cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bs275
title: Data from: The role of pleiotropy and linkage in genes affecting a sexual ornament and bone allocation in the chicken

description: Sexual selection and the ornaments that inform such choices have been
 extensively studied, particularly from a phenotypic perspective. Although
 more is being revealed about the genetic architecture of sexual ornaments,
 much still remains to be discovered. The comb of the chicken is one of the
 most widely recognized sexual ornaments, which has been shown to be
 correlated with both fecundity and bone allocation. In this study we use a
 combination of multiple intercrosses between White Leghorn populations and
 wild-derived Red Junglefowl to firstly map QTL for bone allocation, and
 secondly to identify eQTL that correlate and colocalise with comb mass.
 These candidate quantitative genes were then assessed for potential
 pleiotropic effects on bone tissue and fecundity traits. We identify genes
 that correlate with both relative comb mass and bone traits suggesting a
 combination of both pleiotropy and linkage mediate gene regulatory
 variation of these traits.
description: Comb microarray data
 (raw and RMA preprocessed)Microarray data for the
 39 individual comb base samples. This files contains the raw as well as
 RMA preprocessed gene expression values, and design files for the custom
 NimbleGen gene expression chip used.comb_microarray_data.tar.gzComb eQTL data (R/qtl format)Residual comb masses, preprocessed gene expression data and genotypes of the 39 individuals of the comb eQTL study in R/qtl csv input format.comb_eQTL_data_Rqtl_format.csvRJF x OS genotypes (QTL Express format)Genotype data from the Red Jungefowl x Obese strain White Leghorn intercross in QTL Express format.OS_genotypes_QTLexpress_format.txtRJF x OS genetic map (QTL Express format)Genetic map file for the Red Junglefowl x Obese strain White Leghorn intercross in QTL Express format.OS_map_QTLexpress_format.txtRJF x OS bone phenotypes (QTL express format)Bone phenotypes (residual values after adjusting for body weight) from the Red Junglefowl x Obese strain White Leghorn intercross in QTL Express format.OS_phenotypes_QTLexpress_format.txtBone eQTL data (R/qtl format)Residual bone and fecundity phenotypes (adjusted for body weight), preprocessed gene expression data and genotypes of the 127 individuals of the bone eQTL study in R/qtl csv input format.bone_eQTL_data_Rqtl_format.csvBone microarray data (raw and RMA preprocessed)Microarray data for the 127 individual bone samples. This files contains the raw as well as RMA preprocessed gene expression values, and design files for the custom NimbleGen gene expression chip used.bone_microarray_data.tar.gz
DOI: 10.5061/dryad.09j54
title: Data from: Responses of interspecific associations in mixed-species bird flocks to selective logging

description: 1. Non-trophic interactions (or, inter-species associations) play a
 prominent role in determining community structure and function.
 Mixed-species bird flocks are networks of non-trophic associations that
 confer foraging and anti-predator benefits to participant species. Yet,
 the responses of these interspecific associations to anthropogenic
 environmental change are poorly understood. 2. Selective logging is
 pervasive in the tropics, and can affect associations in mixed-species
 bird flocks by altering resource availability and/or predation risk, or
 through the altered abundances of species participating in mixed flocks.
 Across a gradient of logging intensity, we examined how the number and
 strength of associations in two different mixed-species flock types
 responded to logging intensity, while simultaneously controlling
 statistically for changes in the abundances of species in response to
 logging. 3. Across the logging gradient, we used network analyses to: (a)
 quantify the proportion of potentially realisable associations, and (b)
 measure the strengths of these realised associations. For both these
 analyses, we used null models to investigate whether changes in the
 network properties of mixed flocks were simply abundance-driven, or
 congruent with expectations of how flock properties might be modified by
 selective logging. 4. In understorey flocks, after controlling
 statistically for changing abundances of participant species, the
 proportion of realised associations decreased with increasing logging
 intensity, whereas mean association strength did not show any relation
 with logging intensity. In midstorey flocks, both the proportion and mean
 strength of realised associations increased with increasing logging
 intensity. 5. Synthesis and application: By statistically separating
 abundance and behaviour-mediated effects, we show that interspecific
 associations in mixed-species bird flocks respond to potential resource
 and/or predation changes from logging, but that their functional roles
 persist in logged forest. We show that logged forests can conserve not
 only community richness, but also function. Thus, these logged forests
 must be prevented from ongoing conversion into non-forest habitats such as
 agriculture and plantation.21-Dec-2017
description: Midstorey flock
 matricesThe file contains the
 plot wise recording of midstorey flocks. The rows are the flock ID and the
 columns are the species. The cell entries are the conspecific group sizes
 in mixed-flocks.Understorey flock
 matricesThe file contains the
 plot wise recording of understorey flocks. The rows are the flock ID and
 the colums are the species. The cell entries are the conspecific group
 size in mixed-species flocks.Species_weightsThe file contains the plot wise abundance estimation of flocking species. Please read the readme file for details.
DOI: 10.5061/dryad.t741c
title: Data from: Brain size affects the behavioral response to predators in female guppies (Poecilia reticulata)

