cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.690jk
title: Data from: Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic Forest

description: Morphological similarity associated to restricted distributions and low
 dispersal abilities make the direct developing “Terrarana” frogs of the
 genus Euparkerella a good model for examining diversification processes.
 We here infer phylogenetic relationships within the genus Euparkerella,
 using DNA sequence data from one mitochondrial and four nuclear genes
 coupled with traditional Bayesian phylogenetic reconstruction approaches
 and more recent coalescent methods of species tree inference. We also used
 Bayesian clustering analysis and a recent Bayesian coalescent-based
 approach specifically to infer species delimitation. The analysis of 39
 individuals from the four known Euparkerella species uncovered high levels
 of genetic diversity, especially within the two previously
 morphologically-defined E. cochranae and E. brasiliensis. Within these
 species, the gene trees at five independent loci and trees from combined
 data (concatenated dataset and the species tree) uncovered six deeply
 diverged and geographically coherent evolutionary units, which may have
 diverged between the Miocene and the Pleistocene. These six units were
 also uncovered in the Bayesian clustering analysis, and supported by the
 Bayesian coalescent-based species delimitation (BPP), and Genealogical
 Sorting Index (GSI), providing thus strong evidence for underestimation of
 the current levels of diversity within Euparkerella. The cryptic diversity
 now uncovered opens new opportunities to examine the origins and
 maintenance of microendemism in the context of spatial heterogeneity
 and/or human induced fragmentation of the highly threatened Brazilian
 Atlantic forest hotspot.
description: Fusinatto et
 al.CrypticGeneticDiversityEuparkerellaFolder with all data and
 main input files used in this manuscript and a read-me file with
 instructions
DOI: 10.15468/dl.nws6ee
title: Occurrence Download

description: A dataset containing 1098 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Germany",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pipistrellus pipistrellus",
 "Year 2024-2026"
 ]
}

 The dataset includes 1098 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000683-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vg7r3
title: Data from: Dmrt1 polymorphism and sex-chromosome differentiation in Rana temporaria

description: Sex-determination mechanisms vary both within and among populations of
 common frogs, opening opportunities to investigate the molecular pathways
 and ultimate causes shaping their evolution. We investigated the
 association between sex-chromosome differentiation (as assayed from
 microsatellites) and polymorphism at the candidate sex-determining gene
 Dmrt1 in two Alpine populations. Both populations harboured a diversity of
 X-linked and Y-linked Dmrt1 haplotypes. Some males had fixed male-specific
 alleles at all markers (“differentiated” Y chromosomes), others only at
 Dmrt1 (“proto-” Y chromosomes), while still others were genetically
 indistinguishable from females (undifferentiated X chromosomes). Besides
 these XX males, we also found rare XY females. The several Dmrt1 Y
 haplotypes differed in the probability of association with a
 differentiated Y chromosome, which we interpret as a result of differences
 in the masculinizing effects of alleles at the sex-determining locus. From
 our results, the polymorphism in sex-chromosome differentiation and its
 association with Dmrt1, previously inferred from Swedish populations, are
 not just idiosyncratic features of peripheral populations, but also
 characterize highly diverged populations in the central range. This
 implies that an apparently unstable pattern has been maintained over long
 evolutionary times.
description: TableS1Raw genotype data, individual scores for discriminant factors and cluster assignments. Y and X-specific haplotypes are highlighted (the latter in pale yellow).
DOI: 10.5061/dryad.cp405
title: Data from: Direct evidence for encoding of motion streaks in human visual cortex

description: Temporal integration in the visual system causes fast-moving objects to
 generate static, oriented traces (‘motion streaks’), which could be used
 to help judge direction of motion. While human psychophysics and
 single-unit studies in non-human primates are consistent with this
 hypothesis, direct neural evidence from the human cortex is still lacking.
 First, we provide psychophysical evidence that faster and slower motions
 are processed by distinct neural mechanisms: faster motion raised human
 perceptual thresholds for static orientations parallel to the direction of
 motion, whereas slower motion raised thresholds for orthogonal
 orientations. We then used functional magnetic resonance imaging to
 measure brain activity while human observers viewed either fast
 (‘streaky’) or slow random dot stimuli moving in different directions, or
 corresponding static-oriented stimuli. We found that local spatial
 patterns of brain activity in early retinotopic visual cortex reliably
 distinguished between static orientations. Critically, a multivariate
 pattern classifier trained on brain activity evoked by these static
 stimuli could then successfully distinguish the direction of fast
 (‘streaky’) but not slow motion. Thus, signals encoding static-oriented
 streak information are present in human early visual cortex when viewing
 fast motion. These experiments show that motion streaks are present in the
 human visual system for faster motion.
description: Psychophysical
 adaptation dataRaw contrast thresholds,
 and threshold elevations in decibels (dB) after adaptation to either fast
 (13 deg/s) or slow (1.6 deg/s) motion, testing with either parallel or
 orthogonal low-contrast gratings. The stimuli were programmed in Matlab
 version 7.4, using the Psychophysics Toolbox, and thresholds were fitted
 using custom software written in Matlab.Psychophysical_adapt_anonymised.xlsxRanked SVM for all conditionsRanked accuracies from the support vector machine analysis described in the paper for all of the classification analyses. The first column of each tab contains the subject number (1-8), the second column the number of voxels selected from each region (1 - 250), and the remaining columns give the proportion of accuracy for each region of interest.Ranked_SVM_all_Conditions.xlsx
DOI: 10.5061/dryad.s0885
title: Data from: Landscape composition has limited impact on local genetic structure in mountain clover, Trifolium montanum L.

