cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6tv35cc2
title: Data from: Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies

description: Association mapping of important traits of crop plants relies on first
 understanding the extent and patterns of linkage disequilibrium (LD) in
 the particular germplasm being investigated. We characterize here the
 genetic diversity, population structure and genome wide LD patterns in a
 set of asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm
 from China. A diverse collection of 99 asparagus bean and normal cowpea
 accessions were genotyped with 1127 expressed sequence tag-derived single
 nucleotide polymorphism markers (SNPs). The proportion of polymorphic SNPs
 across the collection was relatively low (39%), with an average number of
 SNPs per locus of 1.33. Bayesian population structure analysis indicated
 two subdivisions within the collection sampled that generally represented
 the ‘standard vegetable’ type (subgroup SV) and the ‘non-standard
 vegetable’ type (subgroup NSV), respectively. Level of LD (r2) was higher
 and extent of LD persisted longer in subgroup SV than in subgroup NSV,
 whereas LD decayed rapidly (0–2 cM) in both subgroups. LD decay distance
 varied among chromosomes, with the longest (≈5 cM) five times longer than
 the shortest (≈1 cM). Partitioning of LD variance into within- and
 between-subgroup components coupled with comparative LD decay analysis
 suggested that linkage group 5, 7 and 10 may have undergone the most
 intensive epistatic selection toward traits favorable for vegetable use.
 This work provides a first population genetic insight into domestication
 history of asparagus bean and demonstrates the feasibility of mapping
 complex traits by genome wide association study in asparagus bean using a
 currently available cowpea SNPs marker platform.
description: Xu et al raw SNP
 genotyping data_HeredityThis file contains the
 raw genotyping data of the 1102 EST-derived SNPs loci with successful
 calls in the sample set used in this study. Column A: IDs of the plant
 materials; Line1: names of the SNP markers. Question marks indicate
 unsuccessful or ambiguous calls.
DOI: 10.5061/dryad.v837d
title: Data from: Obesity and the role of short duration submaximal work on cardiovascular and cerebral hemodynamics

description: The objective of this study was to compare gas exchange, cardiac and
 cerebral hemodynamic responses between 10 non-obese and 10 obese men
 during submaximal work. With the increasing prevalence of obesity, there
 is a need to understand the impact of obesity on work-induced responses.
 Participants completed a step-wise incremental cycling until they reached
 60% of their age-predicted maximum heart rate. Gas exchange, cardiac and
 pre-frontal cortex hemodynamic responses were simultaneously measured
 during rest, work, and recovery. The non-obese group reached ~43% of their
 predicted maximal aerobic capacity as compared to ~34% in the obese group,
 with the non-obese working at a relatively higher workload and for more
 duration than the obese. The obese had elevated baseline heart rate and
 reduced whole-body oxygen uptake per body weight at baseline and task
 termination. Other cardiac and cerebral responses, although increased from
 baseline, were similar between groups during submaximal effort. In the
 obese, during recovery oxygen uptake and heart-rate recovery were slowest;
 cardiac output and rate pressure product were greatest, and left ventricle
 ejection time was shortest. However, both groups exhibited similar
 cerebral hemodynamics during recovery. These finding imply that,
 irrespective of their low aerobic fitness, obesity does not impair
 myocardial performance and cerebrovascular function during graded
 submaximal work, however, recovery from a short duration of work was
 influenced by their fitness level. Since a majority of activities of daily
 living are performed at individual’s submaximal level, understanding
 influence of obesity on submaximal work is critical.
description: Cycling
 Cardiorespiratory ResponsesCardiorespiratory
 responses measured during a submaximal cycling task to 60% of
 age-predicted maximum heart rate. Measurements were made using a Cosmed
 k4b2 portable system.Cycling
 Data.zip
DOI: 10.5061/dryad.7vd0160
title: Data from: Effector gene birth in plant parasitic nematodes: neofunctionalization of a housekeeping glutathione synthetase gene

