cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ns7bv
title: Data from: Plant-soil feedbacks shift from negative to positive with decreasing light in forest understory species

description: Net pairwise plant–soil feedbacks (PSF) may be an important factor
 structuring plant communities, yet the influence of abiotic context on PSF
 is not yet understood. Abiotic factors such as light availability can
 alter plant–soil interactions, potentially resulting in strong context
 dependence of PSF. Here, we present an experiment in which we measured
 whole-soil net pairwise feedbacks amongst six common forest understory
 species across a gradient of light availability. Light treatments were
 imposed throughout both phases (the conditioning phase and the response
 phase) of the feedback experiment. Across the plant community, PSF shifted
 from negative at high light availability to weakly positive under low
 light (P = 0.013). Differences in the biomass of plants during the
 conditioning phase did not fully explain light-imposed differences in
 feedbacks, indicating that reduced light availability qualitatively
 changes the nature of PSF rather than simply weakening feedbacks by
 reducing plant growth. Results indicate that abiotic context can
 fundamentally alter the role of PSF in structuring plant communities.
description: SmithandReynolds_Ecology_2015_datasetFile includes biomass data from a two-phase greenhouse experiment designed to measure net pairwise plant-soil feedback in understory species from Eastern deciduous forests of the United States. In Phase I each species was grown under each light treatment. In Phase II, soil from each Phase I pot was divided and used to inoculate a new set of plants so that each species was grown in soil conditioned by a conspecific and all possible heterospecifics.
DOI: 10.5061/dryad.bd1s3
title: Data from: Latitudinal variation in thermal reaction norms of post-winter pupal development in two butterflies differing in phenological specialization

description: Latitudinal clines in thermal reaction norms of development are a common
 phenomenon in temperate insects. Populations from higher latitudes often
 develop faster throughout the range of relevant temperatures (i.e
 countergradient variation) because they must be able to complete their
 life cycle within a shorter seasonal time window compared to populations
 at lower latitudes. In the present study, we experimentally demonstrate
 that two species of butterflies Anthocharis cardamines (L.) and Pieris
 napi (L.) instead show a cogradient variation in thermal reaction norms of
 post-winter pupal development so that lower latitude populations develop
 faster than higher latitude populations. The two species share host plants
 but differ in the degree of phenological specialization, as well as in the
 patterns of voltinism. We suggest that the pattern in A. cardamines, a
 univoltine phenological specialist feeding exclusively on flowers and
 seedpods, is the result of selection for matching to the phenological
 pattern of its local host plants. The other species, P. napi, is a
 phenological generalist feeding on the leaves of the hosts and it shows a
 latitudinal cline in voltinism. Because the latitudinal pattern in P. napi
 was an effect of slow development in a fraction of the pupae from the most
 northern population, we hypothesize that this population may include both
 bivoltine and univoltine genotypes. Consequently, although the two species
 both showed cogradient patterns in thermal reaction norms, it appears
 likely that this was for different reasons.
description: Latitudinal variation in
 thermal reaction norms of post-winter pupal development in two butterflies
 differing in phenological specializationExcel
 fileDryad
 dataset.xlsx
DOI: 10.5061/dryad.ht357
title: Data from: Preschool children’s vision screening in New Zealand: a retrospective evaluation of referral accuracy

description: Objectives: To assess the accuracy of preschool vision screening in a
 large, ethnically diverse, urban population in South Auckland, New
 Zealand. Design: Retrospective longitudinal study. Methods: B4 School
 Check vision screening records (n=5572) were compared with hospital eye
 department data for children referred from screening due to impaired
 acuity in one or both eyes who attended a referral appointment (n=556).
 False positive screens were identified by comparing screening data from
 the eyes that failed screening with hospital data. Estimation of false
 negative screening rates relied on data from eyes that passed screening.
 Data were analysed using logistic regression modelling accounting for the
 high correlation between results for the two eyes of each child. Primary
 outcome measure: Positive predictive value of the preschool vision
 screening programme. Results: Screening produced high numbers of false
 positive referrals, resulting in poor positive predictive value (PPV=31%,
 95% CI 26% to 38%). High estimated negative predictive value (NPV=92%, 95%
 CI 88% to 95%) suggested most children with a vision disorder were
 identified at screening. Relaxing the referral criteria for acuity from
 worse than 6/9 to worse than 6/12 improved PPV without adversely affecting
 NPV. Conclusions: The B4 School Check generated numerous false positive
 referrals and consequently had a low PPV. There is scope for reducing
 costs by altering the visual acuity criterion for referral.
description: B4SC Visual screening -
 DataData analysed from B4
 School Check vision screening referrals 1 March 2010 to 28 February
 2011Copy of
 Langeslag et al - B4SC Visual screening -
 Data.xlsx
DOI: 10.5061/dryad.dp24m
title: Data from: Responses of common and rare aliens and natives to nutrient availability and fluctuations

