cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g2j62
title: Data from: Association between the severity of influenza A(H7N9) virus infections and length of the incubation period

description: Background: In early 2013, a novel avian-origin influenza A(H7N9) virus
 emerged in China, and has caused sporadic human infections. The incubation
 period is the delay from infection until onset of symptoms, and varies
 from person to person. Few previous studies have examined whether the
 duration of the incubation period correlates with subsequent disease
 severity. Methods and Findings: We analyzed data of period of exposure on
 395 human cases of laboratory-confirmed influenza A(H7N9) virus infection
 in China in a Bayesian framework using a Weibull distribution. We found a
 longer incubation period for the 173 fatal cases with a mean of 3.7 days
 (95% credibility interval, CrI: 3.4–4.1), compared to a mean of 3.3 days
 (95% CrI: 2.9–3.6) for the 222 non-fatal cases, and the difference in
 means was marginally significant at 0.47 days (95% CrI: -0.04, 0.99).
 There was a statistically significant correlation between a longer
 incubation period and an increased risk of death after adjustment for age,
 sex, geographical location and underlying medical conditions (adjusted
 odds ratio 1.70 per day increase in incubation period; 95% credibility
 interval 1.47–1.97). Conclusions: We found a significant association
 between a longer incubation period and a greater risk of death among human
 H7N9 cases. The underlying biological mechanisms leading to this
 association deserve further exploration.
description: Read me (data file
 explanations)Data on H7N9 cases in
 ChinaThis data file contains
 information on 395 human cases of laboratory-confirmed H7N9 infection in
 China between Mar 2013 and Aug 2014.data_h7n9_severity.csvSimple MCMC function scriptsR syntax to define the MCMC functions to be used in other scriptsmcmc_function_incubation.rTable 1 scriptsTable_1.rTable 2 scriptsTable_2.rTable 3 scriptsTable_3.rTable 4 scriptsTable_4.rFigure 1 scriptsFigure_1.rFigure 2 scriptsFigure_2.r
DOI: 10.5061/dryad.3g9s2
title: Data from: Bayesian hierarchical models for spatially misaligned data in R

description: Spatial misalignment occurs when at least one of multiple outcome
 variables is missing at an observed location. For spatial data, prediction
 of these missing observations should be informed by within location
 association among outcomes and by proximate locations where measurements
 were recorded. This study details and illustrates a Bayesian regression
 framework for modelling spatially misaligned multivariate data. Particular
 attention is paid to developing valid probability models capable of
 estimating parameter posterior distributions and propagating uncertainty
 through to outcomes' predictive distributions at locations where some
 or all of the outcomes are not observed. Models and associated software
 are presented for both Gaussian and non-Gaussian outcomes. Model parameter
 and predictive inference within the proposed framework is illustrated
 using a synthetic and forest inventory data set. The proposed Markov chain
 Monte carlo samplers were written in c++ and leverage R's Foreign
 Language Interface to call fortran blas (Basic Linear Algebra Subprograms)
 and lapack (Linear Algebra Package) libraries for efficient matrix
 computations. The models are implemented in the spMisalignLM and
 spMisalignGLM functions within the spBayes r package available via the
 Comprehensive R Archive Network (cran) (http://cran.r-project.org).
description: Data for Section
 4.2Data for Section
 4.2example-data.tar.gzR code for Section 4R code for Section 4FBC13.R
DOI: 10.15468/dl.5f94sa
title: Occurrence Download

description: A dataset containing 3664 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Solanum lycopersicum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 3664 records from 270 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001005-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cq8bh
title: Data from: Genetic sorting of subordinate species in grassland modulated by intraspecific variation in dominant species.

