cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4s61t
title: Data from: Sex-specific fitness effects of unpredictable early life conditions are associated with DNA methylation in the avian glucocorticoid receptor

description: Organisms can adapt to variable environments by using environmental cues
 to modulate developmental gene expression. In principle, maternal
 influences can adaptively adjust offspring phenotype when early life and
 adult environments match, but they may be maladaptive when future
 environments are not predictable. One of the best-studied ‘maternal
 effects’ is through modification of the offspring's
 hypothalamic–pituitary–adrenal (HPA) axis, the neuroendocrine system that
 controls responses to stress. In addition to the direct transfer of
 glucocorticoids from mother to offspring, offspring HPA function and other
 phenotypes can also be affected by epigenetic modifications like DNA
 methylation of the glucocorticoid receptor promoter. Here we examine how
 among-year variation in rainfall is related to DNA methylation during
 development and fitness in adulthood in the superb starling (Lamprotornis
 superbus), which lives in a climatically unpredictable environment where
 early life and adult environments are unlikely to match. We found that DNA
 methylation in the putative promoter of the glucocorticoid receptor gene
 is reduced in chicks – particularly in males – born following drier
 prebreeding periods. Additionally, DNA methylation is lower in males that
 become breeders than those that never breed. However, there is no
 relationship in females between DNA methylation and the likelihood of
 dispersing from the natal group to breed elsewhere. These results suggest
 that early life conditions may positively affect fitness in a sex-specific
 manner through chemical modification of an HPA-associated gene. This study
 is the first to show that epigenetic modifications during early life may
 influence the fitness of free-living organisms adapted to unpredictable
 environments.
description: Raw Data: DNA
 methylation, behavior and rainfall(1) Whole Region DNA
 Methyl: DNA methylation of the coding and regulatory region for 11 birds.
 (2) Regulatory region DNA Methyl: DNA methylation in the regulatory region
 for 96 birds, including behavior and rainfall data. (3) Recapture DNA
 Methyl: DNA methylation in a portion of the regulatory region for 12 birds
 recaptured after initial sampling.Rubenstein Methylation
 Data.xlsx
DOI: 10.5061/dryad.t446r
title: Data from: Bottom-up effects of a no-take zone on endangered penguin demographics

description: Marine no-take zones can have positive impacts for target species and are
 increasingly important management tools. However, whether they indirectly
 benefit higher order predators remains unclear. The endangered African
 penguin (Spheniscus demersus) depends on commercially exploited forage
 fish. We examined how chick survival responded to an experimental 3-year
 fishery closure around Robben Island, South Africa, controlling for
 variation in prey biomass and fishery catches. Chick survival increased by
 18% when the closure was initiated, which alone led to a predicted 27%
 higher population compared with continued fishing. However, the modelled
 population continued to decline, probably because of high adult mortality
 linked to poor prey availability over larger spatial scales. Our results
 illustrate that small no-take zones can have bottom-up benefits for highly
 mobile marine predators, but are only one component of holistic,
 ecosystem-based management regimes.
description: Penguin nest days
 dataAfrican penguin chick
 survival data, collected on Robben Island, South Africa. Nest
 identifications (ID) are unique between years; repeated nest numbers
 within years denote repeat clutches or multiple chicks per
 brood.Sherley_et_al._Biol_Lett_penguindata.csv
DOI: 10.5061/dryad.1n3n6
title: Data from: Improving early diagnosis of pulmonary infections in patients with febrile neutropenia using low-dose chest computed tomography