description: Large brains are thought to result from selection for cognitive benefits,
 but how enhanced cognition leads to increased fitness remains poorly
 understood. One explanation is that increased cognitive ability results in
 improved monitoring and assessment of predator threats. Here, we use male
 and female guppies (Poecilia reticulata), artificially selected for large
 and small brain size, to provide an experimental evaluation of this
 hypothesis. We examined their behavioural response as singletons, pairs or
 shoals of four towards a model predator. Large-brained females, but not
 males, spent less time performing predator inspections, an inherently
 risky behaviour. Video analysis revealed that large-brained females were
 further away from the model predator when in pairs but that they
 habituated quickly towards the model when in shoals of four. Males stayed
 further away from the predator model than females but again we found no
 brain size effect in males. We conclude that differences in brain size
 affect the female predator response. Large-brained females might be able
 to assess risk better or need less sensory information to reach an
 accurate conclusion. Our results provide experimental support for the
 general idea that predation pressure is likely to be important for the
 evolution of brain size in prey species.
description: Processed_inspection_dataData table with meta data for all the trials and inspection variables.Raw_inspection_dataRaw JWatcher files for the inspection data.Raw_tracks_control_trialsRaw ctrax output (after manual correction) for novel object control trials.Raw_tracks_predator_trialsRaw ctrax output (after manual correction) for predator model trials.Processed_tracksLocation and orientation data (video tracking) for both predator and control trials, after processing.Video_snapshotsScreen grabs that may be used to process the raw tracking data.
DOI: 10.5061/dryad.7c730
title: Data from: Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia: genomic heterogeneity and temporal stability

description: Non-random association of alleles in the nucleus and cytoplasmic
 organelles, or cyto-nuclear linkage disequilibrium (LD), is both an
 important component of a number of evolutionary processes and a
 statistical indicator of others. The evolutionary significance of
 cyto-nuclear LD will depend on both its magnitude and how stable those
 associations are through time. Here, we use a longitudinal population
 genetic data set to explore the magnitude and temporal dynamics of
 cyto-nuclear disequilibria through time. We genotyped 135 and 170
 individuals from 16 and 17 patches of the plant species Silene latifolia
 in Southwestern VA, sampled in 1993 and 2008, respectively. Individuals
 were genotyped at 14 highly polymorphic microsatellite markers and a
 single-nucleotide polymorphism (SNP) in the mitochondrial gene, atp1.
 Normalized LD (D′) between nuclear and cytoplasmic loci varied
 considerably depending on which nuclear locus was considered (ranging from
 0.005–0.632). Four of the 14 cyto-nuclear associations showed a
 statistically significant shift over approximately seven generations.
 However, the overall magnitude of this disequilibrium was largely stable
 over time. The observed origin and stability of cyto-nuclear LD is most
 likely caused by the slow admixture between anciently diverged lineages
 within the species’ newly invaded range, and the local spatial structure
 and metapopulation dynamics that are known to structure genetic variation
 in this system.
description: FullDatasetThis file is a tab-delimited text file of genotype information formatted in the CONVERT file format (1). The marker ATP1 is not diploid, but rather is formatted in a manner that allows for direct import, along with the actually diploid microsatellites, into a number of population genetics softwares, including the utilized GenoDive (2). FullDataset.txt contains genotype information deriving from 14 microsatellites and one mtDNA SNP, deriving from 135 and 170 individuals deriving from a metapopulation of the flowering plant, Silene latifolia, located in Giles County, VA, USA, in 1993 and 2008, respectively. References: 1). Glaubitz JC (2004). convert: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol Ecol Notes 4(2): 309-310. 2). Meirmans PG, Van Tienderen PH (2004). GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes 4(4): 792-794.
DOI: 10.5061/dryad.pf684
title: Data from: Derivation of occupational thresholds of toxicological concern for airborne systemically-acting non-carcinogenic organic chemicals

