cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bs8c4
title: Data from: A systematic review and meta-analysis of gene therapy in animal models of cerebral glioma: why did promise not translate to human therapy?

description: Background: The development of therapeutics is often characterized by
 promising animal research that fails to translate into clinical efficacy;
 this holds for the development of gene therapy in glioma. We tested the
 hypothesis that this is because of limitations in the internal and
 external validity of studies reporting the use of gene therapy in
 experimental glioma. Method: We systematically identified studies testing
 gene therapy in rodent glioma models by searching three online databases.
 The number of animals treated and median survival were extracted and
 studies graded using a quality checklist. We calculated median survival
 ratios and used random effects meta-analysis to estimate efficacy. We
 explored effects of study design and quality and searched for evidence of
 publication bias. Results: We identified 193 publications using gene
 therapy in experimental glioma, including 6,366 animals. Overall, gene
 therapy improved median survival by a factor of 1.60 (95% CI 1.53–1.67).
 Study quality was low and the type of gene therapy did not account for
 differences in outcome. Study design characteristics accounted for a
 significant proportion of between-study heterogeneity. We observed similar
 findings in a data subset limited to the most common gene therapy.
 Conclusion: As the dysregulation of key molecular pathways is
 characteristic of gliomas, gene therapy remains a promising treatment for
 glioma. Nevertheless, we have identified areas for improvement in conduct
 and reporting of studies, and we provide a basis for sample size
 calculations. Further work should focus on genes of interest in paradigms
 recapitulating human disease. This might improve the translation of such
 therapies into the clinic.
description: Gene therapy in
 experimental glioma: raw data & analysisData extracted directly
 from studies included in the systematic review. Data were entered into the
 CAMARADES data manager (Access database) and analysed. Both the raw data
 and results have been exported to Excel file (note there are several pages
 to the spreadsheet).Hirst_gene therapy_raw
 data.xls
DOI: 10.5061/dryad.j2k54s8
title: Data from: Understory succession after burial by tephra from Mount St. Helens

description: 1. Successional change following disturbance is a fundamental ecological
 process that remains central to understanding patterns in plant ecology.
 Although succession has been studied for well over a century,
 understanding of the patterns and processes of change is still inadequate,
 partly because of the dearth of long-term studies. 2. Here, we use, as a
 model system, a volcanic disturbance that is widespread and of global
 relevance. We examine succession in old-growth conifer forest understories
 following burial by tephra (aerially transported volcanic ejecta) in the
 1980 eruption of Mount St. Helens. Using four sites with different initial
 conditions and amounts of disturbance (tephra burial), we sampled plant
 communities at years 1, 20 and 36 since the eruption using permanent plots
 representing two treatments: undisturbed tephra and control plots from
 which tephra was experimentally removed. By using this long-term data, we
 were able to gauge change through time and differences between
 tephra-disturbed and control plots. 3. In tephra-impacted plots, cover
 reached pre-eruption levels by year 36 except for bryophytes at three
 sites and shrubs at one site. Cover in control plots also increased
 significantly for all growth forms except bryophytes, remaining above that
 on tephra plots at the same site in most situations. Sites generally
 increased in species richness first, and then gradually increased in
 evenness and Shannon’s diversity; after 36 years, differences between
 control and tephra-impacted plots remained at only one site. Community
 composition was stable in one site and shifted gradually through time at
 the two other sites, and differences between plot types persisted at one
 site. Communities change over 36 years could relate to various endogenic
 and abiotic factors. 4. Synthesis: These data suggest that, while recovery
 to the pre-disturbance status occurs in some cases, recovery is
 site-specific. Understory communities can be dynamic, even in old-growth
 forests, and may still be responding to disturbance over three decades
 later. Long-term experimental studies are key to understanding succession
 patterns and generalizations about the importance of initial conditions,
 disturbance intensity, and the complexity of interactions that determine
 vegetation change.
description: Community Data From
 Mount St. Helens Tephra plots in years 1980-2016 (less common species
 duplicates and short-names not corrected)This file contains
 community % cover data for tephra and control plots at Mount St. Helens in
 the tephra disturbance zone for years 1980, 2000, and 2016. Some species
 names may have changed or may have been combined for final analysis.
 Contact the authors directly with any questions or
 clarifications.Fischer_et_al_MTSH_DRYAD_80_2000_2016.xlsx
DOI: 10.5061/dryad.4t8c7
title: Data from: Lost at sea: ocean acidification undermines larval fish orientation via altered hearing and marine soundscape modification

