cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hk46g
title: Data from: Vertically transmitted symbiont reduces host fitness along temperature gradient

description: Parasites with exclusive vertical transmission from host parent to
 offspring are an evolutionary puzzle. With parasite fitness entirely
 linked to host reproduction, any fitness cost for infected hosts risks
 their selective elimination. Environmental conditions likely influence
 parasite impact, and thereby the success of purely vertical transmission
 strategies. We tested for temperature-dependent virulence of Caedibacter
 taeniospiralis, a vertically transmitted bacterial symbiont of the
 protozoan Paramecium tetraurelia. We compared growth of infected and cured
 host populations at five temperatures (16-32°C). Infection reduced host
 density at all temperatures, with a peak at 28°C. These patterns were
 largely consistent across five infected Paramecium strains. Similar to
 Wolbachia symbionts, C. taeniospiralis may compensate fitness costs by
 conferring to the host a 'killer trait', targeting uninfected
 competitors. Considerable loss of infection at 32°C suggests that killer
 efficacy is not universal and that limited heat tolerance restricts the
 conditions for persistence of C. taeniospiralis.
description: growth curve and
 carrying capacityDate set contains the
 data for growth curve and carrying capacity data for 5 strain identitis at
 5 temperatures in 3 replicatesData_set.txt
DOI: 10.5061/dryad.d632k
title: Data from: Maternal antibodies contribute to sex based difference in hantavirus transmission dynamics

description: Individuals often differ in their ability to transmit disease and
 identifying key individuals for transmission is a major issue in
 epidemiology. Male hosts are often thought to be more important than
 females for parasite transmission and persistence. However, the role of
 infectious females, particularly the transient immunity provided to
 offspring through maternal antibodies (MatAbs), has been neglected in
 discussions about sex-biased infection transmission. We examined the
 effect of host sex upon infection dynamics of zoonotic Puumala hantavirus
 (PUUV) in semi-natural, experimental populations of bank vole (Myodes
 glareolus). Populations were founded with either females or males that
 were infected with PUUV while the other sex was immunized against PUUV
 infection. The likelihood of the next generation being infected was lower
 when the infected founders were females, underlying the putative
 importance of adult males in PUUV transmission and persistence in host
 populations. However, we show that this effect likely results from
 transient immunity that infected females provide to their offspring,
 rather than any sex-biased transmission efficiency per se. Our study
 proposes a potential contrasting nature of female and male hosts in the
 transmission dynamics of hantaviruses.
description: Kallio et al_raw
 dataIndividual level data
 for 77 bank voles. Headings of the columns: Individual from 1 to 77, sex
 of the animal, f= female, m=males; PUUV serostatus in September, 0=
 seronegative, 1=seropositive; MatAb carrier in September, 0= no, 1=yes;
 PUUV infected = seropositive in November, 0=no, 1= yes, enclosure where
 the animal has been captured, MatAb prevalence in September = number of
 MatAb carriers/(Matab carriers+seronegative) in September, treatment
 FI=founder females infected, MI=founder males infected
DOI: 10.5061/dryad.s147c
title: Data from: Niche differentiation in the dynamics of host-symbiont interactions: symbiont prevalence as a coexistence problem

description: Heritable symbioses can have important ecological effects and have
 triggered important evolutionary innovations. Current predictions for
 long-term symbiont prevalence are based on their fitness benefits and
 vertical transmission rates but ignore non-linear competitive feedbacks
 among symbiotic and symbiont-free hosts. We hypothesized that such
 feedbacks function as stabilizing mechanisms, promoting coexistence of
 host types and maintaining intermediate symbiont frequency at the
 population scale. Using a model grass / endophyte symbiosis, we
 manipulated competition within and between endophyte-symbiotic (E+) and
 endophyte-free (E-) hosts and fit competition models to experimental data.
 We show for the first time that symbiont-structured competition can
 generate stable coexistence of E+ and E- hosts, even under perfect
 vertical transmission. Niche differentiation was the key to coexistence,
 causing hosts of each type to limit themselves more strongly than each
 other. These results establish roles for non-linear competitive dynamics
 and niche differentiation in the ecology and evolution of heritable
 symbionts.
description: Miller&Rudgers_Dryad_data_submission_18Nov2013
DOI: 10.5061/dryad.fk472
title: Data from: The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies

