cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.th725q8
title: Data from: Association between commercial funding of Canadian patient groups and their views about funding of medicines: an observational study

description: Background: Patient groups represent the interest of their members when it
 comes to drug funding. Many patient groups receive grants from
 pharmaceutical companies that make products being considered for funding.
 This research examines whether there is an association between the
 positions that Canadian groups take about the products and conflicts of
 interest with the companies. Methods: The Common Drug Review (CDR) and
 panCanadian Oncology Drug Review (pCODR) make recommendations to Canadian
 provincial and federal drug plans about funding particular
 drug-indications. Both utilize input from patient groups in making their
 recommendations. Patient group submissions are available from both
 organizations and these submissions contain statements about conflicts of
 interest. Views of the patient groups, with and without a conflict with
 the company making the drug under consideration and without any conflicts
 at all, were assessed and then compared with the recommendations from CDR
 and pCODR. Results: There was a total of 222 reports for drug-indications.
 There were 372 submissions from 93 different patient groups. Groups
 declared a total of 1896 conflicts with drug companies in 324 (87.1%)
 individual submissions. There were 268 submissions where groups declared a
 conflict with the company making the product or said they had no conflict.
 Irrespective of whether there was a conflict, the views of patient groups
 about the drug-indications under consideration were the same. There was no
 statistically significant difference between views of patient groups and
 the recommendations from CDR and/or pCODR. Conclusions: The large majority
 of patient groups making submissions about funding of particular
 drug-indications had conflicts with the companies making the products and
 their views about the products were almost always positive. This
 association between funding and views needs to be further investigated to
 determine if a true cause and effect exists.
description: Patient groups and
 funding recommendationsComplete data set for
 articleSupplementary
 File.csvEvaluation of patient
 group viewsEvaluation of patient
 group views by individual reviewers and final decision as to whether view
 is positive, neutral or negative
DOI: 10.5061/dryad.329b0m6
title: Data from: Identifying drivers of parallel evolution: a regression model approach

description: Parallel evolution, defined as identical changes arising in independent
 populations, is often attributed to similar selective pressures favoring
 the fixation of identical genetic changes. However, some level of parallel
 evolution is also expected if mutation rates are heterogeneous across
 regions of the genome. Theory suggests that mutation and selection can
 have equal impacts on patterns of parallel evolution; however empirical
 studies have yet to jointly quantify the importance of these two
 processes. Here, we introduce several statistical models to examine the
 contributions of mutation and selection heterogeneity to shaping parallel
 evolutionary changes at the gene-level. Using this framework, we analyze
 published data from forty experimentally evolved Saccharomyces cerevisiae
 populations. We can partition the effects of a number of genomic variables
 into those affecting patterns of parallel evolution via effects on the
 rate of arising mutations, and those affecting the retention versus loss
 of the arising mutations (i.e. selection). Our results suggest that
 gene-to-gene heterogeneity in both mutation and selection, associated with
 gene length, recombination rate, and number of protein domains drive
 parallel evolution at both synonymous and nonsynonymous sites. While there
 are still a number of parallel changes that are not well described, we
 show that allowing for heterogeneous rates of mutation and selection can
 provide improved predictions of the prevalence and degree of parallel
 evolution.
description: Example R-script for
 regression procedureThis is an example
 R-script showing how our regression model was implemented, the model
 selection procedure, and P-value estimation using a permutation
 procedure.regression
 procedure.RCombined
 dataThe full integrated data
 set used in the regression analysis. Data sources are list in table 1 of
 the GBE article.combined
 data.csv
DOI: 10.5061/dryad.hj722
title: Data from: Landscape genetics of the nonnative red fox of California

description: Invasive mammalian carnivores contribute disproportionately to declines in
 global biodiversity. In California, nonnative red foxes (Vulpes vulpes)
 have significantly impacted endangered ground-nesting birds and native
 canids. These foxes derive primarily from captive-reared animals
 associated with the fur-farming industry. Over the past five decades, the
 cumulative area occupied by nonnative red fox increased to cover much of
 central and southern California. We used a landscape-genetic approach
 involving mitochondrial DNA (mtDNA) sequences and 13 microsatellites of
 402 nonnative red foxes removed in predator control programs to
 investigate source populations, contemporary connectivity, and
 metapopulation dynamics. Both markers indicated high population
 structuring consistent with origins from multiple introductions and low
 subsequent gene flow. Landscape-genetic modeling indicated that population
 connectivity was especially low among coastal sampling sites surrounded by
 mountainous wildlands but somewhat higher through topographically flat,
 urban and agricultural landscapes. The genetic composition of populations
 tended to be stable for multiple generations, indicating a degree of
 demographic resilience to predator removal programs. However, in two sites
 where intensive predator control reduced fox abundance, we observed
 increases in immigration, suggesting potential for recolonization to
 counter eradication attempts. These findings, along with continued genetic
 monitoring, can help guide localized management of foxes by identifying
 points of introductions and routes of spread and evaluating the relative
 importance of reproduction and immigration in maintaining populations.
 More generally, the study illustrates the utility of a landscape-genetic
 approach for understanding invasion dynamics and metapopulation structure
 of one of the world's most destructive invasive mammals, the red fox.
description: DryadDatabaseAccessionFinalContains sample data and genetic data, including identifiers, museum accession Nos (where applicable), location, date, mtDNA haplotype names (identifiable in Genbank), alleles at 13 microsatellite loci
DOI: 10.5061/dryad.q164g
title: Data from: Groups of related belugas (Delphinapterus leucas) travel together during their seasonal migrations in and around Hudson Bay

