cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.16b00
title: Data from: Morphological, ecological and genetic aspects associated with endemism in the Fly Orchid group

description: The European genus Ophrys (Orchidaceae) is famous for its insect-like
 floral morphology, an adaptation for a pseudocopulatory pollination
 strategy involving Hymenoptera males. A large number of endemic Ophrys
 species have recently been described, especially within the Mediterranean
 Basin, which is one of the major species diversity hotspots. Subtle
 morphological variation and specific pollinator dependence are the two
 main perceptible criteria for describing numerous endemic taxa. However,
 the degree to which endemics differ genetically remains a challenging
 question. Additionally, knowledge regarding the factors underlying the
 emergence of such endemic entities is limited. To achieve new insights
 regarding speciation processes in Ophrys, we have investigated species
 boundaries in the Fly Orchid group (Ophrys insectifera sensu lato) by
 examining morphological, ecological and genetic evidence. Classically,
 authors have recognized one widespread taxon (O. insectifera) and two
 endemics (O. aymoninii from France and O. subinsectifera from Spain). Our
 research has identified clear morphological and ecological factors
 segregating among these taxa; however, genetic differences were more
 ambiguous. Insights from cpDNA sequencing and amplified fragment length
 polymorphisms genotyping indicated a recent diversification in the three
 extant Fly Orchid species, which may have been further obscured by active
 migration and admixture across the European continent. Our genetic results
 still indicate weak but noticeable phylogeographic clustering that
 partially correlates with the described species. Particularly, we report
 several isolated haplotypes and genetic clusters in central and
 southeastern Europe. With regard to the morphological, ecological and
 genetic aspects, we discuss the endemism status within the Fly Orchid
 group from evolutionary, taxonomical and conservation perspectives.
description: Final DNA sequence
 assembledAFLP
 matrixMorphological
 dataEcological
 data
DOI: 10.5061/dryad.23p42
title: Data from: The effect of colour-producing mechanisms on plumage sexual dichromatism in passerines and parrots

description: Sexual dichromatism (SD) often reflects intense sexual selection on males.
 It has been hypothesized that sexual selection should favour the
 elaboration of those male colours that honestly signal quality and that
 such colours should therefore show higher SD. Costliness of colours is
 expected to vary according to their production mechanism (pigment type,
 feather microstructure and combinations thereof). Carotenoid-based
 colours, due to their dietary origin and competing functions of carotenoid
 pigments, are the best documented costly colours, while endogenous
 pigments and structural colours are expected to be less costly. However,
 how SD varies with colour-producing mechanism has not been systematically
 addressed. Here, we test the link between SD and mechanisms of colour
 production across nearly all Australian passerines (n = 302) and parrots
 (n = 48), using reflectance spectrometry and visual models. We quantified
 SD [chromatic (hue and saturation) and achromatic (light to dark)] for
 individual plumage patches as well as for the whole plumage. We then
 compared whether these SD estimates vary for plumage produced by different
 mechanisms of colour production. Not unexpectedly, individual plumage
 patches were most sexually dichromatic when males and females have
 different mechanisms of colour production. In most cases however, both
 sexes share the same mechanism. Among these, red carotenoid-based plumage
 in passerines showed the highest SD, while in passerines as well as in
 parrots, melanin-based plumage and white plumage have the lowest levels of
 SD. Average SD within species is weakly predicted by the proportion of the
 plumage produced by different mechanisms. This effect is strongest for red
 carotenoids, but equally so for males and females. In contrast, effects of
 structural and pheomelanin-based colours are different between sexes,
 highlighting the links between high SD and the evolution of different
 mechanisms of colour production in males and females. While our analysis
 showed that colours based on red carotenoids have higher levels of SD, the
 differences were small, and most mechanisms of colour production were able
 to produce a similar range of SD. These results do not support the
 hypothesis that sexual selection should preferentially lead to the
 elaboration of some types of colours over others.
description: Plumage patch level
 sexual dichromatismPlumage patch level
 sexual dichromatism data on Australian passerines and
 parrots.patch.level.sexual.dichromatism.csvSpecies level sexual dichromatismSpecies-level sexual dichromatism for Australian passerines and parrots.species.level.sexual.dichromatism.csv
DOI: 10.5061/dryad.m1j968g3
title: Data from: Selection and microevolution of coat pattern are cryptic in a wild population of sheep