description: The dispersal of larvae and their settlement to suitable habitat is
 fundamental to the replenishment of marine populations and the communities
 in which they live. Sound plays an important role in this process because
 for larvae of various species, it acts as an orientational cue towards
 suitable settlement habitat. Because marine sounds are largely of
 biological origin, they not only carry information about the location of
 potential habitat, but also information about the quality of habitat.
 While ocean acidification is known to affect a wide range of marine
 organisms and processes, its effect on marine soundscapes and its
 reception by navigating oceanic larvae remains unknown. Here, we show that
 ocean acidification causes a switch in role of present-day soundscapes
 from attractor to repellent in the auditory preferences in a temperate
 larval fish. Using natural CO2 vents as analogues of future ocean
 conditions, we further reveal that ocean acidification can impact marine
 soundscapes by profoundly diminishing their biological sound production.
 An altered soundscape poorer in biological cues indirectly penalizes
 oceanic larvae at settlement stage because both control and CO2-treated
 fish larvae showed lack of any response to such future soundscapes. These
 indirect and direct effects of ocean acidification put at risk the complex
 processes of larval dispersal and settlement.
description: Lost at sea Rossi et al.
 datasetIn this excel files the
 data are organized in 5 sheets (1) contains the data behind the power
 spectrum of White Island (2) contains the mulloway fish auditory
 preference data (3) contains mulloway otoliths size (4) contains the water
 chemistry data recorded during the rearing period of mulloway in the lab
 (5) contains the water chemistry data recorded on the vents at White
 Islandlost
 at sea TRossi dataset dryad.xlsx
DOI: 10.5061/dryad.5dn48
title: Data from: Quantifying behavioral changes in territorial animals caused by sudden population declines

description: Although territorial animals are able to maintain exclusive use of certain
 regions of space, movement data from neighboring individuals often suggest
 overlapping home ranges. To explain and unify these two aspects of animal
 space use, we use recently developed mechanistic models of collective
 animal movement. We apply our approach to a natural experiment on an urban
 red fox (Vulpes vulpes) population that underwent a rapid decline in
 population density due to a sarcoptic mange epizooty. By extracting
 details of movement and interaction strategies from location data, we show
 how foxes alter their behavior, taking advantage of sudden
 population-level changes by acquiring areas vacated due to neighbor
 mortality, while ensuring territory boundaries remain contiguous. The rate
 of territory border movement increased eightfold as the population
 declined and the foxes’ response time to neighboring scent reduced by a
 third. By demonstrating how observed, fluctuating territorial patterns
 emerge from movements and interactions of individual animals, our results
 give the first data-validated, mechanistic explanation of the elastic disc
 hypothesis, proposed nearly 80 years ago.
description: Pre-mange
 datapre-mange-online.xlsxPost-mange datapost-mange-online.xlsx
DOI: 10.5061/dryad.55p22
title: Data from: Ecological and historical determinants of population genetic structure and diversity in the Mediterranean shrub Rosmarinus officinalis (Lamiaceae)

