cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d0gm2
title: Data from: How many more? Sample size determination in studies of morphological integration and evolvability

description: The variational properties of living organisms are an important component
 of current evolutionary theory. As a consequence, researchers working on
 the field of multivariate evolution have increasingly used integration and
 evolvability statistics as a way of capturing the potentially complex
 patterns of trait association and their effects over evolutionary
 trajectories. Little attention has been paid, however, to the cascading
 effects that inaccurate estimates of trait covariance have on these widely
 used evolutionary statistics. Here, we analyze the relationship between
 sampling effort and inaccuracy in evolvability and integration statistics
 calculated from 10-trait matrices with varying patterns of covariation and
 magnitudes of integration. We then extrapolate our initial approach to
 different numbers of traits and different magnitudes of integration and
 estimate general equations relating the inaccuracy of the statistics of
 interest to sampling effort. We validate our equations using a dataset of
 cranial traits, and use them to make sample size recommendations. Our
 results suggest that highly inaccurate estimates of evolvability and
 integration statistics resulting from small sample sizes are likely common
 in the literature, given the sampling effort necessary to properly
 estimate them. We also show that patterns of covariation have no effect on
 the sampling properties of these statistics, but overall magnitudes of
 integration interact with sample size and lead to varying degrees of bias,
 imprecision, and inaccuracy. Finally, we provide R functions that can be
 used to calculate recommended sample sizes or to simply estimate the level
 of inaccuracy that should be expected in these statistics, given a
 sampling design.
description: R
 codesZip file containing the
 R codes needed to run the simulations reported in this manuscript. Please
 see Main_simulation_starter.R for details of the simulation
 setup.Formatted_outputFormatted output files from our simulation run. Variable names follow the convention established in the R codes. Row IDs correspond to the number of individuals sampled.
DOI: 10.5061/dryad.s21k2
title: Data from: Evolution and spread of glyphosate resistance in Conyza canadensis in California

description: Recent increases in glyphosate use in perennial crops of California, USA,
 are hypothesized to have led to an increase in selection and evolution of
 resistance to the herbicide in Conyza canadensis populations. To gain
 insight into the evolutionary origins and spread of resistance and to
 inform glyphosate resistance management strategies, we investigated the
 geographical distribution of glyphosate resistance in C. canadensis across
 and surrounding the Central Valley, its spatial relationship to
 groundwater protection areas (GWPA), and the genetic diversity and
 population structure and history using microsatellite markers. Frequencies
 of resistant individuals in 42 sampled populations were positively
 correlated with the size of GWPA within counties. Analyses of population
 genetic structure also supported spread of resistance in these areas.
 Bayesian clustering and approximate Bayesian computation (ABC) analyses
 revealed multiple independent origins of resistance within the Central
 Valley. Based on parameter estimation in the ABC analyses, resistant
 genotypes underwent expansion after glyphosate use began in agriculture,
 but many years before it was detected. Thus, diversity in weed control
 practices prior to herbicide regulation in GWPA probably kept resistance
 frequencies low. Regionally coordinated efforts to reduce seed dispersal
 and selection pressure are needed to manage glyphosate resistance in C.
 canadensis.
description: Conyza_canadensis_microsat
DOI: 10.5061/dryad.3ms19
title: Data from: Clade-specific positive selection on a developmental gene: branchless trichome and the evolution of stellate trichomes in Physaria (Brassicaceae)

