cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.84vc24v
title: Data from: Quantifying temporal change in plant population attributes: insights from a resurrection approach

description: Rapid evolution in annual plants can be quantified by comparing phenotypic
 and genetic changes between past and contemporary individuals from the
 same populations over several generations. Such knowledge will help
 understand the response of plants to rapid environmental shifts, such as
 the ones imposed by global climate change. To that end, we undertook a
 resurrection approach in Spanish populations of the annual plant
 Arabidopsis thaliana that were sampled twice over a decade. Annual weather
 records were compared to their historical records to extract patterns of
 climatic shifts over time. We evaluated the differences between samplings
 in flowering time, a key life-history trait with adaptive significance,
 with a field experiment. We also estimated genetic diversity and
 differentiation based on neutral nuclear markers and nucleotide diversity
 in candidate flowering time (FRI and FLC) and seed dormancy (DOG1) genes.
 The role of genetic drift was estimated by computing effective population
 sizes with the temporal method. Overall, two climatic scenarios were
 detected: intense warming with increased precipitation and moderate
 warming with decreased precipitation. The average flowering time varied
 little between samplings. Instead, within-population variation in
 flowering time exhibited a decreasing trend over time. Substantial
 temporal changes in genetic diversity and differentiation were observed
 with both nuclear microsatellites and candidate genes in all populations,
 which were interpreted as the result of natural demographic fluctuations.
 We conclude that drought stress caused by moderate warming with decreased
 precipitation may have the potential to reduce within-population variation
 in key life-cycle traits, perhaps as a result of stabilising selection on
 them, and to constrain the genetic differentiation over time. Besides, the
 demographic behaviour of populations probably accounts for the substantial
 temporal patterns of genetic variation, while keeping rather constant
 those of phenotypic variation.
description: Arabidopsis_resurrection_13sep18Flowering time data, microsatellite data and weather data from Iberian Arabidopsis thaliana accessions included in the resurrection experiments.
DOI: 10.5061/dryad.v30kv
title: Data from: Impacts of regular and random noise on the behaviour, growth and development of larval Atlantic cod (Gadus morhua)

description: Anthropogenic noise impacts behaviour and physiology in many species, but
 responses could change with repeat exposures. As repeat exposures can vary
 in regularity, identifying regimes with less impact is important for
 regulation. We use a 16-day split-brood experiment to compare effects of
 regular and random acoustic noise (playbacks of recordings of ships),
 relative to ambient-noise controls, on behaviour, growth and development
 of larval Atlantic cod (Gadus morhua). Short-term noise caused startle
 responses in newly hatched fish, irrespective of rearing noise. Two days
 of both regular and random noise regimes reduced growth, while regular
 noise led to faster yolk sac use. After 16 days, growth in all three sound
 treatments converged, although fish exposed to regular noise had lower
 body width–length ratios. Larvae with lower body width–length ratios were
 easier to catch in a predator-avoidance experiment. Our results
 demonstrate that the timing of acoustic disturbances can impact
 survival-related measures during development. Much current work focuses on
 sound levels, but future studies should consider the role of noise
 regularity and its importance for noise management and mitigation
 measures.
description: Startles
 dataStartles_data_for_submission.xlsxYolk sac centroid sizeYolk_sac_centroid_size_for_submission.xlsxBody length results with figureBody_length_results_with_figure.xlsxBody width-length ratio results with figureBody_width-length_ratio_results_with_figure.xlsxTime to catch data with figureTime_to_catch_data_for_submission_with_figure.xlsx
DOI: 10.5061/dryad.3kt7fc2
title: Data from: Epidemiological relationship between Mycoplasma pneumoniae pneumonia and recurrent wheezing episode in children: an observational study at a single hospital in Korea

