cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h3r11
title: Data from: Baseline glucocorticoids are drivers of body mass gain in a diving seabird

description: Life-history trade-offs are influenced by variation in individual state,
 with individuals in better condition often completing life-history stages
 with greater success. Although resource accrual significantly impacts key
 life-history decisions such as the timing of reproduction, little is known
 about the underlying mechanisms driving resource accumulation. Baseline
 corticosterone (CORT, the primary avian glucocorticoid) mediates daily and
 seasonal energetics, responds to changes in food availability, and has
 been linked to foraging behavior, making it a strong potential driver of
 individual variation in resource accrual and deposition. Working with a
 captive colony of white-winged scoters (Melanitta fusca deglandi), we
 aimed to causally determine whether variation in baseline CORT drives
 individual body mass gains mediated through fattening rate (plasma
 triglycerides corrected for body mass). We implanted individuals with each
 of three treatment pellets to elevate CORT within a baseline range in a
 randomized order: control, low dose of CORT, high dose of CORT, then blood
 sampled and recorded body mass over a two-week period to track changes in
 baseline CORT, body mass, and fattening rates. The high CORT treatment
 significantly elevated levels of plasma hormone for a short period of time
 within the biologically relevant, baseline range for this species, but
 importantly did not inhibit the function of the HPA
 (hypothalamic–pituitary–adrenal) axis. Furthermore, an elevation in
 baseline CORT resulted in a consistent increase in body mass throughout
 the trial period compared to controls. This is some of the first empirical
 evidence demonstrating that elevations of baseline CORT within a
 biologically relevant range have a causal, direct, and positive influence
 on changes in body mass.
description: Hennin 2016 - WWSC
 DataThese are data from an
 experiment in captive white-winged scoters in which we manipulated
 corticosterone to examine the profile of release of corticosterone over
 time, the impact on the HPA axis and subsequent changes in mass and
 fattening.
DOI: 10.5061/dryad.1v4t5
title: Data from: Mammalian herbivores affect leafhoppers associated with specific plant functional types at different timescales

description: 1. Theory predicts that mammalian herbivores affect the quantity and
 quality of plants on which they preferentially feed in the short term. In
 the longer term, they can promote either preferred or less preferred
 plants, depending on whether preferred plants are adapted or sensitive to
 grazing. Less clear are the short- and long-term responses of herbivorous
 insects to mammalian herbivory, and how these responses depend on the
 specific plants or plant functional types on which the insects feed. 2. We
 progressively excluded large, medium, and small mammals for five growing
 seasons in two subalpine vegetation types with long-term differences in
 mammalian grazing intensity. Short-grass vegetation has a history of
 intensive grazing, while tall-grass vegetation has been grazed less
 intensively. We tested whether mammals altered the abundance and body size
 of leafhoppers specialized on specific plant functional types (grasses,
 sedges, forbs, or legumes/forbs), distinguishing between short-term
 (exclosures) and long-term (vegetation types) differences in mammalian
 grazing pressure. Furthermore, we assessed whether leafhoppers’ responses
 were explained by changes in biomass or quality of the plant functional
 types on which they feed. 3. In the short term, mammal exclosures
 increased the abundance of grass- and forb-feeding leafhoppers via
 increases in the biomass of grasses and forbs, regardless of vegetation
 type. Both grasses and forbs are preferred food plants of mammals. In the
 long term, the biomass of sedges, which are less preferred by mammals,
 increased in the less intensively grazed tall-grass vegetation. This
 resulted in a higher abundance of sedge-feeding leafhoppers. The small
 size of these sedge feeders lowered the average leafhopper body size in
 the tall-grass vegetation. Plant nutritional quality did not explain any
 effects of exclusions or vegetation types. 4. Our results demonstrate that
 both short- and long-term effects of mammalian herbivores on the biomass
 of specific plant functional types caused concurrent changes in the
 abundance of specialized herbivorous insects, which scaled up to
 community-wide shifts in insect body size, a key life-history trait. A
 plant-functional-type approach can thus help to predict how overabundance
 or extinction of mammalian herbivores impacts on other components of the
 food web at various timescales.
description: Data_FE-2017-00030.R1
DOI: 10.5061/dryad.h5d55
title: Data from: A universal and reliable assay for molecular sex identification of three-spined sticklebacks (Gasterosteus aculeatus)

