cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gd8038s
title: Data from: Conserving evolutionary history does not result in greater diversity over geological timescales

description: Alternative prioritization strategies have been proposed to safeguard
 biodiversity over macro-evolutionary timescales. The first prioritizes the
 most distantly related species (maximizing phylogenetic diversity) in the
 hopes of capturing at least some lineages that will successfully diversify
 into the future. The second prioritizes lineages that are currently
 speciating, in the hopes that successful lineages will continue to
 generate species into the future. These contrasting schemes also map onto
 contrasting predictions about the role of slow diversifiers in the
 production of biodiversity over paleontological time scales. We consider
 the performance of the two schemes across ten dated species-level
 paleo-phylogenetic trees ranging from foraminifera to dinosaurs. We find
 that prioritizing phylogenetic diversity for conservation generally led to
 fewer subsequent lineages, while prioritizing diversifiers led to modestly
 more subsequent diversity, compared to random sets of lineages.
 Importantly for conservation, the tree shape when decisions are made
 cannot predict which scheme will be most successful. These patterns are
 inconsistent with the notion that long-lived lineages are the source of
 new species. While there may be sound reasons for prioritizing
 phylogenetic diversity for conservation, long-term species production
 might not be one of them.
description: Datasets S1 to S10.
 Phylogenetic datasetsPhylogenetic datasets
 used in our analyses. Each dataset is a nexus file including a tree
 distribution with 100 trees (except for planktonic
 foraminifera).Phylogenetic Datasets
 S1-S10.zip
DOI: 10.5061/dryad.41bh21r
title: Data from: Bird services and disservices to strawberry farming in Californian agricultural landscapes

description: 1.Bird conservation in agricultural settings can be controversial. While
 some bird species damage some crops, others suppress insect pests. Few
 studies have simultaneously compared bird services and disservices to
 assess their net impact. 2.Using an exclusion experiment in six California
 strawberry farms, we show that bird suppression of berry damage by insect
 pests (about 3.8% of berries) is similar in magnitude to the damage birds
 inflict on strawberries (about 3.2% of berries). 3.Across 27 farms, we
 found that bird species richness and the relative abundance of
 insectivorous birds increased, while the relative abundance of
 strawberry‐eating birds and bird damage decreased on farms with more
 semi‐natural land cover in the surrounding landscapes (1000m radius).
 4.Relative to homogeneous farms, those that implemented diversification
 practices, such as hedgerows, flower strips, or increased crop diversity,
 had greater bird species richness, total relative abundance, insectivore
 abundance, and strawberry‐eating bird abundance. 5.Synthesis and
 applications. Conserving semi‐natural land cover in the surrounding
 landscape benefits bird species richness locally and aids farmers through
 reduced abundance of strawberry‐eating birds and bird damage. These
 results highlight the need to consider both the services and disservices
 of birds when making management decisions.
description: JAPPL-2018-00005.R3_DatasetsDatasets for the bird exclosure experiment and the local and landscape factors impacting bird community variables
DOI: 10.5061/dryad.s31rc70
title: Data from: Birth-and-death evolution of the fatty acyl-CoA reductase (FAR) gene family and diversification of cuticular hydrocarbon synthesis in Drosophila