description: Genetic variation in a single species can have predictable and heritable
 effects on associated communities and ecosystem processes, however little
 is known about how genetic variation of a dominant species affects plant
 community assembly. We characterized the genetic structure of a dominant
 grass (Sorghastrum nutans) and two subordinate species (Chamaecrista
 fasciculata, Silphium integrifolium), during the third growing season in
 grassland communities established with genetically distinct (cultivated
 varieties or local ecotypes) seed sources of the dominant grasses. There
 were genetic differences between subordinate species growing in the
 cultivar versus local ecotype communities, indicating that intraspecific
 genetic variation in the dominant grasses affected the genetic composition
 of subordinate species during community assembly. A positive association
 between genetic diversity of S. nutans, C. fasciculata, and S.
 integrifolium and species diversity established the role of an
 intraspecific biotic filter during community assembly. Our results show
 that intraspecific variation in dominant species can significantly
 modulate the genetic composition of subordinate species.
description: Chamaecrista
 fasciculata, Silphium integrifolium, and Sorghastrum nutans ISSR data
 (1.22.14)Individual (1/0) and
 plot level frequency Inter Simple Sequence Repeat (ISSR) data for
 Chamaecrista fasciculata, Silphium integrifolium, and Sorghastrum
 nutans
DOI: 10.5061/dryad.v8bn7
title: Data from: Persistent anthrax as a major driver of wildlife mortality in a tropical rainforest

description: Anthrax is a globally significant animal disease and zoonosis. Despite
 this, current knowledge of anthrax ecology is largely limited to arid
 ecosystems, where outbreaks are most commonly reported. We reveal cryptic
 the dynamics of an anthrax causing agent, Bacillus cereus biovar
 anthracis, in a tropical rainforest with severe consequences for local
 wildlife communities. Using data and samples collected over three decades
 we found that rainforest anthrax is a persistent and widespread cause of
 death for a broad range of mammalian hosts. We predict that this pathogen
 will accelerate the decline and possibly result in the extirpation of
 local chimpanzee (Pan troglodytes verus) populations. Our findings
 illuminate the epidemiology of a cryptic pathogen and have important
 implications for conservation and public health.
description: SNP_Alignment_TNP_Bcbva_ChromosomeAlignment of variant sites of chromosomal Bcbva sequences from TNP (Côte d’Ivoire, n=124) and Grebo (Liberia, n=2). One sequence per host hosts (mammals/flies, two divergent isolates for fly 600) was included and the final alignment of variant sites is 298bp long.SNP_Alignment_TNP_Bcbva_pXO1Alignment of variant sites of Bcbva plasmid pXO1 sequences from TNP (Côte d’Ivoire, n=124) and Grebo (Liberia, n=2). One sequence per host hosts (mammals/flies, two divergent isolates for fly 600) was included and the final alignment of variant sites is 18bp long.SNP_Alignment_TNP_Bcbva_pXO2Alignment of variant sites of Bcbva plasmid pXO2 sequences from TNP (Côte d’Ivoire, n=124) and Grebo (Liberia, n=2). One sequence per host hosts (mammals/flies, two divergent isolates for fly 600) was included and the final alignment of variant sites is 11bp long.SNP_Alignment_sub-Saharan_Africa_Bcbva_ChromosomeAlignment of variant sites of chromosomal Bcbva sequences from Côte d'Ivoire (CI), Cameroon (CAM), Liberia (505-4 and 506-4) and CAR (363-2 and 364-1). The final alignment of variant sites is 1016bp long.
DOI: 10.5061/dryad.f3b66
title: Data from: A phylogenetic analysis of trait convergence in the spring flora

description: In temperate deciduous forests, spring flowering plants exhibit remarkable
 similarity in a number of characteristics, including reproductive,
 vegetative, and ecological traits. The apparent convergence of floral
 traits, especially corolla colour, among spring flowering species has been
 well documented, but remains poorly understood. Here we review adaptive
 hypotheses and predictions that have been proposed to explain the apparent
 correlation between spring flowering and a suite of traits. We
 investigated the correlation between flowering phenology (i.e., spring or
 nonspring) and several key traits using phylogenetic comparative methods.
 Through this analysis we were able to confirm the existence of a
 correlation for five of the six traits examined. Specifically, spring
 flowering is shown to have evolved in a correlated fashion with
 reproductive schedule (perennial vs. annual), light corolla colour, fruit
 type, growth form, and forest strata layer. In general, our survey
 determined that spring flowering species are perennial, have light
 coloured corollas, a herbaceous growth form, and tend to occupy the
 understory of the forest. These results are discussed in light of the
 reviewed adaptive hypotheses and the spring pollination environment.
description: Hensel and Sargent
 Botany dataThe file contains two
 worksheets. One sheet contains phenology, fruit type, growth form, forest
 strata layer, floral colour, and reproductive schedule data for 465
 temperate deciduous forest species. The second sheet contains a legend
 explaining the coding of the character states of the traits. The data was
 collected from the The New Britton and Brown Illustrated Flora of the
 Northeastern United States and Adjacent Canada (Gleason 1952) and was used
 to investigate correlated evolution between flowering phenology and a
 suite of ecological, reproductive, and vegetative
 traits.
DOI: 10.5061/dryad.0908bq0
title: Data from: Heat hardening capacity in Drosophila melanogaster is life stage specific and juveniles show the highest plasticity

