cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.65r9c
title: Data from: Does selection on increased cold tolerance in the adult stage confer resistance throughout development?

description: Artificial selection is a powerful approach to unravel constraints on
 genetic adaptation. While it has been frequently used to reveal genetic
 trade-offs among different fitness-related traits, only a few studies have
 targeted genetic correlations across developmental stages. Here we test
 whether selection on increased cold tolerance in the adult stage increases
 cold resistance throughout ontogeny in the butterfly Bicyclus anynana. We
 used lines selected for decreased chill-coma recovery time and according
 controls, which had originally been set up from three levels of inbreeding
 (outbred control, one or two full-sib matings). Four generations after
 having terminated selection, a significant response to selection was found
 in one day-old butterflies (the age at which selection took place). Older
 adults showed a very similar though weaker response. Nevertheless, cold
 resistance did not increase in either egg, larval or pupal stage in the
 selection lines, but was even lower compared to control lines for eggs and
 young larvae. These findings suggest a cost of increased adult cold
 tolerance, presumably reducing resource availability for offspring
 provisioning and thereby stress tolerance during development, which may
 substantially affect evolutionary trajectories.
description: development
 stagesSurvival of eggs, larvae
 and pupae after cold shocks and chill coma recovery times of
 adults
DOI: 10.5061/dryad.tt29d
title: Data from: Evaluation of Xpert® MTB/RIF assay in induced sputum and gastric lavage samples from young children with suspected tuberculosis from the MVA85A TB vaccine trial

description: Objective: Diagnosis of childhood tuberculosis is limited by the
 paucibacillary respiratory samples obtained from young children with
 pulmonary disease. We aimed to compare accuracy of the Xpert® MTB/RIF
 assay, an automated nucleic acid amplification test, between induced
 sputum and gastric lavage samples from young children in a tuberculosis
 endemic setting. Methods: We analyzed standardized diagnostic data from
 HIV negative children younger than four years of age who were investigated
 for tuberculosis disease near Cape Town, South Africa [2009–2012]. Two
 paired, consecutive induced sputa and early morning gastric lavage samples
 were obtained from children with suspected tuberculosis. Samples underwent
 Mycobacterial Growth Indicator Tube [MGIT] culture and Xpert MTB/RIF
 assay. We compared diagnostic yield across samples using the two-sample
 test of proportions and McNemar’s χ2 test; and Wilson’s score method to
 calculate sensitivity and specificity. Results: 1,020 children were
 evaluated for tuberculosis during 1,214 admission episodes. Not all
 children had 4 samples collected. 57 of 4,463[1.3%] and 26 of 4,606[0.6%]
 samples tested positive for Mycobacterium tuberculosis on MGIT culture and
 Xpert MTB/RIF assay respectively. 27 of 2,198[1.2%] and 40 of 2,183[1.8%]
 samples tested positive [on either Xpert MTB/RIF assay or MGIT culture] on
 induced sputum and gastric lavage samples, respectively. 19/1,028[1.8%]
 and 33/1,017[3.2%] admission episodes yielded a positive MGIT culture or
 Xpert MTB/RIF assay from induced sputum and gastric lavage, respectively.
 Sensitivity of Xpert MTB/RIF assay was 8/30[26.7%; 95% CI: 14.2–44.4] for
 two induced sputum samples and 7/31[22.6%; 11.4–39.8] [p = 0.711] for two
 gastric lavage samples. Corresponding specificity was
 893/893[100%;99.6–100] and 885/890[99.4%;98.7–99.8] respectively [p =
 0.025]. Conclusion: Sensitivity of Xpert MTB/RIF assay was low, compared
 to MGIT culture, but diagnostic performance of Xpert MTB/RIF did not
 differ sufficiently between induced sputum and gastric lavage to justify
 selection of one sampling method over the other, in young children with
 suspected pulmonary TB.
description: Data from: Evaluation of
 Xpert® MTB/RIF assay in induced sputum and gastric lavage samples from
 young children with suspected tuberculosis from the MVA85A TB vaccine
 trialThese data were derived
 from an infant Tuberculosis disease vaccine trial conducted near Cape Town
 in South Africa, sub-Saharan Africa. We included diagnostic data that
 enabled us to evaluate diagnostic accuracy of Xpert MTB/RIF in induced
 sputum as compared to gastric lavage.Diagnostic accuracy_minimalist
 dataset_2nd revision.xlsx
DOI: 10.5061/dryad.j1b7h
title: Data from: Species limits, quarantine risk and the intrigue of a polyphagous invasive pest with highly restricted host relationships in its area of invasion

