cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j3127
title: Data from: Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations

description: Humans have exploited the earth's metal resources for thousands of
 years leaving behind a legacy of toxic metal contamination and poor water
 quality. The southwest of England provides a well-defined example, with a
 rich history of metal mining dating to the Bronze Age. Mine water washout
 continues to negatively impact water quality across the region where brown
 trout (Salmo trutta L.) populations exist in both metal-impacted and
 relatively clean rivers. We used microsatellites to assess the genetic
 impact of mining practices on trout populations in this region. Our
 analyses demonstrated that metal-impacted trout populations have low
 genetic diversity and have experienced severe population declines.
 Metal-river trout populations are genetically distinct from clean-river
 populations, and also from one another, despite being geographically
 proximate. Using approximate Bayesian computation (ABC), we dated the
 origins of these genetic patterns to periods of intensive mining activity.
 The historical split of contemporary metal-impacted populations from
 clean-river fish dated to the Medieval period. Moreover, we observed two
 distinct genetic populations of trout within a single catchment and dated
 their divergence to the Industrial Revolution. Our investigation thus
 provides an evaluation of contemporary population genetics in showing how
 human-altered landscapes can change the genetic makeup of a species.
description: Salmo trutta
 genotypesGenotypes for 15
 populations (641 individuals - full-sibs removed) at 23 microsatellite
 loci in Genalex formatDryad_Genotypes_Masterfile.xlsx
DOI: 10.5061/dryad.74hp1kt
title: Data from: Low siring success of females with an acquired male function illustrates the legacy of sexual dimorphism in constraining the breakdown of dioecy

description: Evolutionary transitions from dioecy to functional hermaphroditism must
 overcome the inertia of sexual dimorphism because modified males or
 females will express the opposite sexual function for which their
 phenotypes have been optimized. We tested this prediction by assessing the
 siring success of monoecious individuals of the plant Mercurialis annua
 with an acquired male function but that are phenotypically still
 female-like. We found that pollen dispersed by female-like monoecious
 individuals was ~ 1/3 poorer at siring outcrossed offspring than pollen
 from monoecious individuals with an alternative male-like inflorescence.
 We conclude that whereas dioecy might evolve from functional
 hermaphroditism by conferring upon individuals certain benefits of sexual
 specialization, reversion from a strategy of separate to one of combined
 sexes must overcome constraints imposed by the advantages of sexual
 dimorphism. The breakdown of dioecy must therefore often be limited to
 situations in which outcrossing cannot be maintained and where selection
 favors a capacity for inbreeding by functional hermaphrodites.
description: dataset_Santos_et al.
 2018 Ecol lettPlant phenotypic data
 from experiments 1, and 2 as described in the
 manuscript.
DOI: 10.5061/dryad.f8426
title: Data from: Carotenoid-based bill coloration functions as a social, not sexual, signal in songbirds (Aves: Passeriformes)

description: Many animals use coloration to communicate with other individuals. While
 the signalling role of avian plumage colour is relatively well studied,
 there has been much less research on coloration in avian bare parts.
 However, bare parts could be highly informative signals as they can show
 rapid changes in coloration. We measured bill colour (a ubiquitous bare
 part) in over 1600 passerine species and tested whether interspecific
 variation in carotenoid-based coloration is consistent with signalling to
 potential mates or signalling to potential rivals in a competitive
 context. Our results suggest that carotenoid bill coloration primarily
 evolved as a signal of dominance, as this type of coloration is more
 common in species that live in social groups in the non-breeding season,
 and species that nest in colonies; two socio-ecological conditions that
 promote frequent agonistic interactions with numerous and/or unfamiliar
 individuals. Additionally, our study suggests that carotenoid bill
 coloration is independent of the intensity of past sexual selection, as it
 is not related to either sexual dichromatism or sexual size dimorphism.
 These results pose a significant challenge to the conventional view that
 carotenoid-based avian coloration has evolved as a developmentally costly,
 condition-dependent sexual signal. We also suggest that bare part
 ornamentation may often signal different information than plumage
 ornaments.
description: Bill Colour in
 PasserinesBill colour and life
 history variables for 1605 species of Passerine birds, from Africa,
 Australia and New Zealand. This data set includes red-chromaticity values
 for the upper and lower mandible of male and female specimens for each
 species, as measured from plates in bird handbooks (see text of article
 for details). Additionally we include data on non-breeding sociality,
 breeding dispersion, sexual size dimorphism, sexual dichromatism and body
 size, collected from bird handbooks and from Dale et al. 2007. Proc R Soc
 B 274:2971-2979 (see text for details).
DOI: 10.5061/dryad.81k4v
title: Data from: Does source population size affect performance in new environments?

