cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t0k5k
title: Data from: Sixty-year legacy of human impacts on a high Arctic ecosystem

description: The high Arctic is the world's fasting warming biome, allowing access
 to sections of previously inaccessible land for resource extraction.
 Starting in 2011, exploration of one of the Earth's largest
 undeveloped coal seams was initiated in a relatively pristine, polar
 desert environment in the Canadian high Arctic. Due to the relative lack
 of historic anthropogenic disturbance, significant gaps in knowledge exist
 on how the landscape will be impacted by development. At an abandoned
 airstrip located near the area of current exploration, we used a
 disturbance case–control approach to evaluate the long-term ecological
 consequences of high Arctic infrastructure disturbance to vegetation and
 sensitive, ice-rich permafrost. We quantified: (i) long-term effects on
 vegetation diversity, soil nutrients, and abiotic ground conditions and
 (ii) the alteration of the ground surface topography and legacy of
 subsurface thermal changes. We found that in over sixty years since
 abandonment, the disturbed landscape has not recovered to initial
 conditions but instead reflects a disturbance-initiated succession towards
 a different stable-state community. Microtopography greatly influenced
 recovery patterns in the landscape. The terrain overlaying buried ice (ice
 wedge polygon troughs) was the most sensitive to disturbance and had a
 different species composition, decreased plot-level species richness,
 significant increases in vegetation cover, and a drastically reduced
 seasonal fluctuation in subsurface temperatures. In contrast, disturbed
 polygon tops showed resiliency in vegetation recovery, but still had
 remarkable increases of depth of seasonal soil thaw (active layer).
 Synthesis and applications. Our results indicate that disturbance effects
 differ depending on microtopographic features, leading to an increased
 patchiness of the landscape as found elsewhere in the Arctic. Managers who
 wish to lessen their impact on high Arctic environments should avoid areas
 of sensitive, ice-rich permafrost, constrain the geographic scale of
 near-surface ground disturbance, limit vegetation removal where possible
 and reseed disturbed areas with native species.
description: Airfield Vegetation
 Community CompositionPlot-level community
 composition data of 80 plots of vascular vegetation data from a site of
 anthropogenic disturbance on Ellesmere Island, Nunavut, Canada. Please
 refer to Becker & Pollard, 2015 for more
 information.Airfield_Community_Composition.csvAirfield Plot MetadataCorresponding metadata of plot environmental variables matching 80 plots of vascular vegetation data from a site of anthropogenic disturbance on Ellesmere Island, Nunavut, Canada. Please refer to Becker & Pollard, 2015 for more information.Airfield_Plot_Metadata.csv
DOI: 10.5061/dryad.11vs5
title: Data from: Facial attractiveness is related to women’s cortisol and body fat, but not with immune responsiveness

description: Recent studies suggest that facial attractiveness indicates immune
 responsiveness in men and that this relationship is moderated by stress
 hormones which interact with testosterone levels. However, studies testing
 whether facial attractiveness in women signals their immune responsiveness
 are lacking. Here, we photographed young Latvian women, vaccinated them
 against hepatitis B and measured the amount of specific antibodies
 produced, cortisol levels and percentage body fat. Latvian men rated the
 attractiveness of the women's faces. Interestingly, in women, immune
 responsiveness (amount of antibodies produced) did not predict facial
 attractiveness. Instead, plasma cortisol level was negatively associated
 with attractiveness, indicating that stressed women look less attractive.
 Fat percentage was curvilinearly associated with facial attractiveness,
 indicating that being too thin or too fat reduces attractiveness. Our
 study suggests that in contrast to men, facial attractiveness in women
 does not indicate immune responsiveness against hepatitis B, but is
 associated with two other aspects of long-term health and fertility:
 circulating levels of the stress hormone cortisol and percentage body fat.
description: Data about
 womenRantala
 et al.xlsx
DOI: 10.5061/dryad.hf792
title: Data from: Disentangling direct and indirect fitness effects of microbial dormancy