description: For nearly 100 years serotyping has been the gold standard for the
 identification of Salmonella serovars. Despite the increasing adoption of
 DNA-based subtyping approaches, serotype information remains a cornerstone
 in food safety and public health activities aimed at reducing the burden
 of salmonellosis. At the same time, recent advances in whole-genome
 sequencing (WGS) promise to revolutionize our ability to perform advanced
 pathogen characterization in support of improved source attribution and
 outbreak analysis. We present the Salmonella In Silico Typing Resource
 (SISTR), a bioinformatics platform for rapidly performing simultaneous in
 silico analyses for several leading subtyping methods on draft Salmonella
 genome assemblies. In addition to performing serovar prediction by
 genoserotyping, this resource integrates sequence-based typing analyses
 for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core
 genome MLST (cgMLST). We show how phylogenetic context from cgMLST
 analysis can supplement the genoserotyping analysis and increase the
 accuracy of in silico serovar prediction to over 94.6% on a dataset
 comprised of 4,188 finished genomes and WGS draft assemblies. In addition
 to allowing analysis of user-uploaded whole-genome assemblies, the SISTR
 platform incorporates a database comprising over 4,000 publicly available
 genomes, allowing users to place their isolates in a broader phylogenetic
 and epidemiological context. The resource incorporates several metadata
 driven visualizations to examine the phylogenetic, geospatial and temporal
 distribution of genome-sequenced isolates. As sequencing of Salmonella
 isolates at public health laboratories around the world becomes
 increasingly common, rapid in silico analysis of minimally processed draft
 genome assemblies provides a powerful approach for molecular epidemiology
 in support of public health investigations. Moreover, this type of
 integrated analysis using multiple sequence-based methods of sub-typing
 allows for continuity with historical serotyping data as we transition
 towards the increasing adoption of genomic analyses in epidemiology. The
 SISTR platform is freely available on the web at
 https://lfz.corefacility.ca/sistr-app/.
description: 4330 Salmonella genome
 assemblies7-Zip archive of 4330
 Salmonella genomes for validation of Salmonella In Silico Typing Resource
 (SISTR). Salmonella whole genome sequences used were obtained from the
 public repositories of WGS data at the National Center for Biotechnology
 Information (NCBI). These included fully assembled genomes from NCBI
 Assembly (http://www.ncbi.nlm.nih.gov/assembly/), and unassembled genomes
 downloaded from the NCBI SRA repository (http://www.ncbi.nlm.nih.gov/sra).
 Unassembled genomes were assembled using SPAdes
 (v3.1.1).SISTR-4330-fastas.7zcgMLST_3307-Zip archive of 330 cgMLST loci and multi-fasta files with existing alleles for each locus.
DOI: 10.5061/dryad.393n5
title: Data from: Experimental small-scale flower patches increase species density but not abundance of small urban bees

