cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.crgm63
title: Occurrence Download

description: A dataset containing 3401 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Empoasca vitis"
 ]
}

 The dataset includes 3401 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001382-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2c8m3
title: Data from: A potential case of reinforcement in a facultatively sexual unicellular eukaryote

description: The origin of a new species requires a mechanism to prevent divergent
 populations from interbreeding. In the classic allopatric model, divided
 populations evolve independently and accumulate genetic differences. If
 contact is restored, hybrids suffer reduced fitness and selection may
 favor traits that prevent mistakes in mating, a process known as
 reinforcement. This decisive but transient phase is challenging to
 document and has been reported mostly in macroorganisms. Very little is
 known about the processes through which new microbial species originate.
 In particular, it is unclear whether microbial eukaryotes, many of which
 can reproduce sexually during complex life cycles, speciate in much the
 same way as do well-studied plants and animals. Using individual cellular
 mate choice trials, we investigated the mating behavior of sympatric and
 allopatric woodland populations of the yeast Saccharomyces paradoxus. We
 find evidence consistent with reinforcement, potentially representing an
 example of microbial speciation in progress.
description: Mating
 DataThis file contains the
 results of mate choice trials in Saccharomyces paradoxus strains from
 three different populations/groups. Each mating trial contained two spores
 from one strain (the chooser strain) and one spore from another strain
 (the option strain). If the two spores from one strain mated, it was
 classified as inbreeding; if two spores from different strains mated, it
 was classified as outcrossing. The data are in columns with the following
 headers: Chooser Group; Option Group; Chooser Strain; Option Strain;
 Number of Outcrossing; Number of Inbreeding; Total
 Trials.Sp_Data_Counts.csvSpSporeViabilityThese are spore viability data for individual Saccharomyces paradoxus strains, as well as crosses between them. There are numerous columns with different identifiers (genetic group, strain, within/between population, etc.) for different analyses.GerminationTimingThis file contains data collected by monitoring the amount of time it took for spores from different Saccharomyces paradoxus strains to germinate. Each column is a different strain (headers included).
DOI: 10.15468/dl.uk2y7d
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Torreya fargesii yunnanensis"
 ]
}

 The dataset includes 37 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001383-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.84687q
title: Occurrence Download

description: A dataset containing 214 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Ziziphus jujuba spinosa",
 "Year 1975-2026"
 ]
}

 The dataset includes 214 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001381-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cs0qv
title: Data from: Many-to-many mapping of phenotype to performance: an extension of the F-matrix for studying functional complexity

description: Performance capacity influences ecology, behavior and fitness, and is
 determined by the underlying phenotype. The phenotype-performance
 relationship can influence the evolutionary trajectory of an organism.
 Several types of phenotype-performance relationships have been described,
 including one-to-one relationships between a single phenotypic trait and
 performance measure, trade-offs and facilitations between a phenotypic
 trait and multiple performance measures, and redundancies between multiple
 phenotypic traits and a single performance measure. The F-matrix is an
 intraspecific matrix of measures of statistical association between
 phenotype and performance that is used to quantify these relationships. We
 extend the F-matrix in two ways. First, we use the F-matrix to describe
 how the different phenotype-performance relationships occur simultaneously
 and interact in functional systems, a phenomenon we call many-to-many
 mapping. Second, we develop methods to compare F-matrices among species
 and compare phenotype-performance relationships at microevolutionary and
 macroevolutionary levels. We demonstrate the expanded F-matrix approach
 with a dataset of eight phrynosomatine lizard species, including six
 phenotypic traits and two measures of locomotor performance. Our results
 suggest that all types of relationships occur in this system and that
 phenotypic traits involved in trade-offs are more functionally constrained
 and tend evolve slower interspecifically than those involved in
 facilitations or one-to-one relationships.
description: Bergmann_and_McElroy_individual_dataIndividual-level dataset used in the publication.Bergmann_and_McElroy_species_dataSpecies-level data used in the publication
DOI: 10.5061/dryad.rd4j5
title: Data from: Convergent evolution as a generator of phenotypic diversity in threespine stickleback