description: Disentangling individual selection from kin selection is one of the
 greatest challenges of evolutionary biology. Even solitary organisms that
 do not interact directly with conspecifics may interact indirectly with
 them through competition for resources. As a result, traits that appear to
 affect individual fitness alone can also modify the fitness of relatives
 nearby and thus may evolve partially through these cryptic indirect
 fitness effects. Here we develop a method to quantitatively separate
 direct and indirect fitness consequences when some microbes become
 dormant, while neighbors of the same genotype remain active. Dormant
 microbes typically survive stresses that kill metabolically active cells,
 but dormancy also has a social side effect, sparing resources that may be
 used by nondormant individuals for growth. In structured populations,
 spared resources may be preferentially consumed by nondormant clonemates,
 providing an indirect benefit. Without population structure, however,
 exploitation by a never-dormant competitor imposes an indirect fitness
 cost on dormant cells. Cryptic indirect fitness effects may play a
 significant role in the evolution of many ostensibly asocial traits.
description: DataAmNatThis datafile contains the data from the yeast experiment in which three strains of Saccharomyces cerevisiae strain Y55 were mixed together (non-labeled spores, GFP and BFP vegetative cells), then grown with limited carbon. FACS generated counts of cells (and calculated cells/mL) were reported for each sample at the beginning and end of the experiment.
DOI: 10.5061/dryad.28dj1
title: Data from: Environmental changes drive the temporal stability of semi-arid natural grasslands through altering species asynchrony

description: Stability is an important property of ecological systems, many of which
 are experiencing increasing levels of anthropogenic environmental changes.
 However, how these environmental changes influence ecosystem stability
 remains poorly understood. We conducted an 8-year field experiment in a
 semi-arid natural grassland to explore the effects of two common
 environmental changes, precipitation and nitrogen enrichment, on the
 temporal stability of plant above-ground biomass. A split-plot design,
 with precipitation as the main plot factor and nitrogen as the sub-plot
 factor, was used. Temporal stability was related to potential explanatory
 abiotic and biotic variables using regressions and structural equation
 modelling. Increase in growing season precipitation enhanced plant species
 richness and promoted temporal stability of plant above-ground biomass.
 Nitrogen fertilization, however, reduced both plant species richness and
 temporal stability of plant above-ground biomass. Contrary to
 expectations, species richness was not an important driver of stability.
 Instead, community temporal stability was mainly driven by water and
 nitrogen availability that modulated the degree of species asynchrony,
 and, to a lesser extent, by the stability of dominant plant species.
 Synthesis. Our results highlight the importance of limiting resources for
 regulating community biomass stability, and suggest that the projected
 increase in growing season precipitation may potentially offset negative
 effects of increased atmospheric nitrogen deposition on species diversity
 and community stability in semi-arid grasslands.
description: Soil and vegetation
 variables
DOI: 10.5061/dryad.428q1
title: Data from: Primary ecological succession in vascular epiphytes: the species accumulation model

description: Epiphytes are integral to tropical forests yet little is understood about
 how succession proceeds in these communities. As trees increase in size
 they create microhabitats for late-colonizing species in both small and
 large branches while maintaining small tree microhabitats for early
 colonizing species in the small and young branches. Thus, epiphyte
 succession may follow different models depending on the scale: at the
 scale of the entire tree, epiphytes may follow a species accumulation
 model where species are continuously added to the tree as trees increase
 in size but at the scale of one zone on a branch (e.g., inner crown: 0–2 m
 from the trunk), they may follow the replacement model of succession seen
 in terrestrial ecosystems. Assuming tree size as an indicator of tree age,
 I surveyed 61 Virola koschnyi trees of varying size (2.5–103.3 cm diameter
 at breast height) in lowland wet tropical forest in Costa Rica to examine
 how epiphyte communities change through succession. Epiphyte communities
 in small trees were nested subsets of those in large trees and epiphyte
 communities became more similar to the largest trees as trees increased in
 size. Furthermore, epiphyte species in small trees were replaced by mid-
 and late-successional species in the oldest parts of the tree crown but
 dispersed toward the younger branches as trees increased in size. Thus,
 epiphyte succession followed a replacement model in particular zones
 within treecrowns but a species accumulation model at the scale of the
 entire tree crown.
description: Vascular epiphyte
 community data on different-sized treesThe attached data file
 contains the abundance and species richness of vascular epiphytes on each
 of 61 Virola koschnyi trees of varying sizes at La Selva Biological
 Research Station, Costa Rica.Woods Epiphyte
 Data.xlsx
DOI: 10.5061/dryad.qj4h3
title: Data from: The effects of habitat management on the species, phylogenetic and functional diversity of bees are modified by the environmental context

