cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.15dv41nx3
title: Limited potential for bird migration to disperse plants to cooler latitudes

description: Climate change is forcing the redistribution of life on Earth at an
 unprecedented velocity. Migratory birds are thought to help plants to
 track climate change via long-distance seed dispersal. However, seeds may
 be consistently dispersed towards cooler or warmer latitudes depending on
 whether a plant species fruiting period coincides with the northward or
 southward migrations. Here we assess the potential of plant communities to
 keep pace with climate change via long-distance seed dispersal by
 migratory birds. To do so, we combine phenological and migration
 information with data on 949 seed-dispersal interactions between 46 bird
 and 81 plant species from 13 woodland communities across Europe. While
 most plant species (86%) in these communities are dispersed by birds
 migrating south, only 35% are dispersed by birds migrating north, a subset
 phylogenetically clustered in lineages with fruiting periods that overlap
 with the spring migration. Moreover, only a few Palearctic migrant species
 provide most of this critical dispersal service northwards. The potential
 of migratory birds to assist a small non-random sample of plants to track
 climate change latitudinally is expected to strongly influence the
 formation of novel plant communities, thereby affecting their ecosystem
 functions and community assembly at higher trophic levels.
DOI: 10.5061/dryad.m0cfxpp3r
title: False and true positives in arthropod thermal adaptation candidate gene lists

description: Genome-wide studies are prone to false positives due to inherently low
 priors and statistical power. One approach to ameliorate this problem is
 to seek validation of reported candidate genes across independent studies:
 genes with  repeatedly discovered effects are less likely to be
 false positives. Inversely, genes reported only as many times as expected
 by chance alone, while possibly representing novel discoveries, are also
 more likely to be false positives. We show that, across over 30
 genome-wide studies that reported Drosophila and Daphnia genes with
 possible roles in thermal adaptation, the combined lists of candidate
 genes and orthologous groups are rapidly approaching the total number of
 genes and orthologous groups in the genome, respectively, consistent with
 the expectation of high frequency of false positives. The majority of
 these spurious candidates have been identified by one or a few studies, as
 expected by chance alone. In contrast, a noticeable minority of genes have
 been identified by numerous studies with the probabilities of such
 discoveries occurring by chance alone being exceedingly small. For this
 subset of genes, different studies are in agreement with each other
 despite differences in the ecological settings, genomic tools and
 methodology, and reporting thresholds.  We provide a reference
 set of presumed true positives among Drosophila candidate genes and
 orthologous groups involved in response to changes in temperature,
 suitable for cross-validation purposes. Despite this approach being prone
 to false negatives, this list of presumed true positives includes several
 hundred genes, consistent with the "omnigenic" concept of
 genetic architecture of complex traits.
description: Meta-analysis of literature data. Studies included used either
 transcriptomics or GWAS/local adaptation approaches.
DOI: 10.5061/dryad.kkwh70s4d
title: The role of extreme rain events in driving tree growth across a continental-scale climatic range in Australia

