cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.040jp22
title: Data from: Plant economic strategies of grassland species control soil carbon dynamics through rhizodeposition

description: 1. The plant economics spectrum is increasingly recognized as a major
 determinant of plant species effects on terrestrial ecosystem functioning
 related to carbon cycling. However, the role of plant economic strategies
 in the effects of living root activity on soil organic carbon (SOC)
 dynamics through rhizodeposition remains unexplored, despite SOC being the
 largest terrestrial carbon pool. 2. Using a continuous 13C-labeling method
 allowing partitioning of plant and soil sources to carbon fluxes and
 pools, we studied here the linkages between plant economic strategies and
 SOC cycling processes in a ‘common garden’ greenhouse experiment. It
 includes a panel of 12 grassland species selected along a gradient of
 economic traits and belonging to three functionnal groups (C3 grasses,
 forbs and legumes). 3. All species induced an acceleration of native SOC
 mineralization but this rhizosphere priming effect (RPE) substantially
 differed across species and varied eleven-fold by the end of the
 experiment (from +26 to +295 % relative to unplanted soil). Interspecific
 variation in RPE was primarily linked to plant photosynthetic activity
 associated to species economic strategies of light and CO2 resource
 acquisition and processing. Fast-growing acquisitive species, such as
 legumes, featured large RPE, in relation with their high canopy
 photosynthesis coupled to high leaf photosynthetic capacity and large net
 primary productivity allocated aboveground. This large RPE was further
 associated with high root metabolic activity, rhizodeposition and soil
 microbial activity. In contrast, fine-root growth and economic traits
 related to soil resource foraging ability were poor predictors of RPE. 4.
 The formation of new root-derived SOC varied nine-fold across species and
 was similarly positively related to the net primary productivity allocated
 aboveground. Fast-growing acquisitive species with a high photosynthetic
 activity induced a disproportionately large RPE relative to SOC formation.
 5. Synthesis. Overall, our study demonstrates that rhizodeposition is a
 major mechanism through which plant economic strategies of grassland
 species control soil carbon dynamics. Acquisitive versus conservative
 species were associated with high versus low rates of photosynthesis and
 rhizodeposition, in turn leading to fast versus slow SOC turnover. This
 emphasizes the importance of considering rhizosphere processes for
 understanding plant species effects on soil biogeochemistry.
description: JEcol-2019-Henneron et
 alThis excel file is
 composed of two set of data: the first contains data available for each
 CO2 sampling time; the second contains data with cumulative or final C
 fluxes and pools. Each set had three excel sheets: the first contains the
 metadata describing each variable, the second contains the data for each
 microcosm, and the third contains the data for each treatment (with the
 means of the replicate microcosms for each treatment).
DOI: 10.5061/dryad.7fq25s8
title: Data from: Do people imitate when making decisions? - evidence from a spatial prisoners dilemma experiment

description: How do people decide which action to take? This question is best answered
 using Game Theory, which has proposed a series of decision mechanisms that
 people potentially use. In network simulations, wherein games are repeated
 and payoff differences can be observed, those mechanisms rely often on
 imitation of successful behavior. Surprisingly, little to no evidence has
 been provided about whether, how and what people actually use to alter
 their actions in that context. By comparing two experimental treatments
 wherein participants play in a network the iterated Prisoner's
 Dilemma game, we aim to answer whether more successful actions are
 imitated. Whereas in the first treatment, participants have the
 possibility to use payoff differences in making their decision, the second
 treatment hinders such imitation as no information about the gains is
 provided. If imitation of the more successful plays a role then there
 should be a difference in how players switch from cooperation to defection
 between both treatments. Although, cooperation and payoff levels appear
 not to be significantly different between both treatments, detailed
 analysis shows that there are behavioral differences: When confronted with
 a more successful co-player, the focal player will imitate that behavior
 as the switching is related to the experienced payoff inequality.
description: Iterated Multiplayer
 Prisoner's Dilemma experiment on a square latticeDataSet.csv
DOI: 10.5061/dryad.8g69b06
title: Data from: Making Brexit work for the environment and livelihoods: delivering a stakeholder informed vision for agriculture and fisheries

