cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.2s47km
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: DNA barcoding of Sialis sp. (Megaloptera) in Portugal: the missing tool to species identification"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000535-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f5229
title: Data from: Estimating the effective number of breeders from single parr samples for conservation monitoring of wild populations of Atlantic salmon Salmo salar

description: This study assesses whether the effective number of breeders (Nb) can be
 estimated using a time and cost-effective protocol using genetic sibship
 reconstruction from a single sample of young-of-the-year (YOY) for the
 purposes of Atlantic salmon Salmo salar population monitoring. Nb was
 estimated for 10 consecutive reproductive seasons for S. salar in the
 River Nivelle, a small population located at the rear-edge of the species
 distribution area in France, chronically under its conservation limit and
 subjected to anthropogenic and environmental changes. Subsampling of real
 and simulated data showed that accurate estimates of Nb can be obtained
 from YOY genotypes, collected at moderate random sampling intensity,
 achievable using routine juvenile electrofishing protocols. Spatial bias
 and time elapsed since spawning were found to affect estimates, which must
 be accounted for in sampling designs. Nb estimated in autumn for S. salar
 in the River Nivelle was low and variable across years from 23 (95% C.I.
 14–41) to 75 (53–101) and was not statistically correlated with the
 estimated number of returning adults, but it was positively correlated
 with the estimated number of YOY at age 9 months. Nb was found to be lower
 for intermediate levels of redd aggregation, suggesting that the strength
 of the competition between males to access females affects reproductive
 success variance depending on redd spatial configuration. Thus,
 environmental factors such as habitat availability and quality for
 spawning and YOY development predominate over demographic ones (number of
 returning adults) in driving long-term population viability for S. salar
 in the River Nivelle. This study showcases Nb as an integrated parameter,
 encompassing demographic and ecological information about a reproductive
 event, relevant to the assessment of both short-term effects of management
 practices and long-term population conservation status.
description: Multilocus
 microsatellites dataDryad_Bacles-et-al_JFB-2018.xlsx
DOI: 10.5061/dryad.5v1r5
title: Data from: Phylogeographical patterns of an alpine plant, Rhodiola dumulosa (Crassulaceae), inferred from chloroplast DNA sequences

description: The phylogeographical patterns of Rhodiola dumulosa, an alpine plant
 species restrictedly growing in the crevices of rock piles, were
 investigated based on 4 fragments of the chloroplast genome. To cover the
 full distribution of R. dumulosa in China, 19 populations from 3 major
 disjunct distribution areas (northern, central, and northwestern China)
 were sampled. A total of 5881bp (after alignment) of chloroplast DNA
 (cpDNA) from 100 individuals were sequenced. The combined cpDNA data set
 yielded 36 haplotypes. The total genetic diversity of R. dumulosa was
 remarkably high (H T = 0.981). The interpopulation genetic differentiation
 was significantly large (F ST = 0.8537, P &lt; 0.001), possibly due to
 the long-term isolation of the natural populations. N ST was significantly
 larger than G ST (P &lt; 0.001), indicating the presence of
 phylogeographical structure among the R. dumulosa populations. We propose
 2 migration steps to explain the current distribution of R. dumulosa in
 China. First, this species migrated from refugia in the Qinghai-Tibetan
 Plateau to northern areas via the intervening highlands when temperatures
 increased; second, the highland populations migrated toward the
 mountaintops when temperatures increased further because R. dumulosa is
 adapted to cold environments. During the second migration step, the common
 ancestral haplotypes may have been gradually lost.
description: combined cpDNA
 sequences_alignedan aligned sequence file
 of combined cpDNA sequences from 100 individual samples
DOI: 10.5061/dryad.6c9143t
title: Data from: Nitrogen and chlorine co-doped carbon dots as probe for sensing and imaging in biological samples