description: Population genetic studies of widespread Mediterranean shrubs are scarce
 compared with those of trees and narrow endemics or studies from
 phylogeographical perspectives, despite the key role these species may
 play in Mediterranean ecosystems. Knowledge on the effect of ecological
 factors in shaping their genetic patterns is also limited. In this study
 we investigate genetic diversity and population structure across 18
 populations of Rosmarinus officinalis, a Mediterranean shrubland plant.
 Populations were sampled along two elevational gradients, one each on
 calcareous and siliceous soils in a mountain system in the eastern Iberian
 Peninsula, to decipher the effect of ecological factors on the genetic
 diversity and structure based on 11 microsatellite loci. We found overall
 high levels of genetic diversity and weak population structure. Genetic
 diversity increased with elevation, whereas population differentiation was
 stronger among populations growing on siliceous soils. The nested analysis
 of elevational gradients within soil types revealed that these general
 patterns were mostly driven by siliceous populations, whereas calcareous
 populations were more homogeneous along elevational belts. Bayesian
 analysis of population structure revealed genetic membership of lowland
 and high-elevation populations to different genetic clusters and a higher
 admixture of intermediate-elevation populations to both clusters.
 High-elevation populations were less differentiated from a hypothetical
 ancestral cluster, suggesting the persistence of their gene pool during
 the Pleistocene glaciations. In contrast, lowland populations resulted
 from more recent divergence. We propose that life-history and reproductive
 traits mostly contribute to explain the high levels of genetic diversity
 and weak population structure, whereas ecological and historical factors
 mostly contribute to the stronger differentiation of siliceous populations
 and a rapid expansion of R. officinalis on calcareous soils possibly
 mediated by human landscape transformations.
description: Rosmarinus officinalis
 genotypic dataContains gentotypic data
 of 1728 individuals (96 each from 18 populations) for eleven nuclear
 microsatellite loci. For each individual, geographical coordinates are
 given in two extra columns following the individual identification
 code.
DOI: 10.5061/dryad.453v0
title: Data from: Rock wrens preferentially use song types that improve long distance signal transmission during natural singing bouts

description: When animals are capable of producing variable signals they may
 preferentially use some signal types over others. Among songbirds,
 individuals are known to alter song type form and usage patterns in
 contest and mating situations, but studies have not examined how song
 choice improves signal efficacy during broadcast song. For this study we
 investigated rock wren Salpinctes obsoletus song type use rates during
 natural singing bouts. We tested three hypotheses for adaptive song use
 during broadcast song: 1) birds improve signal content by increasing the
 use of high quality songs, 2) birds optimize for signal propagation by
 preferentially using songs that transmit well, and 3) birds maintain
 energy by reducing the use of costly songs. The study included 19 058
 songs sung by 12 individuals, each of which had a measured song repertoire
 of between 52 and 117 song types which were produced at highly variable
 rates. Results indicated that rock wrens did not preferentially sing song
 types with shorter durations or fewer frequency switches, as would be
 expected if they selected song types to minimize delivery costs. They also
 did not favor songs with more rapid trills or more frequency switches, as
 would be expected if they adjusted song use primarily to indicate quality.
 Focal birds did preferentially sing significantly longer songs with lower
 bandwidths, lower frequencies, and slower trill rates. Results suggest
 that natural broadcast singing patterns are shaped more by the benefits of
 long distance transmission than by the benefits of advertising performance
 ability or the costs of song production.
description: Rock Wren song data -
 Benedict and Warning JAB 2017Spreadsheet containing
 song type measurement and use data for all song types sung by 12
 individual rock wrens included in the study.
DOI: 10.5061/dryad.5gs75
title: Data from: Male clasping ability, female polymorphism and sexual conflict: fine-scale elytral morphology as a sexually antagonistic adaptation in female diving beetles

description: During sexual conflict, males and females are expected to evolve traits
 and behaviours with a sexually antagonistic function. Recently, sexually
 antagonistic coevolution was proposed to occur between male and female
 diving beetles (Dytiscidae). Male diving beetles possess numerous suction
 cups on their forelegs whereas females commonly have rough structures on
 their elytra. These rough structures have been suggested to obstruct
 adhesion from male suction cups during mating attempts. However, some
 diving beetle species are dimorphic, where one female morph has a rough
 elytra and the other has a smooth elytra. Here, we used biomechanics to
 study the adhesive performance of male suction cups on the female morphs
 in two diving beetle species: Dytiscus lapponicus and Graphoderus zonatus.
 We compared adhesion on the rough and the smooth female morphs to infer
 the function of the rough elytral modifications. We found that the
 adhesive force on the rough structures was much lower than on other
 surfaces. These findings support the suggestion of sexual conflict in
 diving beetles and a sexually antagonistic function of the rough female
 structures. In addition, males differed in their adhesive capacity on
 different female surfaces, indicating a male trade-off between adhering to
 smooth and rough female morphs.
description: Adhesion of male diving
 beetles suction cupsData from adhesion
 measurements of male diving beetle suction cups on different surfaces. The
 surfaces include glass (measured both with the sensor operated by a
 manipulator and manually) and the elytra and pronotum of both males and
 two female morphs. Data comes from two species (Dytiscus lapponicus and
 Graphoderus zonatus) and two different locations (Östra Skivsjön and
 Lomtjärn). The data file includes the maximum, minimum and mean of each
 adhesion event, the time of the measurment, the baseline, the calibration
 factor used for calculations and the calculated adhesion and loading
 force.DataDryadAdhesionKKGetal.xlsx
DOI: 10.5061/dryad.fr2k8
title: Data from: Epigenetic variation predicts regional and local intraspecific functional diversity in a perennial herb

