cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m8q8bn3
title: Data from: Passive acoustics and sound recognition provide new insights on status and resilience of an iconic endangered marsupial (koala Phascolarctos cinereus) to timber harvesting

description: Retention forestry aims to mitigate impacts of native forestry on
 biodiversity, but data are limited on its effectiveness for threatened
 species. We used acoustics to investigate the resilience of a folivorous
 marsupial, the koala Phascolarctos cinereus, to timber harvesting where a
 key mitigation practice is landscape exclusion of harvesting. We deployed
 acoustic recorders at 171 sites to record male bellows (~14,640 hours) for
 use in occupancy modelling and for comparisons of bellow rate (bellows
 night-1). Surveys targeted modelled medium-high quality habitat, with
 sites stratified by time since logging and logging intensity, including
 old growth as a reference. After scanning recordings with software to
 identify koala bellows, we found a high probability of detection (~0.45
 per night), but this varied with minimum temperature and recorder type.
 Naïve occupancy was ~ 64 % across a broad range of forests, which was at
 least five times more than expected based on previous surveys using
 alternative methods. After accounting for imperfect detection, probability
 of occupancy was influenced by elevation (-ve), cover of important browse
 trees (+ve), landscape NDVI (+ve) and extent of recent wildfire (-ve, but
 minor effect). Elevation was the most influential variable, though the
 relationship was non-linear and low occupancy was most common at tableland
 elevations (&gt; 1000 m). Neither occupancy nor bellow rate were
 influenced by timber harvesting intensity, time since harvesting or local
 landscape extent of harvesting or old growth. Extrapolation of occupancy
 across modelled habitat indicates that the hinterland forests of
 north-east NSW support a widespread, though likely low density koala
 population that is considerably larger than previously estimated.
 Retention forestry has a significant role to play in mitigating harvesting
 impacts on biodiversity, including for forest specialists, but localised
 studies are needed to optimise prescriptions for koalas.
description: Raw PRESENCE data for
 PONE-D-18-22682Presence/Absence data
 for koalas surveyed across 171 sites on the NSW North Coast and Hinterland
 forests between 2015 and 2017. Also included in the file are data on site
 and sampling covariates that were used in PRESENCE for occupancy
 modelling.
DOI: 10.5061/dryad.810f1
title: Data from: The role of glucosinolates and the jasmonic acid pathway in resistance of Arabidopsis thaliana against molluskan herbivores

description: Although slugs and snails play important roles in terrestrial ecosystems
 and cause considerable damage on a variety of crop plants, knowledge about
 the mechanisms of plant immunity to mollusks is limited. We found slugs to
 be natural herbivores of Arabidopsis thaliana and therefore investigated
 possible resistance mechanisms of this species against several molluskan
 herbivores. Treating wounded leaves with the mucus residue (“slime trail”)
 of the Spanish slug Arion lusitanicus increased wound-induced jasmonate
 levels, suggesting the presence of defense elicitors in the mucus. Plants
 deficient in jasmonate biosynthesis and signaling suffered more damage by
 molluskan herbivores in the laboratory and in the field, demonstrating
 that JA-mediated defenses protect A. thaliana against slugs and snails.
 Furthermore, experiments using A. thaliana mutants with altered levels of
 specific glucosinolate classes revealed the importance of aliphatic
 glucosinolates in defending leaves and reproductive structures against
 mollusks. The presence in mollusk feces of known and novel metabolites
 arising from glutathione conjugation with glucosinolate hydrolysis
 products suggests that molluskan herbivores actively detoxify
 glucosinolates. Higher levels of aliphatic glucosinolates were found in
 plants during the night compared to the day, which correlated well with
 the nocturnal activity rhythms of slugs and snails. Our data highlight the
 function of well-known anti-herbivore defense pathways in resistance
 against slugs and snails and suggest an important role for the diurnal
 regulation of defense metabolites against nocturnal molluskan herbivores.
description: updated data
 filethis data file contains
 the final data for the submitted manuscriptupdated data for
 database.xlsxR script for analyzing
 field data from experiments in MichiganR script for analyzing
 field data from experiments in Michigan
DOI: 10.5061/dryad.r1m19
title: Data from: Effect of ultrasonography surveillance in patients with liver cancer: a population-based longitudinal study