description: We performed a prospective study in patients with chemotherapy induced
 febrile neutropenia to investigate the diagnostic value of low-dose
 computed tomography compared to standard chest radiography. The aim was to
 compare both modalities for detection of pulmonary infections and to
 explore performance of low-dose computed tomography for early detection of
 invasive fungal disease. The low-dose computed tomography remained blinded
 during the study. A consensus diagnosis of the fever episode made by an
 expert panel was used as reference standard. We included 67 consecutive
 patients on the first day of febrile neutropenia. According to the
 consensus diagnosis 11 patients (16.4%) had pulmonary infections.
 Sensitivity, specificity, positive predictive value and negative
 predictive value were 36%, 93%, 50% and 88% for radiography, and 73%, 91%,
 62% and 94% for low-dose computed tomography, respectively. An uncorrected
 McNemar showed no statistical difference (p = 0.197). Mean radiation dose
 for low-dose computed tomography was 0.24 mSv. Four out of 5 included
 patients diagnosed with invasive fungal disease had radiographic
 abnormalities suspect for invasive fungal disease on the low-dose computed
 tomography scan made on day 1 of fever, compared to none of the chest
 radiographs. We conclude that chest radiography has little value in the
 initial assessment of febrile neutropenia on day 1 for detection of
 pulmonary abnormalities. Low-dose computed tomography improves detection
 of pulmonary infiltrates and seems capable of detecting invasive fungal
 disease at a very early stage with a low radiation dose.
description: rawdata_PLOS_ONEExcel file containing radiologists scoring results and the consensus diagnosis per patient.result_form_PLOS_ONE.xls
DOI: 10.5061/dryad.71q32
title: Data from: Global decline of bumblebees is phylogenetically structured and inversely related to species range size and pathogen incidence

description: Conservation biology can profit greatly from incorporating a phylogenetic
 perspective into analyses of patterns and drivers of species extinction
 risk. We applied such an approach to analyse patterns of bumblebee
 (Bombus) decline. We assembled a database representing approximately 43%
 of the circa 260 globally known species, which included species extinction
 risk assessments following the International Union fo Conservation of
 Nature Red List categories and criteria, and information on species traits
 presumably associated with bumblebee decline. We quantified the strength
 of phylogenetic signal in decline, range size, tongue length and parasite
 presence. Overall, about one-third of the assessed bumblebees are
 declining and declining species are not randomly distributed across the
 Bombus phylogeny. Susceptible species were over-represented in the
 subgenus Thoracobombus (approx. 64%) and under-represented in the subgenus
 Pyrobombus (approx. 6%). Phylogenetic logistic regressions revealed that
 species with small geographical ranges and those in which none of three
 internal parasites were reported (i.e. Crithidia bombi, Nosema spp. or
 Locustacarus buchneri) were particularly vulnerable. Bumblebee
 evolutionary history will be deeply eroded if most species from threatened
 clades, particularly those stemming from basal nodes, become finally
 extinct. The habitat of species with restricted distribution should be
 protected and the importance of pathogen tolerance/resistance as
 mechanisms to deal with pathogens needs urgent research.
description: Complete database Bombus
 declineThe complete database,
 for GLOBAL DECLINE OF BUMBLEBEES IS PHYLOGENETICALLY STRUCTURED AND
 INVERSELY RELATED TO SPECIES RANGE SIZE AND PATHOGEN INCIDENCE, including
 potential variables associated with decline, described in the main
 text.Dryad_Arbetman.xls
DOI: 10.5061/dryad.1981
title: Data from: Differential niche modification by males and females of a dioecious herb: extending the Jack Sprat effect

description: Males and females of dioecious plants often differ in morphological,
 physiological, and life-history traits, probably as a result of their
 different requirements for reproduction. Here, we show that the growth and
 reproductive effort of individuals of the dioecious herb Mercurialis annua
 depended on whether males or females had been growing in the soil
 previously. This suggests that males and females of M. annua
 differentially modify the soil in which they are growing. Our study
 indicates that sexual dimorphism in dioecious plants can give rise to
 increased environmental heterogeneity as a consequence of sex-specific
 niche modification.
description: NicheModificationMercurialisExcel file
DOI: 10.5061/dryad.2pq32
title: Data from: Nuclear and mitochondrial patterns of population structure in North Pacific false killer whales (Pseudorca crassidens)

