cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q6789
title: Data from: Plant and soil microbe responses to light, warming and nitrogen addition in a temperate forest

description: 1. Temperate forests across Europe and eastern North America have become
 denser since the 1950s due to less intensive forest management and global
 environmental changes such as nitrogen deposition and climate warming.
 Denser tree canopies result in lower light availability at the forest
 floor. This shade may buffer the effects of nitrogen deposition and
 climate warming on understorey plant communities. 2. We conducted an
 innovative in-situ field experiment to study the responses of co-occurring
 soil microbial and understorey plant communities to nitrogen addition,
 enhanced light availability, and experimental warming in a full-factorial
 design. 3. We determined the effects of multiple environmental drivers and
 their interactions on the soil microbial and understorey plant
 communities, and assessed to what extent the soil microbial and
 understorey plant communities co-vary. 4. High light led to lower biomass
 of the soil microbes (analysed by phospholipid fatty acids), but the soil
 microbial structure, i.e., the ratio of fungal biomass to bacterial
 biomass, was not affected by light availability. The composition of the
 soil bacterial community (analysed by high-throughput sequencing) was
 affected by both light availability and warming (and their interaction),
 but not by nitrogen addition. Yet, the number of unique operational
 taxonomic units was high in plots with nitrogen addition, and there were
 significant interactive effects of light and nitrogen addition. Light
 availability also determined the composition of the plant community; no
 effects of nitrogen addition and warming were observed. The soil bacterial
 and plant communities were co-structured, and light availability explained
 most variance of this co-structure. 5. We provide robust evidence for the
 key role of light in affecting both the soil microbial and plant
 communities in forest understoreys. Our results advocate for more
 multifactor global-change experiments that investigate the mechanism
 underlying the (in)direct effects of light on the plant–soil continuum in
 forests.
description: Soil microbial community
 and plant coverThe data file contains
 three datasets.The folder PrimerClipped contains the primerclipped V3-V4
 region 16SrRNA gene amplicon sequence files. The excel file Plant cover
 contains plant species and cover in each plot. The PLFA concentrations
 file contains all PLFA biomarkers. The READ ME file indicates the details
 of sequence files.Raw
 data.zip
DOI: 10.5061/dryad.4s5r6
title: Data from: The genome of the yellow potato cyst nematode Globodera rostochiensis reveals insights into the basis of parasitism and virulence

description: Background: The yellow potato cyst nematode Globodera rostochiensis is a
 devastating plant pathogen of global economic importance. This biotrophic
 parasite secretes effectors from pharyngeal glands, some of which were
 acquired by horizontal gene transfer, to manipulate host processes and
 promote parasitism. G. rostochiensis is classified into pathotypes with
 different plant resistance-breaking phenotypes. Results: We generate a
 high-quality genome assembly for G. rostochiensis pathotype Ro1, identify
 putative effectors and horizontal gene transfer events, map gene
 expression through the life cycle focusing on key parasitic transitions,
 and sequence the genomes of eight populations including four additional
 pathotypes to identify variation. Horizontal gene transfer contributes
 3.5% of the predicted genes, of which approximately 8.5% are deployed as
 effectors. Over one-third of all effector genes are clustered in 21
 putative "effector islands" in the genome. We identify a dorsal
 gland promoter element motif present upstream of 26 out of 28
 representative dorsal gland effector families, and predict a putative
 effector superset associated with this motif. We validate gland cell
 expression in two novel genes by in situ hybridisation, and catalogue
 dorsal gland promoter element-containing effectors from available cyst
 nematode genomes. Comparison of effector diversity between pathotypes
 highlights correlation with plant resistance-breaking. Conclusions: These
 G. rostochiensis genome resources will facilitate major advances in
 understanding nematode plant-parasitism. Dorsal gland promoter
 element-containing effectors are at the front line of the evolutionary
 arms race between plant and parasite, and the ability to predict gland
 cell expression a priori promises rapid advances in understanding their
 roles and mechanisms of action.
description: Clusters and normalized
 expression tablesFor each gene, lists the
 normalized expression data for each life stage, and (if significantly
 differentially expressed) which expression super cluster it is grouped
 into.nGr.v1.0.annotation+TEGFF file with locations of all gene calls in the G. rostochiensis genome and all transposable element predictions.nGr.v1.0.blast2goblast2go annotation as gff3 filenGr.v1.0.blast2go.txtblast2go annotation as gzipped text filenGr.v1.0.iprscan.xmlinter pro scan as gzipped xmlnGr.v1.0.iprscan.xmlinterproscan as tsvGr_pops.new.vs.nGr.v1.1.GQ.vcf.norm.filtered.vcf.snpeff.vcf.gz.data.txtsnpeff parsed vcf for G. rostochiensis pathotypes Ro1, 2, 3, 4, 5.Gr_pops.new.vs.nGr.v1.1.GQ.vcf.norm.filtered.vcf.snpeff.vcfRaw VCF for G. rostochiensis pathotypes Ro1, 2, 3, 4, 5.
DOI: 10.5061/dryad.hr0qt
title: Data from: BsRADseq: screening DNA methylation in natural populations of non-model species

