cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0453k
title: Data from: Mitochondrial DNA as a tool for reconstructing past life-history traits in mammals

description: Reconstructing the ancestral characteristics of species is a major goal in
 evolutionary and comparative biology. Unfortunately, fossils are not
 always available and sufficiently informative, and phylogenetic methods
 based on models of character evolution can be unsatisfactory. Genomic data
 offer a new opportunity to estimate ancestral character states, through:
 (i) the correlation between DNA evolutionary processes and species
 life-history traits, and (ii) available reliable methods for ancestral
 sequence inference. Here we assess the relevance of mitochondrial DNA –
 the most popular molecular marker in animals – as a predictor of ancestral
 life-history traits in mammals, using the order of Cetartiodactyla as a
 benchmark. Using the complete set of 13 mitochondrial protein-coding
 genes, we show that the lineage-specific nonsynonymous over synonymous
 substitution rate ratio (dN/dS) is closely correlated with the species
 body mass, longevity and age of sexual maturity in Cetartiodactyla, and
 can be used as a marker of ancestral traits provided that the noise
 introduced by short branches is appropriately dealt with. Based on
 ancestral dN/dS estimates, we predict that the first cetartiodactyls were
 relatively small animals (around 20 kg). This finding is in accordance
 with Cope's rule and the fossil record but could not be recovered via
 continuous character evolution methods.
description: Cetartiodactyla_life-historyTraitsLife-history traits values (body mass, longevity and age of sexual maturity) used in the analysis for the 201 Cetartiodactyla species (values were extracted from both AnAge and PanTHERIA databases and the mean was calculated).Higher-order_taxaList of Cetartiodactyla species within each of the 24 clusters (higher-order taxa) in the main analysis.ClustersSuperGeneMito_Cetartio_alignmentNucleotide alignment of the concatenation of the 13 mitochondrial protein-coding genes for 201 Cetartiodactyla species (and five outgroups).SuperGeneMito_Cetartio.fastacompleteMito_phyloBayes.trCetartiodactyla phylogenetic tree obtained from PhyloBayes (CAT GTR Gamma 4 model). Branch lengths are given in number of substitutions per nucleotide site.completeMito_phyloBayes_initial_branchLength_nucleotide.trSuperGeneMito_Cetartio_bppml_branchLength_codon.trCetartiodactyla phylogenetic tree after optimization of branch lengths with bppml (using the YN98 codon model). Branch lengths are given in number of substitutions per codon site.
DOI: 10.5061/dryad.j42c6
title: Data from: Automated DNA-based plant identification for large-scale biodiversity assessment

description: Rapid degradation of tropical forests urges to improve our efficiency in
 large-scale biodiversity assessment. DNA-barcoding can assist greatly in
 this task, but commonly used phenetic approaches for DNA-based
 identifications rely on the existence of comprehensive reference
 databases, which are infeasible for hyperdiverse tropical ecosystems.
 Alternatively, phylogenetic methods are more robust to sparse taxon
 sampling but time-consuming, while multiple alignment of
 species-diagnostic, typically length-variable markers can be problematic
 across divergent taxa. We advocate the combination of phylogenetic and
 phenetic methods for taxonomic assignment of DNA-barcode sequences against
 incomplete reference databases such as GenBank, and we developed a
 pipeline to implement this approach on large-scale plant diversity
 projects. The pipeline workflow includes several steps: database
 construction and curation, query sequence clustering, sequence retrieval,
 distance calculation, multiple alignment and phylogenetic reconstruction.
 We describe the strategies used to establish these steps and the
 optimisation of parameters to fit the selected psbA-trnH marker. We tested
 the pipeline using infertile plant samples and herbivore diet sequences
 from the highly threatened Nicaraguan seasonally dry forest and exploiting
 a valuable purpose-built resource: a partial local reference database of
 plant psbA-trnH. The selected methodology proved efficient and reliable
 for high-throughput taxonomic assignment, and our results corroborate the
 advantage of applying ‘strict’ tree-based criteria to avoid false
 positives. The pipeline tools are distributed as the scripts suite
 ‘BAGpipe’ (pipeline for Biodiversity Assessment using GenBank data), which
 can be readily adjusted to the purposes of other projects and applied to
 sequence-based identification for any marker or taxon.
description: BAGpipe
 AlignmentsMafft Alignments of
 psbA-trnH sequences produced by the BAGpipe.BAGpipeAlignments.zipNicaraguan SDTF Database psbA-trnH SequencesA fasta file containing psbA-trnH sequences of 450 angiosperm samples from the Nicaraguan Seasonally Dry Tropical Forest, with taxonomic and geographic informationNicaraguanSDTFDatabase_psbAtrnH_Seqs.fasta
DOI: 10.82294/dvnfxr9oe
title: COPUS. Territorio: Caquetá. Sector: Cultura. Año: 2025
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2025 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 Caquetá.
DOI: 10.5061/dryad.j326j
title: Data from: Evolutionary origins of a bioactive peptide buried within preproalbumin

