cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.68722
title: Data from: Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae)

description: The phylogenies of allopolyploids take the shape of networks and cannot be
 adequately represented as bifurcating trees. Especially for
 high-polyploids (i.e., organisms with more than six sets of nuclear
 chromosomes), the signatures of gene homoeolog loss, deep coalescence and
 polyploidy may become confounded, with the result that gene trees may be
 congruent with more than one species network. Herein, we obtained the most
 parsimonious species network by objective comparison of competing
 scenarios involving polyploidization and homoeolog loss in a
 high-polyploid lineage of violets (Viola, Violaceae) mostly or entirely
 restricted to North America, Central America, or Hawaii. We amplified
 homoeologs of the low-copy nuclear gene GPI by single-molecule PCR and the
 chloroplast trnL-F region by conventional PCR for 51 species and
 subspecies. Topological incongruence among GPI homoeolog subclades, owing
 to deep coalescence and two instances of putative loss (or lack of
 detection) of homoeologs, were reconciled by applying the maximum tree
 topology for each subclade. The most parsimonious species network and the
 fossil-based calibration of the homoeolog tree favored monophyly of the
 high-polyploids, which has resulted from allodecaploidization 9–14 Ma ago,
 involving sympatric ancestors from the extant Viola sections
 Chamaemelanium (diploid), Plagiostigma (paleotetraploid), and Viola
 (paleotetraploid). While two of the high-polyploid lineages
 (Boreali-Americanae, Pedatae) remained decaploid, recurrent
 polyploidization with tetraploids of section Plagiostigma within the last
 5 Ma has resulted in two 14-ploid lineages (Mexicanae, Nosphinium) and one
 18-ploid lineage (Langsdorffianae). This implies a more complex
 phylogenetic and biogeographic origin of the Hawaiian violets (Nosphinium)
 than that previously inferred from rDNA data and illustrates the necessity
 of considering polyploidy in phylogenetic and biogeographic
 reconstruction.
description: Online_appendix_1_BEAST_input_fileInput file for BEAST generated using BEAUTY for GPI homoeolog and fossil data. Will open in a text editorOnline_appendix_2_BEAST_output_chronogramChronogram obtained with BEAST based on GPI homoeolog sequence and fossil data, edited in FigTree. Will open in FigTree or another tree editing software.Online_appendix_3_PADRE analysesInput multilabelled GPI gene trees (as .newick files) for PADRE, and output species networks (as graphics) from PADRE. Pdf file.
DOI: 10.5061/dryad.9m6vp
title: Data from: Long-term species loss and homogenization of moth communities in Central Europe

description: As global biodiversity continues to decline steeply, it is becoming
 increasingly important to understand diversity patterns at local and
 regional scales. Changes in land use and climate, nitrogen deposition and
 invasive species are the most important threats to global biodiversity.
 Because land use changes tend to benefit a few species but impede many,
 the expected outcome is generally decreasing population sizes, decreasing
 species richness at local and regional scales, and increasing similarity
 of species compositions across sites (biotic homogenization).
 Homogenization can be also driven by invasive species or effects of soil
 eutrophication propagating to higher trophic levels. In contrast, in the
 absence of increasing aridity, climate warming is predicted to generally
 increase abundances and species richness of poikilotherms at local and
 regional scales. We tested these predictions with data from one of the few
 existing monitoring programmes on biodiversity in the world dating to the
 1960s, where the abundance of 878 species of macro-moths have been
 measured daily at seven sites across Hungary. Our analyses revealed a
 dramatic rate of regional species loss and homogenization of community
 compositions across sites. Species with restricted distribution range,
 specialized diet or dry grassland habitat were more likely than others to
 disappear from the community. In global context, the contrasting effects
 of climate change and land use changes could explain why the predicted
 enriching effects from climate warming are not always realized.
description: Moth captures
 (1962-2009) at seven sites in HungaryThe count of individuals
 of each species at each site and year.valtonen_etal_JAE.xlsx
DOI: 10.5061/dryad.9pn45
title: Data from: Body size evolution in Titanosauriformes (Sauropoda, Macronaria)