description: Epigenetic modifications are expected to occur at a much faster rate than
 genetic mutations, potentially causing isolated populations to
 stochastically drift apart, or if they are subjected to different
 selective regimes, to directionally diverge. A high level of genome-wide
 epigenetic divergence between individuals occupying distinct habitats is
 therefore predicted. Here, we introduce bisulfite-converted restriction
 site associated DNA sequencing (bsRADseq), an approach to quantify the
 level of DNA methylation differentiation across multiple individuals. This
 reduced representation method is flexible in the extent of DNA sequence
 interrogated. We showcase its applicability in three natural systems, each
 comprising individuals adapted to divergent environments: a diploid plant
 (Heliosperma, Caryophyllaceae), a tetraploid plant (Dactylorhiza,
 Orchidaceae) and an animal (Gasterosteusaculeatus, Gasterosteidae). We
 present a robust bioinformatic pipeline, combining tools for RAD locus
 assembly, SNP calling, bisulfite-converted read mapping and DNA
 methylation calling to analyse bsRADseq data with or without a reference
 genome. Importantly, our approach accurately distinguishes between SNPs
 and methylation polymorphism (SMPs). Although DNA methylation frequency
 between different positions of a genome varies widely, we find a
 surprisingly high consistency in the methylation profile between
 individuals thriving in divergent ecological conditions, particularly in
 Heliosperma. This constitutive stability points to significant molecular
 or developmental constraints acting on DNA methylation variation.
 Altogether, by combining the flexibility of RADseq with the accuracy of
 bisulfite sequencing in quantifying DNA methylation, the bsRADseq
 methodology and our bioinformatic pipeline open up the opportunity for
 genome-wide epigenetic investigations of evolutionary and ecological
 relevance in non-model species, independent of their genomic features.
description: Reduced reference genome
 and bismark output filesReduced representation
 genome sequences built concatenating RADseq loci in Heliosperma and
 Dactylorhiza. Bismark output files for the three experiment described in
 the paper.bsRADseq_ref_bismark_output.tar.gz
DOI: 10.5061/dryad.db470
title: Data from: Genomics of end-Pleistocene population replacement in a small mammal

