cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dh5qs
title: Data from: SNP discovery and high resolution melting analysis from massive transcriptome sequencing in the California red abalone Haliotis rufescens

description: The California red abalone, Haliotis rufescens that belongs to the
 Haliotidae family, is the largest species of abalone in the world that has
 sustained the major fishery and aquaculture production in the USA and
 Mexico. This native mollusk has not been evaluated or assigned a
 conservation category even though in the last few decades it was heavily
 exploited until it disappeared in some areas along the California coast.
 In Chile, the red abalone was introduced in the 1970's from
 California wild abalone stocks for the purposes of aquaculture.
 Considering the number of years that the red abalone has been cultivated
 in Chile crucial genetic information is scarce and critical issues remain
 unresolved. This study reports and validates novel single nucleotide
 polymorphisms (SNP) markers for the red abalone H. rufescens using cDNA
 pyrosequencing. A total of 622 high quality SNPs were identified in 146
 sequences with an estimated frequency of 1 SNP each 1,000 bp. Forty-five
 SNPs markers with functional information for gene ontology were selected.
 Of these, 8 were polymorphic among the individuals screened: Heat shock
 protein 70 (HSP70), vitellogenin (VTG), lysin, Alginate lyase enzyme (AL),
 Glucose-regulated protein 94 (GRP94), fructose-bisphosphate aldolase
 (FBA), sulfatase 1A precursor (S1AP) and ornithine decarboxylase antizyme
 (ODC). Two additional sequences were also identified with polymorphisms
 but no similarities with known proteins were achieved. To validate the
 putative SNP markers, High Resolution Melting Analysis (HRMA) was
 conducted in a wild and hatchery-bred population. Additionally, SNP
 cross-amplifications were tested in two further native abalone species, H.
 fulgens and H. corrugata. This study provides novel candidate genes that
 could be used to evaluate loss of genetic diversity due to hatchery
 selection or inbreeding effects.
description: SNP_Hr_astringenteFasta file with assembled sequences used for SNP miningMulti BLAST (149 sequences)_HrBlast performed to 149 sequences containing SNPsHr summary reportDe novo assembly report from H. rufescens EST-data setHr de novo assembly SNP Detection TableSNP detection table
DOI: 10.5061/dryad.437t2
title: Data from: Experimental illumination of a forest: no effects of lights of different colours on the onset of the dawn chorus in songbirds

description: Light pollution is increasing exponentially, but its impact on animal
 behaviour is still poorly understood. For songbirds, the most repeatable
 finding is that artificial night lighting leads to an earlier daily onset
 of dawn singing. Most of these studies are, however, correlational and
 cannot entirely dissociate effects of light pollution from other effects
 of urbanization. In addition, there are no studies in which the effects of
 different light colours on singing have been tested. Here, we investigated
 whether the timing of dawn singing in wild songbirds is influenced by
 artificial light using an experimental set-up with conventional street
 lights. We illuminated eight previously dark forest edges with white,
 green, red or no light, and recorded daily onset of dawn singing during
 the breeding season. Based on earlier work, we predicted that onset of
 singing would be earlier in the lighted treatments, with the strongest
 effects in the early-singing species. However, we found no significant
 effect of the experimental night lighting (of any colour) in the 14
 species for which we obtained sufficient data. Confounding effects of
 urbanization in previous studies may explain these results, but we also
 suggest that the experimental night lighting may not have been strong
 enough to have an effect on singing.
description: Recordingdata2013allspeciesThe data was collected in the field from 15 April to 15 May (from 27 April to 15 May for the Voorstonden location). The first column shows the 7 sites (from 1 to 7) used in the models as random effects. Site 1 corresponds to a location called ‘Lebret’s Hoeve’, site 2 to ‘Voorstonden’, site 3 to ‘Radio Kootwijk’, and site 7 to ‘Hijkerveld’. Sites 4 and 5 are adjacent spatially and correspond to a location called ‘ASK Doornspijk’. Finally, site 6 consists of two sites merged together because they overlap in a location called ‘Klaterweg’. The onsets (column 7) have therefore been obtained from the mean onsets in the two former sites for each light treatment on each day. The second column shows the 3 levels of 'Treatment', which represents the transects where the data has been collected (green, red, or white light transect). The third column shows the 'Formal date', i.e., the date at which the bird was singing (in calendar days). The fourth column shows the (relative) ‘date', which is the date relative to 15 April (0 = 15 April), and which has been used in the models as a random slope. The fifth column shows the 'onset relative to control'. This variable is calculated for each species, at each site and on each day, as the difference (in min) in the onset of dawn song between each light treatment (red/green/white) and the dark control. The sixth and last column shows the 'species' for which the onset is shown (14 levels, vernacular names shown).DaSilvaetal_data.xlsx
DOI: 10.5061/dryad.n71684c
title: Data from: Exploring emergency department 4-hour target performance and cancelled elective operations: a regression analysis of routinely collected and openly reported NHS trust data.