description: Small populations are predicted to perform poorly relative to large
 populations when experiencing environmental change. To explore this
 prediction in nature, data from reciprocal transplant, common garden, and
 translocation studies were compared meta-analytically. We contrasted
 changes in performance resulting from transplantation to new environments
 among individuals originating from different sized source populations from
 plants and salmonids. We then evaluated the effect of source population
 size on performance in natural common garden environments and the
 relationship between population size and habitat quality. In ‘home-away’
 contrasts, large populations exhibited reduced performance in new
 environments. In common gardens, the effect of source population size on
 performance was inconsistent across life-history stages (LHS) and
 environments. When transplanted to the same set of new environments, small
 populations either performed equally well or better than large
 populations, depending on life stage. Conversely, large populations
 outperformed small populations within native environments, but only at
 later life stages. Population size was not associated with habitat
 quality. Several factors might explain the negative association between
 source population size and performance in new environments: (i) stronger
 local adaptation in large populations and antagonistic pleiotropy, (ii)
 the maintenance of genetic variation in small populations, and (iii)
 potential environmental differences between large and small populations.
description: Source.Population.Size.Performance.In.Novel.EnvironmentsMeta-analysis data: Performance of natural populations when transplanted to novel natural environments, with associated source population size information.
DOI: 10.5061/dryad.p2h11s7
title: Data from: Rodent seed predators and a dominant grass competitor affect coexistence of co-occurring forb species that vary in seed size

description: 1. Propagule size and number often vary by several orders of magnitude
 among co-occurring plant species. Explaining the maintenance of this
 variation and understanding how propagule size contributes to coexistence
 remains a central challenge for community ecologists. The dominant
 paradigm is that a competition-colonization trade-off maintains
 interspecific variation in seed size, but empirical support is limited and
 other coexistence mechanisms, such as size-dependent seed predation, have
 not been examined. 2. We examined how seed size, fecundity, and other
 functional traits of 18 co-occurring perennial forbs trade-off with both
 vulnerability to rodent seed predation and competitive response to a
 community dominant perennial bunchgrass. We added seeds of these species
 to 1 m2 plots at 10 sites where we factorially manipulated rodent seed
 predation and competition from the community dominant, Festuca campestris.
 For a given plot, seeds of each species were added at densities that
 reflected the fecundity (i.e. per capita seed production) for each
 species. Moreover, we varied total seed density among plots by adding
 seeds at one of five relative densities (0, 0.25. 0.5, 1.0 and 1.5 times
 each species’ fecundity) to examine how fecundity affected overall
 recruitment for each species. 3. There was a trade-off between seed size
 and fecundity, as expected, but larger seed size was also associated with
 greater plant height, lower C/N ratios, and lower water use efficiency,
 suggesting that seed size represented a “resource acquisitive” trait
 syndrome (as quantified by trait principal component scores). 4. In the
 field experiment, the suppressive effects of seed predation on seed
 recruitment rate increased with increasing seed size. In contrast,
 smaller-seeded species with less resource acquisitive traits were more
 negatively affected by competition from F. campestris than were species
 with more resource acquisitive traits. 5. Synthesis. While the
 competition-colonization trade-off has been the predominant mechanism
 thought to maintain coexistence among species that vary in fecundity and
 seed size, our work suggests that susceptibility to rodent seed predation
 and competitive response to community dominants represent alternative
 mechanisms that can differentially influence plant recruitment of species
 based on their seed size and associated traits.
description: Maronetal2018JEcolThis file contains data on recruitment from experimental seed additions. All data were collected in the blackfoot valley in western Montana by the authors. Please refer to the README file for metadata.
DOI: 10.5061/dryad.133b9
title: Data from: BMI and WHR are reflected in female facial shape and texture: a geometric morphometric image analysis

description: Facial markers of body composition are frequently studied in evolutionary
 psychology and are important in computational and forensic face
 recognition. We assessed the association of body mass index (BMI) and
 waist-to-hip ratio (WHR) with facial shape and texture (color pattern) in
 a sample of young Middle European women by a combination of geometric
 morphometrics and image analysis. Faces of women with high BMI had a wider
 and rounder facial outline relative to the size of the eyes and lips, and
 relatively lower eyebrows. Furthermore, women with high BMI had a brighter
 and more reddish skin color than women with lower BMI. The same facial
 features were associated with WHR, even though BMI and WHR were only
 moderately correlated. Yet BMI was better predictable than WHR from facial
 attributes. After leave-one-out cross-validation, we were able to predict
 25% of variation in BMI and 10% of variation in WHR by facial shape.
 Facial texture predicted only about 3-10% of variation in BMI and WHR.
 This indicates that facial shape primarily reflects total fat proportion,
 rather than the distribution of fat within the body. The association of
 reddish facial texture in high-BMI women may be mediated by increased
 blood pressure and superficial blood flow as well as diet. Our study
 elucidates how geometric morphometric image analysis serves to quantify
 the effect of biological factors such as BMI and WHR to facial shape and
 color, which in turn contributes to social perception.
description: BMI &
 WHRBody mass index (BMI)
 and waist-to-hip ratio (WHR) for all 49 females used in the
 study.bmiwhr.txtProcrustes shape coordinatesThis 49 x 138 matrix contains for each of the 49 individuals the x and y coordinates of the 69 landmarks. The landmark configurations are Procrustes aligned and symmetrized.proc_coord.txtPC scores of texturePrincipal component scores of facial texture (RGB values of the pixels of the standardized images) for the 49 individuals.PCscores_texture.txt
DOI: 10.5061/dryad.vn63n
title: Data from: Apolipoprotein (ApoE) polymorphism is related to differences in potential fertility in women: a case of antagonistic pleiotropy?