description: Convergent evolution, in which populations produce similar phenotypes in
 response to similar selection pressure, is strong evidence for the role of
 natural selection in shaping biological diversity. In some cases, closely
 related populations can produce functionally similar but phenotypically
 divergence forms in response to selection. Functional convergence with
 morphological divergence has been observed in laboratory selection
 experiments and computer simulations, but while potentially common, is
 rarely recognized in nature. Here, we present data from the North Pacific
 threespine stickleback radiation showing that ecologically and
 functionally similar, but morphologically divergent phenotypes rapidly
 evolved when an ancestral population colonized freshwater benthic habitats
 in parallel. Additionally, we show that in this system, functional
 convergence substantially increases morphospace occupation relative to
 ancestral phenotypes, which suggests that convergent evolution may,
 paradoxically, be an important and previously underappreciated source of
 morphological diversity.
description: McGeeWainwright_ConvergenceFile contains standard length and Suction Index measurements for all fish used in the study, as well as the final Suction Index calculation. Please email the primary author for more information, or if your calculated Suction Index values do not match the values listed in the paper.
DOI: 10.5061/dryad.t2v1b
title: Data from: Drop spreading with random viscosity

description: We examine theoretically the spreading of a viscous liquid drop over a
 thin film of uniform thickness, assuming the liquid’s viscosity is
 regulated by the concentration of a solute that is carried passively by
 the spreading flow. The solute is assumed to be initially heterogeneous,
 having a spatial distribution with prescribed statistical features. To
 examine how this variability influences the drop’s motion, we investigate
 spreading in a planar geometry using lubrication theory, combining
 numerical simulations with asymptotic analysis. We assume diffusion is
 sufficient to suppress solute concentration gradients across but not along
 the film. The solute field beneath the bulk of the drop is stretched by
 the spreading flow, such that the initial solute concentration immediately
 behind the drop’s effective contact lines has a long-lived influence on
 the spreading rate. Over long periods, solute swept up from the precursor
 film accumulates in a short region behind the contact line, allowing
 patches of elevated viscosity within the precursor film to hinder
 spreading. A low-order model provides explicit predictions of the
 variances in spreading rate and drop location, which are validated against
 simulations.
description: Simulation codes for PDE
 and generalised Landau– Levich equationCodes.zip
DOI: 10.5061/dryad.43b52
title: Data from: Rapid evolution of antioxidant defense in a natural population of Daphnia magna

description: Natural populations can cope with rapid changes in stressors by relying on
 sets of physiological defense mechanisms. Little is known onto what extent
 these physiological responses reflect plasticity and/or genetic
 adaptation, evolve in the same direction and result in an increased
 defense ability. Using resurrection ecology, we studied how a natural
 Daphnia magna population adjusted its antioxidant defense to ultraviolet
 radiation (UVR) during a period with increasing incident UVR reaching the
 water surface. We demonstrate rapid evolution of the induction patterns of
 key antioxidant enzymes under UVR exposure in the laboratory. Notably,
 evolutionary changes strongly differed among enzymes and mainly involved
 the evolution of UV-induced plasticity. While D. magna evolved a strong
 plastic upregulation of glutathione peroxidase under UVR, it evolved a
 lower plastic upregulation of glutathione S-transferase and superoxide
 dismutase, and a plastic downregulation of catalase. The differentially
 evolved antioxidant strategies were collectively equally effective in
 dealing with oxidative stress since they resulted in the same high levels
 of oxidative damage (to lipids, proteins and DNA) and lowered fitness
 (intrinsic growth rate) under UVR exposure. The lack of better protection
 against UVR may suggest that the UVR exposure did not increase between
 both periods. Predator-induced evolution to migrate to lower depths that
 occurred during the same period may have contributed to the evolved
 defense strategy. Our results highlight the need for a multiple trait
 approach when focusing on the evolution of defense mechanisms.
description: Evo_antioxidant defence_
 dataData file contains all
 measurements for antioxidant enzyme activities, oxidative damage and
 life-history parameters. Data presented are averaged values for each
 measurement.
DOI: 10.5061/dryad.t72b0
title: Data from: Ecological forensics: using single point stable isotope values to infer seasonal schedules of animals after two diet switches

