cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hb653
title: Data from: Phylogenetic relationships and timing of diversification in gonorynchiform fishes inferred using nuclear gene DNA sequences (Teleostei: Ostariophysi)

description: The Gonorynchiformes are the sister lineage of the species-rich Otophysi
 and provide important insights into the diversification of ostariophysan
 fishes. Phylogenies of gonorynchiforms inferred using morphological
 characters and mtDNA gene sequences provide differing resolutions with
 regard to the sister lineage of all other gonorynchiforms (Chanos vs.
 Gonorynchus) and support for monophyly of the two miniaturized lineages
 Cromeria and Grasseichthys. In this study the phylogeny and divergence
 times of gonorynchiforms are investigated with DNA sequences sampled from
 nine nuclear genes and a published morphological character matrix.
 Bayesian phylogenetic analyses reveal substantial congruence among
 individual gene trees with inferences from eight genes placing Gonorynchus
 as the sister lineage to all other gonorynchiforms. Seven gene trees
 resolve Cromeria and Grasseichthys as a clade, supporting previous
 inferences using morphological characters. Phylogenies resulting from
 either concatenating the nuclear genes, performing a multispecies
 coalescent species tree analysis, or combining the morphological and
 nuclear gene DNA sequences resolve Gonorynchus as the living sister
 lineage of all other gonorynchiforms, strongly support the monophyly of
 Cromeria and Grasseichthys, and resolve a clade containing Parakneria,
 Cromeria, and Grasseichthys. The morphological dataset, which includes 13
 gonorynchiform fossil taxa that range in age from Early Cretaceous to
 Eocene, was analyzed in combination with DNA sequences from the nine
 nuclear genes and a relaxed molecular clock to estimate times of
 evolutionary divergence. This “tip dating” strategy accommodates
 uncertainty in the phylogenetic resolution of fossil taxa that provide
 calibration information in the relaxed molecular clock analysis. The
 estimated age of the most recent common ancestor (MRCA) of living
 gonorynchiforms is slightly older than estimates from previous node dating
 efforts, but the molecular tip dating estimated ages of Kneriinae (Kneria,
 Parakneria, Cromeria, and Grasseichthys) and the two paedomorphic
 lineages, Cromeria and Grasseichthys, are considerably younger.
description: gonorynchALLinterleaved alignment of all 9 nuclear genes in nexus formatgonorynchENCalignment of ENC1 nuclear gene in nexus formatgonorynchGLYTalignment of Glyt nuclear gene in nexus formatgonorynchMYHalignment of myh6 nuclear gene in nexus formatgonorynchPLAGalignment of plagl2 nuclear gene in nexus formatgonorynchPTRalignment of Ptr nuclear gene in nexus formatgonorynchRAGalignment of rag1 nuclear gene in nexus formatgonorynchSH3alignment of SH3PX3 nuclear gene in nexus formatgonorynchTBRalignment of tbr1 nuclear gene in nexus formatgonorynchZICalignment of zic1 nuclear gene in nexus formatgonorynchTOTinterleaved alignment of all 9 nuclear genes and morphological data in nexus formatgonorynchTIPaBEAST input file for divergence time estimation
DOI: 10.5061/dryad.321bv
title: Data from: The origin and evolution of phototropins