description: Plant pathogens and parasites are a major threat to global food security.
 Plant parasitism has arisen four times independently within the phylum
 Nematoda, resulting in at least one parasite of every major food crop in
 the world. Some species within the most economically important order
 (Tylenchida) secrete proteins termed effectors into their host during
 infection to re-programme host development and immunity. The precise
 detail of how nematodes evolve new effectors is not clear. Here we
 reconstruct the evolutionary history of a novel effector gene family. We
 show that during the evolution of plant parasitism in the Tylenchida, the
 housekeeping glutathione synthetase (GS) gene was extensively replicated.
 New GS paralogues acquired multiple dorsal gland promoter elements,
 altered spatial expression to the secretory dorsal gland, altered temporal
 expression to primarily parasitic stages, and gained a signal peptide for
 secretion. The gene products are delivered into the host plant cell during
 infection, giving rise to “GS-like effectors”. Remarkably, by solving the
 structure of GS-like effectors we show that during this process they have
 also diversified in biochemical activity, and likely represent the
 founding members of a novel class of GS-like enzyme. Our results
 demonstrate the re-purposing of an endogenous housekeeping gene to form a
 family of effectors with modified functions. We anticipate that our
 discovery will be a blueprint to understand the evolution of other
 plant-parasitic nematode effectors, and the foundation to uncover a novel
 enzymatic function.
description: All GS-like protein
 sequences from 11 nematode species.180 GS-like protein
 sequences from 11 nematode species across the phylum. Deduced amino acid
 sequences from genome and/or transcriptome assemblies.PLOS_GEN_.treeorder.one_per_line.new_namesAll GS-like nucleotide sequences from 10 nematode species176 GS-like nucleotide sequences from 10 nematode species across the phylum. Sequences are not available for M. incognita. sequences encode the entire transcript, and in some cases 5' and/or 3' UTRsPLOS_GEN_.treeorder.one_per_line.new_names.cds
DOI: 10.5061/dryad.4085r
title: Data from: Toxin-resistant isoforms of Na+/K+-ATPase in snakes do not closely track dietary specialization on toads

description: Toads are chemically defended by bufadienolides, a class of cardiotonic
 steroids that exert toxic effects by binding to and disabling the
 Na+/K+-ATPases of cell membranes. Some predators, including a number of
 snakes, have evolved resistance to the toxic effects of bufadienolides and
 prey regularly on toads. Resistance in snakes to the acute effects of
 these toxins is conferred by at least two amino acid substitutions in the
 cardiotonic steroid binding pocket of the Na+/K+-ATPase. We surveyed 100
 species of snakes from a broad phylogenetic range for the presence or
 absence of resistance-conferring mutations. We found that such mutations
 occur in a much wider range of taxa than previously believed. Although all
 sequenced species known to consume toads exhibited the resistance
 mutations, many of the species possessing the mutations do not feed on
 toads, much less specialize on that food source. This suggests that either
 there is little performance cost associated with these mutations or they
 provide an unknown benefit. Furthermore, the distribution of the mutation
 among major clades of advanced snakes suggests that the origin of the
 mutation reflects evolutionary retention more than dietary constraint.
description: Script for stochastic
 character mappingThis R script was used
 for stochastic character mapping of the resistance mutations. It relies on
 phytools and data files (character states and a tree) that are included in
 this submission.fitAnc.RReistance mutation character stateThis matrix provides the mutation state for each snake species (NA for missing data). Resistance mutations are encoded with 1, and the non-resistant mutation with 0. The two data columns give the two mutations in order.charMatrixCor.txtNucleotide mutation matrixThis matrix provides the mutation state for each snake species (NA for missing data), but here the two different resistance mutations (A to G vs. A to C) at codon 120 are considered separately. Specifically, resistance mutations are encoded with 1 or 2 (2 only applies to codon 120), and the non-resistant mutation with 0. The two data columns give the two mutations in ordercharMatrixAA.txtPhylogenetic treeThis is the tree we used for the analyses. This tree was originally published by Zhen and Weins (2016), and is simply included here to ensure our analyses can be recreated from the data on Dryad.mmc3.txt
DOI: 10.5061/dryad.63m17n5
title: Data from: Accuracy of node and bud-scar counts for aging two dominant conifers in western North America

