cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rxwdbrv5z
title: Data from: Evolution and epidemic spread of SARS-CoV-2 in Brazil

description: Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in
 the world. Owing to limited available data, assessments of the impact of
 non-pharmaceutical interventions (NPIs) on virus spread remain
 challenging. Using a mobility-driven transmission model, we show that NPIs
 reduced the reproduction number from &gt;3 to 1–1.6 in São Paulo and
 Rio de Janeiro. Sequencing of 427 new genomes and analysis of a
 geographically representative genomic dataset identified &gt;100
 international virus introductions in Brazil. We estimate that most (76%)
 of the Brazilian strains fell in three clades that were introduced from
 Europe between 22 February11 March 2020. During the early epidemic phase,
 we found that SARS-CoV-2 spread mostly locally and within-state borders.
 After this period, despite sharp decreases in air travel, we estimated
 multiple exportations from large urban centers that coincided with a 25%
 increase in average travelled distances in national flights. This study
 sheds new light on the epidemic transmission and evolutionary trajectories
 of SARS-CoV-2 lineages in Brazil, and provide evidence that current
 interventions remain insufficient to keep virus transmission under control
 in the country.
description: Please see Materials and Methods section in Supplementary
 Materials. 
description: This REPOSITORY contains the data used for the main figures of
 the manuscript. Data for main figures:
 Figure 1 Fig1a: Cumulative number of Covid-19
 confirmed cases and deaths until the 30th of April 2020, as provided by
 the Brazilian ministry of Health at https://covid.saude.gov.br/;<br>
 Fig1b: number of Covid-19 confirmed cases and deaths until the 30th of
 April 2020, as provided by the Brazilian ministry of Health at
 https://covid.saude.gov.br/;<br> Fig1c: reproduction number (Rt)
 estimates and confidence intervals for São Paulo city.<br> Fig1d:
 reproduction number (Rt) estimates and confidence intervals for Rio de
 Janeiro city. Figue 2 Fig2a: Dates
 of first confirmed Covid-19 case and death for each Brazilian state. Dates
 and states of collection of all 427 sequences generated in this
 study.<br> Fig2b: Number of SARI Covid-19 confirmed cases and number
 of novel genomes generated in this study per Brazilian state.<br>
 Fig3c: Number of samples per lag time (in days) between symptom onset and
 collection date. Figure 3 Fig3a:
 Maximum Clade Credibility (MCC)  tree of 1,182 SARS-CoV-2 genomes,
 including 427 novel genomes for Brazil. For details, see supplementary
 data.<br> Fig3c: Number of national and international air passengers
 in Brazil per flight and per day from January to 30th April
 2020. Figue 4<br> Fig4a: Continuous
 phylogeography<br> Fig4b: Discrete phylogeography<br> Fig4c:
 Average distance of air travel in Brazil
DOI: 10.5061/dryad.n02v6wwv4
title: Analysis of land cover evolution within the built-up areas of provincial capital cities in northeastern China based on nighttime light data and Landsat data

description: Mastering the evolution of urban land cover is important for urban
 management and planning. In this paper, a method for analyzing land cover
 evolution within urban built-up areas based on nighttime light data and
 Landsat data is proposed. The method solves the problem of inaccurate
 descriptions of urban built-up area boundaries from the use of
 single-source diurnal or nocturnal remote sensing data and was able to
 achieve an effective analysis of land cover evolution within built-up
 areas. Four main procedures are involved: (1) The neighborhood extremum
 method and maximum likelihood method are used to extract nighttime light
 data and the urban built-up area boundaries from the Landsat data,
 respectively; (2) multisource urban boundaries are obtained using boundary
 pixel fusion of the nighttime light data and Landsat urban built-up area
 boundaries; (3) the maximum likelihood method is used to classify Landsat
 data within multisource urban boundaries into land cover classes, such as
 impervious surface, vegetation and water, and to calculate landscape
 indexes, such as overall landscape trends, degree of fragmentation and
 degree of aggregation; (4) the changes in the multisource urban boundaries
 and landscape indexes were obtained using the abovementioned methods,
 which were supported by multitemporal nighttime light data and Landsat
 data, to model the urban land cover evolution. Using the cities of
 Shenyang, Changchun and Harbin in northeastern China as experimental
 areas, the multitemporal landscape index showed that the integration and
 aggregation of land cover in the urban areas had an increasing trend, the
 natural environment of Shenyang and Harbin was improving, while Changchun
 laid more emphasis on the construction of artificial facilities. At the
 same time, the method proposed in this paper to extract built-up areas
 from multi-source city data showed that the user accuracy, production
 accuracy, overall accuracy and Kappa coefficient are at least 3%, 1%, 1%
 and 0.04 higher than the single-source data method.
DOI: 10.5061/dryad.d2547d816
title: Data from: Fungal volatiles influence plant defence against aboveground and belowground herbivory