description: Anthropogenic landscape elements, such as roadsides, hedgerows, field
 edges, and power line clearings, can be managed to provide important
 habitats for wild bees. However, the effects of habitat improvement
 schemes in power line clearings on components of diversity are poorly
 studied. We conducted a large-scale experiment to test the effects of
 different management practices on the species, phylogenetic, and
 functional diversity of wild bees in power line clearings (n = 19 sites
 across southeastern Norway) and explored whether any treatment effects
 were modified by the environmental context. At each site, we conducted the
 following treatments: (1) Cut: all trees cut and left to decay in the
 clearing; (2) Cut + Remove: all trees cut and removed from the plot; and
 (3) Uncut: uncleared. The site-specific environmental context (i.e.,
 elevation and floral diversity) influenced the species, phylogenetic, and
 functional diversity within bee species assemblages. The largest number of
 species was found in the Cut + Remove treatment in plots with a high forb
 species richness, indicating that the outcome of management practices
 depends on the environmental context. Clearing of treatment plots with
 many forb species also appeared to alter the phylogenetic composition of
 bee species assemblages, that is, more closely related species were found
 in the Cut and the Cut + Remove plots than in the Uncut plots. Synthesis
 and applications: Our experimental simulation of management practices in
 power line clearings influenced the species, phylogenetic, and functional
 diversity of bee species assemblages. Frequent clearing and removal of the
 woody debris at low elevations with a high forb species richness can
 increase the value of power line clearings for solitary bees. It is
 therefore important for managers to consider the environmental context
 when designing habitat improvement schemes for solitary bees.
description: Bee community data
 frameData frame including the
 abundance of solitary bees sampled within experimental treatment
 plots.Environmental
 dataData frame containing
 the site identity, treatment type, number of traps successfully emptied
 per treatment plot (sampintensity), the logarithm of the sample intensity
 (logsampintensity) used as an offset variable in the analysis, the species
 richness of forbs within treatment plots and the species richness of
 ericaceous shrubs within treatment plots.
DOI: 10.5061/dryad.nq070
title: Data from: Construction of a virtual Mycobacterium tuberculosis consensus genome and its application to data from a next generation sequencer

description: Background: Although Mycobacterium tuberculosis isolates are consisted of
 several different lineages and the epidemiology analyses are usually
 assessed relative to a particular reference genome, M. tuberculosis H37Rv,
 which might introduce some biased results. Those analyses are essentially
 based genome sequence information of M. tuberculosis and could be
 performed in sillico in theory, with whole genome sequence (WGS) data
 available in the databases and obtained by next generation sequencers
 (NGSs). As an approach to establish higher resolution methods for such
 analyses, whole genome sequences of the M. tuberculosis complexes (MTBCs)
 strains available on databases were aligned to construct virtual reference
 genome sequences called the consensus sequence (CS), and evaluated its
 feasibility in in sillico epidemiological analyses. Results: The consensus
 sequence (CS) was successfully constructed and utilized to perform
 phylogenetic analysis, evaluation of read mapping efficacy, which is
 crucial for detecting single nucleotide polymorphisms (SNPs), and various
 MTBC typing methods virtually including spoligotyping, VNTR, Long sequence
 polymorphism and Beijing typing. SNPs detected based on CS, in comparison
 with H37Rv, were utilized in concatemer-based phylogenetic analysis to
 determine their reliability relative to a phylogenetic tree based on whole
 genome alignment as the gold standard. Statistical comparison of
 phylogenic trees based on CS with that of H37Rv indicated the former
 showed always better results that that of later. SNP detection and
 concatenation with CS was advantageous because the frequency of crucial
 SNPs distinguishing among strain lineages was higher than those of H37Rv.
 The number of SNPs detected was lower with the consensus than with the
 H37Rv sequence, resulting in a significant reduction in computational
 time. Performance of each virtual typing was satisfactory and accorded
 with those published when those are available. Conclusions: These results
 indicated that virtual CS constructed from genome sequence data is an
 ideal approach as a reference for MTBC studies.
description: MTBC_SNP_align_200.phy_phyml_treeH37Rv_SNP_align_200.phy_phyml_treewhole_genome_phymlwhole_genome_BayesH37Rv_SNP_BayesMTBC_SNP_Bayes
DOI: 10.5061/dryad.8m67m
title: Data from: Landscape diversity moderates the effects of bee visitation frequency to flowers on crop production.

