cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2j5s7
title: Data from: Are variations of direct and indirect plant interactions along a climatic gradient dependent on species' strategies? An experiment on tree seedlings

description: Investigating how interactions among plants depend on environmental
 conditions is key to understand and predict plant communities’ response to
 climate change. However, while many studies have shown how direct
 interactions change along climatic gradients, indirect interactions have
 received far less attention. In this study, we aim at contributing to a
 more complete understanding of how biotic interactions are modulated by
 climatic conditions. We investigated both direct and indirect effects of
 adult tree canopy and ground vegetation on seedling growth and survival in
 five tree species in the French Alps. To explore the effect of
 environmental conditions, the experiment was carried out at 10 sites along
 a climatic gradient closely related to temperature. While seedling growth
 was little affected by direct and indirect interactions, seedling survival
 showed significant patterns across multiple species. Ground vegetation had
 a strong direct competitive effect on seedling survival under warmer
 conditions. This effect decreased or shifted to facilitation at lower
 temperatures. While the confidence intervals were wider for the effect of
 adult canopy, it displayed the same pattern. The monitoring of
 micro-environmental conditions revealed that competition by ground
 vegetation in warmer sites could be related to reduced water availability;
 and weak facilitation by adult canopy in colder sites to protection
 against frost. For a cold-intolerant and shade-tolerant species (Fagus
 sylvatica), adult canopy indirectly facilitated seedling survival by
 suppressing ground vegetation at high temperature sites. The other more
 cold tolerant species did not show this indirect effect (Pinus uncinata,
 Larix decidua and Abies alba). Our results support the widely observed
 pattern of stronger direct competition in more productive climates.
 However, for shade tolerant species, the effect of direct competition may
 be buffered by tree canopies reducing the competition of ground
 vegetation, resulting in an opposite trend for indirect interactions
 across the climatic gradient.
description: Seedling first year
 survivalData used seedling
 survival analysis (see
 https://github.com/kunstler/indirect.effect.climaten for R
 code)data.seedling.survival.csvSeedling growth dataData for seedling growth analysis (see https://github.com/kunstler/indirect.effect.climate)data.seedling.growth.csvDaily climatic data per plotDaily climatic data per plotdata.climate.all.csvData on ground vegetation cover and light interceptiondata.herb.light.csvAnnual climatic data per site in open areadata.clim.mean.csv
DOI: 10.5061/dryad.nh6hm
title: Data from: Geographic ranges of genera and their constituent species: structure, evolutionary dynamics, and extinction resistance

description: We explore the relationships among the geographic ranges of genera, the
 ranges and positions of their constituent species, and the number of
 species they contain, considering variation among coeval genera and
 changes within genera over time. Measuring range size as the maximal
 distance, or extent, between occurrences within a taxon, we find that the
 range of the most widespread species is a good predictor of the range of
 the genus, and that the number of species is a better predictor still.
 This analysis is complicated by a forced correlation: the range of a genus
 must be at least as large as that of each of its constituent species. We
 therefore focus on a second measure of range, the mean squared distance,
 or dispersion, of occurrences from the geographic centroid, which, by
 analogy to the analysis of variance, allows the total dispersion of a
 genus to be compared to the mean within-species dispersion and the
 dispersion among species centroids. We find that among-species dispersion
 is the principal determinant of genus dispersion. Within-species
 dispersion also plays a major role. The role of species richness is
 relatively small. Our results are not artifacts of temporal variation in
 the geographic breadth of sampled data. The relationship between changes
 in genus dispersion and changes in within- and among-species dispersion
 shows a symmetry, being similar in cases when the genus range is expanding
 and when it is contracting. We also show that genera with greater
 dispersion have greater extinction resistance, but that within- and
 among-species dispersion are not demonstrable predictors of survival once
 the dispersion of the genus is accounted for. Thus it is the range of the
 genus, rather than how it is attained, that is most relevant to its fate.
 Species richness is also a clear predictor of survival, beyond its effects
 on geographic range.
description: Supplementary Table
 1This
 file is a table containing data on fossil marine animal genera used in the
 referenced publication. Fields include: genus name; class; stratigraphic
 interval; species richness; number of occurrences; and characteristics of
 the geographic ranges of these genera. Data are derived from the
 Paleobiology Database, with modification.SupplementaryTable1Final.csv
DOI: 10.5061/dryad.37hr9
title: Data from: A framework for detecting natural selection on traits above the species level

