cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2h0cc57
title: Data from: Effects of a systematically offered social and preventive medicine consultation on training and health attitudes of young people not in employment, education or training (NEETs): an interventional study in France

description: Background NEETs (young people not in employment, education or training)
 are at higher risk for poorer mental and physical health. In France, the
 Missions locales (MLs) are the only social structures dedicated to this
 population. We sought to determine whether the systematic offer of a
 social and preventive medicine consultation at a ML might increase NEET
 participants’ access to training in the 12 months following the
 intervention. Methods This intervention research was a parallel randomised
 controlled interventional study conducted at five MLs in mainland France
 in 2011-2012. It included 976 NEETs aged 18 to 25 years who attended one
 of the five MLs. At inclusion, participants were randomly assigned (1:1:1)
 to three groups: those in the first group were invited to see a social
 worker (not studied in this paper), those in the second group were invited
 to see a doctor and a social worker (intervention group), and the third
 was a control group. The primary outcome was participation in at least one
 training session during the year following study inclusion. Results Among
 the 976 participants, 504 were randomly assigned to the intervention group
 and 472 to the control group; 704 (72.1%) were included in the analyses. A
 significantly higher proportion of the participants in the intervention
 group participated in a training session in the 12 months following the
 intervention than of those in the control group (63.3% vs 55.6%; p=0.04).
 This difference was significantly greater for women, those less than 21
 years of age, those unstably housed and those with a lower level of
 education. Conclusions Social and preventive medicine consultations that
 are fully integrated into the social services for NEETs have an impact on
 their access to training and contribute to changing some of their
 health-related behaviours. This may improve their access to the labour
 market.
description: Data PRESAJE Dryad
 eng
DOI: 10.5061/dryad.qb2s9f2
title: Data from: Climate-niche factor analysis: a spatial approach to quantifying species vulnerability to climate change

description: Climate change vulnerability assessments are an important tool for
 understanding the threat that climate change poses to species and
 populations, but do not generally yield insight into the spatial variation
 in vulnerability throughout a species' habitat. We demonstrate how to
 adapt the method of ecological-niche factor analysis (ENFA) to objectively
 quantify aspects of species sensitivity to climate change. We then expand
 ENFA to quantify aspects of exposure and vulnerability to climate change
 as well, using future projections of global climate models. This approach
 provides spatially-explicit insight into geographic patterns of
 vulnerability, relies only on readily-available spatial data, is suitable
 for a wide range of species and habitats, and invites comparison between
 different species. We apply our methods to a case study of two species of
 montane mammals, the American pika Ochotona princeps and the
 yellow-bellied marmot Marmota flaviventris.
description: Sensitivity, exposure
 and vulnerability maps of Marmota flaviventris.Zipped file containing
 sensitivity, exposure and vulnerability maps for the IUCN range map of
 Marmota flaviventris. Exposure and vulnerability maps are based on the
 MIROC5 global climate model projections for 2050 and for RCPs 4.5 and
 8.5.Marmota
 flaviventris.zipSensitivity, exposure
 and vulnerability maps for Ochotona princeps.Zipped file containing
 sensitivity, exposure and vulnerability maps for the IUCN range map of
 Ochotona princeps. Exposure and vulnerability maps are based on the MIROC5
 global climate model projections for 2050 and for RCPs 4.5 and
 8.5.Ochotona
 princeps.zipSensitivity, exposure
 and vulnerability predictions for Marmota flaviventrisZipped file containing
 sensitivity, exposure and vulnerability maps with predictions outside the
 range of Marmota flaviventris. Exposure and vulnerability maps are based
 on the MIROC5 global climate model projections for 2050 and for RCPs 4.5
 and 8.5.Marmota flaviventris
 predictions.zipSensitivity, exposure
 and vulnerability predictions for Ochotona princepsZipped file containing
 sensitivity, exposure and vulnerability maps with predictions outside the
 range of Ochotona princeps. Exposure and vulnerability maps are based on
 the MIROC5 global climate model projections for 2050 and for RCPs 4.5 and
 8.5.Ochotona princeps
 predictions.zip
DOI: 10.5061/dryad.1n064hg
title: Data from: Low modularity and specialization in a commensalistic epiphyte–phorophyte network in a tropical cloud forest

