cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kh587f2
title: Data from: Negative biotic interactions drive predictions of distributions for species from a grassland community

description: Understanding the factors that determine species’ geographic distributions
 is important for addressing a wide range of biological questions,
 including where species will be able to maintain populations following
 environmental change. New methods for modelling species distributions
 include the effects of biotic interactions alongside more commonly used
 abiotic variables such as temperature and precipitation; however, it is
 not clear which types of interspecific relationship contribute to shaping
 species distributions and should therefore be prioritised in models. Even
 if some interactions are known to be influential at local spatial scales,
 there is no guarantee they will have similar impacts at macroecological
 scales. Here we apply a novel method based on information theory to
 determine which types of interspecific relationship drive species
 distributions. Our results show that negative biotic interactions such as
 competition have the greatest effect on model predictions for species from
 a California grassland community. This knowledge will help focus data
 collection and improve model predictions for identifying at-risk species.
 Furthermore, our methodological approach is applicable to any kind of
 species distribution model that can be specified with and without
 interspecific relationships.
description: Code accompanying
 Biology Letters article, "Negative biotic interactions drive
 predictions of distributions for species from a grassland
 community"Code to perform total
 length analysisBiologyLetters_StaniczenkoSuttlePearson_Code.zip
DOI: 10.5061/dryad.gh162v1
title: Data from: Explaining the ocean’s richest biodiversity hotspot and global patterns of fish diversity

description: For most marine organisms, species richness peaks in the Central
 Indo-Pacific region and declines longitudinally, a striking pattern that
 remains poorly understood. Here, we used phylogenetic approaches to
 address the causes of richness patterns among global marine regions,
 comparing the relative importance of colonization time, number of
 colonization events, and diversification rates (speciation minus
 extinction). We estimated regional richness using distributional data for
 almost all percomorph fishes (17,435 species total, including ~72% of all
 marine fishes and ~33% of all freshwater fishes). The high diversity of
 the Central Indo-Pacific was explained by its colonization by many
 lineages 5.3–34 million years ago. These relatively old colonizations
 allowed more time for richness to build up through in-situ diversification
 compared to other warm-marine regions. Surprisingly, diversification rates
 were decoupled from marine richness patterns, with clades in low-richness
 cold-marine habitats having the highest rates. Unlike marine richness,
 freshwater diversity was largely derived from a few ancient colonizations,
 coupled with high diversification rates. Our results are congruent with
 the geological history of the marine tropics, and thus may apply to many
 other organisms. Beyond marine biogeography, we add to the growing number
 of cases where colonization and time-for-speciation explain large-scale
 richness patterns instead of diversification rates.
description: Data and scripts from
 Miller et al.: Explaining the ocean’s dominant species richness gradient
 and global patterns of fish diversityData and R scripts from:
 Explaining the ocean’s dominant species richness gradient and global
 patterns of fish diversity Authors: Elizabeth Christina Miller, Kenji T.
 Hayashi, Dongyuan Song, and John J. Wiens Corresponding author: EC Miller
 (ecmiller 'at' email.arizona.edu or lizmiller2633@gmail.com)
 Please contact with questions or requests for additional material. R
 scripts are ordered following the Material and Methods section. Input
 files are included.Miller et al. Dryad September
 11 2018.zip
DOI: 10.5061/dryad.g0db883
title: Data from: Model choice, missing data and taxon sampling impact phylogenomic inference of deep Basidiomycota relationships

