cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.12758
title: Data from: Quantitative genetic variation in, and environmental effects on, pathogen resistance and temperature-dependent disease severity in a wild trout

description: Health after pathogen contact varies among individuals because of
 differences in pathogen load (which is limited by resistance) and disease
 severity in response to pathogen load (which is limited by tolerance). To
 understand pathogen-induced host evolution, it is critical to know not
 only the relative contributions of nongenetic and genetic variation to
 resistance and tolerance but also how they change environmentally. We
 quantified nongenetic and genetic variation in parasite load and the
 associated temperature-dependent disease among trout siblings from two
 rivers. We detected a genetic variance for parasite load 6.6 times as
 large in the colder river. By contrast, genetic variance for disease
 traits tended to be larger in the warmer river, where the disease was
 manifested more severely. The relationships between disease severity and
 pathogen load (tolerance) exhibited plateaus at low pathogen load and
 stronger steepening slopes at high pathogen load in the warmer river. Our
 study demonstrates the environmental influence on disease severity,
 nongenetic and genetic variance for health-damage-limiting host abilities,
 and the shape of tolerance curves. Environmental variability is predicted
 to govern the presence and intensity of selection, change the relative
 contributions of nongenetic and genetic variance, and therefore hamper
 evolution toward more resistant and tolerant hosts.
description: Genotypes_AltjaSTR genotypes for Salmo trutta individuals from River AltjaGenotypes_MustojaSTR genotypes for Salmo trutta individuals from River MustojaMarkerTypeErrorRateSTR genotyping error file used in parental reconstruction analysis using the program ColonyMinerData.All.EcorrqPCR quantification cycle as inferred by the online tool 'Real-time PCR Miner' http://miner.ewindup.info/ given per plate and well, including amplification efficiencies and efficiency-corrected quantification cyclePhenotypeDataPhenotype and sampling information for Salmo trutta individuals from rivers Altja and Mustoja.PKD.NegativeDataPhenotype data on parasite free Salmo trutta individuals from three Estonian rivers.qPCR.Tm.DataqPCR melting curve data per plate, well, and cycle.
DOI: 10.5061/dryad.9km73
title: Data from: Evolutionary adaptation to environmental stressors: A common response at the proteomic level

description: Mechanistic trade-offs between traits under selection can shape and
 constrain evolutionary adaptation to environmental stressors. However, our
 knowledge of the quantitative and qualitative overlap in the molecular
 machinery among stress tolerance traits is highly restricted by the
 challenges of comparing and interpreting data between separate studies and
 laboratories, as well as to extrapolating between different levels of
 biological organization. We investigated the expression of the
 constitutive proteome (833 proteins) of 35 Drosophila melanogaster
 replicate populations artificially selected for increased resistance to
 six different environmental stressors. The evolved proteomes were
 significantly differentiated from replicated control lines. A targeted
 analysis of the constitutive proteomes revealed a regime-specific
 selection response among heat shock proteins, which provides evidence that
 selection also adjusts the constitutive expression of these molecular
 chaperones. While the selection response in some proteins was regime
 specific, the results were dominated by evidence for a ‘common stress
 response’. With the exception of high temperature survival, we found no
 evidence for negative correlations between environmental stress resistance
 traits, meaning that evolutionary adaptation is not constrained by
 mechanistic trade-offs in regulation of functional important proteins.
 Instead, standing genetic variation and genetic trade-offs outside
 regulatory domains likely constrain the evolutionary responses in natural
 populations.
description: Proteomic data in long
 formatProtein abundances used
 for all analyses.All Replica_Multiconsensus from
 5 Reports_long_dryad.csv
DOI: 10.5061/dryad.n856r
title: Data from: Long-term declines in dietary nutritional quality for North American cattle

description: With over 1 billion cattle in the world as well as over 2 billion sheep,
 goats and buffalo, these animals contribute approximately 15% of the
 global human protein supply while producing a significant proportion of
 anthropogenic emissions of greenhouse gases and global nutrient fluxes.
 Despite increasing reliance on grazers for protein production globally,
 the future of grazers in a changing world is uncertain. Factors such as
 increased prevalence of drought, rising atmospheric CO2 concentrations,
 and sustained nutrient export all have the potential to reduce cattle
 performance by reducing the nutritional quality of forage. However, there
 are no analyses to quantify changes in diet quality, subsequent impact on
 cattle performance and cost of supplementation necessary to mitigate any
 predicted protein deficiency. To quantify the trajectory of nutritional
 stress in cattle, we examined more than 36 000 measurements of dietary
 quality taken over 22 yr for US cattle. Here, we show that standardizing
 for spatial and temporal variation in drought and its effects on forage
 quality, cattle have been becoming increasingly stressed for protein over
 the past two decades, likely reducing cattle weight gain. In economic
 terms, the replacement costs of reduced protein provision to US cattle are
 estimated to be the equivalent of $1.9 B annually. Given these trends,
 nitrogen enrichment of grasslands might be necessary if further reduction
 in protein content of forages is to be prevented.
description: Forage quality
 dataForage quality data for
 main analyses. Note that location data have been rounded to nearest 0.1
 degrees to maintain privacy.InputGanlabquality.csvWeight gain model resultsNutbal output dataNutbal.csvR script for analysesR file for analysesModelPlotGANLABDietQuality2.R
DOI: 10.5061/dryad.t6292
title: Data from: Phylogenetic relationships in Senegalia (Leguminosae-Mimosoideae) emphasizing the South American lineages

