cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0q2mq
title: Data from: Qualitative study of physicians' varied uses of biomedical research in the USA

description: Objective To investigate the nature of physicians' use of research
 evidence in experimental conditions of open access to inform training and
 policy. Design This qualitative study was a component of a larger
 mixed-methods initiative that provided 336 physicians with relatively
 complete access to research literature via PubMed and UpToDate, for 1 year
 via an online portal, with their usage recorded in web logs. Using a
 semistructured interview protocol, a subset of 38 physician participants
 were interviewed about their use of research articles in general and were
 probed about their reasons for accessing specific articles as identified
 through their web logs. Transcripts were analysed using a general
 inductive approach. Setting Physician participants were recruited from and
 registered in the USA. Participants 38 physicians from 16 US states,
 engaged in 22 medical specialties, possessing more than 1 year of
 experience postresidency training participated. Results 26 participants
 attested to the value of consulting research literature within the context
 of the study by making reference to their roles as clinicians, educators,
 researchers, learners, administrators and advocates. The physicians
 reported previously encountering what they experienced as a prohibitive
 paywall barrier to the research literature and other frustrations with the
 nature of information systems, such as the need for passwords. Conclusions
 The findings, against the backdrop of growing open access to biomedical
 research, indicate that a minority of physicians, at least initially, is
 likely to seek out and use research and do so in a variety of common
 roles. Physicians' use of research in these roles has not
 traditionally been part of their training or part of the considerations
 for open access policies. The findings have implications for educational
 and policy initiatives directed towards increasing the effectiveness of
 this access to and use of research in improving the quality of healthcare.
description: Physician
 TranscriptsIn this data set, we
 provide access to the transcripts of interviews of 36 physicians in the
 United States (US) about their use of information. These physician
 interviews represents the qualitative component of a larger mixed-methods
 research initiative funded by the National Science Foundation, led by this
 author team (Grant No. #1158673).Clean Transcripts
 3.zip
DOI: 10.5061/dryad.br45b
title: Data from: The relationship between diet and body mass in terrestrial mammals

description: Diet and body mass are highly important factors in mammalian ecology, and
 they have also proven to be powerful paleoecological indicators. Our
 previous research has proposed a new classification scheme for mammals
 with more dietary divisions that emphasizes the primary resource in a
 given diet. We analyzed a database summarizing the dietary preferences of
 139 species of marsupial and placental terrestrial mammals (including 14
 orders) and their average body masses in order to explore whether this new
 classification better highlights ecomorphological differences between
 species. Additionally, the dietary diversity of every species in the data
 set was quantified by applying the inverse Simpson index to stomach
 content percentages. We observed a decrease in maximum dietary diversity
 with increasing body mass. Having lower requirements for energy and
 nutrients per unit of body weight or ecological advantages such as larger
 home ranges allows larger mammals to feed on less nutritive feeding
 resources (i.e., structural plant material). Our results also suggest that
 body-size ranges are different across dietary specializations. Smaller
 mammals (&lt;1 kg) are mainly insectivores, granivores, or mixed
 feeders, while bigger animals (&gt;30 kg) are usually either
 carnivores or herbivores that feed specifically on grasses and leaves. The
 medium-size range (1–30 kg) is mostly composed of frugivorous species that
 inhabit tropical and subtropical rain forests. Thus, the near absence of
 medium-sized mammals in open environments such as savannas can be linked
 to the decreasing density of fruit trees needed to support a pure
 frugivorous diet year-round. In other words, seasonality of precipitation
 prevents species from specializing on a totally frugivorous diet. Our
 results suggest that this new classification scheme correlates well with
 body mass, one of the most studied morphological variables in paleoecology
 and ecomorphology. Therefore, the classification should serve as a useful
 basis for future paleoclimatological studies.
description: Suplementary
 informationFiles as described in
 main text in the publication
DOI: 10.5061/dryad.79dq1
title: Data from: New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