description: Rainfall regimes in many parts of the world have become increasingly
 dominated by fewer, but more extreme, rainfall events. Understanding how
 tree growth responds to changes in the frequency and intensity of rain
 events is critical to predicting how climate change will impact on forests
 and woodlands in the future. In this study, we used five tree-ring records
 of the native Australian conifer Callitris columellaris that span a large
 (&gt; 20 degree) latitudinal and climatic gradient from the mesic
 (tropical) north to the xeric (semi-arid) south of Australia to
 investigate how inter-annual and spatial variation in the delivery of
 rainfall (the intensity and frequency of rain events) influences tree
 growth. In semi-arid biomes (~300-400 mm rainfall annually), tree growth
 is most strongly related to the amount of rainfall from heavy (&gt;
 75th percentile) rain days or the number of extreme (&gt; 90th
 percentile) rain days, regardless of differences in the seasonal
 distribution and average intensity of rainfall among sites. Our findings
 also indicate that there is likely a minimum threshold amount of daily
 rainfall (~5 mm) that is required to stimulate tree growth in the
 semi-arid zone. In contrast, in the tropics (&gt; 800 mm annual
 rainfall), inter-annual variation in growth is best explained by total
 growing season rainfall or the number of rain days &gt; ~5 mm (~50th
 percentile of rain days) rather than extreme rainfall. Our findings
 indicate that not all rain events are important for driving tree growth,
 which has important implications for interpreting climatic signals in tree
 rings. Our findings also indicate that projected increases in the
 intensity of extreme rain events are likely to have contrasting impacts on
 tree growth across biomes, with greater and positive impacts on growth in
 semi-arid biomes and potentially negative impacts on growth in tropical
 biomes of Australia.
description: To account for potential age-related decline in ring width, we
 statistically detrended the raw ring-width measurements to remove
 age-related (non-climatic) trends and converted them to ring-width indices
 (RWI) as residuals from the detrending curve (Cook and Peters 1997).
 Ring-width series were first power-transformed to stabilise variance (Cook
 and Peters 1997) and detrended using an age-dependent spline. All series
 for all sites were detrended in a signal free environment (Melvin and
 Briffa 2008) using the RCSigFree program (http://www.ldeo.columbia.edu/tree-ring-laboratory/resources/software).
description: This dataset contains three tree-ring width chronologies from
 Western Australia. Data are stored in decadal (Tucson) format. 
 All tree rings are dated using the Schulman convention - the year
 refers to the calendar year in which growth began. For the CHR
 site (tropical northern Australia), growth begins in the Austral summer
 (~Oct-Nov). For the LTY and LDE sites (Mediterranean semi-arid southern
 Australia), growth begins in Austal Autumn (~Feb-Mar).
DOI: 10.6078/d1898w
title: Cytotype and genotype predict mortality and recruitment in Colorado quaking aspen (Populus tremuloides)

description: Species responses to climate change depend on environment, genetics, and
 interactions among these factors. Intraspecific cytotype (ploidy level)
 variation is a common type of genetic variation in many species. However,
 the importance of intraspecific cytotype variation in determining
 demography across environments is poorly known. We studied the tree
 species quaking aspen (Populus tremuloides), which occurs in diploid and
 triploid cytotypes. This widespread species is experiencing contractions
 in its western range, which could potentially be linked to
 cytotype-dependent drought tolerance. We found that interactions between
 cytotype and environment drive mortality and recruitment across 503 plots
 in Colorado. Triploids were more vulnerable to mortality relative to
 diploids and had reduced recruitment on more drought-prone and disturbed
 plots relative to diploids. Furthermore, there was substantial
 genotype-dependent variation in demography. Thus, cytotype and genotype
 variation are associated with decline in this foundation species. Future
 assessment of demographic responses under climate change will require
 knowledge of how genetic and environmental mosaics interact to determine
 species’ ecophysiology and demography.
DOI: 10.5061/dryad.sn02v6x3z
title: Hematoma expansion shift analysis to assess acute intracerebral hemorrhage treatments

description: Objective: Hematoma expansion (HE) is commonly analyzed as a dichotomous
 outcome in intracerebral hemorrhage (ICH) trials.  In this
 proof-of-concept study, we propose a “HE shift” analysis model as a method
 to improve the evaluation of candidate ICH therapies. Methods: Using data
 from the Antihypertensive Treatment of Acute Cerebral Hemorrhage II
 (ATACH-2) trial, we performed HE shift analysis in response to intensive
 blood pressure lowering by generating polychotomous strata based on a)
 previously established HE definitions, b) percentile/absolute quartiles of
 hematoma volume change, and c) quartiles of 24-hour follow-up hematoma
 volumes. The relationship between blood pressure treatment and HE shift
 was explored using proportional odds models. Results: The primary analysis
 population included 863 patients. In both treatment groups, approximately
 one-third of patients exhibited no HE. Using a trichotomous HE
 stratification, the highest strata of ≥33% revealed a 5.8% reduction in
 hematoma growth for those randomized to intensive therapy (aOR: 0.77 [95%
 CI: 0.60-0.99]). Using percentile quartiles of hematoma volume change, we
 observed a favorable shift to reduce growth in patients treated with
 intensive therapy: aOR: 0.73 (0.57-0.93). Similarly, in a tetrachotomous
 analysis of 24-hour follow-up hematoma volumes, shifts in the highest
 stratum (&gt; 21.9 mL) was most notable. Conclusions: Our findings
 suggest that intensive blood pressure reduction may preferentially
 mitigate growth in patients at risk of high volume HE. A shift analysis
 model of HE provides additional insights into the biological effects of a
 given therapy and may be an additional way to assess hemostatic agents in
 future studies. Registration: ClinicalTrials.gov Identifier: NCT01176565
DOI: 10.5061/dryad.3bk3j9kjs
title: The δ13C series of different components from Masson pine