description: Social structure involving long-term associations with relatives should
 facilitate the learning of complex behaviours such as long-distance
 migration. In and around Hudson Bay (Canada), three stocks of beluga
 whales form a panmictic unit, but have different migratory behaviours
 associated with different summering areas. We analysed genetic variation
 at 13 microsatellite loci among 1524 belugas, to test hypotheses about
 social structure in belugas. We found significant proportions of
 mother–offspring pairs throughout the migratory cycle, but average
 relatedness extended beyond close kinship only during migration. Average
 relatedness was significantly above random expectations for pairs caught
 at the same site but on different days or months of a year, suggesting
 that belugas maintain associations with a network of relatives during
 migration. Pairs involving a female (female–female or male–female) were on
 average more related than pairs of males, and males seemed to disperse
 from their matrilineal group to associate with other mature males.
 Altogether, our results indicate that relatives other than strictly
 parents, and especially females, play a role in maintaining a social
 structure that could facilitate the learning of migration routes. Cultural
 conservatism may limit contributions from nearby summer stocks to
 endangered stocks such as the Eastern Hudson Bay beluga.
description: ColbeckAl_RSPB-2012-2552_DataDryad.xlsxExcel file containing information for 1524 belugas, namely: Code, Location of capture, code of location of capture, Day (if available), month(if available), and year of capture, age (if available), sex (if available), and multilocus genotype at 13 microsatellite loci (in pb, one allele per column)
DOI: 10.15468/dl.qgacbs
title: Occurrence Download

description: A dataset containing 5152 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tetragonisca angustula, Puma concolor)",
 "HasCoordinate is true",
 "Country is Brazil"
 ]
}

 The dataset includes 5152 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000652-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.923n7
title: Data from: A common-garden experiment to quantify evolutionary processes in copepods: the case of emamectin benzoate resistance in the parasitic sea louse Lepeophtheirus salmonis

description: Background:The development of pesticide resistance represents a global
 challenge to food production. Specifically for the Atlantic salmon
 aquaculture industry, parasitic sea lice and their developing resistance
 to delousing chemicals is challenging production. In this study, seventeen
 full sibling families, established from three strains of Lepeophtheirus
 salmonis displaying differing backgrounds in emamectin benzoate (EB)
 tolerance were produced and quantitatively compared under a common-garden
 experimental design. Lice surviving to the preadult stage were then
 exposed to EB and finally identified through the application of DNA
 parentage testing. Results: With the exception of two families (19 and
 29%), survival from the infectious copepod to preadult stage was very
 similar among families (40-50%). In contrast, very large differences in
 survival following EB exposure were observed among the families (7.9-74%).
 Family survival post EB exposure was consistent with the EB tolerance
 characteristics of the strains from which they were established and no
 negative effect on infection success were detected in association with
 increased EB tolerance. Two of the lice families that displayed reduced
 sensitivity to EB were established from a commercial farm that had
 previously used this chemical. This demonstrates that resistant alleles
 were present on this farm even though the farm had not reported treatment
 failure. Conclusions: To our knowledge, this represents the first study
 where families of any multi-cellular parasite have been established and
 compared in performance under communal rearing conditions in a
 common-garden experiment. The system performed in a predictable manner and
 permitted, for the first time, elucidation of quantitative traits among
 sea lice families. While this experiment concentrated on, and provided a
 unique insight into EB sensitivity among lice families, the experimental
 design represents a novel methodology to experimentally address both
 resistance development and other evolutionary questions in parasitic
 copepods.
description: Common-garden and EB
 trial data from 17 families of Lepeophtheirus salmonisBackground data and
 results for: 1. Production of families in single tanks, and 2: All
 individual lice sampled from a common-garden infection in four tanks and
 subsequently exposed to emamectin benzoate in a one-dose
 trial.Data_CommonGarden_EBTrial.xls
DOI: 10.5061/dryad.67225
title: Data from: Temporal variability and cooperative breeding: testing the bet-hedging hypothesis in the acorn woodpecker