description: The alleles that are detrimental to health, especially in older age, are
 thought to persist in populations because they also confer some benefits
 for individuals (through antagonistic pleiotropy). The ApoE4 allele at the
 ApoE locus, encoding apolipoprotein E (ApoE), significantly increases risk
 of poor health, and yet it is present in many populations at relatively
 high frequencies. Why has it not been replaced by natural selection with
 the health-beneficial ApoE3 allele? ApoE is a major supplier of
 cholesterol precursor for the production of ovarian oestrogen and
 progesterone, thus ApoE has been suggested as the potential candidate gene
 that may cause variation in reproductive performance. Our results support
 this hypothesis showing that in 117 regularly menstruating women those
 with genotypes with at least one ApoE4 allele had significantly higher
 levels of mean luteal progesterone (144.21 pmol l−1) than women with
 genotypes without ApoE4 (120.49 pmol l−1), which indicates higher
 potential fertility. The hormonal profiles were based on daily data for
 entire menstrual cycles. We suggest that the finding of higher
 progesterone in women with ApoE4 allele could provide first strong
 evidence for an evolutionary mechanism of maintaining the ancestral and
 health-worsening ApoE4 allele in human populations.
description: participantsBasic data about study participants.ESTRADIOL dataCumulative, log transformed data on estradiol. Estradiol values were obtained from daily collected saliva samples.PROGESTERONE_dataCumulative, log transformed data on progesterone. Progesterone values were obtained from daily collected saliva samples.
DOI: 10.5061/dryad.s38s0g00
title: Data from: Characteristics of randomised trials on diseases in the digestive system registered in ClinicalTrials.gov - a retrospective analysis

description: Objectives: To evaluate the adequacy of reporting of protocols for
 randomised trials on diseases of the digestive system registered in
 ClinicalTrials.gov and the consistency between primary outcomes, secondary
 outcomes and sample size specified in ClinicalTrials.gov and published
 trials. Design: Randomised phase III trials on adult patients with
 gastrointestinal diseases registered before January 2009 in
 ClinicalTrials.gov were eligible for inclusion. From ClinicalTrials.gov
 all data elements in the database required by the International Committee
 of Medical Journal Editors (ICMJE) member journals were extracted. The
 subsequent publications for registered trials were identified. For
 published trials, data concerning publication date, primary and secondary
 endpoint, sample size, and whether the journal adhered to ICMJE principles
 were extracted. Differences between primary and secondary outcomes, sample
 size and sample size calculations data in ClinicalTrials.gov and in the
 published paper were registered. Results: 105 trials were evaluated.
 Sixty-six trials (63%) were published. Thirty-one percent of trials were
 registered incorrectly after their completion date. Several data elements
 of the required ICMJE data list were not filled in, with lacking data in
 22% and 11% of cases concerning the primary outcome measure and sample
 size. In 26% of the published papers data of sample size calculations were
 missing and discrepancies between sample size reporting in
 ClinicalTrials.gov and published trials existed. Conclusion: The quality
 of registration of randomised controlled trials still needs improvement.
description: updated_english_version_of_trial_registration_study, finalAn Excel file, with data extracted from the database: ClinicalTrials.gov and related publications. Abbreviations for column headings - see the uploaded ReadMe file.
DOI: 10.5061/dryad.cf137
title: Data from: Sex-specific genetic analysis indicates low correlation between demographic and genetic connectivity in the Scandinavian brown bear (Ursus arctos)