description: Species interactions can shape the structure of natural communities. Such
 sets of interactions have been described as complex ecological networks,
 an example of which is the commensal network formed by epiphyte–phorophyte
 interactions. Vascular epiphytes germinate and grow on phorophytes
 (support trees), assuming a horizontal distribution (among the phorophyte
 species) and a vertical distribution (from the base of the tree trunk to
 the crown of phorophytes, i.e., through ecological zones). Here we
 investigated the organization of these structural dimensions of the
 epiphyte–phorophyte network in a Brazilian tropical montane cloud forest.
 The analyzed network, comprising 66 epiphyte species and 22 phorophyte
 species, exhibited a nested structure with a low degree of specialization,
 a typical pattern for epiphyte–phorophyte networks in forests. The network
 was slightly modular, with 65% of the species common to three modules, and
 had vertical structure corresponding to the vertical organization of the
 phorophytes. The size (diameter at breast height) of phorophyte
 individuals influenced the network structure, possibly due to the increase
 in habitat area, the time available for colonization by epiphytes, and a
 greater number of microenvironments. We found that the distribution of the
 epiphyte species differed between the phorophyte ecological zones, with
 greater richness in the lower portions and greater abundance in the upper
 portions of the phorophytes. The results provide relevant guidance for
 future research on the characteristics and the vertical and horizontal
 organization of vascular epiphyte and phorophyte networks.
description: Epiphyte–phorophyte
 network in a tropical cloud forestFrancisco et
 al..xlsx
DOI: 10.5061/dryad.2vp18qv
title: Data from: Using a multi-stage hESC model to characterize BDE-47 toxicity during neurogenesis

description: While the ramifications associated with polybrominated diphenyl ethers
 (PBDE) exposures during human pregnancy have yet to be determined,
 increasing evidence in humans and animal models suggests that these
 compounds cause neurodevelopmental toxicity. Human embryonic stem cell
 models (hESCs) can be used to study the effects of environmental chemicals
 on the successive stages of neuronal development. Here, using a hESC
 differentiation model, we investigated the effects of common PBDE
 congeners (BDE-47 or -99) on the successive stages of early neuronal
 development. First, we determined the points of vulnerability to PBDEs
 across four stages of in vitro neural development by using assays to
 assess for cytotoxicity. Differentiated neural progenitors were identified
 to be more sensitive to PBDEs than their less differentiated counterparts.
 In follow-up investigations, we observed BDE-47 to inhibit functional
 processes critical for neurogenesis (e.g., proliferation, migration) in
 hESC-derived neural precursor cells (NPCs) at sub-lethal concentrations.
 Finally, to determine the mechanism(s) underlying PBDE-toxicity, we
 conducted global transcriptomic and methylomic analyses of BDE-47. We
 identified 589 genes to be differentially expressed (DE) due to BDE-47
 exposure, including molecules involved in oxidative stress mediation, cell
 cycle, hormone signaling, steroid metabolism, and neurodevelopmental
 pathways. In parallel analyses, we identified a significant increase in
 CpG methylation. In summary, our results suggest, on a cellular level,
 PBDEs induce human neurodevelopmental toxicity in a
 concentration-dependent manner and sensitivity to these compounds is
 dependent on the developmental stage of exposure. Proposed mRNA and
 methylomic perturbations may underlie toxicity in early embryonic neuronal
 populations.
description: Supplemental Video
 1_Neurosphere_expansion
DOI: 10.15468/dl.zw44gc
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Fish collection of the Kagoshima University Museum",
 "TaxonKey is Lophius"
 ]
}