description: 1. Global environmental change not only includes changes in mean
 environmental conditions but also in temporal environmental fluctuations.
 Because it is frequently suggested that common species, and particularly
 invasive alien species, are phenotypically highly plastic, they might
 benefit more from these fluctuations than rare native and rare alien
 species. Experimental tests, however, are still lacking. 2. Here, we
 tested whether alien plant species take more advantage of increases in
 resource levels and fluctuations therein than native species, and whether
 common species do so more than rare species. Therefore, we grew seven
 common alien, seven rare alien, nine common native and six rare native
 herbaceous plants, in one treatment with constantly low nutrient
 availability and five treatments with high nutrient availability that
 differed in temporal availability of nutrients (constant, increasing,
 decreasing, single large pulse, multiple smaller pulses). 3. We found that
 all species produced more biomass and longer roots, and had a lower root
 mass fraction under high nutrient conditions than under low nutrient
 conditions, irrespective of their origin and commonness. Among the high
 nutrient treatments, the temporal pattern of nutrient supply also
 influenced biomass production, root allocation and root thickness, but the
 magnitude and/or directions of these responses varied among the groups of
 species. Particularly, we found that alien plant species, irrespective of
 whether they are common or rare, produced more biomass, and had a higher
 root mass fraction when nutrients were supplied as a single pulse in the
 middle of the growth period instead of supplied at a constant rate,
 whereas the reverse was true for the native species. 4.
 Synthesis: Our study suggests that species origin does not drive
 differences in plant biomass production, root morphology and allocation in
 response to changes in mean environmental nutrient availability. However
 in our study, alien plant species, in contrast to native plant species,
 benefited from a large nutrient pulse. This suggests that increased
 fluctuations in nutrient availability might promote alien plant invasions.
description: RFE2014_YJL_MvK.xlsx: Species: Species
 name Family: Family name Origin:
 Alien or Native Commonness: Common or Rare
 Treatment: Nutrient Treatment Total_LA: Total
 leaf area whole plant(mm2) Initial_H: Initial
 height(cm) Total_biomass: Total biomass(g)
 RMF: Root mass fraction Length: Total Root
 length of the whole plant(m) Diam: Average Diameter of
 whole plant(mm) SRL: Specific root length
 (m/g) NA: Data missing because the plant died or sample
 lossing
DOI: 10.5061/dryad.27056
title: Data from: Assessing environmental pollution in birds: a new methodological approach for interpreting bioaccumulation of trace elements in feather shafts using geochemical sediment data

