cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17630/ebb59c38-7285-4590-89e9-81e5dfe122f2
title: MOF-based Membranes for Challenging Gas Separations (thesis data)

description: The following file types and formats include:
Raw data of sample adsorption (which were measured on IGA and 2020);
Raw data of AFM, IR, NMR, SEM,XRD,XPS
XRD refinement,
and membrane gas permeation.
Indefinite embargo applied. Embargo reason: permission not provided to allow public access
DOI: 10.5061/dryad.2rq05
title: Data from: Gut microbiota dynamics during dietary shift in Eastern African cichlid fishes

description: The gut microbiota structure reflects both a host phylogenetic history and
 a signature of adaptation to the host ecological, mainly trophic niches.
 African cichlid fishes, with their array of closely related species that
 underwent a rapid dietary niche radiation, offer a particularly
 interesting system to explore the relative contribution of these two
 factors in nature. Here we surveyed the host intra- and interspecific
 natural variation of the gut microbiota of five cichlid species from the
 monophyletic tribe Perissodini of lake Tanganyika, whose members
 transitioned from being zooplanktivorous to feeding primarily on fish
 scales. The outgroup riverine species Astatotilapia burtoni, largely
 omnivorous, was also included in the study. Fusobacteria, Firmicutes and
 Proteobacteria represented the dominant components in the gut microbiota
 of all 30 specimens analysed according to two distinct 16S rRNA markers.
 All members of the Perissodini tribe showed a homogenous pattern of
 microbial alpha and beta diversities, with no significant qualitative
 differences, despite changes in diet. The recent diet shift between
 zooplantkon- and scale-eaters simply reflects on a significant enrichment
 of Clostridium taxa in scale-eaters where they might be involved in the
 scale metabolism. Comparison with the omnivorous species A. burtoni
 suggests that, with increased host phylogenetic distance and/or increasing
 herbivory, the gut microbiota begins differentiating also at qualitative
 level. The cichlids show presence of a large conserved core of taxa and a
 small set of core OTUs (average 13–15%), remarkably stable also in
 captivity, and putatively favoured by both restricted microbial
 transmission among related hosts (putatively enhanced by mouthbrooding
 behavior) and common host constraints. This study sets the basis for a
 future large-scale investigation of the gut microbiota of cichlids and its
 adaptation in the process of the host adaptive radiation.
description: V12_OTU_biom_tableBiom Table for V1-2 16S ampliconV34_OTU_biom_tableBiom table for V3-4 16S ampliconV12_OTUs_alignmentOTU fasta alignment for V1-2 16S ampliconV34_OTUs_alignmentOTU fasta alignment of V3-4 16S amplicon
DOI: 10.5061/dryad.8602
title: Data from: Environmental niche divergence between genetically distant lineages of an endangered water beetle

description: Historically, there has been considerable disagreement between researchers
 about the criteria used to discriminate among species. Decisions based on
 traditional morphological and genetic data alone can be potentially
 problematic, especially if the hypotheses are contradictory. Today,
 taxonomy is integrating new methods from different disciplines that study
 species’ limits and evolution; this diverse range of evidence aids
 researchers in the recognition of species. Differences in niche
 characteristics could become a new and useful criterion in helping to
 decide the status of conflicting taxonomical entities. Ochthebius glaber
 (family Hydraenidae) is an endangered water beetle typical from southeast
 Iberian hypersaline streams that shows three clear discrete genetic units
 within its distribution range. However, there is no evidence to date that
 these lineages of O. glaber exhibit any adaptive morphological or
 ecological divergence. Using a modelling approach directed to generate
 niche representation from distributional data, we found a significant
 environmental niche divergence for allopatric lineages of O. glaber that
 followed an aridity gradient. Although we can not conclude firmly at
 present that the separate populations of O. glaber studied represent
 separate, reproductively isolated species, this study complements and
 supports previous phylogeographic analyses through the inclusion of
 measures of another form of evolutionary change; in this case, ecological
 diversification. Despite the existence of some methodological limitations,
 also discussed in this work, we emphasise the importance of recent
 conceptual advances that allow taxonomy to improve species delimitation
 practices through the integration of theory and methods from disciplines
 that study the origin and evolution of species.
description: DataGeographical, Climatic,
 Geological information of the pixels used in the paper (including
 ocurrence localities from each lineage).
DOI: 10.18167/dvn1/7n2btu
title: Code for: Spatial scenario of tropical deforestation and carbon emissions for the 21st century
title: Code pour: Scénario spatialisé de la déforestation tropicale et des émissions de carbone pour le 21e siècle

