cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8rv46
title: Data from: Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

description: 1. Coalescent-based species delimitation methods combine population
 genetic and phylogenetic theory to provide an objective means for
 delineating evolutionarily significant units of diversity. The Generalized
 Mixed Yule Coalescent (GMYC) and the Poisson Tree Process (PTP) are
 methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene
 trees as input, intended for use mostly with single-locus data such as DNA
 barcodes. 2. Here we assess how robust the GMYC and PTP are to different
 phylogenetic reconstruction and branch smoothing methods. We reconstruct
 over 400 ultrametric trees using up to 30 different combinations of
 phylogenetic and smoothing methods and perform over 2,000 separate species
 delimitation analyses across 16 empirical datasets. We then assess how
 variable diversity estimates are, in terms of richness and identity, with
 respect to species delimitation, phylogenetic and smoothing methods. 3.
 The PTP method generally generates diversity estimates that are more
 robust to different phylogenetic methods. The GMYC is more sensitive, but
 provides consistent estimates for BEAST trees. The lower consistency of
 GMYC estimates is likely a result of differences among gene trees
 introduced by the smoothing step. Unresolved nodes (real anomalies or
 methodological artefacts) affect both GMYC and PTP estimates, but have a
 greater effect on GMYC estimates. Branch smoothing is a difficult step and
 perhaps an underappreciated source of bias that may be widespread among
 studies of diversity and diversification. 4. Nevertheless, careful choice
 of phylogenetic method does produce equivalent PTP and GMYC diversity
 estimates. We recommend simultaneous use of the PTP model with any
 model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees
 for obtaining species hypotheses.
description: Gene trees generated and
 usedAll gene trees generated
 and used. Includes raw unsmoothed gene trees, and those smoothed using
 branch smoothing methods. Each of the 16 datasets has up to 30 gene trees
 (exceptions are explained in the main text). File designation includes the
 dataset followed by the phylogenetic method followed by the smoothing
 method. All gene trees are in the NEWICK format.MEE-14-05-266-R1
 TREES.rar
DOI: 10.15159/phytop.160
title: Juusa

description: Phytoplankton biomass, diversity and abundance in samples collected from Lake Juusa during the period 1954-1989.
DOI: 10.5061/dryad.j2n18
title: Data from: Peroxisomal lactate dehydrogenase is generated by basal translational readthrough in mammals

description: Translational readthrough gives rise to low abundance proteins with
 C-terminal extensions beyond the stop codon. To identify functional
 translational readthrough, we estimated the readthrough propensity (RTP)
 of all stop codon contexts of the human genome by a new regression model
 in silico, identified a nucleotide consensus motif for high RTP by using
 this model, and analyzed all readthrough extensions in silico with a new
 predictor for peroxisomal targeting signal type 1 (PTS1). Lactate
 dehydrogenase B (LDHB) showed the highest combined RTP and PTS1
 probability. Experimentally we show that at least 1.6% of the total
 cellular LDHB getting targeted to the peroxisome by a conserved hidden
 PTS1. The readthrough-extended lactate dehydrogenase subunit LDHBx can
 also co-import LDHA, the other LDH subunit into peroxisomes. Peroxisomal
 LDH is conserved in mammals and likely contributes to redox equivalent
 regeneration in peroxisomes.
description: Dataset1Genome-wide in silico analysis of basal translational readthrough. Calculation of readthrough propensity (RTP) of stop codon contexts (SCCs), peroxisomal targeting signals type 1 (PTS) in the extensions. RTP * PTS1 product scores, and other functional elements. Applet for RTP calculation of user-entered SCCs.
DOI: 10.5061/dryad.sd784
title: Data from: Genome data from a 16th century pig illuminate modern breed relationships

