cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.742564m
title: Data from: Out of the testis, into the ovary: biased outcomes of gene duplication and deletion in Drosophila

description: Gene turnover is a key source of adaptive variation. Yet most evolutionary
 studies have focused on gene duplication, dismissing gene deletion as a
 mechanism that simply eradicates redundancy. Here I utilize genome-scale
 sequence and multi-tissue expression data from Drosophila melanogaster and
 Drosophila pseudoobscura to simultaneously assess the evolutionary
 outcomes of gene duplication and deletion in Drosophila. I find that gene
 duplication is more frequent than gene deletion in both species,
 indicating that it may play a more important role in Drosophila evolution.
 However, examination of several genic properties reveals that genes likely
 possess distinct functions after duplication that diverge further before
 deletion, suggesting that loss of redundancy cannot explain a majority of
 gene deletion events in Drosophila. Moreover, in addition to providing
 support for the well-known “out of the testis” origin of young duplicate
 genes, analyses of gene expression profiles uncover a preferential bias
 against deletions of old ovary-expressed genes. Therefore, I propose a
 novel “into the ovary” hypothesis for gene deletion in Drosophila, in
 which gene deletion may promote adaptation by salvaging genes that
 contribute to the evolution of female reproductive phenotypes. Under this
 combined “out of the testis, into the ovary” evolutionary model, gene
 duplication and deletion work in concert to generate and maintain a
 balanced repertoire of genes that may promote sex-specific adaptation in
 Drosophila.
description: Absolute
 quantile-normalized log2(FPKM) in six tissues of D.
 melanogasterColumns: Flybase ID,
 Muller Element, Female Head FPKM, Ovary FPKM, Male Head FPKM, Testis FPKM,
 Accessory Gland FPKM, Carcass FPKMDmel.log2FPKM.quantNorm.absoluteRelativized quantile-normalized log2(FPKM) in six tissues of D. melanogasterColumns: Flybase ID, Muller Element, Female Head FPKM, Ovary FPKM, Male Head FPKM, Testis FPKM, Accessory Gland FPKM, Carcass FPKMDmel.log2FPKM.quantNorm.relativeAbsolute quantile-noramlized log2(FPKM) in six tissues of D. pseudoobscuraColumns: Flybase ID, Muller Element, Female Head FPKM, Ovary FPKM, Male Head FPKM, Testis FPKM, Accessory Gland FPKM, Carcass FPKMDpse.log2FPKM.quantNorm.absoluteRelativized quantile-normalized log2(FPKM) in six tissues of D. pseudoobscuraColumns: Flybase ID, Muller Element, Female Head FPKM, Ovary FPKM, Male Head FPKM, Testis FPKM, Accessory Gland FPKM, Carcass FPKMDpse.log2FPKM.quantNorm.relative
DOI: 10.5061/dryad.sh5b962
title: Data from: Sequence capture phylogenomics of historical ethanol-preserved museum specimens: unlocking the rest of the vault