description: Scirtothrips aurantii is a generalist horticultural pest in its African
 range and recently established quite widely in Australia on the invasive
 succulent weed Bryophyllum. Paradoxically, this thrips is not polyphagous
 in its incursive range. The issue is principally one of quarantine. Will
 the thrips in Australia shift, perhaps adaptively, to citrus, and should
 the primary focus be on containment around Australian citrus, or does the
 real quarantine risk exist offshore with thrips present on citrus in
 Africa? We examined the phylogenetic relationships of Bryophyllum
 associated thrips populations in Australia and populations sampled from
 various host plant species in South Africa (including Bryophyllum) using
 both CO1 and28s markers. Eight variable microsatellite markers were
 developed to assess the extent of gene flow between the thrips on
 different hosts in South Africa. The COI phylogeny resolved S. aurantii
 into three distinct clades with samples collected from B. delagoense in
 South Africa and Australia representing a single clade, a second clade
 associated with Gloriosa lilies and the third with horticultural hosts.
 The microsatellite analysis confirmed that the populations associated with
 citrus and Bryophyllum do not hybridize with one another in sympatry. We
 conclude that the citrus damaging thrips are not currently present in
 Australia and remain a serious quarantine concern in relation to
 Australian horticulture.
description: Genotyping_S.
 aurantiiGenotypes of screened
 Scirtothrips aurantii from 11 host associated populations across Australia
 and South Africa using eight microsatellite loci. Population/host plant
 codes: MBd (Miles, Bryophyllum delagoense), BBd (Brisbane, Bryophyllum
 delagoense), NBd (Nelspruit, Bryophyllum delagoense), NCs (Nelspruit,
 Citrus sinensis), NMi (Nelspruit, Macadamia integrifolia), NCp (Nelspruit,
 Caesalpinia pulcherrima), PCs (Pretoria, Citrus sinensis), PCm (Pretoria,
 Crassula multicava), PKb (Pretoria, Kalanchoe blossfeldiana), WCs (Western
 Cape, Citrus sinensis), WPg (Western Cape, Punica granatum). Contact: Dr
 Michelle Rafter - m.rafter@uq.edu.auMale_genotyping_S.aurantiiMicrosatellite optimization conducted on 45 males using the 8 loci used in the study to determine male Scirtothrips aurantii haploidy and further screen the loci for non-specific amplification. Population/host plant codes: MBd (Miles, Bryophyllum delagoense), BBd (Brisbane, Bryophyllum delagoense), NBd (Nelspruit, Bryophyllum delagoense), NCs (Nelspruit, Citrus sinensis), NMi (Nelspruit, Macadamia integrifolia), NCp (Nelspruit, Caesalpinia pulcherrima), PCs (Pretoria, Citrus sinensis), PCm (Pretoria, Crassula multicava), PKb (Pretoria, Kalanchoe blossfeldiana), WCs (Western Cape, Citrus sinensis), WPg (Western Cape, Punica granatum). Contact: Dr Michelle Rafter - m.rafter@uq.edu.au
DOI: 10.5061/dryad.r4j63pg0
title: Data from: Reconciling extremely strong barriers with high levels of gene exchange in annual sunflowers