description: Current species’ distributions at high latitudes are the product of
 expansion from glacial refugia into previously uninhabitable areas at the
 end of the last glaciation. The traditional view of postglacial
 colonization is that southern populations expanded their ranges into
 unoccupied northern territories. Recent findings on mitochondrial DNA
 (mtDNA) of British small mammals have challenged this simple colonization
 scenario by demonstrating a more complex genetic turnover in Britain
 during the Pleistocene-Holocene transition where one mtDNA clade of each
 species was replaced by another mtDNA clade of the same species. Here, we
 provide evidence for one of those small mammals, the bank vole
 (Clethrionomys glareolus), that the replacement was genome-wide. Using
 more than 10,000 autosomal SNPs we found that similar to mtDNA, bank vole
 genomes in Britain form two (north and south) clusters which admix.
 Therefore, the genome of the original post-glacial colonists (the northern
 cluster) was likely replaced by another wave of migration from a different
 continental European population (the southern cluster), and we gained
 support for this by modelling with approximate Bayesian computation. This
 finding emphasises the importance of analysis of genome-wide diversity
 within species under changing climate in creating opportunities for
 sophisticated testing of population history scenarios.
description: Reference
 transcriptomeReference transcriptome
 reconstructed from de novo assembly produced with program Trinity by
 merging isoforms into gene models.reference_transcriptome.faGenotype information for 59 individualsVariant Call Format filevar.flt.vcf.zipPython script to retain a single, random SNP per geneTo run this script, type: python SNPs_oneSNPperContig.py SNPs_oneSNPperContig.pyPython script to run a HWE testThis Python script calls a perl script written by Joshua C. Randall (available at: http://www.sph.umich.edu/csg/abecasis/Exact/) to perform an exact Hardy-Weinberg Equilibrium test (Wigginton et al., 2005, Am J Hum Genet, 76: 887-893) for each SNP separately. To run this script, type: python P_value_HWE.py $outfile1.txtP_value_hwe.pyPython script to make an input file for the script P_value_HWE.pyTo run this script, type: python script_hwe_testing.py $infile.vcf $outfile1.txthwe_testing.py
DOI: 10.15468/dl.m4dgqr
title: Occurrence Download

description: A dataset containing 286023 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-148.44 59.27,-118.08 59.27,-118.08 69.77,-148.44 69.77,-148.44 59.27))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 286023 records from 300 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000309-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/qbnd9w
title: First description of the female of Hypotrabala tabithae and new collection localities for the species (Lepidoptera, Lasiocampidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Prozorova, Tatiana A., Sulak, Harald, Yakovlev, Roman V., Saldaitis, Aidas, Volkova, Julia S., Revay, Edita E., Müller, Günter C., Prozorov, Alexey M. (2025): First description of the female of Hypotrabala tabithae and new collection localities for the species (Lepidoptera, Lasiocampidae). Zootaxa 5728 (2): 352-364, DOI: 10.11646/zootaxa.5728.2.6, URL: https://doi.org/10.11646/zootaxa.5728.2.6AbstractTwo males and two females of Hypotrabala tabithae Takano & László, 2024 were found in the Ditsong National Museum of Natural History (Pretoria, Republic of South Africa) during a short visit in 2016. Females and their genitalia are illustrated and described here for the first time for H. tabithae, previously known after two type males. In addition, the male and its genitalia and geographic and ecoregional maps with four new collection localities in Zambia are illustrated.
DOI: 10.5061/dryad.m1c04
title: Data from: Measuring the biodiversity of microbial communities by flow cytometry

description: 1. Measuring the microbial diversity in natural and engineered
 environments is important for ecosystem characterization, ecosystem
 monitoring and hypothesis testing. Although the conventional assessment
 through single marker gene surveys has resulted in major advances, the
 complete procedure remains slow (i.e., weeks to months), labour-intensive
 and susceptible to multiple sources of laboratory and data processing
 bias. Growing interest, in highly resolved, temporal surveys of microbial
 diversity, necessitates rapid, inexpensive and robust analytical platforms
 that require limited computational effort. 2. Here, we demonstrate that
 sensitive single-cell measurements of phenotypic attributes, obtained via
 flow cytometry, can provide fast (i.e., within minutes) first-line
 assessments of microbial diversity dynamics, without demanding extensive
 sample preparation and downstream data processing. We developed a data
 processing pipeline that fits bivariate kernel density functions to
 phenotypic parameter combinations of an entire microbial community, and
 concatenates them to a single one-dimensional phenotypic fingerprint. By
 calculating established diversity metrics from such phenotypic
 fingerprints, we construct an alternative interpretation of the microbial
 diversity that incorporates distinct phenotypic traits underlying
 cell-to-cell heterogeneity (i.e., morphology and nucleic acid content). 3.
 Based on a detailed longitudinal study of a highly dynamic microbial
 ecosystem, our approach delivered temporal alpha diversity profiles that
 strongly correlated with the reference diversity, as estimated by 16S rRNA
 amplicon sequencing. This strongly suggests that the distribution of a
 limited amount of phenotypic features within a microbial community already
 provides sufficient resolving power for the measurement of diversity
 dynamics at the species level. 4. We present a fast, robust analysis
 method for monitoring the microbial biodiversity of natural and engineered
 ecosystems that correlates well with the conventional marker gene surveys.
 Our work has both applied and fundamental implications that stretch from
 ecosystem monitoring and studies on microbial community dynamics, to
 supervised sampling strategies. Furthermore, our approach offers
 perspectives for the development of on-line and in situ monitoring systems
 for microbial ecosystems.
description: Flow cytometry
 dataThis data set contains
 two flow cytometry data (.fcs format) surveys for a cooling water
 microbial community. In the metadata, additional information (e.g.,
 temperature, taxonomic diversity) has been included as well. For details
 about the ecosystem we refer to SI figure 2 of the paper. More information
 about the metadata can be found in the ReadMe file. For a selected subset
 of datapoints, 16S rRNA gene amplicon sequencing was performed and this
 data can be found here:
 http://www.ncbi.nlm.nih.gov/sra/?term=SRP066190.FlowRepository_FR-FCM-ZZNA_files.zip
DOI: 10.5061/dryad.fp45s43
title: Data from: Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila

description: The adherens junction couples the actin cytoskeletons of neighboring cells
 to provide the foundation for multicellular organization. The core of the
 adherens junction is the cadherin-catenin complex that arose early in the
 evolution of multicellularity to link actin to intercellular adhesions.
 Over time, evolutionary pressures have shaped the signaling and mechanical
 functions of the adherens junction to meet specific developmental and
 physiological demands. Evolutionary rate covariation (ERC) identifies
 proteins with correlated fluctuations in evolutionary rate that can
 reflect shared selective pressures and functions. Here we use ERC to
 identify proteins with evolutionary histories similar to the Drosophila
 E-cadherin (DE-cad) ortholog. Core adherens junction components α-catenin
 and p120-catenin displayed positive ERC correlations with DE-cad,
 indicating that they evolved under similar selective pressures during
 evolution between Drosophila species. Further analysis of the DE-cad ERC
 profile revealed a collection of proteins not previously associated with
 DE-cad function or cadherin-mediated adhesion. We then analyzed the
 function of a subset of ERC-identified candidates by RNAi during border
 cell (BC) migration and identified novel genes that function to regulate
 DE-cad. Among these, we found that the gene CG42684, which encodes a
 putative GTPase activating protein (GAP), regulates BC migration and
 adhesion. We named CG42684 raskol (“to split” in Russian) and show that it
 regulates DE-cad levels and actin protrusions in BCs. We propose that
 Raskol functions with DE-cad to restrict Ras/Rho signaling and help guide
 BC migration. Our results demonstrate that a coordinated selective
 pressure has shaped the adherens junction and this can be leveraged to
 identify novel components of the complexes and signaling pathways that
 regulate cadherin-mediated adhesion.
description: ERC_calculation
 compressed directory, code and dataCompressed directory
 contains all code and data to calculate gene-by-gene ERC values for the
 Drosophila genome. Follow steps and file decriptions in the README.txt
 file.ERC_calculation.zip
DOI: 10.5061/dryad.1n542
title: Data from: Homeostasis of metabolites in Escherichia coli on transition from anaerobic to aerobic conditions and the transient secretion of pyruvate

description: We have developed a method for rapid quenching of samples taken from
 chemostat cultures of Escherichia coli that gives reproducible and
 reliable measurements of extracellular and intracellular metabolites by 1H
 NMR and have applied it to study the major central metabolites during the
 transition from anaerobic to aerobic growth. Almost all metabolites showed
 a gradual change after perturbation with air, consistent with immediate
 inhibition of pyruvate formate-lyase, dilution of overflow metabolites and
 induction of aerobic enzymes. Surprisingly, although pyruvate showed
 almost no change in intracellular concentration, the extracellular
 concentration transiently increased. The absence of intracellular
 accumulation of pyruvate suggested that one or more glycolytic enzymes
 might relocate to the cell membrane. To test this hypothesis, chromosomal
 pyruvate kinase (pykF) was modified to express either PykF-green
 fluorescent protein or PykF-FLAG fusion proteins. Measurements showed that
 PykF-FLAG relocates to the cell membrane within 5 min of aeration and then
 slowly returns to the cytoplasm, suggesting that on aeration, PykF
 associates with the membrane to facilitate secretion of pyruvate to
 maintain constant intracellular levels.
description: NMR
 datazipped archive of
 representative NMR spectrafluorescence images and
 datazipped archive of
 fluorescence data at different time points and excel files listing data,
 fitting and calculations of point spread functionsTEM
 imageszipped archive of TEM
 images of nanogold-antibody labelling of FLAG-tagged PykF at different
 time points
DOI: 10.5061/dryad.23d0f
title: Data from: Detecting recent selective sweeps while controlling for mutation rate and background selection