description: &lt;p&gt;This dataset includes the code used to produce the results of the following scientific article:&lt;/p&gt;

&lt;p&gt;
&lt;strong&gt;Vieilledent G., C. Vancutsem, C. Bourgoin, P. Ploton, P. Verley and F. Achard.&lt;/strong&gt; Spatial scenario of tropical deforestation and carbon emissions for the 21&lt;sup&gt;st&lt;/sup&gt; century. &lt;i&gt;bioRxiv&lt;/i&gt;. doi: &lt;a href="https://doi.org/10.1101/2022.03.22.485306"&gt;10.1101/2022.03.22.485306&lt;/a&gt;.&lt;/p&gt;

&lt;p&gt;
A development version of this code is available on GitHub: &lt;a href="https://github.com/ghislainv/forestatrisk-tropics"&gt;ghislainv/forestatrisk-tropics&lt;/a&gt;.
&lt;/p&gt;
description: This dataset is part of the ForestAtRisk project: https://forestatrisk.cirad.fr.
DOI: 10.82294/dvnavxkqn
title: COPUS. Territorio: Cali. Sector: Cultura. Año: 2023
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2023 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector Cultura (educación informal) en la ciudad de Cali.
DOI: 10.5061/dryad.7vs3d
title: Data from: Patterns of niche filling and expansion across the invaded ranges of an Australian lizard

description: Studies of realized niche shifts in alien species typically ignore the
 potential effects of intraspecific niche variation and different
 invaded-range environments on niche lability. We incorporate our detailed
 knowledge of the native-range source populations and global introduction
 history of the delicate skink Lampropholis delicata to examine
 intraspecific variation in realized niche expansion and unfilling, and
 investigate how alternative niche modelling approaches are affected by
 that variation. We analyzed the realized niche dynamics of L. delicata
 using an ordination method, ecological niche models (ENMs), and occurrence
 records from 1) Australia (native range), 2) New Zealand, 3) Hawaii, 4)
 the two distinct native-range clades that were the sources for the New
 Zealand and Hawaii introductions, and 5) the species’ global range
 (including Lord Howe Island, Australia). We found a gradient of realized
 niche change across the invaded ranges of L. delicata: niche stasis on
 Lord Howe Island, niche unfilling in New Zealand (16%), and niche
 unfilling (87%) and expansion (14%) in Hawaii. ENMs fitted to native-range
 data generally identified suitable climatic conditions at sites where the
 species has established non-native populations, whereas ENMs based on
 native-range source clades and non-native populations had lower spatial
 transferability. Our results suggest that the extent to which realized
 niches are maintained during invasion does not depend on species-level
 traits. When realized niche shifts are predominately due to niche
 unfilling, fully capturing species’ responses along climatic gradients by
 basing ENMs on native distributions may be more important for accurate
 invasion forecasts than incorporating phylogenetic differentiation, or
 integrating niche changes in the invaded range.
description: Occurrence records of
 Lampropholis delicataGeographic coordinates
 where Lampropholis delicata has been detected. See main manuscript for
 data sources and additional details.L delicata
 occurrence.xls
DOI: 10.5061/dryad.0g6m2
title: Data from: Effect of host plant and immune challenge on the levels of chemosensory and odorant-binding proteins in caterpillar salivary glands