description: Semi-dry grasslands in the European Alps have been increasingly fragmented
 over the last 150 years. Few studies have investigated the implications of
 landscape configuration for genetic structure and gene flow among remnant
 habitat patches. Conservation management of semi-dry grassland plants
 rarely accounts for possible effects of major landscape elements; such as
 forest patches, as barriers to gene flow and dispersal via seed and
 pollen, despite their potential importance for biodiversity conservation.
 Using 1,416 individuals from 61 sampling sites across two valleys in
 South-Eastern Switzerland and AFLP fingerprints we applied a spatial strip
 and a circle approach to determine the impact of different landscape
 elements on genetic differentiation in the semi-dry grassland herb
 Trifolium montanum (mountain clover). Overall genetic differentiation
 among sampling sites was low (overall FST = 0.044). Forest area had no
 effect on gene flow at the landscape scale but area of semi-dry grassland,
 the potential habitat of T. montanum, road area and altitude influenced
 genetic differentiation among sampling sites. The observed pattern of
 genetic differentiation suggests that a future increase in forest area,
 due to land use abandonment, at least in the short term, are unlikely to
 directly impact patterns of genetic variation in T. montanum.
description: AFLPdata_HR_73lociAFLP genotypes of 721 plant individuals of Trifolium montanum, 31 sampling sites, 73 loci, sampled in Hinterrheintal (HR)AFLPdata_VL_78lociAFLP genotypes of 695 plant individuals of Trifolium montanum, 30 sampling sites, 78 loci, sampled in Val Lumnezia (VL)
DOI: 10.5061/dryad.8qk33
title: Data from: Novel genetic capacitors and potentiators for the natural genetic variation of sensory bristles and their trait-specificity in Drosophila

description: Cryptic genetic variation (CGV) is defined as the genetic variation that
 has little effect on phenotypic variation under a normal condition, but
 contributes to heritable variation under environmental or genetic
 perturbations. Genetic buffering systems that suppress the expression of
 CGV and store it in a population are called genetic capacitors, and the
 opposite systems are called genetic potentiators. One of the best-known
 candidates for a genetic capacitor and potentiator is the molecular
 chaperone protein, HSP90, and one of its characteristics is that it
 affects the genetic variation in various morphological traits. However, it
 remains unclear whether the wide-ranging effects of HSP90 on a broad range
 of traits are a general feature of genetic capacitors and potentiators. In
 the current study, I searched for novel genetic capacitors and
 potentiators for quantitative bristle traits of Drosophila melanogaster,
 and then investigate the trait-specificity of their genetic buffering
 effect. Three bristle traits of D. melanogaster were used as the target
 traits, and the genomic regions with genetic buffering effects were
 screened using the 61 genomic deficiencies examined previously for genetic
 buffering effects in wing shape. As a result, four and six deficiencies
 with significant effects on increasing and decreasing the broad-sense
 heritability of the bristle traits were identified, respectively. Of the
 18 deficiencies with significant effects detected in the current study
 and/or by the previous study, 14 showed trait-specific effects, and four
 affected the genetic buffering of both bristle traits and wing shape. This
 suggests that most genetic capacitors and potentiators exert
 trait-specific effects, but that general capacitors and potentiators with
 effects on multiple traits also exist.
description: Bristle dataset of D.
 melanogasterBristle counts of
 sternopleurals (SP), ocellar bristles (OC), and orbital bristles (OB) for
 61 deficinecy/wild-type genotypes of Drosophila melanogaster. Each entry
 represents mean bristle counts at replication vial
 level.DRYAD_Takahashi.xlsx
DOI: 10.5061/dryad.jv98k
title: Data from: Setup in a clinical workflow and impact on radiotherapy routine of an in vivo dosimetry procedure with an electronic portal imaging device