description: A composite likelihood ratio test implemented in the program SweepFinder
 is a commonly used method for scanning a genome for recent selective
 sweeps. SweepFinder uses information on the spatial pattern (along the
 chromosome) of the site frequency spectrum (SFS) around the selected
 locus. To avoid confounding effects of background selection and variation
 in the mutation process along the genome, the method is typically applied
 only to sites that are variable within species. However, the power to
 detect and localize selective sweeps can be greatly improved if invariable
 sites are also included in the analysis. In the spirit of a
 Hudson-Kreitman-Aguadé test, we suggest adding fixed differences relative
 to an outgroup to account for variation in mutation rate, thereby
 facilitating more robust and powerful analyses. We also develop a method
 for including background selection, modeled as a local reduction in the
 effective population size. Using simulations we show that these advances
 lead to a gain in power while maintaining robustness to mutation rate
 variation. Furthermore, the new method also provides more precise
 localization of the causative mutation than methods using the spatial
 pattern of segregating sites alone.
description: SF2 input
 filesFrequencies of European
 human SNPs and fixed differences (x=n) to chimpanzee that was used as
 input file for SweepFinder2. Original data from: Drmanac R, Sparks AB,
 Callow MJ et al. (2010) Human genome sequencing using unchained base reads
 on self-assembling DNA Nanoarrays. Science, 327, 78–81.input_frequencies.zipRecombination ratesSex-averaged pedigree-based human recombination rates from deCODE Genetics that was used as input file for SweepFinder2. Original data from: Kong A, Thorleifsson G, Gudbjartsson DF et al. (2010) Fine-scale recombination rate differences between sexes, populations and individuals. Nature, 467, 1099–1103.input_recombination_rates.zipinput_BvaluesB-value map that was used as input file for SweepFinder2. Original data from: McVicker G, Gordon D, Davis C, Green P (2009) Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet, 5, e1000471. Note that the positions correspond to the positions of the recombination rate and frequency files.Human-chimpanzee site frequency spectrumWhole-genome site frequency spectrum (SFS) that includes the proportion of sites that are fixed to chimpanzee (x=n). This file was used as background SFS for SweepFinder2.humanChimpSpectrum.txt
DOI: 10.5061/dryad.pm3g4r3
title: Data from: Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development

description: The ancient mechanisms that caused developmental gene regulatory networks
 to diversify among distantly related taxa are not well understood. Here we
 use ancestral protein reconstruction, biochemical experiments, and
 developmental assays of transgenic animals carrying reconstructed
 ancestral genes to investigate how the transcription factor Bicoid (Bcd)
 evolved its central role in anterior-posterior patterning in flies. We
 show that most of Bcd's derived functions are attributable to
 evolutionary changes within its homeodomain (HD) during a phylogenetic
 interval &gt;140 million years ago. A single substitution from this
 period (Q50K) accounts almost entirely for the evolution of Bcd's
 derived DNA specificity in vitro. In transgenic embryos expressing the
 reconstructed ancestral HD, however, Q50K confers activation of only a few
 of Bcd's transcriptional targets and yields a very partial rescue of
 anterior development Adding a second historical substitution (M54R)
 confers regulation of additional Bcd targets and further rescues anterior
 development. These results suggest that two epistatically interacting
 mutations played a major role in the evolution of Bcd's controlling
 regulatory role in early development.
description: PBM_resultsRaw and processed data from protein binding microarray experiments.