description: The birth-and-death evolutionary model proposes that some members of a
 multigene family are phylogenetically stable and persist as a single copy
 over time whereas other members are phylogenetically unstable and undergo
 frequent duplication and loss. Functional studies suggest that stable
 genes are likely to encode essential functions, while rapidly evolving
 genes reflect phenotypic differences in traits that diverge rapidly among
 species. One such class of rapidly diverging traits are insect cuticular
 hydrocarbons (CHCs), which play dual roles in chemical communications as
 short-range recognition pheromones as well as protecting the insect from
 desiccation. Insect CHCs diverge rapidly between related species leading
 to ecological adaptation and/or reproductive isolation. Because the CHC
 and essential fatty acid biosynthetic pathways share common genes, we
 hypothesized that genes involved in the synthesis of CHCs would be
 evolutionary unstable, while those involved in fatty acid-associated
 essential functions would be evolutionary stable. To test this hypothesis,
 we investigated the evolutionary history of the fatty acyl-CoA reductases
 (FARs) gene family that encodes enzymes in CHC synthesis. We compiled a
 unique dataset of 200 FAR proteins across 12 Drosophila species. We
 uncovered a broad diversity in FAR content which is generated by gene
 duplications, subsequent gene losses, and alternative splicing. We also
 show that FARs expressed in oenocytes and presumably involved in CHC
 synthesis are more unstable than FARs from other tissues. Taken together,
 our study provides empirical evidence that a comparative approach
 investigating the birth-and-death evolution of gene families can identify
 candidate genes involved in rapidly diverging traits between species.
description: amino acid alignment -
 tree figure 2Aalignment_aa.fastaOutput RAxML tree - figure 2ARAxML_tree_figure 2APhyloBayes_tree_figure 2A
DOI: 10.5061/dryad.6v2k320
title: Data from: Negative frequency-dependent foraging behaviour in a generalist herbivore (Alces alces) and its stabilizing influence on food-web dynamics

description: 1.Resource selection is widely appreciated to be context‐dependent and
 shaped by both biological and abiotic factors. However, few studies have
 empirically assessed the extent to which selective foraging behaviour is
 dynamic and varies in response to environmental conditions for
 free‐ranging animal populations. 2.Here, we assessed the extent that
 forage selection fluctuated in response to different environmental
 conditions for a free‐ranging herbivore, moose (Alces alces) in Isle
 Royale National Park, over a 10‐year period. More precisely, we assessed
 how moose selection for coniferous versus deciduous forage in winter
 varied between geographic regions and in relation to: (i) the relative
 frequency of forage types in the environment (e.g., frequency‐dependent
 foraging behaviour), (ii) moose abundance, (iii) predation rate (by gray
 wolves), and (iv) snow depth. These factors are potentially important for
 their influence on the energetics of foraging. We also built a series of
 food‐chain models to assess the influence of dynamic foraging strategies
 on the stability of food‐webs. 3.Our analysis indicates that moose
 exhibited negative frequency‐dependence, by selectively exploiting rare
 resources. Frequency‐dependent foraging was further mediated by
 density‐dependent processes, which are likely to be predation, moose
 abundance, or some combination of both. In particular,
 frequency‐dependence was weaker in years when predation risk was high
 (i.e., when the ratio of moose to wolves was relatively low). Selection
 for conifers was also slightly weaker during deep snow years. 4.The
 food‐chain analysis indicates that the type of frequency‐dependent
 foraging strategy exhibited by herbivores had important consequences for
 the stability of ecological communities. In particular, the dynamic
 foraging strategy that we observed in the empirical analysis (i.e.
 negative frequency‐dependence being mediated by density‐dependent
 processes) was associated with more stable food‐web dynamics compared to
 fixed foraging strategies. 5.The results of this study indicated that
 forage selection is a complex ecological process, varying in response to
 both biological (predation and moose density) and abiotic factors (snow
 depth) and over relatively small spatial scales (between regions). This
 study also provides a useful framework for assessing the influence of
 other aspects of foraging behavior on the stability of food‐web dynamics.
description: Data file for
 analysisThis file contains all
 of the data used in the empirical analysis of moose selection for conifer
 and balsam fir in Isle Royale National Parkisro.data.for.dryad.txt
DOI: 10.5061/dryad.5g4409r
title: Data from: Cognitive function and mood at high altitude following acclimatization and use of supplemental oxygen and adaptive servoventilation sleep treatments

