cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fc1m8
title: Data from: Transcriptional profile and differential fitness in a specialist milkweed insect across host plants varying in toxicity

description: Interactions between plants and herbivorous insects have been models for
 theories of specialization and coevolution for over a century.
 Phytochemicals govern many aspects of these interactions and have fostered
 the evolution of adaptations by insects to tolerate or even specialize on
 plant defensive chemistry. While genomic approaches are providing new
 insights into the genes and mechanisms insect specialists employ to
 tolerate plant secondary metabolites, open questions remain about the
 evolution and conservation of insect counter-defenses, how insects respond
 to the diversity defenses mounted by their host plants, and the costs and
 benefits of resistance and tolerance to plant defenses in natural
 ecological communities. Using a milkweed-specialist aphid (Aphis nerii)
 model, we test the effects of host plant species with increased toxicity,
 likely driven primarily by increased secondary metabolites, on aphid life
 history traits and whole body gene expression. We show that more toxic
 plant species have a negative effect on aphid development and lifetime
 fecundity. When feeding on more toxic host plants with higher levels of
 secondary metabolites, aphids regulate a narrow, targeted set of genes,
 including those involved in canonical detoxification processes (e.g.,
 cytochrome P450s, hydrolases, UDP-glucuronosyltransferases, and ABC
 transporters). These results indicate that A. nerii marshal a variety of
 metabolic detoxification mechanisms to circumvent milkweed toxicity and
 facilitate host plant specialization, yet, despite these detoxification
 mechanisms, aphids experience reduced fitness when feeding on more toxic
 host plants. Disentangling how specialist insects respond to challenging
 host plants is a pivotal step in understanding the evolution of
 specialized diet breadths.
description: Development to Adult
 dataEach aphid is
 represented with a line; day column indicates day aphid matured to
 adult.adult_total.csvFecundity dataEach line represents a plant; number of adults and offspring each day were counted for daily average fecundity.fecundity_total.csvSurvival dataEach line represents an aphid; day column represents the experimental day the aphid died.survival_total.csvMicrosatellite dataMicrosatellite lengths (bp) are indicated for three A. nerii genotypes at six loci.microsats.xlsxDESEQ2 for A. nerii transcriptomeFile is output of DESEQ2 showing differential expression for all A. nerii transcripts. Ax3 = mean expression on A. incarnata; Bx3 = mean expression on G. physocarpus.APHNE_DESEQ.csvA. nerii transcriptome sequencesAssembled A. nerii nucleotide sequences (APHNE).A.nerii.coding.sequences.fa
DOI: 10.5061/dryad.4fv71
title: Data from: Maternal effects in a wild songbird are environmentally plastic but only marginally alter the rate of adaptation

description: Despite ample evidence for the presence of maternal effects (MEs) in a
 variety of traits and strong theoretical indications for their
 evolutionary consequences, empirical evidence to what extent MEs can
 influence evolutionary responses to selection remains ambiguous. We tested
 the degree to which MEs can alter the rate of adaptation of a key
 life-history trait, clutch size, using an individual-based model approach
 parameterized with experimental data from a long-term study of great tits
 (Parus major). We modeled two types of MEs: (i) an environmentally plastic
 ME, in which the relationship between maternal and offspring clutch size
 depended on the maternal environment via offspring condition, and (ii) a
 fixed ME, in which this relationship was constant. Although both types of
 ME affected the rate of adaptation following an abrupt environmental
 shift, the overall effects were small. We conclude that evolutionary
 consequences of MEs are modest at best in our study system, at least for
 the trait and the particular type of ME we considered here. A closer link
 between theoretical and empirical work on MEs would hence be useful to
 obtain accurate predictions about the evolutionary consequences of MEs
 more generally.
description: Phenotypes (clutch size)
 to calculate heritabilityClutchSize_heritability_data.csvPedigree associated with the phenotype filePedigree.csvManipulated clutch sizes with fledgling weightsManipulated_Weights.csvFledgling weights and survival of chicksSurvival_Weights.csvData for calculating maternal effectMaternalEffect.csv
DOI: 10.5061/dryad.1607
title: Data from: Conservation genetics of Neotropical pollinators revisited: microsatellite analysis suggests that diploid males are rare in orchid bees