description: The discovery of four new Xenoturbella species from deep waters of the
 eastern Pacific Ocean is reported here. The genus and two nominal species
 were described from the west coast of Sweden1, 2, but their taxonomic
 placement remains unstable3, 4. Limited evidence placed Xenoturbella with
 molluscs5, 6, but the tissues can be contaminated with prey7, 8. They were
 then considered deuterostomes9, 10, 11, 12, 13. Further taxon sampling and
 analysis have grouped Xenoturbella with acoelomorphs (=Xenacoelomorpha) as
 sister to all other Bilateria (=Nephrozoa)14, 15, or placed
 Xenacoelomorpha inside Deuterostomia with Ambulacraria
 (Hemichordata + Echinodermata)16. Here we describe four new species of
 Xenoturbella and reassess those hypotheses. A large species (&gt;20 cm
 long) was found at cold-water hydrocarbon seeps at 2,890 m depth in
 Monterey Canyon and at 1,722 m in the Gulf of California (Mexico). A
 second large species (~10 cm long) also occurred at 1,722 m in the Gulf of
 California. The third large species (~15 cm long) was found at ~3,700 m
 depth near a newly discovered carbonate-hosted hydrothermal vent in the
 Gulf of California. Finally, a small species (~2.5 cm long), found near a
 whale carcass at 631 m depth in Monterey Submarine Canyon (California),
 resembles the two nominal species from Sweden. Analysis of whole
 mitochondrial genomes places the three larger species as a sister clade to
 the smaller Atlantic and Pacific species. Phylogenomic analyses of
 transcriptomic sequences support placement of Xenacoelomorpha as sister to
 Nephrozoa or Protostomia.
description: Mitochondrial Genome
 AlignmentConcatenated
 Mitochondrial Protein Alignment file and gene partition text
 file.1Mito.zipPhylogenomic SupermatricesTranslated homologous gene alignments from transcriptome data. There are two datasets with the partition files. The 70% complete supermatrix and the 80% complete supermatrix. See text for more details.2SupermatrixPartitions.zipSowhat Constraint TreesConstriant trees used for SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori).3Sowhat.zip
DOI: 10.5061/dryad.88354
title: Data from: Patterns and limitations of urban human mobility resilience under the influence of multiple types of natural disaster

description: Natural disasters pose serious threats to large urban areas, therefore
 understanding and predicting human movements is critical for evaluating a
 population’s vulnerability and resilience and developing plans for
 disaster evacuation, response and relief. However, only limited research
 has been conducted into the effect of natural disasters on human mobility.
 This study examines how natural disasters influence human mobility
 patterns in urban populations using individuals’ movement data collected
 from Twitter. We selected fifteen destructive cases across five types of
 natural disaster and analyzed the human movement data before, during, and
 after each event, comparing the perturbed and steady state movement data.
 The results suggest that the power-law can describe human mobility in most
 cases and that human mobility patterns observed in steady states are often
 correlated with those in perturbed states, highlighting their inherent
 resilience. However, the quantitative analysis shows that this resilience
 has its limits and can fail in more powerful natural disasters. The
 findings from this study will deepen our understanding of the interaction
 between urban dwellers and civil infrastructure, improve our ability to
 predict human movement patterns during natural disasters, and facilitate
 contingency planning by policymakers.
description: Patterns and Limitations
 of Urban Human Mobility Resilience under the Influence of Multiple Types
 of Natural Disaster (Original Data)The file includes the
 location data from 15 natural disaster events that are used for this
 research.
DOI: 10.5061/dryad.k1c4j
title: Data from: The accumulation of reproductive isolation in early stages of divergence supports a role for sexual selection