description: Understanding the maintenance of genetic variation in natural populations
 is a core aim of evolutionary genetics. Insight can be gained by
 quantifying selection at the level of the genotype, as opposed to the
 phenotype. Here, we show that in a natural population of Soay sheep which
 is polymorphic for coat pattern, recessive genetic variants at the causal
 gene, agouti signalling protein (ASIP), are associated with reduced
 lifetime fitness. This was due primarily to a reduction in juvenile
 survival of uniformly coloured (self-type) sheep, which are homozygous
 recessive, and occurs despite significantly higher reproductive success in
 surviving self-type adults. Consistent with their relatively low fitness,
 we show that the frequency of self-type individuals has declined from 1985
 to 2008. Remarkably though, the frequency of the underlying self-allele
 has increased, because the frequency of heterozygous individuals (who
 harbour the majority of all self alleles) has increased. Indeed, the ratio
 of observed:expected heterozygous individuals has increased during the
 study, such that there is now a significant excess of heterozygotyes. By
 employing gene-dropping simulations, we show that microevolutionary trends
 in the frequency and excess of ASIP heterozygotes are too pronounced to be
 caused by genetic drift. Studying this polymorphism at the level of
 phenotype rather than underlying genotype would have failed to detect
 cryptic fitness differences. We would also have been unable to rule out
 genetic drift as an evolutionary force driving genetic change. This
 highlights the importance of resolving the underlying genetic basis of
 phenotypic variation in explaining evolutionary dynamics.
description: Gratten_etal_Dryad
DOI: 10.5061/dryad.5nq06fj
title: Data from: Assessing feeding preferences of a consumer guild: partitioning variation among versus within species

description: Interspecific variation in resource use is critical to understanding
 species diversity, coexistence, and ecosystem functioning. A growing body
 of research describes analogous intraspecific variation and its potential
 importance for population dynamics and community outcomes. However, the
 magnitude of intraspecific variation relative to interspecific variation
 in key dimensions of consumer-resource interactions remains unknown, and
 is critical for understanding the importance of this variation for
 population and community processes. In this study, we examine feeding
 preference through repeated laboratory choice feeding assays of 444
 wild-caught individuals of eight invertebrate grazer species on rocky
 reefs in northern California, USA. Between-species variation accounted for
 25-33% of the total variation in preference for the preferred resource,
 while between-individual variation accounted for 4-5% of total variation.
 For two of the eight species, between-individual variation was
 significantly different from zero and contributed on-average 14% and 17%
 of the total diet variation, even after accounting for differences due to
 size and sex. Therefore, even with clearly distinguishable between-species
 differences in mean preference, diet variation between and within
 individuals can contribute to the dietary niche width of species and
 guilds, which may be overlooked by focusing solely on species' mean
 resource use patterns.
description: OK Rhoades Am Nat
 dataData from choice
 preference laboratory experiment with eight species of mobile invertebrate
 herbivores.
DOI: 10.5061/dryad.0m801b4
title: Data from: Life in the cystic fibrosis upper respiratory tract influences competitive ability of the opportunistic pathogen Pseudomonas aeruginosa

description: Understanding characteristic differences between host-associated and
 free-living opportunistic pathogens can provide insight into the
 fundamental requirements for success after dispersal to the host
 environment, and more generally into the ecological and evolutionary
 processes by which populations respond to simultaneous selection on
 complex interacting traits. We examined how cystic fibrosis (CF)
 associated and environmental isolates of the opportunistic pathogen
 Pseudomonas aeruginosa differ in the production of an ecologically
 important class of proteinaceous toxins known as bacteriocins, and how
 overall competitive ability depends on the production of and resistance to
 these bacteriocins. We determined bacteriocin gene content in a diverse
 collection of environmental and CF isolates and measured
 bacteriocin-mediated inhibition, resistance, and the outcome of
 competition in a shared environment between all possible pairs of these
 isolates at 25 °C and 37 °C. Although CF isolates encoded significantly
 more bacteriocin genes, our phenotypic assays suggest that they have
 diminished bacteriocin-mediated killing and resistance capabilities
 relative to environmental isolates, regardless of incubation temperature.
 Notably, however, although bacteriocin killing and resistance profiles
 significantly predicted head to head competitive outcomes, CF and
 environmental isolates did not differ significantly in their competitive
 ability. This suggests that the contribution of bacteriocins to
 competitive ability involves selection on other traits that may be
 pleiotropically linked to interference competition mediated by
 bacteriocins.
description: pyocin inhibition
 dataread me file for
 cross-streak dataPyocin haplotype
 dataSAS model for pyocin
 inhibitionSAS code used to analyze
 pyocin inhibition dataSAS model for
 competition by EOISAS code used to analyze
 outcome of cross-streak data by environment of
 isolationSAS model for
 competition by inhibitionSAS code used to analyze
 outcome of cross-streak data by pyocin inhibition
DOI: 10.5061/dryad.ph826
title: Data from: Why have multiple plastic responses? Interactions between color change and heat avoidance behavior in Battus philenor larvae

