cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v6b8c
title: Data from: Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana

description: Understanding the causes and architecture of genetic differentiation
 between natural populations is of central importance in evolutionary
 biology. Crosses between natural populations can result in heterosis if
 recessive or nearly recessive deleterious mutations have become fixed
 within populations because of genetic drift. Divergence between
 populations can also result in outbreeding depression because of genetic
 incompatibilities. The net fitness consequences of between-population
 crosses will be a balance between heterosis and outbreeding depression. We
 estimated the magnitude of heterosis and outbreeding depression in the
 highly selfing model plant Arabidopsis thaliana, by crossing replicate
 line pairs from two sets of natural populations (C↔R, B↔S) separated by
 similar geographic distances (Italy↔Sweden). We examined the contribution
 of different modes of gene action to overall differences in estimates of
 lifetime fitness and fitness components using joint scaling tests with
 parental, reciprocal F1 and F2, and backcross lines. One of these
 population pairs (C↔R) was previously demonstrated to be locally adapted,
 but locally maladaptive quantitative trait loci were also found,
 suggesting a role for genetic drift in shaping adaptive variation. We
 found markedly different genetic architectures for fitness and fitness
 components in the two sets of populations. In one (C↔R), there were
 consistently positive effects of dominance, indicating the masking of
 recessive or nearly recessive deleterious mutations that had become fixed
 by genetic drift. The other set (B↔S) exhibited outbreeding depression
 because of negative dominance effects. Additional studies are needed to
 explore the molecular genetic basis of heterosis and outbreeding
 depression, and how their magnitudes vary across environments.
description: Oakleyetal_2015_Heredity_JLineCross_Growout_RawDataRaw dataOakleyetal_2015_Heredity_JointScale_FruitNExample Python script for performing the joint scaling analyses
DOI: 10.5061/dryad.mr0n8
title: Data from: Top-down effects of a lytic bacteriophage and protozoa on bacteria in aqueous and biofilm phases

description: Lytic bacteriophages and protozoan predators are the major causes of
 bacterial mortality in natural microbial communities, which also makes
 them potential candidates for biological control of bacterial pathogens.
 However, little is known about the relative impact of bacteriophages and
 protozoa on the dynamics of bacterial biomass in aqueous and biofilm
 phases. Here, we studied the temporal and spatial dynamics of bacterial
 biomass in a microcosm experiment where opportunistic pathogenic bacteria
 Serratia marcescens was exposed to particle-feeding ciliates,
 surface-feeding amoebas, and lytic bacteriophages for 8 weeks, ca. 1300
 generations. We found that ciliates were the most efficient enemy type in
 reducing bacterial biomass in the open water, but least efficient in
 reducing the biofilm biomass. Biofilm was rather resistant against
 bacterivores, but amoebae had a significant long-term negative effect on
 bacterial biomass both in the open-water phase and biofilm. Bacteriophages
 had only a minor long-term effect on bacterial biomass in open-water and
 biofilm phases. However, separate short-term experiments with the
 ancestral bacteriophages and bacteria revealed that bacteriophages crash
 the bacterial biomass dramatically in the open-water phase within the
 first 24 h. Thereafter, the bacteria evolve phage-resistance that largely
 prevents top-down effects. The combination of all three enemy types was
 most effective in reducing biofilm biomass, whereas in the open-water
 phase the ciliates dominated the trophic effects. Our results highlight
 the importance of enemy feeding mode on determining the spatial
 distribution and abundance of bacterial biomass. Moreover, the enemy type
 can be crucially important predictor of whether the rapid defense
 evolution can significantly affect top-down regulation of bacteria.
description: Biomass dynamics in free
 water and biofilmAmoeba and ciliate
 dynamics
DOI: 10.5061/dryad.th251
title: Data from: Exposure to an environmental estrogen breaks down sexual isolation between native and invasive species