description: Natural history collections play a crucial role in biodiversity research
 and museum specimens are increasingly being incorporated into modern
 genetics-based studies. Sequence capture methods have proven incredibly
 useful for phylogenomics, providing the additional ability to sequence
 historical museum specimens with highly degraded DNA, which until recently
 have been deemed less valuable for genetic work. The successful sequencing
 of ultraconserved elements (UCEs) from historical museum specimens has
 been demonstrated on multiple tissue types including dried bird skins,
 formalin-fixed squamates, and pinned insects. However, no study has
 thoroughly demonstrated this approach for historical ethanol-preserved
 museum specimens. Alongside sequencing of “fresh” specimens preserved in
 &gt;95% ethanol and stored at -80 ºC, we used extraction techniques
 specifically designed for degraded DNA coupled with sequence capture
 protocols to sequence UCEs from historical museum specimens preserved in
 70–80% ethanol and stored at room temperature, the standard for such
 ethanol-preserved museum collections. Across 35 fresh and 15 historical
 museum samples of the arachnid order Opiliones, an average of 345 UCE loci
 were included in phylogenomic matrices, with museum samples ranging from
 6–495 loci. We successfully demonstrate the inclusion of historical
 ethanol-preserved museum specimens in modern sequence capture phylogenomic
 studies, show high frequency of variant bases at the species and
 population-level, and from off-target reads successfully recover multiple
 loci traditionally sequenced in multi-locus studies including
 mitochondrial loci and nuclear rRNA loci. The methods detailed in this
 study will allow researchers to potentially acquire genetic data from
 millions of ethanol-preserved museum specimens held in collections
 worldwide.
description: 65/65 CORE 50% coverage
 treeResulting RAxML
 phylogeny for the 65/65 CORE dataset with 50% taxon
 coverage65:65_CORE_50PercentTaxon_RAxML_bipartitions.result.tre82/80 CORE 50% coverage treeResulting RAxML phylogeny for the 82/80 CORE dataset with 50% taxon coverage82:80_CORE_50PercentTaxon_RAxML_bipartitions.result.tre65/65 CORE 50% coverage matrixConcatenated UCE matrix for the 65/65 CORE dataset with 50% taxon coverage65:65_CORE_50PercentTaxon.phylip82/80 CORE 50% coverage matrixConcatenated UCE matrix for the 82/80 CORE dataset with 50% taxon coverage82:80_CORE_50PercentTaxon.phylip65/65 CORE 50% coverage UCE lociAll individual UCE loci included in the 65/65 CORE 50% coverage matrix65:65_CORE_50PercentTaxon_UCEloci.zip82/80 CORE 50% coverage UCE lociAll individual UCE loci included in the 82/80 CORE 50% coverage matrix82:80_CORE_50PercentTaxon_UCEloci.zip
DOI: 10.5061/dryad.2h412kh
title: Data from: Genome-wide variation in DNA methylation is associated with stress resilience and plumage brightness in a wild bird

description: Individuals often differ in their ability to cope with challenging
 environmental and social conditions. Evidence from model systems suggests
 that patterns of DNA methylation are associated with variation in coping
 ability. These associations could arise directly if methylation plays a
 role in controlling the physiological response to stressors by, among
 other things, regulating the release of glucocorticoids in response to
 challenges. Alternatively, the association could arise indirectly if
 methylation and resilience have a common cause, such as early life
 conditions. In either case, methylation might act as a biomarker for
 coping ability. At present, however, relatively little is known about
 whether variation in methylation is associated with organismal performance
 and resilience under natural conditions. We studied genome-wide patterns
 of DNA methylation in free-living female tree swallows (Tachycineta
 bicolor) using methylated DNA immunoprecipitation (MeDIP) and a tree
 swallow genome that was assembled for this study. We identified areas of
 the genome that were differentially methylated with respect to social
 signal expression (breast brightness) and physiological traits (ability to
 terminate the glucocorticoid stress response through negative feedback).
 We also asked whether methylation predicted resilience to a subsequent
 experimentally imposed challenge. Individuals with brighter breast plumage
 and higher stress resilience had lower methylation at differentially
 methylated regions across the genome. Thus, widespread differences in
 methylation predicted both social signal expression and the response to
 future challenges under natural conditions. These results have
 implications for predicting individual differences in resilience, and for
 understanding the mechanistic basis of resilience and its environmental
 and social mediators.
description: MEDIP_ANALYSIS_COMMANDSExample of the commands used for MEDIP analysis and obtaining rpkm valuesSequence data aligned to the T. bicolor genomeSequence data for each individual included in the study aligned to the reference genomeAligned_MEDIP_data.tar.gz
DOI: 10.15468/dl.mg4frd
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Englerina triplinervia"
 ]
}

 The dataset includes 40 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001820-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.32svnz
title: Occurrence Download

description: A dataset containing 134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rumex gmelinii"
 ]
}