description: Objective: This study was aimed to evaluate epidemiological and clinical
 relationship between MP infection and childhood recurrent wheezing episode
 (RWE). Design: Retrospective case note review. Setting: Paediatric
 department at a single Korean institution. Participants: Consecutive
 admitted patients with MP pneumonia and RWE (0-15 years of age) between
 2003 and 2014. Methods: The retrospective medical records of patients with
 MP pneumonia (n=793 for epidemiological analysis and n=501 for clinical
 analysis) and those with RWE (n=384) from 2003 to 2014 were analyzed.
 Diagnosis of MP pneumonia was made based on 2-times titration of IgM
 antibody during hospitalization. An RWE patient was defined as one with
 expiratory wheezing with at least one or more wheezing episodes based on
 medical records. Results: During 3 MP pneumonia epidemics, there were no
 corresponding increases of patients with RWE in the epidemic years. In the
 501 MP pneumonia patients, 52 (10.4%) had wheezing at presentation and 15
 (3%) had RWE. The MP pneumonia patients with wheezing at presentation
 (n=52) were younger and were more likely to have an allergic disease
 history than those without wheezing (n=449). Among wheezing patients at
 presentation, 10 patients had previously RWE history. In a follow-up
 study, 13 patients (including 5 RWE) with initial wheezing and 25 patients
 (including 2 RWE) without wheezing had wheezy episodes after discharge.
 Among the total 501 patients, it was estimated that at least 31 MP
 pneumonia patients (6.2%) showed recurrent wheezing after initial MP
 infection. Conclusions: A small part of children with MP pneumonia showed
 recurrent wheezing after MP pneumonia, and patients with RWE had a greater
 likelihood of experiencing wheezing when they had an initial MP infection.
 However, there were no increased admitted patients with RWE in MP
 pneumonia epidemic periods because of rarity of MP reinfection in children
 including patients with RWE or asthma.
description: Data for MP and
 asthmaData of
 "Epidemiological relationship between Mycoplasma pneumoniae Pneumonia
 and recurrent wheezing episode in children"Data (LeeKY)
 2.xlsx
DOI: 10.5061/dryad.vt8t7
title: Data from: Recent admixture generates heterozygosity-fitness correlations during the range expansion of an invading species

description: Admixture, the mixing of historically isolated gene pools, can have
 immediate consequences for the genetic architecture of fitness traits.
 Admixture may be especially important for newly colonized populations,
 such as during range expansion and species invasions, by generating
 heterozygosity that can boost fitness through heterosis. Despite
 widespread evidence for admixture during species invasions, few studies
 have examined the demographic history leading to admixture, how admixture
 affects the heterozygosity and fitness of invasive genotypes, and whether
 such fitness effects are maintained through time. We address these
 questions using the invasive plant Silene vulgaris, which shows evidence
 of admixture in both its native Europe and in North America where it has
 invaded. Using multilocus genotype data in conjunction with approximate
 Bayesian computation analysis of demographic history, we showed that
 admixture during the invasion of North America was independent from and
 much younger than admixture in the native range of Europe. We tested for
 fitness consequences of admixture in each range and detected a significant
 positive heterozygosity–fitness correlation (HFC) in North America; in
 contrast, no HFC was present in Europe. The lack of HFC in Europe may
 reflect the longer time since admixture in the native range, dissipating
 associations between heterozygosity at markers and fitness loci. Our
 results support a key short-term role for admixture during the early
 stages of invasion by generating HFCs that carry populations past the
 threat of extinction from inbreeding and demographic stochasticity.
description: heterozygosity-fitness
 data for Silene vulgarisThese data provide
 sampling meta-data, genetic summary statistics (multi-locus heterozygosity
 and STRUCTURE Q-scores), and common garden fitness data for 163 families
 of Silene vulgaris collected from across Europe (native) and North America
 (introduced)Keller_etal_JEB2014_HFC_DRYAD.xlsxMicrosatellite genotypes from 15 loci for Silene vulgarisThese data are diploid microsatellite genotypes, in units of allele size (bp), for 15 co-dominant loci. Data are formatted as an input file for STRUCTURE, with missing values are coded as '-9'.Keller_etal_JEB2014_MICROSATS_STR.txtGenotype data for DIYABC analysis of demographic history for Silene vulgarisThese data provide sampling meta-data, microsatellite genotypes, and input file formatting for the DIYABC approximate Bayesian computation analysis. Two sheets are provided: sheet "data, K=2" provides the genotype data and accompanying metadata used to produce the input file for DIYABC; sheet "forDIYABC" provides the formatted input file for the DIYABC analysisKeller_etal_JEB2014_DIYABC_DRYAD.xlsxDIYABC reftable.header for ABC demographic analysis in Silene vulgarisThis file contains the metadata necessary to run approximate Bayesian computation in DIYABC for 2 historical demographic scenarios in Silene vulgaris.Keller_etal_JEB2014_DIYABC_reftable.header
DOI: 10.5061/dryad.bt29j
title: Data from: Contrasted invasion processes imprint the genetic structure of an invasive scale insect across southern Europe