description: Ancient DNA (aDNA) provides direct evidence of historical events that have
 modeled the genome of modern individuals. In livestock, resolving the
 differences between the effects of initial domestication and of subsequent
 modern breeding is not straight forward without aDNA data. Here, we have
 obtained shotgun genome sequence data from a sixteenth century pig from
 Northeastern Spain (Montsoriu castle), the ancient pig was obtained from
 an extremely well-preserved and diverse assemblage. In addition, we
 provide the sequence of three new modern genomes from an Iberian pig,
 Spanish wild boar and a Guatemalan Creole pig. Comparison with both
 mitochondrial and autosomal genome data shows that the ancient pig is
 closely related to extant Iberian pigs and to European wild boar. Although
 the ancient sample was clearly domestic, admixture with wild boar also
 occurred, according to the D-statistics. The close relationship between
 Iberian, European wild boar and the ancient pig confirms that Asian
 introgression in modern Iberian pigs has not existed or has been
 negligible. In contrast, the Guatemalan Creole pig clusters apart from the
 Iberian pig genome, likely due to introgression from international breeds.
description: Ancient Pig and modern
 samples primary dataHDY_AncientPig.zip
DOI: 10.5061/dryad.94nk8
title: Data from: Improving the efficacy of web-based educational outreach in ecology

description: Scientists are increasingly engaging the web to provide formal and
 informal science education opportunities. Despite the prolific growth of
 web-based resources, systematic evaluation and assessment of their
 efficacy remains limited. We used clickstream analytics, a widely
 available method for tracking website visitors and their behavior, to
 evaluate &gt;60,000 visits over three years to an educational website
 focused on ecology. Visits originating from search engine queries were a
 small proportion of the traffic, suggesting the need to actively promote
 websites to drive visitation. However, the number of visits referred to
 the website per social media post varied depending on the social media
 platform and the quality of those visits (e.g., time on site and number of
 pages viewed) was significantly lower than visits originating from other
 referring websites. In particular, visitors referred to the website
 through targeted promotion (e.g., inclusion in a website listing classroom
 teaching resources) had higher quality visits. Once engaged in the
 site's core content, visitor retention was high; however, visitors
 rarely used the tutorial resources that serve to explain the site's
 use. Our results demonstrate that simple changes in website design,
 content and promotion are likely to increase the number of visitors and
 their engagement. While there is a growing emphasis on using the web to
 broaden the impacts of biological research, time and resources remain
 limited. Clickstream analytics provides an easily accessible, relatively
 fast and quantitative means by which those engaging in educational
 outreach can improve upon their efforts.
description: Data used for the
 analysis of visitation and visitor behavior to the website Canopy in the
 CloudsThe file
 Goldsmithetal_datafile.csv contains the data used for the analysis of
 visitation and visitor behavior to the website Canopy in the Clouds
 (www.canopyintheclouds.com) associated with Goldsmith et al. (2014) in
 Ecosphere. The file Goldsmithetal_readme.txt contains the relevant
 description, permissions and contacts.Goldsmithetal_datafile.csv
DOI: 10.5061/dryad.52j55
title: Data from: Long-term observation of amphibian populations inhabiting urban and forested areas in Yekaterinburg, Russia

description: This article presents data derived from a 36 year-long uninterrupted
 observational study of amphibian populations living in the city and
 vicinity of Yekaterinburg, Russia. This area is inhabited by six amphibian
 species. Based on a degree of anthropogenic transformation, the urban
 territory is divided into five highly mosaic zones characterized by
 vegetation, temperature, and a distinctive water pollution profile.
 Population data is presented year-by-year for the number of animals, sex
 ratio, and species-specific fecundity including the number and quality of
 spawns for the following amphibian species: Salamandrella keyserligii,
 Rana arvalis, R. temporaria, Lissotriton vulgaris, and Pelophylax
 ridibundus. These data provide an excellent opportunity to assess an urban
 environment from an animal population-wide perspective, as well as
 revealing the forces driving animal adaptation to the anthropogenic
 transformation of habitats.
description: Readme Vershinin et al
 2015Contains descriptions
 and column headings for all files included in this data
 package.Egg_size_Rana_arvalis_engFecundity_Salamandrella_engTemperature_April_May_engFecundity_Rana_temporaria_engPopulations_status_1977_2013_engPopulations_status_1977_2013_eng.csv contains information about presence of particular species of amphibians each year from 1977 to 2013. Each species is marked by a number: 1 – S. keyserlingii, 2 – L. vulgaris, 3 – B. bufo, 4 – R. arvalis, 5 – R. temporaria, 6 – P. ridibundus. Column headings: 1.1. Habitat: The identifier for each wetland where amphibian species were mentioned. 1.2. Zone: The identifier of the urbanization degree at the sample collection site based on our landscape typification scheme for each habitat where amphibian species were registered. Columns 1977 up to 2013 show year-by-year information on the species presence (or disappearance and habitat destruction).Fecundity_Rana_arvalis_engLissotriton_juveniles_morphology_engPelophylax_ridibundus_juveniles_morphology_engRana_arvalis_juv_morphology_engRana_arvalis_ juveniles_morphology_eng.csvRana_temporaria_juv_morphology_engSpawns_number_Rana_arvalis_engSpawns_number_Rana_temporaria_engWater_1980_2013_short_engSpawns_number_Salamandrella_engVegetation_description_engHabitats_coordinates
DOI: 10.5061/dryad.84t75
title: Data from: Gradual assembly of avian body plan culminated in rapid rates of evolution across dinosaur-bird transition