description: To what extent can natural selection act on groupings above the species
 level? Despite extensive theoretical discussion and growing practical
 concerns over increased rates of global ecological turnover, the question
 has largely evaded empirical resolution. A flexible and robust
 hypothesis-testing framework for detecting the phenomenon could facilitate
 significant progress in resolving this issue. We introduce a
 permutation-based approach, implemented in the R package perspectev, which
 provides an explicit test of whether empirical patterns of correlation
 between upper level trait values and survivorship are reducible to
 correlations manifested at lower levels. The package is applicable to
 virtually any nested set of upper- and lower level groupings, a wide
 variety of upper level traits, and both historical and contemporary
 occurrence data. We apply this approach to five paleontological data sets
 that represent different magnitudes of extinction and differ in taxonomic
 breadth, geological timing and geographic extent. Using simulations, we
 demonstrate that this method is a robust means of detecting irreducibility
 in the relationship between upper level traits and survivorship, and
 outline circumstances in which the method is less effective. We also find
 evidence consistent with previous findings of selection above the species
 level for geographic range size in North American K-Pg molluscs and show
 that this phenomenon was evident for the same molluscan genera globally.
 Ultimately, we conclude that at certain points in history, some higher
 level taxonomic groups have survived differentially with respect to
 geographic range size in a manner that is not explained by the same trait
 at the species level, and we show that evidence for this phenomenon varies
 across taxa and extinction events. We release our method as a flexible and
 easy-to-use R package that will allow others to help determine the
 relative frequency of this macroevolutionary phenomenon, both in the
 fossil record and in estimates of contemporary extinction risk.
description: Data and Analysis
 ScriptsContains raw and
 filtered data sets used in analyses (MNAK, MGK, etc), and scripts for
 performing the analyses in the paper. The scripts are in R and require
 perspectev to be in installed (see
 https://cran.r-project.org/web/packages/perspectev/). Further information
 about using perspectev can be found here:
 http://evolve.zoo.ox.ac.uk/Evolve/Perspectev.htmlperspectev_DRYAD.zip
DOI: 10.5061/dryad.3hc5t
title: Data from: Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution

description: Background. The Marburg virus (MARV) has a negative-sense single-stranded
 RNA genome, belongs to the family Filoviridae, and is responsible for
 several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns
 of viruses reflect a series of evolutionary changes that enable viruses to
 shape their survival rates and fitness toward the external environment
 and, most importantly, their hosts. To understand the evolution of MARV at
 the codon level, we report a comprehensive analysis of synonymous codon
 usage patterns in MARV genomes. Multiple codon analysis approaches and
 statistical methods were performed to determine overall codon usage
 patterns, biases in codon usage, and influence of various factors,
 including mutation pressure, natural selection, and its two hosts, Homo
 sapiens and Rousettus aegyptiacus. Results. Nucleotide composition and
 relative synonymous codon usage (RSCU) analysis revealed that MARV shows
 mutation bias and prefers U- and A-ended codons to code amino acids.
 Effective number of codons analysis indicated that overall codon usage
 among MARV genomes is slightly biased. The Parity Rule 2 plot analysis
 showed that GC and AU nucleotides were not used proportionally which
 accounts for the presence of natural selection. Codon usage patterns of
 MARV were also found to be influenced by its hosts. This indicates that
 MARV have evolved codon usage patterns that are specific to both of its
 hosts. Moreover, selection pressure from R. aegyptiacus on the MARV RSCU
 patterns was found to be dominant compared with that from H. sapiens.
 Overall, mutation pressure was found to be the most important and dominant
 force that shapes codon usage patterns in MARV. Conclusions. To our
 knowledge, this is the first detailed codon usage analysis of MARV and
 extends our understanding of the mechanisms that contribute to codon usage
 and evolution of MARV.
description: marburg.full.nucleotideFull genome nucleotide sequences of Marburg viruses taken from NCBI GenBank and used for codon usage analysis.Marburg.codon.analysis.outputRAW output of codon analysis steps for Marburg virus genomes.
DOI: 10.5061/dryad.hn16c
title: Data from: Reversible, specific, active aggregates of endogenous proteins assemble upon heat stress

