cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mv580
title: Data from: Local adaptation of reproductive performance during thermal stress

description: Considerable evidence exists for local adaptation of critical thermal
 limits in ectotherms following adult temperature stress, but fewer studies
 have tested for local adaptation of sublethal heat stress effects across
 life-history stages. In organisms with complex life cycles, such as
 holometabolous insects, heat stress during juvenile stages may severely
 impact gametogenesis, having downstream consequences on reproductive
 performance that may be mediated by local adaptation, although this is
 rarely studied. Here, we tested how exposure to either benign or heat
 stress temperature during juvenile and adult stages, either independently
 or combined, influences egg-to-adult viability, adult sperm motility and
 fertility in high- and low-latitude populations of Drosophila subobscura.
 We found both population- and temperature-specific effects on survival and
 sperm motility; juvenile heat stress decreased survival and subsequent
 sperm motility and each trait was lower in the northern population. We
 found an interaction between population and temperature on fertility
 following application of juvenile heat stress; although fertility was
 negatively impacted in both populations, the southern population was less
 affected. When the adult stage was also subject to heat stress, the
 southern population exhibited positive carry-over effects whereas the
 northern population's fertility remained low. Thus, the northern
 population is more susceptible to sublethal reproductive consequences
 following exposure to juvenile heat stress. This may be common in other
 organisms with complex life cycles and current models predicting
 population responses to climate change, which do not take into account the
 impact of juvenile heat stress on reproductive performance, may be too
 conservative.
description: Porcelli et al 2016 JEB
 dryadData files used for data
 analysis presented in Porcelli et al JEB Local adaptation of reproductive
 performance during thermal stress
DOI: 10.15468/dl.ux6smb
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.1.13_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Cyanopica cyanus"
 ]
}

 The dataset includes 17 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001094-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ck800
title: Data from: Salinity-induced phenotypic plasticity in threespine stickleback sperm activation

description: Phenotypic expression may be and often is influenced by an organism’s
 developmental environment, referred to as phenotypic plasticity. The sperm
 cells of teleosts have been found to be inactive in the seminal plasma and
 are activated by osmotic shock for most fish species, through release in
 either hypertonic (for marine fish) or hypotonic (for freshwater fish)
 water. If this is the case, the regulatory system of sperm mobility should
 be reversed in salt and freshwater fish. We tested this hypothesis by
 first activating sperm of saltwater and freshwater populations of
 threespine stickleback in salt- and fresh water. The sperm from saltwater
 stickleback could be activated in either salinity, which matches the
 freshwater colonization history of the species, whereas the sperm from the
 freshwater population acted as predicted by the osmotic shock theory and
 was activated in freshwater only. As the freshwater population used here
 was calculated to be thousands of years old, we went on to test whether
 the trait(s) were plastic and sperm from freshwater males still could be
 activated in saltwater after individuals were exposed to saltwater. After
 raising freshwater stickleback in saltwater we found the mature males to
 have active sperm in both salt and freshwater. Further, we also found the
 sperm of wild-caught freshwater stickleback to be active in saltwater
 after exposing those mature males to saltwater for only two days. This
 illustrates that the ability for stickleback sperm to be activated in a
 range of water qualities is an environmentally induced plastic trait.
description: Supplementary_data_sperm_activation_in_sticklebackSperm velocity score numbers for threespine stickleback originating from saltwater and freshwater tested in saltwater and freshwater. Please see Supplementary 1 for a more detailed description.Supplementary_data.xlsx
DOI: 10.5061/dryad.p1006
title: Data from: Imperfect pathogen detection from non-invasive skin swabs biases disease inference

