cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.x69p8czfx
title: Data from: Environmental drivers of femaleness of an inter-Andean monoecious shrub

description: Hetero-and conspecific interactions, nutrient availability, climate,
 habitat heterogeneity and disturbances can generate variation and spatial
 patterns of femaleness in plants. We assessed whether year, site, plant
 size, plant density and canopy area of conspecific neighbors influenced
 the expression and spatial aggregation of femaleness in Croton aff.
 wagneri, a monoecious shrub from dry shrublands of the inter-Andean
 valleys in Ecuador. We georeferenced in two sites (1,700 and 1,400
 m.a.s.l) in five 10x10 m plots, within each site, the position of each
 Croton reproductive plant during first part of flowering season in two
 years, and measured their height, length and width. The femaleness index
 of each plant was determined by the number of female and male buds and
 flowers. Plant density was determined for each plot, along with the number
 of neighbors and the summed canopy area of conspecific neighbors (at 1.0,
 2.0, and 2.5 m radius, and the five closest plants) from each focal plant.
 Croton's femaleness at the lower elevation site was greater than at
 the higher elevation site and increased with plant size and with canopy of
 the closest five neighbors. Soil at the lower elevation site had higher
 temperatures and lower water content. Aggregate patterns of femaleness
 were found in more plots at the lower elevation site. Our results indicate
 that location, plant size and canopies of conspecific neighbors of Croton
 can affect femaleness and its aggregation and support the hypothesis that
 femaleness can be influenced by facilitative interactions.
description: One site was located at 1700 a.s.l. and identified as the higher
 elevation site and the other at 1400  a.s.l., identified as the lower
 elevation site. At each site and within a 70x50 m plot, five subplots of
 10x10 m were established in 2013 and 2016. The subplots were distributed
 as follows: four in the corners and one in the center with respect to the
 larger plot. In each plot, the spatial location of the main stem of each
 reproductive plant was tagged and georeferenced. To estimate plant size,
 plant height as well as length and width of canopy of each sampled plant
 were measured. During the flowering season (November - December) in both
 2013 and 2016, five inflorescences were randomly selected on each plant of
 each 10x10 m plot in both sites (1145 plants and 5725 total
 inflorescences). Then, number of female and male buds and number of female
 and male flowers of each inflorescence were counted in situ and an average
 of female and male flowers per inflorescence was obtained from each plant.
 The standardized phenotypic femaleness index (Gi) of each plant was used
 to estimate the sexual expression of Croton, according to Lloyd
 (1980).
DOI: 10.5061/dryad.kprr4xh2h
title: Data from: Environmental drivers of femaleness of an inter-Andean monoecious shrub

description: Hetero-and conspecific interactions, nutrient availability, climate,
 habitat heterogeneity and disturbances can generate variation and spatial
 patterns of femaleness in plants. We assessed whether year, site, plant
 size, plant density and canopy area of conspecific neighbors influenced
 the expression and spatial aggregation of femaleness in Croton aff.
 wagneri, a monoecious shrub from dry shrublands of the inter-Andean
 valleys in Ecuador. We georeferenced in two sites (1,700 and 1,400
 m.a.s.l) in five 10´10 m plots, within each site, the position of each
 Croton reproductive plant during first part of flowering season in two
 years, and measured their height, length and width. The femaleness index
 of each plant was determined by the number of female and male buds and
 flowers. Plant density was determined for each plot, along with the number
 of neighbors and the summed canopy area of conspecific neighbors (at 1.0,
 2.0, and 2.5 m radius, and the five closest plants) from each focal plant.
 Croton´s femaleness at the lower elevation site was greater than at the
 higher elevation site and increased with plant size and with canopy of the
 closest five neighbors. Soil at the lower elevation site had higher
 temperatures and lower water content. Aggregate patterns of femaleness
 were found in more plots at the lower elevation site. Our results indicate
 that location, plant size and canopies of conspecific neighbors of Croton
 can affect femaleness and its aggregation and support the hypothesis that
 femaleness can be influenced by facilitative interactions.
description: During the winter season, September 2018 to March 2019, HOBO data
 loggers S-TMB-M006 and S-SMC-M005 (Onset, USA) were used to measure soil
 temperature and moisture at a depth of 10 cm, with a sampling interval of
 5 minutes at each site which recorded 66932 and 48931 soil temperature and
 moisture samples for higher elevation site (1700 m) and lower elevation
 site (, respectively.
DOI: 10.5061/dryad.8931zcrnb
title: Reintroduced grazers and prescribed fire effects on beetle assemblage structure and function in restored grasslands