description: Environmental change can increase the likelihood of interspecific
 hybridization by altering properties of mate recognition and
 discrimination between sympatric congeners. We examined how exposure to an
 environmentally widespread endocrine disrupting chemical (EDC), Bisphenol
 A (BPA), affected visual communication signals and behavioral isolation
 between an introduced freshwater fish and a native congener (genus:
 Cyprinella). Exposure to BPA induced changes in the expression of male
 secondary traits as well as male and female mate choice, leading to an
 overall reduction in prezygotic isolation between congeners. Changes in
 female mate discrimination were not tightly linked to changes in male
 phenotypic traits, suggesting that EDC exposure may alter female choice
 thresholds independently of the effects of exposure on males. These
 findings indicate that environmental exposure to EDCs can lead to
 population declines via the erosion of species boundaries and by promoting
 the establishment and spread of non-native species via hybridization.
description: Male_Trial_DataMale behavioural and phenotypic data recorded from interspecific mate choice tests in Control and BPA treatments.Female Trial DataFemale responses to conspecific and heterospecific males recorded during mate choice tests.
DOI: 10.5061/dryad.3jm7h
title: Data from: Parasite transmission in a natural multihost-multiparasite community

description: Understanding the transmission and dynamics of infectious diseases in
 natural communities requires understanding the extent to which the
 ecology, evolution and epidemiology of those diseases are shaped by
 alternative hosts. We performed laboratory experiments to test how
 parasite spillover affected traits associated with transmission in two
 co-occurring parasites: the bacterium Pasteuria ramosa and the fungus
 Metschnikowia bicuspidata. Both parasites were capable of transmission
 from the reservoir host (Daphnia dentifera) to the spillover host
 (Ceriodaphnia dubia), but this occurred at a much higher rate for the
 fungus than the bacterium. We quantified transmission potential by
 combining information on parasite transmission and growth rate, and used
 this to compare parasite fitness in the two host species. For both
 parasites, transmission potential was lower in the spillover host. For the
 bacterium, virulence was higher in the spillover host. Transmission back
 to the original host was high for both parasites, with spillover
 influencing transmission rate of the fungus but not the bacterium. Thus,
 whilst inferior, the spillover host is not a dead-end for either parasite.
 Overall, our results demonstrate that the presence of multiple hosts in a
 community can have important consequences for disease transmission and
 host and parasite fitness.
description: Expt1PastFullFull data for Exp1. Hosts: Daphnia dentifera, Ceriodaphnia dubia. Parasite: Pasteuria ramosa. Variables include host offspring counts, day of death, spores per host, host species and host genotypeExpt1MetschFullFull data for Exp1. Hosts: Daphnia dentifera, Ceriodaphnia dubia. Parasite: Metschnikowia bicuspidata. Variables include host offspring counts, day of death, spores per host, host species and host genotypeExpt1PastBSTTransmission data for Exp1. Hosts: Daphnia dentifera, Ceriodaphnia dubia. Parasite: Pasteuria ramosa. Variables include transmission rate (Beta), parasite growth rate (sigdeath), host species and host clone.Expt1MetschBSTTransmission data for Exp1. Hosts: Daphnia dentifera, Ceriodaphnia dubia. Parasite: Metschnikowia bicuspidata. Variables include transmission rate (Beta), parasite growth rate (sigdeath), host species and host clone.Expt2PastBSTTransmission data for Exp2. Hosts: Daphnia dentifera, Ceriodaphnia dubia. Parasite: Pasteuria ramosa. Variables include transmission rate (beta), parasite growth rate (sigma/tau), overall transmission potential (bs/t), first host species (host 1) and second host clone (host 2).Expt2MetschBSTTransmission data for Exp2. Hosts: Daphnia dentifera, Ceriodaphnia dubia. Parasite: Metschnikowia bicuspidata. Variables include transmission rate (beta), parasite growth rate (sigma/tau), overall transmission potential (bs/t), first host species (host 1) and second host clone (host 2).MHMP_PhilTransCode for all of the analyses within this manuscript
DOI: 10.5061/dryad.dc42s75
title: Data from: Dispositional free riders do not free ride on punishment

