cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b2hc1
title: Data from: Genomic DNA transposition induced by human PGBD5

description: Transposons are mobile genetic elements that are found in nearly all
 organisms, including humans. Mobilization of DNA transposons by
 transposase enzymes can cause genomic rearrangements, but our knowledge of
 human genes derived from transposases is limited. In this study, we find
 that the protein encoded by human PGBD5, the most evolutionarily conserved
 transposable element-derived gene in vertebrates, can induce stereotypical
 cut-and-paste DNA transposition in human cells. Genomic integration
 activity of PGBD5 requires distinct aspartic acid residues in its
 transposase domain, and specific DNA sequences containing inverted
 terminal repeats with similarity to piggyBac transposons. DNA
 transposition catalyzed by PGBD5 in human cells occurs genome-wide, with
 precise transposon excision and preference for insertion at TTAA sites.
 The apparent conservation of DNA transposition activity by PGBD5 suggests
 that genomic remodeling contributes to its biological function.
description: Reads from
 HEK293-GFP-PBwt mapped to hg19+pb-ef1_neo.Reads obtained from
 sequencing FLEA PCR products to amplify transposon reporter insertions in
 sample HEK293-GFP-PBwt, mapped to a hybrid genome consisting of hg19 and
 the reporter plasmid sequence. Reads were mapped with bwa-mem using
 default parameters.pcr1_HEK293-GFP-PBwt.vs.hg19_pbneo.mem.bamReads from HEK293-GFP-PBmut mapped to hg19+pb-ef1-neoReads obtained from sequencing FLEA PCR products to amplify transposon reporter insertions in sample HEK293-GFP-PBmut, filtered, quality trimmed and mapped to a hybrid genome consisting of hg19 and the reporter plasmid sequence. Reads were mapped with bwa-mem using default parameters.pcr2_HEK293-GFP-PBmut.vs.hg19_pbneo.mem.bamReads from HEK293-PGBD5-PBwt mapped to hg19+pb-ef1-neoReads obtained from sequencing FLEA PCR products to amplify transposon reporter insertions in sample HEK293-PGBD5-PBwt, filtered, quality trimmed and mapped to a hybrid genome consisting of hg19 and the reporter plasmid sequence. Reads were mapped with bwa-mem using default parameters.pcr3_HEK293-PGBD5-PBwt.vs.hg19_pbneo.mem.bamReads from HEK293-PGBD5-PBmut mapped to hg19+pb-ef1-neoReads obtained from sequencing FLEA PCR products to amplify transposon reporter insertions in sample HEK293-PGBD5-PBmut, filtered, quality trimmed and mapped to a hybrid genome consisting of hg19 and the reporter plasmid sequence. Reads were mapped with bwa-mem using default parameters.pcr4_HEK293-PGBD5-PBmut.vs.hg19_pbneo.mem.bamSummary table of DNA transposon integration lociSpreadsheet listing human genome and transposon coordinate positions of transposon integrations, integration type (ITR transposition vs non-ITR transposition), and DNA sequences surrounding the genomic integration sites.summary_insertion_sites_pub.xlsxTransposon reporter plasmid sequence: pb-ef1-neoPlasmid sequence of NEO reporter flanked by PiggyBac ITRs. Reads from FLEA PCR were mapped to a hybrid genome consisting of this sequence and the hg19 human genome reference.pb-ef1-neo_seq.fa
DOI: 10.5061/dryad.s6f4q
title: Data from: Marine soundscape shaped by fishing activity

description: Marine communities face anthropogenic pressures that degrade ecosystems.
 Because underwater soundscapes carry information about habitat quality, we
 explored whether destructive impacts of fishing could be evaluated via the
 soundscape. Maerl beds are recognized as biodiversity hotspots and they
 experience major worldwide degradation owing to fishing. We collected
 field acoustic recordings in maerl beds exposed to different fishing
 practices. We found that unfished maerl beds were threefold louder and
 exhibited sound frequencies more diversified than those recorded in fished
 maerl beds. Analyses of associated fauna samples indicated that snapping
 shrimps provided a major contribution to the maerl bed soundscape.
 Moreover, sea urchins and squat lobsters most likely contributed to
 differences between the soundscapes of unfished and fished maerl beds. Our
 results supported the idea that the soundscape can provide valuable
 information on maerl bed ecosystem health related to fishing activity.
description: Raw acoustic
 data10 min recording samples
 of each of the two maerl beds (fished and unfished)Raw_data.zip
DOI: 10.5061/dryad.bv1g6
title: Data from: Can we build it? Yes we can, but should we use it? Assessing the quality and value of a very large phylogeny of campanulid angiosperms

