cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tr62rm1
title: Data from: Urban forest fragments as unexpected sanctuaries for the rare endemic ghost butterfly from the Atlantic forest.

description: Anthropogenic land expansion, particularly urbanization, is pervasive,
 dramatically modifies the environment and is a major threat to wildlife
 with its associated environmental stressors. Urban remnant vegetation can
 help mitigate these impacts and could be vital for species unable to
 survive in harsh urban environments. Although resembling non-urban
 habitats, urban vegetation remnants are subject to additional
 environmental stresses. Here we evaluate the occurrence and density of the
 endemic ghost butterfly (Morpho epistrophus nikolajewna), that was once
 common, in the highly fragmented Atlantic forest of NE Brazil. We tested
 whether this butterfly would be found at lower densities in urban forest
 fragments of contrasting sizes as opposed to rural ones, given the number
 of environmental stressors found in urban areas. We surveyed 14 forest
 fragments (range 2.8 to over 3000 ha) of semi-deciduous Atlantic forest in
 rural and urban locations using transect based distance sampling. The
 ghost butterflies showed strong seasonality; flying only from April to
 June. They were only identified in an urban fragment (515 ha), with an
 estimate of 720 individuals and a density 1.4 ind/ha. All forest fragments
 had experienced some level of logging in the past, which might have had an
 effect in the butterfly population. Nevertheless, rural forest fragments
 were subject to increased particulate matter concentrations, associated to
 biomass burning, that we suggest might have had a more influential role
 driving the collapse of rural populations. Our findings show the
 importance of urban forest remnants to sustain population of this
 endangered species.
description: Data Morpho
 densityThis data set contains
 the records of the ghost butterfly during the surveys in the Mata
 Buraquinho conservation area. Transects names are in portuguese because
 these are the trails names! (this is for the Dryad people who request to
 translate them...)Ghost_MB_density.xls
DOI: 10.5061/dryad.28fr4qh
title: Data from: Patterns of livestock depredation and cost-effectiveness of fortified livestock enclosures in northern Tanzania

description: Human-carnivore conflicts and retaliatory killings contribute to carnivore
 populations’ declines around the world. Strategies to mitigate conflicts
 have been developed, but their efficacy is rarely assessed in a randomized
 case-control design. Further, the economic costs prevent the adoption and
 wide use of conflict mitigation strategies by pastoralists in rural
 Africa. We examined carnivore [African lion (Panthera leo), leopard
 (Panthera pardus), spotted hyena (Crocuta crocuta), jackal (Canis
 mesomelas), and cheetah (Acinonyx jubatus)] raids on fortified (n=45,
 total 631 monthly visits) and unfortified (traditional, n=45, total 521
 monthly visits) livestock enclosures (“bomas”) in northern Tanzania. The
 study aimed to (i) assess the extent of retaliatory killings of major
 carnivore species due to livestock depredation, (ii) describe the
 spatio-temporal characteristics of carnivore raids on livestock enclosures
 (iii) analyze whether spatial covariates influenced livestock depredation
 risk in livestock enclosures, and (iv) examine the cost-effectiveness of
 livestock enclosure fortification. Results suggest that i) majority of
 boma raids by carnivores were caused by spotted hyenas (nearly 90% of all
 raids), but retaliatory killings mainly targeted lions, (ii) carnivore
 raid attempts were rare at individual households (0.081 raid
 attempts/month in fortified enclosures and 0.102 raid attempts/month in
 unfortified enclosures), iii) Spotted hyena raid attempts increased in the
 wet season compared to the dry season, and owners of fortified bomas
 reported less hyena raid attempts than owners of un-fortified bomas.
 Landscape and habitat variables tested, did not strongly drive the spatial
 patterns of spotted hyena raids in livestock bomas. Carnivore raids varied
 randomly both spatially (village to village) and temporally (year to
 year). The cost-benefit analysis suggest that investing in boma
 fortification yielded positive net present values after two to three
 years. Thus, enclosure fortification is a cost-effective strategy to
 promote coexistence of carnivores and humans.
description: Data_Patterns of
 livestock depredation and cost-effectiveness of fortified livestock
 encolosures in northern TanzaniaThis dateset describes
 reports from monthly visits to traditional and enforced livestock
 enclosures. Enclosure owners reported number of successfull and non-
 successfull raid attempts by large carnivores in the past month. Carnivore
 species that attempted to raid livestock enclosures were identified to
 species level adn counted by enclosure owners. The number of injured and
 killed livestock individuals (separated by species and age class) is
 reported as well. The last columns (AE-AW) describe the spatial variables
 for each livestock enclosure. GPS coordinates of livestock enclosures were
 removed.
DOI: 10.5061/dryad.h46b994
title: Data from: Plastome of Quercus xanthoclada and comparison of genomic diversity among selected Quercus species using genome skimming