description: Many substances in workplace do not have occupational exposure limits
 (OELs). The threshold of toxicological concern (TTC) principle is part of
 the hierarchy of approaches useful in occupational health risk assessment.
 The aim of this study was to derive occupational TTCs (OTTCs) reflecting
 the airborne concentrations below which no significant risk to workers
 would be anticipated. A reference dataset consisting of the 8-h threshold
 limit values -Time-Weighted Average (8-h TLV-TWA) for 280 organic
 substances was compiled. Each substance was classified into low (Class I),
 intermediate (Class II) or high (Class III) hazard categories as per
 Cramer rules. For each chemical, n-octanol:water partition coefficient and
 vapor pressure along with the molecular weight were used to predict the
 blood:air partition coefficient. The blood:air partition coefficient along
 with data on water solubility and ventilation rate allowed the prediction
 of pulmonary retention factor and absorbed dose in workers. For each
 Cramer class, the distribution of the predicted doses was analyzed to
 identify the various percentile values corresponding to occupational OTTC.
 Accordingly, for Cramer Classes I, II and III, the OTTCs derived in the
 present study correspond to 0.15, 0.0085 and 0.006 mmol/day at the 10th
 percentile level, while these values were 1.5, 0.09 and 0.03 mmol/day at
 the 25th percentile level. The proposed occupational TTCs are not meant to
 replace the traditional OELs, but can be used in data-poor situations
 along with exposure estimates to support screening level risk assessment
 and prioritization.
description: Organic substances with
 TLV and physicochemical propertiesThe file in the
 supplementary data is a table that lists the organic chemical substances
 that were studied as well as their Cramer classes, CASRN, occupational
 exposure limits (i.e. 8-h TLV-TWA), LogP, and vapor
 pressure.Supplementary_TOXSCI_170119.docx
DOI: 10.5061/dryad.q4sc8
title: Data from: The future of practical skills in undergraduate medical education – an explorative Delphi-Study

description: Background: 64% of young medical professionals in Germany do not feel
 adequately prepared for the practical requirements of the medical
 profession. The goal of “outcome-orientated training” is to structure
 medical curricula based on the skills needed when entering the workforce
 after completing undergraduate medical education, and thus to bridge the
 gap between the skills graduates have attained and those necessary for a
 career in the medical profession. Outcome frameworks (OFs) are used for
 this purpose. In preparation for developing the National Competence-Based
 Catalogue of Learning Objectives for Medicine (NKLM) – the German OF – the
 “Consensus Statement of Practical Skills in Undergraduate Medical
 Education” (which structures the teaching and acquisition of practical
 skills in Germany and which strongly influenced the “Clinical-Practical
 Skills” chapter of the NKLM) was published in 2011. It is not uncommon for
 at least a decade to elapse between the definition and implementation of
 an OF and the students’ graduation, which can further increase the gap
 between necessary and acquired skills. Thus, the purpose of this paper is
 to posit theses for future development in healthcare and to apply these
 theses to a current OF. Methodology: Partially structured interviews with
 experts were used to generate theses pertaining to general, future
 development in healthcare. These theses were assessed by physician experts
 based on the likelihood of implementation by the year 2025. The 288
 learning goals of the consensus statement were assessed for their
 relevance for medical education in the interim. Results: 11 theses were
 generated for the development of medicine, and these theses were assessed
 and discussed by 738 experts. These theses include the increase in
 diseases associated with old age, the increasing significance of
 interprofessional cooperation, and the growing prevalence of telemedicine
 applications. Of the 288 learning goals of the consensus statement, 231 of
 the goals were assessed as relevant, and 57 were deemed irrelevant for the
 short-term future. Discussion: The theses on the future of healthcare,
 which were generated in this study and which were validated by numerous
 experts, provide indications of future developments of overall
 requirements for medical school graduates. For example, when applied to
 the content of the “Clinical-Practical Skills” NKLM chapter, they largely
 validate the future relevance of developing practical skills while also
 providing indications for their further development as applied to the
 consensus statement.
description: Delphi_Rohdaten -
 english
DOI: 10.5061/dryad.gd14g
title: Data from: Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