description: High conformal techniques such as intensity-modulated radiation therapy
 and volumetric-modulated arc therapy are widely used in overloaded
 radiotherapy departments. In vivo dosimetric screening is essential in
 this environment to avoid important dosimetric errors. This work examines
 the feasibility of introducing in vivo dosimetry (IVD) checks in a
 radiotherapy routine. The causes of dosimetric disagreements between
 delivered and planned treatments were identified and corrected during the
 course of treatment. The efficiency of the corrections performed and the
 added workload needed for the entire procedure were evaluated. The IVD
 procedure was based on an electronic portal imaging device. A total of
 3682 IVD tests were performed for 147 patients who underwent head and
 neck, abdomen, pelvis, breast, and thorax radiotherapy treatments. Two
 types of indices were evaluated and used to determine if the IVD tests
 were within tolerance levels: the ratio R between the reconstructed and
 planned isocentre doses and a transit dosimetry based on the γ-analysis of
 the electronic portal images. The causes of test outside tolerance level
 was investigated and corrected and IVD test was repeated during subsequent
 fraction. The time needed for each step of the IVD procedure was
 registered. Pelvis, abdomen, and head and neck treatments had 10% of tests
 out of tolerance whereas breast and thorax treatments accounted for up to
 25%. The patient setup was the main cause of 90% of the IVD tests out of
 tolerance and the remaining 10% was due to patient morphological changes.
 An average time of 42 min per day was sufficient to monitor a daily
 workload of 60 patients in treatment. This work shows that IVD performed
 with an electronic portal imaging device is feasible in an overloaded
 department and enables the timely realignment of the treatment quality
 indices in order to achieve a patient’s final treatment compliant with the
 one prescribed.
description: Data-PONE-D-17-07823_anonymized
DOI: 10.5061/dryad.cd423
title: Data from: Dispersal in a patchy landscape reveals contrasting determinants of infection in a wild avian malaria system

description: 1. Understanding exactly when, where and how hosts become infected with
 parasites is critical to understanding host-parasite coevolution. However,
 for host-parasite systems in which hosts or parasites are mobile (for
 example vector-borne diseases), the spatial location of infection, and the
 relative importance of parasite exposure at successive host life-history
 stages, are often uncertain. 2. Here, using a six-year longitudinal
 dataset from a spatially referenced population of blue tits, we test the
 extent to which infection by avian malaria parasites is determined by
 conditions experienced at natal or breeding sites, as well as by postnatal
 dispersal between the two. 3. We show that the location and timing of
 infection differs markedly between two sympatric malaria parasite species.
 For one species (P. circumflexum), our analyses indicate that infection
 occurs after birds have settled on breeding territories, and because the
 distribution of this parasite is temporally stable, hosts could in
 principle alter their exposure and potentially avoid infection through
 postnatal dispersal. Conversely, the spatial distribution of another
 parasite species (P. relictum) is unpredictable, and infection probability
 is positively associated with postnatal dispersal distance, potentially
 indicating that infection occurs during this major dispersal event. 4.
 These findings suggest that hosts in this population may be subject to
 divergent selection pressures from these two parasites, potentially acting
 at different life-history stages. Because this implies parasite
 species-specific predictions for many coevolutionary processes, they also
 illustrate the complexity of predicting such processes in multi-parasite
 systems.
description: Datafile for statistical
 analysisThis file contains all
 data required for statistical analyses in this paper. it contains one row
 per individual, from 447 locally born blue tit recruits, captured and
 tested for malaria parasites while breeding in the same population. See
 README csv file for a key to the column headings.Dispersal_malaria_DRYAD_final_datafile.csv
DOI: 10.5061/dryad.nn2h5
title: Data from: Consequences of a nectar yeast for pollinator preference and performance