description: In heterogametic species, biological differences between the two sexes are
 ubiquitous, and hence, errors in sex identification can be a significant
 source of noise and bias in studies where sex-related sources of variation
 are of interest or need to be controlled for. We developed and validated a
 universal multi-marker assay for reliable sex identification of
 three-spined sticklebacks (Gasterosteus aculeatus). The assay makes use of
 genotype scores from three sex-linked loci, and utilizes Bayesian
 probabilistic inference to identify sex of the genotyped individuals. The
 results, validated with 286 phenotypically sexed individuals from six
 populations of sticklebacks representing all major genetic lineages (cf.
 Pacific, Atlantic and Japan Sea) indicate that in contrast to commonly
 used single-marker based sex identification assays, the developed
 multi-marker assay should be 100% accurate. Since the markers in the assay
 can be scored from agarose gels, it provides a quick and cost-efficient
 tool for universal sex identification of three-spined sticklebacks. The
 general principle of combining information from multiple markers to
 improve the reliability of sex identification is transferable and can be
 utilized to develop and validate similar assays for other species.
description: Genetic_scoresA table providing individual fish IDs, population IDs, the locus used to test for the sex of the fish, the actual sex of the fish and the sex independently attributed to the fish by four testers based on their reading of the results of the genotyping of the locus in exam.Bayesian-sex-callingThe R script and an example of its use to calculate the posterior that a fish is male after three subsequent genetic tests.
DOI: 10.5061/dryad.b5b77
title: Data from: Food webs obscure the strength of plant diversity effects on primary productivity

description: Plant diversity experiments generally find that increased diversity causes
 increased productivity; however, primary productivity is typically
 measured in the presence of a diverse food web, including pathogens,
 mutualists and herbivores. If food web impacts on productivity vary with
 plant diversity, as predicted by both theoretical and empirical studies,
 estimates of the effect of plant diversity on productivity may be biased.
 We experimentally removed arthropods, foliar fungi and soil fungi from the
 longest-running plant diversity experiment. We found that fungi and
 arthropods removed a constant, large proportion of biomass leading to a
 greater reduction of total biomass in high diversity plots. As a result,
 the effect of diversity on measured plant productivity was much higher in
 the absence of fungi and arthropods. Thus, diversity increases
 productivity more than reported in previous studies that did not control
 for the effects of heterotrophic consumption.
description: e244-mass-diversity-data-output.csvMetadata filee244-mass-diversity-data-output-header.csvMetadata file description
DOI: 10.5061/dryad.jt2jr03
title: Data from: Towards a better understanding of the Chenopodium album aggregate (Amaranthaceae) in the Middle East: a karyological, cytometric and morphometric investigation