description: Animals adjust to seasonal challenges in physical, behavioural and spatial
 ways. Such adjustments are commonly associated with diet changes that
 often can be characterised isotopically. We introduce the ‘double diet
 switch model’, with which the occurrence and timing of two subsequent diet
 switches of an individual animal can be traced with a single sample
 assayed for stable isotopes. We demonstrate the model for Sanderling,
 Calidris alba, a small shorebird that migrates from the Nearctic tundra
 breeding grounds to the intertidal flats of the Wadden Sea; during this
 migration some birds may stage in the North Atlantic areas. The ‘double
 diet switch model’ successfully predicted the occurrence and timing of two
 diet switches in 59 Sanderlings captured in the Wadden Sea in
 July–September. Excluding birds that likely had over-summered at North
 Atlantic staging areas, the model predicted that Sanderlings departed from
 the Arctic on 13 July (range: 9–17 July), had a staging duration of 18·6
 days in the North Atlantic, and arrived in the Wadden Sea on 1 August (31
 July–1 August).The estimated mean Arctic departure dates coincided with
 the mean hatching date, suggesting that many individuals failed to produce
 young or left the care to a partner. Estimated mean arrival date matched
 the main arrival period in the Wadden Sea obtained from observation data.
 In this study we did not use lipid-free tissues, which may bias model
 predictions. After correcting for lipid components, the estimated
 departure date was 11 days later and the staging duration 8·5 days
 shorter, while arrival date was similar. The ‘double diet switch model’
 successfully identified the occurrence and timing of two subsequent diet
 switches. The ‘double diet switch model’ will not only apply to switches
 between three isotopic levels (as in the case study on Sanderling) but
 also to scenarios where the second switch reverses to the initial isotopic
 level. Due to this general applicability, the model can be adapted to a
 wide range of taxa and situations. Foreseeable applications include
 changes in habitat and food type, ontogenetic development or drastic
 phenotypic changes such as the metamorphosis in insects and amphibians.
description: d13C data of (the diet
 of) Sanderlings under three dietsd13C data of Sanderlings
 from the Arctic breeding area, d13C data of prey from the staging area and
 d13C values of prey from the Wadden Sea.Jouta_J.-Using_isotopes_to_infer_seasonal_schedules-MethEcolEvol--data_three_stages.odsd13C data of sanderlings caught in the Wadden Sead13C values of plasma and red blood cells of Sanderlings caught in the Wadden Sea.Jouta_J.-Using_isotopes_to_infer_seasonal_schedules-MethEcolEvol--raw_data_sanderings_WaddenSea.ods
DOI: 10.5061/dryad.75pr0
title: Data from: Species ecological similarity modulates the importance of colonization history for adaptive radiation

description: Adaptive radiation is an important evolutionary process, through which a
 single ancestral lineage rapidly gives rise to multiple newly formed
 lineages that specialize in different niches. In the first-arrival
 hypothesis, David Lack emphasized the importance of species colonization
 history for adaptive radiation, suggesting that the earlier arrival of a
 diversifying species would allow it to radiate to a greater extent. Here,
 we report on the first rigorous experimental test of this hypothesis,
 using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 and six
 different bacterial competitors. We show that the earlier arrival of P.
 fluorescens facilitated its diversification. Nevertheless, significant
 effects of colonization history, which led to alternative diversification
 trajectories, were observed only when the competitors shared similar niche
 and competitive fitness with P. fluorescens. These results highlight the
 important role of species colonization history, modified by their
 ecological differences, for adaptive radiation.
description: Density of SBW25
 phenotypes and competitorsIn this file, we include
 the density of six SBW25 phenotypes and competitors. Data are log10-(x+1)
 transformed.Data for Evolution
 2017.xlsx
DOI: 10.5061/dryad.t441k
title: Data from: Impacts of grazing by different large herbivores in grassland depend on plant species diversity