description: Plant phototropism, the ability to bend toward or away from light, is
 predominantly controlled by blue-light photoreceptors, the phototropins.
 Although phototropins have been well-characterized in Arabidopsis
 thaliana, their evolutionary history is largely unknown. In this study, we
 complete an in-depth survey of phototropin homologs across land plants and
 algae using newly available transcriptomic and genomic data. We show that
 phototropins originated in an ancestor of Viridiplantae (land plants +
 green algae). Phototropins repeatedly underwent independent duplications
 in most major land-plant lineages (mosses, lycophytes, ferns, and seed
 plants), but remained single-copy genes in liverworts and hornworts—an
 evolutionary pattern shared with another family of photoreceptors, the
 phytochromes. Following each major duplication event, the phototropins
 differentiated in parallel, resulting in two specialized, yet partially
 overlapping, functional forms that primarily mediate either low- or
 high-light responses. Our detailed phylogeny enables us to not only
 uncover new phototropin lineages, but also link our understanding of
 phototropin function in Arabidopsis with what is known in Adiantum and
 Physcomitrella (the major model organisms outside of flowering plants). We
 propose that the convergent functional divergences of phototropin paralogs
 likely contributed to the success of plants through time in adapting to
 habitats with diverse and heterogeneous light conditions.
description: phot_alignment_forPhylogenyphototropin alignment trimmed for phylogenetic analysesML_garlimaximum likelihood tree reconstructed using GarliMLBS_raxmlmaximum likelihood bootstrap consensus tree reconstructed using RAxMLBI_mrbayes_conbayesian inference consensus tree reconstructed using MrBayes
DOI: 10.5061/dryad.7k23g
title: Data from: Humans recognize emotional arousal in vocalizations across all classes of terrestrial vertebrates: evidence for acoustic universals

description: Writing over a century ago, Darwin hypothesized that vocal expression of
 emotion dates back to our earliest terrestrial ancestors. If this
 hypothesis is true, we should expect to find cross-species acoustic
 universals in emotional vocalizations. Studies suggest that acoustic
 attributes of aroused vocalizations are shared across many mammalian
 species, and that humans can use these attributes to infer emotional
 content. But do these acoustic attributes extend to non-mammalian
 vertebrates? In this study, we asked human participants to judge the
 emotional content of vocalizations of nine vertebrate species representing
 three different biological classes—Amphibia, Reptilia (non-aves and aves)
 and Mammalia. We found that humans are able to identify higher levels of
 arousal in vocalizations across all species. This result was consistent
 across different language groups (English, German and Mandarin native
 speakers), suggesting that this ability is biologically rooted in humans.
 Our findings indicate that humans use multiple acoustic parameters to
 infer relative arousal in vocalizations for each species, but mainly rely
 on fundamental frequency and spectral centre of gravity to identify higher
 arousal vocalizations across species. These results suggest that
 fundamental mechanisms of vocal emotional expression are shared among
 vertebrates and could represent a homologous signalling system.
description: datafile_Filippi_et_al_2017Data was collected in a laboratory setting. The experimental interface was created in PsychoPy (standalone version). Abbreviations used in column headings: HNR = Harmonic-to-noise-ratio, F0 = mean fundamental frequency, SCG = spectral center of gravity. For each acoustic parameter, ratios between low and high arousal vocalizations within each pair were included in the analysis.data_file.csv
DOI: 10.5061/dryad.v5403
title: Data from: Terminated trials in the ClinicalTrials.gov results database: evaluation of availability of primary outcome data and reasons for termination

