cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8289
title: Data from: Characterization of an intergenic polymorphic site (pp-hC1A_5) in Wolbachia pipientis (wPip)

description: Wolbachia pipientis (w Pip) is an intracellular bacterium causing
 cytoplasmic incompatibility in arthropods including mosquitoes of the
 Culex pipiens complex. Here we present a method useful for genotyping
 within the w Pip group. Primers were designed using a Tandem Repeat Finder
 program to amplify an intergenic, polymorphic site (pp-hC1A_5) of w Pip.
 The polymorphic site is located between genes that code for polynucleotide
 phosphorylase and a hypothetical protein (C1A_5). Comparison of these w
 Pip genomic regions from C. pipiens mosquitoes sampled in different
 geographic regions revealed deletions of fragments that proved useful in
 phyologenetic analysis.
description: Sept2010alignWolbachia pipientis (wPip) sequence alignment of the intergenic region (pp-hC1A_5). The (pp-hC1A_5) region is flanked by a polynucleotide phosphorylase and a hypothetical protein (C1A_5) gene. wPip strains found in C. pipiens complex species were sampled in seven worldwide distributed geographic locations. Single nucleotide differences are marked in gray. Wolbachia pipientis strain source: wPip_mpAR, Argentina; wPip_mpAU, Australia; wPip_mpGR, Greece; wPip_mpIT, Italy; wPip_mpJP, Japan; wPip_mpUS, U.S.A.; wPip_Sang, Sanger Institute.
DOI: 10.5061/dryad.46kk44r
title: Data from: Characterization of cytoplasmic viscosity of hundreds of single tumor cells based on micropipette aspiration

description: Background: Cytoplasmic viscosity (μc) is a key biomechanical parameter
 for evaluating the status of cellular cytoskeletons. Previous studies
 focused on white blood cells, but the data of cytoplasmic viscosity for
 tumor cells were missing. Methodology: Tumor cells (H1299, A549 and
 drug-treated H1299 with compromised cytoskeletons) were aspirated
 continuously through a micropipette at a pressure of -10 kPa or -5 kPa
 where aspiration lengths as a function of time were obtained and
 translated to cytoplasmic viscosity based on a theoretical Newtonian fluid
 model. Quartile coefficients of dispersion were quantified to evaluate the
 distributions of cytoplasmic viscosity within the same cell type while
 neural network based pattern recognitions were used to classify different
 cell types based on cytoplasmic viscosity. Results: The single-cell
 cytoplasmic viscosity with three quartiles and the quartile coefficient of
 dispersion were quantified as 16.7 Pa•S, 42.1 Pa•S, 110.3 Pa•S and 74% for
 H1299 cells at -10 kPa (ncell=652), 144.8 Pa•S, 489.8 Pa•S, 1390.7 Pa•S,
 and 81% for A549 cells at -10 kPa (ncell=785), 7.1 Pa•S, 13.7 Pa•S, 31.5
 Pa•S, and 63% for CD-treated H1299 cells at -10 kPa (ncell=651) and 16.9
 Pa•S, 48.2 Pa•S, 150.2 Pa•S, and 80% for H1299 cells at -5 kPa
 (ncell=600), respectively. Neural network based pattern recognition
 produced successful classification rates of 76.7% for H1299 vs. A549,
 67.0% for H1299 vs. drug-treated H1299 and 50.3% for H1299 at -5 kPa and
 -10 kPa. Conclusion: Variations of cytoplasmic viscosity were observed
 within the same cell type and among different cell types, suggesting the
 potential role of cytoplasmic viscosity in cell status evaluation and cell
 type classification.
description: Cytoplasmic viscosity of
 individual tumor cellsThe file is an Excel
 composed of four sheets, with names of H1299-10 kpa, A549-10 kpa,
 H1299-10kpa-CD and H1299-5 kpa, respectively. In each sheet, there are
 three columns, which are No. Cell, Cell Diameter and Viscosity,
 respectively.data in summary
 20181012.xlsx
DOI: 10.5061/dryad.733tn
title: Data from: Parasites driving host diversity: incidence of disease correlated with Daphnia clonal turnover

