cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7fk21
title: Data from: Social plasticity in choosiness in green tree frogs, Hyla cinerea

description: Mate choice is an important driver of the evolution of sexual traits and
 can promote divergence and speciation. Understanding the underlying
 variation in mate choice decisions is crucial to understand variation in
 the strength and direction of sexual selection. We explored whether
 variation in the social environment influences mate choice decisions and
 focus on the aspect of mate choice termed choosiness (i.e. the effort
 invested in mate assessment and acquisition). Using call playbacks, we
 manipulated the social environment female green tree frogs would
 experience as they entered a chorus, and then we conducted two-choice
 playback trials to assess whether females exhibited social plasticity in
 choosiness. We explored social plasticity at 2 levels: in one experiment,
 we manipulated the presence or absence of preferred (attractive) and less
 preferred (unattractive) conspecific males (i.e. intraspecific context),
 and in the other experiment, we manipulated the presence or absence of
 preferred (conspecific) and less preferred closely related heterospecific
 males (i.e. interspecific context). We found that in the intraspecific
 context, the presence of attractive males increased choosiness, while
 absence of attractive males reduced choosiness. In the interspecific
 context, choosiness remained stable in most treatments, but was lowered
 when females experienced a mixture of conspecific and heterospecific
 calls. We discuss the effect of social plasticity in choosiness on mate
 choice decisions and highlight its evolutionary consequences.
description: Neelon_Hoebel All Data
 for BehavEcolExcel file containing
 all data used for figures and statistical analysis.
DOI: 10.5061/dryad.2qp305p
title: Data from: A probabilistic metric for the validation of computational models

description: A new validation metric is proposed that combines the use of a threshold
 based on the uncertainty in the measurement data with a normalised
 relative error, and that is robust in the presence of large variations in
 the data. The outcome from the metric is the probability that a
 model's predictions are representative of the real world based on the
 specific conditions and confidence level pertaining to the experiment from
 which the measurements were acquired. Relative error metrics are
 traditionally designed for use with series of data values but orthogonal
 decomposition has been employed to reduce the dimensionality of data
 matrices to feature vectors so that the metric can be applied to fields of
 data. Three previously published case studies are employed to demonstrate
 the efficacy of this quantitative approach to the validation process in
 the discipline of structural analysis, for which historical data was
 available; however, the concept could be applied to a wide range of
 disciplines and sectors where modelling and simulation plays a pivotal
 role.
description: ValidationMetricmatlab functionCS_rubber_blockfeature vectors describing data fields for case study 2 (rubber block)CS_ibeamfeature vectors representing data fields in case study 1(i-beam)CS_bonnetfeature vectors describing data in case study 3 (bonne liner)
DOI: 10.5061/dryad.4b565
title: Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees

description: 1.Declining populations of bee pollinators are a cause of concern, with
 major repercussions for biodiversity loss and food security. RNA viruses
 associated with honeybees represent a potential threat to other insect
 pollinators, but the extent of this threat is poorly understood. 2.This
 study aims to attain a detailed understanding of the current and on going
 risk of emerging infectious disease (EID) transmission between managed and
 wild pollinator species across a wide range of RNA viruses. 3.Within a
 structured large-scale national survey across 26 independent sites, we
 quantify the prevalence and pathogen loads of multiple RNA viruses in
 co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus
 spp.) populations. We then construct models that compare virus prevalence
 between wild and managed pollinators. 4.Multiple RNA viruses associated
 with honeybees are widespread in sympatric wild bumblebee populations.
 Virus prevalence in honeybees is a significant predictor of virus
 prevalence in bumblebees, but we remain cautious in speculating over the
 principle direction of pathogen transmission. We demonstrate
 species-specific differences in prevalence, indicating significant
 variation in disease susceptibility or resilience. Pathogen loads within
 individual bumblebees may be high and in the case of at least one RNA
 virus, prevalence is higher in wild bumblebees than in managed honeybee
 populations. 5.Our findings indicate widespread transmission of RNA
 viruses between managed and wild bee pollinators, pointing to an
 interconnected network of potential disease pressures within and between
 pollinator species. In the context of the biodiversity crisis, our study
 emphasizes the importance of targeting a wide range of pathogens and
 defining host associations when considering potential drivers of
 population decline.
description: GLMM and GLM
 modelsIncludes raw MLPA data
 files, R scripts and outputMLPA.zipSequences and treesTree files in newick format for BQCV and SBPV; raw cloned sequences in fasta format for BQCV, SBPV and ABPVMisc statisticsR code script and data for true prevalence estimates, tests of proportions and kolmogorov-smirnov testsTrue Prev-KS tests-proportion tests-Co-infection ChiSq.RqPCRCt values for qPCR data
DOI: 10.5061/dryad.nr716
title: Data from: High-throughput genotyping of Anopheles mosquitoes using intact legs by Agena Biosciences iPLEX