description: Accurately aging trees is critical for understanding tree demography and
 tree responses to environmental change. Given the proliferation of studies
 aimed at understanding the effects of climate and disturbance on forest
 ecosystems, it is important to understand the tradeoffs between
 field-based age estimates and precise dendrochronological techniques. We
 assessed the accuracy of age estimates from node counts in the field
 against precise tree-ring counts at the root-shoot boundary, in 1279
 ponderosa pine and 1268 Douglas-fir seedlings sampled from across three
 study regions in the western U.S. We also assessed the accuracy of age
 estimates from bud-scar counts in the field against node counts and
 precise tree-ring counts in a subset of 757 seedlings from the Northern
 Rockies. Node counts systematically underestimated ring counts by an
 average of 4.1 years, with bias increasing with tree age. At annual, ±1-,
 ±2-, and ±5-yr precision, the accuracy of node counts was 5%, 15%, 29%,
 and 74% across all regions and species, respectively. Similar results were
 found for bud scars. Given the magnitude of the bias between field-based
 methods and ring counts, it is critical to select appropriate aging
 methods, based on the precision required to answer specific ecological
 questions. To improve the accuracy of field-based age estimates in these
 species, we provide a tool for correcting for the bias when precise
 dendrochronological aging is not feasible.
description: ReadMe_DataReadMe_ScriptsData_TreeAgesData_AgeToolTemplate_NodeDataScript_Hankin_et_al_Analysis_CodeScript_Hankin_et_al_Node_to_Age_Tool
DOI: 10.5061/dryad.dr357sv
title: Data from: Impacts of mixed-grazing on root biomass and belowground net primary production in a temperate desert steppe

description: The impacts of large herbivores on plant communities differ depending on
 the plants and the herbivores. Few studies have explored how herbivores
 influence root biomass. Root growth of vegetation was studied in the field
 with four treatments: sheep grazing alone (SG), cattle grazing alone (CG),
 mixed grazing with cattle and sheep (MG) and no grazing (CK). Live and
 total root biomasses were measured using the root ingrowth core and the
 drilling core, respectively. After 2 years of grazing, total root biomass
 showed a decreasing trend while live root biomass increased with time
 during the growing seasons. Belowground net primary production (BNPP)
 among the treatments varied from 166±32 to 501±88 g.m-2 and root turnover
 rates (RTR) varied from 0.25±0.05 to 0.70±0.11 year-1. SG had the greatest
 BNPP and RTR, while the CG had the smallest BNPP and RTR. BNPP and RTR of
 the MG treatment were between those of the CG and SG treatments. BNPP and
 RTR of the CK were similar to MG treatment. Compared with other
 treatments, CG had a greater impact on dominant tall grasses species in
 communities. SG could decrease community diversity. MG eliminated the
 disadvantages of single-species grazing and was beneficial to community
 diversity and stability.
description: Appendix
 S1,S2,S3,S4,S5,S6,S7Appendix S1 Variation in
 root biomass and its proportion of the plant community as measured using
 the drilling method in stratified soil layer in different months of the
 growing season. Appendix S2 Data and statistical analysis on live root
 biomass, total root biomass and proportion of live root to total root
 mass. Appendix S3 Data and statistical analysis on BNPP and root turnover
 rate Appendix S4 Data and statistical analysis on relationships between
 root turnover rate and the ratio of live root mass to total root mass.
 Appendix S5 Data and statistical analysis on aboveground biomass in June,
 July, August and September. Appendix S6 Data and statistical analysis on
 standing live biomass of functional groups of the plant community Appendix
 S7 Primary data of this paper.Wang_et al_Impacts of
 mixed-grazing on root mass on steppe_Appendix
 S1-S7.zip
DOI: 10.5061/dryad.s1634
title: Data from: Validation of the instrument of health literacy competencies for Chinese-speaking health professionals

description: The study aimed to illustrate the constructs and test the psychometric
 properties of an instrument of health literacy competencies (IOHLC) for
 health professionals. A multi-phase questionnaire development method was
 used to develop the scale. The categorization of the knowledge and
 practice domains achieved consensus through a modified Delphi process. To
 reduce the number of items, the 92-item IOHLC was psychometrically
 evaluated through internal consistency, Rasch modeling, and two-stage
 factor analysis. In total, 736 practitioners, including nurses, nurse
 practitioners, health educators, case managers, and dieticians completed
 the 92-item IOHLC online from May 2012 to January 2013. The final version
 of the IOHLC covered 9 knowledge items and 40 skill items containing 9
 dimensions, with good model fit, and explaining 72% of total variance. All
 domains had acceptable internal consistency and discriminant validity. The
 tool in this study is the first to verify health literacy competencies
 rigorously. Moreover, through psychometric testing, the 49-item IOHLC
 demonstrates adequate reliability and validity. The IOHLC may serve as a
 reference for the theoretical and in-service training of Chinese-speaking
 individuals' health literacy competencies.
description: Final Data (N=736)
 20140103Raw data for total
 subjects in EXCELfinaldatan736.xlsx
DOI: 10.5061/dryad.54r13
title: Data from: Development and application of a novel metric to assess effectiveness of biomedical data