description: The genus Quercus L. contains several of the most economically important
 species for timber production in the Northern Hemisphere. It was one of
 the first genera described but genetic diversity at a global scale within
 and among oak species remains unclear, despite numerous regional or
 species-specific assessments. To evaluate global plastid diversity in
 oaks, we sequenced the complete chloroplast of Quercus xanthoclada, and
 compared its sequence those available from other main taxonomic groups in
 Quercus. We quantify genomic divergence among oaks and performed a sliding
 window analysis to detect the most variable regions among members of the
 various clades, as well as divergent regions occurring in specific pairs
 of species. We identified private and shared SNPs among oaks species and
 sections, and stress the need for a large global assessment of the genetic
 diversity in this economically and ecologically important genus.
description: Sequences
 alignmentAlignment of the
 sequences used in the paperQuercus_phytokeys_aligned.fasta
DOI: 10.5061/dryad.8q51152
title: Data from: Gene flow at the leading range edge - the long-term consequences of isolation in European Beech (Fagus sylvatica L. Kuhn)

description: Aim: Isolation is expected to lead to negative impacts on populations due
 to a reduction in effective population size and gene flow, exacerbating
 the effects of genetic drift, which might be stronger in peripheral and
 fragmented populations. Fagus sylvatica (European beech) in southern
 Sweden presents a gradient of isolation towards the leading range edge of
 the species. We sought to determine the impact of long-term isolation on
 genetic diversity and population genetic structure within populations of
 this species. Location: Samples were obtained from 14 sites towards the
 northern edge of the native range of beech in Sweden. Taxon: Fagaceae
 Methods: Using historical sources, we obtained area- and distance-based
 measures of isolation. We measured genetic diversity and structure by
 using nuclear microsatellite marker data, and performed parentage analysis
 to estimate external pollen-mediated gene flow. We implemented a partial
 least squares regression to determine the effects of isolation on each of
 the genetic diversity estimators and the measures of external
 pollen-mediated gene flow. Results: Long-term isolation generally had a
 negative impact on genetic diversity, which is exacerbated over time,
 further affecting progeny and suggesting that isolated populations are
 subject to strong genetic drift, possibly due to the combination of
 founder events and persistent small population sizes. Bayesian cluster
 analysis revealed that isolation was also acting as a barrier to gene flow
 in the north-eastern distribution of beech. Main conclusions: Isolation at
 the leading range edge of beech in Sweden has created gradients of
 contemporary gene flow within the species. The long-term cumulative
 effects of isolation on this wind-pollinated tree species and its negative
 impacts on genetic diversity and gene flow, could lead to inbreeding
 depression and higher extinction risk where populations remain small and
 isolated.
description: SSR with GPS location
 Mature and Seedling Fagus sylvatica treesMicrosatellite (SSR)
 fragment lengths for 13 primers for adult (mature) and seedling beech
 trees (Fagus sylvatica) derived from DNA from leaves sampled in July and
 August 2012. Samples were collected from various sites in Sweden. A
 description of the sites and the data can be found on the sheet entitled
 'Info on Dataset' on the excel file.
DOI: 10.5061/dryad.t91r232
title: Data from: Agroforestry coffee soils increase the insect-suppressive potential offered by entomopathogenic fungi over full-sun soils: a case proposing a "bait-survival technique"

