cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vj645q8
title: Data from: Age-structure and transient dynamics in epidemiological systems

description: Mathematical models of childhood diseases date back to the early twentieth
 century. In several cases, models that make the simplifying assumption of
 homogeneous time-dependent transmission rates give good agreement with
 data in the absence of secular trends in population demography or
 transmission. The prime example is afforded by the dynamics of measles in
 industrialized countries in the pre-vaccine era. Accurate description of
 the transient dynamics following the introduction of routine vaccination
 has proved more challenging, however. This is true even in the case of
 measles which has a well-understood natural history and an effective
 vaccine that confers long-lasting protection against infection. Here, to
 shed light on the causes of this problem, we demonstrate that, while the
 dynamics of homogeneous and age-structured models can be qualitatively
 similar in the absence of vaccination, they diverge subsequent to vaccine
 roll-out. In particular, we show that immunization induces changes in
 transmission rates, which in turn reshapes the age distribution of
 infection prevalence, which effectively modulates the amplitude of
 seasonality in such systems. To examine this phenomenon empirically, we
 fit transmission models to measles notification data from London that span
 the introduction of the vaccine. We find that a simple age-structured
 model provides a much better fit to the data than does a homogeneous
 model, especially in the transition period from the pre-vaccine to the
 vaccine era. Thus, we propose that age structure and heterogeneities in
 contact rates are critical features needed to accurately capture transient
 dynamics in the presence of secular trends.
description: CODE_plotsR Code for Plots in "Age-structure and transient dynamics in epidemiological systems"CODE_searchR Code for an initial parameter search to fit models in "Age-structure and transient dynamics in epidemiological systems"
DOI: 10.15468/dl.8gyg7f
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-120.0",
 "HasCoordinate is True",
 "HasGeospatialIssue is False",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae",
 {
 "or" : [
 "GadmGid is U",
 "GadmGid is S",
 "GadmGid is A",
 "GadmGid is .",
 "GadmGid is 3",
 "GadmGid is 9",
 "GadmGid is _",
 "GadmGid is 1"
 ]
 },
 "Year 2015-2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001791-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.sv90027
title: Data from: Interannual variation in season length is linked to strong co-gradient plasticity of phenology in a montane annual plant

description: Species are commonly distributed along latitudinal and elevational
 gradients of growing season length to which they might respond via
 phenotypic plasticity and / or adaptive genetic differentiation. However,
 the relative contribution of these processes and whether plasticity, if it
 occurs, facilitates expansion along season length gradients remains
 unclear but are important for predicting species fates during
 anthropogenic change. We quantified phenological trait variation in the
 montane annual Rhinanthus minor for three generations at 12 sites across
 900 m of elevation in the Canadian Rocky Mountains and conducted a
 reciprocal transplant experiment for two generations among nine sites. We
 compared clines and interannual variation of phenological traits between
 natural and transplanted individuals. Season length declined by ~ 37%
 along our elevational gradient and, as expected, plants emerged, reached
 first flower and made their first seed in ~ 41% fewer growing degree days
 under shorter growing seasons. Although reciprocal transplants revealed
 modest genetic differentiation across elevation, trait clines were
 primarily due to striking co-gradient plasticity that paralleled genetic
 differentiation. Co-gradient plasticity likely evolved in response to
 considerable interannual variation in season length across our elevational
 transect, and should prepare R. minor to make adaptive changes to
 phenology in response to ongoing climate change predicted for montane
 environments.
description: READMEGrowing season
 lengthsGrowing season length
 and elevation data for each study site and year (see overall README
 file).gsl.csvNatural plant phenological phenotypesPhenological measurements and identifying characteristics of naturally occurring Rhinanthus minor individuals.nat.csvTransplanted phenological phenotypesPhenological and site identifying characteristics for all measured transplanted individualstrans.csv
DOI: 10.5061/dryad.328q0b3
title: Data from: Pollen-borne microbes shape bee fitness