description: Environmental trace element composition can have an important impact on
 ecosystem and population health as well individual fitness. Therefore,
 carefully assessing bioaccumulation of trace elements is central to
 studies investigating the ecological impact of pollution. Colonial birds
 are important bioindicators since non-invasive sampling can easily be
 achieved through sampling of chick feathers, which controls for some
 confounding factors of variability (age and environmental heterogeneity).
 However, an additional confounding factor, external contamination (ExCo),
 which remains even after washing feathers, has frequently been overlooked
 in the literature. We developed a new method to reliably interpret
 bioaccumulation of 10 trace elements (As, Cd, Cr, Cu, Hg, Ni, Pb, Se, Sn
 and Zn) in feathers using chicks of a colonial species: the Greater
 Flamingo, Phoenicopterus roseus. First, only shafts were used to remove
 ExCo retained in vanes. Secondly, we applied a thorough washing procedure.
 Thirdly, we applied a new analytical method to control for ExCo, which
 assumes that ExCo is mainly due to adhered sediment particles and that the
 relative concentration of each trace element will be similar to the
 sediment geochemical composition of sampling sites. We validated this new
 methodology by comparing trace element composition and particle
 composition (by scanning electron microscopy and mass spectrometry) of
 washed and unwashed feathers. The washing procedure removed &gt;99% of
 K indicating that most of the ExCo from salt was removed. Scanning
 electron microscopy and mass spectrometry revealed that some sediment
 particles remained after washing, especially clays which are likely to
 severely bias bioaccumulation interpretation. We successfully controlled
 for ExCo by calculating the ratio of ExCo due to sediment using the
 geochemical fingerprint of sediment samples. Our methodology leads to
 conservative estimates of bioaccumulation for As, Cd, Cr, Cu, Hg, Ni, Pb,
 Se, Sn and Zn. We have validated a new more reliable method of analysing
 trace element concentrations in feathers, which effectively controls for
 ExCo, if geochemical sediment data can be meaningfully compared to ExCo of
 feathers. We have demonstrated that overlooking ExCo leads to potentially
 erroneous conclusions, and we urge that the method applied in this study
 be considered in future studies.
description: DryadData of trace elements
 of feathers, sediment and salt from samples collected between July and
 August 2014, during the ringing operations of three breeding colonies of
 Greather flamingo, Phoenicopterus roseus, of the western Mediterranean:
 Aigues-Mortes (AIG), southern France (N 43° 33’, E 4° 11’); Fuente de
 Piedra (FDP), southern Spain (37° 06’N, 04° 45’W) and the heavily polluted
 Odiel marshes (ODI), southern Spain (37º 17′ N, 06º 55′
 W).
DOI: 10.5061/dryad.rh2cf
title: Data from: A new taxon of cistecephalid dicynodont from the upper Permian Kundaram Formation of India

description: A new cistecephalid dicynodont, Sauroscaptor tharavati gen. et sp. nov.,
 is described from the upper Permian Kundaram Formation of India. This
 taxon is represented by specimens formerly referred to the African
 dicynodont genera Cistecephalus and Emydops. Sauroscaptor can be
 distinguished from other cistecephalids by the extremely posterior
 position of the pineal foramen (overhanging the edge of the occiput),
 bipartite nuchal crest, and relatively narrow skull roof. The recognition
 of Sauroscaptor as a distinct cistecephalid taxon adds to the increasing
 evidence for high levels of basinal endemism in this family. However,
 dicynodont biogeographical patterns are complex, and there is no simple
 relationship between inferred dispersal ability based on body size and
 levels of endemicity within clades.
description: Sauroscaptor
 phylogenetic character dataAnomodont data matrix
 (in TNT format) used in phylogenetic analysis of Sauroscaptor
 tharavati.Sauroscaptor.tntCistecephalid MeasurementsMeasurements of total dorsal skull length, anterior and posterior intertemporal width, and post-pineal skull length in cistecephalid dicynodonts.
DOI: 10.5061/dryad.r617g73
title: Data from: Does urbanization cause stress in wild birds during development? insights from feather corticosterone levels in juvenile house sparrows (Passer domesticus)

description: Urban landscapes are associated with abiotic and biotic environmental
 changes that may result in potential stressors for wild vertebrates. Urban
 exploiters have physiological, morphological and behavioral adaptations to
 live in cities. However, there is increasing evidence that urban
 exploiters themselves can suffer from urban conditions, especially during
 specific life-history stages. We looked for a link between the degree of
 urbanization and the level of developmental stress in an urban exploiter
 (the house sparrow, Passer domesticus), which has recently been declining
 in multiple European cities (e.g. London, UK). Specifically, we conducted
 a large-scale study and sampled juvenile sparrows in 11 urban and rural
 sites to evaluate their feather corticosterone (CORT) levels. We found
 that juvenile feather CORT levels were positively correlated with the
 degree of urbanization, supporting the idea that developing house sparrows
 may suffer from urban environmental conditions. However, we did not find
 any correlation between juvenile feather CORT levels and body size, mass,
 or body condition. This suggests either that the growth and condition of
 urban sparrows are not impacted by elevated developmental CORT levels, or
 that urban sparrows may compensate for developmental constraints once they
 have left the nest. Although feather CORT levels were not correlated with
 baseline CORT levels, we found that feather CORT levels were slightly and
 positively correlated with the CORT stress response in juveniles. This
 suggests that urban developmental conditions may potentially have
 long-lasting effects on stress physiology and stress sensitivity in this
 urban exploiter.
description: Beaugeard2018_Data_FeatherCort_HouseSparrow_juv_11sitesData of feathers from juvenile house sparrows captured in 11 sites in France. Data include the date of capture (2 formats), the site of capture, the urbanization score of the site, the level of feather corticosterone expressed either in ng/mg or in ng/mm.Beaugeard2018_Data_FeatherCort_HouseSparrow_juv_4sitesData of juvenile house sparrows captured in 4 sites in France. Data include the date of capture (2 formats), the site of capture, the urbanization score of the site, the feather corticosterone level expressed either in ng/mg or in ng/mm, the sex, the Scaled Mass Index (SMI), the tarsus length, the body mass, and the levels of baseline and stress-induced corticosterone in plasma.
DOI: 10.5061/dryad.hn45t
title: Data from: Effects of deer density and land use on white-tailed deer

