cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8754
title: Data from: A lectin-mediated resistance of higher fungi against predators and parasites

description: Fruiting body lectins are ubiquitous in higher fungi and characterized by
 being synthesized in the cytoplasm and up-regulated during sexual
 development. The function of these lectins is unclear. A lack of phenotype
 in sexual development upon inactivation of the respective genes argues
 against a function in this process. We tested a series of characterized
 fruiting body lectins from different fungi for toxicity towards the
 nematode Caenorhabditis elegans, the mosquito Aedes aegypti and the amoeba
 Acanthamoeba castellanii. Most of the fungal lectins were found to be
 toxic towards at least one of the three target organisms. By altering
 either the fungal lectin or the glycans of the target organisms, or by
 including soluble carbohydrate ligands as competitors, we demonstrate that
 the observed toxicity is dependent on the interaction between the fungal
 lectins and specific glycans in the target organisms. The toxicity was
 found to be dose-dependent such that low levels of lectin were no longer
 toxic but still led to food avoidance by C. elegans. Finally, we show, in
 an ecologically more relevant scenario, that challenging the vegetative
 mycelium of Coprinopsis cinerea with the fungal-feeding nematode
 Aphelenchus avenae induces the expression of the nematotoxic fruiting body
 lectins CGL1 and CGL2. Based on these findings, we propose that
 filamentous fungi possess an inducible resistance against predators and
 parasites mediated by lectins that are specific for glycans of these
 antagonists.
description: Toxicity and induction
 dataIncludes raw data of
 toxicity and induction experiments mentioned in the manuscript. For more
 information refer to the ReadMe file.Glycan array TAP1 and
 XCLContains raw data for
 the Glycan array analysis of the lectins TAP1 and XCL. Files are also
 available at the Consortium for Functional Glycomics (CFG)
 http://www.functionalglycomics.org/static/consortium/resources/resourcecoreh.shtml
DOI: 10.5061/dryad.r8k26cd
title: Data from: Improving estimates of environmental change using multilevel regression models of Ellenberg indicator values

description: Ellenberg indicator values (EIVs) are a widely used metric in plant
 ecology comprising a semi-quantitative description of species‘ ecological
 requirements. Typically, point estimates of mean EIV scores are compared
 to infer differences in the environmental conditions structuring plant
 communities – particularly in resurvey studies with no historical
 environmental data available. However, the use of point estimates as a
 basis for inference does not take into account variance among species EIVs
 within sampled plots, and gives equal weighting to means calculated from
 sites with differing numbers of species. We present a set of multilevel
 models – fitted with and without group-level predictors – to improve
 precision and accuracy of site mean EIV scores, and to provide more
 reliable inference on changing environmental conditions over spatial and
 temporal gradients in re-visitation studies. We compare multilevel model
 performance to GLMM’s fitted to point estimates of site mean EIVs. We also
 test the reliability of this method to improve inferences with incomplete
 species lists in some or all sample sites. Hierarchical modelling led to
 more accurate and precise estimates of site-level differences in mean EIV
 scores between time-periods, particularly for datasets with incomplete
 records of species occurrence. They also revealed directional
 environmental change within ecological habitat types, which estimates from
 GLMM’s were inadequate to detect. Multilevel models also highlighted a
 prominent role of hydrological differences as a driver of community change
 in our case study, which traditional use of EIVs failed to reveal. We have
 demonstrated that multilevel modelling of EIVs allows for a nuanced
 estimation of environmental change underlying ecological communities from
 plant assemblage data, leading to a better understanding of temporal
 dynamics of ecosystems. Further, the ability of these methods to perform
 well with missing data should increase the total set of historical data
 which can be used to this end.
description: Species_level_dataThis file contains data on species occurrences for vascular plant species recorded on the Studland peninsula in the 1930s and 2010s. The data was compiled by the National Trust with the aid of a large cohort of citizen scientists in a project named "The Cyril Diver Project" after the main data collector in the 1930s. The file consists of nine columns on: 1) The name of the sample plot a species was recorded in; 2) The numeric value assigned to specify that plot; 3) The scientific name of the plant species recorded; 4) The time period the species was recorded (0 = 1930s, 1 = 2010s); and 5-9) Ellenberg indicator values for L, F, R, N and S respectively.Plot_level_dataThis file contains information on the plots (or sampling compartments).
DOI: 10.5061/dryad.n872j
title: Data from: Fitness effects of thermoregulation in a thermally changing environment