description: Plants have evolved resistance traits that negatively affect attackers,
 and tolerance traits that sustain plant growth despite herbivore damage.
 These mechanisms often co-occur in a mixed-defence strategy, balancing
 resistance and tolerance. These plant defences can be enhanced upon
 interaction with soil microorganisms. Here, we investigated the effects of
 volatiles emitted by soil-borne fungi on plant defence to insect
 herbivory, and on plant phenology. We exposed roots of Brassica rapa
 plants to volatiles emitted by four soil-borne fungi. As a proxy of plant
 resistance, we assessed the performance of Pieris brassicae, a caterpillar
 feeding on leaves and inflorescences, and of Delia radicum, an insect root
 herbivore. As a proxy of plant tolerance, we compared growth of
 volatile-exposed plants challenged with or without insects. Additionally,
 we assessed the effects on plant phenology by recording bolting time and
 by counting the number of buds and flowers. Plant exposure to fungal
 volatiles differentially affected plant resistance to above- and
 belowground herbivory. Performance of P. brassicae caterpillars differed
 between the fungal volatile-exposed plants but were variable between
 experimental batches. In contrast, the effects of fungal volatiles on D.
 radicum performance was predominantly negative, indicating an increased
 plant resistance. Despite root consumption by D. radicum, root dry weight
 remained unchanged in infested plants compared with uninfested ones,
 irrespectively of the volatile exposure, suggesting compensation for the
 tissue loss, sometimes at the cost of undamaged aboveground tissues. When
 B. rapa plants were attacked by P. brassicae caterpillars, only exposure
 to volatiles of some fungi led to compensation for the loss of aboveground
 tissues consumed by the caterpillars, which differed between leaves and
 inflorescences. Furthermore, bolting was accelerated in response to
 volatiles of some fungi, resulting in more buds and flowers, which
 suggests a potential enhancement of plant fitness. Our data show that
 fungal volatiles can modulate the mixed-defence strategies of B. rapa
 plants, balancing plant resistance and tolerance to above- and belowground
 herbivory. These effects may be variable and were fungus-specific.
 Ultimately, plant fitness may be enhanced upon root exposure to fungal
 volatiles.
DOI: 10.15468/dl.n7xuc7
title: Occurrence Download

description: A dataset containing 23185086 species occurrences available in GBIF matching the query:
{
 "and" : [
 "KingdomKey is Plantae",
 "Country is Australia",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation, Machine Observation)"
 ]
}

 The dataset includes 23185086 records from 512 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002420-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g79cnp5n7
title: HDL particle size and cholesterol content in Heart Failure. Supplementary Material

description: Supplementary material corresponding to the article entitled Particle Size
 and Cholesterol Content of circulating HDL correlate with Cardiovascular
 Death in Chronic Heart Failure.
DOI: 10.5061/dryad.d51c5b00t
title: Supplementary information for integrating sequence capture and restriction-site associated DNA sequencing to resolve recent radiations of Pelagic seabirds