description: Allozyme analyses have suggested that Neotropical orchid bee (Euglossini)
 pollinators are vulnerable because of putative high frequencies of diploid
 males, a result of loss of sex allele diversity in small hymenopteran
 populations with single locus complementary sex determination. Our
 analysis of 1010 males from 27 species of euglossine bees sampled across
 the Neotropics at 2-11 polymorphic microsatellite loci revealed only 5
 diploid males at an overall frequency of 0.005 (95% CIs 0.002-0.010);
 errors through genetic non-detection of diploid males were likely small.
 In contrast to allozyme-based studies, we detected very weak or
 insignificant population genetic structure, even for a pair of populations
 &gt;500 km apart, possibly accounting for low diploid male
 frequencies. Technical flaws in previous allozyme-based analyses have
 probably led to considerable overestimation of diploid male production in
 orchid bees. Other factors may have a more immediate impact on population
 persistence than the genetic load imposed by diploid males on these
 important Neotropical pollinators.
description: Haplotypes/genotypes of
 individuals at microsatellite lociHaplotypes (for diploid
 males: genotypes) of all males collected in the field and analyzed at
 several microsatellite loci, as presented in the original Evolution
 paper.PaxTableS1males.docGenotypes of females at numerous microsatellite lociGenotypes at numerous microsatellite loci of all female euglossine bees presented in the original Evolution paper.PaxTableS2fem.doc
DOI: 10.5061/dryad.8m5v4
title: Data from: Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms

description: Despite recent work to characterize gene expression changes associated
 with larval development in oysters, the mechanism by which the larval
 shell is first formed is still largely unknown. In Crassostrea gigas, this
 shell forms within the first 24 hours post fertilization, and it has been
 demonstrated that changes in water chemistry can cause delays in shell
 formation, shell deformations and higher mortality rates. In this study,
 we use the delay in shell formation associated with exposure to
 pCO2-acidified seawater to identify genes correlated with initial shell
 deposition. By fitting linear models to gene expression data in ambient
 and low aragonite saturation treatments, we are able to isolate 37
 annotated genes correlated with initial larval shell formation, which can
 be categorized into 1) ion transporters, 2) shell matrix proteins and 3)
 protease inhibitors. Clustering of the gene expression data into
 co-expression networks further supports the result of the linear models,
 and also implies an important role of dynein motor proteins as
 transporters of cellular components during the initial shell formation
 process. This work provides a foundation for further studies on how
 genetic variation in these identified genes could affect fitness of oyster
 populations subjected to future environmental changes, such as ocean
 acidification.
description: Experiment 1 (NET3) Raw
 read counts (with duplicates)Experiment 1 (NET3) Raw
 read counts (with duplicates), mapped to the oyster genome v9 coding
 regions.NET3_Counts_with_dups.txtExperiment 2 (NET1) Raw read counts (with duplicates)Experiment 2 (NET1) Raw read counts (with duplicates), mapped against the oyster genome v9 coding regions.NET1_Counts_with_dups.txtExperiment 1 (NET3) Raw read counts (duplicates removed)Experiment 1 (NET3) Raw read counts (duplicates removed), mapped against the oyster genome v9 coding regionsNET3_Counts_dedup.txtExperiment 2 (NET1) Raw read counts (duplicates removed)Experiment 2 (NET1) Raw read counts (duplicates removed), mapped against the oyster genome v9 coding regionsNET1_Counts_dedup.txtSupporting information - ErmineJ Functional enrichment results fileSupporting information - ErmineJ Functional enrichment results fileSI_TableS2_ERMINEJ GSR runs.project
DOI: 10.5061/dryad.8hs71
title: Data from: An in silico comparison of protocols for dated phylogenomics