description: The ecological significance of epigenetic variation has been generally
 inferred from studies on model plants under artificial conditions, but the
 importance of epigenetic differences between individuals as a source of
 intraspecific diversity in natural plant populations remains essentially
 unknown. This paper investigates the relationship between epigenetic
 variation and functional plant diversity by conducting epigenetic
 (methylation-sensitive amplified fragment length polymorphisms, MSAP) and
 genetic (amplified fragment length polymorphisms, AFLP) marker-trait
 association analyses for 20 whole-plant, leaf and regenerative functional
 traits in a large sample of wild-growing plants of the perennial herb
 Helleborus foetidus from ten sampling sites in southeastern Spain. Plants
 differed widely in functional characteristics, and exhibited greater
 epigenetic than genetic diversity, as shown by percent polymorphism of
 MSAP fragments (92%) or markers (69%) greatly exceeding that for AFLP ones
 (41%). After controlling for genetic structuring and possible cryptic
 relatedness, every functional trait considered exhibited a significant
 association with at least one AFLP or MSAP marker. A total of 27 MSAP
 (13.0% of total) and 12 AFLP (4.4%) markers were involved in significant
 associations, which explained on average 8.2% and 8.0% of trait variance,
 respectively. Individual MSAP markers were more likely to be associated
 with functional traits than AFLP markers. Between-site differences in
 multivariate functional diversity was directly related to variation in
 multilocus epigenetic diversity after multilocus genetic diversity was
 statistically accounted for. Results suggest that epigenetic variation can
 be an important source of intraspecific functional diversity in H.
 foetidus, possibly endowing this species with the capacity to exploit a
 broad range of ecological conditions despite its modest genetic diversity.
description: AFLP
 profilesAFLP profiles for 200
 plants of Helleborus foetidus from ten locations in the Sierra de Cazorla,
 southeastern Spain, sampled for the studyAFLP.scores.xlsxMSAP profilesMSAP profiles for 200 plants of Helleborus foetidus from 10 locations in the Sierra de Cazorla, southeastern Spain, sampled for the studyMSAP.scores.xlsxPlant functional traitsWhole-plant, leaf and regenerative functional traits for the 200 individual plants of Helleborus foetidus from 10 locations in Sierra de Cazorla, southeastern Spain, sampled for the study.Functional.traits.xlsx
DOI: 10.5061/dryad.45157
title: Data from: From fine-scale foraging to home ranges: a semi-variance approach to identifying movement modes across spatiotemporal scales

description: Understanding animal movement is a key challenge in ecology and
 conservation biology. Relocation data often represent a complex mixture of
 different movement behaviors, and reliably decomposing this mix into its
 component parts is an unresolved problem in movement ecology. Traditional
 approaches, such as composite random walk models, require that the
 timescales characterizing the movement are all similar to the usually
 arbitrary data-sampling rate. Movement behaviors such as long-distance
 searching and fine-scale foraging, however, are often intermixed but
 operate on vastly different spatial and temporal scales. An approach that
 integrates the full sweep of movement behaviors across scales is currently
 lacking. Here we show how the semivariance function (SVF) of a stochastic
 movement process can both identify multiple movement modes and solve the
 sampling rate problem. We express a broad range of continuous-space,
 continuous-time stochastic movement models in terms of their SVFs, connect
 them to relocation data via variogram regression, and compare them using
 standard model selection techniques. We illustrate our approach using
 Mongolian gazelle relocation data and show that gazelle movement is
 characterized by ballistic foraging movements on a 6-h timescale, fast
 diffusive searching with a 10-week timescale, and asymptotic diffusion
 over longer timescales.
description: data_semiVarianceToIdentifyingMovementModesDescription of columns in data set: "gazelle": identifies individual gazelles. “time”: time is measured in seconds from the first relocation of every gazelle. “x”, “y”: coordinates are measured in meters from the individual mean. The projection was azimuthal equidistant centered at the population mean.
DOI: 10.5061/dryad.n420r
title: Data from: Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