description: Resolving deep divergences in the tree of life is challenging even for
 analyses of genome-scale phylogenetic datasets. Relationships between
 Basidiomycota subphyla, the rusts and allies (Pucciniomycotina), smuts and
 allies (Ustilaginomycotina) and mushroom-forming fungi and allies
 (Agaricomycotina) were found particularly recalcitrant both to traditional
 multigene and genome-scale phylogenetics. Here, we address basal
 Basidiomycota relationships using concatenated and gene-tree based
 analyses of various phylogenomic datasets to examine the contribution of
 several potential sources of bias. We evaluate the contribution of
 biological causes (hard polytomy, incomplete lineage sorting) versus
 unmodeled evolutionary processes and factors that exacerbate their effects
 (e.g. fast-evolving sites and long-branch taxa) to inferences of basal
 Basidiomycota relationships. Bayesian MCMC and likelihood mapping analyses
 reject the hard-polytomy with confidence. In concatenated analyses,
 fast-evolving sites and oversimplified models of amino acid substitution
 favored the grouping of smuts with mushroom-forming fungi, often leading
 to maximal bootstrap support in both concatenation and coalescent
 analyses. On the contrary, the most conserved data subsets grouped rusts
 and allies with mushroom-forming fungi, although this relationship proved
 labile, sensitive to model choice, to different data subsets and to
 missing data. Excluding putative long branch taxa, genes with high
 proportions of missing data and/or with strong signal failed to reveal a
 consistent trend toward one or the other topology, suggesting that
 additional sources of conflict are at play. While concatenated analyses
 yielded strong but conflicting support, individual gene trees mostly
 provided poor support for any resolution of rusts, smuts and
 mushroom-forming fungi, suggesting that the true Basidiomycota tree might
 be in a part of tree space that is difficult to access using both
 concatenation and gene-tree based approaches. Inference-based assessments
 of absolute model fit strongly reject best fit models for the vast
 majority of genes, indicating a poor fit of even the most commonly used
 models. While this is consistent with previous assessments of
 site-homogenous models of amino acid evolution, this does not appear to be
 the sole source of confounding signal. Our analyses suggest that
 topologies uniting smuts with mushroom-forming fungi can arise as a result
 of inappropriate modeling of amino acid sites that might be prone to
 systematic bias. We speculate that improved models of sequence evolution
 could shed more light on basal splits in the Basidiomycota, which, for
 now, remain unresolved despite the use of whole genome data.
description: SupplementPrasanna et al supplement.zip
DOI: 10.5061/dryad.mr677g8
title: Data from: Portable bacteria-capturing chip for direct surface-enhanced Raman scattering identification of urinary tract infection pathogens

description: Acute urinary tract infections (UTIs) are one of the most common
 nosocomial bacterial infections, which affect almost 50% of the population
 at least once in their lifetime. UTIs may lead to lethal consequences if
 they are left undiagnosed and untreated properly. Early, rapid and
 accurate uropathogens detection methods play a pivotal role in clinical
 process. In this work, a portable bacteria-grasping surface-enhanced Raman
 scattering (SERS) chip for identification of three species of uropathogens
 (E. coli CFT 073, P. aeruginosa PAO1, and P. mirabilis PRM1) directly from
 culture matrix was reported. The chip was firstly modified with a
 positively-charged NH3+ group, which enable itself grasp the
 negatively-charged bacterial cells through the electrostatic adsorption
 principle. After the bacterial cells were captured by the chip,
 concentrated Ag nanoparticles (NPs) were used to obtain their Raman
 fingerprint spectra with recognizable characteristic peaks and good
 reproducibility. With the help of chemometric method such as discriminant
 analysis (DA), the SERS based chip allows a rapid, successful
 identification of three species of UTI bacteria with a minimal bacterial
 concentration (105 cells/mL) required for clinical diagnostics. In
 addition, this chip could spot the bacterial SERS fingerprints information
 directly from LB culture medium and artificial urine without sample
 pre-treatment. The portable bacteria-grasping SERS based chip provides a
 possibility for fast and easy detection of uropathogens, and viability of
 future development in healthcare applications.
description: Spectra of three
 strainsSpectra of three strains
 including original dataAg NPs
 absorbanceThe characterization of
 the Ag nanoparticlesClassification of three
 pure bacteria after washClassification of three
 bacteria after wash.opjuClassification of three
 bacteria from LB mediumthree bacteria from LB
 mediumUTI-LB.opjthree bacteria spectra from artificial urineUTI-UA.opj
DOI: 10.15468/dl.zg6vkh
title: Occurrence Download

description: A dataset containing 9127 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Australia",
 "OccurrenceStatus is Present",
 "TaxonKey is Carnivora"
 ]
}

 The dataset includes 9127 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001537-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sv62tu
title: Occurrence Download

description: A dataset containing 7114 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Betula ermanii"
 ]
}

 The dataset includes 7114 records from 194 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001543-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60893/figshare.pte.28135751
title: Mass data and fitting parameters

description: This Excel table gives the raw data and the fitting parameters.
DOI: 10.15468/dl.gs66zz
title: Occurrence Download

description: A dataset containing 491 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Apiomerus lanipes"
 ]
}