description: Models of speciation by sexual selection propose that male-female
 coevolution leads to the rapid evolution of behavioral reproductive
 isolation. Here, we compare the strength of behavioral isolation to
 ecological isolation, gametic incompatibility, and hybrid inviability in a
 group of dichromatic stream fishes. In addition, we examine whether any of
 these individual barriers, or a combined measure of total isolation, is
 predicted by body shape differences, male color differences, environmental
 differences, or genetic distance. Behavioral isolation reaches the highest
 values of any barrier and is significantly greater than ecological
 isolation. No individual reproductive barrier is associated with any of
 the predictor variables. However, marginally significant relationships
 between male color and body shape differences with ecological and
 behavioral isolation are discussed. Differences in male color and body
 shape predict total reproductive isolation between species; hierarchical
 partitioning of these two variables’ effects suggests a stronger role for
 male color differences. Together, these results suggest an important role
 for divergent sexual selection in darter speciation but raise new
 questions about the mechanisms of sexual selection at play and the role of
 male nuptial ornaments.
description: Behavioral Isolation
 DataSpawning events across
 three replicate trails for each species pair.BI.xlsxManual Cross DataData used to compute GI and HI.GI and HI.xlsxEcological Isolation DataHabitat data used to compute EI.EI.xlsxMacroenvironmental DatasetData used to compute Macroenvironmental Differences.
DOI: 10.5061/dryad.4b8j7
title: Data from: Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: a case-study in Carex sect. Racemosae

description: PREMISE OF THE STUDY: Relationships among closely related and recently
 diverged taxa can be especially difficult to resolve. Here we use both
 Sanger sequencing and next-generation RADseq data sets to estimate
 phylogenetic relationships among species of Carex section Racemosae
 (Cyperaceae), a clade largely restricted to high latitudes and elevations.
 Interest in relationships among these taxa derives from questions about
 the species’ biogeographic histories and possible links between
 diversification and Pleistocene glaciations. METHODS: A combination of
 approaches and molecular markers were used to estimate relationships among
 Carex species within sect. Racemosae and taxa from closely related
 sections. Nuclear and chloroplast loci generated by Sanger sequencing were
 analyzed with *BEAST, and SNP data from RADseq loci were analyzed as a
 concatenated data set using maximum likelihood and as independent loci
 using SVDquartets. KEY RESULTS: Sanger sequencing data sets resolved
 relationships among taxa at intermediate phylogenetic depths (albeit with
 low levels of support). Only the RADseq data resolved relationships with
 strong support at all phylogenetic depths. Moreover, different methods and
 data partitions of the RADseq data resulted in nearly identical
 topologies. Carex sect. Racemosae is a strongly supported clade, although
 a handful of species were found to group with closely related sections.
 Herbarium specimens up to 35 yr old successfully produced informative
 RADseq data. CONCLUSIONS: Despite the short read lengths of RADseq data,
 they nevertheless resolved relationships that Sanger sequencing data did
 not. Resolution of the phylogenetic relationships among recently and
 rapidly diversifying taxa within sect. Racemosae clades suggest a role for
 the Pleistocene glaciations in clade diversification.
description: Parameters for
 PyradThis file contains the
 Pyrad parameters file that was used to create the SNP dataset that was
 used (after modification) in ML and SVDquartets
 analyses.params_pyrad_racemosae.txtData file for ML analysesThis file contains the SNP data used for the ML analysis. A key to species codes is given in a separate file.racemosae_ML.txtData file for SVDquartets analysisThis file contains the SNP data for the SVDquartets analysis. A separate file contains the codes for the species names.racemosae_SVDquartets.txtSpecies key, ML analysisThis file provides the species names and codes that are used in the ML data file.species_key_ML_analysis.txtSpecies key for SVDquartets analysisThis file contains the species and codes that are used in the SVDquartets data file.species_key_SVDquartets_analysis.txt
DOI: 10.5061/dryad.g9645
title: Data from: Heritability, environmental effects, and genetic and phenotypic correlations of oxidative stress resistance-related enzyme activities during early life stages in Atlantic salmon