description: In the age of genome-scale DNA sequencing, choice of molecular marker
 arguably remains an important decision in planning a phylogenetic study.
 Using published genomes from 23 primate species, we make a standardized
 comparison of four of the most frequently used protocols in phylogenomics,
 viz., targeted sequence-enrichment using ultraconserved element and
 exon-capture probes, and restriction-site-associated DNA sequencing
 (RADseq and ddRADseq). Here we present a procedure to perform in silico
 extractions from genomes and create directly comparable datasets for each
 class of marker. We then compare these datasets in terms of both
 phylogenetic resolution and ability to consistently and precisely estimate
 clade ages using fossil-calibrated molecular-clock models. Furthermore, we
 were also able to directly compare these results to previously published
 datasets from Sanger-sequenced nuclear exons and mitochondrial genomes
 under the same analytical conditions. Our results show---although with the
 exception of the mitochondrial genome dataset and the smallest ddRADseq
 dataset---that for uncontroversial nodes all data classes performed
 equally well, i.e. they recovered the same well supported topology.
 However, for one difficult-to-resolve node comprising a rapid
 diversification, we report well supported but conflicting topologies among
 the marker classes, consistent with the mismodelling of gene tree
 heterogeneity as demonstrated by species tree analyses of single
 nucleotide polymorphisms. Likewise, clade age estimates showed consistent
 discrepancies between datasets under strict and relaxed clock models; for
 recent nodes, clade ages estimated by nuclear exon datasets were younger
 than those of the UCE, RADseq and mitochondrial data, but vice versa for
 the deepest nodes in the primate phylogeny. This observation is explained
 by temporal differences in phylogenetic informativeness (PI), with the
 datasets with strong PI peaks toward the present underestimating the
 deepest node ages. Finally, we conclude by emphasizing that while huge
 numbers of loci are probably not required for uncontroversial phylogenetic
 questions---for which practical considerations such as cost and ease of
 data generation/sharing/aggregating therefore become increasingly
 important---accurately modelling heterogeneous data remains as relevant as
 ever for the more recalcitrant problems.
description: xml data files for
 BEAST2 analysesxml data files (ddRAD,
 ddRADeco, RAD, Exon, UCE, Perelman and Finstermeier) used in dated BEAST2
 analysesbeast.tar.gzxml data files for SNAPP analyses in BEAST2xml data files (ddRAD, ddRADeco, RAD, Exon and UCE) used in SNAPP analyses implemented in BEAST2snapp.tar.gz
DOI: 10.5061/dryad.fp954
title: Data from: Low rates of hybridization between European wildcats and domestic cats in a human-dominated landscape

description: Hybridization between wild species and their domestic congeners is
 considered a major concern for species conservation. Genetic integrity of
 the European wildcat, for instance, is of interest as the species is
 outnumbered by domestic cats by several orders of magnitude throughout its
 range. We genotyped 1071 individual wildcat samples obtained from hair
 traps and roadkills collected across the highly fragmented forests of
 western central Europe, in Germany and Luxembourg, to assess domestic cat
 introgression in wildcats in human-dominated landscapes. Analyses using a
 panel of 75 autosomal SNPs suggested a low hybridization rate, with 3.5 %
 of wildcat individuals being categorized as F1, F2 or backcrosses to
 either parental taxon. We report that SNP data appeared to be more
 consistent than our set of 14 microsatellite markers and that SNPs showed
 higher accuracy to detect hybrids and their class in simulation analyses
 and were less affected by underlying population structure. Our results
 strongly suggest that very high hybridization rates previously reported
 for central Europe may be partly due to inadequate choice of markers
 and/or sampling design. Our example documents that a carefully selected
 SNP panel for hybrid detection may be used as an alternative to commonly
 applied microsatellite markers, including studies relying on
 non-invasively collected samples. In addition, our finding of overall low
 hybridization rates in central European wildcats provides an example of
 successful wildlife coexistence in human-dominated, fragmented landscapes.
description: Dataset_Low rates of
 hybridisationThis file contains all
 necessary data from the manuscript.
DOI: 10.5061/dryad.2mm71
title: Data from: A high-throughput FTIR spectroscopy approach to assess adaptive variation in the chemical composition of pollen