description: More than half of the proteome from mandibular glands in caterpillars is
 represented by chemosensory proteins. Based on sequence similarity, these
 proteins are putative transporters of ligands to gustatory receptors in
 sensory organs of insects. We sought to determine whether these proteins
 are inducible by comparing, both qualitatively and quantitatively, the
 salivary (mandibular and labial) proteomes from caterpillars (Vanessa
 cardui) reared on different plants and artificial diet containing either
 bacteria or bacterial cell-walls. We included a treatment where the
 caterpillars were switched from feeding on artificial diet to plant
 material at some point in their development. Additionally, we evaluated
 the degree of overlap between the proteomes in the hemolymph-filled coelom
 and salivary glands of caterpillars reared on plant material. We found
 that the quality and quantity of the identified proteins differed clearly
 between hemolymph-filled coelom, labial and mandibular glands. Our results
 indicated that even after molting and two-day feeding on a new diet,
 protein production is affected by the previous food source used by the
 caterpillar. Candidate proteins involved in chemosensory perception by
 insects were detected: three chemosensory (CSPs) and two odorant-binding
 proteins (OBPs). Using the relative amounts of these proteins across
 tissues and treatments as criteria for their classification, we detected
 hemolymph- and mandibular gland-specific CSPs and observed that their
 levels were affected by caterpillar diet. Moreover, we could compare the
 protein and transcript levels across tissues and treatment for at least
 one CSP and one OBP. Therefore, we have identified specific isoforms for
 testing the role of CSPs and OBPs in plant and pathogen recognition. We
 detected catalase, immune-related protein and serine proteases and their
 inhibitors in high relative levels in the mandibular glands in comparison
 to the labial glands. These findings suggest that the mandibular glands of
 caterpillars may play an important role protecting the caterpillar from
 oxidative stress, pathogens and aiding in digestion. Contamination with
 hemolymph proteins during dissection of salivary glands from caterpillars
 may occur but it is not substantial since the proteomes from hemolymph,
 mandibular and labial glands were easily discriminated from each other by
 principal component analysis of proteomic data.
description: V. cardui de novo
 transcriptome assemblyConsensus_Vcardui_de novo
 assembly.fasta
DOI: 10.5061/dryad.k9k23
title: Data from: Using phylogenomics to resolve mega-families: an example from Compositae

description: Next-generation sequencing and phylogenomics hold great promise for
 elucidating complex relationships among large plant families. Here we
 performed targeted capture of low copy sequences followed by
 next-generation sequencing on the Illumina platform in the large and
 diverse angiosperm family Compositae (Asteraceae). The family is
 monophyletic based on morphology and molecular data, yet many areas of the
 phylogeny have unresolved polytomies and interpreting phylogenetic
 patterns has been historically difficult. In order to outline a method and
 provide a framework and for future phylogenetic studies in the Compositae,
 we sequenced 23 taxa from across the family in which the relationships
 were well established as well as a member of the sister family
 Calyceraceae. We generated nuclear data from 795 loci and assembled
 chloroplast genomes from off-target capture reads enabling the comparison
 of nuclear and chloroplast genomes for phylogenetic analyses. We also
 analyzed multi-copy nuclear genes in our data set using a clustering
 method during orthology detection, and we applied a network approach to
 these clusters—analyzing all related locus copies. Using these data we
 produced hypotheses of phylogenetic relationships employing both a
 conservative (restricted to only loci with one copy per targeted locus)
 and a multigene approach (including all copies per targeted locus). The
 methods and bioinformatics workflow presented here provide a solid
 foundation for future work aimed at understanding gene family evolution in
 the Compositae as well as providing a model for phylogenomic analyses in
 other plant mega-families.
description: conservative_COS_concatenated_treeTree file for concatenated conservative COS dataset.conservative_COS_concatenated.treconservative_COS_concatenated_fastafasta file containing concatenated conservative COS lociconservative_COS_concatenated.fastaastral_conservative_COS_treeastral_conservative_COS_treeastral_conservative.trechloroplast_all_treechloroplast.trelow_copy_cluster_trees_used_for_networklow_copy_cluster_trees.zip100_random_cluster_trees_for_networkTrees for 100 random clusters used to generate network in figure 4B100_random_clusters_for_network.trechloroplast_all_finalfasta file for chloroplast datasetGitools_heatmap_all_clustersCSV file used for generating heat map in GitoolsGitools_heatmap_conservative_COSCSV file used for generating heat map in Gitools
DOI: 10.5061/dryad.8623
title: Data from: Bayesian estimation of genomic clines