description: The study of variation in nuclear genome size, especially when combined
 with common garden experiments, significantly contributes to disentangling
 interspecies relationships within taxonomically complicated plant groups.
 The Chenopodium album aggregate is among the morphologically most variable
 groups and consists of many weakly differentiated cosmopolitan entities.
 We analysed nuclear genome size variation in diploid and polyploid species
 of the aggregate from Iran using flow cytometry of 282 accessions from 88
 populations of 7 species. To this end, we also determined chromosome
 numbers and performed a morphometric study to reveal the extent of
 intraspecific morphological variation. We found that Iranian species are
 exclusively diploid (C. vulvaria), tetraploid (C. novopokrovskyanum, C.
 strictum, C. sosnowskyi and C. chaldoranicum) or hexaploid (C. album
 subsp. album, C. album subsp. iranicum and C. opulifolium). Six
 homogeneous relative genome size groups were distinguished among the
 species studied. Our morphometric study surprisingly revealed that under
 similar ecological conditions Chenopodium species are morphologically
 stable and well distinguishable, exhibited very little morphological
 variation. Hence, immense variation in leaf shapes, branching and
 inflorescence organization seen in the field has not been repeated under
 greenhouse conditions. The only exception was C. album s. str. which
 exhibited numerous morphotypes, covering the variation of remaining
 species.
description: Genome sizes of
 individual Chenopodium album aggregate species from
 Iran.Genome sizes of
 individual Chenopodium album aggregate species from Iran. Population codes
 are taken from Table S1.Chenopodium_cytometry.txt.txtAnalysed morphological characters in Chenopodium album aggregate species from Iran.Analysed morphological characters in Chenopodium album aggregate species from Iran. PL - Petiole length, LL - Lamina length, LW - Lamina width, TA - Tip angle of leaf, BA - Base angle of leaf, WV - Length from tip to widest point of the leaf (along the central vein), W1/2 - Lamina width in 1/2 of lamina length, C - Circularity of lamina, A - Area of lamina, A/A_reduced - Area of lamina/Area of lamina without teeth, PL/LL - Petiole length/Lamina length, LW/LL - Lamina width/Lamina length, WV/LL - Length from tip to widest point of the leaf/Lamina length, W1/2/LW - Lamina width in 1/2 of lamina length/Lamina length, area/LW - Area of lamina/Lamina width.Chenopodium_morphometrics.txt
DOI: 10.5061/dryad.8b5n18p
title: Data from: Environmental stress does not increase the mean strength of selection

description: A common intuition among evolutionary biologists and ecologists is that
 environmental stress will increase the strength of selection against
 deleterious alleles and among alternate genotypes. However, the strength
 of selection is determined by the relative fitness differences among
 genotypes, and there is no theoretical reason why these differences should
 be exaggerated as mean fitness decreases. We update a recent review of the
 empirical results pertaining to environmental stress and the strength of
 selection and find that there is no overall trend towards increased
 selection under stress. The majority of past studies measure the strength
 of selection by quantifying the decrease in fitness imposed by single or
 multiple mutations in different environments. However, selection rarely
 acts on one locus independently, and the strength of selection will be
 determined by variation across the whole genome. We used 20 inbred lines
 of Drosophila melanogaster to make repeated fitness measurements of the
 same genotypes in four different environments. This framework allowed us
 to determine the variation in fitness attributable to genotype across
 stressful environments and to calculate the opportunity for selection
 among these genotypes in each stress. While we found significant decreases
 in mean fitness in our stressful environments, we did not find any
 significant differences in the strength of selection among any of the four
 measured environments. Therefore, in agreement with our updated review, we
 find no evidence for the oft-cited verbal model that stress increases the
 strength of selection.
description: Block
 1Data
 from block 1, measuring offspring production of fruit fly pairs raised in
 control or diluted foodBlock
 2Data
 from block 2, which measured offspring production of fruit fly pairs
 raised in control, ethanol, and salt food.
DOI: 10.5061/dryad.7nh1v
title: Data from: Evolutionary shifts in habitat aridity predict evaporative water loss across squamate reptiles