 The dataset includes 134 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001819-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4181mp7
title: Data from: Catalytic self-folding of 2D structures through cascading magnet reactions

description: While thousands of proteins involved in development of the human body are
 capable of self-assembling in a distributed manner from merely 20 types of
 amino acid, macroscopic products that can be assembled spontaneously from
 `alive' components remains an aspiration in engineering. To attain
 such a mechanism, a major challenge lies in understanding which attributes
 from the bio-molecular realm must be leveraged at the macro-scale.
 Inspired by protein folding, we present a centimetre-size 1D tile chain
 whose self-folding processes are directed by structure-embedded magnetic
 interactions, which can theoretically self-assemble into convex 2D
 structures of any size or shape without the aid of a global
 `controller'. Each tile holds two magnets contained in paths designed
 to control their interactions. Once initiated by a magnetic unit (termed
 Catalyst), the chain self-reconfigures by consuming magnetic potential
 energy stored between magnet pairs, until the final 2D structure is
 reached at an energetic minimum. Both simulation and experimental results
 are presented to illustrate the method's efficacy on chains of
 arbitrary length. Results demonstrate the promise of a physically
 implemented, bottom-up, and scalable self-assembly method for novel 2D
 structure manufacturing, bridging the bio-molecular and mechanical realms.
description: Tracked experiments,
 simulations, 3D designsVideos of two
 experiments with accompanying files in Tracker for tracking positions of
 magnets during magnetic catalysis. Simulations in Blender to accompany
 simulation videos. Designs in Autodesk Fusion 360 for each tile type and
 Catalyst holder.SupportingData.zip
DOI: 10.5061/dryad.7rt21s4
title: Data from: Protein deprivation facilitates the independent evolution of behavior and morphology

description: Ecological conditions such as nutrition can change genetic covariances
 between traits and accelerate or slow down trait evolution. Since adaptive
 trait correlations can become maladaptive following rapid environmental
 change, poor or stressful environments are expected to weaken genetic
 covariances, thereby increasing the opportunity for independent evolution
 of traits. Here, we demonstrate the differences in genetic covariance
 among multiple behavioral and morphological traits (exploration,
 aggression and body weight) between southern field crickets (Gryllus
 bimaculatus) raised in favorable (free-choice) versus stressful
 (protein-deprived) nutritional environments. We also quantify the extent
 to which differences in genetic covariance structures contribute to the
 potential for the independent evolution of these traits. We demonstrate
 that protein-deprived environments tend to increase the potential for
 traits to evolve independently, which is caused by genetic covariances
 that are significantly weaker for crickets raised on protein-deprived
 versus free-choice diets. The weakening effects of stressful environments
 on genetic covariances tended to be stronger in males than in females. The
 weakening of the genetic covariance between traits under stressful
 nutritional environments was expected to facilitate the opportunity for
 adaptive evolution across generations. Therefore, the multivariate
 gene-by-environment interactions revealed here may facilitate behavioral
 and morphological adaptations to rapid environmental change.
description: datafile
DOI: 10.5061/dryad.hv10kq1
title: Data from: Spider silk colour co-varies with thermal properties but not protein structure

description: Understanding how and why animal secretions vary in property has important
 biomimetic implications as desirable properties might co-vary. Spider
 major ampullate (MA) silk, for instance, is a secretion earmarked for
 biomimetic applications, but many of its properties vary among and between
 species across environments. Here we tested the hypothesis that MA silk
 colour, protein structure, and thermal properties co-vary when protein
 uptake is manipulated in the spider Trichonephila plumipes. We collected
 silk from adult female spiders maintained on a protein fed or protein
 deprived diet. Based on spectrophotometric quantifications we classified
 half the silks as ‘bee visible’ and the other half ‘bee invisible’. Wide
 Angle X-ray Scattering and Differential Scanning Calorimetry were then
 used to assess the silk’s protein structure, and thermal properties
 respectively. We found that although protein structures and thermal
 properties varied across our treatments only the thermal properties
 co-varied with colour. This ultimately suggests that protein structure
 alone is not responsible for MA silk thermal properties, nor does it
 affect silk colours. We speculate that similar ecological factors act on
 silk colour and thermal properties, which should be uncovered to inform
 biomimetic programs.
description: N_P
 SpecsSpectra across protein
 fed and protein deprived treamentsY_W
 SpecsSpectra of yellow and
 white silks.XRD & DSC
 outputsOutputs from X-ray
 diffraction and Differential Scanning Calorimetry
 procedures.
DOI: 10.5061/dryad.q2d60q3
title: Data from: Evolution of diet across the animal Tree of Life