description: Ecological restoration seeks to re-establish functioning ecosystems, but
 planning and evaluation often focus on taxonomic community structure and
 neglect consumers and their functional roles. The functional trait
 composition of insect assemblages, which make up the majority of animal
 diversity in many systems, can reveal how they are affected by restoration
 management and the consequences for ecosystem function. We sampled ground
 beetle (Coleoptera: Carabidae) assemblages in restored tallgrass prairies
 varying in management with prescribed fire and reintroduced American bison
 (Bison bison) to describe their taxonomic and functional trait structure.
 We also measured seed and arthropod predation to relate management, beetle
 assemblage characteristics, and function, and to test if function is
 maximized by trait diversity, dominant trait values, or beetle abundance.
 Beetle assemblages primarily varied with restoration age, declining over
 time in richness and both taxonomic and functional diversity, but bison
 presence also influenced taxonomic composition. Prescribed fire reduced
 seed predation in summer and arthropod predation in fall. Although seed
 predation was unrelated to beetle assemblages, arthropod predation was
 greater in sites with higher abundances of carnivorous ground beetles. The
 relatively weak impacts of fire and bison on functional assemblage
 structure is a promising sign that these management disturbances, aimed at
 supporting a diverse native plant community, are not detrimental to beetle
 assemblages. The significance of reduced predator function following
 prescribed fire will depend on the restoration context and whether seed or
 arthropod predation relates to management goals.
DOI: 10.5061/dryad.k0p2ngf5z
title: Seismograms and snapshot files for dynamic models (crack and shear sources)

description: This paper presents a numerical investigation on the influence of the
 mining environment on seismic sources with a focus of pillar failure
 mechanisms in tabular mining. We investigate the influence of the stope on
 seismic inversions for the scalar moment, corner frequency, source radius,
 stress drop and moment tensor through dynamic numerical modelling using
 elastodynamic modelling software, WAVE3D. The main objective is to
 determine whether the source parameters calculated from the recorded
 waveforms are due to a combination of the stope source and the pillar
 sources, rather than being related only to crushing of the pillar or
 shearing in the pillar footwall. The main finding is that the presence of
 stopes, and types of pillars, have a significant impact on the seismic
 moment and other source parameters. This is important since moment is
 viewed as a robust parameter on which seismic magnitude is often based,
 however this study indicates that moments calculated for pillar failure in
 a tabular stoping environments are less representative of the shearing or
 crushing source than originally thought.
description: This data was generated by an elastodynamic code called WAVE3D
 and consists of velocity seismograms and snapshots in time in CSV format.
 Eight models were run: 1. Crush source in solid
 (control model) 2. Crush source with a stope
 3. Crush source with a rigid pillar in a stope
 4. Crush source with a soft pillar in a stope
 5. Shear source in solid (control model) 6.
 Shear source with a stope 7. Shear source with a rigid
 pillar in a stope 8. Shear source with a soft pillar in
 a stope
DOI: 10.5061/dryad.jsxksn06j
title: Bayesian inference of tree species using diffusion models: tabulated posterior statistics for SNAPP and SNAPPER analyses

description: We describe a new and computationally efficient Bayesian methodology
 for inferring species trees and demographics from unlinked binary
 markers. Likelihood calculations are carried out using diffusion models of
 allele frequency dynamics combined with novel numerical algorithms. The
 diffusion approach allows for analysis of datasets containing hundreds or
 thousands of individuals. The method, which we call \snapper, 
 has been implemented as part of the BEAST2 package. We conducted
 simulation experiments to assess numerical error, computational
 requirements and accuracy recovering known model parameters. A re-analysis
 of soybean SNP data demonstrates that the models implemented in \snapp and
 \snapper can be difficult to distinguish in practice, a characteristic
 which we tested with further simulations. We demonstrate the scale of
 analysis possible using a SNP dataset sampled from 399 fresh water turtles
 in 41 populations.
description: This data file contains posterior statistics for (1) an analysis
 of soybean SNP data and (2) an analysis of SNP data from 399 fresh water
 turtles in 41 populations.
DOI: 10.5061/dryad.p8cz8w9mv
title: Data from: Pro-inflammatory immune response is linked to wintering habitat in a migratory shorebird