description: In several cases, estimates of gene flow between species appears to be
 higher than predicted given the strength of interspecific barriers.
 However, as far as we are aware, detailed measurements of reproductive
 isolation have not previously been compared with a coalescent-based
 assessment of gene flow. Here, we contrast these two measures in two
 species of sunflower, Helianthus annuus and Helianthus petiolaris. We
 quantified the total reproductive barrier strength between these species
 by compounding the contributions of the following prezygotic and
 postzygotic barriers: ecogeographic isolation, reproductive asynchrony,
 immigrant inviability, pollen competition, hybrid seed formation, hybrid
 seed germination, hybrid pollen fertility, and hybrid seed set. The
 estimated probabilities that a reproductively successful hybrid is
 produced: range from 10^-4 to 10^-6 depending on the direction of the
 cross and the degree of independence among reproductive barriers.
 Population genetic estimates of gene flow estimated between these
 sunflower species (N_e m = 0.34-0.76) are due mainly to their large
 effective population sizes (N_e &gt;10^6). The interspecific migration
 rate (m) is very small (&lt;10^-7) and an order of magnitude lower
 than that expected based on our reproductive barrier strength estimates.
 Thus, even high levels of reproductive isolation (&gt; 0.999) may
 produce genomic mosaics.
description: Sambatti et al data
 archiveThis gives an overview
 of the contents of all remaining data files.
DOI: 10.5061/dryad.1mg5n
title: Data from: Relaxed predation results in reduced phenotypic integration in a suite of dragonflies

description: While changes in magnitude of single traits responding to selective agents
 have been studied intensively, little is known about selection shaping
 networks of traits and their patterns of co-variation. However, this is
 central for our understanding of phenotypic evolution since traits are
 embedded in a multivariate environment with selection affecting a
 multitude of traits simultaneously rather than individually. Here, we
 investigate inter- and intraspecific patterns of trait integration (trait
 correlations) in the larval abdomen of dragonflies as a response to a
 change in predator selection. Species of the dragonfly genus Leucorrhinia
 underwent a larval habitat shift from predatory fish to predatory
 dragonfly dominated lakes with an associated relaxation in selection
 pressure from fish predation. Our results indicate that the habitat-shift
 induced relaxed selection pressure caused phenotypic integration of
 abdominal traits to be reduced. Intraspecific findings matched patterns
 comparing species from both habitats with higher abdominal integration in
 response to predatory fish. This higher integration is probably a result
 of faster burst swimming speed. The abdomen holds the necessary
 morphological machinery to successfully evade predatory fish via burst
 swimming. Hence, abdominal traits have to function in a tight coordinated
 manner, since maladaptive variation and consequently non-optimal burst
 swimming would cause increased mortality. In predatory dragonfly dominated
 lakes no such strong link between burst swimming and mortality is present.
 Our findings highlight the importance of studying multivariate trait
 relationships as a response to selection for understanding patterns of
 phenotypic diversification.
description: Mikolajewski et al.
 JEBAbdominal measures for
 phenotypic integration in Leucorrhinia-species.
DOI: 10.5061/dryad.p039j
title: Data from: Chronic exposure to neonicotinoids reduces honey bee health near corn crops

description: Experiments linking neonicotinoids and declining bee health have been
 criticized for not simulating realistic exposure. Here we quantified the
 duration and magnitude of neonicotinoid exposure in Canada’s corn-growing
 regions and used these data to design realistic experiments to investigate
 the effect of such insecticides on honey bees. Colonies near corn were
 naturally exposed to neonicotinoids for up to 4 months—the majority of the
 honey bee’s active season. Realistic experiments showed that
 neonicotinoids increased worker mortality and were associated with
 declines in social immunity and increased queenlessness over time. We also
 discovered that the acute toxicity of neonicotinoids to honey bees doubles
 in the presence of a commonly encountered fungicide. Our work demonstrates
 that field-realistic exposure to neonicotinoids can reduce honey bee
 health in corn-growing regions.
description: AgrochemicalAgrochemicals found in different colony sample types, location, and time points.agrochemicals.xlsxPollen analysis of NNI positive samplesThe relative proportion of pollen grains from different plants found in samples that tested positive for neonicotinoidsPollen.xlsxOral Toxicity of Clothianadin and Thiamethoxam in the presence of Linuron and BoscalidThe mortality of worker honeybees in cage experiments with different doses of NNIs in the presence of constant levels of either the herbicide linuron or the fungacide boscalid.LD50_NNIs.xlsx
DOI: 10.5061/dryad.3mn5rk4
title: Data from: The pervasive effects of lighting environments on sensory drive in bluefin killifish: an investigation into male/male competition, female choice, and predation