description: Positive selection is known to drive the evolution of genes involved in
 evolutionary arms races, but what role does it play in the evolution of
 genes involved in developmental processes? We used the single-celled
 epidermal trichomes of Brassicaceae as a model to uncover the molecular
 evolutionary processes that contributed to the transition from dendritic
 trichomes, as seen in most species of Brassicaceae, to the distinctive
 stellate trichomes of the genus Physaria. We explored the role of positive
 selection on the evolution of BRANCHLESS TRICHOME (BLT), a candidate gene
 for changes in trichome branching pattern. Maximum likelihood models of
 codon evolution point to a shift in selective pressure affecting the
 evolution of BLT across the entire Physaria clade, and we found strong
 evidence that positive selection has acted on a subset of Physaria BLT
 codons. Almost all of the 10 codon sites with the highest probability of
 having evolved under positive selection are clustered in a predicted
 coiled-coil domain, pointing to changes in protein-protein interactions.
 Thus, our findings suggest that selection acted on BLT to modify its
 interactions with other proteins. The fact that positive selection
 occurred throughout the radiation of Physaria could reflect selection to
 stabilize development in response to an abrupt switch from the dendritic
 form to the stellate form, divergent selection for diversification of the
 stellate form, or both. These results point to the need for evolutionary
 developmental studies of BLT and its interacting proteins in Physaria.
description: BRANCHLESS TRICHOME
 AlignmentPartial sequence
 alignment of Brassicaceae BRANCHLESS TRICHOME (BLT) homologues. Sequences
 were assembled, edited, and manually aligned by codon using Geneious Pro
 (version 5.6.6, Biomatters, Auckland, New Zealand;
 http://www.geneious.com; Kearse et al. 2012).BLTFull.nexITS AlignmentPartial sequence alignment of Brassicaceae ITS homologues. Sequences were assembled, edited, and aligned using Geneious Pro (version 5.6.6, Biomatters, Auckland, New Zealand; http://www.geneious.com; Kearse et al. 2012). Sequences were aligned with the MUSCLE algorithm (Edgar 2004) and then manually adjusted.ITS.nex
DOI: 10.5061/dryad.b1772
title: Data from: Quantitative cross-species extrapolation between humans and fish: the case of the anti-depressant fluoxetine

description: Fish are an important model for the pharmacological and toxicological
 characterization of human pharmaceuticals in drug discovery, drug safety
 assessment and environmental toxicology. However, do fish respond to
 pharmaceuticals as humans do? To address this question, we provide a novel
 quantitative cross-species extrapolation approach (qCSE) based on the
 hypothesis that similar plasma concentrations of pharmaceuticals cause
 comparable target-mediated effects in both humans and fish at similar
 level of biological organization (Read-Across Hypothesis). To validate
 this hypothesis, the behavioural effects of the anti-depressant drug
 fluoxetine on the fish model fathead minnow (Pimephales promelas) were
 used as test case. Fish were exposed for 28 days to a range of measured
 water concentrations of fluoxetine (0.1, 1.0, 8.0, 16, 32, 64 µg/L) to
 produce plasma concentrations below, equal and above the range of Human
 Therapeutic Plasma Concentrations (HTPCs). Fluoxetine and its metabolite,
 norfluoxetine, were quantified in the plasma of individual fish and linked
 to behavioural anxiety-related endpoints. The minimum drug plasma
 concentrations that elicited anxiolytic responses in fish were above the
 upper value of the HTPC range, whereas no effects were observed at plasma
 concentrations below the HTPCs. In vivo metabolism of fluoxetine in humans
 and fish was similar, and displayed bi-phasic concentration-dependent
 kinetics driven by the auto-inhibitory dynamics and saturation of the
 enzymes that convert fluoxetine into norfluoxetine. The sensitivity of
 fish to fluoxetine was not so dissimilar from that of patients affected by
 general anxiety disorders. These results represent the first direct
 evidence of measured internal dose response effect of a pharmaceutical in
 fish, hence validating the Read-Across hypothesis applied to fluoxetine.
 Overall, this study demonstrates that the qCSE approach, anchored to
 internal drug concentrations, is a powerful tool to guide the assessment
 of the sensitivity of fish to pharmaceuticals, and strengthens the
 translational power of the cross-species extrapolation.
description: Effects of fluoxetine on
 fish - Dataset - Margiotta-Casaluci et al. 2014The file provides the
 results of a study during which male fathead minnows were exposed for 28
 days to the anti-depressant fluoxetine.
DOI: 10.5061/dryad.f8c58
title: Data from: Does high relatedness promote cheater-free multicellularity in synthetic lifecycles?