description: To better understand the evolution of phenotypic plasticity and
 thermoregulation and their potential value for ectotherms in the face of
 global warming, we conducted field experiments to measure their effects on
 fitness and their association with reproductive phenology in Plantago
 lanceolata in a thermally variable environment. We measured the
 reproductive timing and success of genotypes varying in thermoregulation,
 as mediated by floral-reflectance plasticity. Results were consistent with
 the hypothesis that thermoregulation is more adaptive when thermally
 variable reproductive seasons are shorter and cooler. Strong
 thermoregulation/plasticity increased reproductive success during the cool
 portion of the reproductive season but not during the warm portion.
 Directional selection that favored strongly thermoregulating genotypes
 early in the season shifted to stabilizing selection that favored
 genotypes with weaker thermoregulation later in the season.
 Thermoregulation and reproductive phenology were negatively correlated.
 Although reproductive onset and duration were similar between genotypes,
 strong thermoregulators produced more and larger spikes (clutches) early;
 weak thermoregulators produced more spikes late. Results suggest that with
 atmospheric warming, the benefit of raising body temperature via
 thermoregulation when it is cool should decline in extant populations. The
 negative correlation between thermoregulation and phenology should
 accelerate the evolutionary shift toward thermoconformity, that is,
 reduced plasticity.
description: Lacey et al. - cum spike
 production csv2012Lacey et al. - cum seed
 production csv2012Lacey et al. - Spike
 size x position csv2012Lacey et al. - seed per
 spike data csv 2012
DOI: 10.5061/dryad.75jp4q7
title: Data from: Multiple infections, relatedness and virulence in the anther-smut fungus castrating Saponaria plants

description: Multiple infections (co-occurrence of multiple pathogen genotypes within
 an individual host) can have important impacts on diseases. Relatedness
 among pathogens can affect the likelihood of multiple infections and their
 consequences through kin selection. Previous studies on the castrating
 anther-smut fungus Microbotryum lychnidis-dioicae have shown that multiple
 infections occur in its host plant Silene latifolia. Relatedness was high
 among fungal genotypes within plants, which could result from competitive
 exclusion between unrelated fungal genotypes, from population structure or
 from interactions between plant and fungal genotypes for infection
 ability. Here, we aimed at disentangling these hypotheses using M.
 saponariae and its host Saponaria officinalis, both experimentally
 tractable for these questions. By analysing populations using
 microsatellite markers, we also found frequent occurrence of multiple
 infections and high relatedness among strains within host plants.
 Infections resulting from experimental inoculations in the greenhouse also
 revealed high relatedness among strains coinfecting host plants, even in
 clonally-replicated plant genotypes, indicating that high relatedness
 within plants did not result merely from plant x fungus interactions or
 population structure. Furthermore, hyphal growth in vitro was affected by
 the presence of a competitor growing nearby and by its genetic similarity,
 although this latter effect was strain-dependent. Altogether, our results
 support the hypothesis that relatedness-dependent competitive exclusion
 occurs in Microbotryum fungi within plants. These micro-organisms can thus
 respond to competitors and to their level of relatedness.
description: Data_natural_populations_genotypes_structure_analyseGenotype data of fungal natural populations used for genetic structure analysis. Genotypes are based on microsatellite markers.Data_natural_populations_genotypes_relatedness_analyseGenotype data of fungal natural populations used for relatedness analysis. Genotypes are based on microsatellite markers.Data_greenhouse_genotypes_relatedness_analyseGenotype data of greenhouse fungal strains used for relatedness analysis. Genotypes based on micorsatellite markers.Data_greenhouse_virulence_probability_infectionVirulence data related to the probability of infection of single or mixture of fungal strains in the greenhouse experiment.Data_greenhouse_virulence_proportion_infected_stemsVirulence data related to the proportion of infected stems of single or mixture of fungal strains in the greenhouse experiment.Data_greenhouse_virulence_flowering_onsetVirulence data related to the flowering onset of plants infected by single or mixture of fungal strains in the greenhouse experiment.Data_greenhouse_virulence_number_sporesVirulence data related to the number of spores produced in plants infected by single or mixture of fungal strains in the greenhouse experiment.
DOI: 10.5061/dryad.9jq7j
title: Data from: Effects of environmental disturbance on phenotypic variation: an integrated assessment of canalization, developmental stability, modularity and allometry in lizard head shape