description: 1. The UK’s decision to leave the EU has far-reaching implications for
 agriculture and fisheries. To ensure the future sustainability of UK
 agricultural and fisheries systems, we argue that it is essential to grasp
 the opportunity that Brexit is providing to develop integrated policies
 that improve the management and protection of the natural environments,
 upon which these industries rely. 2. This article advances a stakeholder
 informed vision of the future design of UK agriculture and fisheries
 policies. We assess how currently emerging UK policy will need to be
 adapted in order to implement this vision. Our starting point is that
 Brexit provides the opportunity to redesign current unsustainable
 practices and can in principle deliver a sustainable future for
 agriculture and fisheries. 3. Underpinning policies with an ecosystem
 approach, with explicit inclusion of public goods provision, and social
 welfare equity were found to be central to the success of this endeavour.
 Recognition of the needs of, and innovative practices in, the devolved UK
 nations is also required as the new policy and regulatory landscape is
 established. 4. Achieving our proposed vision will necessitate drawing on
 best practice and creating more coherent and integrated food, environment
 and rural and coastal economy policies. Sustainable prosperity should and
 can form the core of future post-Brexit environmental policy thinking and
 our findings demonstrate the “bottom-up” and co-production approaches that
 will be key to the development of more environmentally sustainable
 agricultural and fisheries policies.
description: Agriculture &
 Fisheries Workshop Feedback Form Analysis (March 2017)Summary analysis of
 responses to questionnaires issued at the end of our stakeholder workshops
 on agriculture and fisheries in March 2017Fisheries Workshop &
 Questionaire Analysis (March 2017)Summary analysis of
 responses to questionnaires issued before our fisheries stakeholder
 workshop in March 2017, along with analysis of presentations during the
 day, the questionnaire at the end of the day, and additional information
 (as detailed) extracted from online sources
DOI: 10.5061/dryad.1rk753f
title: Data from: K-13 Propeller gene polymorphisms isolated between 2014 and 2017 from Cameroonian Plasmodium falciparum malaria patients

description: The emergence of artemisinin-resistant parasites since the late 2000s at
 the border of Cambodia and Thailand poses serious threats to malaria
 control globally, particularly in Africa which bears the highest malaria
 transmission burden. This study aimed to obtain reliable data on the
 current state of the kelch13 molecular marker for artemisinin resistance
 in Plasmodium falciparum in Cameroon. DNA was extracted from the dried
 blood spots collected from epidemiologically distinct endemic areas in the
 Center, Littoral and North regions of Cameroon. Nested PCR products from
 the Kelch13-propeller gene were sequenced and analyzed on an ABI 3730XL
 automatic sequencer. Of 219 dried blood spots, 175 were sequenced
 successfully. We identified six K13 mutations in 2.9% (5/175) of samples,
 including 2 non-synonymous, the V589I allele had been reported in Africa
 already and one new allele E612K had not been reported yet. These two
 non-synonymous mutations were uniquely found in parasites from the
 Littoral region. One sample showed two synonymous mutations within the
 kelch13 gene. We also observed two infected samples with mixed K13 mutant
 and K13 wild-type infection. Taken together, our data suggested the
 circulation of the non-synonymous K13 mutations in Cameroon. Albeit no
 mutations known to be associated with parasite clearance delays in the
 study population, there is need for continuous surveillance for earlier
 detection of resistance as long as ACTs are used and scaled up in the
 community.
description: Cameroonian Plasmodium
 falciparum isolates and K-13 polymorphisms20190821_Malaria K13 DATA BASE
 REFERENTIAL.xlsx
DOI: 10.5061/dryad.q1h4k0n
title: Data from: Exploring a Pool-seq only approach for gaining population genomic insights in non-model species