description: According to the Red Queen hypothesis, clonal diversity in asexual
 populations could be maintained by negative frequency-dependant selection
 by co-evolving parasites. If common clones are selected against and rare
 clones gain a concomitant advantage, we expect that clonal turnover should
 be faster during parasite epidemics than between them. We tested this
 hypothesis exploring field data of the Daphnia – Caullerya host-parasite
 system. The clonal make-up and turnover of the Daphnia host population was
 tracked with high temporal resolution from 1998 until 2013, using first
 allozyme markers and later microsatellite markers. Significant differences
 in the clonal composition between random and infected sub-samples of
 Daphnia populations were detected on six of seven tested occasions,
 confirming genetic specificity of the host-parasite interaction in this
 system. We used time series analysis to compare the rates of host clonal
 turnover to the incidence of parasitism, and found that Caullerya
 prevalence was significantly associated with microsatellite-based clonal
 turnover. As alternate hypotheses, we further tested whether turnover was
 related to a variety of biotic, abiotic, and host demographic parameters.
 Other significant correlates of turnover were cyanobacterial biomass and
 (weakly) temperature. Overall, parasitism seems to be a strong driver of
 host clonal turnover, in support of the Red Queen hypothesis.
description: Time series data from
 GreifenseeContains all time series
 data files used in the analysis. These are: algae biomass;Daphnia species
 and MLG composition, inferred with both microsatellites and allozymes;
 caullerya abundance; Daphnia demographic parameters; oxygen profiles; and
 temperature profiles.inputs.tar.gz
DOI: 10.5061/dryad.hq8k8
title: Data from: Importance of boreal rivers in providing iron to marine waters

description: This study reports increasing iron concentrations in rivers draining into
 the Baltic Sea. Given the decisive role of iron to the structure and
 biogeochemical function of aquatic ecosystems, this trend is likely one
 with far reaching consequences to the receiving system. What those
 consequences may be depends on the fate of the iron in estuarine mixing.
 We here assess the stability of riverine iron by mixing water from seven
 boreal rivers with artificial sea salts. The results show a gradual loss
 of iron from suspension with increasing salinity. However, the capacity of
 the different river waters to maintain iron in suspension varied greatly,
 i.e. between 1 and 54% of iron was in suspension at a salinity of 30. The
 variability was best explained by iron:organic carbon ratios in the
 riverine waters – the lower the ratio the more iron remained in
 suspension. Water with an initially low iron:organic carbon ratio could
 keep even higher than ambient concentrations of Fe in suspension across
 the salinity gradient, as shown in experiments with iron amendments.
 Moreover, there was a positive relationship between the molecular size of
 the riverine organic matter and the amount of iron in suspension. In all,
 the results point towards a remarkably high transport capacity of iron
 from boreal rivers, suggesting that increasing concentrations of iron in
 river mouths may result in higher concentrations of potentially
 bioavailable iron in the marine system.
description: Data underlying the
 conclusions made in the paperMonitoring and
 experimental data.Archive for PLOS
 ONE.xlsx
DOI: 10.5061/dryad.1c2j6
title: Data from: Intoxicated copepods: ingesting toxic phytoplankton leads to risky behaviour

description: Understanding interactions between harmful algal bloom (HAB) species and
 their grazers is essential for determining mechanisms of bloom
 proliferation and termination. We exposed the common calanoid copepod,
 Temora longicornis to the harmful algal bloom species Alexandrium
 fundyense and examined effects on copepod survival, ingestion, egg
 production and swimming behaviour. A. fundyense was readily ingested by T.
 longicornis and significantly altered copepod swimming behaviour without
 affecting copepod survival or fitness. A. fundyense caused T. longicornis
 to increase their swimming speed and the straightness of their path long
 after the copepods had been removed from the A. fundyense treatment.
 Models suggest that these changes could lead to a 25-56% increase in
 encounter frequency between copepods and their predators. This work
 highlights the need to determine how ingesting HAB species alters grazer
 behaviour as this can have significant impacts on the fate of HAB toxins
 in marine systems.
description: copepod
 kinematicsTemora longicornis
 swimming speed and net:gross displacement ratio affected by Alexandrium
 fundyense and Rhodomonas lenscopepod
 survivalTemora longicornis
 survivorship when exposed to Alexandrium fundyense and Rhodomonas
 lensingestion
 rateTemora longicornis
 ingestion of Alexandrium fundyense and Rhodomonas lensegg
 productionThe effects of
 Alexandrium fundyense (a harmful algal bloom species) on copepod egg
 productionegg hatching
 successThe effect of
 Alexandrium fundyense (harmful algal bloom species) on copepod egg
 hatching success
DOI: 10.5061/dryad.5t2k7
title: Data from: Cumulative early life adversity predicts longevity in wild baboons