description: The evolution of multicellularity is one of the key transitions in
 evolution and requires extreme levels of cooperation between cells.
 However, even when cells are genetically identical, non-cooperative
 cheating mutants can arise that cause a breakdown in cooperation. How
 then, do multicellular organisms maintain cooperation between cells? A
 number of mechanisms that increase relatedness amongst cooperative cells
 have been implicated in the maintenance of cooperative multicellularity
 including single cell bottlenecks and kin recognition. In this study we
 explore how relatively simple biological processes such as growth and
 dispersal can act to increase relatedness and promote multicellular
 cooperation. Using experimental populations of pseudo-organisms, we found
 that manipulating growth and dispersal of clones of a social amoeba to
 create high levels of relatedness was sufficient to prevent the spread of
 cheating mutants. By contrast cheaters were able to spread under low
 relatedness conditions. Most surprisingly, we saw the largest increase in
 cheating mutants under an experimental treatment that should create
 intermediate levels of relatedness. This is because one of the factors
 raising relatedness, structured growth, also causes high vulnerability to
 growth rate cheaters.
description: Flow cytometry
 resultsCells counts of
 fluorescently-labelled and non-labelled D. discoideum spores, that
 underwent varying levels of structured growth and structured
 dispersalGrowth
 RatesComparison of growth
 rates between EC28.2 and NC28.2.Expansion
 rateComparison of the
 expansion rates across a nutrient agar plate of NC28.1 and
 EC28.2.
DOI: 10.5061/dryad.2hr40
title: Data from: What keeps family physicians busy in Portugal? A multi-centre observational study of work other than direct patient contacts

description: Objectives: To quantify the time spent by family physicians (FP) on tasks
 other than direct patient contact, to evaluate job satisfaction, to
 analyse the association between time spent on tasks and physician
 characteristics, the association between the number of tasks performed and
 physician characteristics and the association between time spent on tasks
 and job satisfaction. Design: Cross-sectional, using time-and-motion
 techniques. Two workdays were documented by direct observation. A
 significance level of 0.05 was adopted. Setting: Multicentric in 104
 Portuguese family practices. Participants: A convenience sample of FP,
 with lists of over 1000 patients, teaching senior medical students and
 first-year family medicine residents in 2012, was obtained. Of the 217 FP
 invited to participate, 155 completed the study. Main outcomes measured:
 Time spent on tasks other than direct patient contact and on the
 performance of more than one task simultaneously, the number of direct
 patient contacts in the office, the number of indirect patient contacts,
 job satisfaction, demographic and professional characteristics associated
 with time spent on tasks and the number of different tasks performed, and
 the association between time spent on tasks and job satisfaction. Results:
 FP (n=155) spent a mean of 143.6 min/day (95% CI 135.2 to 152.0)
 performing tasks such as prescription refills, teaching, meetings,
 management and communication with other professionals (33.4% of their
 workload). FP with larger patient lists spent less time on these tasks
 (p=0.002). Older FP (p=0.021) and those with larger lists (p=0.011)
 performed fewer tasks. The mean job satisfaction score was 3.5 (out of 5).
 No association was found between job satisfaction and time spent on tasks.
 Conclusions: FP spent one-third of their workday in coordinating care,
 teaching and managing. Time devoted to these tasks decreases with
 increasing list size and physician age.
description: database
 2013contains every data
 except the ones that could identify partcipants, such as gender and work
 location
DOI: 10.5061/dryad.14vt7
title: Data from: Temporal dynamics of seed excretion by wild ungulates: implications for plant dispersal