description: Cooperative breeding is generally considered an adaptation to ecological
 constraints on dispersal and independent breeding, usually due to limited
 breeding opportunities. Although benefits of cooperative breeding are
 typically thought of in terms of increased mean reproductive success, it
 has recently been proposed that this phenomenon may be a bet-hedging
 strategy that reduces variance in reproductive success (fecundity
 variance) in populations living in highly variable environments. We tested
 this hypothesis using long-term data on the polygynandrous acorn
 woodpecker (Melanerpes formicivorus). In general, fecundity variance
 decreased with increasing sociality, at least when controlling for annual
 variation in ecological conditions. Nonetheless, decreased fecundity
 variance was insufficient to compensate for reduced per capita
 reproductive success of larger, more social groups, which typically
 suffered lower estimated mean fitness. We did, however, find evidence that
 sociality in the form of larger group size resulted in increased fitness
 in years following a small acorn crop due to reduced fecundity variance.
 Bet-hedging, although not the factor driving sociality in general, may
 play a role in driving acorn woodpecker group living when acorns are
 scarce and ecological conditions are poor.
description: HNHR_monthly_weatherMonthly rainfall and temperature data for Hastings Reservation (the study site), 1939 - 2013.Hastings_mean_acorn_cropMean acorn crop data for Hastings Reservation (the study site), between 1980 and 2012. Data are the mean number of acorns counted per 30-s sample across all oak trees sampled (N = 250). Data are both the raw number of acorns counted and the mean log-transformed (ln[x+1]) number of acorns counted. Acorns are counted in the fall of year x, and thus correspond to the acorn woodpecker breeding season of year x+1.AcornWoodpeckerReproDataRaw data for acorn woodpecker group composition and reproductive success (total number of young fledged in the spring breeding season), 1972 - 2013, by territory (group).
DOI: 10.5061/dryad.gp16s
title: Data from: Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions

description: Discrete character-taxon matrices are increasingly being used in an
 attempt to understand the pattern and tempo of morphological evolution;
 however, methodological sophistication and bespoke software
 implementations have lagged behind. In the present study, an attempt is
 made to provide a state-of-the-art description of methodologies and
 introduce a new R package (Claddis) for performing foundational disparity
 (morphologic diversity) and rate calculations. Simulations using its core
 functions show that: (1) of the two most commonly used distance metrics
 (Generalized Euclidean Distance and Gower's Coefficient), the latter
 tends to carry forward more of the true signal; (2) a novel distance
 metric may improve signal retention further; (3) this signal retention may
 come at the cost of pruning incomplete taxa from the data set; and (4) the
 utility of bivariate plots of ordination spaces are undermined by their
 frequently extremely low variances. By contrast, challenges to estimating
 morphologic tempo are presented qualitatively, such as how trees are
 time-scaled and changes are counted. Both disparity and rates deserve
 better time series approaches that could unlock new macroevolutionary
 analyses. However, these challenges need not be fatal, and several
 potential future solutions and directions are suggested.
description: Matrix used for the
 tutorialtutorial_matrix.nexAges file for the tutorial data settutorial_ages.txtR code for the tutorialtutorial_code.rR code used for the simulationssimulation_code.r
DOI: 10.5061/dryad.s074j
title: Data from: Water restriction causes an intergenerational trade-off and delayed mother-offspring conflict in a viviparous lizard

description: 1. Parenting is costly and because the relationship between the mother and
 embryos is not mutualistic, mother-offspring conflicts may exist whenever
 resource are scarce. However, intergenerational trade-offs and conflicts
 resulting from limited access to water, a vital and depreciable resource,
 remain largely overlooked. 2. In this study, we examined the
 physiological, reproductive and life history responses to water
 restriction in the European Common Lizard (Zootoca vivipara). We
 hypothesised that, under water-limited conditions, pregnant females
 experience both short-term and long-term physiological impacts
 (dehydration and stress) underlying an allocation trade-off for water
 between mothers and offspring. 3. Water restriction led to a decrease in
 body mass, and an increase in plasma osmolality (dehydration) and
 corticosterone concentration in both males and females. The extent of the
 dehydration was positively correlated with fecundity in females. This
 suggests a trade-off between maternal water balance and allocation of
 water to developing embryos during reproduction. 4. Water restriction had
 no immediate effect on reproductive output or offspring morphology at
 birth. Yet, water restriction in pregnant females enhanced their
 reproductive effort the following year but reduced the early life growth
 and annual survival of their second-year offspring. 5. These delayed
 fitness responses to water restriction in offspring and mothers suggest
 that water can trigger intergenerational conflicts as demonstrated for
 energy. Although the mediation of this conflict remains to be clarified,
 we hypothesized that it represents a selective force that influences
 reproductive strategies.
description: data_adult_yearlingThis dataset described the physiological responses to water treatment in adults and yearlings. It also includes the data on fitness estimates (annual growth rate, survival rate and reproduction the next year).data_juvenileThis dataset includes juvenile characteristics at birth and after few weeks during september recapture (early body growth rate).
DOI: 10.5061/dryad.fq127
title: Data from: Dynamics of short- and long-term association between a bacterial plant pathogen and its arthropod vector