description: 1.Reductions in natural habitat are implicated in declining honey bee Apis
 mellifera L. and wild bee populations, thereby threatening crop
 production. This concern has stimulated interest in identifying
 landscape-level impacts on bee-mediated pollination services, but previous
 studies have only inferred connections between landscape, bees and yield
 through generalized linear regressions. 2. We examined landscape impacts
 on bee-mediated crop yield using both a traditional linear regression
 approach and conditional process modelling, which combined landscape
 features, bee visits to crop flowers, interactions between landscape and
 bee visits to flowers into a single model predicting crop yield. We used
 the pumpkin Cucurbita pepo L. system in New York State and recorded bees
 visiting pumpkin flowers in 2011 and 2012. Landscape diversity and
 percentage of semi-natural grassland around each pumpkin field were
 calculated. 3. Results from the traditional approach indicated that
 landscape diversity, percentage of grassland in the landscape, bumble bee
 Bombus impatiens Cresson, and honey bee visitation frequency each
 positively predicted yield. A common conclusion from these results is that
 pumpkins grown in highly diverse or high grassland coverage landscapes
 would have greater yields via bumble bee and honey bee visits to flowers.
 However, this inference does not preclude the possibility that landscape
 features may be associated with crop yield, independent of bee visits to
 flowers. 4. Results from conditional process modelling indicated that only
 pumpkins grown in highly diverse landscapes were predicted to have greater
 yields as a consequence of more bumble bee visits to pumpkin flowers. None
 of the landscape features predicted greater fruit yields as a consequence
 of more honey bee visits to pumpkin flowers. This novel analysis indicated
 that traditional approaches may be misinterpreting the relationships among
 these variables. 5. Synthesis and applications. Bumble bees benefited from
 a diverse landscape and their visits to flowers positively impacted
 pumpkin production. Conservation of a diverse landscape should be promoted
 to support improved pumpkin production. Growers can use this information
 to decide where to plant pumpkins to improve the potential for high
 yields, to identify scenarios where landscape diversity could be
 increased, and where supplementation with bees might be beneficial.
description: FactorsThis file contains the data associated with this manuscript on a per field basis including each factor included in the analyses presented.AllData.xlsx
DOI: 10.15468/dl.58nckt
title: Occurrence Download

description: A dataset containing 5594 records in GBIF matching the query:
SELECT
 '411' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 37.42857426825602
 AND decimalLatitude &lt;= 41.89415215079384
 AND decimalLongitude &gt;= 46.05129743524373
 AND decimalLongitude &lt;= 53.94667277126278
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 5594 records were derived from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001363-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.43kp7
title: Data from: Resemblance to the enemy's eyes underlies the intimidating effect of eyespots