description: The study of very large and very old clades holds the promise of greater
 insights into evolution across the tree of life. However, there has been a
 fair amount of criticism regarding the interpretations and quality of
 studies to date, with some suggesting that detailed studies carried out on
 smaller, tractable scales should be preferred over the increasingly grand
 syntheses of these data. Methods - We provided in detail our trials and
 tribulations of compiling a large, sparsely sampled matrix from GenBank
 data and inferring a well-supported, time-calibrated phylogeny of
 Campanulidae. We also used a simulation approach to assess tree quality,
 and to study the value of using very large, comprehensive phylogenies in a
 comparative context. Key results - A robust and well-supported phylogeny
 can be produced as long as automated procedures are supplemented with some
 human intervention. In the case of campanulids, the overall topology may
 be driven not only by particular genes, but also particular sequences for
 a gene. We also determined that estimates of divergence times should be
 fairly robust to issues related to clade-specific heterogeneity. Finally,
 we demonstrated how relying on results from smaller, younger clades are
 prone to produce biased interpretations of tropical to temperate evolution
 across campanulids as a whole. Conclusions - While we were both surprised
 and encouraged by the robust and fairly well-resolved, comprehensive
 phylogeny of campanulids, challenges still remain. Nevertheless, large
 phylogenies are inherently valuable in a comparative context if only to
 attenuate the issue of ascertainment bias.
description: BeaulieuOMearaAllFiles.tarContains all files and scripts used in the paper.
DOI: 10.5281/zenodo.18380236
title: test data for the 'domutils' Python package

description: This dataset allow to perform tests and demonstrations with the domutils Python package.


Source code is available at:


https://github.com/dja001/domutils
DOI: 10.5281/zenodo.3635906
title: test data for the 'domutils' Python package

description: This dataset allow to perform tests and demonstrations with the domutils Python package.


Source code is available at:


https://github.com/dja001/domutils
DOI: 10.5061/dryad.dh88c
title: Data from: Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the Northern Red Sea

description: High-Throughput Sequencing (HTS) of DNA barcodes (metabarcoding),
 particularly when combined with standardized sampling protocols, is one of
 the most promising approaches for censusing overlooked cryptic
 invertebrate communities. We present biodiversity estimates based on
 sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral
 reefs of the Gulf of Aqaba, a semi-enclosed system in the Northern Red
 Sea. Samples were obtained from standardized sampling devices [Autonomous
 Reef Monitoring Structures (ARMS)] deployed for 18 months. DNA barcoding
 of non-sessile specimens &gt;2mm revealed 83 OTUs in six phyla, of
 which only 25% matched a reference sequence in public databases.
 Metabarcoding of the 2mm-500μm and sessile bulk fractions revealed 1197
 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes.
 These results highlight the scarcity of COI data for cryptobenthic
 organisms of the Red Sea. Compared with data obtained using similar
 methods, our results suggest that Gulf of Aqaba reefs are less diverse
 than two Pacific coral reefs but much more diverse than an Atlantic oyster
 reef at a similar latitude. The standardized approaches used here show
 promise for establishing baseline data on biodiversity, monitoring the
 impacts of environmental change, and quantifying patterns of diversity at
 regional and global scales.
description: IonXpress_009_R_2013_05_26_04_37_58_user_SN2-40-MatthieuSampleA_barcodes7-8-9_Auto_user_SN2-40-MatthieuSampleA_barcodes7-8-9_61Raw amplicon sequence (mtCOI) data obtained on the Ion Torrent platform (Thermo Fisher Scientific).IonXpress_016_R_2013_03_29_20_58_02_user_SN2-4-MarineGeo_J_K_L_Auto_user_SN2-4-MarineGeo_J_K_L_31Raw amplicon sequence (mtCOI) data obtained on the Ion Torrent platform (Thermo Fisher Scientific).Jordan_Metabarcode_OTUtableThis table summarize the number of sequences per Operational Taxonomic Units (OTU) and per sample. OTUs were considered matched to a reference barcode when the level of similarity of the Blast search was higher than 97%. In the absence of direct match, the Bayesian phylogenetic approach implemented in the Statistical Assignment Package (Munch et al. 2008) was used for taxonomic assignment. The description of each sample can be found in Table S2 of the manuscript.
DOI: 10.5061/dryad.g08m87q
title: Data from: The nearshore cradle of early vertebrate diversification