description: Entomopathogenic fungi are important natural enemies of insects. However,
 there is little information on the insect-suppressive potential of these
 fungi and possible effects of farming management on this. Meanwhile,
 changes in natural landscapes due to agricultural intensification have
 caused considerable biodiversity loss and consequent decay of ecosystem
 services. However, the adoption of practices such as agroforestry in
 agroecosystems can foster abiotic and biotic conditions that conserve
 biodiversity, consequently restoring the provision of ecosystems services.
 Here, we assessed the effect of management systems (agroforestry or
 full-sun) on the pest-suppressive potential of entomopathogenic fungi in
 Brazilian coffee plantations. We used the insect-bait method coupled with
 survival analyses to assess the speed of kill by entomopathogenic fungi
 and their presence in soil samples from both farming systems. We found
 that insects exposed to agroforestry soils died more quickly than insects
 exposed to full-sun soils. Of the fungi isolated from the insect-baits,
 Metarhizium was found most frequently, followed by Beauveria. Meanwhile,
 Fusarium was frequently isolated as primary or secondary infections. We
 propose that the differential survival of insects is indicative of a
 greater suppressive potential by entomopathogenic fungi in agroforestry,
 and that this could be promoted by the diversified landscape,
 microclimatic stability and reduced soil disturbance in agroforestry
 systems. Furthermore, our results provide a useful demonstration of the
 potential use of the insect bait method to investigate pest suppressive
 potential through insect-bait mortality, and we term this the “bait
 survival technique”.
description: Data_Moreira_et_al_2019_Ecol_and_evolutionThe compressed directory contains the data tables, R code, and and a readme text required to reproduce survival and frequency analysis in the paper.
DOI: 10.5061/dryad.778340g
title: Data from: Direct nano-electrospray ionization tandem mass spectrometry for quantification and identification of metronidazole in its dosage form and human urine

description: A rapid, sensitive, and direct nano-electrospray ionization-tandem mass
 spectrometry (NS-ESI-MS/MS) method using an off-line nanospray (NS)
 capillary has been developed and validated for the analysis of
 metronidazole (MTZ). A mixture of 2µL MTZ sample solution prepared in an
 ionization solvent consisting of methanol: water: formic acid in a ratio
 of 80:20:0.3, together with 2µL of an internal standard (IS),
 1,3,6-polytyrosine, is loaded into the back of the NS capillary. The NS
 capillary was fitted into the ion source at a distance of 3 mm between the
 NS tip and MS orifice. Sample is then analyzed and acquired sustainable
 signal that allowed for data compilation across various data points for
 MTZ identification and quantification. The quantification relied on the
 ratio of the [M+H]+ peaks of MTZ and IS with m/z values of 172.0717 and
 182.0812, respectively, while the identification relied on the MS/MS of
 the precursor ions [M+H]+ of both compounds and their fragments at 128.05
 for MTZ and 165.1 and 136.07 for the IS. The NS-ESI-MS/MS method was
 accurate and precise for the quantification of MTZ over concentration
 range from 2.5 to 25000 ng/mL. The applicability of the method was
 confirmed by MTZ analysis in its pharmaceutical dosage form as well as
 detection of the analyte in clinical human urine samples without any
 sample treatment procedure.
description: MTZRaw Data files of MTZ
 calibration curve
description: Data files were generated as XCalibur raw data files (.raw), and
 can be read using the ThermoScientific XCalibur system. Results were
 extracted manually from these files as described in the published
 method.
DOI: 10.5061/dryad.20v30sm
title: Data from: Integrating palaeontological and molecular data uncovers multiple ancient and recent dispersals in the pantropical Hamamelidaceae

description: Aim: The integration of palaeontological and phylogenetic data can improve
 our understanding in the spatio-temporal evolutionary processes of living
 organisms. However, how best to use fossil data in divergence time
 estimation and ancestral range reconstruction remains challenging. Here,
 we integrated palaeontological and molecular data to investigate the
 historical biogeography of Hamamelidaceae, a pantropical angiosperm family
 with abundant fossils outside its present distribution. Location: Global
 tropical/subtropical areas. Methods: Using seven DNA regions (&gt;
 7,500 bp) from plastid and nuclear genomes, we reconstructed a robust
 phylogenetic framework for Hamamelidaceae with the first complete
 genus-level sampling. We used the tip-dating method with the 22 fossils to
 estimate divergence times for the family, and inferred the ancestral range
 of lineages under the dispersal-extinction-cladogenesis model by
 incorporating the fossils. Results: Our biogeographic analysis indicates
 that extant Hamamelidaceae most likely originated in tropical Asia during
 the mid-Cretaceous, and in the family 20 dispersals occurred during three
 major time intervals: the Upper Cretaceous (c. 93–69 Ma), Paleocene–Eocene
 (c. 63–39 Ma) and late Oligocene (c. 27–23 Ma). Main conclusions: Overland
 migrations through available land bridges and island chains may have been
 mainly responsible for hamamelidaceous range expansions during these three
 episodes. This study contributes to our knowledge on the assembly and
 evolution of angiosperm-dominated tropical and subtropical forests.
description: Hamamelidaceae (69
 taxon)Nexus matrix of extant
 Hamamelidaceae species (69 taxon) for phylogenetic
 analysisHamamelidaceae
 (69-taxon).nexHamamelidaceae (91
 taxon)Nexus matrix of extant
 and extinct Hamamelidaceae species (91 taxon) for
 datingHamamelidaceae91.txt
DOI: 10.5061/dryad.m16d23c
title: Data from: Sampling strategy optimization to increase statistical power in landscape genomics: a simulation-based approach