description: 1. Conservation managers rely on accurate estimates of disease parameters,
 such as pathogen prevalence and infection intensity, to assess disease
 status of a host population. However, these disease metrics may be biased
 if low-level infection intensities are missed by sampling methods or
 laboratory diagnostic tests. These false negatives underestimate pathogen
 prevalence and overestimate mean infection intensity of infected
 individuals. 2. Our objectives were two-fold. First, we quantified false
 negative error rates of Batrachochytrium dendrobatidis on non-invasive
 skin swabs collected from an amphibian community in El Copé, Panama. We
 swabbed amphibians twice in sequence, and we used a recently developed
 hierarchical Bayesian estimator to assess disease status of the
 population. Second, we developed a novel hierarchical Bayesian model to
 simultaneously account for imperfect pathogen detection from field
 sampling and laboratory diagnostic testing. We evaluated the performance
 of the model using simulations and varying sampling design to quantify the
 magnitude of bias in estimates of pathogen prevalence and infection
 intensity. 3. We show that Bd detection probability from skin swabs was
 related to host infection intensity, where Bd infections &lt; 10
 zoospores have &lt; 95% probability of being detected. If imperfect Bd
 detection was not considered, then Bd prevalence was underestimated by as
 much as 16%. In the Bd-amphibian system, this indicates a need to correct
 for imperfect pathogen detection caused by skin swabs in persisting host
 communities with low-level infections. More generally, our results have
 implications for study designs in other disease systems, particularly
 those with similar objectives, biology, and sampling decisions. 4.
 Uncertainty in pathogen detection is an inherent property of most sampling
 protocols and diagnostic tests, where the magnitude of bias depends on the
 study system, type of infection, and false negative error rates. Given
 that it may be difficult to know this information in advance, we advocate
 that the most cautious approach is to assume all errors are possible and
 to accommodate them by adjusting sampling designs. The modeling framework
 presented here improves the accuracy in estimating pathogen prevalence and
 infection intensity.
description: Batrachochytrium
 dendrobatidis infection intensity data of amphibians in El Cope,
 PanamaThis file contains
 Batrachochytrium dendrobatidis (i.e., chytrid) infection intensity data of
 amphibians in El Cope, Panama across &gt; 30 species from 2012 to 2014
 (including wet and dry seasons; and stream and trail habitats). A subset
 of individuals were swabbed twice in sequence. These double swabs were
 used to estimate the sensitivity of swabs to detect pathogen infection.
 Number listed under the column "First_swab" represent the
 chytrid infection load detected on the first swab, and the column
 "Second_swab" is the chytrid infection load detected on the
 second swab.Frog.csv
DOI: 10.5061/dryad.tn8qs35
title: Data from: Methods for normalizing microbiome data: an ecological perspective

description: 1. Microbiome sequencing data often need to be normalized due to
 differences in read depths, and recommendations for microbiome analyses
 generally warn against using proportions or rarefying to normalize data
 and instead advocate alternatives, such as upper quartile, CSS, edgeR-TMM,
 or DESeq-VS. Those recommendations are, however, based on studies that
 focused on differential abundance testing and variance standardization,
 rather than community-level comparisons (i.e., beta diversity), Also,
 standardizing the within-sample variance across samples may suppress
 differences in species evenness, potentially distorting community-level
 patterns. Furthermore, the recommended methods use log transformations,
 which we expect to exaggerate the importance of differences among rare
 OTUs, while suppressing the importance of differences among common OTUs.
 2. We tested these theoretical predictions via simulations and a
 real-world data set. 3. Proportions and rarefying produced more accurate
 comparisons among communities and were the only methods that fully
 normalized read depths across samples. Additionally, upper quartile, CSS,
 edgeR-TMM, and DESeq-VS often masked differences among communities when
 common OTUs differed, and they produced false positives when rare OTUs
 differed. 4. Based on our simulations, normalizing via proportions may be
 superior to other commonly used methods for comparing ecological
 communities.
description: Simulation script
 1This
 R script will simulate two populations of microbiome samples and compare
 normalization methods.Simulation script
 2This
 R script will simulate two populations of microbiome samples and compare
 normalization methods via PcOAs.Sample.OTU.distributionOTU distribution used in the paper: Methods for normalizing microbiome data: an ecological perspective
DOI: 10.5061/dryad.5g52t
title: Data from: Insectivorous bats respond to vegetation complexity in urban green spaces

