cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9p8cz8wk5
title: Are behavioural responses to eyespots in sticklebacks influenced by the visual environment? An experimental examination

description: Eyespots are taxonomically widespread colour patterns consisting of large
 concentric rings that are commonly assumed to protect prey by influencing
 the behaviours of predators. Although there is ample experimental evidence
 supporting an anti-predator function of eyespots in terrestrial animals,
 whether eyespots have a similar deterring function in aquatic animals
 remains unclear. Furthermore, studies in terrestrial systems suggest that
 the protective function of eyespots depends on ambient light conditions
 where predators encounter them, but this effect was never been tested in
 aquatic environments. Here, we examine how eyespots influence behavioural
 responses in an aquatic environment under different visual environments,
 using laboratory-reared three-spined sticklebacks (Gasterosteus aculeatus)
 as model predators. Specifically, we experimentally examined behavioural
 responses of sticklebacks towards artificial prey patterns (control vs
 eyespots) under two different light environment treatments (low vs high).
 We found that eyespots did not postpone attacks from sticklebacks.
 However, sticklebacks approaching eyespots stopped more frequently than
 sticklebacks approaching prey items with a control pattern. Sticklebacks
 were (marginally) slower to attack prey in the low light treatment, but
 light level did not influence stickleback behavioural responses towards
 eyespots. We conclude that that eyespots can modulate some behaviours of
 an aquatic predator, albeit with a different functional role than
 previously demonstrated in terrestrial species.
description: The dataset represents an experimental examination of how
 sticklebacks respond to eyespot and control stimuli under different light
 conditions. The experiments were performed in a controlled laboratory
 setting. The data is derived from real time observation and video
 analyses. 
description: The statistical program R is needed to run the code adn the raw
 data is visible with a program that can read spreadsheets (e.g. Microsof
 Excel).
DOI: 10.5061/dryad.cnp5hqc71
title: Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations

description: Biodiversity varies predictably with environmental energy around the
 globe, but the underlying mechanisms remain incompletely understood. The
 evolutionary speed hypothesis predicts that environmental energy shapes
 variation in speciation rates through temperature- or life
 history-dependent rates of evolution. To test whether variation in
 evolutionary speed can explain the relationship between energy and
 biodiversity in birds, mammals, amphibians, and reptiles, we simulated
 diversification over 65 million years of geological and climatic change
 with a spatially explicit eco-evolutionary simulation model. We modeled
 four distinct evolutionary scenarios in which speciation-completion rates
 were dependent on temperature (M1), life history (M2), temperature and
 life history (M3), or were independent of temperature and life-history
 (M0). To assess the agreement between simulated and empirical data, we
 performed model selection by fitting supervised machine learning models to
 multidimensional biodiversity patterns. We show that a model with
 temperature-dependent rates of speciation (M1) consistently had the
 strongest support. In contrast to statistical inferences, which showed no
 general relationships between temperature and speciation rates in
 tetrapods, we demonstrate how process-based modeling can disentangle the
 causes behind empirical biodiversity patterns. Our study highlights how
 environmental energy has played a fundamental role in the evolution of
 biodiversity over deep time.
description: These data were generated to investigate the role of temperature-
 and body size-dependent rates of speciation on global biodiversity
 patterns in tetrapods (birds, mammals, amphibians, and reptiles). Using
 large, published datasets of spatial, phylogenetic, and body size data, we
 estimated 54 metrics that summarise different kinds of biodiversity
 patterns. We used a spatially-explicit simulation model to generate
 spatial, phylogenetic, and body size data under four alternative models of
 diversification in which speciation-completion rates were dependent on
 temperature (M1), life history (M2), temperature and life history (M3), or
 were independent of temperature and life-history (M0). The simulation
 model used published paleo-reconstructions of temperature and aridity over
 the past 200 Ma as input. From the simulated spatial, phylogenetic, and
 body size data, we estimated the same set of 54 biodiversity metrics. To
 assess the agreement between simulated and empirical data, we performed
 model selection by fitting supervised machine learning models to
 multidimensional biodiversity patterns.
DOI: 10.5061/dryad.qfttdz0kn
title: Herbivory and traits of Lupinus polyphyllus