description: 1. Large flower plantings are often used to combat negative effects of
 habitat loss on pollinators, but whether these floral additions are
 effective at smaller scales remains unclear, particularly in urban
 settings. 2. To test the effectiveness of small-scale floral additions on
 enhancing urban bee populations, as well as their impact from one year to
 the next, different quantities of potted sweet alyssum (Lobularia
 maritima) flowers were placed across sites in Ann Arbor, Michigan for two
 consecutive years and the resulting Halictid bee visitors were monitored.
 3. Overall we found the number of flowers added at the local level was
 significantly and positively correlated with small Halictid bee abundance
 and species density in an urban landscape. At smaller flower quantities
 dynamics were clearly linear, where incremental increases in number of
 flowers showed significant increases in bee abundance and species density.
 At larger quantities of floral additions, however, dynamics were nonlinear
 in that incremental increases in flower quantity had no effect on bee
 abundance and highly variable effects on bee species density. 4. When
 comparing the change in small Halictid bee abundance and species density
 from one year to the next, we found a significant increase in bee species
 density in the second year of small-scale floral additions, but no
 significant difference in bee abundance. 5. Synthesis and applications.
 Our results show that small flower plantings can have positive effects on
 small bee communities in urban systems even over a short period of time,
 and therefore confirm that encouraging citizens to plant flowers can be an
 effective conservation strategy for certain urban pollinator populations.
 In addition, our finding that smaller flower plantings may have higher
 impacts on small pollinators than larger plantings suggests resource
 managers interested in pollinator conservation should consider spreading
 multiple, smaller floral plantings across the urban landscape, rather than
 pooling all resources into one large flower patch.29-Nov-2017
description: Simao_et_al_2018_DataData file contains complete data set from 2015 and 2016 field collections of bees, as well as floral and nesting landscape data.
DOI: 10.15468/dl.rmwvb5
title: Occurrence Download

description: A dataset containing 744 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Monotropastrum humile",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 744 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001384-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bv37v
title: Data from: Has snake fang evolution lost its bite? New insights from a structural mechanics viewpoint

description: Venomous snakes—the pinnacle of snake evolution—are characterized by their
 possession of venom-conducting fangs ranging from grooved phenotypes
 characterizing multiple lineages of rear-fanged taxa to tubular phenotypes
 present in elapids, viperids and atractaspidines. Despite extensive
 research, controversy still exists on the selective pressures involved in
 fang phenotype diversification. Here, we test the hypothesis that larger
 fangs and consequently a shift to an anterior position in the maxilla
 evolved to compensate for the costs of structural changes, i.e. higher
 stress upon impact in tubular fangs compared to grooved fangs. Direct
 voxel-based stress simulations conducted on high-resolution µCT scans,
 analysed within a phylogenetic framework, showed no differences in stress
 distribution between the three fang phenotypes, despite differences in
 (relative) fang length. These findings suggest that additional
 compensatory mechanisms are responsible for the biomechanical optimization
 and that fang length might instead be related to differential striking
 behaviour strategies.
description: Data for
 DryadAbsolute and relatives
 values for various morphological measurements and results from stress
 simulations.
DOI: 10.5061/dryad.f22m3
title: Data from: Observed fitness may affect niche overlap in competing species via selective social information use

description: Social information transmission is important because it enables horizontal
 spread of behaviors, not only between conspecifics, but also between
 individuals of different species. Because interspecific social information
 use is expected to take place among species with similar resource needs,
 it may have major consequences for the emergence of local adaptations,
 resource sharing and community organization. Social information use is
 expected to be selective, but the conditions promoting it in an
 interspecific context are not well known. Here, we experimentally test
 whether pied flycatchers (Ficedula hypoleuca) use the clutch size of great
 tits (Parus major) in determining the quality of the observed individual
 and use it as a basis in decision-making. We show that pied flycatchers
 (Ficedula hypoleuca) copied or rejected a novel nest-site feature
 preference of great tits (Parus major), experimentally manipulated to
 exhibit high or low fitness (clutch size), respectively. Our results
 demonstrate that the social transmission of behaviors across species can
 be highly selective in response to observed fitness, plausibly making the
 phenomenon adaptive. In contrast with the current theory of species
 coexistence, overlap between realized niches of species could dynamically
 increase or decrease depending on the observed success of surrounding
 individuals.
description: Data from the study
 'Observed fitness may affect niche overlap in competing species via
 selective social information use'Data is collected in the
 field. Abbreviations are explained in Sheet 1.Data.csv
DOI: 10.5061/dryad.bb3bm
title: Data from: Molecular phylogenetic evidence corroborates morphology but not chemistry in the Lepraria neglecta group