description: Dispersal is a key process in metapopulation dynamics as it conditions
 species' spatial responses to gradients of abiotic and biotic
 conditions and triggers individual and gene flows. In the numerous plants
 that are dispersed through seed consumption by herbivores (endozoochory),
 the distance and effectiveness of dispersal is determined by the combined
 effects of seed retention time in the vector's digestive system, the
 spatial extent of its movements, and the ability of the seeds to germinate
 once released. Estimating these three parameters from experimental data is
 therefore crucial to calibrate mechanistic metacommunity models of
 plant–herbivore interactions. In this study, we jointly estimated the
 retention time and germination probability of six herbaceous plants
 transported by roe deer (Capreolus capreolus), red deer (Cervus elaphus),
 and wild boar (Sus scrofa) through feeding experiments and a Bayesian
 dynamic model. Retention time was longer in the nonruminant wild boar
 (&gt;36 h) than in the two ruminant species (roe deer: 18–36 h, red
 deer: 3–36 h). In the two ruminants, but not in wild boar, small and round
 seeds were excreted faster than large ones. Low germination probabilities
 of the excreted seeds reflected the high cost imposed by endozoochory on
 plant survival. Trait-mediated variations in retention time and
 germination probability among animal and plant species may impact plant
 dispersal distances and interact with biotic and abiotic conditions at the
 release site to shape the spatial patterns of dispersed plant species.
description: Data: number of seeds
 and seedlingsNumber of seeds counted
 in the dissected sample, number of seedlings in the germinated sample,
 seed and animal characteristics.Data.xlsxData_preparationScript for preparing the data, before running the model.ModelScript of the Bayesian model.
DOI: 10.5061/dryad.jm858
title: Data from: Real-time characterization of the molecular epidemiology of an influenza pandemic

description: Early characterization of the epidemiology and evolution of a pandemic is
 essential for determining the most appropriate interventions. During the
 2009 H1N1 influenza A pandemic, public databases facilitated widespread
 sharing of genetic sequence data from the outset. We employ Bayesian
 phylogenetics to simulate real-time estimation of the evolutionary rate,
 date of emergence and intrinsic growth rate (r0) of the pandemic from
 whole-genome sequences. We investigate the effects of temporal range of
 sampling and dataset size on the precision and accuracy of parameter
 estimation. Parameters can be accurately estimated as early as two months
 after the first reported case, from 100 genomes. Early deleterious
 mutations were purged from the population during the second pandemic wave
 and the choice of growth model is important for accurate estimation of r0.
 This demonstrates the utility of simple coalescent models to rapidly
 inform intervention strategies during a pandemic.
description: XML for input into BEAST
 with increasing temporal sampling rangeXML were created in
 BEAUti v1.5.4 for analysis in BEAST v1.7.4, as described in Hedge et al.
 2013 (Drummond & Rambaut, 2007, Drummond et al. 2012). Each file
 specifies the EpiFlu accession numbers of the segments concatenated into
 the whole-genome sequences and used as input data for the analysis
 (http://platform.gisaid.org/). Each file is labelled with the name of the
 last month during which sequences included in the analysis were sampled
 and the growth modelled employed. For example, June.exp.xml comprises
 EpiFlu accession numbers of sequences sampled from the start of the
 pandemic until June 2009 and specifies the use of an exponential growth
 model. Details of the substitution, clock and coalescent models are
 provided along with the priors placed on the model parameters. An
 additional block implementing the estimation of the marginal likelihood of
 the model using path-sampling is given after the Markov chain Monte Carlo
 (MCMC) block (Baele et al. 2012).BEAST_XML.zip
DOI: 10.5061/dryad.288n0
title: Data from: Fitness cost due to herbicide resistance may trigger genetic background evolution

description: This paper investigates the possible existence of mechanisms
 counterbalancing the negative pleiotropic effects on development and
 reproduction that are conferred by alleles responsible for herbicide
 resistance in the weed Alopecurus myosuroides. We considered three
 herbicide-resistant, mutant acetyl-CoA carboxylase (ACCase) alleles:
 Leu1781, Asn2041 and Gly2078 found in eight resistant populations. Of
 these, Gly2078 is the only allele with a known fitness cost. We compared
 plants homozygous for wild-type ACCase alleles that were siblings of
 plants carrying a given mutant resistant ACCase allele with plants from
 three populations where resistance did not evolve. In each of two series
 of experiments, we measured germination dynamics, seedling vigour, plant
 height, vegetative biomass and seed production. The wild-type siblings of
 plants carrying Gly2078 performed better in the field, on average, than
 wild-type plants that were sibling of plants carrying other mutant ACCase
 alleles, and particularly those carrying Leu1781. We propose that rapid
 evolution of the genetic background of plants from the populations where
 the Gly2078 allele originally arose could partially counterbalance Gly2078
 fitness cost, enhancing the spread of the resistant genotypes.
description: Darmency
 ID-14-0256-R2-GerminationDarmency
 ID-14-0256-R2-FieldDarmency
 ID-14-0256-R2-Seed
DOI: 10.5061/dryad.j0036
title: Data from: Plastic and evolutionary responses to heat stress in a temperate dung fly: negative correlation between basal and induced heat tolerance?