description: Aridity is an important determinant of species distributions, shaping both
 ecological and evolutionary diversity. Lizards and snakes are often
 abundant in deserts, suggesting a high potential for adaptation or
 acclimation to arid habitats. However, phylogenetic evidence indicates
 that squamate diversity in deserts may be more strongly tied to speciation
 within arid habitats than to convergent evolution following repeated
 colonization from mesic habitats. To assess the frequency of evolutionary
 transitions in habitat aridity while simultaneously testing for associated
 changes in water-balance physiology, we analyzed estimates of total
 evaporative water loss (EWL) for 120 squamate species inhabiting arid,
 semiarid, or mesic habitats. Phylogenetic reconstructions revealed that
 evolutionary transitions to and from semiarid habitats were much more
 common than those between arid and mesic extremes. Species from mesic
 habitats exhibited significantly higher EWL than those from arid habitats,
 while species from semiarid habitats had intermediate EWL. Phylogenetic
 comparative methods confirmed this association between habitat aridity and
 EWL despite phylogenetic signal in each. Thus, the historical colonization
 of arid habitats by squamates is repeatedly associated with adaptive
 changes in EWL. This physiological convergence, which may reflect both
 phenotypic plasticity and genetic adaptation, has likely contributed to
 the success of squamates in arid environments.
description: Evaporative Water Loss
 of Squamate SpeciesHabitat type, Mass,
 Evaporative Water Loss, Measurement Conditions and Measurement Code for
 120 species of squamate reptiles. For Habitat Type, A = arid, M= mesic,
 and S = semiarid. TEWL= Total Evaporative Water Loss. Please see
 manuscript for the description of how the habitat types were assigned.
 Please see Supplementary Table S1 for the literature cited associated with
 each species.EWL_pruned.csvSquamate Habitat TypesA list of the habitat types for 860 species of squamate reptiles. A = arid, S=semiarid, and M= mesic. Please see manuscript for details of how habitat type was assigned. Please see supplementary Table S2 for the literature cited associated with this data.Squamate_habitat_expanded.csvHabitat types bordering squamate geographic rangesList of habitat types of species and both the number and types of habitats bordering the geographic range of 227 squamate reptiles from North America. A = arid, S = semiarid, and M = mesic. Please see manuscript for methodology and literature cited associated with this data.Squamates_bordering_habitats_North_America.csv
DOI: 10.5061/dryad.p7q9359
title: Data from: Advanced glycation end products (AGE) and receptor for AGE (RAGE) in patients with active tuberculosis, and their relationship between food intake and nutritional status

description: Introduction: The receptor for advanced glycation end products (RAGE) is
 expressed in normal lungs and is upregulated during infection. AGEs and
 RAGE cause oxidative stress and apoptosis in lung cells. The objective of
 this study is to evaluate levels of AGEs and its soluble receptor (sRAGE),
 and to investigate their relationship with food intake and nutritional
 status, in a university-affiliated hospital in Brazil. Methods:
 Case-control study, from June 2017 to June 2018. AGE (carboxymethyl
 lysine, CML) and sRAGE were measured from blood samples by Elisa.
 Nutritional assessment was performed by body mass index, triceps skin-fold
 thickness, mid-arm circumference, mid-arm muscle circumference,
 bioelectrical impedance analysis, and food frequency questionnaire.
 Results: We included in the study 35 tuberculosis (TB) patients and 35
 controls. The mean sRAGE levels were higher in TB patients than in
 controls (68.5 ± 28.1 vs 57.5 ± 24.0 pg/mL; p=0.046). Among cases that
 were current smokers, lower sRAGE levels were associated with mortality,
 evaluated at the end of hospitalization (p=0.006), and with weight loss
 (p=0.034). There was no statistically significant difference in CML levels
 and diet CML content between cases and controls. Malnutrition was more
 frequent in cases, but there was no correlation between nutritional
 parameters and CML or sRAGE levels. Conclusions: TB patients had higher
 sRAGE levels than controls, although it is not clear that this difference
 is clinically relevant. Also, sRAGE was associated with weight loss and
 mortality.
description: BD_Plos_One
DOI: 10.5061/dryad.nh71t5c
title: Data from: Living shorelines enhanced the resilience of saltmarshes to Hurricane Matthew (2016)

description: Nature-based solutions, such as living shorelines, have the potential to
 restore critical ecosystems, enhance coastal sustainability, and increase
 resilience to natural disasters; however, their efficacy during storm
 events compared to traditional hardened shorelines is largely untested.
 This is a major impediment to their implementation and promotion to
 policy-makers and homeowners. To address this knowledge gap, we evaluated
 rock sill living shorelines as compared to natural marshes and hardened
 shorelines (i.e. bulkheads) in North Carolina, USA for changes in surface
 elevation, Spartina alterniflora stem density, and structural damage from
 2015-2017, including before and after Hurricane Matthew (2016). Our
 results show that living shorelines exhibited better resistance to
 landward erosion during Hurricane Matthew than bulkheads and natural
 marshes. Additionally, living shorelines were more resilient than hardened
 shorelines, as they maintained landward elevation over the two-year study
 period without requiring any repair. Finally, rock sill living shorelines
 were able to enhance S. alterniflora stem densities over time when
 compared to natural marshes. Our results suggest that living shorelines
 have the potential to improve coastal resilience while supporting
 important coastal ecosystems.
description: ElevationVegetationSpartina alterniflora stem densities (stems m^2) at living shoreline and marsh sites in North Carolina.
DOI: 10.5061/dryad.sd6jq
title: Data from: Behavioural phenotypes predict disease susceptibility and infectiousness