description: Teeming within pollen provisions are diverse communities of symbiotic
 microbes, which provide a variety of benefits to bees. Microbes themselves
 may represent a major dietary resource for developing bee larvae. Despite
 their apparent importance in sustaining bee health, evidence linking
 pollen-borne microbes to larval health is currently lacking. We examined
 the effects of microbe-deficient diets on the fitness of larval mason
 bees. In a series of diet manipulations, microbe-rich maternally collected
 pollen provisions were replaced with increasing fractions of sterilized,
 microbe-deficient pollen provisions before being fed to developing larvae.
 Convergent findings from amino acid and fatty acid trophic biomarker
 analyses revealed that larvae derived a substantial amount of nutrition
 from microbial prey and occupied a significantly higher trophic position
 than that of strict herbivores. Larvae feeding on increasingly sterile
 diets experienced significant adverse effects on growth rates, biomass and
 survivorship. When completely deprived of pollen-borne microbes, larvae
 consistently exhibited marked decline in fitness. We conclude that
 microbes associated with aged pollen provisions are central to bee health,
 not only as nutritional mutualists, but also as a major dietary component.
 In an era of global bee decline, the conservation of such bee–microbe
 interactions may represent an important facet of pollinator protection
 strategies.
description: CSIA for Trophic
 positiond15N data from amino
 acids used for TP calculationOsmia pollen chemistry
 analysis tableProximate nutrient
 chemistry analysis of natural and sterilized and natural Osmia
 pollen
DOI: 10.15468/dl.tchpqy
title: Occurrence Download

description: A dataset containing 7141 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "DatasetKey is EOD – eBird Observation Dataset",
 "IucnRedListCategory is CR",
 "OccurrenceStatus is Present",
 "Year 2024-2026"
 ]
}

 The dataset includes 7141 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001795-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t513409
title: Data from: Assessing specialized metabolite diversity in the cosmopolitan plant genus Euphorbia L.

description: Coevolutionary theory suggests that an arms race between plants and
 herbivores yields increased plant specialized metabolite diversity and the
 geographic mosaic theory of coevolution predicts that coevolutionary
 interactions vary across geographic scales. Consequently, plant
 specialized metabolite diversity is expected to be highest in
 coevolutionary hotspots, geographic regions, which exhibit strong
 reciprocal selection on the interacting species. Despite being well
 established theoretical frameworks, technical limitations have precluded
 rigorous hypothesis testing. Here we aim at understanding how geographic
 separation over evolutionary time may have impacted chemical
 differentiation in the cosmopolitan plant genus Euphorbia. We use a
 combination of state-of-the-art computational mass spectral metabolomics
 tools together with cell-based high-throughput immunomodulatory testing.
 Our results show significant differences in specialized metabolite
 diversity across geographically separated phylogenetic clades. Chemical
 structural diversity of the highly toxic Euphorbia diterpenoids is
 significantly reduced in species native to the Americas, compared to
 Afro-Eurasia. The localization of these compounds to young stems and
 roots, suggest a possible ecological relevance in herbivory defense. This
 is further supported by reduced immunomodulatory activity in the American
 subclade as well as herbivore distribution patterns. We conclude that
 computational mass spectrometric metabolomics coupled with relevant
 ecological data provide a strong tool for exploring plant specialized
 metabolite diversity in a chemo-evolutionary framework.
description: Euphorbia Bayesian
 phylogenetic tree50% majority rule
 consensus tree from Bayesian analysis of 11587 bps of DNA markers spanning
 all three plant genomes: chloroplast, mitochondrial,
 nuclear.EuphorbiaMBPF15_HornSet.con.tre
DOI: 10.5061/dryad.n53sh18
title: Data from: Fish assemblage convergence along stream environmental gradients: an intercontinental analysis

description: Species that pass through similar environmental filters, regardless of
 geographic proximity or evolutionary history, are expected to share many
 traits, resulting in similar assemblage trait distributions. Convergence
 of assemblage trait distributions among different biotic regions would
 indicate that consistent ecological processes produce repeated patterns of
 adaptive evolution. This study analyzes trait-environment relationships
 across multiple stream fish assemblages representing evolutionarily
 divergent faunas. We hypothesized that trait-environment patterns converge
 across regional faunas in response to a common set of environmental
 filters acting on functional traits. One hundred and ninety-seven species
 and forty streams were sampled from five regions: Belize, Benin, Brazil,
 Cambodia, and United States of America. By examining trait-environment
 plots, multiple congruent trait-environment patterns were found across all
 regions, indicative of a consistent set of environmental filters acting on
 local community assembly. The consistency of these patterns strongly
 suggests that water velocity and habitat structural complexity function as
 universal environmental filters, producing similar assemblage trait
 distributions in streams across all regions. Bivariate relationships were
 not universal, and only one of the associations between a single
 functional trait and single environmental variable was statistically
 significant across all five regions. Strong phylogenetic signal was found
 in traits and habitat use, which implies that niche conservatism also
 influenced assemblage trait distributions. Overall, results support the
 idea that habitat templates structure trait distributions of stream fish
 assemblages and do so in a consistent manner.
description: Species
 abundance-traits-habitat dataThe standardized
 morphological traits, abundance, and microhabitat data for all species
 collected. Field number and location provided.Data_traits_species_enviro.xlsx
DOI: 10.5061/dryad.5172532
title: Data from: Integrated genome-scale analysis identifies novel genes and networks underlying senescence in maize

