cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cj4c2s1
title: Data from: A family-based study into penetrance in facioscapulohumeral muscular dystrophy type 1

description: Objective: An observational cross-sectional study was conducted in a
 national facioscapulohumeral muscular dystrophy (FSHD) expertise center to
 estimate the penetrance of FSHD1 and to evaluate phenotype–genotype
 correlations. Methods: Ten FSHD1 probands carrying 4–9 D4Z4 unit alleles
 and 140 relatives were examined. All 150 participants were genetically
 characterized, including D4Z4 methylation levels in the mutation carriers.
 Mutation carriers were classified as (1) symptomatic: with symptoms of
 muscle weakness on history and muscle FSHD signs on examination; (2)
 asymptomatic: without symptoms of muscle weakness but with muscle FSHD
 signs on examination; and (3) nonpenetrant: without symptoms of muscle
 weakness on history and without muscle FSHD signs on examination. We
 assessed the relationship between age-corrected clinical severity score
 and repeat size, sex, and D4Z4 methylation levels. Results: The maximum
 likelihood estimates of symptomatic and those of symptomatic plus
 asymptomatic FSHD showed that penetrance depends on repeat size and
 increases until late adulthood. We observed many asymptomatic carriers
 with subtle facial weakness with or without mild shoulder girdle weakness
 (25% [17/69]). Nonpenetrance was observed less frequently than in recent
 population studies (17% [12/69]), and most asymptomatic patients reported
 some shoulder pain. D4Z4 methylation tended to be lower in moderately to
 severely affected mutation carriers with 7 or 9 repeats. Discussion: This
 family-based study detected a lower overall nonpenetrance than previously
 observed, probably due to many asymptomatic mutation carriers identified
 by careful examination of facial and shoulder muscles. The recognition of
 asymptomatic mutation carriers is essential for selection of participants
 for future trials, and the likelihood estimates are helpful in counseling.
description: Supplemental data
 Pedigrees_20170209_Revision NeurologyThis file contains the
 pedigrees of the families described in: A family-based study into
 penetrance in facioscapulohumeral muscular dystrophy type 1. The file
 numbers refer to the family numbers in the text and supplemental data 2.
 All participants have a patient number that is designated in the file.
 Patients without number were below 18 years.
DOI: 10.5061/dryad.sh546k0
title: Data from: Insular woody daisies (Argyranthemum , Asteraceae) are more resistant to drought-induced hydraulic failure than their herbaceous relatives

description: 1. Insular woodiness refers to the evolutionary transition from
 herbaceousness towards derived woodiness on (sub)tropical islands, and
 leads to island floras that have a higher proportion of woody species
 compared to floras of nearby continents. 2. Several hypotheses have tried
 to explain insular woodiness since Darwin’s original observations, but
 experimental evidence why plants became woody on islands is scarce at
 best. 3. Here, we combine experimental measurements of hydraulic failure
 in stems (as a proxy for drought stress resistance) with stem anatomical
 observations in the daisy lineage (Asteraceae), including insular woody
 Argyranthemum species from the Canary Islands and their herbaceous
 continental relatives. 4. Our results show that stems of insular woody
 daisies are more resistant to drought-induced hydraulic failure than the
 stems of their herbaceous counterparts. The anatomical character that best
 predicts variation in embolism resistance is intervessel pit membrane
 thickness (TPM), which can be functionally linked with air bubble dynamics
 throughout the 3D vessel network. There is also a strong link between TPM
 vs degree of woodiness and thickness of the xylem fiber wall vs embolism
 resistance, resulting in an indirect link between lignification and
 resistance to embolism formation. 5. Thicker intervessel pit membranes in
 Argyranthemum functionally explain why this insular woody genus is more
 embolism resistant to drought-induced failure compared to the herbaceous
 relatives from which it has evolved, but additional data are needed to
 confirm that palaeoclimatic drought conditions has triggered wood
 formation in this daisy lineage.
description: Hydraulic measurements
 of Argyranthemum speciesHydraulic measurements
 performed with cavitron for the five Argyranthemum species studied. The
 file contain the P50, P12, P88 and Kmax values of each branch used, with
 the individual and species average.Cavitron_argyranthemum.xlsHydraulic measurements of daisy herbaceous speciesHydraulic measurements performed with cavitron for the five daisy herbaceous species studied. The file contain the P50, P12, P88 and Kmax values of each branch used, with the individual and species average.Cavitron_daisy_herbaceous.xlsStem anatomical measurementsMeasurements of stem anatomical characters of woody and herbaceous daisies. For each feature were measured at least 2 individuals per species, except for Cladanthus mixtus, for which we have measured 9 individuals for proportion of lignified area over stem area 4 individuals for thickness of intervessel pit membrane
DOI: 10.5061/dryad.hm60m7n
title: Data from: Evaluation of acoustic telemetry grids for determining aquatic animal movement and survival