description: In humans and other animals, harsh circumstances in early life predict
 morbidity and mortality in adulthood. Multiple adverse conditions are
 thought to be especially toxic, but this hypothesis has rarely been tested
 in a prospective, longitudinal framework, especially in long-lived
 mammals. Here we use prospective data on 196 wild female baboons to show
 that cumulative early adversity predicts natural adult lifespan. Females
 who experience ≥3 sources of early adversity die a median of 10 years
 earlier than females who experience ≤1 adverse circumstances (median
 lifespan is 18.5 years). Females who experience the most adversity are
 also socially isolated in adulthood, suggesting that social processes
 partially explain the link between early adversity and adult survival. Our
 results provide powerful evidence for the developmental origins of health
 and disease and indicate that close ties between early adversity and
 survival arise even in the absence of health habit and health care-related
 explanations.
description: Tung et al data for
 survival analysesThis file contains data
 to test for the effects of early adversity on adult
 survival.Tung_etal_survival_dryad.xlsxTung et al data for analyses of social connectednessThis file contains data to test the effects of early adversity on social connectedness in adulthood.Tung_etal_SocConnectedness.xlsx
DOI: 10.15468/dl.vn4wvu
title: Occurrence Download

description: A dataset containing 266 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Carex remotiuscula"
 ]
}

 The dataset includes 266 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000773-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7tr51
title: Data from: Genetic diversity of the endemic Canary Island pine tree, Pinus canariensis (Ph.D. thesis)

description: The Canary Island pine, Pinus canariensis, is an endemic tree that forms
 one of the main forest ecosystems within the archipelago, and whose
 distribution has been reduced in the last five centuries by clear cutting
 for the extraction of timber and tar. It was in the XXth century that
 exploitation declined and reforestation programs were brought forward for
 the restoration of an ecosystem that harbours a number of endangered
 endemic species of plants and animals. In addition to reforestation
 efforts, an understanding of population genetic processes is also
 necessary for the successful conservation management of the Canarian pine
 forest, particularly in light of gathering evidence for local adaptation.
 In this thesis historical and contemporary gene flow within P. canariensis
 was studied with nuclear and chloroplast microsatellite markers. High
 immigration rates (0.68–0.75) were estimated as expected for an
 outcrossing wind-pollinated tree. Nevertheless, significant population
 differentiation (FST=0.019, RST=0.044) was detectable for sites separated
 by only a few kilometres. Within the context of reforestation programs the
 high levels of gene flow detected would appear to have a positive effect,
 by facilitating the immigration of local alleles from natural stands into
 potentially genetically depauperate first generation gene pools of
 reforested stands. Historical population growth was revealed with
 chloroplast microsatellites for most populations of P. canariensis.
 Population expansions for the pine parasite weevil Brachyderes rugatus
 were also detected, broadly coinciding with the population expansions
 within the Canary Island pine forests. Given the estimated times of
 expansion, these population demographic increases would seem likely
 related to the process of colonisation of newly emerged islands or local
 patches after volcanic disturbance. Detection and dating of these
 expansions from chloroplast microsatellites was, to some degree,
 negatively affected by homoplasy (i.e. parallel and back mutations).
 Coalescent simulations of the evolution of chloroplast microsatellites
 were applied to study the effects of homoplasy in the statistical analysis
 of population structuring. Measures of genetic diversity based on number
 of haplotypes and measures based on genetic distances were differently
 affected. Genetic distances were underestimated but were proportional to
 the actual value. These effects help to explain the lower performance of
 statistical analyses for the detection and dating of population
 expansions. Further research on the effects of homoplasy in the analysis
 of population differentiation using chloroplast microsatellites is
 essential.
description: Navascues.PhD.DATANuclear and chloroplast microsatellite data
DOI: 10.5061/dryad.1hg55vm
title: Data from: Field metabolic rates of teleost fishes are recorded in otolith carbonate