description: Impairments in cognitive function, mood, and sleep quality occur following
 ascent to high altitude. Low oxygen (hypoxia) and poor sleep quality are
 both linked to impaired cognitive performance but their independent
 contributions at high altitude remain unknown. Adaptive servoventilation
 (ASV) improves sleep quality by stabilizing breathing and preventing
 central apneas without supplemental oxygen. We compared the efficacy of
 ASV and supplemental oxygen sleep treatments for improving daytime
 cognitive function and mood in high-altitude visitors (N = 18) during
 acclimatization to 3,800 m. Each night, subjects were randomly provided
 with ASV, supplemental oxygen (SpO₂ &gt; 95%), or no treatment. Each
 morning subjects completed a series of cognitive function tests and
 questionnaires to assess mood and multiple aspects of cognitive
 performance. We found that both ASV and supplemental oxygen (O2) improved
 daytime feelings of confusion (ASV: p &lt; 0.01; O₂: p &lt; 0.05)
 and fatigue (ASV: p &lt; 0.01; O₂: p &lt; 0.01) but did not
 improve other measures of cognitive performance at high altitude. However,
 performance improved on the trail making tests (TMT) A and B (p &lt;
 0.001), the balloon analog risk test (p &lt; 0.0001), and the
 psychomotor vigilance test (p &lt; 0.01) over the course of three days
 at altitude after controlling for effects of sleep treatments. Compared to
 sea level, subjects reported higher levels of confusion (p &lt; 0.01)
 and performed worse on the TMT A (p &lt; 0.05) and the emotion
 recognition test (p &lt; 0.05) on nights when they received no
 treatment at high altitude. These results suggest that stabilizing
 breathing (ASV) or increasing oxygenation (supplemental oxygen) during
 sleep can reduce feelings of fatigue and confusion but that daytime
 hypoxia may play a larger role in other cognitive impairments reported at
 high altitude. Furthermore, this study provides evidence that some aspects
 of cognition (executive control, risk inhibition, sustained attention)
 improve with acclimatization.
description: High-altitude cognition
 dataResults from cognitive
 function test battery.high_altitude_cognition_data.csv
DOI: 10.5061/dryad.8f7112b
title: Data from: Phenology in a warming world: differences between native and non-native plant species

description: Phenology is a harbinger of climate change, with many species advancing
 flowering in response to rising temperatures. However, there is tremendous
 variation among species in phenological response to warming, and any
 phenological differences between native and non‐native species may
 influence invasion outcomes under global warming. We simulated global
 warming in the field and found that non‐native species flowered earlier
 and were more phenologically plastic to temperature than natives, which
 did not accelerate flowering in response to warming. Non‐native
 species' flowering also became more synchronous with other community
 members under warming. Earlier flowering was associated with greater
 geographic spread of non‐native species, implicating phenology as a
 potential trait associated with the successful establishment of non‐native
 species across large geographic regions. Such phenological differences in
 both timing and plasticity between native and non‐natives are hypothesised
 to promote invasion success and population persistence, potentially
 benefiting non‐native over native species under climate change.
description: Phenology in a warming
 world_phenology datasetThis file contains the
 phenological data used in the manuscript.Phenology in a warming
 world_community synchronyThis file contains the
 phenological synchrony data used in the manuscript.Phenology in a warming
 world_invasion spread and timeThis file contains the
 data on geographic spread and time since invasion used in the
 manuscript.
DOI: 10.5061/dryad.nt288h1
title: Data from: Ecosystem services provided by bromeliad plants: a systematic review