description: The de novo evolution of proteins is now considered a frequented route for
 biological innovation, but the genetic and biochemical processes that lead
 to each newly created protein are often poorly documented. The common
 sunflower (Helianthus annuus) contains the unusual gene PawS1
 (Preproalbumin with SFTI-1) that encodes a precursor for seed storage
 albumin; however, in a region usually discarded during albumin maturation,
 its sequence is matured into SFTI-1, a protease-inhibiting cyclic peptide
 with a motif homologous to unrelated inhibitors from legumes, cereals, and
 frogs. To understand how PawS1 acquired this additional peptide with novel
 biochemical functionality, we cloned PawS1 genes and showed that this dual
 destiny is over 18 million years old. This new family of mostly
 backbone-cyclic peptides is structurally diverse, but the
 protease-inhibitory motif was restricted to peptides from sunflower and
 close relatives from its subtribe. We describe a widely distributed,
 potential evolutionary intermediate PawS-Like1 (PawL1), which is matured
 into storage albumin, but makes no stable peptide despite possessing
 residues essential for processing and cyclization from within PawS1. Using
 sequences we cloned, we retrodict the likely stepwise creation of PawS1’s
 additional destiny within a simple albumin precursor. We propose that
 relaxed selection enabled SFTI-1 to evolve its inhibitor function by
 converging upon a successful sequence and structure.
description: Elliott et al. (2014).
 Plant Cell 10.1105/tpc.114.123620 Supplemental DataSupplemental Figures
 1-24, Supplemental Tables 1-11, Supplemental Methods, Supplemental Dataset
 1-8tpc123620Supplemental.rartpc123620_README.pdf
DOI: 10.5061/dryad.g8010
title: Data from: Estimating tempo and mode of Y chromosome turnover: explaining Y chromosome loss with the fragile Y hypothesis

description: Chromosomal sex determination is phylogenetically widespread, having
 arisen independently in many lineages. Decades of theoretical work provide
 predictions about sex chromosome differentiation that are well supported
 by observations in both XY and ZW systems. However, the phylogenetic scope
 of previous work gives us a limited understanding of the pace of sex
 chromosome gain and loss and why Y or W chromosomes are more often lost in
 some lineages than others, creating XO or ZO systems. To gain phylogenetic
 breadth we therefore assembled a database of 4724 beetle species’
 karyotypes and found substantial variation in sex chromosome systems. We
 used the data to estimate rates of Y chromosome gain and loss across a
 phylogeny of 1126 taxa estimated from seven genes. Contrary to our initial
 expectations, we find that highly degenerated Y chromosomes of many
 members of the suborder Polyphaga are rarely lost, and that cases of Y
 chromosome loss are strongly associated with chiasmatic segregation during
 male meiosis. We propose the “fragile Y” hypothesis, that recurrent
 selection to reduce recombination between the X and Y chromosome leads to
 the evolution of a small pseudoautosomal region (PAR), which, in taxa that
 require XY chiasmata for proper segregation during meiosis, increases the
 probability of aneuploid gamete production, with Y chromosome loss. This
 hypothesis predicts that taxa that evolve achiasmatic segregation during
 male meiosis will rarely lose the Y chromosome. We discuss data from
 mammals, which are consistent with our prediction.
description: coleoptera.treesThis file contains 2 nexus files each with 100 trees.seq.dataSupplemental Table 1. Sequences retrieved from GenBank.
DOI: 10.6084/m9.figshare.31158262
title: Raw data for a randomized clinical trial on dentin hypersensitivity in MIH-affected permanent molars