description: An increasing number of studies are using landscape genomics to
 investigate local adaptation in wild and domestic populations. The
 implementation of this approach requires the sampling phase to consider
 the complexity of environmental settings and the burden of logistic
 constraints. These important aspects are often underestimated in the
 literature dedicated to sampling strategies. In this study, we computed
 simulated genomic datasets to run against actual environmental data in
 order to trial landscape genomics experiments under distinct sampling
 strategies. These strategies differed by design approach (to enhance
 environmental and/or geographic representativeness at study sites), number
 of sampling locations and sample sizes. We then evaluated how these
 elements affected statistical performances (power and false discoveries)
 under two antithetical demographic scenarios. Our results highlight the
 importance of selecting an appropriate sample size, which should be
 modified based on the demographic characteristics of the studied
 population. For species with limited dispersal, sample sizes above 200
 units are generally sufficient to detect most adaptive signals, while in
 random mating populations this threshold should be increased to 400 units.
 Furthermore, we describe a design approach that maximizes both
 environmental and geographical representativeness of sampling sites and
 show how it systematically outperforms random or regular sampling schemes.
 Finally, we show that although having more sampling locations (between 40
 and 50 sites) increase statistical power and reduce false discovery rate,
 similar results can be achieved with a moderate number of sites (20
 sites). Overall, this study provides valuable guidelines for optimizing
 sampling strategies for landscape genomics experiments.
description: Data and scripts from
 publication This archive contains
 all the codes and data to reproduce the analysis performed in the
 publication. The archive contains the R script to apply the sampling
 design approach described in the publication to any environmental dataset.
 For more information, see the README file in the archive.
 data.zip
DOI: 10.5061/dryad.8n6m564
title: Data from: Social media and Bitcoin Metrics: which words matter

description: We develop a new Data-Driven Phasic Word Identification (DDPWI)
 methodology to determine which words matter as the bitcoin pricing dynamic
 changes from one phase to another. With Google search volumes as a
 baseline, we find that Reddit submissions are both correlated with Google
 and have a comparable relationship with a variety of bitcoin metrics,
 using Spearman’s rho. Reddit provides complete access to the text of
 submissions. Rather than associating sentiment with market activity, we
 describe the DDPWI method for finding specific ‘price dynamic’ words
 associated with changes in the bitcoin pricing pattern through 2017 and
 2018. We assess the significance of these changes using Wilcoxon Rank-Sum
 Tests with Bonferroni corrections. These price dynamic words are used to
 pull out associated words in the submissions thereby providing the context
 to their use. For example, the price dynamic word ‘ban’, which became
 significantly higher in frequency as prices fell, occurred in the context
 of both government regulation and internet companies banning
 cryptocurrency adverts. This approach could be used more generally to look
 at social media and discussion forums at a granular level identifying
 specific words that impact the metric under investigation rather than
 overall sentiment.
description: Social media and Bitcoin
 Metrics: which words matter Code and DataThe data and code for
 preparation and analysis of data for the paper "Social media and
 Bitcoin Metrics: which words matter".BurnieYilmazRS19.zip
DOI: 10.5061/dryad.dm5j73r
title: Data from: A natural gene drive system influences bovine tuberculosis susceptibility in African buffalo: possible implications for disease management