 The dataset includes 491 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001536-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60893/figshare.pte.28135751.v1
title: Mass data and fitting parameters

description: This Excel table gives the raw data and the fitting parameters.
DOI: 10.15468/dl.kg69un
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Living Specimen)",
 "Country is one of (China, Chinese Taipei, Hong Kong)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Taxus chinensis"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001538-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.88qs138
title: Data from: If you build it, they may not come: modifiable barriers to patient portal use among pre- and post-kidney transplant patients

description: Background: Patient access to health information using electronic patient
 portals is increasingly common. Portal use has the potential to improve
 patients' engagement with their health and is particularly important
 for patients with chronic illness; however, patients’ abilities,
 attitudes, and use of portals is poorly understood. Methods: A
 single-center, cross-sectional survey was conducted of 240 consecutive
 pre- and post-kidney transplant patients of all levels of technological
 proficiency who presented to an urban transplant center in the United
 States. The Patient Information and Technology Assessment-Patient Portal
 (PITA-PP) was used to assess patients' attitudes toward the use of
 patient portals. Results: Most patients surveyed did not use the patient
 portal (n = 176, 73%). Patients were more likely to use the patient portal
 if they were White, highly educated, in the post-transplant period, more
 comfortable with technology, and reported being a frequent internet user
 (p &lt; 0.05). The most common reasons for not using the patient
 portal included: (1) preference for traditional communication, (2) not
 being aware of the portal, (3) low technological proficiency, and (4) poor
 interoperability between the portal at the transplant center and the
 patient’s primary care center. Conclusions: We identified several
 modifiable barriers to patient portal use. Some barriers can be addressed
 by patient education and training on portal use, and federal initiatives
 are underway to improve interoperability; however, a preference for
 traditional communications represents the most prominent barrier.
 Additional strategies are needed to improve portal adoption by encouraging
 acceptance of technologies as a way of clinical communication.
description: Lockwood Dryad
 Submission 6-30-18CSV de-identified data
 (3 indirect identifiers included), documentation (codebook, readme), and
 SAS Syntax used to produce the manuscript
DOI: 10.5061/dryad.g6hr11k
title: Data from: Climate change increases ecogeographic isolation between closely related plants

description: 1. Ecogeographic isolation is a fundamental prezygotic barrier to
 reproduction and a step toward diversification in flowering plants.
 However, whether ecogeographic isolation acts as a reproductive barrier
 between species and thus as a mechanism for species divergence is unclear
 and is expected to change as species distributions shift under climate
 change. 2. Using a Maxent framework, we quantified the extent of
 ecogeographic isolation of nine closely related species of the European
 plant genus Pulmonaria, which lack pre-mating barriers and often form
 hybrids. We investigated ecogeographic isolation under both current
 conditions and four climate change scenarios; two unrelated future climate
 models, each with two predictions of the potential trajectories of climate
 change. 3. Compared with current climates, under these future climate
 scenarios, there will be an increase in mean annual temperature, but not
 in mean annual precipitation in the range of Pulmonaria throughout Europe.
 This will result in a range contraction in three of the nine Pulmonaria
 species, a range expansion in two species, and no clear effect of climate
 change on the ranges of four species. 4. Climate change will result in an
 overall increase in ecogeographic isolation between these species in
 future. In particular, species that have low ecogeographic isolation under
 current conditions are predicted to increase the most in their
 ecogeographic isolation under climate change. 5. Synthesis These results
 highlight that climate change can strongly impact on a major premating
 barrier of closely related species, therefore potentially affect the
 evolutionary trajectory of plants in the future.
description: pulmonaria_dryad_data
DOI: 10.60893/figshare.pte.27944226
title: Supplemental material

description: Supplementary material with more information with additional information about the work.
DOI: 10.60893/figshare.pte.27944226.v1
title: Supplemental material

description: Supplementary material with more information with additional information about the work.
DOI: 10.5061/dryad.g5p7d1c
title: Data from: Estimating environmental suitability

description: Methods for modeling species’ distributions in nature are typically
 evaluated empirically with respect to data from observations of species
 occurrence and, occasionally, absence at surveyed locations. Such models
 are relatively “theory‐free.” In contrast, theories for explaining
 species’ distributions draw on concepts like fitness, niche, and
 environmental suitability. This paper proposes that environmental
 suitability be defined as the conditional probability of occurrence of a
 species given the state of the environment at a location. Any quantity
 that is proportional to this probability is a measure of relative
 suitability and the support of this probability is the niche. This
 formulation suggests new methods for presence‐background modeling of
 species distributions that unify statistical methodology with the
 conceptual framework of niche theory. One method, the plug‐and‐play
 approach, is introduced for the first time. Variations on the
 plug‐and‐play approach were studied with respect to their numerical
 performance on 106 species from an exhaustively sampled presence–absence
 survey of vegetation in the Canton of Vaud, Switzerland. Additionally, we
 looked at the robustness of these methods to the presence of irrelevant
 information and sample size. Although irrelevant variables eroded the
 predictive performance of all methods, these methods were found to be both
 numerically and statistically robust.
description: Estimating-environmental-suitabilityThis folder contains the data and code required to replicate the analyses of Drake and Richards (2018). See README for additional details.
DOI: 10.5061/dryad.2vd6386
title: Data from: Directional selection in the evolution of elongated upper canines in clouded leopards and sabre-toothed cats