description: Recent developments in genotyping technologies coupled with the growing
 desire to characterise genome variation in Anopheles populations opens the
 opportunity to develop more effective genotyping strategies for
 high-throughput screening. A major bottleneck of this goal is nucleic acid
 extraction. Here, we examined the feasibility of using intact portions of
 a mosquito's leg as sources of template DNA for whole genome
 amplification (WGA) by Primer-Extension Pre-amplification. We used the
 Agena Biosciences MassARRAY platform (formerly Sequenom) to genotype 78
 SNPs for 265 WGA leg samples. We performed nucleic acid extraction on 36
 mosquito carcasses and compared the genotype call concordance with their
 corresponding legs, and observed full concordance. Using three legs
 instead of one improved genotyping success rates (96% versus 89%,
 respectively), although this difference was not significant. We provide a
 proof of concept that WGA reactions can be performed directly on mosquito
 legs, thereby eliminating the need to extract nucleic acid. This approach
 is straightforward, sensitive and allows both species determination and
 genotyping of Anopheles mosquitoes to be performed in a high-throughput
 manner. Our protocol also leaves the mosquito body intact facilitating
 other experimental analysis to be undertaken on the same sample. Based on
 our findings, this method would also be suitable for use with other insect
 species.
description: SNPdataThis spreadsheet contains the genomic data used to demonstrate the feasability of using intact portions of a mosquito's leg as sources of template DNA for whole genome amplifcation. The "Data" tab contains sample and genotype information on 292 Anopheles gambiae sensu latu samples collected in Uganda.File S1 (1).xlsx
DOI: 10.5061/dryad.16g74
title: Data from: Severe inbreeding depression and no evidence of purging in an extremely inbred wild species - the Chatham Island black robin

description: Although evidence of inbreeding depression in wild populations is well
 established, the impact of genetic purging in the wild remains
 controversial. The contrasting effects of inbreeding depression, fixation
 of deleterious alleles by genetic drift and the purging of deleterious
 alleles via natural selection mean that predicting fitness outcomes in
 populations subjected to prolonged bottlenecks is not straightforward. We
 report results from a long-term pedigree study of arguably the
 world's most inbred wild species of bird: the Chatham Island black
 robin Petroica traversi, in which conditions were ideal for purging to
 occur. Contrary to expectations, black robins showed a strong, negative
 relationship between inbreeding and juvenile survival, yielding lethal
 equivalents (2B) of 6.85. We also determined that the negative
 relationship between inbreeding and survival did not appear to be mediated
 by levels of ancestral inbreeding and may be attributed in part to
 un-purged lethal recessives. Although the black robin demographic history
 provided ideal conditions for genetic purging, our results show no clear
 evidence of purging in the major life-history trait of juvenile survival.
 Our results also show no evidence of fixation of deleterious alleles in
 juvenile survival, but do confirm that continued high levels of
 contemporary inbreeding in a historically inbred population could lead to
 additional severe inbreeding depression.
description: DatasheetAContains pairwise predictor variables, and fledging rate response variable, for analyses presented in Table 1; Table 2; Figure 2; Supplementary Figure 1; Supplementary Table 1; Supplementary Table 2; Supplementary Table 3. For the code used to generate Fa and ll estimates from the pedigree (DatasheetC), see Supplementary R code 1 and 2, published with the manuscript. Under the "Site" variable: "TPB" = Top Bush, "MGR" - Mangere, "WSB" = Woolshed Bush.DatasheetBContains inbreeding (F) and census (N) data per year, over three sites, used to generate Figure 1.DatasheetCContains pedigree of animals included in this study, plus ll estimates for each individual, used to generate Supplementary Figure 2. Missing data = "NA".DatasheetDContains fledging data for all pairs from 1990 onwards, used to generate Supplementary Figure 3.
DOI: 10.5061/dryad.rk37b
title: Data from: Transient negative biochar effects on plant growth are strongest after microbial species loss