description: Background: Clinical trials that end prematurely (or “terminate”) raise
 financial, ethical, and scientific concerns. The extent to which the
 results of such trials are disseminated and the reasons for termination
 have not been well characterized. Methods and Findings: A cross-sectional,
 descriptive study of terminated clinical trials posted on the
 ClinicalTrials.gov results database as of February 2013 was conducted. The
 main outcomes were to characterize the availability of primary outcome
 data on ClinicalTrials.gov and in the published literature and to identify
 the reasons for trial termination. Approximately 12% of trials with
 results posted on the ClinicalTrials.gov results database (905/7,646) were
 terminated. Most trials were terminated for reasons other than accumulated
 data from the trial (68%; 619/905), with an insufficient rate of accrual
 being the lead reason for termination among these trials (57%; 350/619).
 Of the remaining trials, 21% (193/905) were terminated based on data from
 the trial (findings of efficacy or toxicity) and 10% (93/905) did not
 specify a reason. Overall, data for a primary outcome measure were
 available on ClinicalTrials.gov and in the published literature for 72%
 (648/905) and 22% (198/905) of trials, respectively. Primary outcome data
 were reported on the ClinicalTrials.gov results database and in the
 published literature more frequently (91% and 46%, respectively) when the
 decision to terminate was based on data from the trial. Conclusions:
 Trials terminate for a variety of reasons, not all of which reflect
 failures in the process or an inability to achieve the intended goals.
 Primary outcome data were reported most often when termination was based
 on data from the trial. Further research is needed to identify best
 practices for disseminating the experience and data resulting from
 terminated trials in order to help ensure maximal societal benefit from
 the investments of trial participants and others involved with the study.
description: DATA_Terminated Trials
 in ClinicalTrialsgov Results Database (19 Feb 2013)CSV data file containing
 data retrieved from the ClinicalTrials.gov registry and results database
 on February 19, 2013. Additional details are available in the ReadMe
 file.
DOI: 10.5061/dryad.j11m6
title: Data from: Local population density and group composition influence signal-preference relationships in Enchenopa treehoppers (Hemiptera: Membracidae)

description: Many animals exhibit social plasticity—changes in phenotype or behavior in
 response to experience with conspecifics—that change how evolutionary
 processes like sexual selection play out. Here, we asked whether social
 plasticity arising from variation in local population density in male
 advertisement signals and female mate preferences influences the form of
 sexual selection. We manipulated local density and determined whether this
 changed how the distribution of male signals overlapped with female
 preferences—i.e., the signal-mate preference relationship. We specifically
 look at the shape of female mate preference functions, which, when
 compared to signal distributions, provide hypotheses about the form of
 sexual selection. We used Enchenopa binotata treehoppers, a group of plant
 feeding insects that exhibit natural variation in local densities across
 individual host plants, populations, species, and years. We measured male
 signal frequency and female preference functions across the density
 treatments. We found that male signals varied across local social groups,
 but not according to local density. By contrast, female preferences varied
 with local density—favoring higher signal frequencies in denser
 environments. Thus, local density changes the signal-preference
 relationship and, consequently, the expected form of sexual selection. We
 found no influence of sex ratio on the signal-preference relationship. Our
 findings suggest that plasticity arising from variation in local group
 density and composition can alter the form of sexual selection with
 potentially important consequences both for the maintenance of variation
 and for speciation.
description: JEB12994_DryadJEB12994_Fowler-Finn_EbinotataDensities.xlsxJEB12994_Fowler-Finn_EbinotataMalesJEB12994_Fowler-Finn_EbinotataFemalesRawJEB12994_Fowler-Finn_EbinotataFull
DOI: 10.15468/dl.9zxwpm
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-141.31538 62.17086,-133.92481 59.61705,-135.04694 67.87823,-141.06386 70.47073,-141.31538 62.17086))",
 "OccurrenceStatus is Present",
 "TaxonKey is Cephenemyia trompe"
 ]
}

 The dataset includes 22 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000511-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aur7dv
title: Occurrence Download

description: A dataset containing 10027 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bradypus variegatus"
 ]
}

 The dataset includes 10027 records from 175 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000510-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9077
title: Data from: Rapid evolution caused by pollinator loss in Mimulus guttatus