description: Titanosauriformes is a conspicuous and diverse group of sauropod dinosaurs
 that inhabited almost all land masses during Cretaceous times. Besides the
 diversity of forms, the clade comprises one of the largest land animals
 found so far, Argentinosaurus, as well as some of the smallest sauropods
 known to date, Europasaurus and Magyarosaurus. They are therefore good
 candidates for studies on body size trends such as the Cope's rule,
 the tendency towards an increase in body size in an evolutionary lineage.
 We used statistical methods to assess body size changes under both
 phylogenetic and nonphylogenetic approaches to identify body size trends
 in Titanosauriformes. Femoral lengths were collected (or estimated from
 humeral length) from 46 titanosauriform species and used as a proxy for
 body size. Our findings show that there is no increase or decrease in
 titanosauriform body size with age along the Cretaceous and that negative
 changes in body size are more common than positive ones (although not
 statistically significant) for most of the titanosauriform subclades (e.g.
 Saltasaridae, Lithostrotia, Titanosauria and Somphospondyli). Therefore,
 Cope's rule is not supported in titanosauriform evolution. Finally,
 we also found a trend towards a decrease of titanosauriform mean body size
 coupled with an increase in body size standard deviation, both supporting
 an increase in body size variation towards the end of Cretaceous.
description: Appendix
 1Femur and/or humerus
 lengths, associated geologic unit, age interval, geographic localities,
 and identification of the material.Appendix
 2Parenthetical notation
 of the trees used to calculate the supertree.Appendix 3 (Mesquite
 file)Data file used in
 Mesquite.Appendix
 4Linear regression of
 humeral length against femoral length.
DOI: 10.5061/dryad.fm3j5
title: Data from: Bimodality of stable and plastic traits in plants

description: We challenged archived genetic mapping data for 36 fruit, seed, flower and
 yield traits in tomato and found an unexpected bimodal distribution in one
 measure of trait variability, the mean coefficient of variation, with some
 traits being consistently more variable than others. To determine the
 degree of conservation of this distribution among higher plants, we
 compared 18 homologous phenotypes, including yield and seed production,
 across different crop species grown in a common ‘crop garden’ experiment.
 The set included 32 varieties of tomato, eggplant, pepper, melon,
 watermelon, sunflower and maize. Estimates of canalization were obtained
 using a ‘canalization replication’ experimental design that generated
 multiple estimates of the coefficient of variation of traits, as well as
 their reaction norms in optimal and water-stressed field plots. A common
 pattern of bimodal distribution of stable and plastic traits was observed
 for all the varieties, and a wild weed (Solanum nigrum). We propose that
 canalization profiles of traits in a variety of taxa were ancestrally
 selected to maximize adaptation and reproductive success
description: CROP GARDEN
 RAWThe raw data of 2012
 experiment for yield canalization.Data collected at the field and in the
 lab as well.2004
 rawData was collected by
 Yaniv Semel at 2004, this data was reanalyzed for this
 paper.
DOI: 10.5061/dryad.n9s7q
title: Data from: Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells

description: Steroid alkaloids have been shown to elicit a wide range of
 pharmacological effects that include anticancer and antifungal activities.
 Understanding the biosynthesis of these molecules is essential to
 bioengineering for sustainable production. Herein, we investigate the
 biosynthetic pathway to cyclopamine, a steroid alkaloid that shows
 promising antineoplastic activities. Supply of cyclopamine is limited, as
 the current source is solely derived from wild collection of the plant
 Veratrum californicum. To elucidate the early stages of the pathway to
 cyclopamine, we interrogated a V. californicum RNA-seq dataset using the
 cyclopamine accumulation profile as a predefined model for gene expression
 with the pattern-matching algorithm Haystack. Refactoring candidate genes
 in Sf9 insect cells led to discovery of four enzymes that catalyze the
 first six steps in steroid alkaloid biosynthesis to produce verazine, a
 predicted precursor to cyclopamine. Three of the enzymes are cytochromes
 P450 while the fourth is a γ-aminobutyrate transaminase; together they
 produce verazine from cholesterol.
description: p450 Gene Tree Augustin
 et al. 2015Augustin_etal_2015_p450.zip
DOI: 10.5061/dryad.22c9s
title: Data from: Linking macro-trends and micro-rates: re-evaluating micro-evolutionary support for Cope’s rule