description: The two factors defining male reproductive success in plants are pollen
 quantity and quality, but our knowledge about the importance of pollen
 quality is limited due to methodological constraints. Pollen quality in
 terms of chemical composition may be either genetically fixed for high
 performance independent of environmental conditions, or it may be plastic
 to maximize reproductive output under different environmental conditions.
 In this study, we validated a new approach for studying the role of
 chemical composition of pollen in adaptation to local climate. The
 approach is based on high-throughput Fourier infrared (FTIR)
 characterization and biochemical interpretation of pollen chemical
 composition in response to environmental conditions. The study covered
 three grass species, Poa alpina, Anthoxanthum odoratum, and Festuca ovina.
 For each species, plants were grown from seeds of three populations with
 wide geographic and climate variation. Each individual plant was divided
 into four genetically identical clones which were grown in different
 controlled environments (high and low levels of temperature and
 nutrients). In total, 389 samples were measured using a high-throughput
 FTIR spectrometer. The biochemical fingerprints of pollen were species and
 population specific, and plastic in response to different environmental
 conditions. The response was most pronounced for temperature, influencing
 the levels of proteins, lipids, and carbohydrates in pollen of all
 species. Furthermore, there is considerable variation in plasticity of the
 chemical composition of pollen among species and populations. The use of
 high-throughput FTIR spectroscopy provides fast, cheap, and simple
 assessment of the chemical composition of pollen. In combination with
 controlled-condition growth experiments and multivariate analyses, FTIR
 spectroscopy opens up for studies of the adaptive role of pollen that
 until now has been difficult with available methodology. The approach can
 easily be extended to other species and environmental conditions and has
 the potential to significantly increase our understanding of plant male
 function.
description: Spectral
 dataSpectral data containing
 raw FTIR spectra of pollen (first row: wavenumbers, subsequent rows:
 absorbance values)
DOI: 10.5281/zenodo.16918543
title: Data from: "Controlling longitudinal compressive failure in CFRPs through bio-inspired nacre-like microstructural design"

description: The datset contains data collected and processed for the study presented in the journal paper "Controlling longitudinal compressive failure in CFRPs through bio-inspired nacre-like microstructural design".Specifically, it contains machine recorded data, specimen dimensions, pictures and video recordings (either SEM or with optical microscope) taken during and after 3-point-bending tests on small scale specimens having a nacre-like bioinspired microstructure on their compressive side.

For more details, please refer to the full paper.
DOI: 10.5061/dryad.3h185
title: Data from: Coestimating reticulate phylogenies and gene trees from multilocus sequence data

description: The multispecies network coalescent (MSNC) is a stochastic process that
 captures how gene trees grow within the branches of a phylogenetic
 network. Coupling the MSNC with a stochastic mutational process that
 operates along the branches of the gene trees gives rise to a generative
 model of how multiple loci from within and across species evolve in the
 presence of both incomplete lineage sorting (ILS) and reticulation (e.g.,
 hybridization). We report on a Bayesian method for sampling the parameters
 of this generative model, including the species phylogeny, gene trees,
 divergence times, and population sizes, from DNA sequences of multiple
 independent loci. We demonstrate the utility of our method by analyzing
 simulated data and reanalyzing an empirical data set. Our results
 demonstrate the significance of not only co-estimating species phylogenies
 and gene trees, but also accounting for reticulation and ILS
 simultaneously. In particular, we show that when gene flow occurs, our
 method accurately estimates the evolutionary histories, coalescence times,
 and divergence times. Tree inference methods, on the other hand,
 underestimate divergence times and overestimate coalescence times when the
 evolutionary history is reticulate. While the MSNC corresponds to an
 abstract model of ``intermixture," we study the performance of the
 model and method on simulated data generated under a gene flow model. We
 show that the method accurately infers the most recent time at which gene
 flow occurs. Finally, we demonstrate the application of the new method to
 a 106-locus yeast data set.
description: WenNakhleh-SISupplementary Information
DOI: 10.5281/zenodo.16918542
title: Data from: "Controlling longitudinal compressive failure in CFRPs through bio-inspired nacre-like microstructural design"

description: The datset contains data collected and processed for the study presented in the journal paper "Controlling longitudinal compressive failure in CFRPs through bio-inspired nacre-like microstructural design".Specifically, it contains machine recorded data, specimen dimensions, pictures and video recordings (either SEM or with optical microscope) taken during and after 3-point-bending tests on small scale specimens having a nacre-like bioinspired microstructure on their compressive side.