description: Bovine tuberculosis (BTB) is endemic to the African buffalo (Syncerus
 caffer) of Hluhluwe-iMfolozi Park (HiP) and Kruger National Park, South
 Africa. In HiP, the disease has been actively managed since 1999 through a
 test-and-cull procedure targeting BTB-positive buffalo. Prior studies in
 Kruger showed associations between microsatellite alleles, BTB and body
 condition. A sex chromosomal meiotic drive, a form of natural gene drive,
 was hypothesized to be ultimately responsible. These associations indicate
 high-frequency occurrence of two types of male-deleterious alleles (or
 multiple-allele haplotypes). One type negatively affects body condition
 and BTB resistance in both sexes. The other type has sexually antagonistic
 effects: negative in males but positive in females. Here, we investigate
 whether a similar gene drive system is present in HiP buffalo, using 17
 autosomal microsatellites and microsatellite-derived Y-chromosomal
 haplotypes from 401 individuals, culled in 2002-2004. We show that the
 association between autosomal microsatellite alleles and BTB
 susceptibility detected in Kruger, is also present in HiP. Further,
 Y-haplotype frequency dynamics indicated that a sex chromosomal meiotic
 drive also occurred in HiP. BTB was associated with negative selection of
 male-deleterious alleles in HiP, unlike positive selection in Kruger.
 Birth sex ratios were female-biased. We attribute negative selection and
 female-biased sex ratios in HiP to the absence of a Y-chromosomal
 sex-ratio distorter. This distorter has been hypothesized to contribute to
 positive selection of male-deleterious alleles and male-biased birth sex
 ratios in Kruger. As previously shown in Kruger, microsatellite alleles
 were only associated with male-deleterious effects in individuals born
 after wet pre-birth years; a phenomenon attributed to epigenetic
 modification. We identified two additional allele types: male-specific
 deleterious and beneficial alleles, with no discernible effect on females.
 Finally, we discuss how our findings may be used for breeding disease-free
 buffalo and implementing BTB test-and-cull programs.
description: rainfall data HiP per
 year and monthYearly rainfall data in
 HiP from 1978 till 2004, plus average monthly rainfall in the period
 1982-1999.Sex ratio
 dataAge estimate and sex of
 individual buffalo in relation to pre-birth rainfall.Herd
 informationBackground information
 on sampled buffalo herdsmicrosatellite data
 HiPAutosomal and
 Y-chromosomal genotype data.
DOI: 10.17909/jb9y-e692
title: Updating DOI via the form

description: Creating test DOI in DOI Form
DOI: 10.5061/dryad.7tb88vs
title: Data from: Study of the accuracy of a machine learning muscle MRI-based tool for diagnosis the of muscular dystrophies

description: Objective: Genetic diagnosis of muscular dystrophies (MDs) has classically
 been guided by clinical presentation, muscle biopsy and muscle MRI data.
 Muscle MRI suggests diagnosis based on the pattern of muscle fatty
 replacement. However, patterns overlap between different disorders and
 knowledge about disease-specific patterns is limited. Our aim was to
 develop a software-based tool that can recognize muscle MRI patterns and
 thus aid diagnosis of MDs. Methods: We collected 976 pelvic and lower
 limbs T1 weighted muscle MRIs from 10 different MDs. Fatty replacement was
 quantified using Mercuri score and files containing the numeric data were
 generated. Random forest unsupervised machine learning was applied to
 develop a model useful to identify the correct diagnosis. 2000 different
 models were generated and the one with higher accuracy was selected. A new
 set of 20 MRIs was used to test the accuracy of the model, and the results
 were compared with diagnoses proposed by 4 specialists in the field.
 Results: A total of 976 lower limbs MRIs from 10 different MDs were used.
 The best model obtained had a 95.7% accuracy, with 92.1% sensitivity and
 99.4% specificity. When compared with experts on the field, the diagnostic
 accuracy of the model generated was significantly higher in a new set of
 20 MRIs. Conclusion: Machine learning can help medical doctors in the
 diagnosis of muscle dystrophies by analyzing patterns of muscle fatty
 replacement in muscle MRI. This tool can be helpful for daily clinics but
 also in the interpretation of the results of next generation sequencing
 tests. Classification of Evidence: This study provides Class II evidence
 that a muscle MRI-based artificial intelligence tool accurately diagnosis
 muscular dystrophies.
description: Muscle MRI Mercuri
 scoreMercuri score of the 976
 patients studied in this paperDryad
 data.xlsx