description: Variations in stress resistance and adaptive plastic responses during
 ontogeny have rarely been addressed, despite the possibility that
 differences between life stages can affect species' range margins and
 thermal tolerance. Here, we assessed the thermal sensitivity and hardening
 capacity of Drosophila melanogaster across developmental stages from
 larval to the adult stage. We observed strong differences between life
 stages in heat resistance, with adults being most heat resistant followed
 by puparia, pupae and larvae. The impact of heat hardening (1 h at 35°C)
 on heat resistance changed during ontogeny, with the highest positive
 effect of hardening observed in puparia and pupae and the lowest in
 adults. These results suggest that immobile life stages (puparia and
 pupae) have evolved high plasticity in upper thermal limits whereas adults
 and larvae rely more on behavioural responses to heat stress allowing them
 to escape from extreme high temperatures. While most studies on the
 plasticity of heat resistance in ectotherms have focused on the adult life
 stage, our findings emphasize the crucial importance of juvenile life
 stages of arthropods in understanding the thermal biology and life
 stage-specific physiological responses to variable and stressful high
 temperatures. Failure to acknowledge this complication might lead to
 biased estimates of species' ability to cope with environmental
 changes, such as climate change.
description: Thermal resistance of D.
 melanogaster during ontogeny with or without heat
 hardeningData file shows the
 survival (%) of hardened and non-hardened flies at different life stages
 (larvae1, larvae2, larvae3, puparium, pupae, adult1 and adult2) in
 response to five different test temperatures (37, 38, 39, 40 and 41
 ºC)Data for
 Dryad.xlsx
DOI: 10.5061/dryad.5d9s571
title: Data from: Seasonally sympatric but allochronic: differential expression of hypothalamic genes in a songbird during gonadal development

description: Allochrony, the mismatch of reproductive schedules, is one mechanism that
 can mediate sympatric speciation and diversification. In songbirds, the
 transition into breeding condition and gonadal growth is regulated by the
 hypothalamic-pituitary-gonadal (HPG) axis at multiple levels. We
 investigated whether the difference in reproductive timing between two,
 seasonally sympatric subspecies of dark-eyed juncos (Junco hyemalis) was
 related to gene expression along the HPG axis. During the sympatric
 pre-breeding stage, we measured hypothalamic and testicular mRNA
 expression of candidate genes via qPCR in captive male juncos. For
 hypothalamic mRNA, we found our earlier breeding subspecies had increased
 expression of gonadotropin-releasing hormone (GnRH) and decreased
 expression of androgen receptor, estrogen receptor alpha, and
 mineralocorticoid receptor (MR). Subspecies did not differ in expression
 of hypothalamic gonadotropin-inhibitory hormone (GnIH) and glucocorticoid
 receptor (GR). While our earlier breeding subspecies had higher mRNA
 expression of testicular GR, subspecies did not differ in testicular
 luteinizing hormone receptor, follicle-stimulating hormone receptor, or MR
 mRNA expression levels. Our findings indicate increased GnRH production
 and decreased hypothalamic sensitivity to sex steroid negative feedback as
 factors promoting differences in the timing of gonadal recrudescence
 between recently diverged populations. Differential gene expression along
 the HPG axis may facilitate species diversification under seasonal
 sympatry.
description: qPCR data from junco
 hypothalami and testes*The first six tabs each
 display values for hypothalamic genes *The last four tabs each display
 values for testicular genes *Band # refers to the USFWS silver, metal band
 that each, individual bird was banded with *Population refers to residents
 (Junco hyemalis carolinensis) and migrants (Junco hyemalis hyemalis)
 *Hypothalamus reference genes were PPIA and GAPDH *The testicular
 reference gene was RPL4 *For details on how qPCR assays were run, assay
 variation, etc. please see main text and supplementary materials *Note:
 Hypothalamic genes were run so all individuals were on the same plate.
 Testicular genes were run so one plate had all genes from the same
 individual.Supp_Mat_Data_for_Dryad.xlsx
DOI: 10.5061/dryad.m065n
title: Data from: Disturbance-mediated heterogeneity drives pollinator diversity in boreal managed forest ecosystems

