cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q82j0
title: Data from: Snowbeds are more affected than other subalpine-alpine plant communities by climate change in the Swiss Alps

description: While the upward shift of plant species has been observed on many alpine
 and nival summits, the reaction of the subalpine and lower alpine plant
 communities to the current warming and lower snow precipitation has been
 little investigated so far. To this aim, 63 old, exhaustive plant
 inventories, distributed along a subalpine–alpine elevation gradient of
 the Swiss Alps and covering different plant community types (acidic and
 calcareous grasslands; windy ridges; snowbeds), were revisited after 25–50
 years. Old and recent inventories were compared in terms of species
 diversity with Simpson diversity and Bray–Curtis dissimilarity indices,
 and in terms of community composition with principal component analysis.
 Changes in ecological conditions were inferred from the ecological
 indicator values. The alpha-diversity increased in every plant community,
 likely because of the arrival of new species. As observed on mountain
 summits, the new species led to a homogenization of community
 compositions. The grasslands were quite stable in terms of species
 composition, whatever the bedrock type. Indeed, the newly arrived species
 were part of the typical species pool of the colonized community. In
 contrast, snowbed communities showed pronounced vegetation changes and a
 clear shift toward dryer conditions and shorter snow cover, evidenced by
 their colonization by species from surrounding grasslands. Longer growing
 seasons allow alpine grassland species, which are taller and hence more
 competitive, to colonize the snowbeds. This study showed that
 subalpine–alpine plant communities reacted differently to the ongoing
 climate changes. Lower snow/rain ratio and longer growing seasons seem to
 have a higher impact than warming, at least on plant communities dependent
 on long snow cover. Consequently, they are the most vulnerable to climate
 change and their persistence in the near future is seriously threatened.
 Subalpine and alpine grasslands are more stable, and, until now, they do
 not seem to be affected by a warmer climate.
description: Matteodo2016_Freq&Cover changeSpecies of the six plant communities and their corresponding frequencies in the historical and recent surveys, the difference between recent and historical frequency, the p-value derived from the permutation test on frequency, the mean cover in the historical and recent surveys, the difference of mean cover (recent-historical), and the significance value derived from the permutation test on cover. The latter test was applied only on species with historical and recent frequency values ≥ 25%. Species are ordered firstly by increasing p-values for the frequency test and secondly by increasing p-values for the cover test. Species with significant frequency or mean cover changes are in bold.
DOI: 10.5061/dryad.cv37539
title: Data from: Influenza hemagglutination-inhibition antibody titer as a mediator of vaccine-induced protection for influenza B

description: Background: The hemagglutination inhibition (HAI) assay is an established
 correlate of protection for the inactivated influenza vaccine, but the
 proportion of vaccine-induced protection that is mediated by the
 post-vaccination HAI titer has not been assessed. Methods: We used data
 from a randomized placebo-controlled trial of a split-virion inactivated
 influenza vaccine in children 6-17 years of age. Sera were collected
 before and 30 days after receipt of vaccination or placebo, and tested by
 the HAI assay against B/Brisbane/60/2008-like (B/Victoria lineage). We
 fitted Cox proportional hazards models to the time to laboratory-confirmed
 influenza B. We used causal mediation analysis to estimate the proportion
 of the total effect of vaccination that was mediated by higher HAI titers.
 Results: We estimated that vaccine efficacy against confirmed B/Victoria
 infection was 68% (95% CI: 33%, 88%), and post-vaccination HAI titers
 explained 57% of the effect of vaccination on protection. Conclusions: The
 majority of the effect of inactivated influenza vaccination in children is
 mediated by the increased HAI titer after vaccination, but other
 components of the immune response to vaccination may also play a role in
 protection and should be further explored. Causal mediation analysis
 provides a framework to quantify the role of various mediators of
 protection.
description: Read me (data file
 explanations)Data
 fileThis data file contains
 all data information.kid_all.csvScripts for text results and Figure 2R syntax to reproduce descriptive results and Figure 2Results_and_figures.RScripts for functions used in mediation analysisMediation_functions.RScripts for mediation analysisR syntax for mediation analysis results in main text.Mediation_analysis.R
DOI: 10.5061/dryad.64n47
title: Data from: Comparison of solar-induced chlorophyll fluorescence, light-use efficiency, and process-based GPP models in maize