description: Deciphering the colonization processes by which introduced pests invade
 new areas is essential to limit the risk of further expansion and/or
 multiple introductions. We here studied the invasion history of the
 maritime pine bast scale Matsucoccus feytaudi. This host-specific insect
 does not cause any damage in its native area, but it devastated maritime
 pine forests of South-Eastern France where it was detected in the 1960s,
 and since then reached Italy and Corsica. We used population genetic
 approaches to infer the populations’ recent evolutionary history from
 microsatellite markers and Approximate Bayesian Computation. Consistent
 with previous mitochondrial data, we showed that the native range is
 geographically strongly structured, which is probably due to the patchy
 distribution of the obligate host and the limited dispersal capacity of
 the scale. Our results show that the invasion history can be described in
 three successive steps involving different colonization and dispersal
 processes. During the mid-XXth century, massive introductions occurred
 from the Landes planted forest to South-Eastern France, probably due to
 transportation of infested wood material after World War II.
 Stepping-stone expansion, consistent with natural dispersal, then allowed
 M. feytaudi to reach the maritime pine forests of Liguria and Tuscany in
 Italy. The island of Corsica was accidentally colonized in the 1990s, and
 the most plausible scenario involves the introduction of a limited number
 of migrants from the forests of South-Eastern France and Liguria, which is
 consistent with an aerial dispersal due to the dominant winds that blow in
 spring in this region.
description: Kerdelhue2014_Heredity_MicrosatData_Dryad
DOI: 10.5061/dryad.1d3m8
title: Data from: Theoretical, thermodynamic and electrochemical analysis of Biotin drug as an impending corrosion inhibitor for mild steel in 15% HCl

description: The corrosion mitigation efficiency of Biotin drug for mild steel in 15%
 HCl was thoroughly investigated by weight loss and electrochemical
 methods. The surface morphology was studied by Contact angle, Scanning
 electrochemical microscopy (SECM), Atomic force microscope (AFM) and
 Scanning electron microscopy (SEM) methods. Quantum chemical calculation
 and Fukui analysis was done to correlate the experimental and theoretical
 data. The influence of concentration of inhibitor, immersion time,
 temperature, with activation energy, enthalpy and entropy has been
 reported. The mitigation efficiency of Biotin obtained by all methods was
 in good correlation with each other. Polarization studies revealed that
 Biotin acted as mixed inhibitor. The adsorption of Biotin was found to
 obey the Langmuir adsorption isotherm. Surface studies showed the
 hydrophobic nature of the steel with inhibitor and vindicated the
 formation of a film on the metal surface that reduced the corrosion rate.
description: Data used in the
 PaperThe file
 includes,concentration, time, temperature, Langmuir, Contact Angle, Lo CR
 and Log CR versus TData
 files.rar
DOI: 10.5061/dryad.7j8c5s5j
title: Data from: The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss

description: Reductive genomic evolution is common in endosymbiotic bacteria, where it
 is driven by genetic drift. Genome reduction is less common in free-living
 organisms, but it has occurred in the numerically dominant open-ocean
 bacterioplankton Prochlorococcus and Pelagibacter, and in these cases the
 reduction appears to be driven by natural selection rather than drift. The
 loss of certain genes in free-living organisms may leave them dependent on
 co-occurring microbes for the lost metabolic functions. We present the
 Black Queen Hypothesis (BQH), a novel theory of reductive evolution that
 explains how selection leads to such dependencies; its name refers to the
 queen of spades in the game Hearts, where the usual strategy is to avoid
 taking this card. Gene loss can provide a selective advantage by
 conserving an organism’s limiting resources, provided that the gene’s
 function is dispensable. Many vital genetic functions are leaky, thereby
 unavoidably producing public goods that are available to the entire
 community. Such leaky functions are thus dispensable for individuals,
 provided they are not lost entirely from the community. The BQH predicts
 that the loss of a costly, leaky function is selectively favored at the
 individual level and will proceed until the production of public goods is
 just sufficient to support the equilibrium community; at that point, the
 benefit of any further loss would be offset by the cost. Evolution in
 accordance with the BQH thus generates “beneficiaries” of reduced genomic
 content that are dependent on leaky “helpers,” and it may explain the
 observed non-universality of prototrophy, stress resistance, and other
 cellular functions in the microbial world.
description: Phylogenetic analysis of
 16S and catalase-peroxidase genes from CyanobacteriaBQH.zip
DOI: 10.5061/dryad.376jg
title: Data from: Environmental stress increases selection against and dominance of deleterious mutations in inbred families of the Pacific oyster Crassostrea gigas

description: The deleterious effects of inbreeding are well documented and of major
 concern in conservation biology. Stressful environments have generally
 been shown to increase inbreeding depression; however, little is known
 about the underlying genetic mechanisms of the inbreeding-by-stress
 interaction and to what extent the fitness of individual deleterious
 mutations is altered under stress. Using microsatellite marker segregation
 data and quantitative trait locus (QTL) mapping methods, I performed a
 genome scan for deleterious mutations affecting viability (viability or
 vQTL) in two, inbred families of the Pacific oyster Crassostrea gigas,
 reared in a stressful, nutrient-poor diet and a favorable, nutrient-rich
 diet, which had significant effects on growth and survival. Twice as many
 vQTL were detected in the stressful diet compared with the favorable diet,
 resulting primarily from substantially greater mortality of homozygous
 genotypes. At vQTL, estimates of selection (s) and dominance (h) were
 significantly greater in the stressful environment (s ̅ = 0.86 vs. 0.54
 and h ̅ = 0.35 vs. 0.18, in stressful and non-stressful diets,
 respectively). There was no evidence of interaction between vQTL.
 Individual vQTL differed across diets in selection only, or in both
 selection and dominance, and some vQTL were not affected by diet. These
 results suggest that stress-associated increases in selection against
 individual deleterious alleles underlie greater inbreeding depression with
 stress. Furthermore, the finding that inbreeding-by-environment
 interaction appears, to some extent, to be locus-specific, helps to
 explain previous observations of lineage-specific expression of inbreeding
 depression and environment-specific purging, which have important
 implications for conservation and evolutionary biology.
description: Microsatellite genotypes
 for Mol. Ecology environmental stress study in C. gigas
 5_23_12
DOI: 10.5061/dryad.tq106
title: Data from: How do organisational characteristics influence teamwork and service delivery in lung cancer diagnostic assessment programmes? A mixed-methods study