description: Migratory shorebirds (Charadrii) show a strong dichotomy in their breeding
 and wintering strategies: Arctic-breeding species typically spend the
 wintering season in marine habitats, while more southerly breeding species
 tend to do so in freshwater habitats where pathogens and
 parasites, particularly vector-borne blood parasites, are generally more
 abundant. Thus, it has been hypothesized that the former group may reduce
 their investment in immunity, but experimental data supporting this
 hypothesis are lacking.  Moreover, whether this contrasting
 habitat selection can shape investments in immunocompetence among
 populations within a species is uncertain. We experimentally tested the
 hypothesis that there is a significant association between habitat
 occupancy and the strength of a pro-inflammatory immune response in
 Dunlins Calidris alpina, a widely distributed long-distance migratory
 shorebird that breeds in (sub-)arctic areas and winters mainly, but not
 exclusively, in coastal habitats. Overwintering Dunlins occupying inland
 freshwater and marine habitats at a similar latitude were captured and
 acclimated under identical conditions in outdoor aviaries. After an
 acclimation period, they were challenged with phytohemagglutinin to assess
 the pro-inflammatory immune response and its associated energetic costs,
 measured by basal metabolic rate (BMR) and body mass changes. We found
 that freshwater Dunlins exhibited a higher (63%) pro-inflammatory immune
 response than marine Dunlins. Although this difference did not involve
 significant BMR changes, the time course of body mass response differed
 between freshwater and marine individuals. Our findings point to the
 existence of different pro-inflammatory immune and energetic strategies
 associated to the wintering habitat. These intraspecific differences are
 likely due to population adaptation rather than phenotypic plasticity,
 where not only disease risk but also physiological adaptations to
 different salinity levels could play an important role.
description: This is the raw data of the PHA response, BMR and body mass of
 dunlins captured in freshwater and marine habitats and maintained in
 captivity under a freshwater regime.
DOI: 10.5061/dryad.cnp5hqc2q
title: Two photon data from: Functional and structural properties of highly responsive somatosensory neurons in mouse barrel cortex

description: Sparse population activity is a hallmark of supra-granular sensory neurons
 in neocortex. The mechanisms underlying sparseness are not well understood
 because a direct link between the neurons activated in vivo and their
 cellular properties investigated in vitro has been missing. We used
 two-photon calcium imaging to identify a subset of neurons in layer L2/3
 (L2/3) of mouse primary somatosensory cortex that are highly active
 following principal whisker vibrotactile stimulation. These high
 responders were then tagged using photoconvertible green fluorescent
 protein for subsequent targeting in the brain slice using intracellular
 patch-clamp recordings and biocytin staining. This approach allowed us to
 investigate the structural and functional properties of high responders
 that distinguish them from less active control cells. Compared to less
 responsive L2/3 neurons, high responders displayed increased levels of
 stimulus-evoked and spontaneous activity, elevated noise and spontaneous
 pair-wise correlations, and stronger coupling to the population response.
 Intrinsic excitability was reduced in high responders, while other
 electrophysiological and morphological parameters were unchanged. Thus,
 the choice of which neurons participate in stimulus encoding may largely
 be determined by network connectivity rather than by cellular structure
 and function.
description: Single neuron calcium transients collected with two-photon
 microscopy in the somatosensory cortex of anaesthetized mice. The dataset
 contains 2100 neurons from 21 fields of view in 7 animals. Raw movies were
 motion corrected using the registration module from Suite 2p, and ROIs
 manually delineated with a custom matlab software. Local neuropil was
 defined as a 40 µm area surrounding the ROIs, and excluding all ROIs. Are
 provided the raw fluorescence traces for all ROIs and their corresponding
 neuropil, as well as the Field of view they belong to.
description: From the raw fluorescence (source data), and given the provided
 matlab code, it is possible to reproduce all summary panels and statistics
 in figure 2-4 in our publication. Detailed instructions for the use of
 data and code are given in a readme.m file in the Zenodo
 repository.
DOI: 10.5061/dryad.6wwpzgmw4
title: Gut microbiota in non-obese adolescent girls with polycystic ovary syndrome: effects of randomized treatments