description: Oxidative stress (OS) may pose important physiological constraints on
 individuals, affecting trade-offs between growth and reproduction or
 ageing and survival. Despite such evolutionary and ecological importance,
 the results from studies on the magnitude of individual variation in OS
 resistance and the underlying causes of this variation such as genetic,
 environmental, and maternal origins, remain inconclusive. Using a high
 throughput methodology, we investigated the activity levels in three OS
 resistance-related enzymes (superoxide dismutase, SOD; glutathione
 reductase, GR; glutathione S-transferase, GST) during the early life
 stages of 1000 individuals from 50 paternal half-sib families in two
 populations of Atlantic salmon. Using animal mixed models, we detected the
 presence of narrow-sense heritability for SOD and GST; that for GST
 differed between populations due to differences in environmental variance.
 We found support for the presence of common environmental variation,
 including maternal effects, for only GR. Using a bivariate animal model,
 we detected a positive environmental correlation between activity levels
 of SOD and GST but were unable to detect an additive genetic correlation.
 Our results complement previous heritability findings for levels of
 reactive oxygen species or OS resistance by demonstrating the presence of
 heritability for OS-related enzyme activities. Our findings provide a
 foundation for future work, such as investigations on the evolutionary
 importance of variation in enzyme activities. In addition, our findings
 emphasise the importance of accounting for developmental stage,
 environmental variance, and kin relationships when investigating the
 OS-response at the enzyme activity level.
description: EnzymePlateDataEnzyme activity measurement dataProteinPlateDataProtein content measurement data
DOI: 10.15468/dl.79r8m2
title: Occurrence Download

description: A dataset containing 4674448 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is South Africa",
 "DatasetKey is Southern African Bird Atlas Project",
 "Year 1977-2026"
 ]
}

 The dataset includes 4674448 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001417-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.512m0
title: Data from: Different-sized grazers have distinctive effects on plant functional composition of an African savannah

description: Grazing ungulates play a key role in many ecosystems worldwide and can
 form diverse assemblages, such as in African savannahs. In many of these
 ecosystems, present-day ungulate communities are impoverished subsets of
 once diverse assemblages. While we know that excluding all ungulates from
 grasslands can exert major effects on both the structure and composition
 of the vegetation, how different individual ungulate species may have
 contrasting effects on grassland communities remains poorly understood.
 Here, we performed a long term “Russian doll” grazing exclosure experiment
 in an African savannah to test for the effects of different size classes
 of grazers on grassland structure and composition. At five sites, grazer
 species of decreasing size class (ranging from white rhino to scrub hare)
 were excluded using four fence types, to experimentally create different
 realized grazer assemblages. The vegetation structure and the grass
 functional community composition were characterized in six different years
 over a 10 year period. Additionally, animal footprints were counted to
 quantify the abundance of different ungulate species in each treatment. We
 found that while vegetation height was mostly driven by total grazing
 pressure of all species together, ungulate community composition best
 explained the functional community composition of grasses. In the short
 term, smaller ungulate species (‘mesoherbivores’) had strongest effects on
 vegetation composition, by shifting communities towards dominance by
 species with low specific leaf area and low nutritional value. In the long
 term, large grazers had stronger but similar effects on the functional
 composition of the system. Surprisingly, the largest ‘mega-herbivore’,
 white rhinoceros, did not have strong effects on the vegetation structure
 or composition. Synthesis. Our results support the idea that different
 size classes of grazers have varying effects on the functional composition
 of grassland plant communities. Therefore, the worldwide decline in the
 diversity of ungulate species is expected to have (had) major impacts on
 community composition and functioning of grassland ecosystems, even if
 total grazing pressure has remained constant, e.g., due to replacement by
 livestock.
description: long-term database on
 plant observationsDatabase with plant
 observations for different sites (10 in total, but only those 5 with all
 fence types were used in the associated paper) and five different fence
 types, for six different years, collected in Hluhluwe-iMfolozi Park (HiP),
 South Africa.SABRE_ZLTP_Exclosures.accdbgrass trait datain situ measured values of SLA, leaf N content and canopy height. This data was originally collected for the study van der Plas & Olff, 2014, Mesoherbivores affect grasshopper communities in a megaherbivore-dominated South African savannah, Oecologia 175: 639-649grass traits Fons.txtdaily rainfall valuesrainfall data at the exclosure sites, collected on a daily basis.
DOI: 10.5061/dryad.r95s8
title: Data from: Fractal measures of spatial pattern as a heuristic for return rate in vegetative systems