description: Heat causes protein misfolding and aggregation and in eukaryotic cells
 triggers aggregation of proteins and RNA into stress granules. We have
 carried out extensive proteomic studies to quantify heat-triggered
 aggregation and subsequent disaggregation in budding yeast, identifying
 &gt;170 endogenous proteins aggregating within minutes of heat shock
 in multiple subcellular compartments. We demonstrate that these aggregated
 proteins are not misfolded and destined for degradation. Stable-isotope
 labeling reveals that even severely aggregated endogenous proteins are
 disaggregated without degradation during recovery from shock, contrasting
 with the rapid degradation observed for exogenous thermolabile proteins.
 Although aggregation likely inactivates many cellular proteins, in the
 case of a heterotrimeric aminoacyl-tRNA synthetase complex, the aggregated
 proteins remain active with unaltered fidelity. We propose that most
 heat-induced aggregation of mature proteins reflects the operation of an
 adaptive, autoregulatory process of functionally significant aggregate
 assembly and disassembly that aids cellular adaptation to thermal stress.
description: S. cerevisiae protein
 aggregation estimatesEstimates of proportion
 in 100,000g supernatant (pSup) from S. cerevisiae cells grown in
 SC-complete media at 30C, transferred from 30C to 46C for 2, 4, and 8 min
 and to 37C and 42C for 8 min.scer_aggregation_psup.txtS. cerevisiae protein disaggregation and synthesis estimatesProtein disaggregation and new synthesis measured by media-shift SILAC. Cells are grown on a first set of stable-isotope-labeled amino acids, shifted to media containing a second set of labels, then heat shocked at 42C for 10mins and allowed to recover at 30C for 0, 20, 60, or 180 minutes. Upon collection, these cells are mixed with cells from an unshocked (30C) reference sample grown on a third label. Protein in 100,000g supernatant fraction of lysate is measured, intensities and normalized ratios reported.scer_disaggregation_recovery.txtWallace2015-yeast-heat-agg-dryad-packageComplete package including processed data, intermediate data, and processing scripts.
DOI: 10.5061/dryad.g3122
title: Data from: RAD-sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels

description: Measuring the effects of selection on the genome imposed by human-altered
 environment is currently a major goal in ecological genomics. Given the
 polygenic basis of most phenotypic traits, quantitative genetic theory
 predicts that selection is expected to cause subtle allelic changes among
 covarying loci rather than pronounced changes at few loci of large
 effects. The goal of this study was to test for the occurrence of
 polygenic selection in both North Atlantic eels (European Eel, Anguilla
 anguilla and American Eel, A. rostrata), using a method that searches for
 covariation among loci that would discriminate eels from “control” vs.
 “polluted” environments and be associated with specific contaminants
 acting as putative selective agents. RAD-seq libraries resulted in 23,659
 and 14,755 filtered loci for the European and American Eels respectively.
 A total of 142 and 141 covarying markers discriminating European and
 American Eels from “control” vs. “polluted” sampling localities were
 obtained using the Random Forest algorithm. Distance-based redundancy
 analyses (db-RDAs) were used to assess the relationships between these
 covarying markers and concentration of 34 contaminants measured for each
 individual eel. PCB153, 4'4'DDE and selenium were associated
 with covarying markers for both species, thus pointing to these
 contaminants as major selective agents in contaminated sites . Gene
 enrichment analyses suggested that sterol regulation plays an important
 role in the differential survival of eels in “polluted” environment. This
 study illustrates the power of combining methods for detecting signals of
 polygenic selection and for associating variation of markers with putative
 selective agents in studies aiming at documenting the dynamics of
 selection at the genomic level, and particularly so in human altered
 environments.
description: A.anguilla_genotypes.targenepop file for A.anguilla individualsa.anguilla_genotypes.tar.gzA.rostrata_genotypesGenepop file containing genotype for all A. rostrata individualsImportant_marker_annotation.tarAnnotation results for the important markers.Markers and Important markersGenpop files (in a slightly modified format used for the random forest and contaminants work) of all markers for both eel species, in addition to the identification and statistics of important markers, the similarity matrix obtained from these important markers and the PCoAs produced from these similarity matrix.bayescanPollutantsIndividual contamination of 24 organic and 10 metal pollutants for both species.Database link.tarA csv that links each individual with their BioSample Accession in SRAdatabase link.txt
DOI: 10.5281/zenodo.15829577
title: Data for "Diverse Polymorphism in Ruddlesden-Popper Chalcogenides"