description: Species viability is strongly connected to the degree of gene flow within
 and among populations. Such genetic population connectivity may closely
 track demographic population connectivity or, alternatively, the rate of
 gene flow may change relative to the rate of dispersal. In this study, we
 have explored the relationship between genetic and demographic population
 connectivity using the Scandinavian brown bear as model species, due to
 its pronounced male dispersal and female philopatry. Our expectation,
 based on published demographic data, was that the philopatric females
 shape genetic structure locally whereas the dispersing males act as
 genetic mediators among regions. To test this, we used eight validated
 microsatellite markers on 1531 individuals sampled non-invasively during
 country-wide genetic population monitoring in Sweden and Norway from 2006
 to 2013. First, we determined sex-specific genetic structure and
 substructure across the study area. Second, we compared genetic
 differentiation, migration/gene flow patterns and spatial autocorrelation
 results between the sexes both within and among genetic clusters and
 geographic regions. Our results indicated that demographic connectivity
 was not a reliable indicator of genetic connectivity. On larger geographic
 scales, among genetic clusters, we found no consistent difference in long
 term gene flow and estimated current migration rates between males and
 females. On smaller geographic scales, only females consistently displayed
 significant positive spatial autocorrelation, indicating male-biased small
 scale dispersal. An exception was displayed in one cluster, where males
 showed significant positive spatial autocorrelation, similar to the
 females. The Scandinavian brown bear population has experienced
 substantial recovery over the last decades; however, our results did not
 show any changes in the large scale population structure compared to
 previous studies, suggesting that an increase in population size and
 dispersal of individuals does not necessary lead to increased genetic
 connectivity. Thus, we conclude that estimates of both genetic and
 demographic connectivity should be performed so as not to misconceive the
 reality of wildlife populations.
description: Genotype
 profilesGeoreferenced genotypes
 based on 8 microsatellite markers of 1531 brown bears in
 ScandinaviaData_DRYAD.xlsx
DOI: 10.5061/dryad.jc76f
title: Data from: Locating evolutionary precursors on a phylogenetic tree

description: Conspicuous innovations in the history of life are often preceded by more
 cryptic genetic and developmental precursors. In many cases, these appear
 to be associated with recurring origins of very similar traits in close
 relatives (parallelisms) or striking convergences separated by deep time
 (“deep homologies”). Although the phylogenetic distribution of gain and
 loss of traits hints strongly at the existence of such precursors, no
 models of trait evolution currently permit inference about their location
 on a tree. Here we develop a new stochastic model which explicitly
 captures the dependency implied by a precursor and permits estimation of
 precursor locations. We apply it to the evolution of extrafloral nectaries
 (EFNs), an ecologically significant trait mediating a widespread mutualism
 between plants and ants. In legumes, a species-rich clade with
 morphologically diverse EFNs, the precursor model fits the data on EFN
 occurrences significantly better than conventional models. The model
 generates explicit hypotheses about the phylogenetic location of
 hypothetical precursors, which may help guide future studies of molecular
 genetic pathways underlying nectary position, development and function.
description: Trait data in Nexus
 formatThis is a gzip
 compressed tar archive of six nexus files (and a README file). Each nexus
 file contains the trait data for one of the six types of extra-floral
 nectary as described in the paper. Each file also contains a trees block
 with the same MCC tree used in places in the paper. The nexus file is
 plain text.EFN_traits.tar.gz
DOI: 10.5061/dryad.851jr
title: Data from: Assessing the dynamics of natural populations by fitting individual based models with approximate Bayesian computation

description: 1. Individual based models (IBMs) allow realistic and flexible modelling
 of ecological systems, but their parametrization with empirical data is
 statistically and computationally challenging. Approximate Bayesian
 computation (ABC) has been proposed as an efficient approach for inference
 with IBMs, but its applicability to data on natural populations has not
 been yet fully explored. 2. We construct an IBM for the metapopulation
 dynamics of a species inhabiting a fragmented patch network, and develop
 an ABC method for parametrization of the model. We consider several
 scenarios of data availability from count data to combination of
 mark-recapture and genetic data. We analyse both simulated and real data
 on white-starred robin (Pogonocichla stellata), a passerine bird living in
 montane forest environment in Kenya, and assess how the amount and type of
 data affect the estimates of model parameters and indicators of population
 state. 3. The indicators of the population state could be reliably
 estimated using the ABC method, but full parametrization was not achieved
 due to strong posterior correlations between model parameters. While the
 combination of the data types did not provide more accurate estimates for
 most of the indicators of population state or model parameters than the
 most informative data type (ringing data or genetic data) alone, the
 combined data allowed robust simultaneous estimation of all unknown
 quantities. 4. Our results show that ABC methods provide a powerful and
 flexible technique for parametrizing complex IBMs with multiple data
 sources, and assessing the dynamics of the population in a robust manner.
description: Source code and
 dataThe package provides
 Matlab code for the individual based model and approximate Bayesian
 computation based inference introduced in article "Assessing the
 dynamics of natural populations by fitting individual based models with
 approximate Bayesian computation" by Jukka Sirén, Luc Lens, Laurence
 Cousseau and Otso Ovaskainen accepted for publication in Methods in
 Ecology and Evolution. The package includes also the White-starred robin
 data analyzed in the article.Code.zip