cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kh95v21
title: Data from: Combined effects of mutualistic rhizobacteria counteract virus-induced suppression of indirect plant defenses in soybean

description: It is increasingly clear that microbial plant symbionts can influence
 interactions between their plant hosts and other organisms. Yet, such
 effects remain poorly understood, particularly under ecologically
 realistic conditions where plants simultaneously interact with diverse
 mutualists and antagonists. Here we examine how the effects of a plant
 virus on indirect plant defenses against its insect vector are influenced
 by co-occurrence of other microbial plant symbionts. Using a
 multi-factorial design, we manipulated colonization of soybean using three
 different microbes: a pathogenic plant virus (Bean pod mottle virus
 [BPMV]), a nodule-forming beneficial rhizobacterium (Bradyrhizobium
 japonicum), and a plant growth-promoting rhizobacterium (PGPR) (Delftia
 acidovorans). We then assessed recruitment of parasitoids (Pediobious
 foveolatus [Eulophidae]) and parasitism rates following feeding by the
 BPMV vector Epilachna varivestis (Coccinellidae). BPMV infection
 suppressed parasitoid recruitment, prolonged parasitoid foraging time, and
 reduced parasitism rates in semi-natural foraging assays. However,
 simultaneous colonization of BPMV-infected hosts by both rhizobacteria
 restored parasitoid recruitment and rates of parasitism to levels similar
 to uninfected controls. Co-colonization by the two rhizobacteria also
 enhanced parasitoid recruitment in the absence of BPMV infection. These
 results illustrate the potential of plant-associated microbes to influence
 indirect plant defenses, with implications for disease transmission and
 herbivory, but also highlight the potential complexity of such
 interactions.
description: Data from: Combined
 effects of mutualistic rhizobacteria counteract virus-induced suppression
 of indirect plant defenses in soybeanR code and data for the
 analysis reported in the manuscript.Pulido_et_al_20190417.zip
DOI: 10.7284/166516
title: Multibeam Echosounder data collected during research cruise AR85-02 using a Kongsberg EM712 instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.sf755pr
title: Data from: Avian surface reconstruction in free-flight with application to flight stability analysis of a barn owl and peregrine falcon

description: Birds primarily create and control the forces necessary for flight through
 changing the shape and orientation of their wings and tail. Their wing
 geometry is characterised by complex variation in parameters such as
 camber, twist, sweep and dihedral. To characterise this complexity, a
 multi-stereo photogrammetry setup was developed for accurately measuring
 surface geometry in high-resolution during free-flight. The natural
 patterning of the birds was used as the basis for phase correlation-based
 image matching, allowing indoor or outdoor use while being non-intrusive
 for the birds. The accuracy of the method was quantified and shown to be
 sufficient for characterising the geometric parameters of interest, but
 with a reduction in accuracy close to the wing edge and in some localized
 regions. To demonstrate the method's utility, surface reconstructions
 are presented for a barn owl (Tyto alba) and peregrine falcon (Falco
 peregrinus) during three instants of gliding flight per bird. The barn owl
 flew with a consistent geometry, with positive wing camber and
 longitudinal anhedral. Based on flight dynamics theory this suggests it
 was longitudinally statically unstable during these flights. The peregrine
 flew with a consistent glide angle, but at a range of airspeeds with
 varying geometry. Unlike the barn owl, its glide configuration did not
 provide a clear indication of longitudinal static stability/instability.
 Aspects of the geometries adopted by both birds appeared to be related to
 control corrections and this method would be well suited for future
 investigations in this area, as well as for other quantitative studies
 into avian flight dynamics.
description: Flight O1 - original
 uncompressed tif images for flight O1 of the barn owlO1_images.zipFlight O2 - original uncompressed tif images for flight O2 of the barn owlO2_images.zipFlight O3 - original uncompressed tif images for flight O3 of the barn owlO3_images.zipFlight P1 - original uncompressed tif images for flight P1 of the peregrineP1_images.zipFlight P2 - original uncompressed tif images for flight P2 of the peregrineP2_images.zipFlight P3 - original uncompressed tif images for flight P3 of the peregrineP3_images.zipREADME
DOI: 10.7284/166503
title: Radiometer data collected during research cruise AR85-02 using a Eppley RAD instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.587cv26
title: Data from: Incidence of frontotemporal lobar degeneration in Italy: the Salento-Brescia Registry study