description: This record contains:1. `RP_phases.db` database with data from density functional theory calculations used for training a neuroevolution potential (NEP) for the Ruddlesden-Popper chalcogenides2. `nep.txt` the NEP machine learning interatomic potential3. `test.xyz` and `train.xyz` test and training set used to construct the potential 4. `n*_thermo.out` thermodynamic properties from heating run
DOI: 10.5281/zenodo.18386067
title: Data for "Diverse Polymorphism in Ruddlesden-Popper Chalcogenides"

description: This record contains:1. `RP_phases.db` database with data from density functional theory calculations used for training a neuroevolution potential (NEP) for the Ruddlesden-Popper chalcogenides2. `nep.txt` the NEP machine learning interatomic potential3. `test.xyz` and `train.xyz` test and training set used to construct the potential 4. `n*_thermo.out` thermodynamic properties from heating run
DOI: 10.5061/dryad.hf155
title: Data from: Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae)

description: DNA taxonomy has been proposed as a method to quickly assess diversity and
 species limits in highly diverse, understudied taxa. Here we use five
 methods for species delimitation and two genetic markers (COI and ITS2) to
 assess species diversity within the parasitoid genus, Ophion. We searched
 for compensatory base changes (CBC’s) in ITS2, and determined that they
 are too rare to be of practical use in delimiting species in this genus.
 The other four methods used both COI and ITS2, and included distance-based
 (threshold analysis and ABGD) and tree-based (GMYC and PTP) models. We
 compared the results of these analyses to each other under various
 parameters and tested their performance with respect to 11 Nearctic
 species/morphospecies and 15 described Palearctic species. We also
 computed barcode accumulation curves of COI sequences to assess the
 completeness of sampling. The species count was highly variable depending
 on the method and parameters used, ranging from 47 to 168 species, with
 more conservative estimates of 89–121 species. Despite this range, many of
 the Nearctic test species were fairly robust with respect to method. We
 concluded that while there was often good congruence between methods, GMYC
 and PTP were less reliant on arbitrary parameters than the other two
 methods and more easily applied to genetic markers other than COI.
 However, PTP was less successful at delimiting test species than was GMYC.
 All methods, as well as the barcode accumulation curves, indicate that
 several Palearctic species remain undescribed and that we have scarcely
 begun to appreciate the Nearctic diversity within this genus.
description: COI_alignmentComplete COI data matrix used to construct phylogenetic treesITS2_alignmentComplete ITS2 data matrix used to construct phylogenetic analyses
DOI: 10.5061/dryad.h4f7p
title: Data from: Extracting spatio-temporal patterns in animal trajectories: an ecological application of sequence analysis methods