description: The Lepraria neglecta group is a distinctive entity within the sterile,
 asexually reproducing lichen genus Lepraria whose constituent populations
 are united by their occurrence in exposed habitats and the development of
 a pseudocortex on the granules of the thallus. Previous studies have
 concluded that the group represents a monophyletic entity; however the
 question of how to classify the chemical variability exhibited within the
 group has remained unresolved. A phylogeny was inferred from ITS1, 5.8S,
 and ITS2 sequence data generated from a geographically and chemically
 broad sampling of populations within the L. neglecta group. While the
 inferred phylogeny recovered the core L. neglecta group as a strongly
 supported and monophyletic, the chemotypes within L. neglecta s.l. (i.e.,
 the core-neglecta group excluding L. granulata) were not recovered as
 monophyletic and relationships within the group largely remain poorly
 resolved. Based on these results, a pragmatic circumscription for the
 group is proposed that emphasizes the strong correlation between
 morphological, ecological, and molecular characters over the lack of
 resolution between chemical and molecular characters. The names applied to
 members of the group are placed in synonymy with L. neglecta (these are L.
 alpina (basionym Crocynia alpina), L. alpina var. zeorinica, L.
 angardiana, L. borealis, L. caerulescens, L. caesioalba (basionym Crocynia
 caesioalba), L. caesioalba var. groenlandica, L. gelida, L. svalbardensis,
 and L. zonata). The results of these molecular phylogenetic analyses also
 1) did not support the distinction of L. salazinica from L. elobata, thus
 that name is placed in synonymy here, and 2) elucidated the occurrence of
 L. humida in North America.
description: neglecta_datasetsThis zipped folder includes the nucleotide alignments used in this study. 1) original alignment with exclusion set, 2) alignment for MP in NEXUS format including step matrices and INAASE recoded characters, 3) alignment for ML in PHYLLIP format and 4) alignment for BI in NEXUS format
DOI: 10.5061/dryad.g59r413
title: Data from: No trade-offs in interspecific interference ability and predation susceptibility in newt larvae

description: Coexistence of species with similar requirements is allowed, among others,
 through trade-offs between competitive ability and other ecological
 traits. Although interspecific competition is based on two mechanisms,
 exploitation of resources and physical interference, trade-off studies
 largely consider only species’ ability to exploit resources. Using a
 mesocosm experiment, we examined the trade-off between interference
 competition ability and susceptibility to predation in larvae of two newt
 species, Ichthyosaura alpestris and Lissotriton vulgaris. In the presence
 of heterospecifics, L. vulgaris larvae slowed somatic growth and
 developmental rates, and experienced a higher frequency of injuries than
 in conspecific environments which suggests asymmetrical interspecific
 interference. During short-term predation trials, L. vulgaris larvae
 suffered higher mortality than I. alpestris. Larvae of the smaller
 species, L. vulgaris, had both lower interference and antipredator
 performance than the larger I. alpestris, which suggests a lack of
 trade-off between interference competition ability and predator
 susceptibility. We conclude that interference competition may produce a
 positive rather than negative relationship with predation susceptibility,
 which may contribute to the elimination of subordinate species from common
 habitats.
description: Interspecific
 competition between larvae of two newt speciesThe influence of
 heterospecific interactions on initial total length (mean per tank), final
 total length, somatic growth rate, final developmental stage, proportion
 of injured individuals (damaged tail fins or missing limbs), and
 proportion survived in larvae of two newt species, Ichthyosaura alpestris
 and Lissotriton vulgaris.Hlouskova_et_al_competition.txtSusceptibility to predation in larvae of two newt speciesProportion of injured and killed individuals after 24 h exposure to a predator (dragonfly larva) in two newt species.Hlouskova_et_al_predation.txt
DOI: 10.5061/dryad.tv652
title: Data from: Shoot growth of woody trees and shrubs is predicted by maximum plant height and associated traits