description: Biochar has been explored as an organic amendment to improve soil quality
 and benefit plant growth. The overall positive effects of biochar on crop
 yields are generally attributed to abiotic changes, while the alternative
 causal pathway via changes in soil biota is unexplored. We compared plant
 growth effects of legumes in sterile soil inoculated with dilutions of
 soil and soil microbial suspensions to determine the direct effects of
 biochar-induced changes in soil biota on plant growth. Suspensions and
 soil were from soil amended with biochar and soil without biochar. By
 comparing consecutive plant growth phases on the same inoculated soils, we
 also determined the temporal effects of soil biota from biochar-amended
 and control soils. Biota from biochar-amended soil was less beneficial for
 Medicago sativa growth, especially with small amounts of inocula.
 Flowering was delayed in the presence of biota from biochar plots.
 Inoculum with either soil or soil suspension gave similar results for
 plant biomass, indicating that microorganisms play a major role. Vicia
 villosa growth did not respond to the various inocula, even though the
 inoculum quantity strongly affected nematode community composition and
 protozoan abundance. In a later growing phase the negative effect of
 biochar-associated biota on Medicago growth mostly disappeared, which
 leads to the conclusion that the benefits of biochar application via
 abiotic changes may outweigh the negative effects of biochar on soil
 biota.
description: Biochar_dilution_exp_plantbiomass_nematodes_and_protozoaThis excel file contains data from an experiment started July 2011. A paper describing the conclusions from the data is published in Soil Biology and Biochemistry. Basically three times autoclaved soil from Mossel (Ede, NL) is inoculated with soil inoculum or a suspension. The inoculum comes from the Biochar experiment, from treatments control and Biochar600, 6 blocks for each Soil inoculum is applied in 3 densities: 10% live inoculum, 1% and 0,1 % with a total volume of 600 g fw soil/pot Suspensions are made in similar densities, but sieved over 45 um and thus should only contain microbes Non-inoculated control pots are added (6 replicates per block, 36 in total) This dataset contains data from 3 consequtive experiments, presented in one worksheet Dry weight of the soil at the start of the experiment is presented in a separate worksheetmasterdata_Biochar_dilution.xlsx
DOI: 10.5281/zenodo.18382602
title: De-identified dataset for Trends and Seasonality of Hospital-Onset Staphylococcus aureus and MRSA in Western Mexico (2016–2025): Time-Series Analysis at a University Referral Hospital

description: This Zenodo record provides the data and analytical materials supporting the manuscript: Time-Series Analysis of Staphylococcus aureus and MRSA Trends, Seasonality, and Pandemic-Associated Disruptions in a Tertiary-Care University Hospital (2016–2025). The dataset derives from routinely collected clinical microbiology laboratory records (June 2016–March 2025) and includes variables related to specimen source, hospital department, clinical syndrome classification, sex, and antimicrobial susceptibility testing results used to classify isolates as MRSA/MSSA. The analyses described in the manuscript (trend assessment, seasonality analyses, and interrupted time-series modeling around March 2020 and March 2022) were performed in R. Data were prepared to minimize re-identification risk: direct identifiers were removed and data are shared in de-identified form in accordance with ethical approval and institutional requirements.
DOI: 10.5281/zenodo.18382603
title: De-identified dataset for Trends and Seasonality of Hospital-Onset Staphylococcus aureus and MRSA in Western Mexico (2016–2025): Time-Series Analysis at a University Referral Hospital