description: The diversification of modern birds has been shaped by a number of
 radiations. Rapid diversification events make reconstructing the
 evolutionary relationships among taxa challenging due to the convoluted
 effects of incomplete lineage sorting (ILS) and introgression.
 Phylogenomic datasets have the potential to detect patterns of
 phylogenetic incongruence, and to address their causes. However, the
 footprints of ILS and introgression on sequence data can vary between
 different phylogenomic markers at different phylogenetic scales depending
 on factors such as their evolutionary rates or their selection pressures.
 We show that combining phylogenomic markers that evolve at different
 rates, such as paired-end double-digest restriction site-associated DNA
 (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive
 exploration of the causes of phylogenetic discordance associated with
 short internodes at different timescales. We used thousands of UCE and
 PE-ddRAD markers to produce the first well-resolved phylogeny of
 shearwaters, a group of medium-sized pelagic seabirds amongst the most
 phylogenetically controversial and endangered bird groups. We found that
 phylogenomic conflict was mainly derived from high levels of ILS due to
 rapid speciation events. We also documented a case of introgression,
 despite the high philopatry of shearwaters to their breeding sites, which
 typically limits gene flow. We integrated state-of-the-art concatenated
 and coalescent-based approaches to expand on previous comparisons of UCE
 and RAD-Seq datasets for phylogenetics, divergence time estimation and
 inference of introgression, and we propose a strategy to optimise RAD-Seq
 data for phylogenetic analyses. Our results highlight the usefulness of
 combining phylogenomic markers evolving at different rates to understand
 the causes of phylogenetic discordance at different timescales.
description: Blood and tissue samples were collected in the field or from
 museum loans for 26 species of Shearwaters and were sequenced for UCE and
 PE-ddRAD-Seq.
description: This repository contains: 1) Supplementary
 information document 2) Supplementary Table
 S1 3) Supplementary Table S3 4) UCE
 IUPAC consensus loci alignments in fasta format 5)
 PE-ddRAD loci alignments in fasta format 6) UCE
 contig loci alignments in fasta format 7) ExaBayes TENT
 75 tree in newick format 8) MCMCTree control
 file 9) MCMCTree tree in newick format
 10) Concatenated alignment for the TENT 95 dataset for MCMCTree
 analysis in phylip format 11) UCE IUPAC consensus gene
 trees (best tree with bipartitions and bootstrap trees)
 12) PE-ddRAD gene trees (best tree with bipartitions and
 bootstrap trees) 13) Phylogenetic networks from
 PhyloNetworks
DOI: 10.5061/dryad.9ghx3fffg
title: Association of insularity to cloacal bacteria prevalence and body condition in a small shorebird

description: Do islands harbour less diverse disease communities than mainland? The
 island biogeography theory predicts more diverse communities on mainland
 than on islands due to more niches, more diverse habitats and availability
 of greater range of hosts. We compared bacteria prevalences of
 Campylobacter, Chlamydia and Salmonella in cloacal samples of a small
 shorebird, the Kentish plover (Charadrius alexandrinus) between two island
 populations of Macaronesia and two mainland locations in the Iberian
 Peninsula. Bacteria were found in all populations but, contrary to the
 expectations, prevalences did not differ between islands and mainland.
 Females had higher prevalences than males for Salmonella and when three
 bacteria genera were pooled together. Bacteria infection was unrelated to
 bird’s body condition but females from mainland were heavier than males
 and birds from mainland were heavier than those from islands. Abiotic
 variables consistent throughout breeding sites, like high salinity that is
 known to inhibit bacteria growth, could explain the lack of differences in
 the bacteria prevalence between areas. We argue about the possible drivers
 and implications of sex differences in bacteria prevalence in Kentish
 plovers.
description: Data used to conduct the statistical analysis of the paper.
DOI: 10.5061/dryad.0p2ngf1xt
title: Male competition reverses female preference for male chemical cues