description: Field metabolic rate (FMR) is key to understanding individual and
 population-level responses to environmental changes, but is challenging to
 measure in field conditions, particularly in aquatic environments. Here we
 show that FMR can be estimated directly from the isotopic composition of
 carbon in fish otoliths (δ13Coto). We describe the relationship between
 δ13Coto values and oxygen consumption rate, and report results from
 laboratory experiments relating individual-level measurements of oxygen
 consumption rates to δ13Coto values in Atlantic cod (Gadus morhua). We
 apply our new δ13Coto metabolic proxy to existing δ13Coto data from wild
 cod and four deepwater fish species to test the validity of inferred FMR
 estimates. The δ13Coto metabolic proxy offers a new approach to study
 physiological ecology in free-ranging wild fishes. Otolith-based proxies
 for FMR are particularly promising as they allow retrospective assessment
 of time-integrated, individual-level FMR throughout an individual fish’s
 life history.
description: Supplementary Data
 1Otolith d13C derived
 field metabolic rate in four different data sets used in this study,
 including (1) a rearing experiment of Atlantic cod; (2) 76 species from
 literature; (3) wild Atlantic cod from literature; (4) four deep-sea fish
 from literature.
DOI: 10.6084/m9.figshare.31146724
title: Raw data for Tabu-Enhanced Simulated Bifurcation

description: Tests of Tabu-Enhanced Simulated Bifurcation on Ising problems<br>
DOI: 10.6084/m9.figshare.31146724.v1
title: Raw data for Tabu-Enhanced Simulated Bifurcation

description: Tests of Tabu-Enhanced Simulated Bifurcation on Ising problems<br>
DOI: 10.6084/m9.figshare.31146724.v2
title: Raw data for Tabu-Enhanced Simulated Bifurcation

description: Tests of Tabu-Enhanced Simulated Bifurcation on Ising problems<br>
DOI: 10.5061/dryad.45bf4
title: Data from: Division of labor as a bipartite network

description: Bipartite ecological networks are increasingly used to described and model
 relationships between interacting species (e.g. plant-pollinator or host
 parasite). Here, we apply network methods developed in community ecology
 to quantify division of labor in insect societies. We consider two
 quantitative indices (H2' and d') derived from information
 theory that inform on how much the actual patterns of task performance
 deviates from the null expectation that workers perform tasks randomly. In
 addition, we computed network modularity to identify clusters of
 specialized individuals that are preferentially engaged in the completion
 of subset of available tasks. We analyzed both simple synthetic networks,
 varying in size and degree of specialization, and published datasets to
 introduce the metrics and to show that a bipartite approach provides
 useful insights into task allocation. Considering division of labor as a
 bipartite network offers a conceptual framework that could substantially
 increase our understanding of division of labor in animal societies.
description: Division of labor as a
 bipartite networkThis file comprises
 published datasets and simulated data to explore the relationship between
 the different metrics used to quantify specialization and division of
 labor.Data_bipartite_dryad.xlsx
DOI: 10.5061/dryad.55cc1
title: Data from: Maternal loading of a small heat shock protein increases embryo thermal tolerance in Drosophila melanogaster