description: Objective The goal of the present work, based on a collaborative research
 registry in Italy (the Salento-Brescia Registry), was to assess the
 incidence of frontotemporal lobar degeneration (FTLD) and to define the
 frequencies of different FTLD phenotypes in the general population.
 Methods The study was conducted from January 1, 2017, to December 31,
 2017, in 2 Italian provinces: Lecce (in Puglia) in the south (area
 2,799.07 km2, inhabitants 802,082) and Brescia (in Lombardy) in the north
 (area 4,785.62 km2, inhabitants 1,262,678). During the study period, all
 new cases of FTLD (incident FTLD) were counted, and all patients'
 records were reviewed. The incidence was standardized to the Italian
 general population in 2017. Results In the 2 provinces, 63 patients with
 FTLD were diagnosed. The incidence rate for FTLD was 3.05 (95% confidence
 interval [CI] 2.34–3.90) per 100,000 person-years (py), while the age-sex
 standardized incidence rate was 3.09 (95% CI 2.95–3.23) per 100,000 py. In
 the Italian population, the lifetime risk was 1:400. There was a
 progressive increase in FTLD incidence across age groups, reaching its
 peak in the 75- to 79-year-old group, with an incidence rate of 15.97 (95%
 CI 8.94–26.33) per 100,000 py. The behavioral variant of frontotemporal
 dementia was the most common phenotype (37%). No difference in crude
 incidence rate between the 2 provinces was observed. Conclusion FTLD is a
 more common form of dementia than previously recognized, with a risk
 spanning in a wide age range and with maximum incidence in the mid-70s.
 Improved knowledge of FTLD epidemiology will help to provide appropriate
 public health service policies.
description: Supplementary
 Material
DOI: 10.5061/dryad.96n24g7
title: Data from: Extra-pair offspring are less heterozygous than within-pair offspring in American redstarts (Setophaga ruticilla)

description: The vast majority of bird species are socially monogamous; however,
 extra-pair paternity is nearly ubiquitous and a number of theories have
 been proposed to explain the prevalence of this mixed mating strategy.
 Here, we test the genetic compatibility hypothesis—the idea that females
 that are genetically similar to their social partners will mate with
 extra-pair males that are genetically dissimilar to produce offspring that
 are more heterozygous. For this study, we examined eight years of
 paternity data (2004-2011) from a Nearctic-Neotropical migratory bird, the
 American Redstart (Setophaga ruticilla), breeding in southeastern Ontario,
 Canada. We predicted that females paired with genetically similar males
 (higher relatedness) would be more likely to produce extra-pair offspring
 and that extra-pair offspring would have higher levels of heterozygosity
 than within-pair offspring. Alternatively, because this population
 experiences high levels of immigration, females may produce extra-pair
 offspring with more genetically similar males because of the potential for
 outbreeding depression. Using five highly variable microsatellite markers,
 we examined patterns of relatedness among social pairs as well as measures
 of offspring heterozygosity. In contrast to our predictions, we found no
 difference in relatedness between social pairs where the females produced
 extra-pair offspring and social pairs where the females produced only
 within-pair offspring. However, extra-pair offspring were significantly
 less heterozygous than within-pair offspring. Together, these findings
 suggest that females a) are not engaging in extra-pair fertilizations
 based on relatedness to their social mate and b) appear to be mating with
 extra-pair males that are more genetically similar to themselves. We
 suggest there may be benefits for females to mate with genetically similar
 extra-pair males in highly outbred populations with high rates of
 immigration, such as for maintaining co-adapted gene complexes or genes
 coding for local adaptations.
description: relatednessRelatedness values of parents, along with reproductive dataEP heterozygosityOffspring heterozygosity data
DOI: 10.5061/dryad.8n4pn0b
title: Data from: The relationship between geographic range extent, sea surface temperature and adult traits in coastal temperate fishes