description: Developing genomic insights is challenging in non-model species for which
 resources are often scarce and prohibitively costly. Here, we explore the
 potential of a recently established approach using Pool-seq data to
 generate a de novo genome assembly for mining exons, upon which Pool-seq
 data is used to estimate population divergence and diversity. We do this
 for two pairs of sympatric populations of brown trout (Salmo trutta); one
 naturally sympatric set of populations and another pair of populations
 introduced to a common environment. We validate our approach by comparing
 the results to those from markers previously used to describe the
 populations (allozymes and individual based SNPs) and from mapping the
 Pool-seq data to a reference genome of the closely related Atlantic salmon
 (Salmo salar). We find that genomic differentiation (FST) between the two
 introduced populations exceeds that of the naturally sympatric populations
 (FST = 0.13 and 0.03 between the introduced and the naturally sympatric
 populations, respectively), in concordance with estimates from the
 previously used SNPs. The same level of population divergence is found for
 the two genome assemblies but estimates of average genic diversity differ
 (π ≈0.002 and π ≈0.001 when mapping to S. trutta and S. salar,
 respectively), although the relationships between population values are
 largely consistent. This discrepancy might be attributed to biases when
 mapping to a haploid condensed assembly made of highly fragmented read
 data compared to using a high-quality reference assembly from a divergent
 species. We conclude that the Pool-seq only approach can be suitable for
 detecting and quantifying genome wide population differentiation, and for
 comparing genomic diversity in populations of non-model species where
 reference genomes are lacking.
description: Pool-seq assembly only
 gene models for Salmo trutta Pool-seq de novo
 assembly scaffolded using the protein sequences for Salmo trutta via the
 MESPA pipeline. onlygenemodels.fa.gz
DOI: 10.5061/dryad.mg1k6gc
title: Data from: Extracting phylogenetic signal from phylogenomic data: higher-level relationships of the nightbirds (Strisores)

description: A well-resolved phylogeny would facilitate study of adaptation to
 nocturnality in the avian superorder Strisores, a group that includes both
 nocturnal and diurnal lineages. Based on previous estimates, it could be
 hypothesized that there were multiple independent origins of nocturnality
 in this group. In order to refine the Strisores phylogeny, we generated
 genome-scale datasets of 2,289 – 4,243 ultra-conserved elements for 23
 taxa representing all major living lineages in the group. Among the
 considerations for using genome-scale, molecular sequence data in
 phylogenomic analysis are issues related to GC content, GC variance and
 their effects on model selection. In this study, we employed a variety of
 analytical techniques to empirically investigate those issues in our data,
 as well as biases and errors resulting from alignment trimming, taxon
 selection and matrix completeness. Extensive analyses revealed conflict
 within the data, especially in regard to variation in GC content, that
 would not have been detected with more cursory study. Our results indicate
 that readily available models of molecular evolution are insufficient to
 encapsulate all phenomena present in genome-scale matrices, and that this
 problem may be at the root of many current issues in phylogenomic
 analysis. The analytical methods employed in this study are relevant to
 phylogenomic analysis of any large, heterogeneous matrix. In conclusion,
 we present a strongly supported estimate of the Strisores tree and discuss
 potential evolutionary pathways of nocturnality in this clade.
description: MatricesConcatenated, PHYLIP format nucleotide matrices with character sets.Trees concatenated RYNexus-format trees resulting from analysis of concatenated RY-coded matrices.Trees_concatenated_RY.tarTrees concatenated ACGTNexus-format trees resulting from analysis of the concatenated nucleotide matrices.Trees_concatenated_ACGT.tarTrees gene tree summary ACGTNexus-format trees resulting from gene tree summarization over nucleotide locus matrices.Gene_tree_sum_ACGT.tarTrees gene tree summary RYNexus-format trees resulting from gene tree summarization over RY-coded locus matrices.Gene_tree_sum_RY.tarTrees Low GC VarianceNexus-format trees resulting from analysis of concatenated low GC variance matrices.Trees_Low_GC_Variance.tarTrees Partitioned by LocusNexus-format trees resulting from analysis of concatenated matrices partitioned by locus.Trees_Part_by_Locus.tar
DOI: 10.5061/dryad.fc8j47n
title: Data from: Tooth fracture frequency in gray wolves reflects prey availability

