cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c7ss600f
title: Data from: Genetic tradeoffs and conditional neutrality contribute to local adaptation

description: Divergent natural selection promotes local adaptation and can lead to
 reproductive isolation of populations in contrasting environments;
 however, the genetic basis of local adaptation remains largely unresolved
 in natural populations. Local adaptation might result from antagonistic
 pleiotropy, where alternate alleles are favored in distinct habitats, and
 polymorphism is maintained by selection. Alternatively, under conditional
 neutrality some alleles may be favored in one environment but neutral at
 other locations. Antagonistic pleiotropy maintains genetic variation
 across the landscape; however, there is a systematic bias against
 discovery of antagonistic pleiotropy since the fitness benefits of local
 alleles need to be significant in at least two environments. Here, we
 develop a generally applicable method to investigate polygenic local
 adaptation and identify loci that are the targets of selection. This
 approach evaluates allele frequency changes after selection at loci across
 the genome to distinguish antagonistic pleiotropy from conditional
 neutrality and deleterious variation. We investigate local adaptation at
 the QTL-level in field experiments, in which we expose 177 F6 recombinant
 inbred lines (RILs) and parental lines of Boechera stricta (Brassicaceae)
 to their parental environments over two seasons. We demonstrate polygenic
 selection for native alleles in both environments, with 2.8% of the genome
 exhibiting antagonistic pleiotropy, and 8% displaying conditional
 neutrality. Our study strongly supports antagonistic pleiotropy at one
 large-effect flowering phenology QTL (nFT): native homozygotes had
 significantly greater probabilities of flowering than foreign homozygotes
 in both parental environments. Such large-scale field studies are
 essential to elucidate the genetic basis of adaptation in natural
 populations.
description: Flowering status data
 for DryadThese are
 individual-level data on the flowering success of experimental individuals
 (Recombinant Inbred Lines and parental lines) outplanted into Colorado and
 Montana field gardens in September 2008 and 2009. In this file, site
 indicates the common garden where an individual was planted. Cohort refers
 to the year in which we assessed fitness (growing season of 2009 or 2010).
 Family identifies the Recombinant Inbred Line or Parental Line family.
 Block indicates the block into which an individual was planted in each
 garden. Flowered indicates whether an individual flowered (1) or not (0).
 We've included two columns for the genotype at the nFT QTL. The first
 includes heterozygotes, and the second excludes them. Finally %CO is the
 proportion of the genome with Colorado alleles, excluding the nFT region.
 Please see the manuscript for additional information.
DOI: 10.5061/dryad.64n81
title: Data from: Persistence with episodic range expansion from the early Pleistocene: the distribution of genetic variation in the forest tree Corymbia calophylla (Myrtaceae) in south-western Australia

description: Phylogeographic patterns of trees in topographically subdued, unglaciated
 landscapes are under-reported, and might reflect population persistence
 and the influences of environment and distance over historical
 (~2.6Mya-present) and contemporary (recent generations) time-scales. We
 examined this hypothesis using genetic analyses of four slowly evolving
 non-coding chloroplast sequences and 16 nuclear microsatellites in the
 tree Corymbia calophylla from south-western Australia that has been
 unglaciated since the Permian (.300-250Mya). We found strong population
 differentiation for chloroplast DNA and low differentiation for nuclear
 loci, consistent with higher gene flow by pollen than seed. We identified
 three divergent chloroplast lineages distributed in central, north and
 south geographic regions, and diversifying from the early (.3.028Mya),
 mid- (.0.793Mya) and late- (.0.426Mya) Pleistocene, respectively.
 Moderate-high nucleotide diversity with population-specific haplotypes
 supported long-term persistence but diversification of lineages provided
 evidence of unexpected episodic range expansion. We suggest this pattern
 reflects environmental influences of climatic oscillations during
 progressive drying of south-western Australia from the early Pleistocene.
 Significant tests for isolation by environment for nuclear loci also
 supported an influence of contemporary environmental (aridity) conditions
 on genetic structure, but isolation by distance (IBD) was greater.
 Significant chloroplast and nuclear IBD suggested distance was a major
 influence on gene flow at both time-scales.
description: Ccal_genotypes_2017Tab delimited text file of nuclear microsatellite genotypes at 16 loci of 24 individual adult trees from each of 27 populations of Corymbia calophylla (Lindl.) K.D. Hill & L.A.S. Johnson (Myrtaceae) from Western Australia. Coordinate reference system is GDA94. Missing = 0.READ_ME.txt
DOI: 10.5061/dryad.27j11
title: Data from: The optimization of fermentation conditions for producing cellulase of Bacillus amyloliquefaciens and its application to goose feed