description: Intensive forest management, together with fire suppression, have
 decreased structural complexity and altered dynamics of boreal forests
 profoundly. Such management threatens forest biodiversity and can reduce
 the provision of ecosystem services. Although the importance of ecosystem
 services is widely acknowledged, conservation strategies are hindered by
 poor knowledge about diversity patterns of service provider species as
 well as on mechanisms affecting these assemblages at different spatial and
 temporal scales. In this study, we assessed the effect of disturbance
 management on forest pollinator communities. To do so, we used a
 large-scale ecological experiment conducted in year 2000, where forest
 complexity was manipulated with different harvest regimes and prescribed
 fire. Results were consistent with a positive response of pollinators to
 increasing habitat heterogeneity driven by past disturbances. Harvested
 sites harbored a diverse pollinator community, and showed higher spatial
 and temporal turnover in species richness. Conversely, old-growth forest
 communities were a nested subset of harvested sites and contained half of
 their total diversity. Variation in community composition (β diversity)
 was primarily affected by species temporal turnover. Throughout the
 season, β diversity was controlled by fire and harvesting legacies, which
 provide environmental heterogeneity in the form of flowering and nesting
 resources over space and time. Conservation strategies may undervalue
 ecosystem services in dynamic, naturally disturbance-driven, landscapes
 when relying solely on undisturbed forests areas. However, maintaining
 natural dynamics in early successional forests, by emulating natural
 disturbances at harvesting, hold promise for the conservation of both
 biodiversity and ecosystem services in boreal forests.
description: Pollinator_datavariables and their coding are in the ReadMe file
DOI: 10.5061/dryad.3t4g7
title: Data from: Validating genome-wide association candidates controlling quantitative variation in nodulation

description: Genome-wide association (GWA) studies offer the opportunity to identify
 genes that contribute to naturally occurring variation in quantitative
 traits. However, GWA relies exclusively on statistical association, so
 functional validation is necessary to make strong claims about gene
 function. We used a combination of gene-disruption platforms (Tnt1
 retrotransposons, hairpin RNA-interference constructs, and CRISPR/Cas9
 nucleases) together with randomized, well-replicated experiments to
 evaluate the function of genes that an earlier GWA study in Medicago
 truncatula had identified as candidates contributing to variation in the
 symbiosis between legumes and rhizobia. We evaluated ten candidate genes
 found in six clusters of strongly associated single nucleotide
 polymorphisms, selected on the basis of their strength of statistical
 association, proximity to annotated gene models, and root or nodule
 expression. We found statistically significant effects on nodule
 production for three candidate genes, each validated in two independent
 mutants. Annotated functions of these three genes suggest their
 contributions to quantitative variation in nodule production occur through
 processes not previously connected to nodulation, including phosphorous
 supply and salicylic acid-related defense response. These results
 demonstrate the utility of GWA combined with reverse mutagenesis
 technologies to discover and validate genes contributing to naturally
 occurring variation in quantitative traits. The results highlight the
 potential for GWA to complement forward genetics in identifying the
 genetic basis of ecologically and economically important traits.
description: Phenotype data from
 nodule assaysData on leaf number,
 length of the longest branch, root length, and total number of nodules
 produced by plants grown to assay effects of mutations in candidate
 genes.Curtin_etal_PlantPhys_phenotype_data_compiled 17january2017.xlsx
DOI: 10.25919/jp66-pw70
title: Stable isotope data from Nurioopta vineyard field experiment (2023-2025)