description: This Zenodo record provides the data and analytical materials supporting the manuscript: Time-Series Analysis of Staphylococcus aureus and MRSA Trends, Seasonality, and Pandemic-Associated Disruptions in a Tertiary-Care University Hospital (2016–2025). The dataset derives from routinely collected clinical microbiology laboratory records (June 2016–March 2025) and includes variables related to specimen source, hospital department, clinical syndrome classification, sex, and antimicrobial susceptibility testing results used to classify isolates as MRSA/MSSA. The analyses described in the manuscript (trend assessment, seasonality analyses, and interrupted time-series modeling around March 2020 and March 2022) were performed in R. Data were prepared to minimize re-identification risk: direct identifiers were removed and data are shared in de-identified form in accordance with ethical approval and institutional requirements.
DOI: 10.5061/dryad.4tm3v
title: Data from: The effects of inbreeding, genetic dissimilarity and phenotype on male reproductive success in a dioecious plant

description: Pollen fate can strongly affect the genetic structure of populations with
 restricted gene flow and significant inbreeding risk. We established an
 experimental population of inbred and outbred Silene latifolia plants to
 evaluate the effects of (i) inbreeding depression, (ii) phenotypic
 variation and (iii) relatedness between mates on male fitness under
 natural pollination. Paternity analysis revealed that outbred males sired
 significantly more offspring than inbred males. Independently of the
 effects of inbreeding, male fitness depended on several male traits,
 including a sexually dimorphic (flower number) and a gametophytic trait
 (in vitro pollen germination rate). In addition, full-sib matings were
 less frequent than randomly expected. Thus, inbreeding, phenotype and
 genetic dissimilarity simultaneously affect male fitness in this
 animal-pollinated plant. While inbreeding depression might threaten
 population persistence, the deficiency of effective matings between sibs
 and the higher fitness of outbred males will reduce its occurrence and
 counter genetic erosion.
description: Phenotypic and genotypic
 data, as well as pedigree-based relatedness, of experimental plants
 exposed to naturally occurring pollinatorsData obtained in the
 greenhouse, experimental garden and laboratory by direct measurement.
 Relatedness inferred from pedigree data. Format: Excel file. Variable
 definition is provided in the accompanying Read Me
 file.Austerlitz_Silene_data.xlsx
DOI: 10.5061/dryad.16qg8
title: Data from: Adaptation of Escherichia coli to glucose promotes evolvability in lactose

description: The selective history of a population can influence its subsequent
 evolution, an effect known as historical contingency. We previously
 observed that five of six replicate populations that were evolved in a
 glucose-limited environment for 2,000 generations, then switched to
 lactose for 1,000 generations, had higher fitness increases in lactose
 than populations started directly from the ancestor. To test if selection
 in glucose systematically increased lactose evolvability, we started 12
 replay populations—six from a population subsample and six from a single
 randomly selected clone—from each of the six glucose-evolved founder
 populations. These replay populations and 18 ancestral populations were
 evolved for 1,000 generations in a lactose-limited environment. We found
 that replay populations were initially slightly less fit in lactose than
 the ancestor, but were more evolvable, in that they increased in fitness
 at a faster rate and to higher levels. This result indicates that
 evolution in the glucose environment resulted in genetic changes that
 increased the potential of genotypes to adapt to lactose. Genome
 sequencing identified four genes—iclR, nadR, spoT and rbs—that were
 mutated in most glucose-evolved clones and are candidates for mediating
 increased evolvability. Our results demonstrate short-term selective costs
 during selection in one environment can lead to changes in evolvability
 that confer longer-term benefits.
description: Fitness and mutation
 rate dataThe file contains data
 for all fitness assays and mutation rate assays.SubmittedData.xlsx
DOI: 10.5061/dryad.pc683
title: Data from: Development of genetic diversity, differentiation and structure over 500 years in four ponderosa pine populations