description: Senegalia is a genus of the legume family (Leguminosae: Mimosoideae) that
 has a pantropical distribution with centers of diversity in Brazil, Mexico
 and southern Africa. The genus is characterized by plants having bipinnate
 leaves, presence of petiolar nectaries, prickles on the branches, and
 pollen grains arranged in polyads with 16 grains. Morphology is an
 important tool for identification of Senegalia species, but it is not
 sufficient to resolve all taxonomic issues and elucidate the evolutionary
 history of this genus. Prior molecular analyses of Mimosoideae have lacked
 breadth of sampling within Senegalia, leaving many relationships
 uncertain, particularly the relationship among Brazilian species and other
 members of the genus. The aim of this study was to identify Senegalia s.
 s. lineages that contain Brazilian species, and to investigate the
 relationship of these species with non-Brazilian Senegalia species. We
 present the first comprehensively sampled phylogeny of American and
 African Senegalia, however Asian species are not sampled. We sequenced
 four plastid and one nuclear DNA (ITS) regions for 125 samples of 59
 Senegalia and one Parasenegalia species. Both Bayesian and maximum
 likelihood analyses were performed. Neither the American or African
 species form monophyletic lineages. The lack of monophyly of these groups
 suggests a more complicated evolutionary history of the genus than
 previously considered, including probable transatlantic dispersal events.
description: S1Supplementary Figure
 1AppendixAppendix to the species and the GenBank numbers.ap.docx
DOI: 10.5061/dryad.073gb
title: Data from: Coping with strong variations in winter severity: plastic habitat selection of deer at high density

description: Few empirical studies on large herbivores considered how behavioral
 plasticity could enhance their capacity to cope with rapid and extreme
 changes in weather conditions at several spatiotemporal scales. During
 winter, large herbivores living under low predation pressure mainly
 trade-off benefits of forage acquisition with the costs of exposure to
 harsh weather conditions. We assessed the changes in this trade-off for
 white-tailed deer adult females on Anticosti Island (Canada) at different
 scales during 2 contrasted winters (i.e., a harsher and a milder winter).
 We hypothesized that deer should adjust their foraging decisions to avoid
 cold wind-chill temperatures and high locomotion costs in deep snow as
 winter severity increased. We compared habitat selection at the home-range
 scale, habitat selection relative to thermal conditions within the home
 range, and selection for foraging sites relative to snow conditions along
 the foraging tracks between winters. Home-range selection of deer was
 similar between winters. Deer adjusted their within-home-range selection
 relative to thermal conditions: they selected thermal cover during
 cold-stress periods while their selection for open areas increased during
 the warmer periods. Deer showed high behavioral plasticity along their
 foraging tracks: they selected tracks with different forage resources
 between winters and traded-off the locomotion costs in deep snow cover
 with the benefits of forage availability as winter severity increased. We
 discuss how behavioral plasticity of deer in their thermoregulatory
 behavior and foraging site selection allows them to cope with varying
 winter conditions, in a system where their short-term behavioral
 adaptations were already strongly constrained by intraspecific
 competition.
description: Data_HomeRangeScaleData used in the home-range scale analysis.Data_WithinHomeRangeScaleData used in the within-home-range scale analysis.Data_WithinHomeRangeScale_WindchillData used in the within-home-range scale analysis describing wind-chill dataData_ForagingTrackScaleData used in the foraging track scale analysis.
DOI: 10.5061/dryad.qj8gh
title: Data from: A three decade assessment of climate-associated changes in forest composition across the north-eastern USA