description: Extremely developed or specialised traits such as the elongated upper
 canines of extinct sabre-toothed cats are often not analogous to those of
 any extant species, which limits our understanding of their evolutionary
 cause. However, an extant species may have undergone directional selection
 for a similar extreme phenotype. Among living felids, the clouded leopard,
 Neofelis nebulosa, has exceptionally long upper canines for its body size.
 We hypothesised that directional selection generated the elongated upper
 canines of clouded leopards in a manner similar to the process in extinct
 sabre-toothed cats. To test this, we developed an approach that compared
 the effect of directional selection among lineages in a phylogeny using a
 simulation of trait evolution and approximate Bayesian computation. This
 approach was applied to analyse the evolution of upper canine length in
 the Felidae phylogeny. Our analyses consistently showed directional
 selection favouring longer upper canines in the clouded leopard lineage
 and a lineage leading to the sabre-toothed cat with the longest upper
 canines, Smilodon. Most of our analyses detected an effect of directional
 selection for longer upper canines in the lineage leading to another
 sabre-toothed cat, Homotherium, although this selection may have occurred
 exclusively in the primitive species. In all the analyses, the clouded
 leopard and Smilodon lineages showed comparable directional selection.
 This implies that clouded leopards share a selection advantage with
 sabre-toothed cats in having elongated upper canines.
description: Data from Harano &
 Kutsukake 2018 J Evol BiolPosterior observations
 for each parameter (θ0, the trait value for the most recent common
 ancestor; μ0, the baseline evolutionary rate; and drsl, the effect of
 consistent directional selection in a specific branch) of five independent
 MCMC chains.
DOI: 10.5281/zenodo.18327534
title: Multi-objective inverse (MOIn) optimisation proof-of-concept dataset

description: Data set for a case study that serves as proof-of-concept for the multi-objective inverse (MOIn) optimisation methodology.

The case study comprises the Central Western European power system (Belgium, Luxembourg, Netherlands, Germany, France) for 2050 under full decarbonisation. The data is aggregated to 504 timesteps, corresponding to 21 representative days of the year.
DOI: 10.5061/dryad.397c81q
title: Data from: Diversification across biomes in a continental lizard radiation

description: Ecological opportunity is a powerful driver of evolutionary
 diversification, and predicts rapid lineage and phenotypic diversification
 following colonisation of competitor-free habitats. Alternatively,
 topographic or environmental heterogeneity could be key to generating and
 sustaining diversity. We explore these hypotheses in a widespread lineage
 of Australian lizards: the Gehyra variegata group. This clade occurs
 across two biomes: the Australian monsoonal tropics (AMT), where it
 overlaps a separate, larger bodied clade of Gehyra and is largely
 restricted to rocks; and in the larger Australian arid zone (AAZ) where it
 has no congeners and occupies trees and rocks. New phylogenomic data and
 coalescent analyses of AAZ taxa resolve lineages and their relationships
 and reveal high diversity in the western AAZ (Pilbara region). The AMT and
 AAZ radiations represent separate radiations with no difference in
 speciation rates. Most taxa occur on rocks, with small geographic ranges
 relative to widespread generalist taxa across the vast central AAZ.
 Rock-dwelling and generalist taxa differ morphologically, but only the
 lineage-poor central AAZ taxa have accelerated evolution. This accords
 with increasing evidence that lineage and morphological diversity are
 poorly correlated, and suggests environmental heterogeneity and refugial
 dynamics have been more important than ecological release in elevating
 lineage diversity.
description: ASTRAL bootstrap
 trees499 bootstrap trees
 (input file 1 for ASTRAL-II)ASTRAL_499bootstraps_varpuncASTRAL gene trees499 gene trees (input file 2 for ASTRAL-II)ASTRAL_499gene_realbesttrees_varpuncRAxML concatenationConcatenated alignment of 547 loci (input file for RAxML)RAxML_ec_varpunc_alignments_547loci.tar.gzStarBEAST2 alignmentAlignment of 106 loci (input file for StarBEAST2)Gehyra_starBeast2_DNA_106loci_89specimens_complete_aln_seqs_FASTAS.zipReadme fileDetailed information on the data package
DOI: 10.5281/zenodo.15228050
title: Multi-objective inverse (MOIn) optimisation proof-of-concept dataset

description: Data set for a case study that serves as proof-of-concept for the multi-objective inverse (MOIn) optimisation methodology.

The case study comprises the Central Western European power system (Belgium, Luxembourg, Netherlands, Germany, France) for 2050 under full decarbonisation. The data is aggregated to 504 timesteps, corresponding to 21 representative days of the year.