description: Population history plays an important role in shaping contemporary levels
 of genetic variation and geographic structure. This is especially true in
 small, isolated range-margin populations, where effects of inbreeding,
 genetic drift and gene flow may be more pronounced than in large
 continuous populations. Effects of landscape fragmentation and isolation
 distance may have implications for persistence of range-margin populations
 if they are demographic sinks. We studied four small, disjunct populations
 of ponderosa pine over a 500-year period. We coupled demographic data
 obtained through dendroecological methods with microsatellite data to
 discern how and when contemporary levels of allelic diversity, among and
 within-population levels of differentiation, and geographic structure,
 arose. Alleles accumulated rapidly following initial colonization,
 demonstrating proportionally high levels of gene flow into the
 populations. At population sizes of approximately 100 individuals, allele
 accumulation saturated. Levels of genetic differentiation among
 populations (FST and Jost's Dest) and diversity within populations
 (FIS) remained stable through time. There was no evidence of geographic
 genetic structure at any time in the populations' history.
 Proportionally, high gene flow in the early stages of population growth
 resulted in rapid accumulation of alleles and quickly created relatively
 homogenous genetic patterns among populations. Our study demonstrates that
 contemporary levels of genetic diversity were formed quickly and early in
 population development. How contemporary genetic diversity accumulates
 over time is a key facet of understanding population growth and
 development. This is especially relevant given the extent and speed at
 which species ranges are predicted to shift in the coming century.
description: Tree age, position and
 genotypeAges, geographic
 position, and genotype for all Pinus ponderosa individuals in study
 populationsMEC-12-1261_tree_genotypes_ages_ coords.pdf
DOI: 10.5061/dryad.r5q5v1p
title: Data from: Trade‐off between reproductive and anti‐competitor abilities in an insect–parasitic nematode–bacteria symbiosis

description: Mutualistic symbionts can provide diverse benefits to their hosts and
 often supply key trait variation for host adaptation. The bacterial
 symbionts of entomopathogenic nematodes play a crucial role in successful
 colonization of and reproduction in the insect host. Additionally, these
 symbionts can produce a diverse array of antimicrobial compounds to deter
 within‐host competitors. Natural isolates of the symbiont, Xenorhabdus
 bovienii, show considerable variation in their ability to target sympatric
 competitors via bacteriocins, which can inhibit the growth of sensitive
 Xenorhabdus strains. Both the bacteria and its nematode partner have been
 shown to benefit from bacteriocin production when within‐host competition
 with a sensitive competitor occurs. Despite this benefit, several isolates
 of Xenorhabdus do not inhibit sympatric strains. To understand how this
 variation in allelopathy could be maintained, we tested the hypothesis
 that inhibiting isolates face a reproductive cost in the absence of
 competition. We tested this hypothesis by examining the reproductive
 success of inhibiting and non‐inhibiting isolates coupled with their
 natural nematode host in a non‐competitive context. We found that
 nematodes carrying non‐inhibitors killed the insect host more rapidly and
 were more likely to successfully reproduce than nematodes carrying
 inhibitors. Lower reproductive success of inhibiting isolates was
 repeatable across nematode generations and across insect host species.
 However, no difference in insect mortality was observed between inhibiting
 and non‐inhibiting isolates when bacteria were injected into insects
 without their nematode partners. Our results indicate a trade‐off between
 the competitive and reproductive roles of symbionts, such that inhibiting
 isolates, which are better in the face of within‐host competition, pay a
 reproductive cost in the absence of competition. Furthermore, our results
 support the hypothesis that symbiont variation within populations can be
 maintained through context‐dependent fitness benefits conferred to their
 hosts. As such, our study offers novel insights into the selective forces
 maintaining variation within a single host–symbiont population and
 highlights the role of competition in mutualism evolution.
description: Data and SAS code for
 Figures 2 and 3First worksheet holds
 data, 2nd definitions, 3rd SAS codedataFig2and3.xlsxData and SAS code for Figure 4First worksheet holds data, 2nd definitions, 3rd SAS code used in paper.dataFig4.xlsxData and SAS code for Figure 5First worksheet holds data, 2nd definitions, 3rd SAS codedataFig5.xlsx