description: Objective: Design a metric to assess the comparative effectiveness of
 biomedical data elements within a study that incorporates their
 statistical relatedness to a given outcome variable as well as a
 measurement of the quality of their underlying data. Materials and
 methods: The cohort consisted of 874 patients with adenocarcinoma of the
 lung, each with 47 clinical data elements. The p value for each element
 was calculated using the Cox proportional hazard univariable regression
 model with overall survival as the endpoint. An attribute or A-score was
 calculated by quantification of an element's four quality attributes;
 Completeness, Comprehensiveness, Consistency and Overall-cost. An
 effectiveness or E-score was obtained by calculating the conditional
 probabilities of the p-value and A-score within the given data set with
 their product equaling the effectiveness score (E-score). Results: The
 E-score metric provided information about the utility of an element beyond
 an outcome-related p value ranking. E-scores for elements
 age-at-diagnosis, gender and tobacco-use showed utility above what their
 respective p values alone would indicate due to their relative ease of
 acquisition, that is, higher A-scores. Conversely, elements surgery-site,
 histologic-type and pathological-TNM stage were down-ranked in comparison
 to their p values based on lower A-scores caused by significantly higher
 acquisition costs. Conclusions: A novel metric termed E-score was
 developed which incorporates standard statistics with data quality metrics
 and was tested on elements from a large lung cohort. Results show that an
 element's underlying data quality is an important consideration in
 addition to p value correlation to outcome when determining the
 element's clinical or research utility in a study.
description: Lung Cancer Cohort
 Data47 clinical data
 elements for a cohort of 874 patients with adenocarcinoma of the
 lung.CER
 Data.csv
DOI: 10.5061/dryad.8982
title: Data from: Two spinefoot colour morphs: mottled spinefoot Siganus fuscescens and white-spotted spinefoot Siganus canaliculatus are synonyms

description: Mottled spinefoot Siganus fuscescens and white-spotted spinefoot Siganus
 canaliculatus are two similar species that differ subtly in colouration
 and morphology. Three major mtDNA clades were identified for these
 species, but individuals were clustered by amplified fragment length
 polymorphism (AFLP) according to geography rather than morphology,
 suggesting that the colour morphs are interbreeding.
description: Taiwan_Indonesia_AFLP
 data_for_publicationAFLP binary
 data
DOI: 10.5061/dryad.j4n89
title: Data from: ‘Manipulation’ without the parasite: altered feeding behaviour of mosquitoes is not dependent on infection with malaria parasites

description: Previous studies have suggested that Plasmodium parasites can manipulate
 mosquito feeding behaviours such as probing, persistence and engorgement
 rate in order to enhance transmission success. Here, we broaden analysis
 of this ‘manipulation phenotype’ to consider proximate foraging
 behaviours, including responsiveness to host odours and host location.
 Using Anopheles stephensi and Plasmodium yoelii as a model system, we
 demonstrate that mosquitoes with early stage infections (i.e.
 non-infectious oocysts) exhibit reduced attraction to a human host,
 whereas those with late-stage infections (i.e. infectious sporozoites)
 exhibit increased attraction. These stage-specific changes in behaviour
 were paralleled by changes in the responsiveness of mosquito odourant
 receptors, providing a possible neurophysiological mechanism for the
 responses. However, we also found that both the behavioural and
 neurophysiological changes could be generated by immune challenge with
 heat-killed Escherichia coli and were thus not tied explicitly to the
 presence of malaria parasites. Our results support the hypothesis that the
 feeding behaviour of female mosquitoes is altered by Plasmodium, but
 question the extent to which this is owing to active manipulation by
 malaria parasites of host behaviour.
description: Electrophysiology_DataAll EPG recordingsHost_Seeking Data
DOI: 10.5061/dryad.n62p4
title: Data from: Genetic and paleomodelling evidence of the population expansion of the cattle egret Bubulcus ibis in Africa during the climatic oscillations of the Late Pleistocene