description: 1. Acoustic telemetry studies have frequently prioritized linear
 configurations of hydrophone receivers, such as perpendicular from
 shorelines or across rivers, to detect the presence of tagged aquatic
 animals. This approach introduces unknown bias when receivers are
 stationed for convenience at geographic bottlenecks (e.g., at the mouth of
 an embayment or between islands) as opposed to deployments following a
 statistical sampling design. 2. We evaluated two-dimensional acoustic
 receiver arrays (grids: receivers spread uniformly across space) as an
 alternative approach to provide estimates of survival, movement, and
 habitat use. Performance of variably-spaced receiver grids (5–25 km
 spacing) was evaluated by simulating (1) animal tracks as correlated
 random walks (speed: 0.1–0.9 m/s; turning angle standard deviation: 5–30
 degrees); (2) variable tag transmission intervals along each track
 (nominal delay: 15–300 seconds); and (3) probability of detection of each
 transmission based on logistic detection range curves (midpoint: 200–1500
 m). From simulations, we quantified i) time between successive detections
 on any receiver (detection time), ii) time between successive detections
 on different receivers (transit time), and iii) distance between
 successive detections on different receivers (transit distance). 3. In the
 most restrictive detection range scenario (200 m), the 95th percentile of
 transit time was 3.2 days at 5 km grid spacing, 5.7 days at 7 km, and 15.2
 days at 25 km; for the 1500 m detection range scenario, it was 0.1 days at
 5 km, 0.5 days at 7 km, and 10.8 days at 25 km. These values represented
 upper bounds on the expected maximum time that an animal could go
 undetected. Comparison of the simulations with pilot studies on three
 fishes (walleye Sander vitreus, common carp Cyprinus carpio, and channel
 catfish Ictalurus punctatus) from two independent large lake ecosystems
 (lakes Erie and Winnipeg) revealed shorter detection and transit times
 than what simulations predicted. 4. By spreading effort uniformly across
 space, grids can improve understanding of fish migration over the commonly
 employed receiver line approach, but at increased time cost for
 maintaining grids.
description: Acoustic telemetry
 detection dataThis file explains the
 variables in the acoustic telemetry detection dataset that accompanies:
 Kraus et al. 2018, Evaluation of Acoustic Telemetry Grids for Determining
 Aquatic Animal Movement and Survival, in Methods in Ecology and
 Evolution.Kraus-et-al-MEE-telemetry-detection-data-for-Erie-Winnipeg.csv
DOI: 10.5061/dryad.p6qb650
title: Data from: Population need for primary eye care in Rwanda: a national survey