description: Recent advances in the scale and diversity of population genomic datasets
 for bacteria now provide the potential for genome-wide patterns of
 co-evolution to be studied at the resolution of individual bases. Here we
 describe a new statistical method, genomeDCA, which uses recent advances
 in computational structural biology to identify the polymorphic loci under
 the strongest co-evolutionary pressures. We apply genomeDCA to two large
 population data sets representing the major human pathogens Streptococcus
 pneumoniae (pneumococcus) and Streptococcus pyogenes (group A
 Streptococcus). For pneumococcus we identified 5,199 putative epistatic
 interactions between 1,936 sites. Over three-quarters of the links were
 between sites within the pbp2x, pbp1a and pbp2b genes, the sequences of
 which are critical in determining non-susceptibility to beta-lactam
 antibiotics. A network-based analysis found these genes were also coupled
 to that encoding dihydrofolate reductase, changes to which underlie
 trimethoprim resistance. Distinct from these antibiotic resistance genes,
 a large network component of 384 protein coding sequences encompassed many
 genes critical in basic cellular functions, while another distinct
 component included genes associated with virulence. The group A
 Streptococcus (GAS) data set population represents a clonal population
 with relatively little genetic variation and a high level of linkage
 disequilibrium across the genome. Despite this, we were able to pinpoint
 two RNA pseudouridine synthases, which were each strongly linked to a
 separate set of loci across the chromosome, representing biologically
 plausible targets of co-selection. The population genomic analysis method
 applied here identifies statistically significantly co-evolving locus
 pairs, potentially arising from fitness selection interdependence
 reflecting underlying protein-protein interactions, or genes whose product
 activities contribute to the same phenotype. This discovery approach
 greatly enhances the future potential of epistasis analysis for systems
 biology, and can complement genome-wide association studies as a means of
 formulating hypotheses for targeted experimental work.
description: Genome alignment for
 3,156 isolates of S. pneumoniaeFasta formatted genome
 alignment of the Maela Streptococcus pneumoniae isolates considered in the
 study.maela3K.original.zip.7zGenome alignment for 3,442 isolates of S. pyogenesFasta formatted genome alignment of 3,442 isolates of Streptococcus pyogenes considered in the study.M1_3442-postepidemic_strains_alignment.7zTableS5Coupling estimates for the 5078 locus M1 data set
DOI: 10.5061/dryad.f5849
title: Data from: Invasion history alters the behavioural consequences of immune system activation in cane toads.