description: [No abstract entered]
description: Brusatte et al. 2014
 Current Biology Dryad File1Supplementary
 appendices: list of phylogenetic characters, phylogenetic character-taxon
 matrix, list of taxon ages, list of supplementary figure captions
 (relevant to Dryad File 2)BrusatteetalRevisionDryadFile1.docxBrusatte et al. 2014 Current Biology Dryad File2Supplementary figuresBrusatteetalRevisionDryadFile2.pdfBrusatte et al. 2014 Current Biology Dryad File3R code (Graeme T. Lloyd)BrusatteetalRevisionDryadFile3.zip
DOI: 10.82294/dvnm6gxcr
title: COPUS. Territorio: Norte de Santander. Sector: Cultura. Año 2024
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2024 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector Cultura (educación informal) en el departamento de Norte de Santander.
DOI: 10.5061/dryad.p6n9s
title: Data from: Impact on offspring methylation patterns of maternal gestational diabetes mellitus and intrauterine growth restraint suggest common genes and pathways linked to subsequent type 2 diabetes risk

description: Size at birth, postnatal weight gain, and adult risk for type 2 diabetes
 may reflect environmental exposures during developmental plasticity and
 may be mediated by epigenetics. Both low birth weight (BW), as a marker of
 fetal growth restraint, and high birth weight (BW), especially after
 gestational diabetes mellitus (GDM), have been linked to increased risk of
 adult type 2 diabetes. We assessed DNA methylation patterns using a bead
 chip in cord blood samples from infants of mothers with GDM (group 1) and
 infants with prenatal growth restraint indicated by rapid postnatal
 catch-up growth (group 2), compared with infants with normal postnatal
 growth (group 3). Seventy-five CpG loci were differentially methylated in
 groups 1 and 2 compared with the controls (group 3), representing 72
 genes, many relevant to growth and diabetes. In replication studies using
 similar methodology, many of these differentially methylated regions were
 associated with levels of maternal glucose exposure below that defined by
 GDM [the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study] or were
 identified as changes observed after randomized periconceptional
 nutritional supplementation in a Gambian cohort characterized by maternal
 deprivation. These studies provide support for the concept that similar
 epigenetic modifications may underpin different prenatal exposures and
 potentially increase long-term risk for diseases such as type 2 diabetes.
description: Ancillary Datasets S1
 and S2 Quilter et al. FASEB J 2014Sample analysis was
 carried out using the Methylation Module of the Illumina Genome Studio
 software for Ancillary Datasets: S1: results have a cut off values of ±
 10% delta beta at a P value &lt; 0.001 equivalent to a DiffScore of &gt;30
 or &lt;-30 on the Illumina significance threshold scale.S2: results have a
 cut off values of ± 5-10% delta beta at a P value &lt; 0.001 equivalent to
 a DiffScore of &gt;30 or &lt;-30 on the Illumina significance threshold
 scale.Ancillary Dataset S1 and S2
 Quilter et al. FASEB 2014.doc
DOI: 10.5061/dryad.9h42f
title: Data from: A generalized residual technique for analyzing complex movement models using earth mover's distance