description: The unprecedented loss of biological diversity has negative impacts on
 ecosystems and the associated benefits which they provide to humans.
 Bromeliads have high diversity throughout the Neotropics, but they have
 been negatively affected by habitat loss and fragmentation, climate
 change, herbivorous species invasions, and they are also being
 commercialized for ornamental use. These plants provide direct benefits to
 the human society and they also form micro ecosystems in which accumulated
 water and nutrients support the communities of aquatic and terrestrial
 species, thus maintaining local diversity. We performed a systematic
 review of the contribution of bromeliads to ecosystem services across
 their native geographical distribution. We showed that bromeliads provide
 a range of ecosystem services such as maintenance of biodiversity,
 community structure, nutrient cycling, and the availability of food and
 water. Moreover, bromeliads can regulate the spread of diseases, water and
 carbon cycling, and they have the potential to become important sources of
 chemical and pharmaceutical products. The majority of this research was
 performed in Brazil, but future research from other Neotropical countries
 with a high diversity of bromeliads would fill the current knowledge gaps,
 and increase the generality of these findings. This systematic review
 identified that future research should focus on provisioning, regulating
 and cultural services that have been currently overlooked. This would
 improve our understanding of how bromeliad diversity contributes to human
 welfare, and the negative consequences that loss of bromeliad plants can
 have on communities of other species and the healthy functioning of the
 entire ecosystems.
description: Ecosystem services
 provided by bromeliadsA systematic review of
 ecosystem services provided by bromeliad plants following the PRISMA
 (Preferred Reporting Items for Systematic Reviews and Meta-Analyses). The
 file shows the research studies and review articles published between
 January 1981 and June 2017. For each paper, the title, authors, year of
 publication, and ecosystem services are presented.Ecosystem
 services.bromeliads.xls
DOI: 10.5061/dryad.82r5q83
title: Data from: Context-dependent signaling of coincident auditory and visual events in primary visual cortex

description: Detecting rapid, coincident changes across sensory modalities is essential
 for recognition of sudden threats or events. Using two-photon calcium
 imaging in identified cell types in awake, head-fixed mice, we show that,
 among the basic features of a sound envelope, loud sound onsets are a
 dominant feature coded by the auditory cortex neurons projecting to
 primary visual cortex (V1). In V1, a small number of layer 1 interneurons
 gates this cross-modal information flow in a context-dependent manner. In
 dark conditions, auditory cortex inputs lead to suppression of the V1
 population. However, when sound input coincides with a visual stimulus,
 visual responses are boosted in V1, most strongly after loud sound onsets.
 Thus, a dynamic, asymmetric circuit connecting AC and V1 contributes to
 the encoding of visual events that are coincident with sounds.
description: A1V1DataAuditory cortex data and Matlab script for Figure 1
DOI: 10.15468/x767j5
title: Bird Collection (MHNG-AVES) of Muséum d'histoire naturelle de Genève
DOI: 10.5061/dryad.k3c78v7
title: Data from: Carbon use efficiency of mycorrhizal fungal mycelium increases during the growing season but decreases with forest age across a Pinus sylvestris chronosequence

description: 1. In boreal forest soils, mycelium of mycorrhizal fungi is pivotal for
 regulating soil carbon (C) cycling and storage. The carbon use efficiency
 (CUE), a key parameter in C cycling models, can inform on the partitioning
 of C between microbial biomass, and potential soil storage, and
 respiration. Here we test the dependency of mycorrhizal mycelial CUE on
 stand age and seasonality in managed boreal forest stands. 2. Based on
 mycelial production and respiration estimates, derived from sequentially
 incubated ingrowth mesh bags, we estimated CUE on an ecosystem-scale
 during a seasonal cycle and across a chronosequence of eight, 12- to
 158-years-old, managed Pinus sylvestris forest stands characterised by
 decreasing pH and nitrogen (N) availability with increasing age. Mycelial
 respiration was related to total soil respiration, and by using eddy
 covariance flux measurements, primary production (GPP) was estimated in
 the 12- and 100-years-old forests, and related to mycelial respiration and
 CUE. 3. As hypothesized, mycelial CUE decreased significantly with
 increasing forest age by c. 65%, supposedly related to a shift in
 mycorrhizal community composition and a metabolic adjustment to reduce
 their own biomass N demand with declining soil N availability.
 Furthermore, mycelial CUE increased by a factor of five over the growing
 season; from 0.03 in May to 0.15 in November, and we propose that the
 seasonal change in CUE is regulated by a decrease in photosynthate
 production and temperature. The respiratory contribution of mycorrhizal
 mycelium ranged from 14 to 26% of total soil respiration, and was on
 average 17% across all sites and occasions. 4. Synthesis: Carbon is
 retained more efficiently in mycorrhizal mycelium late in the growing
 season, when fungi have access to a more balanced C and nutrient supplies.
 Earlier in the growing season, at maximum host plant photosynthesis, when
 belowground C availability is high in relation to N, the fungi respire
 excess C resulting in lower mycelial CUE. Additionally, C is retained less
 efficiently in mycorrhizal fungal biomass in older forest stands
 characterized by more nutrient depleted soils than younger forest stands.
description: Mycorrhizal fungal
 mycelium - carbon use efficiencyData on respiration,
 carbon use efficiency, mycelial biomass, mycelial production, gross
 primary production and sporocarp production. Biomass estimates are based
 on amounts of ergosterol (a fungal-specific biomass marker), quantified
 using liquid chromatography. Growth estimates are derived from biomass
 estimates and mathematical models. Estimates of carbon use efficiency are
 based on growth and respiration estimates. Gross primary production
 estimates are based on eddy covariance flux
 measurements.Dryad.xlsx
DOI: 10.5281/zenodo.18317742
title: Numerical data for "Transient Dynamical Phase Diagram of the Spin–Boson Model at Finite Temperature"