description: <br>This dataset contains anonymized raw data underpinning the analyses of a randomized clinical trial evaluating the desensitizing effects of fluoride varnish (Duraphat®; GI) and a 10% Biosilicate® suspension (GII) in permanent molars affected by molar–incisor hypomineralization (MIH) in children.The dataset includes Visual Analog Scale (VAS) and Schiff Cold Air Sensitivity Scale (SCASS) scores collected at baseline and during the treatment phase (weeks 2, 3, and 4, corresponding to each application visit), as well as during the follow-up period at 1, 2, 4, and 8 weeks after completion of the treatment protocol.<br>
DOI: 10.6084/m9.figshare.31158262.v2
title: Raw data for a randomized clinical trial on dentin hypersensitivity in MIH-affected permanent molars

description: <br>This dataset contains anonymized raw data underpinning the analyses of a randomized clinical trial evaluating the desensitizing effects of fluoride varnish (Duraphat®; GI) and a 10% Biosilicate® suspension (GII) in permanent molars affected by molar–incisor hypomineralization (MIH) in children.The dataset includes Visual Analog Scale (VAS) and Schiff Cold Air Sensitivity Scale (SCASS) scores collected at baseline and during the treatment phase (weeks 2, 3, and 4, corresponding to each application visit), as well as during the follow-up period at 1, 2, 4, and 8 weeks after completion of the treatment protocol.<br>
DOI: 10.5061/dryad.6vd8p
title: Data from: A framework for analysing colour pattern geometry: adjacent colours

description: The analysis of colour pattern geometry is not as well advanced as the
 analysis of colour, although this reflects a lack of an analytical
 framework. The present study proposes an approach based on a consideration
 of which colours are adjacent to each other. Both vertebrate and
 invertebrate eyes do not take static images of the world but move across
 the field of view. As a consequence, the eye takes transects across the
 field of view responding to the colours and luminances within patches and
 to the colour and/or luminance transitions between patches. The framework
 and methods suggested here are based upon transects across colour patterns
 and make it possible to estimate colour pattern parameters that capture
 not only the relative areas of each patch class, but also the relative
 frequencies of colour/luminance transitions or adjacency. This allows
 tests of new hypotheses about colour patterns at the same time as
 including colour, pattern, and texture. Eleven groups of predictions are
 made with respect to the often conflicting needs of communication with
 conspecifics, avoiding predation, and finding food. New phenomena may be
 discovered as a result of these methods and predictions. For example,
 certain colour transitions may be used for species recognition even though
 the same colours are used by all species.
description: AdjacencyAnalysisAndExampleThis zip file contains a MATLAB .m file with a function to convert a zone map to all of the adjacency statistics in my paper. A subdirectory contains all the material I used to do the Anolis example in the paper. Thanks to Manuel Leal for supplying the photo.
DOI: 10.6084/m9.figshare.31158262.v1
title: Raw data for a randomized clinical trial on dentin hypersensitivity in MIH-affected permanent molars

description: <br>This dataset contains anonymized raw data underpinning the analyses of a randomized clinical trial evaluating the desensitizing effects of fluoride varnish (Duraphat®; GI) and a 10% Biosilicate® suspension (GII) in permanent molars affected by molar–incisor hypomineralization (MIH) in children.The dataset includes Visual Analog Scale (VAS) and Schiff Cold Air Sensitivity Scale (SCASS) scores collected at baseline and during the treatment phase (weeks 2, 3, and 4, corresponding to each application visit), as well as during the follow-up period at 1, 2, 4, and 8 weeks after completion of the treatment protocol.<br>
DOI: 10.5061/dryad.kp14p
title: Data from: Efficient inference of recombination hot regions in bacterial genomes