description: This study addresses the effects of climatic drivers on the tree ring
 width parameters (total ring width, earlywood width, and latewood width)
 and the total ring δ13C series of different wood components (whole wood,
 α-cellulose, and holocelluose) from Masson pine in subtropical China.
 Pairwise correlation is significant between three ring width parameters.
 Earlywood and latewood width did not reveal much stronger climatic
 sensitivity rather than total ring width. This indicates that the use of
 intra-annual ring width have little benefit in extracting more climate
 information. The mean δ13C series of the three components of the total
 ring had the strongest climatic response to the July–September relative
 humidity (r= -0.792 (whole wood, WW), -0.758 (holocellulose, HC) and
 -0.769 (α-cellulose, AC)). Through both stationary temporal and
 spatial-statistical perspectives, the moisture drivers (summer/autumn) had
 a significant impact on three ring width parameters and three components
 of Masson pine. Overall, the tree ring width parameters and the δ13C
 series showed a different response pattern to the same climate drivers
 during the same period. Moreover, the R-squared values of the strongest
 climate-proxy correlation coefficients are smaller than 50% for tree ring
 width. The δ13C series may be a more representative climate proxy than
 tree-ring width parameters for the dendroclimatology in subtropical China.
DOI: 10.5061/dryad.d2547d82n
title: Comparison of SIRS criteria and qSOFA score for identifying culture-positive sepsis in the emergency department: A prospective cross-sectional multicenter study

description: OBJECTIVE: To compare the daily practice of two Emergency Departments (ED)
 in the Netherlands, where SIRS criteria and qSOFA score are used
 differently as screening tool for culture-positive sepsis. DESIGN: A
 prospective cross-sectional multicenter study. SETTING: Two EDs at two
 European clinical teaching hospitals in the Netherlands. PARTICIPANTS: 760
 patients with suspected infection who meet SIRS criteria or have a
 qualifying qSOFA score who were treated at two EDs in the Netherlands from
 1st January 2018 until 1st March 2018 were included. METHODS: SIRS
 criteria and qSOFA score were calculated for each patient. The first
 hospital treated patients who met SIRS criteria following the worldwide
 Surviving Sepsis Campaign protocol. At the second hospital, only patients
 who met the qualifying qSOFA score received this treatment. Therefore,
 patients could be divided into five groups (1: SIRS+, qSOFA-, not treated
 according protocol (reference group); 2: SIRS+, qSOFA-, treated according
 protocol; 3: SIRS+, qSOFA+, treated according protocol; 4: SIRS-, qSOFA+,
 not treated according protocol; 5: SIRS-, qSOFA+, treated according
 protocol). PRIMARY AND SECONDARY OUTCOME MEASURES: To prove
 culture-positive sepsis was present, cultures were used as the primary
 outcome. Secondary outcomes were in-hospital mortality and ICU admission.
 RESULTS: 98.9% met SIRS criteria and 11.7% met qSOFA score. Positive
 predictive values of SIRS criteria and qSOFA score were 41.2% [95%CI
 37.4%-45.2%] and 48.1% [95%CI 37.4%-58.9%], respectively. Hazard ratios
 (HR) were 0.79 [95%CI 0.40-1.56, p=0.500], 3.42 [95%CI 1.82-6.44,
 p&lt;0.001], 18.94 [95%CI 2.48-144.89, p=0.005] and 4.97 [95%CI
 1.44-17.16, p=0.011] for groups two to five, respectively. CONCLUSION:
 qSOFA score performed as well as SIRS criteria for identifying
 culture-positive sepsis and performed significantly better for predicting
 in-hospital mortality and ICU admission. This study showed that SIRS
 criteria are no longer necessary and recommends qSOFA score as the
 standard for identifying culture-positive sepsis in the ED.
DOI: 10.5061/dryad.qrfj6q5fn
title: Plant history and soil history jointly influence the selection environment for plant species in a long‐term grassland biodiversity experiment