description: Strong reciprocity explains prosocial cooperation by the presence of
 individuals who incur costs to help those who helped them (‘strong
 positive reciprocity’) and to punish those who wronged them (‘strong
 negative reciprocity’). Theories of social preferences predict that in
 contrast to ‘strong reciprocators’, self-regarding people cooperate and
 punish only if there are sufficient future benefits. Here, we test this
 prediction in a two-stage design. First, participants are classified
 according to their disposition towards strong positive reciprocity as
 either dispositional conditional cooperators (DCC) or dispositional free
 riders (DFR). Participants then play a one-shot public goods game, either
 with or without punishment. As expected, DFR cooperate only when
 punishment is possible, whereas DCC cooperate without punishment.
 Surprisingly, dispositions towards strong positive reciprocity are
 unrelated to strong negative reciprocity: punishment by DCC and DFR is
 practically identical. The ‘burden of cooperation’ is thus carried by a
 larger set of individuals than previously assumed.
description: WeberWeiselGaechter_Data&CodeThis package contains the data and analysis files of the article "Dispositional free riders do not free ride on punishment", Nature Communications 2018, DOI: 10.1038/s41467-018-04775-8.
DOI: 10.5061/dryad.n63j0
title: Data from: Acute febrile illness and influenza disease burden in a rural cohort dedicated to malaria in Senegal, 2012-2013

description: Background: African populations are considered to be particularly
 vulnerable to fever illnesses, including malaria, and acute respiratory
 disease, owing to limited resources and overcrowding. However, the overall
 burden of influenza in this context is poorly defined and incidence data
 for African countries are scarce. We therefore studied the fever syndrome
 incidence and more specifically influenza incidence in a cohort of
 inhabitants of Dielmo and Ndiop in Sokone district, Senegal. Methods:
 Daily febrile-illness data were prospectively obtained from January 2012
 to December 2013 from the cohort of the villages of Dielmo and Ndiop,
 initially dedicated to the study of malaria. Nasopharyngeal swabs were
 collected from, and malaria diagnosis tests (thick blood smears) carried
 out on, every febrile individual during clinical visits; reverse
 transcriptase-polymerase chain reaction was used to identify influenza
 viruses in the samples. Binomial negative regression analysis was used to
 study the relationship between the monthly incidence rate and various
 covariates. Results: In Dielmo and Ndiop, the incidence of malaria has
 decreased, but fever syndromes remain frequent. Among the 1036 inhabitants
 included in the cohort, a total of 1,129 episodes of fever were reported.
 Influenza was present all year round with peaks in October-December 2012
 and August 2013. The fever, ILI and influenza incidence density rates
 differed significantly between age groups. At both sites, the adjusted
 incidence relative risks for fever syndromes and ILI were significantly
 higher in the [6–24 months) than other age groups: 7.3 (95%CI: [5.7–9.3])
 and 16.1 (95%CI: [11.1–23.3]) respectively. The adjusted incidence
 relative risk for influenza was significantly higher for the [0–6 months)
 than other age groups: 9.9 (95%CI: [2.9–33.6]). At both sites, incidence
 density rates were lowest among adults &gt; = 50 years. Conclusions:
 In this rural setting in Senegal, influenza was most frequent among the
 youngest children. Preventive strategies targeting this population should
 be implemented.
description: Data Influenza
 BurdenComplete data used for
 the articleCOMPLET2.csv
DOI: 10.5061/dryad.120f446
title: Data from: Towards accurate species-level metabarcoding of arthropod communities from the tropical forest canopy