description: Objective Liver cancer is a growing global public health problem.
 Ultrasonography is an imaging tool widely used for the early diagnosis of
 liver cancer. However, the effect of ultrasonography surveillance (US) on
 the survival of patients with liver cancer is unknown. Therefore, this
 study examined the association between survival and US frequency during
 the 2 years preceding patients’ liver cancer diagnosis. Methods This
 population-based longitudinal study was conducted in Taiwan, a region with
 high liver cancer incidence, by using the National Health Insurance
 Research Database. We compared survival between patients who received US
 three times or more (≥3 group) and less than three times (&lt;3 group)
 during the 2 years preceding their liver cancer diagnosis, and identified
 the predictors for the ≥3 group. Results This study enrolled 4621 patients
 with liver cancer who had died between 1997 and 2010. The median survival
 rate was higher in the ≥3 group (1.42 years) than in the &lt;3 group
 (0.51 years). Five-year survival probability was also significantly higher
 in the ≥3 group (14.4%) than in the &lt;3 group (7.7%). The
 multivariate logistic regression results showed that the three most common
 positive predictors for receiving three or more US sessions were
 indications of viral hepatitis, gallbladder diseases, and
 kidney–urinary–bladder diseases; the most common negative predictors for
 receiving three or more US sessions were male sex and indications of
 abdominal pain. Conclusion Patients with liver cancer who received US
 three times or more during the 2 years preceding their liver cancer
 diagnosis exhibited a higher 5-year survival probability.
description: bmjopen-2017-015936the predictors for receiving ultrasonography surveillance three times or more during the 2 years preceding a liver cancer diagnosis
DOI: 10.5061/dryad.gp545
title: Data from: Use of novel psychoactive substances by inpatients on general adult psychiatric wards

description: Objectives: Non-illicit alternatives to controlled drugs, known as Novel
 Psychoactive Substances (NPS) have recently risen to prominence. They are
 readily available with uncertain pharmacology and no widely available
 assay. Given that psychiatric patients are at risk of comorbid substance
 abuse, we hypothesized that NPS use would be present in the psychiatric
 population, and sought to determine its prevalence and investigate the
 characteristics of those who use these drugs with a retrospective review
 of discharge letters. Setting: General adult inpatient wards of a
 psychiatric hospital in a Scottish city. Participants: All adult
 inpatients (18-65) discharged from general psychiatric wards between
 1/7/14 and 31/12/14. 483 admissions identified, 46 were admissions for
 maintenance ECT and were excluded. Of the remaining 437 admissions, 49
 discharge letters were unobtainable, leaving 388 admissions to analyze.
 Primary outcome measure: The mention or lack thereof of NPS use in
 discharge letters was our planned primary outcome measure and was also the
 primary outcome measure we used in our analysis. Results: NPS use was
 identified in 22.2% of admissions, contributing to psychiatric symptoms in
 59.3%. In comparison to non-users, NPS users were younger (p&lt;0.01),
 male and more likely to have a forensic history ((p&lt;0.001) for
 both). The diagnosis of drug-induced psychosis was significantly more
 likely in NPS users (p&lt;0.001, odds ratio (OR) 18.7, 95% confidence
 intervals (CI) 8.1-43.0) and the diagnosis of depression was significantly
 less likely (p&lt;0.005, OR 0.133, CI 0.031-0.558). Use of cannabis
 was significantly more likely in NPS users (p&lt;0.001, OR 4.2, CI
 2.5-7.1), as was substitute opiate prescribing (p&lt;0.001, OR 3.7, CI
 1.8-7.4). Conclusions: NPS use was prevalent amongst young, male
 psychiatric inpatients; in particular those with drug induced psychosis
 and often occurred alongside illicit drug use.
description: Jack Stanley - NPS
 Audit. Age, gender, Employment and Diagnosis edited for anonymisation
 purposesThe original data set
 contained 388 cases. 5 were removed to preserve anonymity. These were
 numbers 12, 160, 232, 387 and 459. Interested parties can contact Jack
 Stanley at s1004557@sms.ed.ac.uk if they would be interested in seeing the
 full data set. Furthermore age has been included as a range, uncommon
 diagnoses grouped as 'other' and data for students and self
 employed individuals has all been grouped as 'employed' for the
 purposes of coding. The frequencies of each of the latter two variables
 remain included in the results section for interest.
DOI: 10.5061/dryad.r140b
title: Data from: A systematic review of cetothere baleen whales (Cetacea, Cetotheriidae) from the Late Miocene of Crimea and Caucasus, with a new genus