description: Cope's rule, wherein a lineage increases in body size through time,
 was originally motivated by macro-evolutionary patterns observed in the
 fossil record. More recently, some authors have argued that evidence
 exists for generally positive selection on individual body size in
 contemporary populations, providing a micro-evolutionary mechanism for
 Cope's rule. If larger body size confers individual fitness
 advantages as the selection estimates suggest, thereby explaining
 Cope's rule, then body size should increase over micro-evolutionary
 time scales. We test this corollary by assembling a large database of
 studies reporting changes in phenotypic body size through time in
 contemporary populations, as well as studies reporting average breeding
 values for body size through time. Trends in body size were quite variable
 with an absence of any general trend, and many populations trended toward
 smaller body sizes. Although selection estimates appear to support
 Cope's rule, our results suggest that actual rates of phenotypic
 change for body size do not. We discuss potential reasons for this
 discrepancy and its implications for the understanding of Cope's
 rule.
description: Copes Rule
 Database.csv file with database
 of phenotypic rates of change for traitsCopesRuleDB.csv
DOI: 10.5061/dryad.h9s55
title: Data from: Bird and bat species' global vulnerability to collision mortality at wind farms revealed through a trait-based assessment

description: Mitigation of anthropogenic climate change involves deployments of
 renewable energy worldwide, including wind farms, which can pose a
 significant collision risk to volant animals. Most studies into the
 collision risk between species and wind turbines, however, have taken
 place in industrialized countries. Potential effects for many locations
 and species therefore remain unclear. To redress this gap, we conducted a
 systematic literature review of recorded collisions between birds and bats
 and wind turbines within developed countries. We related collision rate to
 species-level traits and turbine characteristics to quantify the potential
 vulnerability of 9538 bird and 888 bat species globally. Avian collision
 rate was affected by migratory strategy, dispersal distance and habitat
 associations, and bat collision rates were influenced by dispersal
 distance. For birds and bats, larger turbine capacity (megawatts)
 increased collision rates; however, deploying a smaller number of large
 turbines with greater energy output reduced total collision risk per unit
 energy output, although bat mortality increased again with the largest
 turbines. Areas with high concentrations of vulnerable species were also
 identified, including migration corridors. Our results can therefore guide
 wind farm design and location to reduce the risk of large-scale animal
 mortality. This is the first quantitative global assessment of the
 relative collision vulnerability of species groups with wind turbines,
 providing valuable guidance for minimizing potentially serious negative
 impacts on biodiversity.
description: Bird and bat wind farm
 collision data from a literature review of onshore wind
 farmsThis dataset contains
 information on the collision rates of bird and bat species with onshore
 wind turbines, obtained from a literature review of peer and non-peer
 reviewed studies. Also provided are a list of references reviewed, from
 which data was then obtained.These data fed into the trait-based analysis
 of collision rates of species provided in the main
 paper.Collision data from meta
 analysis and references.xlsx
DOI: 10.5061/dryad.nb3r0
title: Data from: Extent and cost of inappropriate use of tumour markers in patients with pulmonary disease: a multicentre retrospective study in Shanghai, China