description: Anthropogenic perturbations including habitat loss and emerging disease
 are changing pollinator communities and generating novel selection
 pressures on plant populations. Disruption of plant-pollinator
 relationships is predicted to cause plant mating system evolution,
 although this process has not been directly observed. This study
 demonstrates the immediate evolutionary effects of pollinator loss within
 experimental populations of a predominately outcrossing wildflower.
 Initially equivalent populations evolved for five generations within two
 pollination treatments: abundant bumblebee pollinators vs. no pollinators.
 The populations without pollinators suffered greatly reduced fitness in
 early generations but rebounded as they evolved an improved ability to
 self-fertilize. All populations diverged in floral, developmental, and
 life history traits, but only a subset of characters showed clear
 association with pollination treatment. Pronounced treatment effects were
 noted for anther-stigma separation and autogamous seed set. Dramatic
 allele frequency changes at two chromosomal polymorphisms occurred in the
 no pollinator populations, explaining a large fraction of divergence in
 pollen viability. The pattern of phenotypic and genetic changes in this
 experiment favors a sequential model for the evolution of the multi-trait
 ‘selfing syndrome’ observed throughout angiosperms.
description: Fitness and Inbreeding
 EstimatesGeneration 6 Gene-based
 markersGeneration 6
 phenotypesGeneration 6
 polymorphism countsGeneration 7
 phenotypes
DOI: 10.15482/usda.adc/31021342
title: CLIGEN Parameter Set for Mainland China

description: This is a parameter set for the stochastic weather generator, CLIGEN, for Mainland China. The dataset is modified from the original Creative Commons dataset described in the Wang et al. (2021) publication, <i>CLIGEN Parameter Regionalization for M</i><i>ainland China</i>. The gridded dataset has a 10 km spatial resolution and consists of 96,676 individual parameter sets. Modifications include addition of two missing parameter types, dew point temperature and wind, that were not part of the original dataset and were later added for completeness. Dew point temperature was taken from the coarser ERA5 dataset at 0.25 arc degree resolution, resulting in repeat values in neighboring grid points in the 10 km grid. Surrogate wind parameters were found using the "International Conversions Program", which is a CLIGEN tool that assists in finding appropriate values for missing parameters. In this approach, wind parameters are taken from ground stations in the 2015 US CLIGEN network that were found to have similar parameter values to those of the original grid. The surrogate wind stations are indicated at the bottom of each parameter file. The file labeling convention was also modified to embed the latitude and longitude coordinates of each grid point into the file name. The grid numbers associated with the original file labels are shown at the top of each parameter file.The original data article was published in Earth Systems Science Data Journal:Wang, W., Yin, S., Yu, B., & Wang, S. (2021). CLIGEN parameter regionalization for mainland China. <i>Earth System Science Data Discussions</i>, <i>2021</i>, 1-32. https://doi.org/10.5194/essd-13-2945-2021<br>
DOI: 10.15482/usda.adc/31021342.v1
title: CLIGEN Parameter Set for Mainland China

description: This is a parameter set for the stochastic weather generator, CLIGEN, for Mainland China. The dataset is modified from the original Creative Commons dataset described in the Wang et al. (2021) publication, <i>CLIGEN Parameter Regionalization for M</i><i>ainland China</i>. The gridded dataset has a 10 km spatial resolution and consists of 96,676 individual parameter sets. Modifications include addition of two missing parameter types, dew point temperature and wind, that were not part of the original dataset and were later added for completeness. Dew point temperature was taken from the coarser ERA5 dataset at 0.25 arc degree resolution, resulting in repeat values in neighboring grid points in the 10 km grid. Surrogate wind parameters were found using the "International Conversions Program", which is a CLIGEN tool that assists in finding appropriate values for missing parameters. In this approach, wind parameters are taken from ground stations in the 2015 US CLIGEN network that were found to have similar parameter values to those of the original grid. The surrogate wind stations are indicated at the bottom of each parameter file. The file labeling convention was also modified to embed the latitude and longitude coordinates of each grid point into the file name. The grid numbers associated with the original file labels are shown at the top of each parameter file.The original data article was published in Earth Systems Science Data Journal:Wang, W., Yin, S., Yu, B., & Wang, S. (2021). CLIGEN parameter regionalization for mainland China. <i>Earth System Science Data Discussions</i>, <i>2021</i>, 1-32. https://doi.org/10.5194/essd-13-2945-2021<br>
DOI: 10.5061/dryad.t54h6
title: Data from: Amphibian species' traits, evolutionary history, and environment predict Batrachochytrium dendrobatidis infection patterns, but not extinction risk