description: The proper culture conditions for producing cellulase of Bacillus
 amyloliquefaciens S1, isolated from the cecum of goose was optimized by
 single-factor experiment combined with orthogonal test. The properties of
 the cellulase were investigated by DNS method. The appropriate doses of B.
 amyloliquefaciens S1 were obtained by adding them to goose feed. It
 indicated that the suitable culture conditions of producing cellulase were
 the culture temperature of 37°C, the initial pH of 7.0, the incubation
 time of 72 h and the loaded liquid volume of 75 ml per 250 ml. The effects
 of each factor on producing cellulase by B. amyloliquefaciens S1 were as
 follows: initial pH &gt; incubation time = culture
 temperature &gt; loaded liquid volume. The optimum reaction
 temperature and pH were 50°C and 7.0, respectively. This enzyme is a kind
 of neutral cellulase that possesses resistance to heat and acidity. It
 showed high activity to absorbent cotton, soya bean meal and filter paper.
 By adding different doses of B. amyloliquefaciens S1 to the goose feed, it
 was found that the egg production, average egg weight, fertilization rate
 and the hatching rate were promoted both in experiment 1 (1.5 g kg−1) and
 experiment 2 (3 g kg−1). Also the difference of egg production,
 fertilization rate and hatching rate between experiment 1 and control
 group was obvious (p &lt; 0.05), and the average egg weight was
 significantly increased in experiment 2 (p &lt; 0.05).
description: Manuscript
 DataEnzymatic properties,
 optimization of fermentation conditions and feeding experiment
 dataData.xlsx
DOI: 10.5061/dryad.1cf2fb0
title: Data from: New suspension-feeding radiodont suggests evolution of microplanktivory in Cambrian macronekton

description: The rapid diversification of metazoans and their organisation in
 modern-style marine ecosystems during the Cambrian profoundly transformed
 the biosphere. What initially sparked this Cambrian explosion remains
 passionately debated, but the establishment of a coupling between pelagic
 and benthic realms, a key characteristic of modern-day oceans, might
 represent a primary ecological cause. By allowing the transfer of biomass
 and energy from the euphotic zone—the locus of primary production—to the
 sea floor, this biological pump would have boosted diversification within
 the emerging metazoan-dominated benthic communities. However, little is
 known about Cambrian pelagic organisms and their trophic interactions.
 Here we describe a filter-feeding Cambrian radiodont exhibiting
 morphological characters that likely enabled the capture of
 microplankton-sized particles, including large phytoplankton. This
 description of a large free-swimming suspension-feeder potentially engaged
 in primary consumption suggests a more direct involvement of nekton in the
 establishment of an oceanic pelagic-benthic coupling in the Cambrian.
description: List of specimens
 studied.Details about the fossil
 specimens studied.01LeroseyAubril&Pates_MaterialStudied.xlsxCalculation of body length of Pahvantia hastataMeasurements and method used to calculate the maximum body lengths of the specimens of Pahvantia hastata.02LeroseyAubril&Pates_CalculationBodySizePahvantia.xlsxMatrix of characters used in the cladistic analyses.03LeroseyAubril&Pates_MatrixCladisticAnalysis.xlsxCalculation of maximum body lengths of selected radiodonts.Measurements and method used to calculate the maximum body sizes reached in selected radiodonts.04LeroseyAubril&Pates_CalculationBodySizesRadiodonts.xlsx
DOI: 10.5061/dryad.0d377r6
title: Data from: Central place foragers and moving stimuli: a hidden-state model to discriminate the processes affecting movement