description: Objective: To quantify the effect of intra-hospital patient flow on
 Emergency Department (ED) performance targets and indicate if the
 expectations set by the NHS England five year forward review are realistic
 in returning emergency services to previous performance levels. Design:
 Linear regression analysis of routinely reported trust activity and
 performance data using a series of cross-sectional studies. Setting: NHS
 trusts in England submitting routine nationally reported measures to NHS
 England. Participants: 142 acute non-specialist trusts operating in
 England between 2012 and 2016. Main outcome measures: The primary outcome
 measures were: proportion of four-hour waiting time breaches and cancelled
 elective operations. Methods: Univariate and multivariate linear
 regression models were used to show relationships between the outcome
 measures, and various measures of trust activity including: empty
 day-beds, empty night-beds, day-to-night bed ratio, ED conversion ratio
 and delayed transfers of care. Results: Univariate regression results
 using the outcome of four-hour breaches showed clear relationships with:
 empty night-beds and ED conversion ratio between 2012-2016. The
 day-to-night bed ratio showed an increasing ability to explain variation
 in performance between 2015-2016. Delayed transfers of care showed little
 evidence of an association. Multivariate model results indicated that the
 ability of patient flow variables to explain four-hour target performance
 had reduced between 2012-2016 (19% to 12%), and had increased in
 explaining cancelled elective operations (7% to 17%). Conclusions: The
 flow of patients through trusts is shown to influence ED performance,
 however performance has become less explainable by intra-trust patient
 flow between 2012 and 2016. Some commonly stated explanatory factors such
 as delayed transfers of care showed limited evidence of being related. The
 results indicate some of the measures proposed by NHS England to reduce
 pressure on EDs may not have the desired impact on returning services to
 previous performance levels.
description: NHS England acute trust
 performance (data + python code)We have provided data in
 csv format ('variables_yr_acute.csv'). This is data at the
 yearly time period for the acute and teaching trusts investigated in the
 study. The full data set (for all trusts and at quarterly and yearly
 levels) is available at: https://eprints.soton.ac.uk/413163/
 doi:10.5258/SOTON/D0218AandE_datafiles.zip
DOI: 10.15468/dl.xngfvj
title: Occurrence Download

description: A dataset containing 40470 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Balaenopteridae"
 ]
}

 The dataset includes 40470 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000623-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7tv47
title: Data from: The guantitative genetics of sexually selected traits, preferred traits and preference: a review and analysis of the data