description: Fit parameters for different values of s, alpha, and beta, according to Eq. (11) of the paper
DOI: 10.5281/zenodo.18317743
title: Numerical data for "Transient Dynamical Phase Diagram of the Spin–Boson Model at Finite Temperature"

description: Fit parameters for different values of s, alpha, and beta, according to Eq. (11) of the paper
DOI: 10.5061/dryad.tf7s2s5
title: Data from: Evidence of functional species sorting by rainfall and biotic interactions: A community monolith experimental approach

description: 1. Understanding the mechanisms that underlie species assembly is a
 central concern in community ecology. Abiotic and biotic filters are
 probabilistic ‘sieves’ that allow species with certain functional traits
 to become part of the community, or not. We manipulated natural plant
 assemblieses in order to identify variations in the timings of biotic and
 abiotic filters that determine community trait assemblies. 2. We extracted
 soil portions when the investigated annual plant community was in its seed
 phase (‘community monolith’), thereby maintaining the structure and
 similar soil characteristics to the field conditions. Community monoliths
 were subjected to experimental manipulation in terms of the rainfall
 timing and amount, and perturbations of the biological soil crust (BSC;
 intact vs. perturbed). We surveyed the experimental community assembly
 over time based on the functional diversity by considering important
 functional traits in different life stages. 3. We found that autumn
 droughts acted as abiotic filters by favouring the germination and
 establishment of species with greater investment in the root biomass.
 Under severe droughts (66% water reduction), the experimental assemblies
 were dominated by species with functional traits adapted to water shortage
 conditions: high leaf dry matter content, low specific leaf area, small
 individual size, low reproductive ratio, and high root:shoot ratio. We
 identified two roles of BSCs in annual plant species assemblies: 1) as a
 biotic filter that limited the establishment of species based on seed
 size, and 2) as a buffer against water stress conditions by reducing soil
 evapotranspiration. 4. Synthesis. We demonstrated the importance of the
 timing and amount of rainfall for shaping annual plant communities, and
 identified germination filters as the main process that determined
 community assemblies. Our results suggest that the phenotypic integration
 of functional traits facilitates resistance to drought during the life
 cycle. The BSC–annual plant relationship shifted from negative by acting
 as a germination filter to positive by acting as a buffer in later stages.
 Climatic fluctuations and fine scale biotic determinants of spatial
 heterogeneity emerged as sources of changes in the community assembly in
 time and space to possibly promote species coexistence and trait
 differences among the communities studied.
description: species composition,
 traits and factorsThe provided data are
 species traits values, species composition in each experiment and factors
 and treatments for each pot in both experiments. Descriptions of factors
 levels are included as coments in the head title of the colums of the
 excel file. Trait values are the mean of 10 individuals/spp colected in
 the field. Species composition, richness and abundance values have benn
 collected in the pots of the experiment.JE_Peralta et
 al..xlsx