description: Structural complexity is known to determine habitat quality for
 insectivorous bats, but how bats respond to habitat complexity in highly
 modified areas such as urban green spaces has been little explored.
 Furthermore, it is uncertain whether a recently developed measure of
 structural complexity is as effective as field-based surveys when applied
 to urban environments. We assessed whether image-derived structural
 complexity (MIG) was as/more effective than field-based descriptors in
 this environment, and evaluated the response of insectivorous bats to
 structural complexity in urban green spaces. Bat activity and species
 richness were assessed with ultrasonic devices at 180 locations within
 green spaces in Vienna, Austria. Vegetation complexity was assessed using
 17 field-based descriptors and by calculating the mean information gain
 (MIG) using digital images. Total bat activity and species richness
 decreased with increasing structural complexity of canopy cover,
 suggesting maneuverability and echolocation (sensorial) challenges for bat
 species using the canopy for flight and foraging. The negative response of
 functional groups to increased complexity was stronger for open space
 foragers than for edge space foragers. Nyctalus noctula, a species
 foraging in open space, showed a negative response to structural
 complexity, whereas Pipistrellus pygmaeus, an edge space forager, was
 positively influenced by the number of trees. Our results show that MIG is
 a useful, time- and cost-effective tool to measure habitat complexity that
 complemented field-based descriptors. Response of bats to structural
 complexity was group- and species-specific, which highlights the need for
 manifold management strategies (e.g., increasing or reinstating the extent
 of ground vegetation cover) to fulfill different species’ requirements,
 and to conserve insectivorous bats in urban green spaces.
description: Vegetation complexity
 and bats in green spacesBat data were collected
 with acoustic devices in green spaces in Vienna. Bat calls were processed
 using bcAdmin, batIdent, and bcAnalyze. Vegetation structure was measured
 using field-based methods and a digital camera for calgulating mean
 information gain index (MIG). Variables description: point.ID (ID of
 sampling point), type (type of green space), size (size of green space
 [ha]), 0.5-1m, 2-3m, 5-7m, 15m (vertical layering of vegetation at these
 heights), GC (percentage of vegetation cover on the ground), VH (vertical
 heterogeneity), No.trees (number of large trees), DBH (diameter at breast
 height of large trees [cm]), MIG (mean information gain), MIGside (MIG
 side views), MIGtop (MIG top view), activity (bat activity [ms]),
 No.species (number of bat species), edge (activity of edge space
 foragers), open (activity of open space foragers), Nnoc (activity of
 Nyctalus noctula,), Ppyg (activity of Pipistrellus
 pygmaeus).Dryad.xlsx
DOI: 10.5061/dryad.6q023
title: Data from: Is plant fitness proportional to seed set? An experiment and a spatial model

description: Individual differences in fecundity often serve as proxies for differences
 in overall fitness, especially when it is difficult to track the fate of
 an individual's offspring to reproductive maturity. Using fecundity
 may be biased, however, if density-dependent interactions between siblings
 affect survival and reproduction of offspring from high- and low-fecundity
 parents differently. To test for such density-dependent effects in plants,
 we sowed seeds of the wildflower Ipomopsis aggregata (scarlet gilia) to
 mimic partially-overlapping seed shadows of pairs of plants, one of which
 produced twice as many seeds. We tested for differences in offspring
 success using a genetic marker to track offspring to flowering multiple
 years later. Without density dependence the high-fecundity parent should
 produce twice as many surviving offspring. We also developed a model that
 considered the geometry of seed shadows and assumed limited survivors so
 that number of juvenile recruits is proportional to area. Rather than a
 ratio of 2:1 offspring success from high- vs. low-fecundity parents, our
 model predicted a ratio of 1.42 to 1, which would translate into weaker
 selection. Empirical ratios of juvenile offspring and of flowers produced
 conformed well to the model's prediction. Extending the model shows
 how spatial relationships of parents and seed dispersal patterns modify
 inferences about relative fitness based solely on fecundity.
description: Demographic data for
 genotyped juvenile recruitsCampbell et al. Am Nat 2017
 data.xlsx
DOI: 10.5061/dryad.vn23kb7
title: Data from: Resting-state gamma-band power alterations in schizophrenia reveal E/I-balance abnormalities across illness-stages