description: Eyespots of some prey are known to deter predators, but the reason for
 this response has not yet been established, and thus the taxonomically
 widespread occurrence of this color pattern has remained an evolutionary
 conundrum. Two alternative hypotheses propose that (1) the eyelike
 appearance of the pattern falsely indicates the presence of the predator’s
 own enemy or (2) predators are hardwired to be cautious toward conspicuous
 prey. Earlier research has pertained mainly to eyespots in butterflies.
 Here we tested the hypothesis that eyespots resemble eyes by utilizing the
 lateral position of eyes in fishes. This allowed us to produce eyelike
 displays that did not have the round appearance of eyespots. Our study
 indicates that eye mimicry is an important factor evoking hesitation in
 predators. Moreover, we present direct evidence that this is because
 predators associate eyelike displays with the threat posed by their own
 enemies.
description: Kjernsmo & Merilaita
 2017 Raw DataKjernsmo & Merilaita
 2017.xlsx
DOI: 10.5061/dryad.1bt27
title: Data from: Always chew your food: freshwater stingrays use mastication to process tough insect prey

description: Chewing, characterized by shearing jaw motions and high-crowned molar
 teeth, is considered an evolutionary innovation that spurred dietary
 diversification and evolutionary radiation of mammals. Complex
 prey-processing behaviours have been thought to be lacking in fishes and
 other vertebrates, despite the fact that many of these animals feed on
 tough prey, like insects or even grasses. We investigated prey capture and
 processing in the insect-feeding freshwater stingray Potamotrygon motoro
 using high-speed videography. We find that Potamotrygon motoro uses
 asymmetrical motion of the jaws, effectively chewing, to dismantle insect
 prey. However, CT scanning suggests that this species has simple teeth.
 These findings suggest that in contrast to mammalian chewing, asymmetrical
 jaw action is sufficient for mastication in other vertebrates. We also
 determined that prey capture in these rays occurs through rapid uplift of
 the pectoral fins, sucking prey beneath the ray's body, thereby
 dissociating the jaws from a prey capture role. We suggest that the
 decoupling of prey capture and processing facilitated the evolution of a
 highly kinetic feeding apparatus in batoid fishes, giving these animals an
 ability to consume a wide variety of prey, including molluscs, fishes,
 aquatic insect larvae and crustaceans. We propose Potamotrygon as a model
 system for understanding evolutionary convergence of prey processing and
 chewing in vertebrates.
description: Angular
 ProtrusionAngular deviations of
 jaw protrusion during feeding in P. motoro over the course of 15 bites,
 for three different prey items.AngProt.csvSymphyseal flexionSymphyseal flexion during feeding in P. motoro over the course of 15 bites, for three different prey items.AngSym.csvCoarse Processing DataBite rate, number of bites, and prey-handling times during feeding in P. motoro for three different prey items.MotoroCoarseProcessing.csv
DOI: 10.5061/dryad.nk23d
title: Data from: Non-linear costs of reproduction in a long-lived plant

description: A trade-off between current reproduction and future performance is a key
 component of life-history theory, but the shape of this trade-off for any
 specific fitness component remains elusive. We induced 3-5 levels of
 reproductive effort (RE) by manipulating fruit set of a long-lived orchid
 in two populations that differed in the length of the growing season and
 local climate, and examined survival, size and fecundity the following
 year. Natural fruit set was 72% higher in the long-season population, but
 was not associated with a significant survival cost in any population.
 Survival decreased linearly with experimentally increased RE in the
 short-season population. In both populations, natural RE incurred growth
 and fecundity costs, and growth costs increased non-linearly with
 diminishing costs at high RE. Fecundity costs increased linearly with RE
 in the long-season population, but non-linearly with diminishing costs at
 high RE in the other. The results demonstrate that the shape of the cost
 function may be non-linear with context-dependent intercept, slope and
 curvature. They are consistent with the prediction that survival costs
 appear only when RE exceeds natural levels, while growth and fecundity
 costs are evident at natural RE. Synthesis. We suggest that studies
 inducing multiple levels of RE are required to understand life-history
 trade-offs and their context-dependence. This kind of information is
 fundamental for an understanding of the link between environmental
 heterogeneity, adaptive differentiation and life-history evolution.
description: Trait means and
 SDMean and SD of the
 fitness components survival, growth and fecundity for the 3-5 reproductive
 effort treatments in the Sølendet and Tågdalen populations of Dactylorhiza
 lapponica.Dryad_Pop_means.xlsx