description: 1. Human activities can influence the movement of organisms, either
 repelling or attracting individuals depending on whether they interfere
 with natural behavioural patterns or enhance access to food. To discern
 the processes affecting such interactions, an appropriate analytical
 approach must reflect the motivations driving behavioural decisions at
 multiple scales. 2. In this study, we developed a modelling framework for
 the analysis of foraging trips by central place foragers. By recognising
 the distinction between movement phases at a larger scale and movement
 steps at a finer scale, our model can identify periods when animals are
 actively following moving attractors in their landscape. 3. We applied the
 framework to GPS tracking data of northern fulmars Fulmarus glacialis,
 paired with contemporaneous fishing boat locations, to quantify the
 putative scavenging activity of these seabirds on discarded fish and
 offal. We estimated the rate and scale of interaction between individual
 birds and fishing boats and the interplay with other aspects of a foraging
 trip. 4. The model classified periods when birds were heading out to sea,
 returning towards the colony or following the closest boat. The
 probability of switching towards a boat declined with distance and varied
 depending on the phase of the trip. The maximum distance at which a bird
 switched towards the closest boat was estimated around 35 km, suggesting
 the use of olfactory information to locate food. Individuals spent a
 quarter of a foraging trip, on average, following fishing boats, with
 marked heterogeneity among trips and individuals. 5. Our approach can be
 used to characterise interactions between central place foragers and
 different anthropogenic or natural stimuli. The model identifies the
 processes influencing central place foraging at multiple scales, which can
 improve our understanding of the mechanisms underlying movement behaviour
 and characterise individual variation in interactions with a range of
 human activities that may attract or repel these species. Therefore, it
 can be adapted to explore the movement of other species that are subject
 to multiple dynamic drivers.
description: Fulmar tracking
 dataThe spreadsheet contains
 the fulmar tracking data used for the study, collected on Eynhallow
 (Scotland) in July 2009. The data were filtered and interpolated at a
 10-minute resolution using R, as described in the paper. The data set
 includes: the bird and trip ID numbers, the longitude and latitude
 coordinates of a bird at each time step of a trip, the corresponding date
 and time, the step length (in degrees), the bearing (measured from 0
 radians), and the closest boat's longitude, latitude and distance (in
 km) from the bird.Fulmar_trackingData.csv
DOI: 10.5061/dryad.rj10c
title: Data from: Cooperative defence operates by social modulation of biogenic amine levels in the honeybee brain

description: The defence of a society often requires that some specialized members
 coordinate to repel a threat at personal risk. This is especially true for
 honeybee guards, which defend the hive and may sacrifice their lives upon
 stinging. Central to this cooperative defensive response is the sting
 alarm pheromone, which has isoamyl acetate (IAA) as its main component.
 Although this defensive behaviour has been well described, the neural
 mechanisms triggered by IAA to coordinate stinging have long remained
 unknown. Here we show that IAA upregulates brain levels of serotonin and
 dopamine, thereby increasing the likelihood of an individual bee to attack
 and sting. Pharmacological enhancement of the levels of both amines
 induces higher defensive responsiveness, while decreasing them via
 antagonists decreases stinging. Our results thus uncover the neural
 mechanism by which an alarm pheromone recruits individuals to attack and
 repel a threat, and suggest that the alarm pheromone of honeybees acts on
 their response threshold rather than as a direct trigger.
description: Data
 coloniesRaw data supporting the
 information presented in Figure 1.Data
 individualsRaw data supporting the
 information presented in Figures 2 and 3Data
 pharmacoRaw data supporting the
 information presented in Figure 4
DOI: 10.5061/dryad.j13m3
title: Data from: Causes of discordance between allometries at and above species-level: an example with aquatic beetles