description: Long-term biodiversity experiments have shown increasing strengths of
 biodiversity effects on plant productivity over time. However, little is
 known about rapid evolutionary processes in response to plant community
 diversity, which could contribute to explaining the strengthening positive
 relationship. To address this issue, we performed a transplant experiment
 with offspring of seeds collected from four grass species in a 14-year old
 biodiversity experiment (Jena Experiment). We used two- and six-species
 communities and removed the vegetation of the study plots to exclude
 plant-plant interactions. In a reciprocal design, we transplanted five
 “home” phytometers (same origin and actual environment), five “away-same”
 phytometers (same species richness of origin and actual environment, but
 different plant composition), and five “away-different” phytometers
 (different species richness of origin and actual environment) of the same
 species in the study plots. In the establishment year, plants transplanted
 in home soil produced more shoots than plants in away soil indicating that
 plant populations at low and high diversity developed differently over
 time depending on their associated soil community and/or conditions. In
 the second year, offspring of individuals selected at high diversity
 generally had a higher performance (biomass production and fitness) than
 offspring of individuals selected at low diversity, regardless of the
 transplant environment. This suggests that plants at low and high
 diversity showed rapid evolutionary responses measurable in their
 phenotype. Our findings provide first empirical evidence that loss of
 productivity at low diversity is not only caused by changes in abiotic and
 biotic conditions but also that plants respond to this by a change in
 their micro-evolution. Thus, we conclude that eco-evolutionary feedbacks
 of plants at low and high diversity are critical to fully understand why
 the positive influence of diversity on plant productivity is strengthening
 through time.
description: <strong>Data_performance, functional traits,
 infestation</strong> This file contains
 measures of performance (shoot number, biomass production,
 inflorescences), leaf functional traits and leaf infestation of
 phytometers transplanted in low- and high-diversity communities of a
 grassland biodiversity experiment (Jena Experiment). All abbreviations of
 variable names are explained in the data file.
 <strong>Data_survival Poa
 trivialis</strong> This file contains measures of
 survival of <em>Poa trivialis</em> phytometers transplanted in
 low- and high-diversity communities of a grassland biodiversity experiment
 (Jena Experiment). All abbreviations of variable names are explained in
 the data file.
DOI: 10.5061/dryad.kwh70rz3m
title: Many ways to make darker flies: Intra- and inter-specific variation in Drosophila body pigmentation components

description: Body pigmentation is an evolutionarily diversified and ecologically
 relevant trait with substantial variation within and between species, and
 important roles in animal survival and reproduction. Insect pigmentation,
 in particular, provides some of the most compelling examples of adaptive
 evolution, including its ecological significance and genetic bases.
 Pigmentation includes multiple aspects of color and color pattern that may
 vary more or less independently, and can be under different selective
 pressures. We decompose Drosophila thorax and abdominal pigmentation, a
 valuable eco-evo-devo model, into distinct measurable traits related to
 color and color pattern. We investigate intra- and inter-specific
 variation for those traits, and assess its different sources. For each
 body part, we measured overall darkness, as well as four other
 pigmentation properties distinguishing between background color and color
 of the darker pattern elements that decorate each body part. By focusing
 on two standard D. melanogaster laboratory populations, we show that
 pigmentation components vary and co-vary in distinct manners depending on
 sex, genetic background, and temperature during development. Studying
 three natural populations of D. melanogaster along a latitudinal cline and
 five other Drosophila species, we then show that evolution of lighter or
 darker bodies can be achieved by changing distinct component traits. Our
 results paint a much more complex picture of body pigmentation variation
 than previous studies could uncover, including patterns of sexual
 dimorphism, thermal plasticity, and inter-specific diversity. These
 findings underscore the value of detailed quantitative phenotyping and
 analysis of different sources of variation for a better understanding of
 phenotypic variation and diversification, and the ecological pressures and
 genetic mechanisms underlying them.
DOI: 10.5061/dryad.hhmgqnkgj
title: Comparison of size-structured and species-level trophic networks reveals antagonistic effects of temperature on vertical trophic diversity at the population and species level