description: We examined alterations in E/I-balance in schizophrenia (ScZ) through
 measurements of resting-state gamma-band activity in participants meeting
 clinical high-risk (CHR) criteria (n = 88), 21 first episode (FEP)
 patients and 34 chronic ScZ-patients. Furthermore, MRS-data were obtained
 in CHR-participants and matched controls. Magnetoencephalographic (MEG)
 resting-state activity was examined at source level and MEG-data were
 correlated with neuropsychological scores and clinical symptoms.
 CHR-participants were characterized by increased 64–90 Hz power. In
 contrast, FEP- and ScZ-patients showed aberrant spectral power at both
 low- and high gamma-band frequencies. MRS-data showed a shift in
 E/I-balance toward increased excitation in CHR-participants, which
 correlated with increased occipital gamma-band power. Finally,
 neuropsychological deficits and clinical symptoms in FEP and ScZ-patients
 were correlated with reduced gamma band-activity, while elevated psychotic
 symptoms in the CHR group showed the opposite relationship. The current
 study suggests that resting-state gamma-band power and altered Glx/GABA
 ratio indicate changes in E/I-balance parameters across illness stages in
 ScZ.
description: MR-Spectroscopy- and
 RS-high-gamma MEG dataData associated with
 Figure 5 of main manuscript: correlation between high-gamma (64-90 Hz)
 power in occipital regions and MR-Spectroscopy measures of
 Glutamate/Glutamine (GLX) and GABA.DRYAD-PACKAGE-GrenttJong_etal_2018.txt
DOI: 10.5061/dryad.t114v
title: Data from: Description and phylogenetic position of a new species of Oreobates (Anura: Craugastoridae) from northwestern Argentina

description: We describe a new species of Oreobates from Jujuy, Argentina. The new
 species is clearly diagnosable from other species of Oreobates by a
 combination of morphological characters and supported by molecular
 evidence (genetic distance and phylogenetic analysis). We also provide
 taxonomic comments about O. discoidalis and O. barituensis, emphasizing
 the need for an exhaustive revision of these species
description: Oreobates_sequencesCompressed zip file containing the alignments of DNA sequences used in the study in NEXUS formatOreobates_distances_16SFile containing the aligned sequences of 16S gene in NEXUS format
DOI: 10.5061/dryad.1cf35
title: Data from: Reduced hornbill abundance associated with low seed arrival and altered recruitment in a hunted and logged tropical forest

description: Logging and hunting are two key direct threats to the survival of wildlife
 in the tropics, and also disrupt important ecosystem processes. We
 investigated the impacts of these two factors on the different stages of
 the seed dispersal cycle, including abundance of plants and their
 dispersers and dispersal of seeds and recruitment, in a tropical forest in
 north-east India. We focused on hornbills, which are important seed
 dispersers in these forests, and their food tree species. We compared
 abundances of hornbill food tree species in a site with high logging and
 hunting pressures (heavily disturbed) with a site that had no logging and
 relatively low levels of hunting (less disturbed) to understand logging
 impacts on hornbill food tree abundance. We compared hornbill abundances
 across these two sites. We, then, compared the scatter-dispersed seed
 arrival of five large-seeded tree species and the recruitment of four of
 those species. Abundances of hornbill food trees that are preferentially
 targeted by logging were two times higher in the less disturbed site as
 compared to the heavily disturbed site while that of hornbills was 22
 times higher. The arrival of scatter-dispersed seeds was seven times
 higher in the less disturbed site. Abundances of recruits of two tree
 species were significantly higher in the less disturbed site. For another
 species, abundances of younger recruits were significantly lower while
 that of older recruits were higher in the heavily disturbed site. Our
 findings suggest that logging reduces food plant abundance for an
 important frugivore-seed disperser group, while hunting diminishes
 disperser abundances, with an associated reduction in seed arrival and
 altered recruitment of animal-dispersed tree species in the disturbed
 site. Based on our results, we present a conceptual model depicting the
 relationships and pathways between vertebrate-dispersed trees, their
 dispersers, and the impacts of hunting and logging on these pathways.
description: Data of a study
 investigating impacts of hunting and logging on abundance of hornbills,
 dispersed seeds and recuits in north-east IndiaA study was carried out
 to investigate impacts of logging and hunting on hornbills (which are
 important seed dispersers), their large-seeded food plants, arrival of
 scatter-dispersed seeds of these plants and the recruitment pattern of
 these plants across a site experiencing logging and hunting pressures and
 a protected area site which did not experience these anthropogenic
 pressures. The associated data of the study is uploaded
 here.Naniwadekar_etal_PlosOne_Data.zip
DOI: 10.5061/dryad.5v6qm
title: Data from: Multi-serotype pneumococcal nasopharyngeal carriage prevalence in vaccine naïve Nepalese children, assessed using molecular serotyping.