description: Having multiple plastic responses to a change in the environment, such as
 increased temperature, can be adaptive for two major reasons: synergy (the
 plastic responses perform better when expressed simultaneously) or
 complementarity (each plastic response provides a greater net benefit in a
 different environmental context). We investigated these hypotheses for two
 forms of temperature-induced plasticity of Battus philenor caterpillars in
 southern Arizona populations: color change (from black to red at high
 temperatures) and heat avoidance behavior (movement from host to elevated
 refuges at high host temperatures). Field assays using aluminum models
 showed that the cooling effect of the red color is greatly reduced in a
 refuge position relative to that on a host. Field assays with live
 caterpillars demonstrated that refuge seeking is much more important for
 survival under hot conditions than coloration; however, in those assays,
 red coloration reduced the need to seek refuges. Our results support the
 complementarity hypothesis: refuge seeking facilitates survival during
 daily temperature peaks, while color change reduces the need to leave the
 host over longer warm periods. We propose that combinations of rapid but
 costly short-term behavioral responses and slow but efficient long-term
 morphological responses may be common when coping with temperature change.
description: Caterpillar
 ModelsData from experiment
 using aluminum operative temperature models of
 caterpillarscaterpillarModels.csvSpectra of models and caterpillarsReflectance spectra of painted aluminum models and live caterpillarsmodelCaterpillarSpectra.csvEffect of behavior and color on survivalData from experiment on the effects of behavior and color on survival using live caterpillarsbehaviorColorSurvival.csvCalibration of models with caterpillarsData for comparison of temperatures of different colored caterpillars with the corresponding aluminum models.modelCalibration.csvEffect of color on behaviorData from field experiment on the effect of color on refuge-seeking behavior using live caterpillarsbehaviorColor.csv
DOI: 10.15468/dl.tjfbab
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Mollusca Collection (MHNG-MOLL) of Muséum d'histoire naturelle de Genève",
 "OccurrenceStatus is Present",
 "TaxonKey is Hyriidae"
 ]
}

 The dataset includes 87 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000506-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sm5h0
title: Data from: Metabolites of n-Butylparaben and iso-Butylparaben exhibit estrogenic properties in MCF-7 and T47D human breast cancer cell lines

description: Two oxidized metabolites of n-butylparaben (BuP) and iso-butylparaben
 (IsoBuP) discovered in human urine samples exhibit structural similarity
 to endogenous estrogens. We hypothesized that these metabolites bind to
 the human estrogen receptor (ER) and promote estrogen signaling. We tested
 this using models of ER-mediated cellular proliferation. The estrogenic
 properties of 3-hydroxy n-butyl 4-hydroxybenzoate (3OH) and 2-hydroxy
 iso-butyl 4-hydroxybenzoate (2OH) were determined using the ER-positive,
 estrogen-dependent human breast cancer cell lines MCF-7, and T47D. The 3OH
 metabolite induced cellular proliferation with EC50 of 8.2 µM in MCF-7
 cells. The EC50 for 3OH in T47D cells could not be reached. The 2OH
 metabolite induced proliferation with EC50 of 2.2 µM and 43.0 µM in MCF-7
 and T47D cells, respectively. The EC50 for the parental IsoBuP and BuP was
 0.30 and 1.2 µM in MCF-7 cells, respectively. The expression of a
 pro-proliferative, estrogen-inducible gene (GREB1) was induced by these
 compounds and blocked by co-administration of an ER antagonist (ICI 182,
 780), confirming the ER-dependence of these effects. The metabolites
 promoted significant ER-dependent transcriptional activity of an
 ERE-luciferase reporter construct at 10 and 20 µM for 2OH and 10 µM for
 3OH. Computational docking studies showed that the paraben compounds
 exhibited the potential for favorable ligand-binding domain interactions
 with human ERα in a manner similar to known x-ray crystal structures of
 17ß-estradiol in complex with ERα. We conclude that the hydroxylated
 metabolites of BuP and IsoBuP are weak estrogens and should be considered
 as additional components of potential endocrine disrupting effects upon
 paraben exposure.
description: Supplemental Data for
 Paraben Metabolite Characterization 2.22.18Cell culture methods,
 proliferation assay data for dose response curves, and 2D interaction
 diagramsGonzalez_Supplemental_2.22.18.docx
DOI: 10.15468/dl.eub4w5
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Holmesina paulacoutoi"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000505-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k0v67
title: Data from: What is long-distance dispersal? and a taxonomy of dispersal events