description: Metabarcoding of arthropod communities can be used for assessing species
 diversity in tropical forests but the methodology requires validation for
 accurate and repeatable species occurrences in complex mixtures. This
 study investigates how the composition of ecological samples affects the
 accuracy of species recovery. Starting with field-collected bulk samples
 from the tropical canopy, the recovery of specimens was tested for subsets
 of different body sizes and major taxa, by assembling these subsets into
 increasingly complex composite pools. After metabarcoding, we track
 whether richness, diversity and most importantly composition of any size
 class or taxonomic subset is affected by the presence of other subsets in
 the mixture. Operational Taxonomic Units (OTUs) greatly exceeded the
 number of morphospecies in most taxa, even under very stringent sequencing
 read filtering. There was no significant effect on the recovered OTU
 richness of small and medium-sized arthropods when metabarcoded alongside
 larger arthropods, despite substantial biomass differences in the mixture.
 The recovery of taxonomic subsets was not generally influenced by the
 presence of other taxa, although with some exceptions likely due to primer
 mismatches. Considerable compositional variation within size and
 taxon-based subcommunities were evident resulting in high beta diversity
 among samples from within a single tree canopy, but this beta diversity
 was not affected by experimental manipulation. We conclude that OTU
 recovery in complex arthropod communities, with sufficient sequencing
 depth and within reasonable size ranges, is not skewed by variable biomass
 of the constituent species. This could remove the need for time-intensive
 manual sorting prior to metabarcoding. However, there remains a chance of
 taxonomic bias, which may be primer-dependent. There will never be a
 panacea primer; instead, metabarcoding studies should carefully consider
 whether the aim is broad-scale turnover, in which case these biases may
 not be important, or species lists, in which case separate PCRs and
 sequencing might be necessary. OTU number inflation remains an issue in
 metabarcoding and requires bioinformatic development, particularly in read
 filtering and OTU clustering, and/or greater use of species-identifying
 sequences generated outside of bulk sequencing.
description: Metabarcoding
 dataotu.fa: a FASTA format
 file containing the sequences of all of the OTUs generated by the study;
 map.csv: a table reporting the number of reads of each OTU in each
 sequenced library (well); summary_metadata.csv: a table reporting the
 sample data for each welldata.zip
DOI: 10.5061/dryad.116j2
title: Data from: Meta-analysis reveals that hydraulic traits explain cross-species patterns of drought-induced tree mortality across the globe

description: Drought-induced tree mortality has been observed globally and is expected
 to increase under climate change scenarios, with large potential
 consequences for the terrestrial carbon sink. Predicting mortality across
 species is crucial for assessing the effects of climate extremes on forest
 community biodiversity, composition, and carbon sequestration. However,
 the physiological traits associated with elevated risk of mortality in
 diverse ecosystems remain unknown, although these traits could greatly
 improve understanding and prediction of tree mortality in forests. We
 performed a meta-analysis on species’ mortality rates across 475 species
 from 33 studies around the globe to assess which traits determine a
 species’ mortality risk. We found that species-specific mortality
 anomalies from community mortality rate in a given drought were associated
 with plant hydraulic traits. Across all species, mortality was best
 predicted by a low hydraulic safety margin—the difference between typical
 minimum xylem water potential and that causing xylem dysfunction—and xylem
 vulnerability to embolism. Angiosperms and gymnosperms experienced roughly
 equal mortality risks. Our results provide broad support for the
 hypothesis that hydraulic traits capture key mechanisms determining tree
 death and highlight that physiological traits can improve vegetation model
 prediction of tree mortality during climate extremes.
description: Anderegg_Dryad_MortalityDatabase_v1_3-2016Mortality data from Anderegg et al. 2016 PNAS. See publication for details.
DOI: 10.5061/dryad.22300
title: Data from: Phylogenetic revision of the Strophomenida, a diverse and ecologically important palaeozoic brachiopod order

description: The order Strophomenida was an ecologically abundant and taxonomically
 diverse group of Palaeozoic brachiopods that originated in the earliest
 Ordovician and went extinct in the Carboniferous. During their long
 geological range, the Strophomenida survived two of the ‘Big Five’ mass
 extinction events, the Late Ordovician and the Late Devonian, suggesting
 that they are potentially informative taxa for studying the evolutionary
 effects of these two distinct mass extinctions, each with drastically
 different forcing mechanisms. However, while there have been previous
 phylogenetic studies on smaller groups within the Strophomenida, the
 phylogenetic relationships of the whole group are still largely unknown.
 The group has been divided into two major superfamilies, the
 Strophomenoidea (strophomenoids) and the Plectambonitoidea
 (plectambonitoids). Despite being treated as separate clades, the
 plectambonitoids may form a paraphyletic grade into the strophomenoids. We
 present a detailed higher-level parsimony-based phylogenetic analysis of
 the Strophomenida, consisting of 69 characters and 62 exemplar species
 sampled from the majority of the taxonomically defined
 families/subfamilies. Several species of basal chonetids
 (strophochonetids) were also included in this analysis, as they may be
 closely related to the Strophomenida and share several characters with
 both the plectambonitoids and strophomenoids. The phylogenetic analysis
 suggests the plectambonitoids, as originally defined, are paraphyletic to
 the monophyletic strophomenoids. The basal chonetids are reconstructed as
 a monophyletic group that is sister to the strophomenoids, suggesting that
 their proper placement might be within the Strophomenida. The topology
 also suggests that at least 17 of the taxonomically defined strophomenoid
 and plectambonitoid families are likely to be monophyletic. The
 Plectambonitidae and the Taffiidae as defined are paraphyletic, and the
 Grorudiidae and Leptostrophiidae are polyphyletic. Furthermore,
 subfamilies Leptodontellinae, Dicoelostrophiinae, Palaeostrophomeninae and
 Aegiromeninae are raised to the level of family. When analysed within this
 phylogenetic context, the Late Ordovician mass extinction event had little
 effect on the large-scale evolution of the group.
description: S1 - Strophid matrix
 with excluded taxaS2 - Strophid analysis
 with excS3 - Strophid
 matrixS4 - Strophids matrix
 with traditional cardinal process charactersS5 - Strophids matrix
 with microstructure characters
DOI: 10.5061/dryad.vj7k2
title: Data from: Hypogonadism and low bone mineral density in patients on long-term intrathecal opioid delivery therapy