description: We developed a Bayesian genomic cline model to study the genetic
 architecture of adaptive divergence and reproductive isolation between
 hybridizing lineages. This model quantifies locus-specific patterns of
 introgression with two cline parameters that describe the probability of
 locus-specific ancestry as a function of genome-wide admixture.
 "Outlier" loci with extreme patterns of introgression relative
 to most of the genome can be identified. These loci are potentially
 associated with adaptive divergence or reproductive isolation. We
 simulated genetic data for admixed populations that included neutral
 introgression, as well as loci that were subject to directional, epistatic
 or underdominant selection, and analyzed these data using the Bayesian
 genomic cline model. Under many demographic conditions, underdominance or
 directional selection had detectable and predictable effects on cline
 parameters and "outlier" loci were greatly enriched for genetic
 regions affected by selection. We also analyzed previously published
 genetic data from two transects through a hybrid zone between Mus
 domesticus and M. musculus. We found considerable variation in rates of
 introgression across the genome and particularly low rates of
 introgression for two X-linked markers. There were similarities and
 differences in patterns of introgression between the two transects, which
 likely reflects a combination of stochastic variability due to genetic
 drift and geographic variation in the genetic architecture of reproductive
 isolation. By providing a robust framework to quantify and compare
 patterns of introgression among genetic regions and populations, the
 Bayesian genomic cline model will advance our understanding of the
 genetics of reproductive isolation and the speciation process.
description: epistasis_simsData simulated for pairwise epistasis. Each file in the compressed directory is for a different set of model parameters and each file contains ten replicates. Genotypes are given as 0 (homozygote), 1 (heterozygote), or 2 (homozygote).epistasis.tar.gzdirectional_simsData simulated with directional selection. Each file in the compressed directory is for a different set of model parameters and each file contains ten replicates. Genotypes are given as 0 (homozygote), 1 (heterozygote), or 2 (homozygote).directional.tar.gzunderdom.tarData simulated with underdominance. Each file in the compressed directory is for a different set of model parameters and each file contains ten replicates. Genotypes are given as 0 (homozygote), 1 (heterozygote), or 2 (homozygote).neutral_simsData simulated without selection. Each file in the compressed directory is for a different population size and each file contains ten replicates. Genotypes are given as 0 (homozygote), 1 (heterozygote), or 2 (homozygote).neutral.tar.gzbgc_sourceSource code (C++) for the Bayesian genomic cline model. Compilation requires GSL. Simple instructions for compilation, which might need to be modified, are included in bgc_main.C.
DOI: 10.5061/dryad.6nc8c
title: Data from: Size-related scaling of tree form and function in a mixed-age forest