description: When populations experience suboptimal conditions, the mechanisms involved
 in the regulation of phenotypic variation can be challenged, resulting in
 increased phenotypic variance. This kind of disturbance can be diagnosed
 by using morphometric tools to study morphological patterns at different
 hierarchical levels and evaluate canalization, developmental stability,
 integration, modularity, and allometry. We assess the effect of
 urbanization on phenotypic variation in the common wall lizard (Podarcis
 muralis) by using geometric morphometrics to assess disturbance to head
 shape development. The head shapes of urban lizards were more variable and
 less symmetric, suggesting that urban living is more likely to disturb
 development. Head shape variation was congruent within and across
 individuals, which indicated that canalization and developmental stability
 are two related phenomena in these organisms. Furthermore, urban lizards
 exhibited smaller mean head sizes, divergent size-shape allometries, and
 increased deviation from within-group allometric lines. This suggests that
 mechanisms regulating head shape allometry may also be disrupted. The
 integrated evaluation of several measures of developmental instability at
 different hierarchical levels, which provided in this case congruent
 results, can be a powerful methodological guide for future studies, as it
 enhances the detection of environmental disturbances on phenotypic
 variation and aids biological interpretation of the results.
description: LandmarksThis is a tps file containing 2-d digitized landmarks of dorsal head view of 359 Podarcis muralis individuals. 28 landmarks were taken on each specimen. Landmark recording was repeated twice for each animal.P_muralis_asymmetry.TPSClassifier fileThis is a text file containing identifier variables associated with the individuals in the companion tps file.ID numbers corresponding to ID numbers in the tps file. Ind number refers to individual animals, Sex (M or F) indicates animal gender, Pop indicates location where the animals were collected, Type (U or R) indicates type of population, U stands for urban and R for rural population type. Landmark recording was repeated twice for each animal and is indicated by Image (1 or 2).classifier.txt
DOI: 10.5061/dryad.7cq0k
title: Data from: Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information

description: Criollo pig breeds are descendants from pigs brought to the American
 continent starting with Columbus second trip in 1493. Pigs currently play
 a key role in social economy and community cultural identity in Latin
 America. The aim of this study was to establish conservation priorities
 among a comprehensive group of Criollo pig breeds based on a set of 24
 microsatellite markers and using different criteria. Spain and Portugal
 pig breeds, wild boar populations of different European geographic origins
 and commercial pig breeds were included in the analysis as potential
 genetic influences in the development of Criollo pig breeds. Different
 methods, differing in the weight given to within- and between-breed
 genetic variability, were used in order to estimate the contribution of
 each breed to global genetic diversity. As expected, the partial
 contribution to total heterozygosity gave high priority to Criollo pig
 breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds.
 With the combined within- and between-breed approaches, different
 conservation priorities were achieved. The Core Set methodologies highly
 prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano
 and Cr. Guadalupe). However, weighing the between- and within-breed
 components with FST and 1-FST, respectively, resulted in higher
 contributions of Iberian breeds. In spite of the different conservation
 priorities according to the methodology used, other factors in addition to
 genetic information also need to be considered in conservation programmes,
 such as the economic, cultural or historical value of the breeds involved.
description: Breed Pig
 Genotypes1670 Individual
 genotypes, belonging to 45 pig breeds from the Iberian Peninsula (Spain
 and Portugal), Europe (local and commercial breeds), and America, for a
 panel of 24 microsatellitesDatos_Porcino_Dryad.xlsx
DOI: 10.5061/dryad.b2t42
title: Data from: Testing the optimal defense hypothesis in nature: variation for glucosinolate profiles within plants