description: Ancestral vertebrate habitats are subject to controversy and obscured by
 limited, often contradictory paleontological data. We assembled fossil
 vertebrate occurrence and habitat datasets spanning the middle Paleozoic
 (480 million to 360 million years ago) and found that early vertebrate
 clades, both jawed and jawless, originated in restricted, shallow
 intertidal-subtidal environments. Nearshore divergences gave rise to body
 plans with different dispersal abilities: Robust fishes shifted shoreward,
 whereas gracile groups moved seaward. Fresh waters were invaded
 repeatedly, but movement to deeper waters was contingent upon form and
 short-lived until the later Devonian. Our results contrast with the
 onshore-offshore trends, reef-centered diversification, and mid-shelf
 clustering observed for benthic invertebrates. Nearshore origins for
 vertebrates may be linked to the demands of their mobility and may have
 influenced the structure of their early fossil record and diversification.
description: Database
 S1Database S1: Downloaded
 datasets from the Paleobiology Database, regional paleocommunity records
 from Boucot and Lawson, all input files and trees in nexus, txt and csv
 format, R code for analyses and figures, and all results
 files.Nearshore
 Dryad.zip
DOI: 10.5061/dryad.2k6v37j
title: Data from: Placental H3K27me3 establishes female resilience to prenatal insults

description: Although sex biases in disease presentation are well documented, the
 mechanisms mediating vulnerability or resilience to diseases are unknown.
 In utero insults are more likely to produce detrimental health outcomes
 for males versus females. In our mouse model of prenatal stress, male
 offspring experience long-term dysregulation of body weight and
 hypothalamic pituitary adrenal stress axis dysfunction, endophenotypes of
 male-biased neurodevelopmental disorders. Placental function is critical
 for healthy fetal development, and we previously showed that sex
 differences in placental O-linked N-acetylglucosamine transferase (OGT)
 mediate the effects of prenatal stress on neurodevelopmental programming.
 Here we show that one mechanism whereby sex differences in OGT confer
 variation in vulnerability to prenatal insults is by establishing
 sex-specific trophoblast gene expression patterns and via regulation of
 the canonically repressive epigenetic modification, H3K27me3. We
 demonstrate that high levels of H3K27me3 in the female placenta create
 resilience to the altered hypothalamic programming associated with
 prenatal stress exposure.
description: Homer
 OutputChip-Seq for H3K27me3
 was performed on wild type (wt) male, wt female, and trophoblast-specific
 Ogt knock out (ko) male and female placental chromatin. Due to hardware
 failure, raw reads for this experiment were lost. This data package
 contains the output from our downstream analysis using
 Homer.
DOI: 10.5061/dryad.1mr70
title: Data from: Exploring the in meso crystallization mechanism by characterizing the lipid mesophase microenvironment during the growth of single transmembrane α-helical peptide crystals

description: The proposed mechanism for in meso crystallisation of transmembrane
 proteins suggests that a protein or peptide is initially uniformly
 dispersed in the lipid self-assembly cubic phase but that crystals grow
 from a local lamellar phase, which acts as a conduit between the crystal
 and the bulk cubic phase. However, there is very limited experimental
 evidence for this theory. We have developed protocols to investigate the
 lipid mesophase microenvironment during crystal growth using standard
 procedures readily available in crystallography laboratories. This
 technique was used to characterize the microenvironment during crystal
 growth of the DAP12-TM peptide using synchrotron Small Angle X-ray
 Scattering with a micro-sized X-ray beam. Crystal growth was found to
 occur from the Gyroid cubic mesophase. For one in four crystals a
 highly-oriented local lamellar phase was observed, providing supporting
 evidence for the proposed mechanism for in meso crystallisation. A new
 observation of this study was that we can differentiate diffraction peaks
 from crystals grown in meso, from peaks originating from the surrounding
 lipid matrix, potentially opening up the possibility of high-throughput
 SAXS analysis of in meso grown crystals.
description: Database
DOI: 10.5061/dryad.7bn4001
title: Data from: Contemporaneous radiations of fungi and plants linked to symbiosis