 The dataset includes 29 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001672-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0c3gf6j
title: Data from: Extended haplodiploidy hypothesis

description: Evolution of altruistic behaviour was a hurdle for the logic of Darwinian
 evolution. Soon after Hamilton formalised the concept of inclusive
 fitness, which explains how altruism can evolve, he suggested that the
 high sororal relatedness brought by haplodiploidy could be why
 Hymenopterans have a high prevalence in eusocial species, and why helpers
 in Hymenoptera are always female. Later it was noted that in order to
 capitalize on the high sororal relatedness, helpers would need to direct
 help towards sisters, and this would bias the population sex ratio. Under
 a 1:3 males:females sex ratio, the inclusive fitness valuation a female
 places on her sister, brother and an own offspring are equal – apparently
 removing the benefit of helping over independent reproduction. Based on
 this argumentation, haplodiploidy hypothesis has been considered a red
 herring. However, here we show that when population sex ratio, cost of
 altruism, and population growth rate are considered together,
 haplodiploidy does promote female helping even with female-biased sex
 ratio, due the lowered cost of altruism in such populations. Our analysis
 highlights the need to re-evaluate the role of haplodiploidy in the
 evolution of helping, and the importance of fully exploring the model
 assumptions when comparing interactions of population sex ratios and
 social behaviours.
description: SimulationsSupporting Information Mathematica simulation files.
DOI: 10.5061/dryad.mf1gm3p
title: Data from: Effects of early nutritional stress on physiology, life-histories and their trade-offs in a model ectothermic vertebrate

description: Early-life experiences can have far-reaching consequences for phenotypes
 into adulthood. The effect of early-life experiences on fitness,
 particularly under adverse conditions, is mediated by resource allocation
 to particular life-history traits. We examined the effects of early-life
 food restriction on growth, adult body size, physiology and reproduction
 in the checkered garter snake, Thamnophis marcianus. Animals were placed
 on one of two early-life diet treatments: normal-diet (approximating ad
 libitum feeding) or low-diet (restricted to 20% of body mass in food
 weekly). At 15 weeks of age low-diet animals were switched to the
 normal-diet treatment. Individuals fed a restricted diet showed reduced
 growth rates, depressed immunocompetence and a heightened glucocorticoid
 response. Once food restriction was lifted, animals that experienced
 nutritional stress early in life (low-diet) caught up to the normal-diet
 group by increasing their growth, and were able to recover from the
 negative effects of nutritional stress on physiology (immune function and
 stress response). Growth restriction and the subsequent allocation of
 resources into increasing growth rates, however, had a negative effect on
 fitness. Mating success was reduced in low-diet males, while low-diet
 females gave birth to smaller offspring. Our study demonstrates both
 immediate and long-term effects of nutritional stress on physiology and
 growth, reproduction, and trade-offs among them.
description: Growth Phys
 DatasetProvides experimental
 data on morphological measures, and physiological responses to different
 early-life diet treatments. Used for all analyses of growth and physiology
 in manuscriptTm_GrowthPhys_FullDataSet.csvOffspring Size DataProvides data on liveborn offspring sizeTm_OffspringSizeData.csvRepro MeasuresProvides Data on the reproductive effort and successTm_ReproData.csv
DOI: 10.5061/dryad.4nv0nb8
title: Data from: Transgenerational effects in an ecological context: conditioning of adult sea urchins to upwelling conditions alters maternal provisioning and progeny phenotype