description: The fungal pathogen Batrachochytrium dendrobatidis (Bd) has emerged as a
 major agent of amphibian extinction, requiring conservation intervention
 for many susceptible species. Identifying susceptible species is
 challenging, but many aspects of species’ biology are predicted to
 influence the evolution of host resistance, tolerance, or avoidance
 strategies towards disease. In turn, we may expect species exhibiting
 these distinct strategies to differ in their ability to survive epizootic
 disease outbreaks. Here we test for phylogenetic and trait-based patterns
 of Bd infection risk and infection intensity among 302 amphibian species
 by compiling a global dataset of Bd infection surveys across 95 sites. We
 then use best-fit models that associate traits, taxonomy, and environment
 with Bd infection risk and intensity to predict host disease mitigation
 strategies (tolerance, resistance, avoidance) for 122 Neotropical
 amphibian species that experienced epizootic Bd outbreaks, and noted
 species’ persistence or extinction from these events. Aspects of amphibian
 species’ life history, habitat use, and climatic niche were consistently
 linked to variation in Bd infection patterns across sites around the
 world. However, predicted Bd infection risk and intensity based on site
 environment and species traits did not reveal a consistent pattern between
 the predicted host disease mitigation strategy and extinction outcome.
 This suggests that either tolerant or resistant species may have no
 advantage in ameliorating disease during epizootic events, or that other
 factors drive the persistence of amphibian populations during
 chytridiomycosis outbreaks. These results suggest that using a trait-based
 approach may allow us to identify species with resistance or tolerance to
 endemic Bd infections, but that this approach may be insufficient to
 ultimately identify species at risk of extinction from epizootics.
description: Full dataset on disease
 patterns and traitsData on species'
 infection patterns (prevalence and intensity) and survival during
 epizootic events (testing dataset) with full suite of traits. Raw trait
 data (unimputed) is also included. See the Appendix for full details of
 trait data collection and explanation.Greenberg_Evol_Appl_full_dataset.xlsPhylogenyPhylogeny used for testing patterns of phylogenetic signal. Modified from Pyron & Wiens 2013. See Appendix for details on how species were added to the tree.Greenberg_phylo
DOI: 10.5061/dryad.40jd1
title: Data from: Group size differences may mask underlying similarities in social structure: a comparison of female elephant societies

description: Fission-fusion dynamics allow for the costs and benefits of sociality to
 be regulated through changes in group size. There are different modal
 fission-fusion societies, and female Asian and African elephant
 populations examined so far have shown different social structures and
 average group sizes. We report on female Asian elephant social structure
 in Nagarahole and Bandipur National Parks (Kabini population), southern
 India, and examine the role of group size in affecting the outcome of
 social structure analysis in female elephants. Based on five years of
 data, we found the Kabini association network structured into highly
 modular communities that we call clans. A comparison of the Kabini
 dataset, modified to match sampling methods, with previously published Uda
 Walawe Asian elephant and Samburu African elephant data showed that
 measures of association and network structure were more similar amongst
 the Asian elephant populations compared to Samburu. The Samburu population
 formed a hierarchically-nested multilevel society whereas the Asian
 populations did not. However, we found hierarchical levels in all three
 populations using Louvain community detection. Moreover, the average
 community sizes obtained through the Louvain method were not significantly
 different across populations, indicating basic similarities in social
 structure. We examined the effect of average group size on association and
 network statistics. Higher average association index and degree, and lower
 average path length in Samburu compared to Kabini were explained by larger
 average group size in Samburu. Thus, underlying similarities in the social
 networks of species showing fission-fusion dynamics may be obscured by
 differences in average group size.
description: data_for_DryadWe provide data on association indices between individuals that were used for analyses in this paper. Data from Kabini and the Kabini 500-m dataset are provided.