description: Accurately quantifying cropland gross primary production (GPP) is of great
 importance to monitor cropland status and carbon budgets. Satellite-based
 light-use efficiency (LUE) models and process-based terrestrial biosphere
 models (TBMs) have been widely used to quantify cropland GPP at different
 scales in past decades. However, model estimates of GPP are still subject
 to large uncertainties, especially for croplands. More recently,
 space-borne solar-induced chlorophyll fluorescence (SIF) has shown the
 ability to monitor photosynthesis from space, providing new insights into
 actual photosynthesis monitoring. In this study, we examined the potential
 of SIF data to describe maize phenology and evaluated three GPP modeling
 approaches (space-borne SIF retrievals, a LUE-based Vegetation
 Photosynthesis Model (VPM), and a process-based Soil Canopy Observation of
 Photochemistry and Energy flux (SCOPE) model constrained by SIF) at a
 maize (Zea mays L.) site in Mead, Nebraska, USA. The result shows that SIF
 captured the seasonal variations (particularly during the early and late
 growing season) of tower-derived GPP (GPP_EC) much better than did
 satellite-based vegetation indices (enhanced vegetation index, EVI and
 land surface water index, LSWI). Consequently, SIF was strongly correlated
 with GPP_EC than were EVI and LSWI. Evaluation of GPP estimates against
 GPP_EC during the growing season demonstrated that all three modeling
 approaches provided reasonable estimates of maize GPP, with Pearson's
 correlation coefficients (r) of 0.97, 0.94, and 0.93 for the SCOPE, VPM,
 and SIF models, respectively. The SCOPE model provided the best simulation
 of maize GPP when SIF observations were incorporated through optimizing
 the key parameter of maximum carboxylation capacity (Vcmax). Our results
 illustrate the potential of SIF data to offer an additional way to
 investigate the seasonality of photosynthetic activity, to constrain
 process-based models for improving GPP estimates, and to reasonably
 estimate GPP by integrating SIF and GPP_EC data without dependency on
 climate inputs and satellite-based vegetation indices.
description: Vegeation index, SIF and
 VPM model resultsThe data includes PAR,
 air temperature, EVI, LSWI, APAR and SIF. The parameters for the VPM model
 are also included.data_submit.xlsx
DOI: 10.5061/dryad.6rg10
title: Data from: Intrasexual competition underlies sexual selection on male breeding coloration in the orangethroat darter, Etheostoma spectabile

description: Elaborate, sexually dimorphic traits are widely thought to evolve under
 sexual selection through female preference, male–male competition, or
 both. The orangethroat darter (Etheostoma spectabile) is a sexually
 dichromatic fish in which females exhibit no preferences for male size or
 coloration. We tested whether these traits affect individual reproductive
 success in E. spectabile when multiple males are allowed to freely compete
 for a female. The quality and quantity of male coloration were associated
 with greater success in maintaining access to the female and in spawning
 as the primary male (first male to participate). On the other hand,
 sneaking behavior showed little correlation with coloration. Male breeding
 coloration in E. spectabile may therefore demonstrate how intrasexual
 competition can be a predominant factor underlying the evolution of male
 ornaments.
description: zhou&fuller_malecompBehavioral and chromatic data for male E. spectabile
DOI: 10.5061/dryad.b2v51
title: Data from: Ecological niche differentiation in peripheral populations: a comparative analysis of eleven Mediterranean plant species