description: Glyphosate is the most widely used non-selective herbicide in the world.
 Glyphosate residues in soil can affect plant quality by modifying plant
 physiology, hormonal pathways, and traits, with potential consequences for
 plants’ interactions with herbivores. We explored these indirect effects
 in the context of plant-herbivore interactions in a perennial,
 nitrogen-fixing herb. We quantified leaf herbivory for glyphosate-exposed
 and control plants grown in phosphorus-fertilised and non-fertilised
 soils, and assessed the impacts of glyphosate treatment on traits related
 to plant resistance against herbivores (leaf trichome density, leaf mass
 per area) and performance (aboveground biomass, root:shoot ratio, nodule
 number, nodule activity). Moreover, we conducted a laboratory feeding
 experiment to compare the palatability of leaves from glyphosate-exposed
 and control plants to a generalist mollusc herbivore. Herbivore damage and
 intensity in situ increased during the growing season regardless of
 glyphosate or phosphorus treatment. Glyphosate treatment reduced leaf
 trichome density, but had no effect on the other plant traits considered.
 Herbivore damage was negatively associated with leaf trichome density. The
 feeding experiment revealed no difference in the feeding probability of
 mollusc herbivores between glyphosate-exposed and control plants. However,
 there was an interaction between glyphosate treatment and initial leaf
 area for leaf consumption by herbivores: leaf consumption increased with
 increasing leaf area in both groups, but at a lower rate for
 glyphosate-exposed plants than for control plants. Our results show that
 glyphosate residues in soil have the potential to indirectly affect
 aboveground herbivores through changes in leaf quality, which may have
 mixed consequences for folivore damage.
description: Individuals of<em>
 Lupinus polyphyllus</em> were grown from seed in a greenhouse, and
 seedlings were planted in the common garden to observe the effects of
 glyphosate residues on folivory and plant traits during June-August 2020.
 Leaf consumption between glyphosate-exposed and control plants was
 explored in a laboratory feeding experiment by using a generalist
 herbivore, the land snail (<em>Arianta arbustorum</em>,
 Helicidae).
description: Excel, Notepad
DOI: 10.5061/dryad.qfttdz0kp
title: Phenotypic plasticity and the leaf economics spectrum: plasticity is positively associated with specific leaf area

description: Phenotypic plasticity is a key mechanism by which plants respond to
 changing or heterogeneous conditions. Efforts to predict phenotypic
 plasticity across plant species have mainly focused on environmental
 variability or abiotic conditions, i.e., site characteristics. However,
 the considerable variation in phenotypic plasticity within sites calls for
 alternative approaches. Different functional groups are thought to differ
 in their plasticity levels. Further, traits such as leaf specific area
 (SLA), leaf area (LA) and maximum photosynthetic rate (Amax) reflect
 central aspects of plant strategies. Lower values of SLA, LA and Amax are
 indicative of a resource-conservative strategy, which is thought to be
 associated with lower phenotypic plasticity. We used meta-analytical data
 to test whether plant functional group (herbs, woody deciduous and woody
 evergreens) and SLA, LA and Amax are associated with phenotypic plasticity
 in four trait types: biomass allocation, plant size, leaf morphology and
 physiology. We obtained data from 168 plant species and accounted for
 phylogenetic relationships in all analyses. We found a positive
 relationship between SLA and phenotypic plasticity in biomass allocation,
 leaf morphology and physiology, with differences across functional groups.
 In contrast, there was no evidence of greater plasticity in plant size in
 species with higher SLA; rather the opposite was true for woody
 evergreens. Amax and LA showed similar, but less consistent associations
 with phenotypic plasticity. Our results show the potential of building
 predictive frameworks for phenotypic plasticity based on easily measured
 plant functional characteristics. Results also provide insights into plant
 strategies and suggest the existence of potential compromises:
 resource-conservative, low-SLA species tend to be more stress-tolerant but
 may be less able to cope with variable conditions due to their generally
 lower phenotypic plasticity. Further studies are needed to explore the
 mechanisms and the potential implications of this association.
description: We used a subsample of Stotz et al. 2021 (Ecology Letters,
 doi.org/10.1111/ele.13827) dataset. Details on the study selection
 criteria are described in Stotz et al. 2021. 
 This dataset,
 includes only those species for which the authors measured and reported
 specific leaf area (SLA), leaf area (LA) or maximum photosynthetic
 capacity (Amax), and with available information on growth form and leaf
 habit. Phenotypic plasticity of each
 trait was estimated as the absolute value of the effect size (Hedges'
 g) between the two most extreme treatments, as done in Stotz et al. 2021.
 Traits were classified into four trait types: biomass allocation, plant
 size, leaf morphology and physiology. When more than one trait per trait
 type was measured, we selected the most plastic trait (max plasticity).
 Alternatively, we also calculated average (pooled) plasticity of all
 traits within trait type.  
description: Excel.
DOI: 10.5061/dryad.9w0vt4bj8
title: Morphological evolution during the last hurrah of the trilobites: Morphometric analysis of the Devonian asteropyginid trilobites