description: False killer whales (Pseudorca crassidens) are large Delphinids typically
 found in deep water far offshore. However, in the Hawaiian Archipelago
 there are two resident island-associated populations of false killer
 whales, one in the waters around the main Hawaiian Islands (MHI) and one
 in the waters around the Northwestern Hawaiian Islands (NWHI). We use
 mitochondrial DNA (mtDNA) control region sequences and genotypes from 16
 nuclear (nucDNA) microsatellite loci from 206 individuals to examine
 levels of differentiation among the two island-associated populations and
 offshore animals from the central and eastern North Pacific. Both mtDNA
 and nucDNA exhibit highly significant differentiation between populations,
 confirming limited gene flow in both sexes. The mtDNA haplotypes exhibit a
 strong pattern of phylogeographic concordance, with island-associated
 populations sharing three closely related haplotypes not found elsewhere
 in the Pacific. However, nucDNA data suggests that NWHI animals are at
 least as differentiated from MHI animals as they are from offshore
 animals. The patterns of differentiation revealed by the two marker types
 suggest that the island-associated false killer whale populations likely
 share a common colonization history, but have limited contemporary gene
 flow.
description: FKW genotypes for
 DryadNuclear genotype data
 for false killer whales. Genotypes are from 16 nuclear microsatellite
 loci. AnimalID is the identifier from the SWFSC Tissue Archive. The column
 Stratum specifies the way in which samples were stratified in Martien et
 al., 2014, Journal of Heredity. Abbreviations are CNP=Central North
 Pacific, ETP=Eastern Tropical Pacific, MHI=Main Hawaiian Islands,
 NWHI=Northwest Hawaiian Islands
DOI: 10.5061/dryad.925cb
title: Data from: Scale insect host ranges are broader in the tropics

description: The specificity of the interactions between plants and their consumers
 varies considerably. The evolutionary and ecological factors underlying
 this variation are unclear. Several potential explanatory factors vary
 with latitude, for example plant species richness and the intensity of
 herbivory. Here, we use comparative phylogenetic methods to test the
 effect of latitude on host range in scale insects. We find that, on
 average, scale insects that occur in lower latitudes are more polyphagous.
 This result is at odds with the general pattern of greater host-plant
 specificity of insects in the tropics. We propose that this disparity
 reflects a high cost for host specificity in scale insects, stemming from
 unusual aspects of scale insect life history, for example, passive
 wind-driven dispersal. More broadly, the strong evidence for pervasive
 effects of geography on host range across insect groups stands in stark
 contrast to the weak evidence for constraints on host range due to genetic
 trade-offs.
description: Hardy_etal_BioLet_2015_comp_dataComparative data used in Hardy et al. 2015. The scale insect data is from ScaleNet (http://scalenet.info).Hardy_etal_BioLet_2015_Coccoidea_phylogenyTime-scaled Coccoidea phylogeny in newick format.
DOI: 10.5061/dryad.fv58t
title: Data from: Effects of fragmentation on plant adaptation to urban environments

description: Urban ecosystems are relatively recent and heavily human-altered
 terrestrial ecosystems with a surprisingly high diversity of animals,
 plants and other organisms. Urban habitats are also strongly fragmented
 and subject to higher temperatures, providing a compelling model for
 studying adaptation to global change. Crepis sancta (Asteraceae), an
 annual Mediterranean wasteland weed, occupies fragmented urban
 environments as well as certain unfragmented landscapes in southern
 France. We tested for shifts in dispersal, reproductive traits and size
 across a rural–urban gradient to learn whether and how selection may be
 driving changes in life history in urban and fragmented habitats. We
 specifically compared the structure of quantitative genetic variation and
 of neutral markers (microsatellites) between urban and rural and between
 fragmented and unfragmented habitats. We showed that fragmentation
 provides a better descriptor of trait variation than urbanization per se
 for dispersal traits. Fragmentation also affected reproductive traits and
 plant size though one rural population did conform to this scheme. Our
 study shows the role of fragmentation for dispersal traits shift in urban
 environments and a more complex pattern for other traits. We discuss the
 role of pollinator scarcity and an inhospitable matrix as drivers of
 adaptation.
description: phenotypesmeasured quantitative traits from common garden experiment and genetic allelic composition for the 9 microsatellite markersmesured_phenotype.ods
DOI: 10.5061/dryad.v43rd
title: Data from: A relaxed directional random walk model for phylogenetic trait evolution