description: Digital tracking technologies have considerably increased the amount and
 quality of animal trajectories, enabling the study of habitat use and
 habitat selection at a fine spatial and temporal scale. However, current
 approaches do not yet explicitly account for a key aspect of habitat use,
 namely the sequential variation in the use of different habitat features.
 To overcome this limitation, we propose a tree-based approach that makes
 use of sequence analysis methods, derived from molecular biology, to
 explore and identify ecologically relevant sequential patterns in habitat
 use by animals. We applied this approach to ecological data consisting of
 simulated and real trajectories from a roe deer population (Capreolus
 capreolus), expressed as ordered sequences of habitat use. We show that
 our approach effectively captured spatio-temporal patterns of sequential
 habitat use by roe deer. In our case study, individual sequences were
 clustered according to the sequential use of the elevation gradient (first
 order) and of open/closed habitats (second order). We provided evidence
 for several behavioural processes, such as migration and daily alternating
 habitat use. Some unexpected patterns, such as homogeneous sequences of
 use of open habitat, could also be identified. Our findings advocate the
 importance of dealing with the sequential nature of movement data.
 Approaches based on sequence analysis methods are particularly useful and
 effective since they allow exploring temporal patterns of habitat use in a
 synthetic and visually captive manner. The proposed approach represents a
 useful and effective way to classify individual movement behaviour across
 populations and species. Ultimately, this method can be applied to explore
 the temporal scale of ecological processes based on movement.
description: Real and simulated
 habitat use sequencesThis dataset contains
 simulated and real bimonthly spatio-temporal habitat use sequences,
 distinguishing four habitat use classes (high-closed, 4; high-open, 3;
 low-closed, 2; low-open,1). Simulated sequences represent four patterns of
 habitat selection (alternating, random, open, closed) and were simulated
 in 9 different landscapes with different proportions of availability of
 open and closed habitats (10-90% open, each saved as a separate csv-file,
 e.g. Movement_random_10_open_alternance.csv). The real sequences
 (data_real.csv) give the bimonthly sequential habitat use for 26 roe deer,
 in total consisting of 111 sequences. Also several variables were
 associated to the real sequences (e.g. animal, sex, age, migration, home
 range size, proportion of closed, season). In this dataset we also provide
 the raw correlation matrices (e.g. Open_10_) for each of the nine
 landscapes, which were used as input for the substitution weight
 matrices.Datasets.rar
DOI: 10.5061/dryad.v23n2
title: Data from: Chloroplast phylogenomics resolves key relationships in ferns

description: Studies on chloroplast genomes of ferns and lycophytes are relatively few
 in comparison with those on seed plants. Although a basic phylogenetic
 framework of extant ferns is available, relationships among a few key
 nodes remain unresolved or poorly supported. The primary objective of this
 study is to explore the phylogenetic utility of large chloroplast gene
 data in resolving difficult deep nodes in ferns. We sequenced the
 chloroplast genomes from Cyrtomium devexiscapulae (eupolypod I) and
 Woodwardia unigemmata (eupolypod II), and constructed the phylogeny of
 ferns based on both 48 genes and 64 genes. The trees based on 48 genes and
 64 genes are identical in topology, differing only in support values for
 four nodes, three of which showed higher support values for the 48-gene
 dataset. Equisetum was resolved as the sister to the clade of
 Psilotales-Ophioglossales, and the clade of
 Equisetales-Psilotales-Ophioglossales was sister to the clade of the
 leptosporangiate and marattioid ferns. The sister-relationship between the
 tree fern clade and polypods was supported by 82%, and 100%, bootstrap
 values in the 64-gene and the 48-gene trees, respectively. In polypod
 ferns, Pteridaceae was sister to the clade of Dennstaedtiaceae and
 eupolypods with a high support value, and the relationship of
 Dennstaedtiaceae-eupolypods was strongly supported. With recent parallel
 advances in the phylogenetics of ferns using nuclear data, chloroplast
 phylogenomics shows great potential in providing a framework for testing
 the impact of reticulate evolution in the early evolution of ferns.
description: 48genes-36species-latin-name64genes-36species-latin-name
DOI: 10.5518/1502
title: Materials characterisation data on proton conducting arenedisulfonate coordination polymers

description: This dataset contains original characterizations of scanning electron microscopy (SEM), X-ray energy-dispersive spectroscopy (EDS), cryogenic-SEM (cryo-SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), elemental analysis (CHNS), light microscopy, scanning electron diffraction (SED), thermogravimetric analysis (TGA) and differential thermogravimetry (DTG), and electrochemical impedance spectroscopy (EIS) tests on coordination polymers (CPs) and CPs based membranes presented in the linked publication.