description: The Asteropyginae Delo, 1935, is a group of phacopide trilobites in the
 family Acastidae Delo, 1935, that has served as the focus for several
 studies due to their distinctive morphologies and diversity. However,
 despite an interest in these characteristic morphologies, there have been
 very few studies that have examined this group using morphometric
 techniques. In this study, we have utilized both geometric morphometric
 and elliptical Fourier (EF) methods to quantify the morphology of cephalic
 sclerites of specimens representing a wide taxonomic sampling of the
 clade. We constructed a phylomorphospace that shows temporal and spatial
 patterns of phenotypic evolution within the framework of an updated
 tip-dated phylogenetic tree generated using Bayesian inference. Of
 particular note was the recovery of similar patterns, regardless of the
 morphometric approach. These further illustrated that there were marked
 expansions into morphospace throughout the temporal range of the clade.
 This study highlights the utility of employing different methodologies to
 quantitatively explore the disparity of fossil taxa. It also illustrates
 some of the patterns of morphologic change occurring during one of the
 final and major evolutionary radiations within Phacopida.
DOI: 10.5281/zenodo.18400838
title: Multi-Messenger B-L Scotogenic Dark Matter: Complete Analysis Package (Phases 0-22) with chi-Inflaton Validation

description:  

Complete computational framework and results for the U(1)_{B-L} extended

 

Scotogenic Dark Matter model with chi-Inflaton cosmological embedding.

 

This release includes all 22 phases of analysis.

 

 

 

NEW in v9.0.0 - Phase 22: chi-Inflaton Validation (32/32 Checks)

 

- B-L singlet chi as inflaton via non-minimal coupling (xi=10267)

 

- 2-loop RGE: 6 couplings stable to 10^16 GeV

 

- CMB: n_s=0.9667, r=0.0033 (Planck 2-sigma compatible)

 

- Leptogenesis: eta_B=6.39e-10 (4.3% precision vs Planck+BBN)

 

- Self-consistent Casas-Ibarra with lambda_5=0.1, K=367

 

- Unitarity resolved via 5 independent approaches

 

- Reheating: T_rh=5.4e10 GeV >> 15 TeV

 

- 4 validation scripts (<1s each, fully reproducible)

 

 

 

Previous phases: Theoretical framework (0-7), Phenomenology (8-13),

 

Precision MCMC (14-17), Collider projections (18-19), Public tools (20),

 

Global fit (21).
DOI: 10.5061/dryad.x69p8czmn
title: Data from: Fossilisation can mislead analyses of phenotypic disparity

description: Analyses of morphological disparity can incorporate living and fossil taxa
 to facilitate the exploration of how phenotypic variation changes through
 time. However, taphonomic processes introduce non-random patterns of data
 loss in fossil data and their impact on perceptions of disparity is
 unclear. To address this, we characterise how measures of disparity change
 when simulated and empirical data are degraded through random and
 structured data loss. We demonstrate that both types of data loss can
 distort the disparity of clades, and that the magnitude and direction of
 these changes varies between the most commonly employed distance metrics
 and disparity indices. The inclusion of extant taxa and exceptionally
 preserved fossils mitigates these distortions and clarifies the full
 extent of the data lost, most of which would otherwise go uncharacterised.
 This facilitates the use of ancestral state estimation and evolutionary
 simulations to further control for the effects of data loss. Where the
 addition of such reference taxa is not possible, we urge caution in the
 extrapolation of general patterns in disparity from datasets that
 characterise subsets of phenotype, which may represent no more than the
 traits that they sample.
description: # Data from: Fossilisation can mislead analyses of phenotypic disparity
 Thomas J. Smith, Robert S.
 Sansom, Davide Pisani & Philip C. J. Donoghue (2022) ## Description of
 the data and file structure folder:"empirical_data" Contains
 both the small (rep1) and large (complete) mammal datasets in both nexus
 and RDS formats, and the mammal tree. folder:"simulations"
 Contains tree and model used to simulate discrete character data.
 folder:"scripts" Contains all R scripts used to conduct analyses
 and plot figures. folder:"tables"
 subfolder:"simulated" Contains the summary statistics for the
 changes in disparity induced through the removal of data from the
 simulated matrix for all combinations of data loss type, proportion of
 data removed, distance metric, and disparity index.
 subfolder:"empirical" Contains the summary statistics for the
 changes in disparity induced through the removal of data from the
 empirical matrices (small and large) for all combinations of data loss
 type, proportion of data removed, distance metric, and disparity index.
 Summary statistic CSV file naming key: sim = simulated matrix small =
 small mammal matrix large = large mammal matrix all = extant + fossil
 disparity fossil = fossil disparity GED = generalised Euclidean distance
 MORD = maximum observable rescaled distance R = random data loss NR =
 non-random data loss 1-4 = proportion of data removed (1 being least, 4
 being most) Abbreviations inside summary statistic CSV files: MPD = mean
 pairwise distance MPEFD = mean pairwise extant-fossil distance MaxPD =
 maximum pairwise distance SOV = sum of variances SOR = sum of ranges DBEFC
 = distance between extant and fossil centroids
DOI: 10.5061/dryad.t4b8gtj4q
title: Thermal mixing regimes in ponds and shallow lakes