description: The maintenance of variation in sexually selected traits is a puzzle that
 has received increasing attention in the past several decades. Traits that
 are related to fitness, such as life-history or sexually selected traits,
 are expected to have low additive genetic variance (and hence,
 heritability) due to the rapid fixation of advantageous alleles. However,
 previous analyses have suggested that the heritabilities of sexually
 selected traits are on average higher than nonsexually selected traits. We
 show that the heritabilities of sexually selected traits are not
 significantly different from those of nonsexually selected traits overall
 or when separated into the three trait categories: behavioural,
 morphological and physiological. In contrast with previous findings, the
 heritability of preference is quite low (h2 = 0.25 ± 0.06) and is in the
 same range as life-history traits. We distinguish preferred traits as a
 category of sexually selected traits and find that the heritability of the
 former is not significantly different than sexually selected traits
 overall (0.48 ± 0.04 vs. 0.46 ± 0.03). We test the hypothesis that the
 heritability of sexually selected traits is negatively correlated with the
 strength of sexual selection. As predicted, there is a significant
 negative correlation between the heritabilities of sexually selected
 traits and the strength of selection. This suggests that heritabilities do
 indeed decrease as sexual selection increases but sexual selection is not
 strong enough to cause heritabilities of sexually selected traits to
 deviate from the same type of nonsexually selected traits.
description: Final MA Spreadsheet for
 DRYADHeritability,
 correlations and misc variables
DOI: 10.5061/dryad.204bc
title: Data from: Population properties affect inbreeding avoidance in moose

description: Mechanisms reducing inbreeding are thought to have evolved owing to
 fitness costs of breeding with close relatives. In small and isolated
 populations, or populations with skewed age- or sex distributions, mate
 choice becomes limited, and inbreeding avoidance mechanisms ineffective.
 We used a unique individual-based dataset on moose from a small island in
 Norway to assess whether inbreeding avoidance was related to population
 structure and size, expecting inbreeding avoidance to be greater in years
 with larger populations and even adult sex ratios. The probability that a
 potential mating event was realized was negatively related to the
 inbreeding coefficient of the potential offspring, with a stronger
 relationship in years with a higher proportion or number of males in the
 population. Thus, adult sex ratio and population size affect the degree of
 inbreeding avoidance. Consequently, conservation managers should aim for
 sex ratios that facilitate inbreeding avoidance, especially in small and
 isolated populations.
description: Realised and
 non-realised mating events in moosePotential mating events
 between adult male and female moose at Vega, Norway, and the associated
 F-value of the (potential) offspring. Annual values of population
 properties are also provided.Herfindal_et_al_Inbreeding_Avoidance.xls
DOI: 10.5061/dryad.760t1
title: Data from: Sex-dependent expression of behavioural genetic architectures and the evolution of sexual dimorphism

description: Empirical studies imply that sex-specific genetic architectures can
 resolve evolutionary conflicts between males and females, and thereby
 facilitate the evolution of sexual dimorphism. Sex-specificity of
 behavioural genetic architectures have, however, rarely been considered.
 Moreover, as the expression of genetic (co)variances is often
 environment-dependent, general inferences on sex-specific genetic
 architectures require estimates of quantitative genetics parameters under
 multiple conditions. We measured exploration and aggression in pedigreed
 populations of southern field crickets (Gryllus bimaculatus) raised on
 either naturally balanced (free-choice) or imbalanced (protein-deprived)
 diets. For each dietary condition, we measured for each behavioural trait
 (i) level of sexual dimorphism, (ii) level of sex-specificity of survival
 selection gradients, (iii) level of sex-specificity of additive genetic
 variance, and (iv) strength of the cross-sex genetic correlation. We
 report here evidence for sexual dimorphism in behaviour as well as
 sex-specificity in the expression of genetic (co)variances as predicted by
 theory. The additive genetic variances of exploration and aggression were
 significantly greater in males compared to females. Cross-sex genetic
 correlations were highly positive for exploration but deviating
 (significantly) from one for aggression; findings were consistent across
 dietary treatments. This suggests that genetic architectures characterize
 the sexually dimorphic focal behaviours across various key environmental
 conditions in the wild. Our finding also highlights that sexual conflict
 can be resolved by evolving sexually independent genetic architectures.
description: DATAFILE_HAN_DINGEMANSE_2017_PRSB
DOI: 10.5066/p14ahtlk
title: Sierra Nevada Tree Mortality Data for Global Analysis