description: Exceptionally high rates of tooth fracture in large Pleistocene
 carnivorans imply intensified interspecific competition, given that tooth
 fracture rises with increased bone consumption, a behavior that likely
 occurs when prey are difficult to acquire. To assess the link between prey
 availability and dental attrition, we documented dental fracture rates
 over decades among three well-studied populations of extant gray wolves
 that differed in prey:predator ratio and levels of carcass utilization.
 When prey:predator ratios declined, kills were more fully consumed, and
 rates of tooth fracture more than doubled. This supports tooth fracture
 frequency as a relative measure of the difficulty of acquiring prey, and
 reveals a rapid response to diminished food levels in large carnivores
 despite risks of infection and reduced fitness due to dental injuries.
 More broadly, large carnivore tooth fracture frequency likely reflects
 energetic stress, an aspect of predator success that is challenging to
 quantify in wild populations.
description: Data used for the
 analyses of gray wolf dental wear and fracture.The file contains data
 on dental wear stage and number of teeth broken by position (e.g.
 incisors, canines, etc.) along with specimen numbers, estimated age at
 death, sex, and length of the first lower molar for the three gray wolf
 samples included in the paper.Dryad data file- Wolf
 paper.xlsxData on elk carcass
 utilization in Yellowstone National ParkThe file contains data
 on the total number and identity of bones remaining at adult elk kills
 made by gray wolves during winter in Yellowstone National Park for the
 years 1995 through 2016. The data were collected by National Park Service
 scientists and volunteers. Also shown is the calculated mean percent of
 bones that were removed by wolves annually.YNP Elk Carcass data for
 Dryad.xlsx
DOI: 10.5061/dryad.655cc36
title: Data from: Nitrogen enrichment accelerates mangrove range expansion in the temperate-tropical ecotone

description: Climate change and nutrient enrichment are two phenomena impacting coastal
 ecosystems. In coastal wetlands, mangroves in temperate-tropical ecotones
 are encroaching on adjacent saltmarshes, a pattern that is primarily
 attributed to warmer winter temperatures. Climate change is also expected
 to increase the vulnerability of coastal wetlands to eutrophication, and
 increases in nutrient availability may further mediate the rate of
 mangrove expansion. We investigated the consequences of nutrient
 enrichment on coastal wetlands in the mangrove-saltmarsh ecotone near the
 temperate edge of mangrove distribution along the northeast coast of
 Florida. We tested the hypothesis that nutrient enrichment enhances the
 ongoing, climate-driven expansion of mangroves into areas historically
 dominated by saltmarshes by increasing mangrove growth and cover, allowing
 them to outcompete and overgrow adjacent saltmarsh plants. We manipulated
 nitrogen (N) and phosphorus (P) availability and measured the effects on
 growth, cover, diversity, leaf traits and nutrient dynamics of Avicennia
 germinans. We found that A. germinans shrubs growing in the
 saltmarsh-mangrove ecotone in northern Florida grew taller, increased
 their canopies, and had higher reproductive output when enriched with N
 compared to control plants and P-enriched plants. Nutrient enrichment did
 not alter Sarcocornia perennis growth, and increased Batis maritima height
 but did not alter density or biomass. Nitrogen addition caused an increase
 in A. germinans cover and decreases in B. maritima cover and Simpson’s
 index of diversity, suggesting that N enrichment, an ongoing phenomenon,
 can hasten the invasion of mangroves into saltmarshes by favoring mangrove
 growth and reproduction without significantly enhancing saltmarsh plant
 growth.
description: DangremondEtAlNorthMatanzasMangroveSaltmarshFertilizationData collected in the field between 2012 and 2016. File created with Microsoft Excel and consists of 4 sheets, one with metadata. LAI stands for leaf area index.
DOI: 10.5061/dryad.2f25cj0
title: Data from: Sputum microbiota and inflammation at stable state and during exacerbations in a cohort of chronic obstructive pulmonary disease (COPD) patients