description: A facile one step hydrothermal synthesis approach was proposed to prepare
 nitrogen and chlorine co-doped carbon dots using l-ornithine hydrochloride
 as the sole precursor. The configuration and component of carbon dots were
 characterized by TEM, XPS, and FTIR. The obtained CDs (Orn-CDs) with a
 mean diameter of 2.1 nm were well monodispersed in aqueous solutions. The
 as-prepared CDs exhibited a bright blue fluorescence with a high yield of
 60%, good photostability and low cytotoxicity. The emission of Orn-CDs
 could be selectively and effectively suppressed by Fe3+. Thus, a
 quantitative assay of Fe3+ was realized by this nanoprobe with a detection
 limit of 95.6 nmol L-1 in the range of 0.3-50 µmol L-1. Furthermore,
 ascorbic acid could recover the fluorescence of Orn-CDs suppressed by
 Fe3+, owing to the transformation of Fe3+ to Fe2+ by ascorbic acid. The
 limit of detection for ascorbic acid was 137 nmol L-1 in the range of
 0.5-10 µmol L-1. In addition, the established method was successfully
 applied for Fe3+ and ascorbic acid sensing in human serum and urine
 specimans and for imaging of Fe3+ in living cells. With merits of low
 economic cost, easy to scale up, without additional functionalized and
 sample pretreatment, Orn-CDs based sensing platform showed its potential
 to be used for biomedical related study.
description: Raw
 dataraw
 data.rar
DOI: 10.5061/dryad.bc60cd5
title: Data from: A shady phytoplankton paradox: when phytoplankton increases under low light

description: Light is a fundamental driver of ecosystem dynamics, affecting the rate of
 photosynthesis and primary production. In spite of its importance, less is
 known about its community-scale effects on aquatic ecosystems compared
 with those of nutrient loading. Understanding light limitation is also
 important for ecosystem management, as human activities have been rapidly
 altering light availability to aquatic ecosystems. Here we show that
 decreasing light can paradoxically increase phytoplankton abundance in
 shallow lakes. Our results, based on field manipulation experiments, field
 observations, and models, suggest that, under competition for light and
 nutrients between phytoplankton and submersed macrophytes, alternative
 stable states are possible under high light supply. In a
 macrophyte-dominated state, as light decreases phytoplankton density
 increases, because macrophytes (which effectively compete for nutrients
 released from the sediment) are more severely affected by light reduction.
 Our results demonstrate how species interactions with spatial
 heterogeneity can cause an unexpected outcome in complex ecosystems. An
 implication of our findings is that partial surface shading for
 controlling harmful algal bloom may, counterintuitively, increase
 phytoplankton abundance by decreasing macrophytes. Therefore, to predict
 how shallow lake ecosystems respond to environmental perturbations, it is
 essential to consider effects of light on the interactions between pelagic
 and benthic producers.
description: Data and R
 codesData and R codes for
 "A shady phytoplankton paradox: When phytoplankton increases under
 low light" by Yamamichi et al.fig.tar
DOI: 10.5061/dryad.qn24m
title: Data from: Potential for local adaptation in response to an anthropogenic agent of selection: effects of road deicing salts on amphibian embryonic survival and development