description: Measurement of population persistence is a long-standing problem in
 ecology; in particular, whether it is possible to gain insights into
 persistence without long time-series. Fractal measurements of spatial
 patterns, such as the Korcak exponent or boundary dimension, have been
 proposed as indicators of the persistence of underlying dynamics. Here we
 explore under what conditions a predictive relationship between fractal
 measures and persistence exists. We combine theoretical arguments with an
 aerial snapshot and time series from a long-term study of seagrass. For
 this form of vegetative growth, we find that the expected relationship
 between the Korcak exponent and persistence is evident at survey sites
 where the population return rate can be measured. This highlights a
 limitation of the use of power-law patch-size distributions and other
 indicators based on spatial snapshots. Moreover, our numeric simulations
 show that for a single species and a range of environmental conditions
 that the Korcak–persistence relationship provides a link between temporal
 dynamics and spatial pattern; however, this relationship is specific to
 demographic factors, so we cannot use this methodology to compare between
 species.
description: Scilly_seagrass_data
DOI: 10.5061/dryad.p00gd
title: Data from: Genomewide introgressive hybridization patterns in wild Atlantic salmon influenced by inadvertent gene flow from hatchery releases

description: Many salmonid fish populations are threatened by genetic homogenization,
 primarily due to introgressive hybridization with hatchery-reared
 conspecifics. By applying genomewide analysis using two molecular marker
 types (1986 SNPs and 17 microsatellites), we assessed the genetic impacts
 of inadvertent gene flow via straying from hatchery releases on wild
 populations of Atlantic salmon in the Gulf of Finland, Baltic Sea, over 16
 years (1996–2012). Both microsatellites and SNPs revealed congruent
 population genetic structuring, indicating that introgression changed the
 genetic make-up of wild populations by increasing genetic diversity and
 reducing genetic divergence. However, the degree of genetic introgression
 varied among studied populations, being higher in the eastern part and
 lower in the western part of Estonia, which most likely reflects the
 history of past stocking activities. Using kernel smoothing and
 permutation testing, we detected considerable heterogeneity in
 introgression patterns across the genome, with a large number of regions
 exhibiting nonrandom introgression widely dispersed across the genome. We
 also observed substantial variation in nonrandom introgression patterns
 within populations, as the majority of genomic regions showing elevated or
 reduced introgression were not consistently detected among temporal
 samples. This suggests that recombination, selection and stochastic
 processes may contribute to complex nonrandom introgression patterns. Our
 results suggest that (i) some genomic regions in Atlantic salmon are more
 vulnerable to introgressive hybridization, while others show greater
 resistance to unidirectional gene flow; and (ii) the hybridization of
 previously separated populations leads to complex and dynamic nonrandom
 introgression patterns that most likely have functional consequences for
 indigenous populations.
description: Individual genotypes (17
 microsatellites)Individual genotype data
 assessed at 17 microsatellite lociOzerov_et_al_2016_Individual_microsatellite_genotypes.xlsxEstimated SNP allele frequenciesSNP name, chromosome position on the female and male map (cM) and estimated allele A frequency of pooled DNA samplesOzerov_et_al_2016_estimated_SNP_allele_frequencies.xlsxKernel smoothing & permutation test R scriptCustom-made R script to perform kernel smoothing and permutation testsKernel_smoothing&permutation_test_script.R