description: 1. It is well documented that large herbivores have pronounced effects on
 plant communities in grassland ecosystems, and the extent and course of
 their effects can largely depend on both plant and herbivore
 characteristics. Previous studies highlighted the importance of plant
 productivity in predicting the impact of herbivores on grasslands. Yet,
 there has been little consideration of how different herbivores affect
 plant communities that, in turn, differ in plant diversity. 2. In a 2-year
 grazing experiment, we tested the effects of large herbivores (cattle or
 sheep, or both together) on plant communities under high and low plant
 diversity levels in eastern Eurasian steppe. 3. We found that, for high
 plant diversity grassland, mixed grazing by cattle and sheep significantly
 increases plant diversity, but we found no effect of grazing by cattle or
 sheep alone. Grazing by cattle or sheep alone or mixed grazing by cattle
 and sheep did not significantly affect plant biomass in the high diversity
 grassland. However, for low plant diversity grassland, grazing by cattle
 alone and mixed grazing by cattle and sheep significantly increased plant
 diversity, but significantly decreased plant biomass. There was no
 significant impact on both plant diversity and biomass from sheep grazing.
 4. Synthesis and applications. We conclude that the effects of grazing in
 grassland strongly depend on herbivore assemblages and pre-grazing plant
 diversity. Herbivore grazing might contribute more to the maintenance of
 grassland structure and ecosystem functioning under high plant diversity
 compared with low plant diversity. Furthermore, our data suggest that
 multiple-species mixed grazing regimes in grassland systems with high
 plant diversity could represent the optimal protocol for grazing
 management. This study emphasizes the importance of maintaining both plant
 and herbivore diversity to optimize ecosystem functioning.
description: Vegetation data of
 Songnen grassland in ChinaInclude veagetation data
 of the original source of replicate plots and different treatments, such
 as plant species richness, Shannon-Wiener index,Pielou's index ,
 density, height, coverage, and aboveground biomass.JAPPL-2014-01146.R1 -vegetation
 data.xlsx
DOI: 10.5061/dryad.3tk33c9j
title: Data from: Early evolutionary differentiation of morphological variation in the mandible of South American caviomorph rodents (Rodentia, Caviomorpha)

description: Caviomorphs are a clade of South American rodents recorded at least since
 the early Oligocene (&gt;31.5 Ma) that exhibit ample eco-morphological
 variation. It has been proposed that phylogenetic structure is more
 important than ecological factors for understanding mandibular shape
 variation in this clade. This was interpreted as a result of the
 long-standing evolutionary history of caviomorphs and the early divergence
 of major lineages. In this work we test this hypothesis through analysis
 of morphological variation in the mandible of living and extinct species,
 and compare this information with that obtained through comparative
 phylogenetic analyses. Our results support the hypothesis of early origin
 of mandibular variation; moreover, they suggest conservation of early
 differentiated morphologies, which could indicate the existence of
 constrained evolutionary diversification.
description: RWs extant taxa
 7landmarksRelative Warp Analysis
 of aligned landmark coordinates representing alveolar region of caviomorph
 mandible. Landmark coordinates were adquired using tpsDig. Relative Warp
 Analysis was conducted using tpsRelw.RWs extant and fossil
 taxa 7landmarksRelative Warp Analysis
 of aligned landmark coordinates representing alveolar region of caviomorph
 mandible. This file contains data for extant and fossil caviomorph
 rodents. Landmark coordinates were adquired using tpsDig. Relative Warp
 Analysis was conducted using tpsRelw.habits_dummy
 variableDummy variables
 representing caviomorph rodents habits (i.e. subterranean, fossorial and
 epigean). Data were obtained from specialized
 literature.
DOI: 10.5061/dryad.k1g95
title: Data from: Comparing the responses of bryophytes and short-statured vascular plants to climate shifts and eutrophication