description: The application of millions of tons of road deicing salts every winter in
 North America presents significant survival challenges to amphibians
 inhabiting road-side habitats. While much is known of the effects of NaCl
 on anuran tadpoles, less is known of effects on amphibian eggs, or any
 caudate life-stage. In addition, little is known of the effects of MgCl2,
 which is now the 2nd most commonly used road deicer. Most studies have
 considered amphibians to be helpless victims of deicing salts, and ignore
 the possibility of the evolution of local adaptation to this stressor. We
 attempt to address these knowledge gaps and explore this evolutionary
 potential by examining the effects of NaCl and MgCl2 on the survival and
 development of eggs from different female rough-skinned newts (Taricha
 granulosa) from the same population. We demonstrate that both salts, at
 environmentally relevant concentrations, severely affect the embryonic
 survival and development of this amphibian, but that the effects of the
 salt are dependent on the identity of the mother. This female x treatment
 interaction results in substantial variation in tolerance to road deicing
 salts among newt families, providing the raw material necessary for
 natural selection and the evolution of local adaptation in this amphibian.
description: Female Newt
 Morphometrics DataFemale Newt
 Morphometrics (SVL, Mass, TL, Egg Diameter, Number of Eggs Laid) for
 animals used in studyDryadData_FemaleMorphometrics_Hopkinsetal2012.xlsPrimary Data File - Embryonic Survival and DevelopmentPrimary Data File used in analysis of effects of salt treatment and female identity on newt embryonic survival and developmentDryadData_Hopkins_etal_2012_EvolApl.xls
DOI: 10.15468/dl.zmxsg2
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: DNA Barcoding reveals sexual dimorphism in Isotrias penedana Trematerra, 2013 (Lepidoptera: Tortricidae, Chlidanotinae)"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000534-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kfajdh
title: Occurrence Download

description: A dataset containing 6739 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Dalbergia ecastaphyllum"
 ]
}

 The dataset includes 6739 records from 294 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000538-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f4f6b
title: Data from: Can phenotypic rescue from harvest refuges buffer wild sheep from selective hunting?

description: Human harvests can unwittingly drive evolution on morphology and life
 history, and these selective effects may be detrimental to the management
 of natural resources. Although theory suggests that harvest refuges, as
 sources of unselected animals, could buffer the effects of human
 exploitation on wild populations, few studies have assessed their
 efficiency. We analyzed records from &gt;7000 trophy bighorn rams
 (Ovis canadensis) harvested in Alberta, Canada, between 1974 and 2011 to
 investigate if the movement of rams from refuges toward harvested areas
 reduced the effects of selective harvesting on horn size through
 phenotypic rescue. Rams taken near refuges had horns on average about 3%
 longer than rams shot far from refuges and were slightly older, suggesting
 migration from refuges into hunted areas. Rams from areas adjacent to and
 far from harvest refuges, however, showed similar declines in horn length
 and increases in age at harvest over time, indicating a decreasing rate of
 horn growth. Our study suggests that the influx of rams from refuges is
 not sufficient to mitigate the selective effects of sheep trophy harvest.
 Instead, we suggest that selective hunting of highly mobile animals may
 affect the genetic structure of populations that spend part of the year
 inside protected areas.
description: Pelletier et
 al_DATARecords from &gt;7000
 trophy bighorn rams (Ovis canadensis) harvested in Alberta, Canada,
 between 1974 and 2011
DOI: 10.15468/dl.k7heau
title: Occurrence Download

description: A dataset containing 35739 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Callisaurus draconoides"
 ]
}

 The dataset includes 35739 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000536-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7747n
title: Data from: Temperature-dependent resetting of the molecular circadian oscillator in Drosophila.

description: Circadian clocks responsible for daily time keeping in a wide range of
 organisms synchronize to daily temperature cycles via pathways that remain
 poorly understood. To address this problem from the perspective of the
 molecular oscillator, we monitored temperature-dependent resetting of four
 of its core components in the fruitfly Drosophila melanogaster: the
 transcripts and proteins for the clock genes period (per) and timeless
 (tim). The molecular circadian cycle in adult heads exhibited parallel
 responses to temperature-mediated resetting at the levels of per
 transcript, tim transcript and TIM protein. Early phase adjustment
 specific to per transcript rhythms was explained by clock-independent
 temperature-driven transcription of per. The cold-induced expression of
 Drosophila per contrasts with the previously reported heat-induced
 regulation of mammalian Period 2. An altered and more readily
 re-entrainable temperature-synchronized circadian oscillator that featured
 temperature-driven per transcript rhythms and phase-shifted TIM and PER
 protein rhythms was found for flies of the ‘Tim 4’ genotype, which lacked
 daily tim transcript oscillations but maintained post-transcriptional
 temperature entrainment of tim expression. The accelerated molecular and
 behavioural temperature entrainment observed for Tim 4 flies indicates
 that clock-controlled tim expression constrains the rate of temperature
 cycle-mediated circadian resetting.
description: GodaSharpWijnen2014Fig13S2S3S5TabS2S3SPSS data file for the gene expression measures used for Figures 1,3,S2,S3,S5 and Tables S2,S3GodaSharpWijnenFig2Excel file containing the TopCount in vivo luciferase data plotted in Figure 2.GodaSharpWijnen2014FigS1SPSS data file containing the behavioural measures quantified in Figure S1.GodaSharpWijnen2014TabS1SPSS data files describing the circadian locomotor behaviour measures represented in Table S1.GodaSharpWijnen2014TabS4SPSS data file containing the circadian in vivo luminescence measures represented in Table S4
DOI: 10.5061/dryad.2kj82
title: Data from: Heterozygosity–fitness correlations in a wild mammal population: accounting for parental and environmental effects