description: Invasive pneumococcal disease is one of the major causes of death in young
 children in resource poor countries. Nasopharyngeal carriage studies
 provide insight into the local prevalence of circulating pneumococcal
 serotypes. There are very few data on the concurrent carriage of multiple
 pneumococcal serotypes. This study aimed to identify the prevalence and
 serotype distribution of pneumococci carried in the nasopharynx of young
 healthy Nepalese children prior to the introduction of a pneumococcal
 conjugate vaccine using a microarray-based molecular serotyping method
 capable of detecting multi-serotype carriage. We conducted a
 cross-sectional study of healthy children aged 6 weeks to 24 months from
 the Kathmandu Valley, Nepal between May and October 2012. Nasopharyngeal
 swabs were frozen and subsequently plated on selective culture media. DNA
 extracts of plate sweeps of pneumococcal colonies from these cultures were
 analysed using a molecular serotyping microarray capable of detecting
 relative abundance of multiple pneumococcal serotypes. 600 children were
 enrolled into the study: 199 aged 6 weeks to &lt;6 months, 202 aged 6
 months to &lt; 12 months, and 199 aged 12 month to 24 months. Typeable
 pneumococci were identified in 297/600 (49·5%) of samples with more than
 one serotype being found in 67/297 (20·2%) of these samples. The serotypes
 covered by the thirteen-valent pneumococcal conjugate vaccine were
 identified in 44·4% of samples containing typeable pneumococci.
 Application of a molecular serotyping approach to identification of
 multiple pneumococcal carriage demonstrates a substantial prevalence of
 co-colonisation. Continued surveillance utilising this approach following
 the introduction of routine use of pneumococcal conjugate vaccinates in
 infants will provide a more accurate understanding of vaccine efficacy
 against carriage and a better understanding of the dynamics of subsequent
 serotype and genotype replacement.
description: Microarray
 summarySummary of microarray
 detection of pneumococcal serotypes present in nasopharyngeal
 specimensSP-CPS_Oxford-3_Summary_170413.xlsx
DOI: 10.5061/dryad.2rh61k0
title: Data from: Age and infection history are revealed by different ornaments in a warbler

description: Female preference for older or more disease-resistant males are both
 possible outcomes of parasite-mediated sexual selection, but the extent to
 which infection alters the development of ornaments to yield signals of
 male age and health has rarely been explored. In a longitudinal study of
 61 male common yellowthroats (Geothlypis trichas), age-related increases
 in the size of the melanin-based mask and carotenoid-based bib were not
 correlated among young males, likely owing to differences in how blood
 parasites affect ornament development. Infection with trypanosomes and
 hemosporidians in a male’s first breeding season was associated with
 slower growth of the mask; uninfected males attained large masks in their
 second breeding season, while infected males attained large masks in their
 third breeding season. In contrast, the bib size of males increased every
 year regardless of infection. As a consequence, different populations of
 males are identified by the largest ornaments – older males in the case of
 bib and a combination of older males and young, uninfected males in the
 case of mask. Although mask is thus the more informative trait with
 respect to male health, females prefer large bibs in our population. If
 infection is opportunistic, young, uninfected males may not possess good
 genes for parasite resistance but simply good luck, and it may benefit
 females to prefer older males who are more likely to have withstood prior
 episodes of selection. A “pure” signal of age may be a more reliable
 signal of resistance to parasites than an ornament whose expression is
 modulated by infection.
description: Age, Ornamentation, and
 Parasite Status and History in Common YellowthroatsDryad.xlsx