description: Increasing aridity during glacial periods produced the retraction of
 forests and the expansion of arid and semi-arid environments in Africa,
 with consequences for birds. Cattle egret (Bubulcus ibis) is a dispersive
 species that prefers semiarid environments and requires proximity to
 bodies of water. We expected that climatic oscillations led to the
 expansion of the range of the cattle egret during arid periods, such as
 the Last Maximum Glacial (LGM) and contraction of distribution during the
 Last Interglacial (LIG) period, resulting in contact of populations
 previously isolated. We investigated this hypothesis by evaluating the
 genetic structure and population history of 15 cattle egret breeding
 colonies located in West and South Africa using the mitochondrial DNA
 (mtDNA) control region, mtDNA ATPase 8 and 6, and an intron of nuclear
 gene transforming growth factor beta-2. Occurrence data and bioclimatic
 information were used to generate ecological niche models of three periods
 (present, LGM and LIG). We used the genetic and paleomodelling data to
 assess the responses of the cattle egret from Africa to the climatic
 oscillations during the late Pleistocene. Genetic data revealed low levels
 of genetic differentiation, signs of isolation-by-distance, as well as
 recent increases in effective population size that started during the LGM.
 The observed low genetic structure may be explained by recent colonization
 events due to the demographic expansion following the last glacial period
 and by dispersal capacity of this species. The paleomodels corroborated
 the expansion during the LGM, and a more restricted potential distribution
 during the LIG. Our findinds supports the hypothesis that the species
 range of the cattle egret expanded during arid periods and contracted
 during wet periods.
description: Nexus file of DNA
 sequence alignments for mtDNA control region without nine positions with
 signs of homoplasyCR.nexusNexus file of DNA sequence alignments for ATPase 6 and 8ATPase.nexusNexus file of DNA sequence alignments for phased alleles of the intron 5 of the TGFB2TGFB2.nexus
DOI: 10.5061/dryad.q4747
title: Data from: Correlation between the green-island phenotype and Wolbachia infections during the evolutionary diversification of Gracillariidae leaf-mining moths

description: Internally feeding herbivorous insects such as leaf miners have developed
 the ability to manipulate the physiology of their host plants in a way to
 best meet their metabolic needs and compensate for variation in food
 nutritional composition. For instance, some leaf miners can induce
 green-islands on yellow leaves in autumn, which are characterized by
 photosynthetically active green patches in otherwise senescing leaves. It
 has been shown that endosymbionts, and most likely bacteria of the genus
 Wolbachia, play an important role in green-island induction in the apple
 leaf-mining moth Phyllonorycter blancardella. However, it is currently not
 known how widespread is this moth-Wolbachia-plant interaction. Here, we
 studied the co-occurrence between Wolbachia and the green-island phenotype
 in 133 moth specimens belonging to 74 species of Lepidoptera including 60
 Gracillariidae leaf miners. Using a combination of molecular phylogenies
 and ecological data (occurrence of green-islands), we show that the
 acquisitions of the green-island phenotype and Wolbachia infections have
 been associated through the evolutionary diversification of
 Gracillariidae. We also found intraspecific variability in both
 green-island formation and Wolbachia infection, with some species being
 able to form green-islands without being infected by Wolbachia. In
 addition, Wolbachia variants belonging to both A and B supergroups were
 found to be associated with green-island phenotype suggesting several
 independent origins of green-island induction. This study opens new
 prospects and raises new questions about the ecology and evolution of the
 tripartite association between Wolbachia, leaf miners, and their host
 plants.
description: alignement for
 leaf-miner phylogenyalignement for
 leaf-miner phylogeny based on COI, Ef1-alpha, histone3 and
 wingless.4genes_alignment.nex16S gene alignement for Wolbachia phylogeny16S gene alignement for Wolbachia phylogeny16S.nxswsp based alignment for Wolbachia phylogenywsp based alignment for Wolbachia phylogenywsp.nxs