description: HFCs (heterozygosity–fitness correlations) measure the direct relationship
 between an individual's genetic diversity and fitness. The effects of
 parental heterozygosity and the environment on HFCs are currently
 under-researched. We investigated these in a high-density U.K. population
 of European badgers (Meles meles), using a multimodel
 capture–mark–recapture framework and 35 microsatellite loci. We detected
 interannual variation in first-year, but not adult, survival probability.
 Adult females had higher annual survival probabilities than adult males.
 Cubs with more heterozygous fathers had higher first-year survival, but
 only in wetter summers; there was no relationship with individual or
 maternal heterozygosity. Moist soil conditions enhance badger food supply
 (earthworms), improving survival. In dryer years, higher indiscriminate
 mortality rates appear to mask differential heterozygosity-related
 survival effects. This paternal interaction was significant in the most
 supported model; however, the model-averaged estimate had a relative
 importance of 0.50 and overlapped zero slightly. First-year survival
 probabilities were not correlated with the inbreeding coefficient (f);
 however, small sample sizes limited the power to detect inbreeding
 depression. Correlations between individual heterozygosity and inbreeding
 were weak, in line with published meta-analyses showing that HFCs tend to
 be weak. We found support for general rather than local heterozygosity
 effects on first-year survival probability, and g2 indicated that our
 markers had power to detect inbreeding. We emphasize the importance of
 assessing how environmental stressors can influence the magnitude and
 direction of HFCs and of considering how parental genetic diversity can
 affect fitness-related traits, which could play an important role in the
 evolution of mate choice.
description: Annavi et al Datafile
 (Dryad)This file contain
 climate, demographic, survival, inbreeding and single-locus (SCL)
 individual, maternity and paternity data
DOI: 10.5061/dryad.37cc5
title: Data from: Agricultural practices for food safety threaten pest control services for fresh produce

description: Over the past decade, several foodborne disease outbreaks provoked
 widespread reforms to the fresh produce industry. Subsequent concerns
 about wildlife vectors and contaminated manures created pressure on
 growers to discontinue use of manure-based composts and remove nearby
 semi-natural vegetation. Despite widespread adoption, impacts of these
 practices on ecosystem services such as pest control have not been
 assessed. We used a landscape-scale field experiment to quantify
 associations between compost applications, semi-natural vegetation, pest
 control services and lettuce yields on organic farms throughout
 California's Central Coast, a region experiencing food safety
 reforms. We found that farms with surrounding semi-natural vegetation
 supported a diverse arthropod assemblage, whereas a herbivore-dominated
 assemblage occupied farms in simplified landscapes. Moreover, predatory
 arthropods consumed more herbivores at sites with more surrounding
 non-crop vegetation and reduced aphid pest infestations in lettuce.
 Compost improved lettuce yields by increasing soil nutrients and organic
 matter, but affected neither pest control nor Escherichia coli prevalence.
 Synthesis and applications. Food safety concerns are prompting practices
 that simplify farms and landscapes. Our results demonstrate that two
 practices – elimination of manure-based composts and removal of non-crop
 vegetation – are likely having negative impacts on arthropod biodiversity,
 pest control and soil quality. Critically, our findings and previous
 research suggest that compost can be applied safely and that habitat
 removal is likely ineffective at mitigating food safety risk. There is
 thus scope for co-managing fresh produce fields for food safety, ecosystem
 services, and biodiversity through applying appropriately treated composts
 and stopping habitat removal.
description: Pest control, yield, and
 soil data.See attached readme
 file.Karpetal_PestControl_Data.xlsx
DOI: 10.5061/dryad.rk5fp6n9
title: Data from: Fitness of Arabidopsis thaliana mutation accumulation lines whose spontaneous mutations are known