description: The dynamics of association between pathogens and vectors can strongly
 influence epidemiology. It has been proposed that wilt disease epidemics
 in cucurbit populations are sustained by persistent colonization of beetle
 vectors (Acalymma vittatum) by the bacterial phytopathogen Erwinia
 tracheiphila. We developed a qPCR method to quantify E. tracheiphila in
 whole beetles and frass and used it to assess pathogen acquisition and
 retention following variable exposure to infected plants. We found that
 (i) E. tracheiphila is present in frass in as little as three hours after
 feeding on infected plants and can be transmitted with no incubation
 period by vectors given brief exposure to infected plants, but also by
 persistently colonized vectors several weeks following exposure; (ii)
 duration of exposure influences rates of long-term colonization; (iii)
 frass infectivity (assessed via inoculation experiments) reflects
 bacterial levels in frass samples across time; and (iv) vectors rarely
 clear E. tracheiphila infections, but suffer no apparent loss of fitness.
 These results describe a pattern conducive to the effective maintenance of
 E. tracheiphila within cucurbit populations.
description: Dryad_Frass_qPCRThis file contains the raw and processed qPCR reads from the frass experimentsDryad_Beetle_qPCRThis file contains the qPCR raw and processed data from the whole beetle experimentsDryad_Transmission_and_FitnessData from the pathogen transmission and fitness experiments are contained in this file
DOI: 10.5061/dryad.g333421
title: Data from: Adaptation and constraint in the evolution of the mammalian backbone

description: Background: The axial skeleton consists of repeating units (vertebrae)
 that are integrated through their development and evolution. Unlike most
 tetrapods, vertebrae in the mammalian trunk are subdivided into distinct
 thoracic and lumbar modules, resulting in a system that is constrained in
 terms of count but highly variable in morphology. This study asks how
 thoracolumbar regionalization has impacted adaptation and evolvability
 across mammals. Using geometric morphometrics, we examine evolutionary
 patterns in five vertebral positions from diverse mammal species
 encompassing a broad range of locomotor ecologies. We quantitatively
 compare the effects of phylogenetic and allometric constraints, and
 ecological adaptation between regions, and examine their impact on
 evolvability (disparity and evolutionary rate) of serially-homologous
 vertebrae. Results: Although phylogenetic signal and allometry are evident
 throughout the trunk, the effect of locomotor ecology is partitioned
 between vertebral positions. Lumbar vertebral shape correlates most
 strongly with ecology, differentiating taxa based on their use of
 asymmetric gaits. Similarly, disparity and evolutionary rates are also
 elevated posteriorly, indicating a link between the lumbar region,
 locomotor adaptation, and evolvability. Conclusion: Vertebral
 regionalization in mammals has facilitated rapid evolution of the
 posterior trunk in response to selection for locomotion and static body
 support.
description: LandmarksLandmark datalabelsSpecies and ecological data associated with the landmark data
DOI: 10.5061/dryad.b8262
title: Data from: Genetic diversification and dispersal of taro (Colocasia esculenta (L.) Schott)

description: Taro (Colocasia esculenta (L.) Schott) is widely distributed in tropical
 and sub-tropical areas. However, its origin, diversification and dispersal
 remain unclear. While taro genetic diversity has been documented at the
 country and regional levels in Asia and the Pacific, few reports are
 available from Americas and Africa where it has been introduced through
 human migrations. We used eleven microsatellite markers to investigate the
 diversity and diversification of taro accessions from nineteen countries
 in Asia, the Pacific, Africa and America. The highest genetic diversity
 and number of private alleles were observed in Asian accessions, mainly
 from India. While taro has been diversified in Asia and the Pacific mostly
 via sexual reproduction, clonal reproduction with mutation appeared
 predominant in African and American countries investigated. Bayesian
 clustering revealed a first genetic group of diploids from the
 Asia-Pacific region and to a second diploid-triploid group mainly from
 India. Admixed cultivars between the two genetic pools were also found. In
 West Africa, most cultivars were found to have originated from India. Only
 one multi-locus lineage was assigned to the Asian pool, while cultivars in
 Madagascar originated from India and Indonesia. The South African
 cultivars shared lineages with Japan. The Caribbean Islands cultivars were
 found to have originated from the Pacific, while in Costa Rica they were
 from India or admixed between Indian and Asian groups. Taro dispersal in
 the different areas of Africa and America is thus discussed in the light
 of available records of voyages and settlements.
description: Chair_2016_dataGenotypica data (SSR) and descriptive data