description: Background: Universal access to Primary Eye Care (PEC) is a key global
 initiative to reduce and prevent avoidable causes of visual impairment
 (VI). PEC can address minor eye conditions, simple forms of uncorrected
 refractive error (URE) and create a referral pathway for specialist eye
 care, thus offering a potential solution to a lack of eye health
 specialists in low-income countries. However, there is little information
 on the population need for PEC, including prevalence of URE in all ages in
 Sub-Saharan Africa. Methods: A national survey was conducted of people
 aged 7 and over in Rwanda in September-December 2016. Participants were
 selected through two-stage probability proportional to size sampling and
 compact segment sampling. VI (visual acuity&lt;6/12) was assessed
 using Portable Eye Examination Kit (PEEK); URE was detected using a
 pinhole and presbyopia using local near vision test. We also used
 validated questionnaires to collect socio-demographic and minor eye
 symptoms information. Prevalence estimates for VI, URE and need for PEC
 (URE, presbyopia with good distance vision, need for referrals and minor
 eye conditions) were age and sex standardized to the Rwandan population.
 Associations between age, sex, socio-economic status and the key outcomes
 were examined using logistic regression. Results: 4618 participants were
 examined and interviewed out of 5361 enumerated (86% response rate). The
 adjusted population prevalence of VI was 3.7% (95%CI=3.0-4.5%), URE was
 2.2% (95%CI=1.7-2.8%) and overall need for PEC was 34.0%
 (95%CI=31.8-36.4%). Women and older people were more likely to need PEC
 and require a referral. Conclusions: Nearly a third of the population in
 Rwanda has the potential to benefit from PEC, with greater need identified
 in older people and women. Universal access to PEC can address unmet eye
 health needs and public health planning needs to ensure equitable access
 to older people and women.
description: household
 questionnaireindividual
 questionnairedatabase
 vfan
DOI: 10.15468/dl.r3a4ph
title: Occurrence Download

description: A dataset containing 195 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Madagascar",
 "OccurrenceStatus is Present",
 "TaxonKey is Orania"
 ]
}

 The dataset includes 195 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001529-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.19cf1c2
title: Data from: Environmental filtering and competitive exclusion drive biodiversity-invasibility relationships in shallow lake plant communities

description: 1. Understanding the processes that influence the diversity of ecological
 communities and their susceptibility to invasion by exotic species remains
 a challenge in ecology. In many systems, a positive relationship between
 the richness of native species and exotic species has been observed at
 larger spatial (e.g., regional) scales, while a negative pattern has been
 observed at local (e.g., plot) scales. These patterns are widely
 attributed to (1) biotic interactions, particularly biotic resistance,
 limiting invasions in high-diversity locations, producing negative
 local-scale relationships, and (2) native and exotic richness covarying at
 larger spatial scales as a function of environmental conditions and
 heterogeneity, producing positive large-scale relationships. However,
 alternative processes can produce similar patterns and need to be
 critically evaluated to make sound inferences about underlying mechanisms.
 2. We aggregated a large dataset of aquatic vegetation surveys from 1,102
 Minnesota shallow lakes collected over 13 years to quantify spatial and
 temporal patterns of community composition. Using those data and
 additional information on environmental conditions we evaluated evidence
 for four distinct mechanisms that could drive patterns of native and
 exotic species richness: biotic resistance, competitive exclusion,
 environmental filtering, and environmental heterogeneity. 3. We found the
 classic pattern of a negative native-exotic richness relationship at local
 scales and a positive relationship at lake scales. However, we found no
 evidence for local-scale biotic resistance; instead, competitive exclusion
 by invasive species appeared to reduce native richness after locations
 became invaded. Evaluating the influence of environmental filtering and
 heterogeneity, we found that native and exotic species occupied somewhat
 different niches. Invaders were less sensitive to environmental gradients
 and more tolerant of a wider range of conditions. This segregation of
 habitat preferences alone could produce a negative local native-exotic
 richness relationship and a positive regional pattern without the
 involvement of biotic interactions. 4. Synthesis: Our findings somewhat
 conflict with established expectations, which come from research
 predominantly conducted in terrestrial ecosystems. This illustrates the
 importance of explicitly evaluating underlying mechanisms in
 diversity-invasibility research and for comparisons across different types
 of ecosystems. Identification of different drivers of diversity also has
 direct implications for decisions about management of freshwater plant
 communities.
description: Compressed data archive
 fileThis compressed archive
 includes multiple other files including data files (in .csv format for
 tabular data) and the R code for all analyses (a series of .R scripts).
 Specific descriptions of each file are supplied in the ReadMe.txt
 file.Data_archive.zip
DOI: 10.5061/dryad.k55hh8f
title: Data from: A practical introduction to random forest for genetic association studies in ecology and evolution