description: Lakes are classified by thermal mixing regimes, with shallow waterbodies
 historically categorized as continuously mixing systems. Yet, recent
 studies demonstrate extended summertime stratification in ponds,
 underscoring the need to reassess thermal classifications for shallow
 waterbodies. To evaluate the mixing regimes of shallow waters, we measured
 summertime thermal dynamics in 34 ponds and shallow lakes across temperate
 North America and Europe. This dataset provides a time series dataset of
 water temperatures across the water column along with characteristics of
 each study waterbody, including some physical, chemical, and biological
 parameters. This dataset accompanies a manuscript entitled
 "Classifying mixing regimes in ponds and shallow lakes,"
 published in Water Resources Research (10.1029/2022WR032522).
description: Please see details of data collection in the associated
 manuscript. DOI: 10.1029/2022WR032522
description: Files are saved as either CSV or Excel documents.
DOI: 10.5061/dryad.v15dv41zf
title: Plant invasion modifies isohydricity in Mediterranean tree species

description: Understanding of plant hydraulic strategies (i.e., the degree of
 iso-/anisohydricity) is crucial to predict the response of plants to
 changing environmental conditions such as climate-change induced extreme
 drought. Several abiotic factors, including evaporative demand, have been
 shown to seasonally modify the isohydricity of plants. However, the impact
 of biotic factors such as plant-plant interactions on hydraulic strategies
 has seldom been explored. Here, we investigated adaptations and changes in
 hydraulic strategies of two woody species in response to seasonal abiotic
 conditions, experimental drought, and plant invasion in a Mediterranean
 cork oak (Quercus suber) ecosystem with a combined shrub invasion (Cistus
 ladanifer) and rain exclusion experiment. From the dry to wet season, Q.
 suber shifted from a partial isohydric to an anisohydric behaviour while
 C. ladanifer shifted from strict anisohydric to partial isohydric. During
 drought, water competition by plant invasion significantly modified the
 hydraulic strategy of invaded Q. suber, which was accompanied by lower
 pre-dawn leaf water potentials, sap flow density, leaf area index, and
 trunk increment rates. This altered isohydricity of invaded Q. suber trees
 was most likely caused by interspecific competition for water resources by
 water spending C. ladanifer shrubs. Both species do have the highest
 proportion of fine roots in the topsoil and thus, an additional water
 consumer, such as C. ladanifer can lead to more stressful conditions for
 Q. suber during times of water scarcity. Further underlying mechanisms of
 the altered isohydricity of Q. suber, such as potential allelopathic
 effects of C. ladanifer exudates on root growth of Q. suber, have to be
 investigated in the future. In conclusion, we demonstrate that the degree
 of isohydricity of two woody Mediterranean plant species is dynamically
 determined by the interplay of species-specific hydraulic traits and their
 abiotic and biotic environment.
DOI: 10.5061/dryad.qz612jmj8
title: Global potential invasion maps of traded birds under climate and land-cover change

description: Biological invasions rank among the top five threatening factors affecting
 biodiversity, but ongoing changes in climate and land cover might
 exacerbate risks. We used species distribution models for 609 traded bird
 species on the CITES list to examine the combined effects of projected
 climate change and land-cover change worldwide on the potential range
 expansion of bird species with commercial value as pets. The maps of
 potential invasion (may be inferred as the invasion risk) have been
 provided in the main manuscript and here, the potential invasion dataset
 for the current and future times is provided including the species
 distribution maps, all as GeoTiff files. The maps for the future time are
 provided for different future years and over a range of climate scenarios
 (SSP245, SSP370, and SSP585).
description: The data are the outcomes of the species distribution models
 (SDMs), trained by using 609 species data (known to be traded from
 appendix II of CITES [Convention on International Trade in Endangered
 Species] database; available online at https://trade.cites.org) and the Worldclim climate dataset (version 2.1). The sdm R package (https://onlinelibrary.wiley.com/doi/full/10.1111/ecog.01881) was used to fit the models and generate the ensemble of predictions (for the current time) and projections (for the future times). The details are provided in the main manuscript published in Global Change Biology. The zip files contain the species distribution maps for each individual species (for the current and future times), and the individual GeoTiff files (not those that are within the zip files) are the maps based on combining all the species to generate potential invasion risk (also presented in the manuscript).
description: Any software that can handle GIS data (raster formats) can be
 used to open and explore the data (e.g., ArcGIS, QGIS, R).