description: Nine taxa of Miocene baleen whales were described from the Black Sea
 region under the name Cetotherium before 1951, and a further four closely
 related species representing three genera have been added in recent years.
 This rich diversity requires taxonomic revision and ordering. Here, a new
 genus, Mithridatocetus, is described from the Tortonian of Crimea and
 Caucasus, with two species, M. eichwaldi and M. adygeicus (originally
 Kurdalagonus adygeicus); ‘Cetotherium’ mayeri (a nomen dubium) is also a
 member of this genus. In comparison with other Cetotheriinae,
 Mithridatocetus is distinguished by the autapomorphic shape of the
 tympanic bulla with the swollen main ridge, the lowered anterior portion
 of the involucrum and the oblique anterolateral margin; such
 synapomorphies, as a transversely narrow squamosal with the ventromedially
 oriented postglenoid process (shared with Eucetotherium), a squamosal
 cleft (shared with Kurdalagonus) and an oval surface of the compound
 posterior process of the tympanoperiotic on the posterolateral skull wall
 (shared with Brandtocetus); and a unique combination of a high
 neurocranium and a long and robust paroccipital process. The genus
 Kurdalagonus is redefined here as containing only one described species,
 K. mchedlidzei. Therefore, the group Cetotheriinae is now restricted to
 the latest Serravallian and Tortonian of the Eastern Paratethys and
 includes at least five genera: Cetotherium, Brandtocetus, Kurdalagonus,
 Mithridatocetus and Zygiocetus. In addition, ?Cetotherium priscum and C.
 incertum are considered to be nomina dubia; ‘Cetotherium’ klinderi and
 ‘Cetotherium’ pusillum require more complete specimens for reassessment;
 ‘Cetotherium’ maicopicum and Eucetotherium helmersenii require further
 research to identify their taxonomical affinities.
description: Goldin_Startsev_PALA-05-16-3818-OA-R2_suppl
DOI: 10.5061/dryad.sb30r
title: Data from: Dissecting molecular stress networks: identifying nodes of divergence between life-history phenotypes

description: The complex molecular network that underlies physiological stress response
 is comprised of nodes (proteins, metabolites, mRNAs, etc.) whose
 connections span cells, tissues and organs. Variable nodes are points in
 the network upon which natural selection may act. Thus, identifying
 variable nodes will reveal how this molecular stress network may evolve
 among populations in different habitats and how it might impact
 life-history evolution. Here, we use physiological and genetic assays to
 test whether laboratory-born juveniles from natural populations of garter
 snakes (Thamnophis elegans), which have diverged in their life-history
 phenotypes, vary concomitantly at candidate nodes of the stress response
 network, (i) under unstressed conditions and (ii) in response to an
 induced stress. We found that two common measures of stress (plasma
 corticosterone and liver gene expression of heat shock proteins) increased
 under stress in both life-history phenotypes. In contrast, the phenotypes
 diverged at four nodes both under unstressed conditions and in response to
 stress: circulating levels of reactive oxygen species (superoxide, H2O2);
 liver gene expression of GPX1 and erythrocyte DNA damage. Additionally,
 allele frequencies for SOD2 diverge from neutral markers, suggesting
 diversifying selection on SOD2 alleles. This study supports the hypothesis
 that these life-history phenotypes have diverged at the molecular level in
 how they respond to stress, particularly in nodes regulating oxidative
 stress. Furthermore, the differences between the life-history phenotypes
 were more pronounced in females. We discuss the responses to stress in the
 context of the associated life-history phenotype and the evolutionary
 pressures thought to be responsible for divergence between the phenotypes.
description: HeatStressPhysiology_Data_DryadPhysiological and Genetic data (Q-PCR and RNA-seq) collected by Tonia Schwartz and Anne Bronikowski between 2008-2012 from a Heat Stress Experiment on 1.2 year old lab born babies (2007) of the Western Terrestrial Garter snake (Thamnophis elegans).
DOI: 10.5061/dryad.pc7pg
title: Data from: Homing pigeons respond to time-compensated solar cues even in sight of the loft