description: Transgenerational plasticity occurs when the conditions experienced by the
 parental generation influences the phenotype of their progeny. This may in
 turn affect progeny performance and physiological tolerance, providing a
 means by which organisms cope with rapid environmental change. We
 conditioned adult purple sea urchins, Strongylocentrotus purpuratus, to
 combined pCO⁠2 and temperature conditions reflective of in situ conditions
 of their natural habitat, the benthos in kelp forests of nearshore
 California, and then assessed the performance of their progeny raised
 under different pCO⁠2 levels. Adults were conditioned during gametogenesis
 to treatments that reflected static non-upwelling (~650 μatm pCO⁠2, ~17°C)
 and upwelling (~1300 μatm pCO⁠2, ~13°C) conditions. Following
 approximately 4 months of conditioning, the adults were spawned and
 embryos were raised under low pCO⁠2 (~450 μatm pCO⁠2) or high pCO⁠2 (~1050
 μatm pCO⁠2) treatments to determine if differential maternal conditioning
 impacted the progeny response to a single abiotic stressor: pCO⁠2. We
 examined the size, protein content, and lipid content of eggs from both
 sets of conditioned female urchins. Offspring were sampled at four stages
 of early development: hatched blastula, gastrula, prism, and
 echinopluteus. This resulted in four sets of offspring: (1) progeny from
 non-upwelling-conditioned mothers raised under low pCO⁠2, (2) progeny from
 non-upwelling-conditioned mothers raised under high pCO⁠2, (3) progeny
 from upwelling-conditioned mothers raised under low pCO⁠2, and (4) progeny
 from upwelling-conditioned mothers raised under high pCO⁠2. We then
 assessed the effects of maternal conditioning along with the effects of
 developmental pCO⁠2 levels on body size of the progeny. Our results showed
 that differential maternal conditioning had no impact on average egg size,
 although non-upwelling females produced eggs that were more variable in
 size. Maternal conditioning did not affect protein content but did have a
 modest impact on egg lipid content. Developing embryos whose mothers were
 conditioned to simulated upwelling conditions (~1300 μatm pCO⁠2, ~13°C)
 were greater in body size, although this effect was no longer evident at
 the echinopluteus larval stage. Although maternal conditioning affected
 offspring body size, the pCO⁠2 levels under which the embryos were raised
 did not. Overall, this laboratory study provides insight into how
 transgenerational effects may function in nature. The impacts of parental
 environmental history on progeny phenotype during early development have
 important implications regarding recruitment success and population-level
 effects.
description: Morphometric, protein,
 lipid dataMorphometric data for
 the egg, hatched blastula, gastrula, prism, and echinopluteus stages.
 Protein and lipid data for the eggs.JEMBE_Data.zip
DOI: 10.5061/dryad.hp2fr73
title: Data from: Pluripotency and the origin of animal multicellularity

description: \A widely held—but rarely tested—hypothesis for the origin of animals is
 that they evolved from a unicellular ancestor, with an apical cilium
 surrounded by a microvillar collar, that structurally resembled modern
 sponge choanocytes and choanoflagellates. Here we test this view of animal
 origins by comparing the transcriptomes, fates and behaviours of the three
 primary sponge cell types—choanocytes, pluripotent mesenchymal
 archaeocytes and epithelial pinacocytes—with choanoflagellates and other
 unicellular holozoans. Unexpectedly, we find that the transcriptome of
 sponge choanocytes is the least similar to the transcriptomes of
 choanoflagellates and is significantly enriched in genes unique to either
 animals or sponges alone. By contrast, pluripotent archaeocytes upregulate
 genes that control cell proliferation and gene expression, as in other
 metazoan stem cells and in the proliferating stages of two unicellular
 holozoans, including a colonial choanoflagellate. Choanocytes in the
 sponge Amphimedon queenslandica exist in a transient metastable state and
 readily transdifferentiate into archaeocytes, which can differentiate into
 a range of other cell types. These sponge cell-type conversions are
 similar to the temporal cell-state changes that occur in unicellular
 holozoans5. Together, these analyses argue against homology of sponge
 choanocytes and choanoflagellates, and the view that the first
 multicellular animals were simple balls of cells with limited capacity to
 differentiate. Instead, our results are consistent with the first animal
 cell being able to transition between multiple states in a manner similar
 to modern transdifferentiating and stem cells.
description: Additional supplementary
 data for Sogabe et al. 2019This archive contains
 additional supplementary data for Pluripotency and the Origin of Animal
 Multicellularity by Sogabe et al. 2019. The archive contains 12 folders
 with data corresponding to analyses reported in the paper. All folders
 that do not simply contain a fully labelled table include a README file
 explaining the folder's contents.Sogabe et al. 2019
 Dryad.zip
DOI: 10.5061/dryad.d76v3p1
title: Data from: Phylogenomics of Aplacophora (Mollusca, Aculifera) and a solenogaster without a foot