description: This data presents stable isotope data collected over two growing seasons (2023-2035) in order to partition irrigation sources. Stable isotope ratios of hydrogen (H), oxygen (O) and strontium (Sr) were measured in soil, irrigation, precipitation and Vitis vinifera (grapes, canes, and leaves).
DOI: 10.5061/dryad.rp5ht80
title: Data from: Better the devil you know? how familiarity and kinship affect prey responses to disturbance cues

description: Prey can greatly improve their odds of surviving predator encounters by
 eavesdropping on conspecific risk cues, but the reliability of these cues
 depends on both previous accuracy as well as the cue’s relevance. During a
 predator chase, aquatic prey release chemical disturbance cues that may
 vary in their reliability depending on the individuals receiving them.
 Thus, prey may rely differentially on disturbance cues from familiar
 individuals (due to previous experience) or from kin (due to their
 relatedness). We examined the responses of wood frog (Lithobates
 sylvaticus) tadpoles to disturbance cues from familiar vs. unfamiliar
 conspecifics and kin vs. non-kin. In accordance with our prediction,
 tadpoles responded differently to disturbance cues from familiar vs.
 unfamiliar conspecifics. Tadpoles receiving disturbance cues from
 unfamiliar individuals displayed a fright response, whereas tadpoles
 ignored disturbance cues from familiar individuals. Tadpoles may have
 habituated to familiar cues since they were unaccompanied by a true
 threat, hence rendering these cues functionally unreliable. Tadpoles
 responded similarly to disturbance cues from related and unrelated
 individuals suggesting they were similarly reliable and this mirrors the
 matching reliability of prey responses to damage-released alarm cues from
 kin and non-kin. Our findings shed light on a seldom-studied chemical
 communication system in aquatic prey.
description: RawData_for_Bairos-Novak_et_alThe raw data in an Excel spreadsheet used in the R analysis. See the 'metadata' tab of the spreadsheet for more information.Bairos-Novaketal_Rdata.xlsxR_Script_for_Bairos-Novak_et_alThe R programming language script used for loading, analyzing, and plotting the data. See the comments throughout the script for more information (lines preceeded by '#').Bairos-Novaketal_Rcode.R
DOI: 10.5061/dryad.gj4rp
title: Data from: Coinfection timing drives host population dynamics through changes in virulence

description: Infections of one host by multiple parasites are common, and several
 studies have found that the order of parasite invasion can affect both
 within-host competition and disease severity. However, it is unclear to
 what extent coinfection timing might be important to consider when
 modeling parasite impacts on host populations. Using a model system of two
 viruses infecting barley, we found that simultaneous infections of the two
 viruses were significantly more damaging to hosts than sequential
 coinfections. While priority effects were evident in within-host
 concentrations of sequential coinfections, priority did not influence any
 parameters, such as virulence or transmission rate, that affect host
 population dynamics. We built a susceptible-infected model to examine
 whether the observed difference in coinfection virulence could impact host
 population dynamics under a range of scenarios. We found that coinfection
 timing can have an important, but context dependent, effect on projected
 host population dynamics. Studies that examine only simultaneous
 coinfections could inflate disease impact predictions.
description: BSMV-BYDV_TiterDataRelative viral titer data from enzyme-linked immunosorbent assays over a 7 week period for Barley yellow dwarf virus-PAV and Barley stripe mosaic virus infecting Hordeum vulgare var. Conlon.MarchettoBSMV-BYDV_TiterData.csvBSMV-BYDV_HorizontalTransmissionHorizontal transmission data for Barley yellow dwarf virus and Barley stripe mosaic virus in Hordeum vulgare var. Conlon. Barley yellow dwarf virus was transmitted by aphid vectors and Barley stripe mosaic virus was transmitted through contact by rubbing.MarchettoBSMV-BYDV_HorizontalTrans.csvBSMV_VerticalTransmissionVertical transmission data for Barley stripe mosaic virus.MarchettoBSMV-BYDV_VerticalTrans.csvBSMV-BYDV_BiomassDataBiomass data for Hordeum vulgare var. Conlon plants infected with Barley yellow dwarf virus-PAV and/ or Barley stripe mosaic virus.MarchettoBSMV-BYDV_BiomassData.csv