description: 1. Acute activation of the immune system often initiates a suite of
 behavioural changes. These ‘sickness behaviours’—involving lethargy and
 decreased activity—may be particularly costly on invasion fronts, where
 evolutionary pressures on dispersal favour individuals that move large
 distances. 2. We used a combination of field and laboratory studies to
 compare sickness behaviours of cane toads from populations differing in
 invasion history. To do this we stimulated immune system activation by
 injecting lipopolysaccharide (LPS) to mimic bacterial infection. 3. We
 predicted that LPS would result in less severe sickness behaviour in toads
 from invasion-front populations because they had undergone selection for
 rapid and sustained dispersal (activities in conflict with lethargy and
 decreased activity). 3. Contrary to our prediction, LPS injection caused a
 greater reduction in dispersal-relevant traits in invasion-front
 individuals than in conspecifics from the range core. 4. Our data suggest
 that the rapid invasion of cane toads through tropical Australia has seen
 an evolutionary shift in the magnitude of sickness behaviour elicited by
 pathogen infection. The increased sickness behaviour among invasion-front
 toads suggests a shift away from pathogen tolerance (seen in range-core
 populations) towards resistance to pathogen attack. But as a consequence,
 when pathogens do become successfully established, toads from
 invasion-front populations may have less capacity to tolerate their
 ill-effects.
description: dryad
 datasetThe first page of the
 spreadsheet contains data used to generate Table 1 in the manuscript. The
 second spreadsheet page contains data used to generate Table
 2.
DOI: 10.5061/dryad.8066v
title: Data from: The opportunity for balancing selection in experimental populations of Caenorhabditis elegans

description: The role of balancing selection in maintaining diversity during the
 evolution of sexual populations to novel environments is poorly
 understood. To address this issue, we studied the impact of two mating
 systems, androdioecy and dioecy, on genotype distributions during the
 experimental evolution of Caenorhabditis elegans. We analyzed the temporal
 trajectories of 334 single nucleotide polymorphisms (SNPs), covering 1/3
 of the genome, and found extensive allele frequency changes and little
 loss of heterozygosities after 100 generations. As modeled with numerical
 simulations, SNP differentiation was consistent with genetic drift and
 average fitness effects of 2%, assuming that selection acted independently
 at each locus. Remarkably, inbreeding by self-fertilization was of little
 consequence to SNP differentiation. Modeling selection on deleterious
 recessive alleles suggests that the initial dynamics can be explained by
 associative overdominance, but not the later stages since much lower
 heterozygosities would be maintained. By contrast, models with selection
 on true overdominant loci can explain the heterozygote excess observed at
 all periods, particularly when negative epistasis or independent fitness
 effects were considered. Overall, these findings indicate that selection
 at single loci, including purging of recessive alleles, underlies most of
 the genetic differentiation accomplished during the experiment.
 Nonetheless they also imply that maintenance of genetic diversity may be
 due to balancing selection.
description: Genotype
 dataGenotype_data.txtSimulated data - deleterious recessive alleles - A populationsDel_recessive_A.RSimulated data - deleterious recessive alleles - D populationsDel_recessive_D.RSimulated data - balancing selection - A populationsBalancing_A.RSimulated data - balancing selection - D populationsBalancing_D.R
DOI: 10.5061/dryad.hp4b4
title: Data from: Panmixia in a critically endangered fish: the totoaba (Totoaba macdonaldi) in the Gulf of California

description: Conservation of the evolutionary legacy of endangered species is a key
 component for long-term persistence. Totoaba is a long-lived fish endemic
 to the Gulf of California and is considered critically endangered. There
 is currently a debate concerning its conservation status and whether it
 can be used as a fishery resource. Unfortunately, basic information on
 biological and genetic population structure of the species is lacking. We
 sampled 313 individuals and employed 16 microsatellite loci and 3
 mitochondrial DNA markers (16S, 547 pb; COI, 619 pb; control region, 650
 pb) to assess population structure and demography of totoaba in the Gulf
 of California, with samples from locations that encompass nearly all of
 its recognized geographic distribution. We could not reject a hypothesis
 of panmixia for totoaba, using nuclear or mitochondrial markers.
 Demographic analysis of mtDNA suggests a sudden population expansion
 model. The results have important implications for totoaba conservation
 because poaching is a significant conservation challenge and could have
 additive negative effects over the single population of totoaba in the
 Gulf of California.
description: Totoaba_GenotypesTotoaba genotypes from 16 microsatellite loci in 310 individuals. Data file is in Genepop format.