description: What an animal eats is a fundamental aspect of its biology, but the
 evolution of diet has not been studied across animal phylogeny. Here, we
 performed a large-scale phylogenetic analysis to address three unresolved
 questions about the evolution of animal diets. (i) Are diets conserved
 across animal phylogeny? (ii) Does diet influence rates of species
 proliferation (diversification) among animal phyla? (iii) What was the
 ancestral diet of animals and major animal clades? We analyzed diet data
 for 1,087 taxa, proportionally sampled among animal phyla based on the
 relative species richness of phyla. Our survey suggests that across
 animals, carnivory is most common (~63%), herbivory less common (~32%),
 and omnivory relatively rare (~3%). Despite considerable controversy over
 whether ecological traits are conserved or labile, we found strong
 conservatism in diet over extraordinarily deep timescales. We found that
 diet is unrelated to rates of species diversification across animal phyla,
 contrasting with previous studies showing that herbivory increased
 diversification within some important groups (e.g. crustaceans, insects,
 mammals). Finally, we estimated that the ancestor of all animals was most
 likely carnivorous, as were many major phyla (e.g. arthropods, mollusks,
 chordates). Remarkably, our results suggest that many carnivorous species
 living today may have maintained this diet through a continuous series of
 carnivorous ancestors for &gt;800 million years.
description: Supplementary
 MaterialSupplementary_Material.docxDataset S1Dataset S1. Diet data for each taxon in the tree, and supporting referencesDataset S2Time-calibrated animal phylogeny usedDataset S3Diet data for each taxon in the tree, with data modified for four phyla
DOI: 10.5061/dryad.712hc6m
title: Data from: Distinct telomere differences within a reproductively bimodal common lizard population

description: 1. Different strategies of reproductive mode, either oviparity
 (egg-laying) or viviparity (live-bearing), will be associated with a range
 of other life history differences that are expected to affect patterns of
 ageing and longevity. It is usually difficult to compare the effects of
 alternative reproductive modes because of evolutionary and ecological
 divergence. However, the very rare exemplars of reproductive bimodality,
 in which different modes exist within a single species, offer an
 opportunity for robust and controlled comparisons. 2. One trait of
 interest that could be associated with life history, ageing and longevity
 is the length of the telomeres, which form protective caps at the
 chromosome ends and are generally considered a good indicator of cellular
 health. The shortening of these telomeres has been linked to stressful
 conditions; therefore, it is possible that differing reproductive costs
 will influence patterns of telomere loss. This is important because a
 number of studies have linked a shorter telomere length to reduced
 survival, and even population extinction. 3. Here we have studied maternal
 and offspring telomere dynamics in the common lizard (Zootoca vivipara).
 Our study has focused on a population where oviparous and viviparous
 individuals co-occur in the same habitat and occasionally interbreed to
 form admixed individuals. 4. While viviparity confers many advantages for
 offspring, it might also incur substantial costs for the mother, e.g.
 require more energy. Therefore, we predicted that viviparous mothers would
 have relatively shorter telomeres than oviparous mothers, with admixed
 mothers having intermediate telomere lengths. There is thought to be a
 heritable component to telomere length; therefore, we also hypothesised
 that offspring would follow the same pattern as the mothers. 5. Contrary
 to our predictions, the viviparous mothers and offspring had the longest
 telomeres, the oviparous mothers and offspring had the shortest telomeres.
 The differing telomere lengths may have evolved as an effect of the life
 history divergence between the reproductive modes, e.g. due to the
 increased growth rate that viviparous individuals may undergo to reach a
 similar size at reproduction.
description: Dataset for repository -
 McLennan et al. 2019xlsxData corresponding to
 all analyses
DOI: 10.5061/dryad.230j5ch
title: Data from: A highly-resolved food web for insect seed predators in a species-rich tropical forest