description: Aim: The “central-peripheral” hypothesis has provided a baseline for many
 studies of population dynamics and genetic variability at species
 distribution limits. Although peripheral populations are often assumed to
 occur in ecologically marginal conditions, little is known about whether
 they effectively occur in a distinct ecological niche. Location: Western
 Mediterranean basin. Time Period: 2013-2014. Major taxa studied: A
 cross-taxa analysis of 11 Mediterranean vascular plants. Methods: We
 quantified variation in the ecological niche between populations at the
 northern range limits of species in Mediterranean France and those in the
 central part of the distribution in continental Spain or Italy. We
 analyzed both the macro-ecological niche where populations occur in terms
 of broad habitat and altitudinal range and the micro-ecological niche
 where individual plants grow in terms of soil and structural biotic and
 abiotic characteristics. Results: Most species occur in a single broad
 habitat type common to central and peripheral populations and have a
 narrower altitudinal range in the latter. In contrast, for the
 micro-ecological niche we detected marked variation in several niche
 parameters among central and peripheral populations. Although many
 differences are species-specific some are common to several species. We
 found a trend towards narrower micro-niche breadth in peripheral
 populations. Main conclusions: Our results illustrate the importance of
 studying the precise ecological characteristics where plants grow and the
 pertinence of a multi-species approach to correctly assess niche
 variation. The ecological originality of peripheral populations underlines
 their evolutionary potential and conservation significance.
description: DRYAD_ms.ecography_quadThis excel file synthesis all data used for the quadratic analysis. Columns headers are detailed within the manuscript.
DOI: 10.5061/dryad.q446n6q
title: Data from: Costs of walking: differences in egg size and starvation resistance of females between strains of the red flour beetle (Tribolium castaneum) artificially selected for walking ability

description: In many animals, movement often affects fitness components such as
 foraging or migration. On the other hand, individuals with higher mobility
 also often have fitness costs. This trade-off between movement and other
 traits may explain the maintenance of variation in moving ability in a
 population. However, few studies have focused on movement by walking,
 although many previous studies of insects have investigated the evolution
 of variations in mobility with wing polymorphism. In the present study, we
 focused on the walking ability of the red flour beetle (Tribolium
 castaneum), and investigated whether females with higher than lower
 walking ability have fitness costs. The present results showed that
 females with genetically higher walking ability produced smaller eggs and
 had lower starvation resistance than females with lower walking ability.
 These results suggest that higher walking ability is costly for females,
 and this fitness cost may explain maintenance of variations of walking
 ability in a population.
description: JEB-201800183_main_data
DOI: 10.5061/dryad.h58q6
title: Data from: Morphological convergence of the prey-killing arsenal of sabertooth predators

description: Sabertooth members of the Felidae, Nimravidae, and Barbourofelidae are
 well-known for their elongated saber-shaped canines. However, within these
 groups, there is a wide range of independently derived tooth shapes and
 lengths, including dirk-tooth and scimitar-tooth morphs. In conjunction
 with the saberteeth, forelimbs were also used to subdue prey. Thus, there
 may be a functional link between canine shape and forelimb morphology.
 Because there are no living sabertooth forms for comparison, extant felids
 make a good proxy for examining the morphology of these extinct organisms.
 Here, I examine the forelimb morphology of different sabertooth groups
 from across North America; I address whether forelimb morphologies are
 associated with tooth morphologies, and whether these associated tooth and
 forelimb morphologies are convergent among different families. To answer
 these questions, I analyzed six functional indices of the forelimbs and
 two canine characters for 13 species of sabertooth predators and 15 extant
 felid species. Results indicate that sabertooth morphs with longer,
 thinner canines show more robust limb proportions. These patterns were
 convergent among sabertooth felids, nimravids, and barbourofelids, and
 indicate a positive functional relationship between saber elongation and
 increased forelimb robustness. This suggests that sabertooth carnivorans
 demonstrated niche partitioning of predation strategies according to
 canine shape and corresponding forelimb morphology.
description: Convergence in
 Sabertooths Appendix 1Appendix 1: Measurements
 of species used in this studyConvergence in
 Sabertooths Appendix 2Appendix 2: List of all
 specimens used in this project.
DOI: 10.5061/dryad.nk453
title: Data from: Quantitative time-resolved analysis reveals intricate, differential regulation of standard- and immuno-proteasomes