description: Interactions between fungi and plants, including parasitism, mutualism,
 and saprotrophy, have been invoked as key to their respective
 macroevolutionary success. Here we evaluate the origins of plant-fungal
 symbioses and saprotrophy using a time-calibrated phylogenetic framework
 that reveals linked and drastic shifts in diversification rates of each
 kingdom. Fungal colonization of land was associated with at least two
 origins of terrestrial green algae and preceded embryophytes (as evidenced
 by losses of fungal flagellum, ca. 720 Ma), likely facilitating
 terrestriality through endomycorrhizal and possibly endophytic symbioses.
 The largest radiation of fungi (Leotiomyceta), the origin of arbuscular
 mycorrhizae, and the diversification of extant embryophytes occurred ca.
 480 Ma. This was followed by the origin of extant lichens. Saprotrophic
 mushrooms diversified in the Late Paleozoic as forests of seed plants
 started to dominate the landscape. The subsequent diversification and
 explosive radiation of Agaricomycetes, and eventually of ectomycorrhizal
 mushrooms, were associated with the evolution of Pinaceae in the Mesozoic,
 and establishment of angiosperm-dominated biomes in the Cretaceous.
description: Lutzoni_fungi_alignmentMolecular alignment used for dating analyses of fungiLutzoni_fungi_timetreeAnnotated time tree for fungiLutzoni_plants_alignmentMolecular alignment used for dating analyses of plantsLutzoni_plants_timetreeAnnotated time tree for plantsdls-node-age-analysesThis archive contains all scripts that were used to extract node ages from the posterior tree samples, summarize posterior distributions for target clades, plot figures, and compute tabular summaries.
DOI: 10.5061/dryad.7dm4d
title: Data from: Canine mammary tumours are affected by frequent copy number aberrations, including amplification of MYC and loss of PTEN

description: Background: Copy number aberrations frequently occur during the
 development of many cancers. Such events affect dosage of involved genes
 and may cause further genomic instability and progression of cancer. In
 this survey, canine SNP microarrays were used to study 117 canine mammary
 tumours from 69 dogs. Results: We found a high occurrence of copy number
 aberrations in canine mammary tumours, losses being more frequent than
 gains. Increased frequency of aberrations and loss of heterozygosity were
 positively correlated with increased malignancy in terms of
 histopathological diagnosis. One of the most highly recurrently amplified
 regions harbored the MYC gene. PTEN was located to a frequently lost
 region and also homozygously deleted in five tumours. Thus, deregulation
 of these genes due to copy number aberrations appears to be an important
 event in canine mammary tumour development. Other potential contributors
 to canine mammary tumour pathogenesis are COL9A3, INPP5A, CYP2E1 and RB1.
 The present study also shows that a more detailed analysis of chromosomal
 aberrations associated with histopathological parameters may aid in
 identifying specific genes associated with canine mammary tumour
 progression. Conclusions: The high frequency of copy number aberrations is
 a prominent feature of canine mammary tumours as seen in other canine and
 human cancers. Our findings share several features with corresponding
 studies in human breast tumours and strengthen the dog as a suitable model
 organism for this disease.
description: ReadMeFile containing detailed
 information about the different data files in this
 submission.Tumor_BAF_117origOriginal B allele frequency values for the 117 tumour samples studied.Tumor_LogR_117origOriginal Log R Ratio values for the 117 tumour samples studied.Tumor_LogR.GCadjusted_qnorm_117Adjusted Log R Ratio values for the 117 tumour samples studied, after the application of the GC correction method and quantile normalization.Germline_BAF_117B allele frequency values for the blood samples for each of the 71 dogs in the study.Germline_LogR_117Log R Ratio values for the blood samples for each of the 71 dogs in the study.Diagnoses and histopathologic scores_ASCAT tumoursHistopathomorphological diagnoses and histopathologic score values for all tumours that achieced an ASCAT output (113 of 117 tumours). These diagnoses/scores were used in further analysis of the ASCAT output.
DOI: 10.5061/dryad.90005
title: Data from: Convergence analysis of a finite element skull model of Herpestes javanicus (Carnivora, Mammalia): implications for robust comparative inferences of biomechanical function