description: 1. The rate of elongation and thickening of individual branches (shoots)
 varies across plant species. This variation is important for the outcome
 of competition and other plant-plant interactions. Here we compared rates
 of shoot growth across 44 species from tropical, warm temperate, and cool
 temperate forests of eastern Australia. 2. Shoot growth rate was found to
 correlate with a suite of traits including the potential height of the
 species, xylem-specific conductivity, leaf size, leaf area per xylem
 cross-section, twig diameter (at 40 cm length), wood density and modulus
 of elasticity. 3. Within this suite of traits, maximum plant height was
 the clearest correlate of growth rates, explaining 50 to 67% of the
 variation in growth overall (p &lt; 0.0001), and 23 to 32% of the
 variation (p &lt; 0.05) in growth when holding the influence of the
 other traits constant. Structural equation models suggest that traits
 associated with ‘hydraulics’, ‘biomechanics’, and the ‘leaf economics
 spectrum’ represent three clearly separated axes of variation, with the
 hydraulic axis exhibiting the strongest alignment with height and largest
 independent contribution to growth (in the case of branch thickening).
 However most of the capacity of these axes to predict growth was also
 associated with maximum height, presumably reflecting coordinated
 selection on multiple traits that together influence life histories. 4.
 Growth rates were not strongly correlated with leaf nitrogen or leaf mass
 per unit leaf area. 5. Correlations between growth and maximum height
 arose both across latitude (47%, p &lt; 0.0001) and from within-site
 differences between species (30%, p &lt; 0.0001). Covariation between
 growth and maximum height was driven in part by variation in irradiance
 across sites as well as among canopy positions within sites (23%, p
 &lt; 0.0001). A significant fraction of this shared variation was
 independent of irradiance (45%, p &lt; 0.0001), reflecting intrinsic
 differences across species and sites.
description: trait_data_Gleason_et_al_2017Leaf, stem, xylem, height, shoot growth data for 44 Australian woody dicotyledon species. Trait descriptions and units are given in the last column.trait_publish.csv
DOI: 10.5061/dryad.fd0qm
title: Data from: Monarch butterfly population decline in North America: identifying the threatening processes

description: The monarch butterfly (Danaus plexippus) population in North America has
 sharply declined over the last two decades. Despite rising concern over
 the monarch butterfly's status, no comprehensive study of the factors
 driving this decline has been conducted. Using partial least-squares
 regressions and time-series analysis, we investigated climatic and
 habitat-related factors influencing monarch population size from 1993 to
 2014. Potential threats included climatic factors, habitat loss (milkweed
 and overwinter forest), disease and agricultural insecticide use
 (neonicotinoids). While climatic factors, principally breeding season
 temperature, were important determinants of annual variation in abundance,
 our results indicated strong negative relationships between population
 size and habitat loss variables, principally glyphosate use, but also
 weaker negative effects from the loss of overwinter forest and breeding
 season use of neonicotinoids. Further declines in population size because
 of glyphosate application are not expected. Thus, if remaining threats to
 habitat are mitigated we expect climate-induced stochastic variation of
 the eastern migratory population of monarch butterfly around a relatively
 stationary population size.
description: Threats Associated with
 the Decline of Monarch ButterflyData are population size
 estimates for monarch butterflies overwintering in Mexico as well as 76
 potential stressors and 3 correlates. These stressors include disease,
 pesticide, herbicide, temperature, precipitation, and habitat loss
 measured for Mexican overwintering area and Southern, North Central, and
 Northeastern breeding areas. Data were collected to understand the broad
 array of potential stressors affecting monarch butterfly population
 dynamics.FullThreatsData.csv
DOI: 10.15468/dl.rgynu5
title: Occurrence Download

description: A dataset containing 3714 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euscelidius variegatus"
 ]
}

 The dataset includes 3714 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001385-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.