description: Plants employ highly variable chemical defenses against a broad community
 of herbivores, which vary in their susceptibilities to specific compounds.
 Variation in chemical defenses within the plant has been found in many
 species; the ecological and evolutionary influences on this variation,
 however, are less well-understood. One central theory describing the
 allocation of defenses in the plant is the Optimal Defense Hypothesis
 (ODH), which predicts that defenses will be concentrated in tissues that
 are of high fitness value to the plant. Although the ODH has been
 repeatedly supported within vegetative tissues, few studies have compared
 vegetative and reproductive tissues, and the results have not been
 conclusive. We quantified variation in glucosinolate profile and tissue
 value between vegetative and reproductive tissues in Boechera stricta, a
 close relative of Arabidopsis. B. stricta manufactures glucosinolates, a
 set of defensive compounds that vary genetically and are straightforward
 to quantify. Genetic diversity in glucosinolate profile has been
 previously demonstrated to be important to both herbivory and fitness in
 B. stricta; however, the importance of glucosinolate variation among
 tissues has not. Here, we investigate whether allocation of glucosinolates
 within the plant is consistent with the ODH. We used both clipping
 experiments on endogenous plants and ambient herbivory in a large-scale
 transplant experiment at three sites to quantify fitness effects of loss
 of rosette leaves, cauline leaves, and flowers and fruits. We measured
 glucosinolate concentration in leaves and fruits in the transplant
 experiment, and asked whether more valuable tissues were more defended. We
 also investigated within-plant variation in other aspects of the
 glucosinolate profile. Our results indicated that damage to fruits had a
 significantly larger effect on overall fitness than damage to leaves, and
 that fruits had much higher concentrations of glucosinolates, supporting
 the ODH. This is, to the best of our knowledge, the first study to
 explicitly compare both tissue value and chemical defense concentrations
 between vegetative and reproductive tissues under natural conditions.
description: Glucosinolate
 dataA
 spreadsheet with glucosinolate data for individual samples, identified by
 genotype, subspecies, site, and tissue.GSvar_dryad.xlsxAmbient Herbivory datasetA spreadsheet of individuals in three common gardens, showing levels of ambient herbivory on three tissues and fruit number for each individual.ambientherb_dryad.xlsxGlucosinolates and herbivoryA spreadsheet of family ls means for glucosinolate traits and herbivore damage on three tissues.GS_herb_dryad.xlsxClipping datasetA spreadsheet of data for endogenous plants, indicating which treatment plants were assigned (which tissue was removed) and fruit number.Clipping_dryad.xlsx
DOI: 10.5061/dryad.vr28vf67
title: Data from: Tempo of trophic evolution and its impact on mammalian diversification

description: Mammals are characterized by the complex adaptations of their dentition,
 which are an indication that diet has played a critical role in their
 evolutionary history. Although much attention has focused on diet and the
 adaptations of specific taxa, the role of diet in large-scale
 diversification patterns remains unresolved. Contradictory hypotheses have
 been proposed, making prediction of the expected relationship difficult.
 We show that net diversification rate (the cumulative effect of speciation
 and extinction), differs significantly among living mammals, depending
 upon trophic strategy. Herbivores diversify fastest, carnivores are
 intermediate, and omnivores are slowest. The tempo of transitions between
 the trophic strategies is also highly biased: the fastest rates occur into
 omnivory from herbivory and carnivory and the lowest transition rates are
 between herbivory and carnivory. Extant herbivore and carnivore diversity
 arose primarily through diversification within lineages, whereas omnivore
 diversity evolved by transitions into the strategy. The ability to
 specialize and subdivide the trophic niche allowed herbivores and
 carnivores to evolve greater diversity than omnivores.
description: DatasetA database of diets of mammalian species was constructed from published accounts drawn from primary research with data obtained through analysis of stomach or cheek pouch contents or the contents of food stores, direct behavioral observation, or fecal analysis. Please see the ReadMe file for further details.References for datasetThis contains a list of every reference used to create the dataset.omnivory_diet_refs.txt
DOI: 10.5061/dryad.kd8cj
title: Data from: Isocitrate lyase mediates broad antibiotic tolerance in Mycobacterium tuberculosis