description: Proteasomal protein degradation is a key determinant of protein half-life
 and hence of cellular processes ranging from basic metabolism to a host of
 immunological processes. Despite its importance the mechanisms regulating
 proteasome activity are only incompletely understood. Here we use an
 iterative and tightly integrated experimental and modelling approach to
 develop, explore and validate mechanistic models of proteasomal
 peptide-hydrolysis dynamics. The 20S proteasome is a dynamic enzyme and
 its activity varies over time because of interactions between substrates
 and products and the proteolytic and regulatory sites; the locations of
 these sites and the interactions between them are predicted by the model,
 and experimentally supported. The analysis suggests that the rate-limiting
 step of hydrolysis is the transport of the substrates into the proteasome.
 The transport efficiency varies between human standard- and
 immuno-proteasomes thereby impinging upon total degradation rate and
 substrate cleavage-site usage.
description: Proteasomal degradation
 kinetics of short fluorogenic peptidespeptide digestions using
 mouse proteasome, human s- and -i proteasome. Substrates: Suc-LLVY-MCA,
 Z-LLE-MCA, Bz-VGR-MCA.Data.xlsx
DOI: 10.5061/dryad.jk2qr
title: Data from: Male eyespan size is associated with meiotic drive in wild stalk-eyed flies (Teleopsis dalmanni)

description: This study provides the first direct evidence from wild populations of
 stalk-eyed flies to support the hypothesis that male eyespan is a signal
 of meiotic drive. Several stalk-eyed fly species are known to exhibit
 X-linked meiotic drive. A recent QTL analysis in Teleopsis dalmanni, found
 a potential link between variation in male eyespan, a sexually selected
 ornamental trait, and the presence of meiotic drive. This was based on
 laboratory populations subject to artificial selection for male eyespan.
 In this study we examined the association between microsatellite markers
 and levels of sex ratio bias (meiotic drive) in 12 wild T. dalmanni
 populations. We collected two data sets: a) brood sex ratios of
 wild-caught males mated to standard laboratory females, and b) variation
 in a range of phenotypic traits associated with reproductive success of
 wild- caught males and females. In each case, we typed individuals for 8
 X-linked microsatellite markers, including several that previously were
 shown to be associated with male eyespan and meiotic drive. We found that
 one microsatellite marker was very strongly associated with meiotic drive
 whilst a second showed a weaker association. We also found that, using
 both independent datasets, meiotic drive was strongly associated with male
 eyespan, with smaller eyespan males being associated with more
 female-biased broods. These results suggest that mate preference for
 exaggerated male eyespan allows females to avoid mating with males
 carrying the meiotic drive gene and is thus a potential mechanism for the
 maintenance and evolution of female mate preference.
description: Cotton et al. Wild Males
 Sex RatioCotton et al. Adult
 Data
DOI: 10.5061/dryad.55203
title: Data from: Does functional trait diversity predict aboveground biomass and productivity of tropical forests? Testing three alternative hypotheses

description: 1. Tropical forests are globally important, but it is not clear whether
 biodiversity enhances carbon storage and sequestration in them. We tested
 this relationship focusing on components of functional trait biodiversity
 as predictors. 2. Data are presented for three rain forests in Bolivia,
 Brazil and Costa Rica. Initial above-ground biomass and biomass increments
 of survivors, recruits and survivors + recruits (total) were estimated for
 trees ≥10 cm d.b.h. in 62 and 21 1.0-ha plots, respectively. We determined
 relationships of biomass increments to initial standing biomass (AGBi),
 biomass-weighted community mean values (CWM) of eight functional traits
 and four functional trait variety indices (functional richness, functional
 evenness, functional diversity and functional dispersion). 3. The forest
 continuum sampled ranged from ‘slow’ stands dominated by trees with tough
 tissues and high AGBi, to ‘fast’ stands dominated by trees with soft,
 nutrient-rich leaves, lighter woods and lower AGBi. 4. We tested whether
 AGBi and biomass increments were related to the CWM trait values of the
 dominant species in the system (the biomass ratio hypothesis), to the
 variety of functional trait values (the niche complementarity hypothesis),
 or in the case of biomass increments, simply to initial standing biomass
 (the green soup hypothesis). 5. CWMs were reasonable bivariate predictors
 of AGBi and biomass increments, with CWM specific leaf area SLA, CWM leaf
 nitrogen content, CWM force to tear the leaf, CWM maximum adult height
 Hmax and CWM wood specific gravity the most important. AGBi was also a
 reasonable predictor of the three measures of biomass increment. In
 best-fit multiple regression models, CWMHmax was the most important
 predictor of initial standing biomass AGBi. Only leaf traits were selected
 in the best models for biomass increment; CWM SLA was the most important
 predictor, with the expected positive relationship. There were no
 relationships of functional variety indices to biomass increments, and
 AGBi was the only predictor for biomass increments from recruits. 6.
 Synthesis. We found no support for the niche complementarity hypothesis
 and support for the green soup hypothesis only for biomass increments of
 recruits. We have strong support for the biomass ratio hypothesis. CWMHmax
 is a strong driver of ecosystem biomass and carbon storage and CWM SLA,
 and other CWM leaf traits are especially important for biomass increments
 and carbon sequestration.
description: Finegan et al master
 matrix 62 plotssee readme
 file.
DOI: 10.5061/dryad.47n3q
title: Data from: Heritability of flight and resting metabolic rates in the Glanville fritillary butterfly