description: Females must choose among potential mates with different phenotypes in a
 variety of social contexts. Many male traits are inherent and unchanging,
 but others are labile to social context. Competition, for example, can
 cause physiological changes that reflect recent wins and losses which
 fluctuate throughout time. We may expect females to respond
 differently to males depending on the outcome of their most recent fight.
 In Bolitotherus cornutus (forked fungus beetles), males compete for access
 to females, but copulation requires female cooperation. In this study we
 use behavioural trials to determine if females use chemical cues to
 differentiate between males and if the outcome of recent male competition
 alters female preference. We measured female association time with
 chemical cues of two size-matched males both before and after male-male
 competition. Females in our study preferred to associate with future
 losers before males interacted, but changed their preference for realized
 winners following male competitive interactions. Our study provides the
 first evidence of change in female preference based solely on the outcome
 of male-male competition.
DOI: 10.15468/dl.qyvpft
title: Occurrence Download

description: A dataset containing 668 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((159.00094 -48.95058,200.03306 -48.95058,200.03306 -32.54476,159.00094 -32.54476,159.00094 -48.95058))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhynchostegium tenuifolium"
 ]
}

 The dataset includes 668 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002453-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.02v6wwq19
title: St Kitts Mosquito Survey and Model November 2017 to March 2019

description: Background: High quality mosquito surveys that collect fine resolution
 local data on mosquito species’ abundances provide baseline data to help
 us understand potential host-pathogen-mosquito relationships, accurately
 predict disease transmission, and target mosquito control efforts in areas
 at risk of mosquito borne diseases. Methods: As part of an investigation
 into arboviral sylvatic cycles on the Caribbean island of St. Kitts, we
 carried out an island wide mosquito survey from November 2017 to March
 2019. Using Biogents Sentinel 2 and miniature CDC light traps that were
 set monthly and run for 48 hour intervals, we collected mosquitoes from a
 total of 30 sites distributed across the five common land covers on the
 island (agricultural, mangrove, rainforest, scrub, and urban). We
 developed a mixed effects negative binomial regression model to predict
 the effects of land cover, seasonality, and precipitation on observed
 counts of the most abundant mosquito species we found. Results: We
 captured 10 of the 14 mosquito species reported on the island, the four
 most abundant being Aedes taeniorhynchus , Culex quinquefasciatus , Aedes
 aegpyti , and Deinocerites magnus. Sampling in the mangroves yielded the
 most mosquitoes, with Ae. taeniorhynchus, Cx. quinquefasciatus, and De.
 magnus predominating. Aedes aegypti was recovered primarily from urban and
 agricultural habitats, but also at lower frequency in other land covers.
 Psorophora pygmaea and Toxorhynchites guadeloupensis were only captured in
 scrub habitat. Capture rates in rainforests were low. Our models indicated
 the relative abundance of the four most common species varied seasonally
 and with land cover. They also suggested that the extent to which monthly
 average precipitation influenced counts varied according to species.
 Conclusions: This study demonstrates there is high seasonality in mosquito
 abundances and that land cover influenced the distribution and abundance
 of mosquito species on St. Kitts. Further, human-adapted mosquito species
 (e.g. Ae. aegypti and Cx. quinquefasciatus ) that are known vectors for
 many human relevant pathogens are the most wide-spread (across land
 covers) and the least responsive to seasonal variation in precipitation.
description: Excel files, HTML document, r and rmd files for
 modelling scripts
 Diversity_Analysis.r   SKmosq.Rmd   
 SKmosq.html    dat7.csv   
 lc.csv
DOI: 10.5061/dryad.xsj3tx9cc
title: Data S2. CMR data from: Measuring the fitness advantage conferred by autotomy in the wild

description: Data S2. CMR data. The composition is summarized in tables S2, S3, and
 S10. Autotomy, the self-amputation of body parts, serves as an
 anti-predator defense in many taxonomic groups of animals. However, its
 adaptive value has seldom been quantified. Here, we propose a novel
 modeling approach for measuring the fitness advantage conferred by the
 capability for autotomy in the wild. Using a predator-prey system where a
 land snail autotomizes and regenerates its foot specifically in response
 to snake bites, we conducted a laboratory behavioral experiment and a
 3-year multi-event capture–mark–recapture (CMR) study. Combining these
 empirical data, we developed a hierarchical model and estimated the basic
 life history parameters of the snail. Using samples from the posterior
 distribution, we constructed the snail’s life table as well as that of a
 snail variant incapable of foot autotomy. As a result of our analyses, we
 estimated the monthly encounter rate with snake predators at 3.3% (95% CI:
 1.6–4.9%), the contribution of snake predation to total mortality until
 maturity at 43.3% (15.0–95.3%), and the fitness advantage conferred by
 foot autotomy at 6.5% (2.7–11.5%). This study demonstrated the utility of
 the multi-method hierarchical modeling approach for the quantitative
 understanding of the ecological and evolutionary processes of
 anti-predator defenses in the wild.
DOI: 10.5061/dryad.2v6wwpzk0
title: Data S1. Laboratory behavioral data from: Measuring the fitness advantage conferred by autotomy in the wild