description: Behavioural phenotypes may provide a means for identifying individuals
 that disproportionally contribute to disease spread and epizootic
 outbreaks. For example, bolder phenotypes may experience greater exposure
 and susceptibility to pathogenic infection because of distinct
 interactions with conspecifics and their environment. We tested the value
 of behavioural phenotypes in larval amphibians for predicting ranavirus
 transmission in experimental trials. We found that behavioural phenotypes
 characterized by latency-to-food and swimming profiles were predictive of
 disease susceptibility and infectiousness defined as the capacity of an
 infected host to transmit an infection by contacts. While viral shedding
 rates were positively associated with transmission, we also found an
 inverse relationship between contacts and infections. Together these
 results suggest intrinsic traits that influence behaviour and the quantity
 of pathogens shed during conspecific interactions may be an important
 contributor to ranavirus transmission. These results suggest that
 behavioural phenotypes provide a means to identify individuals more likely
 to spread disease and thus give insights into disease outbreaks that
 threaten wildlife and humans.
description: Aruajo et al. Biology
 Letters DataBehavioral data for
 larval wood frog exposed to ranavirus during disease trials. The data is
 separated into focal animals, infected with a lethal dose of ranavirus,
 and non-focal animals that were exposed to the focals for 24 hour
 transmission trials. Non-focal animals were monitored for survival until
 metamorphosis.
DOI: 10.15468/dl.9fjv7z
title: Occurrence Download

description: A dataset containing 511 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Berneuxia thibetica",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 511 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001124-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1g9d4
title: Data from: A review of the lichen genus Phlyctis in North America (Phlyctidaceae) including the description of a new widespread saxicolous species from eastern North America

description: A review of the crustose lichen genus Phlyctis in North America is
 presented derived from large-scale studies of chemical, morphological, and
 molecular data (ITS and mtSSU). Five species are recognized based on a
 combination of morphological and chemical characters, namely P. agelaea,
 P. argena, P. boliviensis, P. speirea and the newly described P. petraea.
 Analyses of molecular data supported the recognition of P. boliviensis and
 P. petraea but recovered P. agelaea, P. argena or P. speirea in a single
 clade with little internal phylogenetic structure, suggesting their
 circumscription based on reproductive mode and thallus morphology requires
 further study. An account is provided that includes an identification key,
 discussion of each species, distribution maps and illustrations of
 morphology. Phlyctis petraea, provisionally named more than a decade ago,
 is described as new to science. Molecular phylogenetic analyses using ITS
 and mtSSU sequence data both confirm the placement of P. petraea in
 Phlyctis and demonstrate two known chemotypes (one with norstictic acid
 and one with norstictic and stictic acids) are not reciprocally
 monophyletic and should be treated as variants of a single species.
 Psathyrophlyctis, described as a member of the Phlyctidaceae, is discussed
 and treated as a member of the Lecanorales incertae sedis.
description: data_packetThis is a zipped folder (add .zip to the file name) that contains the following items: 1) original mtSSU and nuITS alignments compiled for this study, 2) mtSSU and nuITS alignments used for Bayesian analyses ("BI.nex" files), 3) mtSSU and nuITS alignments used for likelihood analyses ("ML.phy" files) together with relevant partition files ("ML_partition_file.txt" files), and 4) mtSSU and nuITS alignments used to generate distance matrices ("distance.matrix.nex" files).