description: Local and regional land use changes, such as the expansion of cellulosic
 biofuels, and population density of deer can affect the health and body
 mass of white-tailed deer (Odocoileus virginianus). We collected
 hunter-harvest data for 1,731 white-tailed deer from DeSoto National
 Wildlife Refuge (DNWR) in eastern Nebraska and western Iowa, USA from
 2003-2010. We used linear mixed-effects models and information theoretic
 methods to estimate effects of density of deer and proportion of total
 landcover area converted from cropland to cool- or warm-season grassland
 on body mass of white-tailed deer. Density of deer at DNWR ranged from
 36.5 deer/km2-50.6 deer/km2 and the proportion of landcover at DNWR that
 remained cropland each year ranged from 14.9%-23.2%. Body mass was
 inversely related to population density (−1.4 kg/5.5 deer/km2) and
 proportion of cropland (−1.3 kg/3.1% conversion of total land area from
 cropland to grassland). We used auxiliary harvest data collected at Boyer
 Chute National Wildlife Refuge (BCNWR) to validate our models and found
 our models performed well. We estimate densities of deer must be reduced
 by 1.7 (SE=0.6) deer/km2 for every 1% change in total landcover from
 cropland to grassland in order for deer to maintain body mass. Our results
 indicate increased harvest of deer, resulting in a reduction in population
 density, will offset negative effects a decline in the amount of available
 cropland could have on the body mass and health of white-tailed deer.
description: Deer Body Mass
 Data
DOI: 10.5061/dryad.364b3
title: Data from: Climatic effects on population declines of a rare wetland species and the role of spatial and temporal isolation as barriers to hybridization

description: Climate change and climatic extremes may affect species directly or
 indirectly. While direct climatic effects have been intensively studied,
 indirect effects, such as increasing hybridization risk, are poorly
 understood. The goal of our study was to analyse the impact of climate on
 population dynamics of a rare habitat specialist, Chorthippus montanus, as
 well as the fine-scale spatial overlap with a sympatric habitat
 generalist, Chorthippus parallelus and the dispersion of hybrids. We were
 particularly interested in the role of spatiotemporal overlap on
 heterospecific encounter frequencies. We conducted high-precision
 mark-recapture studies on two sites over 7 years and genotyped 702
 individuals of two C. montanus generations to detect hybrids. We tested
 the performance of three programs (structure, newhybrids and adegenet) and
 accepted only hybrids detected by the two best performing programs. We
 then tested for correlations between yearly population trends and climatic
 variables. Furthermore, we analysed the spatial dispersion of both taxa
 and the hybrids to calculate variation in spatial and temporal overlap and
 infer heterospecific encounter probabilities. Our results revealed that
 droughts during the egg phase and rainy weather during nymphal development
 were strongly correlated with population declines in the habitat
 specialist. The highest hybridization rate (19·6%) was found in the
 population with lowest population size. The combined effects of spatial
 and temporal niche overlap decreased heterospecific encounter
 probabilities to 4·2–7·6% compared to 20–28% and 11–19% calculated alone
 from phenology or spatial overlap respectively. Hybrids were detected in
 areas of higher heterospecific encounter probability, mainly at the edge
 of the specialists’ occupied habitat in areas with intermediate soil
 moisture conditions compared to the parental species. This illustrates
 that the combination of spatial and temporal segregation provides an
 effective barrier to hybridization. However, the high hybridization rate
 in one of the populations suggests that this function may decrease with
 decreasing population size. This supports the hypothesis that climatic
 extremes threaten rare species directly by reducing reproductive success
 and may indirectly increase hybridization risk.
description: Microsatellite
 dataMicrosatellite data of
 Ch. montanus and Ch. parallelus used for hybrid detection and calculation
 of genetic parameters. DNA was extracted using the DNeasy Blood &
 Tissue Kit (Qiagen). All individuals were genotyped at ten polymorphic
 microsatellite loci. Fragment lengths of PCR products were determined on a
 MEGABACE1000 automated sequencer (GE Healthcare) and scored with Fragment
 Profiler 1.2 (Amersham Biosciences).Dryad Data Rohde et al 2016
 functional ecology.xlsx
DOI: 10.5061/dryad.mk815
title: Data from: Metazoan parasites of African annual killifish (Nothobranchiidae): abundance, diversity, and their environmental correlates