description: Maternal investment is likely to have direct effects on offspring
 survival. In oviparous animals whose embryos are exposed to the external
 environment, maternal provisioning of molecular factors like mRNAs and
 proteins may help embryos cope with sudden changes in the environment.
 Here we sought to modify the maternal mRNA contribution to offspring
 embryos and test for maternal effects on acute thermal tolerance in early
 embryos of Drosophila melanogaster. We drove in vivo overexpression of a
 small heat shock protein gene (Hsp23) in female ovaries and measured the
 effects of acute thermal stress on offspring embryonic survival and larval
 development. We report that overexpression of the Hsp23 gene in female
 ovaries produced offspring embryos with increased thermal tolerance. We
 also found that brief heat stress in the early embryonic stage (0 to 1
 hour-old) caused decreased larval performance later in life (5 to 10
 days-old), as indexed by pupation height. Maternal overexpression of Hsp23
 protected embryos against this heat-induced defect in larval performance.
 Our data demonstrate that transient products of single genes have large
 and lasting effects on whole-organism environmental tolerance. Further,
 our results suggest that maternal effects have a profound impact on
 offspring survival in the context of thermal variability.
description: Thermal phenotypic data
 and qPCR dataData are organized into
 separate sheets in the .xlsx file. Use the tabs to access each subset of
 the data.Lockwood_2017_JEB_data.xlsx
DOI: 10.5061/dryad.f1c5j
title: Data from: Complex consequences of herbivory and interplant cues in three annual plants

description: Information exchange (or signaling) between plants following herbivore
 damage has recently been shown to affect plant responses to herbivory in
 relatively simple natural systems. In a large, manipulative field study
 using three annual plant species (Achyrachaena mollis, Lupinus nanus, and
 Sinapis arvensis), we tested whether experimental damage to a neighboring
 conspecific affected a plant's lifetime fitness and interactions with
 herbivores. By manipulating relatedness between plants, we assessed
 whether genetic relatedness of neighboring individuals influenced the
 outcome of having a damaged neighbor. Additionally, in laboratory feeding
 assays, we assessed whether damage to a neighboring plant specifically
 affected palatability to a generalist herbivore and, for S. arvensis, a
 specialist herbivore. Our study suggested a high level of contingency in
 the outcomes of plant signaling. For example, in the field, damaging a
 neighbor resulted in greater herbivory to A. mollis, but only when the
 damaged neighbor was a close relative. Similarly, in laboratory trials,
 the palatability of S. arvensis to a generalist herbivore increased after
 the plant was exposed to a damaged neighbor, while palatability to a
 specialist herbivore decreased. Across all species, damage to a neighbor
 resulted in decreased lifetime fitness, but only if neighbors were closely
 related. These results suggest that the outcomes of plant signaling within
 multi-species neighborhoods may be far more context-specific than has been
 previously shown. In particular, our study shows that herbivore
 interactions and signaling between plants are contingent on the genetic
 relationship between neighboring plants. Many factors affect the outcomes
 of plant signaling, and studies that clarify these factors will be
 necessary in order to assess the role of plant information exchange about
 herbivory in natural systems.
description: Complex consequences of
 herbivory and interplant cues in three annual plantsAn excel file with
 comments on columns. The data file has information pertaining to damage,
 biomass and seedset of plants in the field as well as the results of
 palatability trials to potted plants.dryad_archive.xlsx
DOI: 10.5061/dryad.4k739
title: Data from: Reduced fitness of Atlantic salmon released in the wild after one generation of captive-breeding

description: Salmonids rank among the most socio-economically valuable fishes and the
 most targeted species by stocking with hatchery-reared individuals. Here,
 we used molecular parentage analysis to assess the reproductive success of
 wild- and hatchery- born Atlantic salmon over three consecutive years in a
 small river in Québec. Yearly restocking in this river follows a single
 generation of captive breeding. Among the adults returning to the river to
 spawn, between 11% and 41% each year were born in hatchery. Their relative
 reproductive success (RRS) was nearly half that of wild-born fish (0.55).
 RRS varied with life stage, being 0.71 for fish released at the fry stage
 and 0.42 for fish released as smolt. The lower reproductive success of
 salmon released as smolt was partly mediated by modification of the
 proportion of single-sea-winter/multi-sea-winter fish. Overall, our
 results suggest that modifications in survival and growth rates alter the
 life-history strategies of these fish at the cost of their reproductive
 success. Our results underline the potential fitness decrease, warn on
 long-term evolutionary consequences for the population of repeated
 stocking and support the adoption of more natural rearing conditions for
 captive juveniles and their release at a younger stage, such as unfed fry.
description: MILOTEVA2012DATAGenotypes at 8 microsatellite loci (coded by three digits) of adults and juveniles Salmo salar sampled in the Malbaie River from 2002 to 2005 and and at the local hatchery (order explained in the first line of the file).