description: Aim: We use publicly available data to assess the influence of ocean
 basin, various biological traits and sea surface temperature on
 biogeographic range extent for temperate, continental shelf fish species
 spanning 141 families. Location: Coastal waters of the temperate Northern
 Hemisphere. Taxon: Teleost Fishes (Infraclass Teleostei). Methods: We
 assess the relationship between species range extent and depth range,
 maximum body length, schooling behaviour and use of multiple habitats for
 1,251 species of northern, temperate, continental shelf fishes in
 different basins (Atlantic vs. Pacific) and margins (east vs. west) using
 linear mixed‐effect models with family and genus as nested random effects.
 We further assess the relationship between species range endpoint
 distribution and latitudinal temperature gradient using generalized linear
 models. Results: We found strong positive relationships between the number
 of species northern range endpoints and the steepness of the latitudinal
 sea surface temperature gradient on the western margins of the Atlantic
 and Pacific Oceans, but no relationship on the eastern margins of these
 ocean basins. The strongest predictors of range extent in our global model
 are ocean basin/margin and depth range. Maximum body length, schooling
 behaviour and use of multiple habitats are also significant predictors of
 range extent in the global model. The factors influencing range extent
 differ by basin and margin. Main conclusions: There are broad differences
 in patterns of species range extent and distribution of species ranges
 among basins/margins. These differences appear to be driven in part by
 variation in latitudinal water temperature gradient between basin margins.
 Our data suggest that sharp latitudinal temperature gradients may pose a
 barrier to dispersal and range expansion along the western margins of the
 Atlantic and Pacific Oceans, but not necessarily on the eastern margins.
 Our work also suggests that several post‐settlement traits may be
 associated with range extent either globally or in some temperate basins.
description: Appendix
 S2Appendix S2 Table of
 range extent and traits for all species included in the
 study.Dataset_S2.csvAppendix S3Appendix S3 Table of temperature gradients, range endpoint frequencies, and species richness across latitude in each basin/margin.Dataset_S3.xlsx
DOI: 10.5061/dryad.t7r6kg5
title: Data from: Differences in flowering time maintain species boundaries in a continental radiation of Viburnum

description: Premise of the study: We take an integrative approach in assessing how
 introgression and Pleistocene climate fluctuations have shaped the
 diversification of the Viburnum lentago clade, a group of five
 inter-fertile species with broad areas of sympatry. We specifically tested
 whether flowering time plays a role in maintaining species isolation.
 Methods: RAD-seq data for 103 individuals were used to infer the species
 relationships and the genetic structure within each species. Flowering
 times were compared among species based on historical flowering dates
 documented in herbarium specimens. Key Results: Within each species we
 found a strong relationship between flowering date and latitude, such that
 southern populations flower earlier than northern ones. In areas of
 sympatry, the species flower in sequence rather than simultaneously, with
 flowering dates offset by at least nine days for all species pairs. In two
 cases it appears that the offset in flowering times is an incidental
 consequence of adaptation to differing climates, but in the recently
 diverged sister species V. prunifolium and V. rufidulum, we find evidence
 that reinforcement led to reproductive character displacement. Long-term
 trends suggest that the two northern-most species are flowering earlier in
 response to recent climate change. Conclusions: We argue that speciation
 in the Lentago clade has primarily occurred through ecological divergence
 of allopatric populations, but differences in flowering time were
 essential to maintain separation of incipient species when they came into
 secondary contact. This combination of factors may underlie
 diversification in many other plant clades.
description: lentago_collections_tableTable with individuals collected for this study. The state and county are listed for each individualPhenology_dataTable of phenology data collected from herbarium specimens. This file contains information on ther Herbarium, species, collector, collection number, locality, date, and phenological stage. In this file the phenology is scored: 0 = leaves, small flower buds, 1 = flower buds with expanded inflorescences, 2 = flowering, 3 = past flowering, small fruits visible, 4 = young fruits, 5 = mature fruits, 6 = fruits fallen off, 7 = no leaves or fruits (winter), NA = infertile.core_lentago-c88-d6-min24_outfilesAll ipyrad outfiles for the entire V. lentago clade + outgroups with all loci shared across at least 24 individuals.core_lentago-c88-d6-min49_outfilesAll ipyrad outfiles for the entire V. lentago clade + outgroups with all loci shared across at least 49 individuals.core_lentago-c88-d6-min73_outfilesAll ipyrad outfiles for the entire V. lentago clade + outgroups with all loci shared across at least 73 individuals.core_lentago_combined_floral_trait_dataMorphological trait data for the core Lentago species.cleaned_occurrences_lentago_cladeTable of occurrence information compiled from multiple sources and cleaned according to the processes described in our manuscript.
DOI: 10.5061/dryad.5p489m3
title: Data from: Guiding carbon farming using interdisciplinary mixed methods mapping