description: Recent molecular phylogenetic investigations strongly supported placement
 of the shell-less, worm-shaped aplacophoran molluscs (Solenogastres and
 Caudofoveata) and chitons (Polyplacophora) in a clade called Aculifera,
 which is the sister taxon of all other molluscs. Thus, understanding the
 evolutionary history of aculiferan molluscs is important for understanding
 early molluscan evolution. In particular, fundamental questions about
 evolutionary relationships within Aplacophora have long been unanswered.
 Here, we supplemented the paucity of available data with transcriptomes
 from 25 aculiferans and conducted phylogenomic analyses on datasets with
 up to 525 genes and 75,914 amino acid positions. Our results indicate that
 aplacophoran taxonomy requires revision as several traditionally
 recognized groups are non-monophyletic. Most notably, Cavibelonia, the
 solenogaster taxon defined by hollow sclerites, is polyphyletic,
 suggesting parallel evolution of hollow sclerites in multiple lineages.
 Moreover, we describe Apodomenia enigmatica sp. nov., a bizarre new
 species that appears to be a morphological intermediate between
 Solenogastres and Caudofoveata. This animal is not a missing link however;
 molecular and morphological studies show that it is a derived solenogaster
 that lacks a foot, mantle cavity, and radula. Taken together, these
 results shed light on the evolutionary history of Aplacophora and reveal a
 surprising degree of morphological plasticity within the group.
description: Supplementary data for
 Phylogenomics of Aplacophora (Mollusca, Aculifera) and a solenogaster
 without a footThis archive contains
 assemblies for all transcriptomes sequenced for this project
 ("Assembled_transcriptomes" folder), input and output files of
 all phylogenetic analyses ("Phylogenetic_analysis_results"
 folder), the custom Solenogastres HaMStR core ortholog set produced for
 this study ("Solenogastres_hmmer3_core_ortholog_set_for_HaMStR"
 folder), a file with all COI sequences extracted from the newly sequenced
 transcriptomes ("COI_mined_from_transcriptomes.fas"), and the
 script used to process the HaMStR output and generate the datasets
 analyzed in this study
 ("Dataset_assembly_script.sh").Kocot_et_al_2019_supplementary_data.zip
DOI: 10.5061/dryad.2gh0ht2
title: Data from: Allopolyploidy in the Wintergreen Group of tribe Gaultherieae (Ericaceae) inferred from low-copy nuclear genes

description: DNA sequence data from the low-copy nuclear genes waxy (GBSSI) and leafy
 were compared with plastid sequence data from prior studies to reconstruct
 phylogenetic relationships in the Wintergreen Group of tribe Gaultherieae
 (Ericaceae). We conducted phylogenetic analysis with 109 species that
 includes representatives of all 15 major clades previously diagnosed in
 the Wintergreen Group and that together span its circum-Pacific
 distribution. Results yielded two distinct homeologous copies of waxy for
 two of the clades, each in widely separated parts of the tree. It also
 yielded two copies of leafy for one of the clades; only one copy of leafy
 was found for the other clade, but it was placed in the same major clade
 as its waxy counterpart and well away from its placement in a prior
 plastid analysis. A combined four-locus (waxy, leafy, ITS, and plastid
 loci) phylogenetic analysis of all available relevant data placed the
 copies of each of the clades in two distinct positions in the phylogeny
 with strong overall statistical support. In combination with evidence from
 morphology, reproductive biology, and cytology, the results suggest that
 these clades arose through allopolyploid hybridization between lineages
 deep in the phylogeny but relatively close geographically. This finding
 confirms previous assumptions that hybridization plays an important role
 in the evolution of the Gaultherieae.
description: four_locus_dataset.nexfour_locus_dataset.phyleafy_dataset.nexleafy_dataset.phywaxy_dataset.nexwaxy_dataset.phy