description: Large genomic studies are becoming increasingly common with advances in
 sequencing technology, and our ability to understand how genomic variation
 influences phenotypic variation between individuals has never been
 greater. The exploration of such relationships first requires the
 identification of associations between molecular markers and phenotypes.
 Here we explore the use of Random Forest (RF), a powerful machine learning
 algorithm, in genomic studies to discern loci underlying both discrete and
 quantitative traits, particularly when studying wild or non-model
 organisms. RF is becoming increasingly used in ecological and population
 genetics because, unlike traditional methods, it can efficiently analyze
 thousands of loci simultaneously and account for non-additive
 interactions. However, understanding both the power and limitations of
 Random Forest is important for its proper implementation and the
 interpretation of results. We therefore provide a practical introduction
 to the algorithm and its use for identifying associations between
 molecular markers and phenotypes, discussing such topics as data
 limitations, algorithm initiation and optimization, as well as
 interpretation. We also provide short R tutorials as examples, with the
 aim of providing a guide to the implementation of the algorithm. Topics
 discussed here are intended to serve as an entry point for molecular
 ecologists interested in employing Random Forest to identify trait
 associations in genomic data sets.
description: Input data file for
 classification Random Forest tutorial in Rdata_classification_RF_tutorial.csvR script for classification Random Forest tutorialclassification_RF_tutorial.RInput data file for regression Random Forest tutorial in Rdata_regression_RF_tutorial.csvR script for regression Random Forest tutorialregression_RF_tutorial.RInput data files and results of simulations to quantify the effectiveness of a method to correct for population stratificationDatasets and results of simulations.xlsxR scripts for simulations to quantify the effectiveness of a method to correct for population stratificationR scripts for simulations to correct for pop structure.zipInput data files and R code to examine overfitting by Random Forest for 1,000 loci and 10,000 loci data setsInput data files and R code to examine overfitting by Random Forest.zip
DOI: 10.5061/dryad.q00k37c
title: Data from: Conservation of a domestic metapopulation structured into related and partly admixed strains

description: Preservation of genetic diversity is one of the most pressing challenges
 in the planetary boundaries concept. Within this context, we focused on
 genetic diversity in a native, unselected and highly admixed domesticated
 metapopulation. A set of 1828 individuals from 60 different cattle breeds
 was analysed using a medium density SNP chip. Among these breeds, 14 Buša
 strains formed a metapopulation represented by 350 individuals, while the
 remaining 46 breeds represented the global cattle population. Genetic
 analyses showed that the scarcely selected and less differentiated Buša
 metapopulation contributed a substantial proportion (52.6%) of the neutral
 allelic diversity to this global taurine population. Consequently, there
 is an urgent need for synchronised maintenance of this highly fragmented
 domestic metapopulation, which is distributed over several countries
 without sophisticated infrastructure and highly endangered by continuous
 replacement crossing as part of the global genetic homogenisation process.
 This study collected and evaluated samples, data and genome-wide
 information and developed genome-assisted cross-border conservation
 concepts. To detect and maintain genetic integrity of the metapopulation
 strains, we designed and applied a composite test that combines six
 metrics based on additive genetic relationships, a nearest neighbour graph
 and the distribution of semi-private alleles. Each metric provides
 distinct information components about past admixture events and offers an
 objective and powerful tool for the detection of admixed outliers. The
 here developed conservation methods and presented experiences could easily
 be adapted to comparable conservation programmes of domesticated or other
 metapopulations bred and kept in captivity or under some other sort of
 human control.
description: The genotypes from
 55,266 SNP scored in 1,210 cattleThis file contains the
 genotypes from 55,266 SNP markers scored in 1,210 cattle. Samples were
 genotyped with the Illumina BovineSNP50 BeadChip version 1 and version 2.
 Genotypes were called using GenomeStudio.BushaLive_MC-17-1542.zip
DOI: 10.5061/dryad.cj262df
title: Data from: Anchored phylogenomics of burrowing mayflies (Ephemeroptera) and the evolution of tusks