description: 1. Climate-associated changes in forest composition have been widely
 reported, particularly where changes in abiotic conditions have resulted
 in high mortality of sensitive species and have disproportionately favored
 certain species better adapted to these newer conditions. In the
 northeastern USA and southeastern Canada, few studies have examined
 climate-related influences associated on forest composition, and none have
 considered broad-scale changes over a long temporal (&gt;25 years)
 period. 2. We used US Forest Service Forest Inventory and Analysis data
 from 1983-2014 across four northeastern states (Maine, New Hampshire, New
 York, and Vermont) to assess temporal and spatial changes in the
 occurrence and abundance of American beech, sugar maple (Acer sacharum
 L.), red maple (A. rubrum L.), and birch (Betula spp.) saplings. We also
 tested the effects of biotic and abiotic factors on the distribution of
 the four studied deciduous species over the entire studied period. 3.
 Occurrence and abundance of American beech have increased substantially
 over the past three decades, whereas the occurrence and abundance of
 three-other deciduous species have decreased in all ecological provinces
 of the northeastern USA, except the Midwest Broadleaf ecological province.
 Consequently, a clear shift in species composition is currently underway
 in the beech-maple-birch (BMB) forests of the northeastern USA, with
 uncertain consequences for future ecosystem structure and function. 4. In
 the studied region and over the entire studied period, the distribution of
 increased occurrence and abundance of beech relative to three-other
 deciduous species were associated with the higher temperature and
 precipitation as well as higher conspecific basal area and dead tree basal
 area. 5. Synthesis and applications: The change from BMB forests to
 beech-dominated forests and beech encroachment to new forest areas across
 the northeast may expand in areas where higher intensity
 harvesting/disturbances (i.e., large-scale canopy openings) do not occur,
 which would be a management concern as the beech is associated with the
 beech-bark disease. Our results emphasize the need for management
 strategies such as higher intensity harvesting methods, vegetation
 management, and controlling browsing pressure to reduce the beech
 dominance.
description: Hardwood sapling
 composition of north-eastern forestsThe data file contains
 response and explanatory variables of the analysis for sapling occurrence,
 absolute, and relative abundances of major hardwood species of
 north-eastern USA forests.Data_Dryad_ARUN.csv
DOI: 10.5061/dryad.rc416
title: Data from: Phylogenetically informed spatial planning is required to conserve the mammalian tree of life

description: In the face of the current extinction crisis and severely limited
 conservation resources, safeguarding the tree of life is increasingly
 recognized as a high priority. We conducted a first systematic global
 assessment of the conservation of phylogenetic diversity (PD) that uses
 realistic area targets and highlights the key areas for conservation of
 the mammalian tree of life. Our approach offers a substantially more
 effective conservation solution than one focused on species. In many
 locations, priorities for PD differ substantially from those of a
 species-based approach that ignores evolutionary relationships. This
 discrepancy increases rapidly as the amount of land available for
 conservation declines, as does the relative benefit for mammal
 conservation (for the same area protected). This benefit is equivalent to
 an additional 5900 Myr of distinct mammalian evolution captured simply
 through a better informed choice of priority areas. Our study uses area
 targets for PD to generate more realistic conservation scenarios, and
 tests the impact of phylogenetic uncertainty when selecting areas to
 represent diversity across a phylogeny. It demonstrates the opportunity of
 using rapidly growing phylogenetic information in conservation planning
 and the readiness for a new generation of conservation planning
 applications that explicitly consider the heritage of the tree of
 life's biodiversity.
description: Mammal PD Conservation
 planning data filesThis zipped archive
 contains a) all data used in this study b) a version of the data formatted
 for use with Marxan and c) a sample parameter file and results for one
 conservation scenario. A help file is also included.MammalPDConservation_data_files.zip
DOI: 10.5061/dryad.q6s1m
title: Data from: Convergence of gut microbiotas in the adaptive radiations of African cichlid fishes

description: Ecoevolutionary dynamics of the gut microbiota at the macroscale level,
 that is, in across-species comparisons, are largely driven by ecological
 variables and host genotype. The repeated explosive radiations of African
 cichlid fishes in distinct lakes, following a dietary diversification in a
 context of reduced genetic diversity, provide a natural setup to explore
 convergence, divergence and repeatability in patterns of microbiota
 dynamics as a function of the host diet, phylogeny and environment. Here
 we characterized by 16S rRNA amplicon sequencing the gut microbiota of 29
 cichlid species from two distinct lakes/radiations (Tanganyika and Barombi
 Mbo) and across a broad dietary and phylogenetic range. Within each lake,
 a significant deviation between a carnivorous and herbivorous lifestyle
 was found. Herbivore species were characterized by an increased bacterial
 taxonomic and functional diversity and converged in key compositional and
 functional community aspects. Despite a significant lake effect on the
 microbiota structure, this process has occurred with remarkable parallels
 in the two lakes. A metabolic signature most likely explains this trend,
 as indicated by a significant enrichment in herbivores/omnivores of
 bacterial taxa and functions associated with fiber degradation and
 detoxification of plant chemical compounds. Overall, compositional and
 functional aspects of the gut microbiota individually and altogether
 validate and predict main cichlid dietary habits, suggesting a fundamental
 role of gut bacteria in cichlid niche expansion and adaptation.
description: Cichlids_representative_OTUs_aligned16S V3-V4 alignment of 22869 representative OTUs, without lanemaskCichlids_ISME_OTUs_aligned.fasta
DOI: 10.5061/dryad.8k3q2
title: Data from: De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech

description: Despite the ecological and economic importance of European beech (Fagus
 sylvatica L.) genomic resources of this species are still limited. This
 hampers an understanding of the molecular basis of adaptation to stress.
 Since beech will most likely be threatened by the consequences of climate
 change, an understanding of adaptive processes to climate change-related
 drought stress is of major importance. Here, we used RNA-seq to provide
 the first drought stress-related transcriptome of beech. In a drought
 stress trial with beech saplings, 50 samples were taken for RNA extraction
 at five points in time during a soil desiccation experiment. De novo
 transcriptome assembly and analysis of differential gene expression
 revealed 44,335 contigs, and 662 differentially expressed genes between
 the stress and normally watered control group. Gene expression was
 specific to the different time points, and only five genes were
 significantly differentially expressed between the stress and control
 group on all five sampling days. GO term enrichment showed that mostly
 genes involved in lipid- and homeostasis-related processes were
 upregulated, whereas genes involved in oxidative stress response were
 downregulated in the stressed seedlings. This study gives first insights
 into the genomic drought stress response of European beech, and provides
 new genetic resources for adaptation research in this species.
description: De novo transcriptome
 assembly of European beechDe novo assembly of a
 drought-related transcriptome of European beech.De novo assembly_European
 beech.fa
DOI: 10.5061/dryad.f0g32
title: Data from: Signatures of optimal control in pairs of schooling zebrafish

description: Animals moving in groups coordinate their motion to remain cohesive. A
 large amount of data and analysis of movement coordination has been
 obtained in several species, but we are lacking theoretical frameworks
 that can derive the form of coordination rules. Here, we examine whether
 optimal control theory can predict the rules underlying social
 interactions from first principles. We find that a control rule which is
 designed to minimize the time it would take a pair of schooling fish to
 form a cohesively moving unit correctly predicts the characteristics of
 social interactions in fish. Our methodology explains why social
 attraction is negatively modulated by self-motion velocity and positively
 modulated by partner motion velocity, and how the biomechanics of fish
 swimming can shape the form of social forces. Crucially, the values of all
 parameters in our model can be estimated from independent experiments that
 need not relate to measurement of social interactions. We test our theory
 by showing a good match with experimentally observed social interaction
 rules in zebrafish. In addition to providing a theoretical rationale for
 observed decision rules, we suggest that this framework opens new
 questions about tuning problems and learnability of collective behaviours.
description: materialsThis zipped file consists of four folders. The first folder forcemaps contains all the trajectory data as well as functions used to calculate the forcemaps. The second folder models contains code used to visualize the decision boundaries as predicted from theory. The folder simulation contains materials needed to reproduce all the numerical simulations of schooling behavior. The folder tracefitters has all the code needed to fit velocity traces.
DOI: 10.5061/dryad.178vs
title: Data from: Conflicts at work are associated with a higher risk of cardiovascular disease

description: Background: Only few authors have analyzed the impact of workplace
 conflicts and the resulting stress on the risk of developing
 cardiovascular disorders. The goal of this study was to analyze the
 association between workplace conflicts and cardiovascular disorders in
 patients treated by German general practitioners. Methods: Patients with
 an initial documentation of a workplace conflict experience between 2005
 and 2014 were identified in 699 general practitioner practices (index
 date). We included only those that were between the ages of 18 and 65
 years, had a follow-up time of at least 180 days after the index date, and
 had not been diagnosed with angina pectoris, myocardial infarction,
 coronary heart diseases, or stroke prior to the documentation of the
 workplace mobbing. In total, this study consisted of 7,374 patients who
 experienced conflicts and 7,374 controls for analysis. The main outcome
 measure was the incidence of angina pectoris, myocardial infarction, and
 stroke correlated with workplace conflict experiences. Results: After a
 maximum of five years of follow-up, 2.9% of individuals who experienced
 workplace conflict were affected by cardiovascular diseases, while only
 1.4% were affected in the control group (p-value&lt;0.001). Workplace
 conflict was associated with a 1.63-fold increase in the risk of
 developing cardiovascular diseases. Finally, the impact of workplace
 conflict was higher for myocardial infarction (OR=2.03) than for angina
 pectoris (OR=1.79) and stroke (OR=1.56). Conclusions: Overall, we found a
 significant association between workplace conflicts and cardiovascular
 disorders.
description: MobbingPatients with and without workplace mobbing experience treated in German general practitioner practices