For more details, please refer to the full paper.
DOI: 10.5061/dryad.6gh40
title: Data from: Temporal genetic patterns of diversity and structure evidence sweepstakes in reproductive success of a spiny lobster

description: Population structure of many marine organisms is spatially patchy and
 varies within and between years, a phenomenon defined as chaotic genetic
 patchiness. This results from the combination of planktonic larval
 dispersal and environmental stochasticity. Additionally, in species with
 bi-partite life, post-settlement selection can magnify these genetic
 differences. The high fecundity (up to 500,000 eggs annually) and
 protracted larval duration (12-24 months) and dispersal of the southern
 rock lobster, Jasus edwardsii, make it a good test species for chaotic
 genetic patchiness and selection during early benthic life. Here we used
 double digest restriction-site associated DNA sequencing (ddRADseq) to
 investigate chaotic genetic patchiness and post-settlement selection in
 this species. We assessed differences in genetic structure and diversity
 of recently settled pueruli across four settlement years and between two
 sites in southeast Australia separated by approximately 1,000 km.
 Post-settlement selection was investigated by identifying loci under
 putative positive selection between recently settled pueruli and
 post-pueruli and quantifying differences in the magnitude and strength of
 the selection at each year and site. Genetic differences within and among
 sites through time in neutral SNP markers indicated chaotic genetic
 patchiness. Recently settled pueruli at the southernmost site exhibited
 lower genetic diversity during years of low pueruli catches, further
 supporting this hypothesis. Finally, analyses of outlier SNPs detected
 fluctuations in the magnitude and strength of the markers putatively under
 positive selection over space and time. One locus under putative positive
 selection was consistent at both locations during the same years,
 suggesting the existence of weak post-settlement selection.
description: Reference
 lociReference catalogue
 containing 900 loci obtained after SNP filtering for MAF, LD, missing data
 and retaining one SNP per locusReference_loci_005MAF.faVariant calling format (VCF) fileVCF file generated using the software GATK v.3.3_0combined_samples.vcf
DOI: 10.5281/zenodo.18372737
title: Gaussian output data for protonated proton sponges

description: This dataset contains Gaussian output files (.log.gz) corresponding to quantum-chemical calculations performed on protonated proton sponge systems investigated in the published study: Phosphazenyl Phosphine Proton Sponges: Does the Proton-Chelating Effect Enhance Their Basicity?, Int. J. Mol. Sci. 2025, 26, 5058, DOI: 10.3390/ijms26115058.

The output files include the complete computational setup for each calculation, including the full route section, molecular input geometries, program version information, and all reported electronic and thermodynamic properties. Separate Gaussian input files are therefore not provided, as all necessary information to reconstruct each calculation is explicitly contained within the corresponding output file.

The dataset represents part 2 of a three-part collection, with files grouped according to logical subsets of the studied systems. The complete collection is distributed across three Zenodo records due to file number limitations.

The data are provided as raw computational outputs and are intended to support transparency, reproducibility, and reuse of the reported computational results.
DOI: 10.5281/zenodo.18372738
title: Gaussian output data for protonated proton sponges

description: This dataset contains Gaussian output files (.log.gz) corresponding to quantum-chemical calculations performed on protonated proton sponge systems investigated in the published study: Phosphazenyl Phosphine Proton Sponges: Does the Proton-Chelating Effect Enhance Their Basicity?, Int. J. Mol. Sci. 2025, 26, 5058, DOI: 10.3390/ijms26115058.

The output files include the complete computational setup for each calculation, including the full route section, molecular input geometries, program version information, and all reported electronic and thermodynamic properties. Separate Gaussian input files are therefore not provided, as all necessary information to reconstruct each calculation is explicitly contained within the corresponding output file.

The dataset represents part 2 of a three-part collection, with files grouped according to logical subsets of the studied systems. The complete collection is distributed across three Zenodo records due to file number limitations.

The data are provided as raw computational outputs and are intended to support transparency, reproducibility, and reuse of the reported computational results.