description: Predictions of skull biomechanical capability based on virtual models
 constitute a valuable data source for testing hypotheses about
 craniodental form and feeding behavior. Such comparative analyses also
 inform dietary reconstruction in extinct species. 3D modeling using Finite
 Element (FE) methods is a common technique applied to the comparative
 analysis of craniodental function in extinct and extant vertebrates.
 However, taxonomically diverse skull models in the literature often are
 not directly comparable to each other, in part because of distinctions in
 how boundary conditions are defined, but also because of substantial
 differences in the number of FEs composing the models. In this study, we
 test whether a conventional convergence test is adequate in identifying
 the minimum number of FEs needed to achieve internally stable results for
 a single species. We constructed a series of skull models of Herpestes
 javanicus, and simulated unilateral biting across the dentition; the
 models differed in the number of FEs, degrees of freedom at the joint and
 bite point constraints, and type of tetrahedral FEs used. We found that
 convergence patterns differed across constraint types, FE quantities, and
 bite position simulated. Four-noded tetrahedral (tet-4) FE models with
 relaxed constraints produced the most stable measurements compared to
 over-constrained tet-4 models and to relaxed tet-10 models. In absence of
 an optimal FE quantity from convergence testing, we propose a broadly
 applicable sub-sampling protocol, whereby average measurement values
 across multiple models per specimen are used for among-species
 comparisons. A regime of sampling three low FE quantity models produced
 the closest estimates of mean measurement values relative to larger model
 sets, being within the 95% bootstrap estimated confidence intervals.
 Future studies should focus on identifying sources of variation associated
 with other FE modeling protocols, so that they can be accounted for before
 biomechanical attributes from these simulations are used to infer
 form–function linkage.
description: Tseng&Flynn_Herpestes_FEMsIndividual Finite Element models in the 3 datasets described in Tseng and Flynn. All files are loaded with simulated muscle forces using BoneLoad. All models are in the Strand7 (*.st7) format, version 2.4.6.
DOI: 10.5061/dryad.vf8sm
title: Data from: Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

description: Chromosomal rearrangement can be an important mechanism driving population
 differentiation and incipient speciation. In the mountain pine beetle
 (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are
 polymorphic among populations are associated with reproductive
 incompatibility. Here we used RAD sequencing across the entire MPB range
 in western North America to reveal the extent of the phylogeographic
 differences between Y haplotypes compared to autosomal and X-linked loci.
 Clustering and gene flow analyses revealed three distinct Y haplogroups
 geographically positioned within and on either side of the Great Basin
 Desert. Despite close geographic proximity between populations on the
 boundaries of each Y haplogroup, there was extremely low Y haplogroup
 mixing among populations, and gene flow on the autosomes was reduced
 across Y haplogroup boundaries. These results are consistent with a
 previous study suggesting that independent degradation of a recently
 evolved neo-Y chromosome in previously isolated populations causes male
 sterility or inviability among Y haplotype lineages. Phylogeographic
 results supported historic contraction of MPB into three separate
 Pleistocene glacial refugia followed by post-glacial range expansion and
 secondary contact. Distinct sets of SNPs were statistically associated
 with environmental data among the most genetically distinct sets of
 geographic populations. This finding suggests that the process of
 adaptation to local climatic conditions is influenced by population
 genetic structure, with evidence for largely independent evolution in the
 most genetically isolated Y haplogroup.
description: S2CollectionInformationInformation regarding collection sites etc. Old codes are used in indexing files this file contains the link between the old and the new codes in the manuscript.Index for Plates 1-7 MPBIndex's for demulitplexing plates. File name indicates plate name. Raw sequencing data is available from NCBI: bioproject PRJNA398557IndexPlateMPB.zipRaw SNP calls for all samplesRaw SNP calls for all samples. Calls made via GATK. File in vcf formatmergedGATKsnpsPineNofilter.vcf.gzScaffold Chromosome InformationFile with scaffold information for autosomal, x chromosome and y chromosome. Scaffolds relate to the names on the MPB genomeScaffoldChromosomeInformation.zip