description: Dispersal capacity is a key life history trait especially in species
 inhabiting fragmented landscapes. Evolutionary models predict that, given
 sufficient heritable variation, dispersal rate responds to natural
 selection imposed by habitat loss and fragmentation. Here, we estimate
 phenotypic variance components and heritability of flight and resting
 metabolic rates in an ecological model species, the Glanville fritillary
 butterfly, in which flight metabolic rate is known to correlate strongly
 with dispersal rate. We modeled a two-generation pedigree with the animal
 model to distinguish additive genetic variance from maternal and common
 environmental effects. The results show that flight metabolic rate is
 significantly heritable, with additive genetic variance accounting for
 about 40% of total phenotypic variance; thus flight metabolic rate has the
 potential to respond to selection on dispersal capacity. Maternal
 influences on flight metabolism were negligible. Heritability of flight
 metabolism was context-dependent, as in stressful thermal conditions
 environmentally induced variation dominated over additive genetic effects.
 There was no heritability in resting metabolic rate, which was instead
 strongly influenced by maternal effects. This study contributes to a
 mechanistic understanding of the evolution of dispersal-related traits, a
 pressing question in view of the challenges posed to many species by
 changing climate and fragmentation of natural habitats.
description: Mattila_Hanski_Heritability of flight and resting metabolic rate_dataThe file includes family and rearing information as well as metabolic rate, morphological and Pgi genotype data for individual butterflies in the first and second generation. Descriptions of data columns are specified in the title row of the data file.
DOI: 10.5061/dryad.jt052vq
title: Data from: Quantitative trait loci for cold tolerance in chickpea

description: Fall-sown chickpea (Cicer arietinum L.) yields are often double those of
 spring-sown chickpea in regions with Mediterranean climates that have mild
 winters. However, winter kill can limit the productivity of fall-sown
 chickpea. Developing cold-tolerant chickpea would allow the expansion of
 the current geographic range where chickpea is grown and also improve
 productivity. The objective of this study was to identify the quantitative
 trait loci (QTL) associated with cold tolerance in chickpea. An
 interspecific recombinant inbred line population of 129 lines derived from
 a cross between ICC 4958, a cold-sensitive desi type (C. arietinum), and
 PI 489777, a cold-tolerant wild relative (C. reticulatum Ladiz), was used
 in this study. The population was phenotyped for cold tolerance in the
 field over four field seasons (September 2011–March 2015) and under
 controlled conditions two times. The population was genotyped using
 genotyping-by-sequencing, and an interspecific genetic linkage map
 consisting of 747 single nucleotide polymorphism (SNP) markers, spanning a
 distance of 393.7 cM, was developed. Three significant QTL were found on
 linkage groups (LGs) 1B, 3, and 8. The QTL on LGs 3 and 8 were
 consistently detected in six environments with logarithm of odds score
 ranges of 5.16 to 15.11 and 5.68 to 23.96, respectively. The QTL CT Ca-3.1
 explained 7.15 to 34.6% of the phenotypic variance in all environments,
 whereas QTL CT Ca-8.1 explained 11.5 to 48.4%. The QTL-associated SNP
 markers may become useful for breeding with further fine mapping for
 increasing cold tolerance in domestic chickpea.
description: Mugabe Supplemental
 Table S1 through S8Cold tolerance of
 chickpea, phenotypic and genotypic data files, SNPs associated with QTL
 conferring cold tolerance identified in a Cicer arietinum x C.
 reticulaturm RIL population.