description: Understanding the processes that give rise to quantitative measurements
 associated with molecular sequence data remains an important issue in
 statistical phylogenetics. Examples of such measurements include
 geographic coordinates in the context of phylogeography and phenotypic
 traits in the context of comparative studies. A popular approach is to
 model the evolution of continuously varying traits as a Brownian diffusion
 process acting on a phylogenetic tree. However, standard Brownian
 diffusion is quite restrictive and may not accurately characterize certain
 trait evolutionary processes. Here, we relax one of the major restrictions
 of standard Brownian diffusion by incorporating a nontrivial estimable
 mean into the process. We introduce a relaxed directional random walk
 (RDRW) model for the evolution of multivariate continuously varying traits
 along a phylogenetic tree. Notably, the RDRW model accommodates
 branch-specific variation of directional trends while preserving model
 identifiability. Furthermore, our development of a computationally
 efficient dynamic programming approach to compute the data likelihood
 enables scaling of our method to large data sets frequently encountered in
 phylogenetic comparative studies and viral evolution. We implement the
 RDRW model in a Bayesian inference framework to simultaneously reconstruct
 the evolutionary histories of molecular sequence data and associated
 multivariate continuous trait data, and provide tools to visualize
 evolutionary reconstructions. We demonstrate the performance of our model
 on synthetic data, and we illustrate its utility in two viral examples.
 First, we examine the spatiotemporal spread of HIV-1 in central Africa and
 show that the RDRW model uncovers a clearer, more detailed picture of the
 dynamics of viral dispersal than standard Brownian diffusion. Second, we
 study antigenic evolution in the context of HIV-1 resistance to three
 broadly neutralizing antibodies. Our analysis reveals evidence of a
 continuous drift at the HIV-1 population level towards enhanced resistance
 to neutralization by the VRC01 monoclonal antibody over the course of the
 epidemic.
description: BEAST XML input files
 used for the data analysisRDRWXMLs.zip
DOI: 10.15468/dl.h9zywg
title: Occurrence Download

description: A dataset containing 12681 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is one of (Paraguay, Argentina, Chile)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Campephilus magellanicus",
 "Year 2000-2026"
 ]
}

 The dataset includes 12681 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000952-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g8g7r71
title: Data from: Presence of blood in gastric juice: a sensitive marker for gastric cancer screening in a poor resource setting

description: Background: Gastric cancer survival rates in Africa are low as many cases
 are diagnosed late. Currently, there are no inexpensive, non-invasive and
 simple techniques that can be employed in poor resource settings for early
 case detection. In this study, we explored the possibility using blood in
 gastric juice as a screening tool to identify patients requiring referral
 for endoscopy. Methods: The study was conducted at the University Teaching
 Hospital endoscopy unit in Lusaka, Zambia. During endoscopy, gastric juice
 was aspirated and the pH determined using pH paper test strips. The
 presence of blood was tested using urinalysis reagent strips. Results: We
 enrolled 276 patients; 147(53%) were female and median age was 49 years
 (IQR 40-64 years). The presence of blood was associated with mucosal
 lesions, [OR 2.1; 95% CI 1.2-3.7, P=0.004]. It was also associated with
 gastric cancer, [OR 6.7; 95% CI 2-35, P=0.0005], even at 1:10 and 1:100
 dilutions, [OR 5.4; 95% CI 2.3-13.8, P&lt;0.0001] and [OR 9.1; 95% CI
 3.5-23, P&lt;0.0001] respectively. The sensitivity for gastric cancer
 detection using blood in gastric juice was 91% and the specificity was
 41%. Analysis using the intensity of blood in gastric juice yielded an
 area under the receiver operating characteristic curve of 0.78; 95% CI
 0.71-0.86 with a sensitivity of 79% and a specificity of 77%. Conclusions:
 The presence of blood in gastric juice is associated with gastric mucosal
 lesions. It has a high sensitivity but low specificity for gastric cancer
 detection.
description: PloSOne Gastric acid
 paperThese are data for study
 participants enrolled in the study. Unique identity numbers are in the
 first column while variables are indicated in the first
 row.
DOI: 10.5061/dryad.v843v
title: Data from: Faunal turnover of marine tetrapods during the Jurassic–Cretaceous transition