description: Premature senescence in annual crops reduces yield while delayed
 senescence, termed stay-green, is known to impose both positive and
 negative impact on yield and nutrition quality. Despite the importance,
 scant information is available on the genetic architecture of senescence
 in maize (Zea mays L.) and other cereals. We combined a systematic
 characterization of natural diversity for senescence in maize and
 co-expression networks derived from transcriptome analysis of normally
 senescing and stay-green lines. Sixty-four candidate genes were identified
 by GWAS, and 14 of these are supported by additional evidence for
 involvement in senescence-related processes including proteolysis, sugar
 transport and signaling, and sink activity. Eight of the GWAS candidates,
 independently supported by a co-expression network underlying stay-green,
 include a trehalose-6-phosphate synthase, a NAC transcription factor, and
 two xylan biosynthetic enzymes. Source-sink communication and the activity
 of cell walls as a secondary sink emerge as key determinants of
 stay-green. Mutant analysis supports the role of a candidate encoding
 cysteine protease in stay-green in Arabidopsis (Arabidopsis thaliana), and
 analysis of natural alleles suggest a similar role in maize. This study
 provides a foundation for enhanced understanding and manipulation of
 senescence for increasing carbon yield, nutritional quality, and stress
 tolerance of maize and other cereals.
description: Cysteine_protease_Newick
 ExportPhylogeny prepared by
 MEGA7Cysteine_protease_alignmentThe sequence alignment prepared in MEGA7 with default settings.
DOI: 10.15468/dl.gxzs77
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation)",
 "Country is Chile",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Leopardus jacobitus"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001794-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rn2j5p0
title: Data from: Industrial bees: the impact of apicultural intensification on local disease prevalence

description: 1) Although it is generally thought that the intensification of farming
 will result in higher disease prevalences there is little specific
 modelling testing this idea. We test this in honeybees by building
 multi-colony models to inform how ‘apicultural intensification’ is
 predicted to impact honeybee pathogen epidemiology at the apiary scale. 2)
 Counter to the prevailing view, our agent-based and analytical models
 predict that intensification, captured though increased population sizes,
 changes in population network structure, and increased between-colony
 transmission, is likely to have little effect on disease prevalence within
 an apiary. Principally this is because even low-intensity apiculture
 exhibits high disease prevalence. 3) The greatest impacts of apicultural
 intensification are found for diseases with relatively low R0 (basic
 reproduction number), however, such diseases cause little overall disease
 prevalence and therefore the impacts of intensification are minor.
 Furthermore, the smallest impacts of intensification are for diseases with
 high R0 values, which we argue are typical of important honeybee diseases.
 4) Policy Implications: Our findings contradict the hypothesis that
 apicultural intensification leads to notably higher disease prevalences
 for established honeybee pathogens with high R0 values. More broadly, our
 work demonstrates the need for informative models of agricultural systems
 and management practices in order to understand the implications of
 management changes on diseases.
description: ABM Simulation Code
 Bartlett and Rozins et al 2019Annotated R script
 documentation implementation of agent-based model of pathogen spread
 across apiaries, as described in 'Industrial bees: the impact of
 apicultural intensification on local disease prevalence' Bartlett,
 Rozins et al. 2019. Journal of Applied Ecology. Note this only includes
 the implementation of the simulation code - downstream output file reading
 and analysis not provided.
DOI: 10.15468/dl.g88m2j
title: Occurrence Download

description: A dataset containing 29849 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Maclura pomifera"
 ]
}