description: Extreme weather events such as heat waves are becoming more frequent and
 intense. Populations can cope with elevated heat stress by evolving higher
 basal heat tolerance (evolutionary response) and/ or stronger induced heat
 tolerance (plastic response). However, there is ongoing debate about
 whether basal and induced heat tolerance are negatively correlated and
 whether adaptive potential in heat tolerance is sufficient under ongoing
 climate warming. To evaluate the evolutionary potential of basal and
 induced heat tolerance, we performed experimental evolution on a temperate
 source population of the dung fly Sepsis punctum. Offspring of flies
 adapted to three thermal selection regimes (Hot, Cold and Reference) were
 subjected to acute heat stress after having been exposed to either a hot-
 or non-acclimation pre-treatment. As different traits may respond
 differently to temperature stress, several physiological and life history
 traits were assessed. Condition-dependence of the response was evaluated
 by exposing juveniles to different levels of developmental (food
 restriction/ rearing density) stress. Heat knockdown times were highest
 while acclimation effects were lowest in the Hot selection regime,
 indicating a negative association between basal and induced heat
 tolerance. However, survival, adult longevity, fecundity and fertility did
 not show such a pattern. Acclimation had positive effects in heat-shocked
 flies, but in the absence of heat stress hot-acclimated flies had reduced
 lifespans relative to non-acclimated ones, thereby revealing a potential
 cost of acclimation. Moreover, body size positively affected heat
 tolerance and unstressed individuals were less prone to heat stress than
 stressed flies, offering support for energetic costs associated with heat
 tolerance. Overall, our results indicate that heat tolerance of temperate
 insects can evolve under rising temperatures, but this response could be
 limited by a negative relationship between basal and induced
 thermotolerance, and may involve some but not other fitness-related
 traits.
description: S. punctum heat shock
 experimentResponses to heat shock
 (15 minutes at 42C) in thermal experimental evolution lines of Sepsis
 punctum (originating from Zurich, Switzerland)sepsis HS
 data.xlsx
DOI: 10.5061/dryad.qj728
title: Data from: Decaying of Artemia salina in clay colloids: 14-month experimental formation of subfossils

description: The mechanism that guides the formation of exceptionally preserved fossils
 with soft tissues variously displayed is a paramount challenge to
 paleontology. The key question for exceptional preservation is the nature
 of the slowdown of decay and acceleration of soft tissue mineralization.
 Here we report the experimental formation of subfossils of the brine
 shrimp Artemia salina (Crustacea, Branchiopoda), which were produced
 during 14 months of aging in a kaolinite clay sediment. EDS/SEM elemental
 analyses showed that the subfossils were preserved as thin clay-organic
 replicas that displayed fine anatomical details. Decomposition in the
 clay-colloidal solution established highly heterogeneous acidic
 conditions, with the lowest pH typically found in the vicinity of the
 buried organisms, and visually manifested in patchy coloration of the
 sediment. Elevated acidity is likely what ultimately slowed the decay. An
 acidic environment increases the rate of clay destruction and,
 consequently, the diffusion rate decline. As a result, the acidic products
 quickly accumulate around a buried body; this in turn inhibits bacterial
 proliferation, accelerates the acidic hydrolysis of clay and, accordingly,
 the release of tanning and mineralizing agents. The subfossils remained
 stable under experimental high pressure and temperature. These model
 subfossils exhibit features that are typical of some Lagerstätten fossils
 preserved in fine-grained sediments.
description: DSC curves of the
 experimental samplesDSC curves for the
 control samples of pure kaolinite (1), dark portion (DL) (2) and top
 portion (TL) (3) of the sediment after 6 months, top portion after the
 adding of CaCl2 (4).Suppl_Data_fig1.jpg