description: Despite the fundamental importance of mutation to the evolutionary
 process, we have little knowledge of the direct consequences of specific
 spontaneous mutations to the fitness of the organism. Combining results of
 whole-genome sequencing with repeated field assays of survival and
 reproduction, we quantify the combined effects on fitness of spontaneous
 mutations identified in Arabidopsis thaliana. We demonstrate that the
 effects are beneficial, deleterious or neutral depending on the
 environmental context. Some lines, bearing mutations disrupting known
 loci, differ strongly in fitness from the founder or premutation genotype.
 Those effects vary across environments, e.g., a line with a major deletion
 spanning a transcription factor gene expressed lower fitness than the
 founder under most conditions but exceeded the founder’s fitness in one
 environment. The large contribution of genotype by environment interaction
 (GxE) to mutation effects on fitness implies spatial and/or temporal
 variation in selection on new mutations and could contribute to the
 maintenance of standing genetic variation.
description: DataSetForPublicationThe data reflect the performance of 5 MA lines and the founder in multiple environments. The 5 MA lines were fully sequenced. The file is an Excel file.
DOI: 10.5061/dryad.q10q6
title: Data from: Phylogeny and new taxonomy of the Booted Eagles (Accipitriformes: Aquilinae)

description: We present a phylogeny of all booted eagles (38 extant and one extinct
 species) based on analysis of published sequences from seven loci. We find
 molecular support for five major clades within the booted eagles: Nisaetus
 (10 species), Spizaetus (4 species), Clanga (3 species), Hieraaetus (6
 species) and Aquila (11 species), requiring generic changes for 14 taxa.
 Additionally, we recommend that the Long-crested Eagle (Lophaetus
 occipitalis) and the Black Eagle (Ictinaetus malaiensis) remain in their
 monotypic genera, due to their distinctive morphology. We apply the
 recently resurrected genus Clanga for the spotted eagles (previously
 Aquila spp.) to resolve the paraphyly of the genus Aquila such that the
 clade including the Booted Eagle (H. pennatus), Little Eagle (H.
 morphnoides), Pygmy Eagle (H. weiskei), Ayres’s Eagle (H. ayresii) and
 Wahlberg’s Eagle (H. wahlbergi) can remain in the genus Hieraaetus. The
 Rufous-bellied Eagle should be retained in the genus Lophotriorchis. For
 consistency in English names, we recommend that the term “hawk-eagles” be
 used only for the species in the genera Nisaetus and Spizaetus. We suggest
 following new or modified English names: Cassin’s Eagle (Aquila africana),
 Bonaparte’s Eagle (A. spilogaster), Ayres’s Eagle (Hieraaetus ayresii),
 and Black-and-chestnut Hawk-Eagle (Spizaetus isidori).
description: infile 41 taxa all
 lociMrBayes input file of 41
 taxa, all loci.allloci_41tax_fig1.nexMrBayes Nuclear 28 taxa (fig2a)MrBayes file for Nuclear dataset with 28 taxa (fig2a)28tax_nuc.PAUMrBayes mt 41 taxa (Fig2b)MrBayes file used to generate figure 2b using mt data for 41 taxa.mt_41tax_pf_sep2016.nex