 The dataset includes 29849 records from 380 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001792-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dm0rq60
title: Data from: Forest amount, not structure, influences fruit removal of two pioneer species in Atlantic forest remnants

description: Fruit removal is a key component of the seed dispersal process with direct
 consequences for plant recruitment. Anthropogenic disturbances might
 affect removal rates by changing frugivore diversity and their behavior.
 Here, we investigated the effects of local forest structure and landscape
 context on fruit removal of two common, pioneer species of Melastomataceae
 family, Clidemia capitellata and Henriettea succosa in 14 Atlantic forest
 sites. We evaluated local forest structure, measured as canopy openness
 and conspecific density, and the amount of forest cover at the landscape
 scale measured in 2000m buffer radius. Our results showed that the
 landscape context was more important than local features to explain fruit
 removal. The percentage of fruits removed from both species sharply
 decreases with forest loss and increases again in highly deforested
 landscapes. We demonstrate changes in fruit removal due to forest loss and
 suggest that both Melastomaceae species rely on the absence of other plant
 species, and consequently, in a less competitive environment to increase
 fruit removal and seed dispersal.
description: Cazetta_removalInformation about fruit removal of two Melastomataceae species (Clidemia capitellata and Henriettea succosa) collected in 14 Atlantic forest sites in Bahia, Brazil. Additionally, information on local forest structure, measured as canopy openness and conspecific density were collected in the field. Forest cover amount in 2000m buffer radius was obtained from each forest site using ArcGIS
DOI: 10.5061/dryad.n3p5086
title: Data from: Centromere satellite repeats have undergone rapid changes in polyploid wheat subgenomes

description: Centromeres mediate the pairing of homologous chromosomes during meiosis;
 this pairing is particularly challenging for polyploid plants such as
 hexaploid wheat (Triticum aestivum), as their meiotic machinery must
 differentiate homologs from similar homoeologs. However, the sequence
 compositions (especially functional centromeric satellites) and
 evolutionary history of wheat centromeres are largely unknown. Here, we
 mapped T. aestivum centromeres by chromatin immunoprecipitation sequencing
 using antibodies to the centromeric-specific histone CENH3; this
 identified two types of functional centromeric satellites that are
 abundant in two of the three subgenomes. These centromeric satellites had
 unit sizes over 500 bp and contained specific sites with highly phased
 binding to CENH3 nucleosomes. Phylogenetic analysis revealed that the
 satellites have diverged in the three T. aestivum subgenomes, and the more
 homogeneous satellite arrays are associated with CENH3. Satellite signals
 decreased and the degree of satellites variation increased from diploid to
 hexaploid wheat. Moreover, several T. aestivum centromeres lack satellite
 repeats. Rearrangements, including local expansion and satellite
 variations, inversions, and changes in gene expression, occurred during
 the evolution from diploid to tetraploid and hexaploid wheat. These
 results reveal the asymmetry in centromere organization among the wheat
 subgenomes, which may play a role in proper homolog pairing during
 meiosis.
description: CL247_CS_cd-hit_cluster_merge_length550All the individual CentT566 repeats were extracted based on BLAST output for each subgenome in wheat. The cd-hit-est software was used to cluster similar CentT566 sequences into clusters using parameters “-c 0.90 -n 10” within each subgenome. The clusters with length larger than 500 bp were used for further analysis. Multiple sequence alignment and phylogenetic analysis of all CentT566 clusters were performed with ClustalW and MEGA7 software using the neighbor-joining method.
DOI: 10.5061/dryad.303jg54
title: Data from: Coping with multiple enemies: pairwise interactions do not predict evolutionary change in complex multitrophic communities

description: Predicting the ecological and evolutionary trajectories of populations in
 multispecies communities is one of the fundamental challenges in ecology.
 Many of these predictions are made by scaling patterns observed from
 pairwise interactions. Here, we show that the coupling of ecological and
 evolutionary outcomes is likely to be weaker in increasingly complex
 communities due to greater chance of life-history trait correlations.
 Using model microbial communities comprising a focal bacterial species
 (Bacillus subtilis), a bacterial competitor, protist predator and phage
 parasite, we found that increasing the number of enemies in a community
 had an overall negative effect on B. subtilis population growth. However,
 only the competitor imposed direct selection for B. subtilis trait
 evolution in pairwise cultures and this effect was weakened in the
 presence of other antagonists that had a negative effect on the
 competitor. In contrast, adaptation to parasites was driven indirectly by
 correlated selection where competitors had a positive and predators a
 negative effect. For all measured traits, selection in pairwise
 communities was a poor predictor of B. subtilis evolution in more complex
 communities. Together, our results suggest that coupling of ecological and
 evolutionary outcomes is interaction-specific and weakly coupled in more
 complex communities. We conclude that understanding the ecological and
 evolutionary mechanisms underpinning trait correlations is crucial to
 predict species response to global change in complex microbial
 communities.
description: McClean_community
 data_ESMMcClean_growth analysis
 data_ESMMcClean_resistance
 data_ESM