description: 1. Complex systems of moving and interacting objects are ubiquitous in the
 natural and social sciences. Predicting their behavior often requires
 models that mimic these systems with sufficient accuracy, while accounting
 for their inherent stochasticity. Though tools exist to determine which of
 a set of candidate models is best relative to the others, there is
 currently no generic goodness-of-fit framework for testing how close the
 best model is to the real complex stochastic system. 2. We propose such a
 framework, using a novel application of the Earth mover's distance,
 also known as the Wasserstein metric. It is applicable to any stochastic
 process where the probability of the model's state at time t is a
 function of the state at previous times. It generalizes the concept of a
 residual, often used to analyze 1D summary statistics, to situations where
 the complexity of the underlying model's probability distribution
 makes standard residual analysis too imprecise for practical use. 3. We
 give a scheme for testing the hypothesis that a model is an accurate
 description of a data set. We demonstrate the tractability and usefulness
 of our approach by application to animal movement models in complex,
 heterogeneous environments. We detail methods for visualizing results and
 extracting a variety of information on a given model's quality, such
 as whether there is any inherent bias in the model, or in which situations
 it is most accurate. We demonstrate our techniques by application to data
 on multi-species flocks of insectivore birds in the Amazon rainforest. 4.
 This work provides a usable toolkit to assess the quality of generic
 movement models of complex systems, in an absolute rather than a relative
 sense.
description: Code for calculating
 Earth Mover's metric, together with associated
 filesContains code for
 generating simulated data and calculating the earth mover's metric
 between a model and data.SI_code.zip
DOI: 10.5061/dryad.00ss6
title: Data from: What’s in an outgroup? The impact of outgroup choice on the phylogenetic position of Thalattosuchia (Crocodylomorpha) and the origin of Crocodyliformes

description: Outgroup sampling is a central issue in phylogenetic analysis. However,
 good justification is rarely given for outgroup selection in published
 analyses. Recent advances in our understanding of archosaur phylogeny
 suggest that many previous studies of crocodylomorph and crocodyliform
 relationships have rooted trees on outgroup taxa that are only very
 distantly related to the ingroup (e.g., Gracilisuchus stipanicicorum), or
 might actually belong within the ingroup. Thalattosuchia, a group of
 Mesozoic marine crocodylomorphs, has a controversial phylogenetic
 position—they are recovered as either the sister group to Crocodyliformes,
 in a basal position within Crocodyliformes, or nested high in the
 crocodyliform tree. Thalattosuchians lack several crocodyliform
 apomorphies, but share several character states with derived long-snouted
 forms with a similar ecological habit, suggesting their derived position
 may be the result of convergent evolution. Several of these “shared”
 characters may result from ambiguously worded character state
 definitions—structures that are superficially similar but anatomically
 different in detail are identically coded. A new analysis of
 crocodylomorphs with increased outgroup sampling recovers Thalattosuchia
 as the sister group to Crocodyliformes, distantly related to long-snouted
 crocodyliforms. I also demonstrate that expanding the outgroup sampling of
 previously published matrices results in the recovery of thalattosuchians
 as sister to Crocodyliformes. The exclusion of thalattosuchians from
 Crocodyliformes has numerous implications for large-scale evolutionary
 trends within the group, including extensive convergence in the evolution
 of the secondary palate characteristic of the group. These results
 demonstrate the importance of careful outgroup sampling and character
 construction, and their profound effect on the position of labile clades.
description: Turner and Buckley 2008
 + PostosuchusCharacter-taxon matrix
 of Turner and Buckley (2008) with added scorings for
 PostosuchusSereno and Larsson 2009
 + outgroupsCharacter-taxon matrix
 of Sereno and Larsson (2009) with added scorings for Gracilisuchus and
 PostosuchusSupplementary figures -
 Rev 1Supplementary
 figuresOnline Appendix 1 -
 materials - Rev 1Materials and references
 utilized in character scoringOnline Appendix 2 -
 character list - Rev 1Character list and state
 descriptions of the data matrix used in the phylogenetic
 analysis.Wilberg SystBiol 12-2014
 - Rev 1Character taxon matrix
 developed for this studyTurner and Buckley 2008
 with modified char scoringThe matrix of Turner and
 Buckley 2008 with three characters recoded
DOI: 10.5878/003008
title: The Gothenburg SOM Survey 2016
title: SOM-undersökningen i Göteborg 2016

description: In the autumn of 2016, the first Gothenburg SOM survey was conducted. A total of 7000 randomly selected citizens of Gothenburg answered questions about attitudes and habits in relation to society, opinion and media. Many of the questions in the Gothenburg survey are of a regional nature, and concern local politicians and infrastructure initiatives.