description: Covariation among organismal traits is nearly universal, occurring both
 within and among species (static and evolutionary allometry,
 respectively). If conserved developmental processes produce similarity in
 static and evolutionary allometry, then when species differ in
 development, it should be expressed in discordance between allometries.
 Here, we investigate whether rapidly evolving developmental processes
 result in discordant static and evolutionary allometries attributable to
 trade-offs in resource acquisition, allocation, or growth across 30
 species of aquatic beetles. The highly divergent sperm phenotypes of these
 beetles might be an important contributor to allometric evolution of
 testis and accessory gland mass through altered requirements for the
 production of sperm and seminal fluids. We documented extensive
 discordance between static and evolutionary allometries, indicating that
 allometric relationships are flexibly modified over short time periods but
 subject to constraint over longer time spans. Among species, sperm
 phenotype did not influence relative investment in accessory glands but
 was weakly associated with investment in testes. Furthermore, except when
 sperm were long and simple, sperm phenotype was not associated with
 species-specific modification of the allometry of testis/accessory gland
 mass and body size. Our results demonstrate the utility of allometric
 discordance to infer species differences in the provisioning and growth of
 concurrently developing traits.
description: Consensus_treeA nexus file containing the majority rule consensus tree produced from 40,000 post burn-in trees.MrBayes_inputA nexus file containing sequence alignments and MrBayes commands. Taxa names correspond to the abbreviations listed in Table2.PATHd8_inputInput file for the program PATHd8. Contains details of the fossil calibration.TableS1Tab delineated file contains raw data (testis, paragonial and body mass) used to calculate inter- and intraspecific allometric relationships.Table S2Tab delineated file contains insect family names, species names, presence and type of conjugation, sample sizes, trait means and standard errors. Missing data is coded with na. For a few species, only minimum sperm length were available (determined from sperm bundles or potentially broken sperm) and is indicated with *.TableS2Table S3Tab delineated file contains species names and accession numbers for mitochondrial DNA sequences. Also includes abbreviated names used in Nexus file.TableS3Ultrametric_treeA nexus file containing a fossil calibrated tree (see article for details) with polytomies randomly resolved in Mesquite.Read MeContains descriptions of other files in this data set.
DOI: 10.15468/dl.rrdwx9
title: Occurrence Download

description: A dataset containing 8361 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Datura stramonium",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 8361 records from 536 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000892-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tp846
title: Data from: The diet of a nocturnal pelagic predator, the Bulwer’s petrel, across the lunar cycle

description: The lunar cycle is believed to strongly influence the vertical
 distribution of many oceanic taxa, with implications for the foraging
 behaviour of nocturnal marine predators. Most studies to date testing
 lunar effects on foraging have focused on predator activity at-sea, with
 some birds and marine mammals demonstrating contrasting behavioural
 patterns, depending on the lunar-phase. However, to date no study has
 focused on how the lunar cycle might actually affect predator-prey
 interactions in the upper layers of the ocean. Here, we tested whether the
 diet of the predominantly nocturnal pelagic predator, the Bulwer’s petrel
 (Bulweria bulwerii) would change throughout the lunar cycle, using
 molecular analysis to augment detection and taxonomic resolution of prey
 collected from stomach-contents. We found no evidence of dietary shifts in
 species composition or diversity, with Bulwer’s petrel always consuming a
 wide range of mesopelagic species. Other co-variables potentially
 affecting light availability at-sea, such as percentage of cloud cover,
 did not confound our results. Moreover, many of the species found are
 thought not to reach the sea-surface. Our findings reveal that nocturnal
 predators are probably more specialized than previously assumed,
 irrespective of ambient-light, but also reveal deficiencies in our current
 understanding of species vertical distribution and predation-dynamics
 at-sea.
description: Prey occurrences in the
 diet of Bulwer´s petrelPresence/absence matrix
 of prey in the diet of Bulweria bulweriiPrey
 occurrences.csvRCodes_Influence of the
 moonRCodes testing the
 influence of the moon at different sites, years and with the interaction
 of cloud coverSpecimens identified
 morphologicallySpecimens with a
 positive morphological identificationTree file of
 cephalopodsRAxML Tree used for
 taxonomic assignment of 16SrRNA sequences of
 cephalopodsCephalopod_Tree.txtAlignment of 16SRNA cephalopod sequencesAligned 16SrRNA mitochondrial sequences of the cephalopod specimens collected in the stomach contents of Bulweria bulwerii and reference sequences
DOI: 10.15468/dl.u6a8mj
title: Occurrence Download

description: A dataset containing 380 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Coniophanes imperialis",
 "Year 1960-2026"
 ]
}