description: Data S1. Laboratory behavioral data. The composition is
 summarized in figure S1. Autotomy, the self-amputation of body parts,
 serves as an anti-predator defense in many taxonomic groups of animals.
 However, its adaptive value has seldom been quantified. Here, we propose a
 novel modeling approach for measuring the fitness advantage conferred by
 the capability for autotomy in the wild. Using a predator-prey system
 where a land snail autotomizes and regenerates its foot specifically in
 response to snake bites, we conducted a laboratory behavioral experiment
 and a 3-year multi-event capture–mark–recapture (CMR) study. Combining
 these empirical data, we developed a hierarchical model and estimated the
 basic life history parameters of the snail. Using samples from the
 posterior distribution, we constructed the snail’s life table as well as
 that of a snail variant incapable of foot autotomy. As a result of our
 analyses, we estimated the monthly encounter rate with snake predators at
 3.3% (95% CI: 1.6–4.9%), the contribution of snake predation to total
 mortality until maturity at 43.3% (15.0–95.3%), and the fitness advantage
 conferred by foot autotomy at 6.5% (2.7–11.5%). This study demonstrated
 the utility of the multi-method hierarchical modeling approach for the
 quantitative understanding of the ecological and evolutionary processes of
 anti-predator defenses in the wild.
DOI: 10.5061/dryad.2z34tmpjg
title: Data from: Climate, soil resources and microbial activity shape the distributions of mountain plants based on their functional traits

description: While soil ecosystems undergo important modi cations due to global change,
 the e ect of soil properties on plant distributions is still poorly
 understood. Plant growth is not only controlled by soil physico-chemistry
 but also by microbial activities through the decomposition of organic
 matter and the recycling of nutrients essential for plants. A growing body
 of evidence also suggests that plant functional traits modulate spe- cies’
 response to environmental gradients. However, no study has yet contrasted
 the importance of soil physico-chemistry, microbial activities and climate
 on plant species distributions, while accounting for how plant functional
 traits can in uence species- speci c responses. Using hierarchical e ects
 in a multi-species distribution model, we investigate how four functional
 traits related to resource acquisition (plant height, leaf carbon to
 nitro- gen ratio, leaf dry matter content and speci c leaf area) modulate
 the response of 44 plant species to climatic variables, soil
 physico-chemical properties and microbial 100 decomposition activity (i.e.
 exoenzymatic activities) in the French Alps. Our hierarchical trait-based
 model allowed to predict well 41 species according to the TSS statistic.
 In addition to climate, the combination of soil C/N, as a measure of
 organic matter quality, and exoenzymatic activity, as a measure of
 microbial decom- position activity, strongly improved predictions of plant
 distributions. Plant traits played an important role. In particular,
 species with conservative traits performed bet- ter under limiting
 nutrient conditions but were outcompeted by exploitative plants in more
 favorable environments. We demonstrate tight associations between
 microbial decomposition activity, plant functional traits associated to di
 erent resource acquisition strategies and plant dis- tributions. is
 highlights the importance of plant–soil linkages for mountain plant
 distributions. ese results are crucial for biodiversity modelling in a
 world where both climatic and soil systems are undergoing profound and
 rapid transformations.
DOI: 10.15468/dl.fgdns2
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sorex alaskanus"
 ]
}

 The dataset includes 13 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002451-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.