description: Objectives: The currently implemented healthcare reform in China requires
 substantial capital investment. Although overtreatment results in serious
 waste, inappropriate laboratory use is widespread, and overuse of tumor
 markers (TMs) has attracted increasing attention. Design: Retrospective
 study. Setting: The respiratory, thoracic surgery, and oncology
 departments of three hospitals in Shanghai, from 2014 to 2015.
 Participants: Patients with chronic obstructive pulmonary disease (COPD)
 and primary bronchogenic lung cancer (PLC). Based on clinical guidelines
 and physician experience, the criteria of suitability of TM examinations
 were determined, and the number, cost, and proportion of inappropriate TM
 requests were analyzed. Results: The area under the receiver operating
 characteristic (ROC) curve for CEA+CYFRA211+SCC+NSE in COPD and PLC
 patients was 0.813, in accordance with the cost-effectiveness principle,
 indicating good clinical and health economics values. In the 2706
 patients, 12,496–16,956 (58.27–79.06%) of TM requests were inappropriate.
 Furthermore, the involved expense was 650,200–1,014,156 yuan, accounting
 for 7.69–12.00% of examination expenses, and 1.35–2.11% of hospitalization
 costs. Conclusions: We found that the inappropriate use of TMs was
 widespread for patients with pulmonary disease. Clinicians should use TMs
 strictly according to the guidelines to effectively manage laboratory
 resources and control costs.
description: data
 reviseddata-revised-bmjopen-2017-019051.R1.xlsx
DOI: 10.5061/dryad.vb1pp
title: Data from: Handicap principle implies emergence of dimorphic ornaments

description: Species spanning the animal kingdom have evolved extravagant and costly
 ornaments to attract mating partners. Zahavi's handicap principle
 offers an elegant explanation for this: ornaments signal individual
 quality, and must be costly to ensure honest signalling, making mate
 selection more efficient. Here, we incorporate the assumptions of the
 handicap principle into a mathematical model and show that they are
 sufficient to explain the heretofore puzzling observation of bimodally
 distributed ornament sizes in a variety of species.
description: ALL-ORNAMENT-DATAThis spreadsheet contains all animal ornament data used for statistical tests. Each column is a list of ornament sizes (or other intensity measure) taken from a population of a particular ornamented species, noted in the column header. All data was either acquired directly from authors or extracted from publications, also noted in the header.Ornament software (main)This Matlab script will reproduce all figures in the main manuscript. The software will numerically integrate the ornament model, plot health versus steady state ornament size, analyze fixed points, etc. All code is commented for easy use.SCDT_032514_antler_clean.mSimulated data (fixed gamma)This zip file contains numerically integrated steady state ornament sizes mat files for many population sizes (indicated in the file name) with fixed gamma = 3/2, s = 1/2. Each row represents one fixed point state.simulatedData_gammaThreeHalves.zipSimulated data (fixed population size N=1000)This zip file contains 6 sets of numerically integrated ornament sizes for various gamma values. Each mat file within the zip file represents a steady state for N = 1000, s = 1/2.simulatedData_variousGammaN1000.zipbimodalTestSimulationsThis Matlab function tests data for bimodality, using the least-unimodal-unimodal (LUU) distribution for comparison.ALL-ORNAMENT-DATA (mat files)This zip file contains all the animal ornament data used in statistical tests (this data is replicated in easier-to-read csv file ALL-ORNAMENT-DATA.csvanimalData_matfiles.zipfindGaussianMixThis Matlab function computes the best fitting Gaussian mixture model for animal data based on AIC/BIC.plotHistogramsThis Matlab function plots histograms of all animal data and overlays kernel density estimates.
DOI: 10.5061/dryad.f7bq534
title: Data from: Boreal tree growth exhibits decadal-scale ecological memory to drought and insect defoliation, but no negative response to their interaction