description: Sensory drive predicts that the conditions under which signaling takes
 place have large effects on signals, sensory systems, and behavior. The
 coupling of an ecological genetics approach with sensory drive has been
 fruitful. An ecological genetics approach compares populations that
 experience different environments and asks whether population differences
 are adaptive and are the result of genetic and/or environmental variation.
 The multi-faceted effects of signaling environments are well-exemplified
 by the bluefin killifish. In this system, males with blue anal fins are
 abundant in tannin-stained swamps that lack UV/blue light but are absent
 in clear springs where UV/blue light is abundant. Past work indicates that
 lighting environments shape genetic and environmental variation in color
 patterns, visual systems, and behavior. Less is known about the selective
 forces creating the across population correlations between UV/blue light
 and the abundance of blue males. Here, we present three new experiments
 that investigate the roles of lighting environments on male competition,
 female mate choice, and predation. We found strong effects of lighting
 environments on male competition where blue males were more likely to
 emerge as dominant in tea-stained water than in clear water. Our
 preliminary study on predation indicated that blue males may be less
 susceptible to predation in tea-stained water than in clear water.
 However, there was little evidence for female preferences favoring blue
 males. The resulting pattern is one where the effects of lighting
 environments on genetic variation and phenotypic plasticity match the
 direction of selection and favor the expression of blue males in swamps.
description: Male competition, female
 choice, predation, and lighting environments in bluefin
 killifishThis excel sheet
 contains 4 data sets. 'maledominance' contains the data from the
 male/male competition experiment. 'female_choice' contains the
 data from the female choice experiment.
 'Preliminary_Bass_Predation_Exp' contains the data from the bass
 predation experiment. 'Clear_Tea_Light' contains the absolute
 and relative irradiance data from clear and tea-stained lighting
 treatments. Each data set has an explanatory header.Mitchem_et_al_Dryad.xlsx
DOI: 10.5061/dryad.3kh41
title: Data from: Adaptation to a novel family environment involves both apparent and cryptic phenotypic changes

description: Cryptic evolution occurs when evolutionary change is masked by concurrent
 environmental change. In most cases, evolutionary changes in the phenotype
 are masked by changing abiotic factors. However, evolutionary change in
 one trait might also be masked by evolutionary change in another trait, a
 phenomenon referred to as evolutionary environmental deterioration.
 Nevertheless, detecting this second type of cryptic evolution is
 challenging and there are few compelling examples. Here, we describe a
 likely case of evolutionary environmental deterioration occurring in
 experimental burying beetle (Nicrophorus vespilloides) populations that
 are adapting to a novel social environment that lacks post-hatching
 parental care. We found that populations rapidly adapted to the removal of
 post-hatching parental care. This adaptation involved clear increases in
 breeding success and larval density (number of dispersing larvae produced
 per gram of breeding carcass), which in turn masked a concurrent increase
 in the mean larval mass across generations. This cryptic increase in
 larval mass was accomplished through a change in the reaction norm that
 relates mean larval mass to larval density. Our results suggest that
 cryptic evolution might be commonplace in animal families, because
 evolving trophic and social interactions can potentially mask evolutionary
 change in other traits, like body size.
description: Schrader et al breeding
 dataMeasures of breeding
 performance for all successful broods across the first 13 generations of
 experimental evolution. The columns are as follow: Carcass_mass_in_grams
 (the mass of the breeding carcass in grams), Environment (Control or No
 Care), Replicate (the replicate population, coded as A or B), Generation
 (the generation of experimental evolution), Pair (the unique breeding pair
 for a given Environment / Replicate / Generation), Brood_size (the number
 of larvae at dispersal), Brood_mass_in_grams (the total mass of all
 dispersing larvae in grams), Mean_larval_mass (the mean mass of dispersing
 larvae in grams, calculated as brood_mass_in
 grams/Brood_size).
DOI: 10.5061/dryad.49rs8
title: Data from: Molecular evolution of anthocyanin pigmentation genes following losses of flower color