description: Pollinators utilize floral resources that vary in colour, scent and reward
 quality. Variation in such traits, including nectar rewards, in addition
 to cues associated with their quality, can influence pollinator foraging
 decisions with consequences for pollinator reproductive success. Nectar is
 commonly subject to colonization by micro-organisms capable of affecting a
 suite of traits important for pollinator attraction and fitness; yet,
 links between microbial presence and changes in pollinator preference and
 performance remain few. Here, we evaluated the effects of a
 nectar-inhabiting micro-organism on pollinator foraging behaviour and
 reproduction using the common eastern bumblebee Bombus impatiens and the
 cosmopolitan nectar yeast Metschnikowia reukaufii. Using a combination of
 choice and no-choice behavioural and feeding assays, we manipulated the
 presence and viability of M. reukaufii in nectar and assessed bumblebee
 foraging and reproductive responses. Bombus impatiens workers responded
 positively to the presence of yeasts. Foragers trained to associate yeast
 presence with flower colour visited a significantly greater proportion of
 flowers inoculated with yeast when subject to a colour discrimination
 test. Moreover, foragers naïve to nectar yeasts incorporated more
 yeast-inoculated flowers into initial foraging bouts when presented with a
 novel floral array. In addition, bees spent significantly longer foraging
 on yeast-inoculated flowers compared to yeast-free flowers. However, when
 we manipulated yeast presence and viability in microcolonies of queenless
 workers, we found no effect of yeast on components of bumblebee
 reproduction, such as initiation of egg laying and number of eggs laid.
 This lack of an effect of yeast persisted even under conditions of pollen
 limitation. Taken together, these results suggest that nectar yeasts can
 enhance floral signalling and alter pollinator foraging behaviour at
 individual flowers, though they may not directly affect pollinator
 performance. Thus, nectar yeasts may play a significant role in mediating
 pollinator foraging behaviour, with consequences for plant fitness and
 evolution of floral traits.
description: PreferenceExperiment1Experimental assessment of nectar-inhabiting yeast impacts on pollinator foraging preference. Metadata is included in the file, outlining the experimental protocol and how preference was scored.PreferenceExperiment2Experimental assessment of impacts of a nectar-inhabiting yeast on foraging behavior of naive bees. Bees were naive with respect to the yeast treatment. Metadata is included in the file, which outlines methodology used in the experiment.PerformanceExperimentNo-choice feeding assay designed to assess costs and benefits of consuming a nectar yeast for bumblebee feeding and reproduction. Metadata is included in the file, outlining methodology used.
DOI: 10.5061/dryad.sc09839
title: Data from: Abundance of an economically important nematode parasite increased in Puget Sound between 1930 and 2016: evidence from museum specimens confirms historical data

description: 1. Does disturbance increase or decrease parasite transmission among
 wildlife hosts? Ecologists cannot answer this controversial question, in
 part because few historical datasets rigorously document parasite
 abundance. Without such a baseline, it is difficult to determine whether
 contemporary ecosystems are experiencing elevated parasite burdens. 2.
 Here, we investigate change over time in the abundance of a parasite that
 affects the economic value of a fish species. Clavinema mariae is a
 nematode parasite of benthic fishes that is common in English sole
 (Parophrys vetulus) of Puget Sound, WA. We obtained historical records of
 its abundance from the literature and from unpublished government agency
 data, and resampled the same locations using the same methods in 2017. We
 also used a new approach by estimating the C. mariae burden for museum
 specimens of English sole collected between 1930 and 2016.3. Both the
 historical data and museum specimen data suggested increases over time in
 C. mariae abundance, with robust agreement between the two approaches. 4.
 In addition to documenting a previously unrecognized ~eightfold increase
 in the burden of an economically important parasite, our work demonstrates
 – for the first time – that parasitological examination of
 liquid-preserved museum specimens can produce reliable data on long-term
 trends in parasite abundance, at a much greater temporal resolution than
 is possible to obtain from historical records. 5. Synthesis and
 applications. Defining a baseline state of infection is vital for natural
 resource management and policy, which must respond to the threat of
 disease; without such a baseline, managers attempting to maintain or
 recover the health of ecosystems under their stewardship are shooting in
 the dark. The method we present here – using museum specimens to
 reconstruct detailed chronologies of parasite abundance change – offers a
 solution. Our approach would allow managers to accurately characterize
 past population disease states, informing the development of appropriate
 disease management targets. Given the broad representation and
 availability of liquid-preserved specimens across ecosystems, geographic
 regions, and host taxa, this solution may be feasible for the management
 of biological resources not only in marine ecosystems, but in freshwater
 and terrestrial ecosystems as well.20-Aug-2018
description: Data from museum
 specimensData from historical
 documents and contemporary sampling
DOI: 10.5061/dryad.j7th2
title: Data from: The effects of age, sex, and habitat on body size and shape of the blackstripe topminnow, Fundulus notatus

description: Lake and stream habitats pose a variety of challenges to fishes due to
 differences in variables such as water velocity, habitat structure, prey
 community, and predator community. These differences can cause divergent
 selection on body size and/or shape. Here, we measured sex, age, length,
 and eight different morphological traits of the blackstripe topminnow,
 Fundulus notatus, from 19 lake and stream populations across four river
 drainages in central Illinois. Our goal was to determine whether size and
 shape differed consistently between lake and stream habitats across
 drainages. We also considered the effects of age and sex as they may
 affect size and morphology. We found large differences in body size of age
 1 topminnows where stream fish were generally larger than lake fish. Body
 shape mainly varied as a function of sex. Adult male topminnows had larger
 morphological traits (with the exception of body width) than females, in
 particular longer dorsal and anal base lengths. Subtle effects of habitat
 were present. Stream fish had a longer dorsal fin base than lake fish.
 These phenotypic patterns may be the result of genetic and/or
 environmental variation. As these lakes are human-made, the observed
 differences, if genetic, would have had to occur relatively rapidly
 (within about 100 years).
description: Fundulus notatus raw
 dataExcel file containing
 the raw data (morphometric measurements as well as data on population,
 drainage, habitat, age, and sex).