete_rootedmtLSU alignment in nexus formatmtlsub.nex4_ITS_haplotypesITS alignment collapsed to haplotypesITS_haplotypes.nex4_GPD_haplotypesGPD alignment collapsed to haplotypesGPD_haplotypes.nex4_mtLSU_haplotypesmtLSU alignment collapsed to haplotypesmtLSU_haplotypes.nex5_ITS_Simmap_60seqsDataset collapsed to haplotypes per geographic region to be used for Stochastic mappingITS60seqsA.nex5_GPD_Simmap_47seqsDataset collapsed to haplotypes per geographic region to be used for Stochastic mappinggpd47seqsa.nex5_mtlsu_Simmap_27seqsDataset collapsed to haplotypes per geographic region to be used for Stochastic mappingmtlsu27seqsA.nex6_ITS_StochasticMaps_transitionsFinal log of the Stochastic character mapping simulations, it was used to generate plots of transitions through time.its_maps.log6_GPD_StochasticMaps_transitionsFinal log of the Stochastic character mapping simulations.gpd_maps.log6_mtLSU_StochasticMaps_transitionsFinal log of the Stochastic character mapping simulations.mtlsu_maps.log6_README_Plot_TransitionsR file used to plot transition through time plotsplotsEnd.r
DOI: 10.5061/dryad.q4g75
title: Data from: A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations

description: Ranaviruses are responsible for a lethal, emerging infectious disease in
 amphibians and threaten their populations throughout the world. Despite
 this, little is known about how amphibian populations respond to ranaviral
 infection. In the United Kingdom, ranaviruses impact the common frog (Rana
 temporaria). Extensive public engagement in the study of ranaviruses in
 the UK has led to the formation of a unique system of field sites
 containing frog populations of known ranaviral disease history. Within
 this unique natural field system, we used RNA sequencing (RNA-Seq) to
 compare the gene expression profiles of R. temporaria populations with a
 history of ranaviral disease and those without. We have applied a RNA read
 filtering protocol that incorporates Bloom filters, previously used in
 clinical settings, to limit the potential for contamination that comes
 with the use of RNA-Seq in non-laboratory systems. We have identified a
 suite of 407 transcripts that are differentially expressed between
 populations of different ranaviral disease history. This suite contains
 genes with functions related to immunity, development, protein transport
 and olfactory reception amongst others. A large proportion of potential
 non-coding RNA transcripts present in our differentially expressed set
 provides first evidence of a possible role for long non-coding RNA
 (lncRNA) in amphibian response to viruses. Our read-filtering approach
 also removed significantly more bacterial reads from libraries generated
 from postitive disease history populations. Subsequent analysis revealed
 these bacterial read sets to represent distinct communities of bacterial
 species, which is suggestive of an interaction between ranavirus and the
 host microbiome in the wild.
description: SRP131529Raw RNA-Seq reads available in NCBI at SRP131529.Expression Counts TableTable of reads per transcript per population sample library as computed using HTSeq.Expression_Counts_Table.tsvProtein AnnotationsList of protein annotations per assembled transcript. Annotations were generated using the Blast+ software package. Using a custom Blast database constructed from Human, Mammalian and Vertebrate Blast databases.Protein_Annotations.txtR. temporaria Final_Denovo AssemblyFinal denovo transcriptome assembly. Assembly incorporates all 6 populations and was constructed using TransAbyss.Rtemporaria_Final_Denovo_Assembly.faBacterial Read Classification Counts TableTable of number of removed reads that mapped to individual bacterial species per sample population library. Read classification was performed using the Kraken classification program.header.tsv
DOI: 10.5061/dryad.44sf1
title: Data from: Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach

description: In recent years, the explosion of affordable next generation sequencing
 technology has provided an unprecedented opportunity to conduct
 genome-wide studies of adaptive evolution in organisms previously lacking
 extensive genomic resources. Here, we characterise genome-wide patterns of
 variability and differentiation using pooled DNA from eight populations of
 the nine-spined stickleback (Pungitius pungitius L.) from marine, lake and
 pond environments. We developed a novel genome complexity reduction
 protocol, defined as paired-end double restriction-site associated DNA (PE
 dRAD), to maximise read coverage at sequenced locations. This allowed us
 to identify over 114,000 short consensus sequences and 15,000 SNPs
 throughout the genome. A total of 6,834 SNPs mapped to a single position
 on the related three-spined stickleback genome, allowing the detection of
 genomic regions affected by divergent and balancing selection, both
 between species and between freshwater and marine populations of the
 nine-spined stickleback. Gene ontology (GO) analysis revealed 15 genomic
 regions with elevated diversity, enriched for genes involved in functions
 including immunity, chemical stimulus response, lipid metabolism and
 signalling pathways. Comparisons of marine and freshwater populations
 identified nine regions with elevated differentiation related to kidney
 development, immunity and MAP kinase pathways. In addition, our analysis
 revealed that a large proportion of the identified SNPs mapping to LG XII
 are likely to represent alternative alleles from divergent X and Y
 chromosomes, rather than true autosomal markers following Mendelian
 segregation. Our work demonstrates how population-wide sequencing and
 combining inter- and intra-specific RAD analysis can uncover genome-wide
 patterns of differentiation and adaptations in a non-model species.
description: s_1_1_sequence_AATTC_start.txts_1_2_sequence_CACTCC_start.txts_1_2_sequence_CTTTCC_start.txts_2_1_sequence_AATTC_start.txts_2_2_sequence_TCTTCC_start.txts_3_1_sequence_AATTC_start.txts_3_2_sequence_CTTTCC_start.txts_3_2_sequence_TTGTCC_start.txts_5_1_sequence_AATTC_start.txts_5_2_sequence_CACTCC_start.txts_5_2_sequence_TCTTCC_start.txts_6_1_sequence_AATTC_start.txts_6_2_sequence_TTGTCC_start.txt