description: Estimates of biodiversity and its global patterns are affected by parasite
 richness and specificity. Despite this, parasite communities are largely
 neglected in biodiversity estimates, especially in the tropics. We studied
 the parasites of annual killifish of the genus Nothobranchius that inhabit
 annually desiccating pools across the African savannah and survive the dry
 period as developmentally arrested embryos. Their discontinuous,
 non-overlapping generations make them a unique organism in which to study
 natural parasite fauna. We investigated the relationship between global
 (climate and altitude) and local (pool size, vegetation, host density and
 diversity, and diversity of potential intermediate hosts) environmental
 factors and the community structure of killifish parasites. We examined
 metazoan parasites from 21 populations of four host species
 (Nothobranchius orthonotus, N. furzeri, N. kadleci, and N. pienaari)
 across a gradient of aridity in Mozambique. Seventeen parasite taxa were
 recorded, with trematode larval stages (metacercariae) being the most
 abundant taxa. The parasites recorded were both allogenic (life cycle
 includes non-aquatic host; predominantly trematodes) and autogenic
 (cycling only in aquatic hosts; nematodes). The parasite abundance was
 highest in climatic regions with intermediate aridity, while parasite
 diversity was associated with local environmental characteristics and
 positively correlated with fish species diversity and the amount of
 aquatic vegetation. Our results suggest that parasite communities of
 sympatric Nothobranchius species are similar and dominated by the larval
 stages of generalist parasites. Therefore, Nothobranchius serve as
 important intermediate or paratenic hosts of parasites, with piscivorous
 birds and predatory fish being their most likely definitive hosts.
description: Environmental and
 similarity datasetssource data for linking
 parasite communities and environmental predictors (one spreadsheet) and
 list of pairwise similarity data (second spreadsheet)Notho_para.xlsx
DOI: 10.5061/dryad.18b1k
title: Data from: Influence of killing method on Lepidoptera DNA barcode recovery

description: The global DNA barcoding initiative has revolutionized the field of
 biodiversity research. Such large-scale sequencing projects require the
 collection of large numbers of specimens, which need to be killed and
 preserved in a way that is both DNA-friendly and which will keep voucher
 specimens in good condition for later study. Factors such as time since
 collection, correct storage (exposure to free water and heat) and DNA
 extraction protocol are known to play a role in the success of downstream
 molecular applications. Limited data are available on the most efficient,
 DNA-friendly protocol for killing. In this study, we evaluate the quality
 of DNA barcode (cytochrome oxidase I) sequences amplified from DNA
 extracted from specimens collected using three different killing methods
 (ethyl acetate, cyanide and freezing). Previous studies have suggested
 that chemicals, such as ethyl acetate and formaldehyde, degraded DNA and
 as such may not be appropriate for the collection of insects for DNA-based
 research. All Lepidoptera collected produced DNA barcodes of good quality,
 and our study found no clear difference in nucleotide signal strength,
 probability of incorrect base calling and phylogenetic utility among the
 three different treatment groups. Our findings suggest that ethyl acetate,
 cyanide and freezing can all be used to collect specimens for DNA
 analysis.
description: Lepidoptera_subsample3_GarliFile contains alignement of sequence data in nexus formatData for Figure 1Contains the average fluorescent values data used to construct Figure 1