description: Objectives: This study aimed to investigate the
 hypothalamic-pituitary-gonadal axis in a sample of male patients
 undertaking intrathecal opioid delivery for the management of chronic
 non-malignant pain and the presence of osteopaenia and/or osteoporosis in
 those diagnosed with hypogonadism. Design: Observational study using
 health data routinely collected for non-research purposes. Setting:
 Department of Pain Management, Russells Hall Hospital, Dudley, UK.
 Patients: Twenty consecutive male patients attending follow-up clinics for
 intrathecal opioid therapy had the gonadal axis evaluated by measuring
 their serum luteinising hormone, follicle stimulating hormone, total
 testosterone, sex hormone binding globulin and calculating the free
 testosterone level. Bone mineral density was measured by DEXA scanning in
 those patients diagnosed with hypogonadism. Results: Based on the
 calculated free testosterone concentrations, 17 (85%) patients had
 biochemical hypogonadism with 15 patients (75%) having free testosterone
 &lt;180 pmol/L and 2 patients (10%) between 180 and 250 pmol/L. Bone
 mineral density was assessed in 14 of the 17 patients after the exclusion
 of 3 patients. Osteoporosis (defined as a T score ≤−2.5 SD) was detected
 in three patients (21.4%) and osteopaenia (defined as a T score between
 −1.0 and −2.5 SD) was observed in seven patients (50%). Five of the 14
 patients (35.7%) were at or above the intervention threshold for hip
 fracture. Conclusions: This study suggests an association between
 hypogonadism and low bone mass density in patients undertaking intrathecal
 opioid delivery for the management of chronic non-malignant pain.
 Surveillance of hypogonadism and the bone mineral density levels followed
 by appropriate treatment may be of paramount importance to reduce the risk
 of osteoporosis development and prevention of fractures in this group of
 patients.
description: Dataset
 DEXAData collected related
 to bone density measurements in an intrathecal drug delivery patient
 sample.
DOI: 10.5061/dryad.qm23g80
title: Data from: Education research: simulation training for neurology residents on acquiring tPA consent: an educational initiative

description: [No abstract entered]
description: IV-tPA consent OSCE
 scriptThis is the actual
 IV-tPA consent OSCE script that was used for the simulation session for
 first year neurology residents.OSCE
 script.pdf
DOI: 10.15468/dl.3649h2
title: Occurrence Download

description: A dataset containing 2873197528 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Theromyzon, Haemadipsa, Haemopis, Alma, Eiseniella, Animalia, Dero, Tubificoides, Barbronia)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2873197528 records from 55949 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000700-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/6xgsoe
title: Impacts of IRC’s Fifth Child community engagement strategy to increase immunisation in northern Uganda

description: Dofiles, ready-for-analysis data used in the analysis published in the Final Report to 3ie on the project, "Impacts of IRC’s Fifth Child community engagement strategy to increase immunisation in northern Uganda" (project code TW10.1018). This project was funded as part of the Innovations in Increasing Immunisation Thematic Window round.