description: Few experimental studies have tested how abundance and diversity of
 grassland bryophytes respond to global environmental changes such as
 climate shifts and eutrophication. Because bryophytes in grasslands are
 low-statured, and because plant height is a key functional trait governing
 plant responses to resource gradients, their responses to these factors
 could resemble those of better-studied small vascular plants.
 Alternatively, traits unique to bryophytes could lead to qualitatively
 different responses than those of small vascular plants. In a semi-arid
 Californian grassland system, where bryophytes are at relatively low
 abundance and their ecology has been little studied, we compared changes
 in cover and species richness of bryophytes and short-statured vascular
 plants in response to 5 years of experimental fertilization, springtime
 watering and fertilization + watering, which produced strong gradients in
 vascular plant biomass. Supporting our hypotheses, the cover and richness
 of both bryophytes and short vascular plants were negatively related to
 total community biomass and tall vascular plant cover, and declined in
 response to the fertilization + watering treatment, in which the cover of
 tall vascular plants most strongly increased. Two divergent responses were
 also observed as follows: watering alone increased the cover of bryophytes
 but not short vascular plants, while fertilization alone reduced the cover
 of short vascular plants but not bryophytes. Bryophytes and short-statured
 vascular plants in grasslands both may be expected to decline under
 projected global changes in climate and nutrient deposition that enhance
 total community biomass and competitive pressure. However, shifts in
 either precipitation or eutrophication regimes alone may have differential
 effects on bryophytes and short vascular plants in grasslands, and
 organism-specific plant functional traits must also be considered.
description: FE_data_for_dryadExperimental treatments as factors (run 2010-2014). Bryophyte taxa (% cover/0.09m2), bryophyte richness (spp/0.09 m2), cover and richness of short and tall vascular plants (spp/m2), biomass+litter (g DW/0.0625m2) measured in 2014.
DOI: 10.5061/dryad.20qv5
title: Data from: Canopy soil greenhouse gas dynamics in response to indirect fertilization across an elevation gradient of tropical montane forests

description: Canopy soils can significantly contribute to aboveground labile biomass,
 especially in tropical montane forests. Whether they also contribute to
 the exchange of greenhouse gases is unknown. To examine the importance of
 canopy soils to tropical forest-soil greenhouse gas exchange, we
 quantified gas fluxes from canopy soil cores along an elevation gradient
 with 4 yr of nutrient addition to the forest floor. Canopy soil
 contributed 5–12 percent of combined (canopy + forest floor) soil CO2
 emissions but CH4 and N2O fluxes were low. At 2000 m, phosphorus decreased
 CO2 emissions (&gt;40%) and nitrogen slightly increased CH4 uptake and
 N2O emissions. Our results show that canopy soils may contribute
 significantly to combined soil greenhouse gas fluxes in montane regions
 with high accumulations of canopy soil. We also show that changes in
 fluxes could occur with chronic nutrient deposition.
description: Canopy soil trace gas
 flux in EcuadorExcel CSV file of canopy
 soil gas flux (CO2, CH4, N2O) measured at 3 elevations (1000 m - Bomb,
 2000 m - ECSF, 3000 m - Caja) in forests of southern Ecuador. Fluxes were
 measured in upper (U) and lower (L) canopy soils from control (C) and
 treatment (added nitrogen (N), phosphorus (P) and N+P) plots; on each date
 intact soil cores were incubated in sealed jars and then returned to the
 tree after measurement.Gas flux all elevations without
 quality.csv