description: Background: Exacerbations of chronic obstructive pulmonary disease (COPD)
 are debilitating events and spur disease progression. Infectious causes
 are frequent; however, it is unknown to what extent exacerbations are
 caused by larger shifts in the airways’ microbiota. The aim of the current
 study was to analyse the changes in microbial composition between stable
 state and during exacerbations, and the corresponding immune response.
 Methods: The study sample included 36 COPD patients examined at stable
 state and exacerbation from the Bergen COPD Cohort and Exacerbations
 studies, and one patient who delivered sputum on 13 different occasions
 during the three-year study period. A physician examined the patients at
 all time points, and sputum induction was performed by stringent protocol.
 Only induced sputum samples were used in the current study, not
 spontaneously expectorated sputum. Sputum inflammatory markers (IL-6,
 IL-8, IL-18, IP-10, MIG, TNF-α) and antimicrobial peptides (AMPs, i.e.
 LL-37/hCAP-18, SLPI) were measured in supernatants, whereas target gene
 sequencing (16S rRNA) was performed on corresponding cell pellets. The
 microbiome bioinformatics platform QIIME2TM and the statistics environment
 R were applied for bioinformatics analyses. Results: Levels of IP-10, MIG,
 TNF-α and AMPs were significantly different between the two disease
 states. Of 36 sample pairs, 24 had significant differences in the 12 most
 abundant genera between disease states. The diversity was significantly
 different in several individuals, but not when data was analysed on a
 group level. The one patient case study showed longitudinal dynamics in
 microbiota unrelated to disease state. Conclusion: Changes in the sputum
 microbiota with ch anging COPD disease states are common, and are
 accompanied by changes in inflammatory markers. However, the changes are
 highly individual and heterogeneous events.
description: COPD_BERGEN_stvsex_MetadataMetadata allowing for sample selection and analyses as performed in the article Sputum microbiota and inflammation at stable state and during exacerbations in a cohort of chronic obstructive pulmonary disease (COPD) patients. To be used with the file: COPD_BERGEN_stvsex_Command and fastq-files (COPD_BERGEN_Fastq175) found at https://doi.org/10.5061/dryad.5gc82COPD_BERGEN_stvsex_CommandCommand file allowing for sample selection as performed for Sputum microbiota and inflammation at stable state and during exacerbations in a cohort of chronic obstructive pulmonary disease (COPD) patients. To be used with the file: COPD_BERGEN_stvsex_Metadata and fastq-files (COPD_BERGEN_Fastq175) found at https://doi.org/10.5061/dryad.5gc82
DOI: 10.5281/zenodo.18393394
title: Tropical stream meiofauna of Prieta Stream, Puerto Rico - post hurricane data

description: Data set on stream meiofauna species richness and abundance and benthic sediments in Quebrada Prieta, El Yunque National Forest, Puerto Rico. The data set corresponds to the 8 months following the impact of Hurricane Maria in September 2017.  Samples were collected in two tributaries, named as QPA and QPB.
DOI: 10.5281/zenodo.18393393
title: Tropical stream meiofauna of Prieta Stream, Puerto Rico - post hurricane data

description: Data set on stream meiofauna species richness and abundance and benthic sediments in Quebrada Prieta, El Yunque National Forest, Puerto Rico. The data set corresponds to the 8 months following the impact of Hurricane Maria in September 2017.  Samples were collected in two tributaries, named as QPA and QPB.
DOI: 10.5061/dryad.47fd240
title: Data from: Post-copulatory sexual selection allows females to alleviate the fitness costs incurred when mating with senescing males

description: Male senescence has detrimental effects on reproductive success and
 offspring fitness. When females mate with multiple males during the same
 reproductive bout, post-copulatory sexual selection that operates either
 through sperm competition or cryptic female choice might allow females to
 skew fertilization success towards young males and as such limit the
 fitness costs incurred when eggs are fertilized by senescing males. Here,
 we experimentally tested this hypothesis. We artificially inseminated
 female North African houbara bustards with sperm from dyads of males of
 different (young and old) or similar ages (either young or old). Then, we
 assessed whether siring success was biased towards young males and we
 measured several life history traits of the progeny to evaluate the
 fitness costs due to advanced paternal age. In agreement with the
 prediction, we found that siring success was biased towards young males,
 and offspring sired by old males had impaired hatching success, growth and
 post-release survival (in females). Overall, our results support the
 hypothesis that post-copulatory sexual selection might represent an
 effective mechanism allowing females to avoid the fitness costs of
 fertilization by senescing partners.
description: Data to evaluate the
 fitness costs incurred when mating with senescing malesThis file contains the
 different datasets to test whether siring success, hatching success,
 offspring growth rate and offspring survival (in captivity and
 post-release in the wild) differ according to paternal
 age.Vuarin
 et al_datasets.xlsx