description: The top-down and indirect effects of insects on plant communities depend
 on patterns of host use, which are often poorly documented, particularly
 in species-rich tropical forests. At Barro Colorado Island, Panama, we
 compiled the first food web quantifying trophic interactions between the
 majority of co-occurring woody plant species and their internally-feeding
 insect seed predators. Our study is based on more than 200,000 fruits
 representing 478 plant species, associated with 369 insect species. Insect
 host-specificity was remarkably high: only 20% of seed predator species
 were associated with more than one plant species, while each tree species
 experienced seed predation from a median of two insect species. Phylogeny,
 but not plant traits, explained patterns of seed predator attack. These
 data suggest that seed predators are unlikely to mediate indirect
 interactions such as apparent competition between plant species, but are
 consistent with their proposed contribution to maintaining plant diversity
 via the Janzen-Connell mechanism.
description: FWData set used for
 construction of quantitative food webInsect
 dataList of observed seed
 predator × plant species interactionsTidyTraitPhyloExtraSpecPhylogeny for plant species. Note that the phylogeny includes a number of species that have been grafted on based purely on taxonomy. Hence, it should not be uncritically used for other purposes.
DOI: 10.5061/dryad.r4mb3h6
title: Data from: Contextual priors do not modulate action prediction in children with autism

description: Bayesian accounts of autism suggest that this disorder may be rooted in an
 impaired ability to estimate the probability of future events, possibly
 due to reduced priors. Here, we tested this hypothesis within the action
 domain in children with and without autism using a behavioural paradigm
 comprising a familiarization and a testing phase. During familiarization,
 children observed videos depicting a child model performing actions in
 diverse contexts. Crucially, within this phase, we implicitly biased
 action-context associations in terms of their probability of
 co-occurrence. During testing, children observed the same videos but
 drastically shortened (i.e., reduced amount of kinematics information) and
 were asked to infer action unfolding. Since during the testing phase
 movement kinematics became ambiguous, we expected children’s responses to
 be biased to contextual priors, thus compensating for perceptual
 uncertainty. While this probabilistic effect was present in controls no
 such modulation was observed in autistic children, suggesting an
 impairment in using prior information when anticipating others’ actions
 under situations of perceptual uncertainty.
description: Contextual
 priors_DatasetDataset.xls
DOI: 10.5061/dryad.tq4qr23
title: Data from: Prescribed burning impacts on ecosystem services in the British uplands: a methodological critique of the EMBER project

description: Due to its novelty and scale, the EMBER project is a key study within the
 prescribed burning evidence base. However, it has several significant but
 overlooked methodological flaws. In this paper, we outline and discuss
 these flaws. In doing so, we aim to highlight the current paucity of
 evidence relating to prescribed burning impacts on ecosystem services
 within the British uplands. We show that the results of the EMBER project
 are currently unreliable because: it used a correlative space‐for‐time
 approach; treatments were located within geographically separate and
 environmentally distinct sites; environmental differences between sites
 and treatments were not accounted for during statistical analysis; and,
 peat surface temperature results are suggestive of measurement error.
 Policy Implications. Given the importance of the EMBER project, our
 findings suggest that (a) government agencies and policymakers need to
 re‐examine the strengths and limitations of the prescribed burning
 evidence base; and, (b) future work needs to control for site‐specific
 differences so that prescribed burning impacts on ecosystem services can
 be reliably identified.
description: Description of
 datasetsA brief description of
 the datasets used in our studyAshby & Heinemeyer 2019
 Data Description.docxCatchment
 DataEnvironmental data for
 each EMBER catchmentAshby & Heinemeyer 2019
 Catchment Data.xlsxPlot
 dataEnvironmental data for
 individual EMBER study plotsAshby & Heinemeyer 2019
 Plot Data.xlsx