description: Dispersal is a key individual-based process influencing many life-history
 attributes and scaling up to population-level properties (e.g.
 metapopulation connectivity). A persistent challenge in dispersal ecology
 has been the robust characterization of dispersal functions (kernels), a
 fundamental tool to predict how dispersal processes respond under global
 change scenarios. Particularly, the rightmost tail of these functions,
 that is the long-distance dispersal (LDD) events, are difficult to
 characterize empirically and to model in realistic ways. But, when is it a
 LDD event? In the specific case of plants, dispersal has three basic
 components: (i) a distinct (sessile) source, the maternal plant producing
 the fruits or the paternal tree acting as a source of pollen; (ii) a
 distance component between source and target locations; and (iii) a vector
 actually performing the movement entailing the dispersal event. Here, I
 discuss operative definitions of LDD based on their intrinsic properties:
 (i) events crossing geographic boundaries among stands; and (ii) events
 contributing to effective gene flow and propagule migration. Strict-sense
 long-distance dispersal involves movement both outside the stand
 geographic limits and outside the genetic neighbourhood area of
 individuals. Combinations of propagule movements within/outside these two
 spatial reference frames result in four distinct modes of LDD. Synthesis.
 I expect truncation of seed dispersal kernels to have multiple
 consequences on demography and genetics, following to the loss of key
 dispersal services in natural populations. Irrespective of neighbourhood
 sizes, loss of LDD events may result in more structured and less cohesive
 genetic pools, with increased isolation by distance extending over broader
 areas. Proper characterization of the LDD events helps to assess, for
 example, how the ongoing defaunation of large-bodied frugivores
 pervasively entails the loss of crucial LDD functions.
description: SupplMat-What is
 long-distance dispersal?Species and study site
 for the case study presented, sampling seeds methods, and lab method for
 genotyping trees and seeds. Summary table on genetic neighborhood
 sizes.SupplMat.pdf
DOI: 10.5061/dryad.rv109
title: Data from: Social effects on foraging behaviour and success depend on local environmental conditions

description: In social groups, individuals' dominance rank, social bonds, and
 kinship with other group members have been shown to influence their
 foraging behavior. However, there is growing evidence that the particular
 effects of these social traits may also depend on local environmental
 conditions. We investigated this by comparing the foraging behavior of
 wild chacma baboons, Papio ursinus, under natural conditions and in a
 field experiment where food was spatially clumped. Data were collected
 from 55 animals across two troops over a 5-month period, including over
 900 agonistic foraging interactions and over 600 food patch visits in each
 condition. In both conditions, low-ranked individuals received more
 agonism, but this only translated into reduced foraging performances for
 low-ranked individuals in the high-competition experimental conditions.
 Our results suggest one possible reason for this pattern may be low-ranked
 individuals strategically investing social effort to negotiate foraging
 tolerance, but the rank-offsetting effect of this investment being
 overwhelmed in the higher-competition experimental environment. Our
 results also suggest that individuals may use imbalances in their social
 bonds to negotiate tolerance from others under a wider range of
 environmental conditions, but utilize the overall strength of their social
 bonds in more extreme environments where feeding competition is more
 intense. These findings highlight that behavioral tactics such as the
 strategic investment of social effort may allow foragers to mitigate the
 costs of low rank, but that the effectiveness of these tactics is likely
 to be limited in certain environments.
description: Marshall et al 2014 - EE
 - experiment agonism dataPlease see ReadMe
 file.Marshall et al 2014 - EE
 - natural agonism dataPlease see ReadMe
 file.Marshall et al 2014 - EE
 - experiment intake rate dataPlease see ReadMe
 file.Marshall et al 2014 - EE
 - natural intake rate dataPlease see ReadMe
 file.Marshall et al 2014 - EE
 - experiment patch residency time dataPlease see ReadMe
 file.Marshall et al 2014 - EE
 - natural patch residency time dataPlease see ReadMe
 file.
DOI: 10.5281/zenodo.18381139
title: SuperDARN data in netCDF format (2005-Jun)

description: 2005-Jun SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5281/zenodo.6633767
title: SuperDARN data in netCDF format (2005-Jun)

description: 2005-Jun SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'