description: 1. Interactions between drought and insect defoliation may dramatically
 alter forest function under novel climate and disturbance regimes, but
 remain poorly understood. We empirically tested two important hypotheses
 regarding tree responses to drought and insect defoliation: 1) trees
 exhibit delayed, persistent, and cumulative growth responses to these
 stressors; 2) physiological feedbacks in tree responses to these stressors
 exacerbate their impacts on tree growth. These hypotheses remain largely
 untested at a landscape scale, yet are critical for predicting forest
 function under novel future conditions given the connection between tree
 growth and demographic processes such as mortality and regeneration. 2. We
 developed a Bayesian hierarchical model to quantify the ecological memory
 of tree growth to past water deficits and insect defoliation events,
 derive antecedent variables reflecting the persistent and cumulative
 effects of these stressors on current growth, and test for their
 interactive effects. The model was applied to extensive tree growth,
 weather, and defoliation survey data from western and eastern regions of
 the Canadian boreal forest impacted by recent drought and defoliation
 events and characterized by contrasting tree compositions, climates, and
 insect defoliators. 3. Results revealed persistent negative tree growth
 responses to past water (all trees) and defoliation (host trees) stress
 lasting 3-6 and 10-12 years, respectively, depending on study region.
 Accounting for the ecological memory of tree growth to water and
 defoliation stress allowed for detection of interactions not previously
 demonstrated. Contrary to expectations, we found evidence for positive
 interactions among non-host trees likely due to reduced water stress
 following defoliation events. Regional differences in ecological memory to
 water stress highlight the role of climate in shaping forest responses to
 drought. 4. Synthesis. Study results suggest negative feedbacks in tree
 responses to drought and insect attack may be weaker than predicted for
 defoliator-dominated boreal forest systems. Instead, insect defoliation
 may offset the impacts of water deficit on boreal tree growth by reducing
 transpirational water demand. This offset mimics increased resistance to
 drought following forest thinning and may lessen growth and mortality
 losses due to increased aridity and more severe insect damage forecast for
 the boreal forest under global change.
description: Tree growth,
 defoliation, and climatic water deficit dataIndividual tree growth
 along with stand-level defoliation and weather data are provided for each
 study region. The individual tree growth data includes ring-width
 observations as well as tree-level variables including age, diameter, and
 species. Detailed information on the growth, defoliation, and weather data
 can be found in the methods section of the accompanying
 article.JEcol-2018-0266.R1.zip
DOI: 10.5061/dryad.0dm8mv1
title: Data from: Fine-scale genetic structure and helping decisions in a cooperatively breeding bird

description: In animal societies, characteristic demographic and dispersal patterns may
 lead to genetic structuring of populations, generating the potential for
 kin selection to operate. However, even in genetically structured
 populations, social interactions may still require kin discrimination for
 cooperative behaviour to be directed towards relatives. Here, we use
 molecular genetics and long-term field data to investigate genetic
 structure in an adult population of long-tailed tits Aegithalos caudatus,
 a cooperative breeder in which helping occurs within extended kin
 networks, and relate this to patterns of helping with respect to kinship.
 Spatial autocorrelation analyses reveal fine-scale genetic structure
 within our population, such that related adults of either sex are
 spatially clustered following natal dispersal, with relatedness among
 nearby males higher than that among nearby females, as predicted by
 observations of male-biased philopatry. This kin structure creates
 opportunities for failed breeders to gain indirect fitness benefits via
 redirected helping, but crucially, most close neighbours of failed
 breeders are unrelated and help is directed towards relatives more often
 than expected by indiscriminate helping. These findings are consistent
 with the effective kin discrimination mechanism known to exist in
 long-tailed tits, and support models identifying kin selection as the
 driver of cooperation.
description: Microsatellite genotypes
 for Aegithalos caudatusContains individual
 genotypes: see ReadMe fileLeedale_2018_data_A_genotypes.txtMicrosatellite genotypes and annual breeding locations of Aegithalos caudatusContains genotypes and annual nest locations of breeding adults: See ReadMe fileLeedale_2018_data_B_breedgenloc.txtSocial pedigree for Aegithalos caudatusContains social pedigree: see ReadMe file.Leedale_2018_data_C_pedigree.txt