description: These data were collected as part of the USGS Sierra Nevada Forest Dynamics Study. They include tree mortality data from 30 plots located along an elevational gradient in the Sierra Nevada of California from 1982 to 2019. Although the data were collected annually, for purposes of compatibility with a global analysis, they were abstracted to five-year census intervals.
DOI: 10.5061/dryad.6523g
title: Data from: Similarity in G matrix structure among natural populations of Arabidopsis lyrata

description: Understanding the stability of the G matrix in natural populations is
 fundamental for predicting evolutionary trajectories, yet, the extent of
 its spatial variation and how this impacts responses to selection remain
 open questions. With a nested paternal half-sib crossing design and plants
 grown in a field experiment, we examined differences in the genetic
 architecture of flowering time, floral display and plant size among four
 Scandinavian populations of Arabidopsis lyrata. Using a multivariate
 Bayesian framework, we compared the size, shape and orientation of G
 matrices and assessed their potential to facilitate or constrain trait
 evolution. Flowering time, floral display and rosette size varied among
 populations and significant additive genetic variation within populations
 indicated potential to evolve in response to selection. Yet, some
 characters, including flowering start and number of flowers, may not
 evolve independently because of genetic correlations. Using a multivariate
 framework, we found few differences in the genetic architecture of traits
 among populations. G matrices varied mostly in size rather than shape or
 orientation. Differences in multivariate responses to selection predicted
 from differences in G were small, suggesting overall matrix similarity and
 shared constraints to trait evolution among populations.
description: Phenotypic data -
 univariate analysesRaw phenotypic data from
 each of the Arabidopsis lyrata populations examined, collected in a common
 garden from offspring of a nested paternal half-sib crossing design. This
 includes plant size and reproduction. Refer to the README for column
 descriptions.puentes_etal_phen_univariate.csvPhenotypic data - multiivariate analyses and G estimationPhenotypic data from each of the Arabidopsis lyrata populations examined, collected in a common garden from offspring of a nested paternal half-sib crossing design. This includes plant size and reproduction. In this file, individuals with missing data have been removed in order to estimate G matrices. Refer to the README for column descriptions.puentes_etal_phen_multivariate_G_matrices.csvPhenotypic data for estimating selection gradientsThis phenotypic field-collected data set (reproduction, plant and flower size of Arabidopsis lyrata for two years) is part of Sandring and Ågren (2009, Evolution). This data allowed estimation of selection gradients that were used in one of the multivariate methods of G matrix comparison (Method 4, Aguirre et al. 2014). Refer to the README file for column names.sandring_agren_2009_selection.csvUnivariate analyses - R scriptAnnotated R script of the univariate analysesPuentes_etal_Evolution_univariate_analyses.RMultivariate analyses and G estimation - R scriptAnnotated R script of the multivariate analyses and G estimationPuentes_et_al_Evolution_multi_G_matrices_analyses.R
DOI: 10.5061/dryad.5qt88
title: Data from: Shifting barriers and phenotypic diversification by hybridisation

description: The establishment of hybrid taxa relies on reproductive isolation from the
 parental forms, typically achieved by ecological differentiation. Here, we
 present an alternative mechanism, in which shifts in the strength and
 location of dispersal barriers facilitate diversification by
 hybridisation. Our case study concerns the highly diverse, stenotopic
 rock-dwelling cichlids of the African Great Lakes, many of which display
 geographic colour pattern variation. The littoral habitat of these fish
 has repeatedly been restructured in the course of ancient lake level
 fluctuations. Genetic data and an experimental cross support the hybrid
 origin of a distinct yellow-coloured variant of Tropheus moorii from
 ancient admixture between two allopatric, red and bluish variants.
 Deficient assortative mating preferences imply that reproductive isolation
 continues to be contingent on geographic separation. Linking
 paleolimnological data with the establishment of the hybrid variant, we
 sketch a selectively neutral diversification process governed solely by
 rearrangements of dispersal barriers.
description: AFLP
 dataAFLP data for 269
 individuals of Tropheus moorii (Cichlidae) from 12 populations. Sample IDs
 are composed of population name and sample number.AFLP dryad
 dataset.txt
DOI: 10.5061/dryad.9c87t
title: Data from: Prescription of antibiotics at drug shops and strategies to improve quality of care and patient safety: a cross-sectional survey in the private sector in Uganda