description: Objectives: Diagnostic assessment programs (DAPs) can reduce wait times
 for cancer diagnosis but optimal DAP design is unknown. This study
 explored how organizational characteristics influenced multidisciplinary
 teamwork and diagnostic service delivery in lung cancer DAPs. Design: A
 mixed methods approach integrated data from descriptive qualitative
 interviews and medical record abstraction at four lung cancer DAPs.
 Findings were analyzed with the Integrated Team Effectiveness Model.
 Setting: Four DAPs at two teaching and two community hospitals in Canada
 Participants: Twenty-two staff were interviewed about organizational
 characteristics, target service benchmarks, and teamwork processes,
 determinants and outcomes; 314 medical records were reviewed for actual
 service benchmarks. Results: Formal, informal and asynchronous team
 processes enabled service delivery and yielded many perceived benefits at
 the patient, staff and service levels. However, several DAP
 characteristics challenged teamwork and service delivery: referral
 volume/workload, time since launch, days per week of operation,
 rural-remote population, number and type of full-time/part-time human
 resources, staff co-location, information systems. As a result, all sites
 failed to meet target benchmarks (from referral to consultation median 4.0
 visits, median wait time 35.0 days). Recommendations included improved
 information systems, more staff in all specialties, staff co-location and
 expanded roles for patient navigators. Findings were captured in a
 conceptual framework of lung cancer DAP teamwork determinants and
 outcomes. Conclusions: This study identified several DAP characteristics
 that could be improved to facilitate teamwork and enhance service
 delivery, thereby contributing to knowledge of organizational determinants
 of teamwork and associated outcomes. Findings can be used to update
 existing DAP guidelines, and by managers to plan or evaluate lung cancer
 DAPs. Ongoing research is needed to identify ideal roles for navigators,
 and staffing models tailored to case volumes.
description: Lung-DAP-February3-2017This file contains data abstracted from medical records including: patient characteristics (age, gender), type of procedure that confirmed the diagnostic result (imaging with computed tomography of the chest; biopsy with fine needle aspiration, bronchoscopy or open biopsy; staging with positron emission tomography or magnetic resonance imaging); and results (positive for cancer, negative for cancer, still suspicious requiring follow-up). Recorded dates included: referral (month and week when referral form received by DAP), confirmatory procedure (month and week when confirmatory diagnostic procedure performed), diagnosis (month and week when finding was recorded in patient record), and consult (month and week of meeting with patient to discuss treatment or follow-up plan)
DOI: 10.5061/dryad.mq5qh
title: Data from: An informational diversity framework, illustrated with sexually deceptive orchids in early stages of speciation

description: Reconstructing evolutionary history for emerging species complexes is
 notoriously difficult, with newly isolated taxa often morphologically
 cryptic and the signature of reproductive isolation often restricted to a
 few genes. Evidence from multiple loci and genomes is highly desirable,
 but multiple inputs require ‘common currency’ translation. Here we deploy
 a Shannon information framework, converting into diversity analogue, which
 provides a common currency analysis for maternally inherited haploid and
 bi-parentally inherited diploid nuclear markers, and then extend that
 analysis to construction of minimum-spanning networks for both genomes.
 The new approach is illustrated with a quartet of cryptic congeners from
 the sexually deceptive Australian orchid genus Chiloglottis, still in the
 early stages of speciation. Divergence is more rapid for haploid plastids
 than for nuclear markers, consistent with the effective population size
 differential (Nep &lt; Nen), but divergence patterns are broadly
 correlated for the two genomes. There are nevertheless intriguing
 discrepancies between the emerging plastid and nuclear signals of early
 phylogenetic radiation of these taxa, and neither pattern is entirely
 consistent with the available information on the sexual cues used by the
 orchids to lure the pollinators enforcing reproductive isolation. We
 describe possible extensions of this methodology to multiple ploidy levels
 and other types of markers, which should increase the range of application
 to any taxonomic assemblage in the very early stages of reproductive
 isolation and speciation.
description: Nuclear microsatellite
 genotype data13 microsatellite loci,
 10 populations, 4 taxon dataset for Chiloglottis orchids. Lat/longs
 included for populations.Chilo-nSSR-Dryad
 v2.xlsxChloroplast haplotype
 data23 indel chloroplast
 haplotype data for 10 populations, 4 taxa of Chiloglottis
 orchids.Chilo-cpIND-Dryad.xlsx