description: Marine and terrestrial animals show a mosaic of lineage extinctions and
 diversifications during the Jurassic–Cretaceous transition. However,
 despite its potential importance in shaping animal evolution, few
 palaeontological studies have focussed on this interval and the possible
 climate and biotic drivers of its faunal turnover. In consequence
 evolutionary patterns in most groups are poorly understood. We use a new,
 large morphological dataset to examine patterns of lineage diversity and
 disparity (variety of form) in the marine tetrapod clade Plesiosauria, and
 compare these patterns with those of other organisms. Although seven
 plesiosaurian lineages have been hypothesised as crossing the
 Jurassic–Cretaceous boundary, our most parsimonious topology suggests the
 number was only three. The robust recovery of a novel group including most
 Cretaceous plesiosauroids (Xenopsaria, new clade) is instrumental in this
 result. Substantial plesiosaurian turnover occurred during the
 Jurassic–Cretaceous boundary interval, including the loss of substantial
 pliosaurid, and cryptoclidid diversity and disparity, followed by the
 radiation of Xenopsaria during the Early Cretaceous. Possible physical
 drivers of this turnover include climatic fluctuations that influenced
 oceanic productivity and diversity: Late Jurassic climates were
 characterised by widespread global monsoonal conditions and increased
 nutrient flux into the opening Atlantic-Tethys, resulting in
 eutrophication and a highly productive, but taxonomically depauperate,
 plankton. Latest Jurassic and Early Cretaceous climates were more arid,
 resulting in oligotrophic ocean conditions and high taxonomic diversity of
 radiolarians, calcareous nannoplankton and possibly ammonoids. However,
 the observation of discordant extinction patterns in other marine tetrapod
 groups such as ichthyosaurs and marine crocodylomorphs suggests that
 clade-specific, factors may be more important than overarching extrinsic
 factors in driving faunal turnover during the Jurassic–Cretaceous boundary
 interval.
description: Data from Benson &
 Druckenmiller (2013)Phylogenetic data
 matrix, R Code for implementing disaprity estimates, and associated
 documentation.DRYAD
 data.zip
DOI: 10.5061/dryad.tg600
title: Data from: Contrasting trait assembly patterns in plant and bird communities along environmental and human-induced land-use gradients

description: Human-driven environmental changes can induce marked shifts in the
 functional structure of biological communities with possible repercussion
 on important ecosystem functions and services. At the same time it remains
 unclear to which extent these changes may differently affect various types
 of organisms. We investigated species richness and community functional
 structure of species assemblages at the landscape scale (1km2 plots) for
 two contrasting model taxa, i.e., plants (producers and sessile organisms)
 and birds (consumers and mobile organisms), along topography, climate,
 landscape heterogeneity, and land-use (agriculture and urbanization)
 gradients in a densely populated region of Switzerland. Our study revealed
 that agricultural and urban land uses drove marked shifts in the
 functional structure of biological communities compared to changes along
 climate and topography gradients, especially for plants, while for birds
 these changes were comparable. Agricultural and urban land uses enhanced
 divergence in traits related to resource use for birds (diet and nesting),
 growth forms, dispersal, and reproductive traits for plants, while it
 induced convergence in vegetative plant traits (plant height and leaf dry
 matter content). These results suggest that contrasting assembly patterns
 may arise within and across taxonomic groups along the same environmental
 gradients as result of distinct underlying processes and
 'organism-specific' environmental perceptions. Our results
 further suggest a potential homogenization of biological communities, as
 well as low functional diversity and redundancy levels of bird assemblages
 in our human-dominated study region. This might potentially compromise the
 maintenance of key ecological processes under future environmental
 changes.
description: SES for plant and bird
 functional traits based on 1000 randomizationsSES_Data.zip