description: The sun has long been thought to guide bird navigation as the second step
 in a two-stage process, in which determining position using a map is
 followed by course setting using a compass, both over unfamiliar and
 familiar terrain. The animal’s endogenous clock time-compensates the solar
 compass for the sun’s apparent movement throughout the day, and this
 allows predictable deflections in orientation to test for the compass’
 influence using clock-shift manipulations. To examine the influence of the
 solar compass during a highly familiar navigational task, 24 clock-shifted
 homing pigeons were precision-tracked from a release site close to and in
 sight of their final goal, the colony loft. The resulting trajectories
 displayed significant partial deflection from the loft direction as
 predicted by either fast or slow clock-shift treatments. The partial
 deflection was also found to be stable along the entire trajectory
 indicating regular updating of orientation via input from the solar
 compass throughout the final approach flight to the loft. Our results
 demonstrate that time-compensated solar cues are deeply embedded in the
 way birds orient during homing flight, are accessed throughout the journey
 and on a remarkably fine-grained scale, and may be combined effectively
 simultaneously with direct guidance from familiar landmarks, even when
 birds are flying towards a directly visible goal.
description: Track data
 depositionLatitude & Longitude
 position fixes recorded at 1Hz for each treatment group
DOI: 10.5061/dryad.f5f60
title: Data from: Diet tracing in ecology: method comparison and selection

description: 1. Determining diet is a key prerequisite for understanding species
 interactions, food web structure and ecological dynamics. In recent years,
 there has been considerable development in both the methodology and
 application of novel and more traditional dietary tracing methods, yet
 there is no comprehensive synthesis that systematically and quantitatively
 compares among the different approaches. 2. Here we conceptualize diet
 tracing in ecology, provide recommendations for method selection, and
 illustrate the advantages of method integration. We summarize empirical
 evidence on how different methods quantify diet mixtures, by contrasting
 estimates of dietary proportions from multiple methods applied to the same
 consumer-resource datasets, or from experimental studies with known diet
 compositions. 3. Our data synthesis revealed an urgent need for more
 experiential comparisons among the dietary methods. The comparison of diet
 quantifications from field observations showed that different techniques
 aligned well in cases with less than six diet items, but diverged
 considerably when applied to more complex diet mixtures. 4. Efforts are
 ongoing to further advance dietary estimation, including how reliably
 compound specific stable isotope analyses and fatty acid profiles can
 quantify more prey items than bulk stable isotope analyses. Similarly, DNA
 analyses, which can depict trophic interactions at a higher resolution
 than any other methods, are generating new ways to better quantify diets
 and differentiate among life-stages of prey. Such efforts, combined with
 more empirical testing of each dietary method and establishment of open
 data repositories for dietary data, promise to greatly advance community
 and ecosystem ecology.
description: Nielsen et al.
 Supplementary material X2 - Data for quantitative
 comparisonData from the 40 studies
 used for the quantitative comparative analyses of diet
 methods.Nielsen et al. Supplementary
 materiaX2.xlsx
DOI: 10.5061/dryad.8gs7g
title: Data from: Development of nuclear microsatellite markers for the Japanese conifers Tsuga diversifolia and T. sieboldii (Pinaceae)

description: Nuclear microsatellite markers were developed for the two Tsuga species
 native to the Japanese Archipelago, Tsuga diversifolia and T. sieboldii,
 and a population with genetic affinities to T. diversifolia on Ulleung
 Island, Korea. Tsuga diversifolia and T. sieboldii are widespread dominant
 trees of temperate and subalpine forests in Japan but to date no genetic
 markers have been developed for these species. Fifteen polymorphic loci
 were developed and characterized, of which 14 are reliably amplified in
 each taxon. Across both species and the Ulleung Island population, the
 number of alleles per locus ranged from 3 to 26 (average = 13.93) and
 observed heterozygosity ranged from 0.005 to 0.935 (average = 0.535). In
 addition, all 15 loci were successfully amplified in a single accession of
 the Chinese species, T. chinensis. These markers will be useful for
 investigating the species’ biogeography, range-wide genetic diversity,
 conservation genetic issues and potential for hybridisation.
description: Tsuga EST sequences
 containing microsatellite regionsThis file contains EST
 sequences containing microsatellite regions for both Tsuga diversifolia
 and Tsuga sieboldii.
DOI: 10.5061/dryad.45q73
title: Data from: Diapause induction and relaxed selection on alternative developmental pathways in a butterfly