description: It is predicted that warmer conditions should lead to a loss of trophic
 levels, as larger bodied consumers, which occupy higher trophic levels,
 experience higher metabolic costs at high temperature. Yet, it is unclear
 whether this prediction is consistent with the effect of warming on the
 trophic structure of natural systems. Furthermore, effects of temperature
 at the species level, which arise through a change in species composition,
 may differ from those at the population level, which arise through a
 change in population structure. We investigate this by building
 species-level trophic networks, and size-structured trophic networks, as a
 proxy for population structure, for 18,648 stream fish communities, from
 4,145,234 individual fish samples, across 7,024 stream locations in France
 from 1980 to 2008. We estimated effects of temperature on total trophic
 diversity (total number of nodes), vertical trophic diversity (mean and
 maximum trophic level), and distribution of biomass across trophic level
 (correlation between trophic level and biomass) in these networks. We
 found a positive effect of temperature on total trophic diversity in both
 species- and size-structured trophic networks. We found that maximum
 trophic level and biomass distribution decreased in species-level and
 size-structured trophic networks, but the mean trophic level decreased
 only in size-structured trophic networks. These results show that warmer
 temperatures associate with a lower vertical trophic diversity in
 size-structured networks, and a higher one in species-level networks. This
 suggests that vertical trophic diversity is shaped by antagonistic effects
 of temperature on population structure and on species composition. Our
 results hence demonstrate that effects of temperature do not only differ
 across trophic levels, but also across levels of biological organisation,
 from population to species level, implying complex changes in network
 structure and functioning with warming.
description: This dataset contains 4,145,234 individual fish samples (e.g.
 body length), from 50 species of fish, across 7,024 stream locations in
 France from 1980 to 2008. This data was collected by ONEMA via electric
 fishing.  In addition, we built species-level trophic networks, and
 size-structured trophic networks, as a proxy for population structure, for
 18,648 stream fish communities, based on body-size dependent prey-predator
 interactions and specific information regarding the diet of fish extracted
 from the literature. All scripts and data set necessary to build the
 networks are provided.
description: It should be noted that the scripts were not intended initially
 for use by a third party and that adjustments may be necessary, such as
 changing the root directory at the beginning of the scripts.
 More information in the README.txt file.
DOI: 10.5061/dryad.3bk3j9kjt
title: Implications of overfishing of frugivorous fishes for cryptic function loss in a Neotropical floodplain

description: Many frugivorous animals act simultaneously as seed predators and
 dispersers, and shifts in the abundance and mean phenotype of the
 frugivore population can alter the prevalence of antagonistic vs
 mutualistic interactions with seeds. Here, we evaluated how a reduction in
 the abundance and species richness of large-bodied frugivorous fishes
 affects their interactions with plants in a Neotropical floodplain.
 Fisheries selectively harvest large frugivorous fishes, which are the most
 effective seed dispersers. Thus, functional extinctions of fish mutualists
 can cascade to secondary extinctions of plants and their biotic
 associates, and ecosystem-level change. We evaluated functional responses
 of wetland communities to changes in fish body size by modeling the
 robustness of plant-frugivore networks to different extinction scenarios,
 using fish body size as a functional trait influencing seed dispersal and
 seed predation. We built ecological networks for frugivory, seed dispersal
 and seed predation. All networks lacked modularity and showed reduced
 nestedness compared with randomized networks. The three networks indicated
 that frugivorous fish have wide niches and low to intermediate degree of
 specialization. Network robustness to extinction of frugivorous fish
 decreased with selective loss of large individuals. Synthesis and
 applications. We predict that reductions in the abundance of large-bodied
 fish species will enhance the dominance of plant species with small seeds
 and decrease plant diversity. The functionally most important species in
 our networks are the most susceptible to overfishing. Therefore,
 sustainable management in these ecosystems needs to contribute to
 protecting interactions and, consequently, ecological, and evolutionary
 processes related to maintaining biodiversity in vast wetland forests.