description: Context: Women and obese adolescent girls with polycystic ovary
 syndrome (PCOS) have altered gut microbiota. 
 Objective: To study the gut microbiota composition of non-obese
 adolescent girls with PCOS and the effects of randomized pharmacological
 treatments. Design: Randomized, open-label, single-center
 controlled trial.  Settings: Endocrinology Department,
 University Hospital.  Participants: 30 girls with PCOS
 [age 15.8 years; body mass index (BMI) 25 kg/ m2] and 31 controls [age
 15.9 years; BMI 22 kg/ m2].  Intervention: PCOS girls
 were randomized to receive an oral contraceptive (OC, N= 15) or
 spironolactone-pioglitazone-metformin (SPIOMET, N= 15) for 1
 year.  Outcomes: 16S ribosomal subunit gene amplicon
 sequencing was used to describe and quantify microbial diversity and
 taxonomic profiles in stool samples from all subjects. Samples from 23 out
 of 30 girls with PCOS (OC, N= 11; SPIOMET, N= 12) were available for
 analysis post-treatment. Correlations between bacterial results and
 endocrine-metabolic variables were performed before and after randomized
 treatments.  Results: Girls with PCOS had decreased
 diversity alpha, altered microbiota pattern and taxonomic profile with
 more abundance of Family XI (P= 0.002), and less
 abundance of family Prevotellaceae (P= 0.0006) and the
 genus Prevotella (P= 0.0001)
 and Senegalimassilia (P&lt; 0.0001), as compared to
 controls. Family XIabundance related positively to
 hepato-visceral fat (R= 0.453; P= 0.0003). SPIOMET treatment, but
 not OC, normalized the abundance of Family
 XI. Prevotellaceae, Prevotella and Senegalimassilia abundance remained unchanged after either treatment.  Conclusion: SPIOMET’s spectrum of normalizing effects in non-obese girls with PCOS is herewith broadened as to include Family XI abundance in gut microbiota.
DOI: 10.5061/dryad.k0p2ngf60
title: Species-specific effects of thermal stress on the expression of genetic variation across a diverse group of plant and animal taxa under experimental conditions

description: Assessing the genetic adaptive potential of populations and species is
 essential for better understanding evolutionary processes. However, the
 expression of genetic variation may depend on environmental conditions,
 which may speed up or slow down evolutionary responses. Thus, the same
 selection pressure may lead to different responses. Against this
 background, we here investigate the effects of thermal stress on genetic
 variation, mainly under controlled laboratory conditions. We estimated
 additive genetic variance (VA), narrow-sense heritability (h2), and the
 coefficient of genetic variation (CVA) under both benign control and
 stressful thermal conditions. We included six species spanning a diverse
 range of plant and animal taxa and a total of 25 morphological and
 life-history traits. Our results show that (1) thermal stress reduced
 fitness components, (2) the majority of traits showed significant genetic
 variation, and that (3) thermal stress affected the expression of genetic
 variation (VA, h2 or CVA) in only one third of the cases (25 of 75
 analyses, mostly in one clonal species). Moreover, effects were highly
 species-specific, with genetic variation increasing in 11 and decreasing
 in 14 cases under stress. Our results hence indicate that thermal stress
 does not generally affect the expression of genetic variation under
 laboratory conditions but, nevertheless, increases or decreases genetic
 variation in specific cases. Consequently, predicting the rate of genetic
 adaptation might not be generally complicated by environmental variation,
 but requires a careful case-by-case consideration.
description: The data were collected in various laboratory experiments. Data
 were not processed in any specific way. Please see the published article
 for details.
DOI: 10.5061/dryad.280gb5mnd
title: Data from: Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus

description: Several factors have been proposed as drivers of species diversification
 in the Neotropics, including environmental heterogeneity, the development
 of drainage systems and historical changes in forest distribution due to
 climatic oscillations. Here, we investigate which drivers contributed to
 the evolutionary history and current patterns of diversity of a
 polymorphic songbird (Arremon taciturnus) that is widely distributed in
 Amazonian and Atlantic forests as well as in Cerrado gallery and
 seasonally-dry forests. We use genomic, phenotypic and habitat
 heterogeneity data coupled with climatic niche modeling. Results suggest
 the evolutionary history of the species is mainly related to paleoclimatic
 changes, although changes in the strength of the Amazon river as a barrier
 to dispersal, current habitat heterogeneity and geographic distance were
 also relevant. We propose an ancestral distribution in the Guyana Shield,
 and recent colonization of areas south of the Amazon river at ~380–166
 kya, expansion of distribution to southern Amazonia, Cerrado and the
 Atlantic Forest. Since then, populations south of the Amazon River have
 been subjected to cycles of isolation and possibly secondary contact due
 to climatic changes that affected habitat heterogeneity and population
 connectivity. Most Amazonian rivers are not associated to long lasting
 isolation of populations, but some might act as secondary barriers,
 susceptible to crossing under specific climatic conditions. Morphological
 variation, while stable in some parts of the distribution, is not a
 reliable indicator of genetic structure or phylogenetic relationships.
description: files descriptions: *UCE.zip - raw data and
 cleanreads for the UCE dataset *ddRAD.zip - raw and
 demultiplexed data for the ddRAD dataset input.zip -
 input files (alignments and SNP matrices) for STRUCTURE, G-PHOCS, IQ-TREE,
 SVDQuartets and ARLEQUIN env.zip - raw environmental
 variables used to generate environmental distances, and isolation by
 resistance matrix generated by circuitscape used as climatic distance
 matrix.  *barcodes information necessary to demultiplex
 files can be found inside each dataset type (UCE/ddRAD) folder.
DOI: 10.5061/dryad.rn8pk0p6x
title: Data from: The impact of personality, morphotype and shore-height on temperature-mediated behavioural responses in the beadlet anemone (Actinia equina)

description: 1. Between-individual variation in behavioural phenotype, termed
 personality, is an important determinant of how populations cope with
 acute environmental fluctuation related to climate change. 2. Personality
 in the beadlet sea anemone (Actinia equina) is linked to genetically
 distinct morphotypes, which are associated with different heights on the
 shore. In the intertidal zone, high-shore environments experience more
 environmental fluctuation due to longer periods of exposure, and animals
 adapted to live in these environments are predicted to deal more
 effectively with environmental perturbation than their low-shore
 counterparts. 3. We collected beadlet anemones of two different
 morphotypes from three different shore-heights. We investigated variation
 in two behaviours at three different temperatures and in a temporal
 control treatment where the temperature was not changed: startle
 response-time, the time it took an anemone to re-extend its tentacles
 after a threatening stimulus, and immersion response-time, the time to
 re-extend tentacles after simulated tidal immersion. These behaviours
 reflect risk taking and allow individuals to be categorised as bold, shy
 or intermediate based upon response-times. 4. Both behaviours showed
 significant changes as the temperature increased. For immersion-response,
 the morphotype associated with the low-shore lengthened response-times at
 high temperatures. For startle-response, all animals lengthened their
 response-times at high temperatures but animals collected from the
 low-shore lengthened theirs to the greatest degree. At the individual
 level, although control individuals exhibited temporal changes in their
 response-times, a clear effect of temperature was present in both
 behaviours. Shy and bold individuals became more intermediate at higher
 temperatures in immersion-response (this effect was present to a lesser
 degree in control individuals), while intermediate individuals raised
 their response-times at higher temperatures for startle-response. 5. Given
 that prolonged tentacle retraction reduces foraging opportunities and can
 negatively impact respiratory efficiency, our data suggest that some
 individuals within a single population of A.equina, particularly those
 associated with the lower-shore, may exhibit less effective behavioural
 responses to temperature-shifts than others. These findings demonstrate
 that acute temperature changes influence risk-taking, and could have
 profound short and long-term implications for survival in the face of
 climate change. 16-Jun-2020