description: 1. Seasonal phenotypic plasticity entails differential trait expression
 depending on the time of season. The facultative induction of winter
 diapause in temperate insects is a developmental switch mechanism often
 leading to differential expression in life history traits. However, when
 there is a latitudinal shift from a bivoltine to univoltine life cycle,
 selection for pathway-specific expression is disrupted, which may allow
 drift towards less optimal trait values within the non-selected pathway.
 2. We use field- and experimental data from five Swedish populations of
 Pararge aegeria to investigate latitudinal variation in voltinism, local
 adaptation in the diapause switch, and footprints of selection on
 pathway-specific regulation of life history traits and sexual dimorphism
 in larval development. 3. Field data clearly illustrated how natural
 populations gradually shift from bivoltinism to univoltinism as latitude
 increases. This was supported experimentally as the decrease in direct
 development at higher latitudes was accompanied by increasing critical
 daylengths, suggesting local adaptation in the diapause switch. 4. The
 differential expression among developmental pathways in development time
 and growth rate was significantly less pronounced in univoltine
 populations. Univoltine populations showed no significant signs of
 protandry during larval development, suggesting that erosion of the direct
 development pathway under relaxed selection has led to the loss of its
 sex-specific modifications.
description: Field observation
 dataField observations of
 Pararge aegeria at five locations in Sweden for years
 2004-2013PropDir_alldata.xlsxCritical daylength experimentCritical daylength experiment of Pararge aegeria from five Swedish populationsLabExp-fix.xlsxLife history traits experimentLife history traits experimentdata2LifeHistoryTraits.txtLife history traits experiment: ProtandryLife history traits experiment: ProtandryDataProtandry2FIX.txt
DOI: 10.5061/dryad.gf83v
title: Data from: Factors contributing to the accumulation of reproductive isolation: A mixed model approach

description: The analysis of large datasets describing reproductive isolation between
 species has been extremely influential in the study of speciation.
 However, the statistical methods currently used for these data limit the
 ability to make direct inferences about the factors predicting the
 evolution of reproductive isolation. As a result, our understanding of
 iconic patterns and rules of speciation rely on indirect analyses that
 have clear statistical limitations. Phylogenetic mixed models are commonly
 used in ecology and evolution, but have not been applied to studies of
 reproductive isolation. Here I describe a flexible framework using
 phylogenetic mixed models to analyze data collected at different
 evolutionary scales, to test both categorical and continuous predictor
 variables, and to test the effect of multiple predictors on rates and
 patterns of reproductive isolation simultaneously. I demonstrate the
 utility of this framework by re-analyzing four classic datasets, from both
 animals and plants, and evaluating several hypotheses that could not be
 tested in the original studies: In the Drosophila and Bufonidae datasets,
 I found support for more rapid accumulation of reproductive isolation in
 sympatric species pairs compared to allopatric species pairs. Using Silene
 and Nolana, I found no evidence supporting the hypothesis that floral
 differentiation elevates postzygotic reproductive isolation. The faster
 accumulation of postzygotic isolation in sympatry is likely the result of
 species coexistence determined by the level of postzygotic isolation
 between species. In addition, floral trait divergence does not appear to
 translate into pleiotropic effects on postzygotic reproductive isolation.
 Overall, these methods can allow researchers to test new hypotheses using
 a single statistical method, while remedying the statistical limitations
 of several previous methods.
description: drosophila_datadrosophila_ultrametric_treeMCMCglmm genetic distance examplenolananolana_ultrametric_treenolanagdsilenesilene citation infosilene_ultrametric_treetoad_treetoaddataedittoad range overlap analysis