description: Objectives: The main objective of this study was to assess antibiotic
 prescription practices at registered drug shops with a focus on upper
 respiratory tract infections among children in order to provide data for
 policy discussions aimed at improving quality of care and patient safety
 in the private health sector in Uganda. Methods: A survey was conducted
 within 57 parishes from August to October 2014 in Mukono district, Uganda.
 Data was captured on the following variables: drug shop characteristics,
 training of staff in management of pneumonia, availability of guidelines
 and basic equipment, available antibiotics, knowledge on treatment of
 pneumonia in children aged &lt; 5 years. The main study outcome was
 the proportion of private health facilities prescribing an antibiotic.
 Results: A total of 170 registered drug shops were surveyed between
 August–October 2014. The majority of drug shops, 93.5% were prescribing
 antibiotics especially Amoxicillin and Trimethoprim-sulfamethoxazole
 (Septrin). The professional qualification of a provider was significantly
 associated with this practice, p=0.04; where lower cadre staff (nursing
 assistants and enrolled nurses) over-prescribed antibiotics. A third,
 29.4% of drug shop providers reported that antibiotics were the first-line
 treatment of children with diarrhoea; yet the standard guideline is to
 give Oral Rehydration Salts (ORS) and zinc tablets. Only few providers,
 8.2%, had training on antibiotics and 10.6% on pneumonia case management.
 Further to this, 7.1% drug shops had WHO- Integrated Management of
 Childhood Illness (IMCI) guidelines; and a negligible proportion
 (&lt;1%) had respiratory timers and baby weighing scales. Although the
 majority of providers, 82.4% knew severe signs and symptoms of pneumonia;
 few, 17.6% knew that amoxicillin was the first-line drug for treatment
 pneumonia in children according to the guidelines. Conclusion: There is
 urgent need to regulate drug shop practices of prescribing and selling
 antibiotics for the safety of patients seeking care at these outlets.
description: Baseline survey private
 sector Feb 27 2016
DOI: 10.5061/dryad.79d15
title: Data from: Comparative analyses of reproductive structures in harvestmen (Opiliones) reveal multiple transitions from courtship to precopulatory antagonism

description: Explaining the rapid, species-specific diversification of reproductive
 structures and behaviors is a long-standing goal of evolutionary biology,
 with recent research tending to attribute reproductive phenotypes to the
 evolutionary mechanisms of female mate choice or intersexual conflict.
 Progress in understanding these and other possible mechanisms depends, in
 part, on reconstructing the direction, frequency and relative timing of
 phenotypic evolution of male and female structures in species-rich clades.
 Here we examine evolution of reproductive structures in the leiobunine
 harvestmen or “daddy long-legs” of eastern North America, a monophyletic
 group that includes species in which males court females using nuptial
 gifts and other species that are equipped for apparent precopulatory
 antagonism (i.e., males with long, hardened penes and females with
 sclerotized pregenital barriers). We used parsimony- and Bayesian
 likelihood-based analyses to reconstruct character evolution in
 categorical reproductive traits and found that losses of ancestral
 gift-bearing penile sacs are strongly associated with gains of female
 pregenital barriers. In most cases, both events occur on the same internal
 branch of the phylogeny. These coevolutionary changes occurred at least
 four times, resulting in clade-specific designs in the penis and
 pregenital barrier. The discovery of convergent origins and/or
 enhancements of apparent precopulatory antagonism among closely related
 species offers an unusual opportunity to investigate how major changes in
 reproductive morphology have occurred. We propose new hypotheses that
 attribute these enhancements to changes in ecology or life history that
 reduce the duration of breeding seasons, an association that is consistent
 with female choice, sexual conflict, and/or an alternative evolutionary
 mechanism.
description: Concatenated mtDNA, 28s
 rDNA, EF1-alpha for eastern North American leiobunine
 harvestmenXML file for BEAST
 ultrametric tree reconstructionLeioBeest.xml