description: Mycobacterium tuberculosis (Mtb) is a persistent intracellular pathogen
 intrinsically tolerant to most antibiotics. The specific factors which
 mediate this tolerance however remain incompletely defined. Here, we apply
 metabolomic profiling to discover a common set of metabolic changes
 associated with the activities of three clinically used TB drugs,
 isoniazid, rifampicin, and streptomycin. Despite targeting diverse
 cellular processes, all 3 drugs trigger activation of Mtb’s isocitrate
 lyases (ICLs), metabolic enzymes commonly assumed to be involved in
 replenishing of tricarboxylic acid (TCA) cycle intermediates. We further
 show that ICL-deficient Mtb strains are significantly more susceptible
 than wild type Mtb to all three antibiotics and that this susceptibility
 can be chemically rescued when Mtb is co-incubated with an anti-oxidant.
 These results identify a previously undescribed role for Mtb’s ICLs in
 antioxidant defense as a mechanism of antibiotic tolerance.
description: Supplementary Data
 1Metabolite abundance (as
 reported by ion intensities) relative to untreated vehicle controls (log2
 transformed).Suppl_data_1.xls
DOI: 10.5061/dryad.gd844
title: Data from: Contrasting genetic metrics and patterns among naturalized rainbow trout (Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture

description: Different pathways of propagation and dispersal of non-native species into
 new environments may have contrasting demographic and genetic impacts on
 established populations. Repeated introductions of rainbow trout
 (Oncorhynchus mykiss) to Chile in South America, initially through
 stocking and later through aquaculture escapes, provide a unique setting
 to contrast these two pathways. Using a panel of single nucleotide
 polymorphisms, we found contrasting genetic metrics and patterns among
 naturalized trout in Lake Llanquihue, Chile’s largest producer of salmonid
 smolts for nearly 50 years, and Lake Todos Los Santos (TLS), a reference
 lake where aquaculture has been prohibited by law. Trout from Lake
 Llanquihue showed higher genetic diversity, weaker genetic structure and
 larger estimates for the effective number of breeders (Nb) than trout from
 Lake TLS. Trout from Lake TLS were divergent from Lake Llanquihue, and
 showed marked genetic structure and a significant isolation-by-distance
 pattern consistent with secondary contact between documented and
 undocumented stocking events in opposite shores of the lake. Multiple
 factors, including differences in propagule pressure, origin of donor
 populations, lake geomorphology, and habitat quality or quantity, may
 concomitantly explain contrasting genetic metrics and patterns for trout
 between lakes. We also discussed violations of assumptions that may lead
 to overestimating Nb . We contend that high propagule pressure from
 aquaculture may not only increase genetic diversity and Nb via demographic
 effects and admixture, but also may impact the evolution of genetic
 structure and increase gene flow, consistent with findings from
 artificially propagated salmonid populations in their native and
 naturalized ranges.
description: Genotype Data for
 Naturalized Rainbow Trout from Lake LLanquihue and Lake Todos Los Santos
 (Lake District X Region - Chile)This dataset corresponds
 to multilocus genotypes for naturalized rainbow trout from Lake Llanquihue
 and Lake Todos Los Santos (Lake District, Chile) screened for 86 single
 nucleotide polymorphisms (coded A=1, C=2, G=3, T=4, Missing=0). Each
 allele (A1 or A2) is found in a separate column (two columns per SNP
 locus). Metadata for sampling location, Lake, Individual ID, Year, Season
 (austral winter or spring) are provided.Canales-Aguirre_etal_2017_Dryad.txt