 The dataset includes 380 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000893-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3913b
title: Data from: Enhancing plant diversity in a novel grassland using seed addition

description: 1.Restoration of novel ecosystems to a historical benchmark may not always
 be possible or advisable. Novel ecosystems may be managed by targeting
 specific components and accepting the novelty of other ecosystem
 attributes. The feasibility of this component-wise management of novel
 ecosystems has rarely been tested. 2.In a novel grassland, where C3
 grasses have replaced C4 grasses, nutrients have been elevated, and
 diversity has been lost due to a history of agricultural land use, we
 aimed to return diversity using seed addition, without altering the
 dominant grass matrix or nutrient status. Using direct seeding, with and
 without soil disturbance, we assessed the ability of 10 species of native
 forbs to establish. 3.Eight of the ten seeded species established in the
 first year. Soil disturbance increased establishment success by 50%, while
 high levels of exotic cover decreased it by 24%. Establishment was
 inversely related to total plant cover at sowing, with a 10% increase in
 initial plant cover decreasing establishment by 47%. 4.By the third year,
 six of the eight species persisted and five were flowering. Survival and
 reproduction in the third year was not associated with the soil
 disturbance treatment or plant cover. 5.Synthesis and applications. We
 show that native plant species can be re-established in grasslands where
 abiotic and biotic conditions are novel relative to their reference state.
 This suggests that the conservation value of novel ecosystems can be
 enhanced using simple restoration tools that target specific ecosystem
 components.
description: covariatesabundance_Y1reprod_Y1survival_reprod_Y2survival_reprod_Y3abundance_Y3community_Y3
DOI: 10.5061/dryad.t8q7t
title: Data from: Somatic deleterious mutation rate in a woody plant: estimation from phenotypic data

description: We conducted controlled crosses in populations of the long-lived clonal
 shrub, Vaccinium angustifolium (lowbush blueberry) to estimate inbreeding
 depression and mutation parameters associated with somatic deleterious
 mutation. Inbreeding depression level was high, with many plants failing
 to set fruit after self-pollination. We also compared fruit set from
 autogamous pollinations (pollen collected from within the same
 inflorescence) to fruit set from geitonogamous pollinations (pollen
 collected from the same plant but from inflorescences separated by several
 meters of branch growth). The difference between geitonogamous versus
 autogamous fitness within single plants is referred to as "autogamy
 depression" (AD). AD can be caused by somatic deleterious mutation.
 AD was significantly different from zero for fruit set. We developed a
 maximum likelihood procedure to estimate somatic mutation parameters from
 AD, and applied it to geitonogamous and autogamous fruit set data from
 this experiment. We infer that on average, approximately three sublethal,
 partially dominant somatic mutations exist within the crowns of the plants
 studied. We conclude that somatic mutation in this woody plant results in
 an overall genomic deleterious mutation rate that exceeds that measured to
 date for annual plants. Some implications of this result for evolutionary
 biology and agriculture are discussed.
description: Data for estimation of
 inbreeding depressionData from 24 fields (12
 putative clones per field). Each clone was self- and cross-pollinated by
 hand. These treatments were conducted at the inflorescence level. At the
 time of pollination, the number of flowers per inflorescence was counted.
 Later, we returned to these clones and counted the number of fruits
 (berries) per clone. The data are proportion of flowers per inflorescence
 that set fruit (Note: if we mis-counted some flowers in the inflorescence,
 then proportion fruit set could be erroneously recorded as a value &gt; 1;
 this happened rarely).Data for estimation of
 somatic mutationProportion of flowers
 setting fruit from autonomously-pollinated inflorescences (Wa), and
 geitonogamously-pollinated inflorescences (Wg). Also included is the
 autogamy depression measure. These measurements were paired as described
 in the article. Clone number refers to a specific clone. There were
 several Wa and Wg measurements for each clone. The measure D is the
 autogamy depression measurement, calculated for each paired autogamous and
 geitonogamous inflorescence cross.Function for calculating
 the likelihoodUsed for maximum
 likelihood estimation of somatic mutation parameters.