description: Young species complexes that are widespread across ecologically disparate
 regions offer important insights into the process of speciation because of
 their relevance to how local adaptation and gene flow influence
 diversification. We used mitochondrial DNA and up to 28,152 genome-wide
 SNPs from polytypic barking frogs (Craugastor augusti complex) to infer
 phylogenetic relationships and test for the signature of introgressive
 hybridization among diverging lineages. Our phylogenetic reconstructions
 suggest (1) a rapid Pliocene-Pleistocene radiation that produced at least
 nine distinct lineages and (2) that geographic features of the arid
 Central Mexican Plateau contributed to two independent northward
 expansions. Despite clear lineage differentiation (many private alleles
 and high between-lineage Fst scores), D-statistic tests, which
 differentiate introgression from ancestral polymorphism, allowed us to
 identify two putative instances of reticulate gene flow. Partitioned
 D-statistics provided evidence that these events occurred in the same
 direction between clades but at different points in time. After correcting
 for geographic distance, we found that lineages involved in hybrid gene
 flow interactions had higher levels of genetic variation than
 independently evolving lineages. These findings suggest that the nature of
 hybrid compatibility can be conserved over long periods of evolutionary
 time and that hybridization between diverging lineages may contribute to
 standing levels of genetic variation.
description: Craugastor_augusti_SNP_dataData included in zipfile: (1) STACKS commands used to process and assemble RADtags, (2) 0.20 missing biallelic data matrix [.stru format], (3) 0.25 missing biallelic data matrix [.stru format], (4) 0.50 missing biallelic data matrix [.stru format], (5) 0.10 missing fixed data matrix [.phy format], (6) 0.25 missing fixed data matrix [.phy format], and (7) 0.50 missing fixed data matrix [.phy format]Craugastor_augusti_data_Mol_Ecol.zipCraugastor_augusti_mtDNA_dataMitochondrial alignment (12S) in .phy format12S_mtDNA_alignment.phy
DOI: 10.5061/dryad.k7797
title: Data from: High fidelity: extra-pair fertilisations in eight Charadrius plover species are not associated with parental relatedness or social mating system

description: Extra-pair paternity is a common reproductive strategy in many bird
 species. However, it remains unclear why extra-pair paternity occurs and
 why it varies among species and populations. Plovers (Charadrius spp.)
 exhibit considerable variation in reproductive behaviour and ecology,
 making them excellent models to investigate the evolution of social and
 genetic mating systems. We investigated inter- and intra-specific patterns
 of extra-pair parentage and evaluated three major hypotheses explaining
 extra-pair paternity using a comparative approach based on the
 microsatellite genotypes of 2,049 individuals from 510 plover families
 sampled from twelve populations that constituted eight species. Extra-pair
 paternity rates were very low (0 to 4.1% of chicks per population). No
 evidence was found in support of the sexual conflict or genetic
 compatibility hypotheses, and there was no seasonal pattern of extra-pair
 paternity (EPP). The low prevalence of EPP is consistent with a number of
 alternative hypotheses, including the parental investment hypothesis,
 which suggests that high contribution to care by males restricts female
 plovers from engaging in extra-pair copulations. Further studies are
 needed to critically test the importance of this hypothesis to plover mate
 choice.
description: High fidelity- EPP in
 plover species_RawDataThis file contains the
 raw microsatellite data for twelve populations and eight species of
 plover. Details of the microsatellite markers and PCR conditions can be
 found in the paper.High fidelity- EPP in plover
 species.xlsx