description: In recognition of the need to address complex environmental problems, some
 ecological studies have adopted social research methods to better
 understand the complexity of social‐ecological systems management. The
 overwhelming majority of these studies stop short of fully embracing
 qualitative methodologies. The lack of integrative social and natural
 science data for a topic such as soil carbon farming is problematic as
 theoretical carbon sequestration opportunities identified through soil
 mapping and process‐based models can fail to deliver the sequestration
 levels promised when introduced on‐the‐ground. Such mapping needs to
 account for the human factors involved in delivering increased soil carbon
 on‐farm. Here, we develop a mixed methods mapping approach to explore the
 potential for increasing soil carbon stocks on upland farms in the UK. Our
 approach considers ecological and social complexity through application of
 soil science, ecology, participant observation, interviews and a focus
 group. Our maps revealed landscapes that are full of carbon farming
 opportunity, but contain previously hidden barriers to the delivery of
 increased soil carbon. For example, they revealed that carbon farming can
 be considered by farmers to work in opposition to perceived ‘good farming’
 practices and be correlated with increased incidents of livestock disease.
 We also discovered that the use of maps in research can be problematic as
 they can close down discussion and exclude local representation of an
 area. Trialling an interdisciplinary mixed methods approach produced new,
 deeper and more richly‐textured understandings about how soil carbon
 management is produced socially as well as ecologically on upland
 livestock farms. Our findings have potential to improve the success of
 future carbon farming initiatives by incorporating farmer knowledge and
 social drivers of implementation.
description: Brockett et al soil
 carbon dataData and code relating
 to the regression krigingbrockett-soilc-suppdata
 (1).zipTranscripts relating to
 soil carbon mapping projectSpatial transcripts,
 focus group transcripts and other transcriptsqual
 data.zip
DOI: 10.5061/dryad.3d63vh5
title: Data from: Hyperandrogenism and insulin resistance induce gravid uterine defects in association with mitochondrial dysfunction and aberrant ROS production

description: Women with polycystic ovary syndrome (PCOS) are at increased risk of
 miscarriage, which often accompanies the hyperandrogenism and insulin
 resistance seen in these patients. However, neither the combinatorial
 interaction between these two PCOS-related etiological factors nor the
 mechanisms of their actions in the uterus during pregnancy are well
 understood. We hypothesised that hyperandrogensim and insulin resistance
 exert a causative role in miscarriage by inducing defects in uterine
 function that are accompanied by mitochondrial-mediated oxidative stress,
 inflammation and perturbed gene expression. Here we tested this hypothesis
 by studying the metabolic, endocrine and uterine abnormalities in pregnant
 rats after exposure to daily injection of 5α-dihydrotestosterone (DHT,
 1.66 mg/kg body weight/day) and/or insulin (6.0 IU/day) from gestational
 day 7.5 to 13.5. We showed that while DHT-exposed and insulin-exposed
 pregnant rats presented impaired insulin sensitivity, DHT+insulin-exposed
 pregnant rats exhibited hyperandrogenism and peripheral insulin
 resistance, which mirrors pregnant PCOS patients. Compared to controls,
 hyperandrogenism and insulin resistance in the dam was associated with
 alterations in uterine morphology and aberrant expression of genes
 responsible for decidualization (Prl8a2, Fxyd2, and Mt1g), placentation
 (Fcgr3 and Tpbpa), angiogenesis (Flt1, Angpt1, Angpt2, Ho1, Ccl2, Ccl5,
 Cxcl9, and Cxcl10) and insulin signaling (Akt, Gsk3 and Gluts). Moreover,
 we observed changes in uterine mitochondrial function and homeostasis
 (i.e. mitochondrial DNA copy number and the expression of genes
 responsible for mitochondrial fusion, fission, biogenesis, and mitophagy)
 and suppression of both oxidative and antioxidative defenses (i.e.
 reactive oxygen species, Nrf2 signaling, and interactive networks of
 antioxidative stress responses) in response to the hyperandrogenism and
 insulin resistance. These findings demonstrate that hyperandrogenism and
 insulin resistance induce mitochondria-mediated damage and a resulting
 imbalance between oxidative and antioxidative stress responses in the
 gravid uterus.
description: Supporting Figures and
 Supplemental TablesSupporting Figures with
 legend and supplemental tables. Note: These figures are also available in
 the file 'Supporting Figure 1 and 2.pptx', and the supplemental
 tables are available in the file 'Suppl
 Tables.docx'.Suppl
 Documentation.pdfSupporting Figure 1 and
 2 (.pptx)Supporting figures in
 pptx format. See 'Supporting Figure legend.docx' for a
 description of the figures.Supporting Figure 1 and
 2.pptxSupporting Figure
 legend.docxSupplmental Tables
 (.docx)Supplemental tables in
 .docx format.Suppl
 Tables.docx
DOI: 10.5061/dryad.5gr7275
title: Data from: Nocturnal torpor by superb fairy-wrens: a key mechanism for reducing winter daily energy expenditure