description: This study investigated the phylogenetic relationships among seven
 burrowing mayfly families. Genetic data from four ribosomal DNA genes
 (12S, 16S, 18S, and 28S) generated with sanger sequencing, 448 protein
 coding loci generated using a novel hybrid enrichment probe set and
 available RNAseq and genome assembly for 19 ingroup taxa and 4 outgroup
 taxa. Maximum Likelihood, and Bayesian analyses were carried out to
 estimate phylogenetic relationships. The results indicated that
 Potamanthidae, Euthyplociidae, Behningiidae, and Palingeniidae were
 recovered as monophyletic. Ephemeridae was not monophyletic. Mandibular
 tusks evolved in the common ancestor of burrowing mayflies and were lost
 in the lineage leading to Behningiidae.
description: READMEREADME File containing
 list of files contained in this dryad packageMAYFLY_refFolder containing the reference sequences by each loci used to make the Mayfly_1 probe kit as well as used as a set of references in IBA assemblyMayfly_1_ProbesMayfly_1 probe kitMiller_et_al_AlignmentsFolder containing the alignments used for analyses. DN12_rDNA_ML.fas was used in IQ-TREE for the DNA1&2 ML analysis (code used is included at top of file). DN12_rDNA_MrBayes.nex was used in the DNA1&2+rDNA MrBayes analysis (code is at bottom of file). AA_for_ML.phy and rDNA_for_ML.phy were used in IQ-TREE for the AA+rDNA ML analysis (code is contained in the AA_rDNA_ML.nex file). AA_rDNA_Bayes.nex was used in the AA+rDNA MrBayes analysis (code included at the bottom).Miller_et_al_LociFolder contains alignments of each loci used in the study.Miller_et_al_ST1-ST2Supplementary tables for Miller_et_al 2017 that include genbank accessions.Miller_et_al_SF1Supplementary figures. Bayesian and Maximum Likelihood trees for AA+rDNA and DNA1&2+rDNA datasets.ML_Bayes_ConTrees in newick format, in the following order: AA+rDNA Bayesian, AA+rDNA ML, DNA1&2+rDNA Bayesian, DNA1&2+rDNA ML, Constraint.
DOI: 10.5061/dryad.g0g5tv8
title: Data from: Phagocytic intracellular digestion in amphioxus (Branchiostoma)

description: The digestive methods employed by amphioxus (Branchiostoma)—both
 intracellular phagocytic digestion and extracellular digestion—have been
 discussed since 1937. Recent studies also show that epithelial cells
 lining the Branchiostoma digestive tract can express many immune genes.
 Here, in Branchiostoma belcheri, using a special tissue fixation method,
 we show that some epithelial cells, especially those lining the large
 diverticulum protruding from the gut tube, phagocytise food particles
 directly, and Branchiostoma can rely on this kind of phagocytic
 intracellular digestion to obtain energy throughout all stages of its
 life. Gene expression profiles suggest that diverticulum epithelial cells
 have functional features of both digestive cells and phagocytes. In
 starved Branchiostoma, these cells accumulate endogenous digestive and
 hydrolytic enzymes, whereas, when sated, they express many kinds of immune
 genes in response to stimulation by phagocytised food particles. We also
 found that the distal hindgut epithelium can phagocytise food particles,
 but not as many. These results illustrate phagocytic intercellular
 digestion in Branchiostoma, explain why. Branchiostoma digestive tract
 epithelial cells express typical immune genes, and suggest that the main
 physiological function of the Branchiostoma diverticulum is different from
 that of the vertebrate liver.
description: Table S3_The total
 information of FullTable S4_The total
 statistics of FullTable S5_Fasta_The
 assembling results of FullTable S6_Fasta_GenBank
 Accession and Clone Id of FullTable S7_The
 total_Information of SSH-DTable S8_The
 total_Statistic of SSH-DTable S9_The
 total_Information of SSH-GTable S10_The
 total_Statistic of SSH-G