description: Background: Phenotypic transitions, such as trait gain or loss, are
 predicted to carry evolutionary consequences for the genes that control
 their development. For example, trait losses can result in molecular decay
 of the pathways underlying the trait. Focusing on the Iochrominae clade
 (Solanaceae), we examine how repeated losses of floral anthocyanin
 pigmentation associated with flower color transitions have affected the
 molecular evolution of three anthocyanin pathway genes (Chi, F3h, and
 Dfr). Results: We recovered intact coding regions for the three genes in
 all of the lineages that have lost floral pigmentation, suggesting that
 molecular decay is not associated with these flower color transitions.
 However, two of the three genes (Chi, F3h) show significantly elevated
 dN/dS ratios in lineages without floral pigmentation. Maximum likelihood
 analyses suggest that this increase is due to relaxed constraint on
 anthocyanin genes in the unpigmented lineages as opposed to positive
 selection. Despite the increase, the values for dN/dS in both pigmented
 and unpigmented lineages were consistent overall with purifying selection
 acting on these loci. Conclusions: The broad conservation of anthocyanin
 pathway genes across lineages with and without floral anthocyanins is
 consistent with the growing consensus that losses of pigmentation are
 largely achieved by changes in gene expression as opposed to structural
 mutations. Moreover, this conservation maintains the potential for regain
 of flower color, and indicates that evolutionary losses of floral
 pigmentation may be readily reversible.
description: Chi, sequence
 alignmentsSequences from a total
 of 22 Iochrominae species were generated from floral bud cDNA prepared
 from greenhouse or field-collected material. Sequences from six outgroup
 taxa were retrieved from Genbank or Solgenomics
 (solgenomics.net).EVOL_CHI_SEQFILE.txtDfr, sequence alignmentsSequences from a total of 22 Iochrominae species were generated from floral bud cDNA prepared from greenhouse or field-collected material. Sequences from six outgroup taxa were retrieved from Genbank or Solgenomics (solgenomics.net).EVOL_DFR_SEQFILE.txtF3h, sequence alignmentsSequences from a total of 22 Iochrominae species were generated from floral bud cDNA prepared from greenhouse or field-collected material. Sequences from six outgroup taxa were retrieved from Genbank or Solgenomics (solgenomics.net).F3H_SEQFILE.txt
DOI: 10.5061/dryad.ds946
title: Data from: Comparing safety climate for nurses working in operating theatres, critical care and ward areas in the UK: a mixed methods study

description: Objectives: The main aim of the study was to explore the potential sources
 of variation and understand the meaning of safety climate for nursing
 practice in acute hospital settings in the UK. Design: A sequential mixed
 methods design included a cross-sectional survey using the Safety Climate
 Questionnaire (SCQ) and thematic analysis of focus group discussions.
 Confirmatory Factor Analysis (CFA) was used to validate the factor
 structure of the SCQ. Factor scores were compared between nurses working
 in operating theatres, critical care and ward areas. Results from the
 survey and the thematic analysis were then compared and synthesised.
 Setting: A London University. Participants: 319 registered nurses working
 in acute hospital settings completed the SCQ and a further 23 nurses
 participated in focus groups. Results: CFA indicated that there was a good
 model fit on some criteria (χ2 = 1683.699, df 824, p &lt; 0.001; χ2/
 df = 2.04; RMSEA = 0.058) but a less acceptable fit on Comparative Fit
 Index (CFI) = 0.804. There was a statistically significant difference
 between clinical specialisms in Management Commitment (F [4,266] = 4.66, p
 = 0.001). Nurses working in operating theatres had lower scores compared
 with ward areas and they also reported negative perceptions about
 management in their focus group. There was significant variation in scores
 for Communication across clinical specialism (F [4,266] = 2.62, p = 0.035)
 but none of the pair-wise comparisons achieved statistical significance.
 Thematic analysis identified themes of Human Factors, Clinical Management
 and Protecting Patients. The System and the Human Side of Caring was
 identified as a meta-theme. Conclusions: The results suggest that the SCQ
 has some utility but requires further exploration. The findings indicate
 that safety in nursing practice is a complex interaction between safety
 systems and the social and interpersonal aspects of clinical practice.
description: Tarling_SCQ_RawDataSafety Climate raw data and demographic dataMTarling_BMJ_dryad.docx