description: Many passerine birds are small and require a high mass-specific rate of
 resting energy expenditure, especially in the cold. The energetics of
 thermoregulation is therefore an important aspect of their ecology, yet
 few studies have quantified thermoregulatory patterns in wild passerines.
 We used miniature telemetry to record the skin temperature (Tskin) of
 free-living superb fairy-wrens (Malurus cyaneus, 8.6 g; n = 6 birds over N
 = 7 to 22 days) and determine the importance of controlled reductions in
 body temperature during resting to their winter energy budgets.
 Fairy-wrens routinely exhibited large daily fluctuations in Tskin between
 maxima of 41.9 ± 0.6°C and minima of 30.4 ± 0.7°C, with overall individual
 minima of 27.4 ± 1.1°C (maximum daily range: 14.7 ± 0.9 °C). These results
 provide strong evidence of nocturnal torpor in this small passerine, which
 we calculated to provide a 42% reduction in resting metabolic rate at a Ta
 of 5 °C compared to active-phase Tskin. A capacity for energy-saving
 torpor has important consequences for understanding the behaviour and
 life-history ecology of superb fairy-wrens. Moreover, our novel field data
 suggest that torpor could be more widespread and important than previously
 thought within passerines, the most diverse order of birds.
description: Tb_SuperbFairyWren_Winter2019_daily valuesDaily values of skin temperature and other relevant variables
DOI: 10.5061/dryad.d40vr87
title: Data from: Are all rivers equal? The role of education in attitudes towards temporary and perennial rivers

description: Temporary rivers (TRs) are prevalent, biodiverse ecosystems yet often
 overlooked and underprotected. This may be because inadequate
 understanding of their ecosystem services leaves them undervalued by
 society. However, evidence of negative attitudes towards TRs is scant. We
 investigated the strength and extent of negative attitudes by surveying
 undergraduate students from Australia, UK, and USA on their agreement
 (positive attitude) or disagreement (negative attitude) with statements
 about the ecosystem services, moral consideration, and protection of
 perennial and TRs. Students were surveyed at the start and end of teaching
 units covering environmental topics. Disagreement with statements was
 uncommon (17% across all statements and surveys) and attitudes towards TRs
 were mostly positive. However, attitudes towards perennial rivers were
 more positive, particularly in comparison with non‐flowing TRs and with
 regard to their aesthetic value and recreational amenity. There were no
 significant differences in attitudes towards perennial and TRs in one
 teaching unit in Australia, and responses were more often more positive at
 the end of teaching units in the UK. Our study indicates education can
 change attitudes. The overall positive response to statements may reflect
 underlying environmental awareness and pre‐existing interest of
 participants enrolled in environmental and biology degrees, but not
 necessarily specific knowledge of TRs. General environmental education
 across the wider community could improve attitudes towards TRs,
 particularly when they are not flowing or in regions where they are
 uncommon or inconspicuous, and could support positive protection measures
 and innovative, inclusive management.
description: Attitudes towards
 temporary and perennial riversSummary statistics for
 responses of anonymous participants to statements about temporary and
 perennial rivers, recorded on a Likert scale of 1 to 5 (strong
 disagreement to strong agreement). Data were collected by survey, in
 accordance with the human research ethics approvals granted by the ethics
 committees and review boards at the respective institutions at which the
 surveys were conducted. Notes defining the abbreviations used are provided
 within the file.LeighEtal2019_PeopleAndNature_Data.xlsx