Purpose:

The purpose of the survey is to study attitudes and opinions among residents in Gothenburg municipality, and to follow these over time.
description: Hösten 2016 genomfördes för första gången en SOM-undersökning i Göteborgs stad, där totalt 7000 slumpmässigt utvalda göteborgare fick svara på frågor om attityder och vanor i relation till samhälle, opinion och medier. Många av frågorna i Göteborgsundersökningen är av regional karaktär, och rör lokala politiker, infrastruktursatsningar, och bilden av Göteborg som stad.

Syfte:

Syftet med undersökningen är att belysa attityder och opinioner bland boende i Göteborgs kommun, samt att följa dessa över tid.
DOI: 10.5061/dryad.694
title: Data from: Phylogeny of Trichoptera (caddisflies): characterization of signal and noise within multiple datasets

description: Trichoptera are holometabolous insects with aquatic larvae that, together
 with the Lepidoptera, comprise the Amphiesmenoptera. Despite extensive
 previous morphological work, there has been little phylogenetic agreement
 over the relationship among the three suborders: Annulipalpia,
 Spicipalpia, and Integripalpia, and conflict over the monophyly of
 Spicipalpia. In an effort to resolve this conflict, we sequenced fragments
 of the large and small subunit nuclear ribosomal RNAs (1078 nts; D1, D3,
 V4-5), the nuclear Elongation factor 1α gene (1098 nts), and a fragment of
 mitochondrial COI (411 nts). Seventy adult and larval morphological
 characters were re-analyzed and added to molecular data in a combined
 analysis. We evaluated signal and homoplasy in each of the molecular
 datasets, and attempted to rank the particular datasets according to how
 approriate they were for inferring relationhip among suborders. This
 evaluation included testing for conflict among datasets, comparing tree
 lengths among alternative hypotheses, measuring the left-skew of
 tree-length distributions from maximally divergent sets of taxa,
 evaluating the recovery of expected clades, visualizing whether or not
 substitutions were accumulating with time, and estimating nucleotide
 compositional bias. All these measures cast doubt on the reliability of
 the deep-level signal coming from the nucleotides of the COI and EF-1α
 genes, yet these data could still be included in combined analyses without
 overturning the results from the most conservative marker; the rRNA. The
 different datasets were found to be evolving under extremely different
 rates. A site-specific likelihood method for dealing with combined data
 when parameters are non-overlapping was proposed, and a similar weighting
 scheme under parsimony was evaluated. Among our phylogenetic conclusions,
 we found Annulipalpia to be the most basal of the three suborders, with
 Spicipalpia and Integripalpia forming a clade. Monophyly of Annulipalpia
 and Integripalpia was confirmed, while the relationships among
 spicipalpians remain equivocal.
description: Explanation of Appendix
 1Kjer_Explanation_of_Ap_1.htmAppendix 2Kjer_Appendix_2.htmCorrected Table 1table.docRNA Data SetKjer_RNA_Syst_Biol.htmTrichoptera Data Settrichoptera.nexusCombined Data Setcombined.nexusCOI Tree Base Data SetKjer_COI_TreeBase_1.htmEF1a TreeBase Data SetKjer_EF1a_TreeBase_1.htmCombined Treebase Data SetKjer_Cmbnd_data_TREEBASE_ 1.htm
DOI: 10.5878/003004
title: The Gothenburg SOM Survey 2016
title: SOM-undersökningen i Göteborg 2016

description: In the autumn of 2016, the first Gothenburg SOM survey was conducted. A total of 7000 randomly selected citizens of Gothenburg answered questions about attitudes and habits in relation to society, opinion and media. Many of the questions in the Gothenburg survey are of a regional nature, and concern local politicians and infrastructure initiatives.

Purpose:

The purpose of the survey is to study attitudes and opinions among residents in Gothenburg municipality, and to follow these over time.
description: Hösten 2016 genomfördes för första gången en SOM-undersökning i Göteborgs stad, där totalt 7000 slumpmässigt utvalda göteborgare fick svara på frågor om attityder och vanor i relation till samhälle, opinion och medier. Många av frågorna i Göteborgsundersökningen är av regional karaktär, och rör lokala politiker, infrastruktursatsningar, och bilden av Göteborg som stad.

Syfte:

Syftet med undersökningen är att belysa attityder och opinioner bland boende i Göteborgs kommun, samt att följa dessa över tid.