description: Many morphological, physiological and ecological traits of trees scale
 with diameter, shaping the structure and function of forest ecosystems.
 Understanding the mechanistic basis for such scaling relationships is key
 to understanding forests globally and their role in Earth's changing
 climate system. Here, we evaluate theoretical predictions for the scaling
 of nine variables in a mixed-age temperate deciduous forest
 (CTFS-ForestGEO forest dynamics plot at the Smithsonian Conservation
 Biology Institute, Virginia, USA) and compare observed scaling parameters
 to those from other forests world-wide. We examine fifteen species and
 various environmental conditions. Structural, physiological and ecological
 traits of trees scaled with stem diameter in a manner that was sometimes
 consistent with existing theoretical predictions – more commonly with
 those predicting a range of scaling values than a single universal scaling
 value. Scaling relationships were variable among species, reflecting
 substantive ecological differences. Scaling relationships varied
 considerably with environmental conditions. For instance, the scaling of
 sap flux density varied with atmospheric moisture demand, and herbivore
 browsing dramatically influenced stem abundance scaling. Thus,
 stand-level, time-averaged scaling relationships (e.g., the scaling of
 diameter growth) are underlain by a diversity of species-level scaling
 relationships that can vary substantially with fluctuating environmental
 conditions. In order to use scaling theory to accurately characterize
 forest ecosystems and predict their responses to global change, it will be
 critical to develop a more nuanced understanding of both the forces that
 constrain stand-level scaling and the complexity of scaling variation
 across species and environmental conditions.
description: Mean annual tree
 diameter growthMean annual diameter
 growth from a 5 year census (2008-2013) for trees at
 SCBI.SCBI_annual_growth.csvSCBI_annual_growth_Metadata.pdfBark depthBark thickness measurements for trees at SCBI.SCBI_bark_depth.csvSCBI_bark_depth_Metadata.pdfCrown dimensionsCrown dimensions measurements for trees at SCBI, including height to base of crown, crown area, and crown volume.SCBI_crown_dimensions.csvSCBI_crown_dimensions_Metadata.pdfDiameter growth from dendrometer bandsMean diameter growth measured using dendrometer bands for trees at SCBI.SCBI_dendroband_growth.csvSCBI_dendrometer_Metadata.pdfSapflowSap flow measurements for trees at SCBI.SCBI_sapflow.csvSCBI_sapflow_Metadata.pdfSapwoodSapwood measurements for trees at SCBI.SCBI_sapwood.csvSCBI_sapwood_Metadata.pdfTree heightsHeight measurements for trees at SCBI.SCBI_tree_heights.csvSCBI_tree_height_Metadata.pdfStem abundanceCount of stems within DBH class for trees at SCBI.SCBI_stem_abundance.csvSCBI_stem_abundance_Metadata.pdfTree mortality ratesMortality rates from a 5 year census (2008-2013) for trees at SCBISCBI_mortality.csvSCBI_mortality_Metadata.pdfSCBI_species_acronymList of species and species acronym used at SCBI
DOI: 10.57745/rqdfbg
title: Gestational Diabetes Mellitus experimental rat model mother plasma metabolomics raw data during mild gestation and lactation

description: Gestational Diabetes Mellitus represents a major public health concern due to adverse maternal post-partum and long-term outcome. Current strategies to manage GDM fail to reduce the maternal risk to develop later impaired glucose tolerance and type 2 diabetes . In a rodent model of diet-induced Gestational Diabetes Mellitus without obesity, we explored the perinatal metabolic adaptations in dams with gestational IGT followed by either persistent or resolved post-partum impaired glucose tolerance. Female Sprague-Dawley rats were fed a High-Fat High-Sucrose or a Chow diet, one week before mating and throughout gestation. Following parturition, High-Fat High-Sucrose dams were randomized to two subgroups: one switched to Chow diet and the other one maintained on High-Fat High-Sucrose diet throughout lactation. Oral glucose tolerance tests were performed at Gestation-days G12 and G18, Lactation-days L12 and L18. Plasma metabolome-lipidome were characterized at G12 and L12. These oral glucose tolerance tests-raw data and metabolomics/lipidomics raw data are synthetized in this dataset
DOI: 10.7927/hjha-bb25
title: IPCC AR6 Synthesis Report SPM.7 (a) and LR Figure 4.4 (a) (Left): Feasibility of climate responses and adaptation in the near-term

description: Selected adaptation options across different systems. Climate responses and adaptation options assessed for their multidimensional feasibility at global scale, in the near term and up to 1.5°C global warming. As literature above 1.5°C is limited, feasibility at higher levels of warming may change, which is currently not possible to assess robustly. The term response is used here in addition to adaptation because some responses, such as migration, relocation and resettlement may or may not be considered to be adaptation. Migration, when voluntary, safe and orderly, allows reduction of risks to climatic and non-climatic stressors. Forest based adaptation includes sustainable forest management, forest conservation and restoration, reforestation and afforestation. WASH refers to water, sanitation and hygiene. Six feasibility dimensions (economic, technological, institutional, social, environmental and geophysical) were used to calculate the potential feasibility of climate responses and adaptation options, along with their synergies with mitigation. For potential feasibility and feasibility dimensions, the figure shows high, medium, or low feasibility. Synergies with mitigation are identified as high, medium, and low.