description: In eukaryotes, detailed surveys of recombination rates have shown
 variation at multiple genomic scales and the presence of “hotspots” of
 highly elevated recombination. In bacteria, studies of recombination rate
 variation are less developed, in part because there are few analysis
 methods that take into account the clonal context within which bacterial
 evolution occurs. Here we focus in particular on identifying “hot regions”
 of the genome where DNA is transferred frequently between isolates. We
 present a computationally efficient algorithm based on the recently
 developed "chromosome painting" algorithm, which characterizes
 patterns of haplotype sharing across a genome. We compare the average
 genome wide painting, which principally reflects clonal descent, with the
 painting for each site which additionally reflects the specific deviations
 at the site due to recombination. Using simulated data, we show that hot
 regions have consistently higher deviations from the genome wide average
 than normal regions. We applied our approach to previously analysed
 Escherichia coli genomes, and revealed that the new method is highly
 correlated with the number of recombination events affecting each site
 inferred by ClonalOrigin, a method that is only applicable to small
 numbers of genomes. Furthermore, we analysed recombination hot regions in
 Campylobacter jejuni by using 200 genomes. We identified three
 recombination hot regions which are enriched for genes related to membrane
 proteins. Our approach and its implementation, which is downloadable from
 https://github.com/bioprojects/orderedPainting, will help to develop a new
 phase of population genomic studies of recombination in prokaryotes.
description: Allele sequences of the
 200 C. jejuni isolatesjejuni200_data.zip
DOI: 10.5061/dryad.7pg3d
title: Data from: From baby birds to feathered dinosaurs incipient wings and the evolution of flight

description: Reconstructing the tree of life requires deciphering major evolutionary
 transformations and the functional capacities of fossils with
 “transitional” morphologies. Some of the most iconic, well-studied fossils
 with transitional features are theropod dinosaurs, whose skeletons and
 feathered forelimbs record the origin and evolution of bird flight.
 However, in spite of over a century of discussion, the functions of
 forelimb feathers during the evolution of flight remain enigmatic. Both
 aerodynamic and non-aerodynamic roles have been proposed, but few of the
 form-function relationships assumed by these scenarios have been tested.
 Here, we use the developing wings of a typical extant ground bird (Chukar
 Partridge) as possible analogues/homologues of historical wing forms to
 provide the first empirical evaluation of aerodynamic potential in
 flapping theropod “protowings.” Immature ground birds with underdeveloped,
 rudimentary wings generate useful aerodynamic forces for a variety of
 locomotor tasks. Feather development in these birds resembles feather
 evolution in theropod dinosaurs, and reveals a predictable relationship
 between wing morphology and aerodynamic performance that can be used to
 infer performance in extinct theropods. By spinning an ontogenetic series
 of spread-wing preparations on a rotating propeller apparatus across a
 range of flow conditions and measuring aerodynamic force, we explored how
 changes in wing size, feather structure, and angular velocity might have
 affected aerodynamic performance in dinosaurs choosing to flap their
 incipient wings. At slow angular velocities, wings produced aerodynamic
 forces similar in magnitude to those produced by immature birds during
 behaviors like wing-assisted incline running. At fast angular velocities,
 wings produced forces sufficient to support body weight during flight.
 These findings provide a quantitative, biologically relevant bracket for
 theropod performance and suggest that protowings could have provided
 useful aerodynamic function early in maniraptoran history, with
 improvements in aerodynamic performance attending the evolution of larger
 wings, more effective feather morphologies, and faster angular velocities.
description: Supplemental
 materialSupplemental tables 1-5,
 figures 1-7 and boxes 1-25. Figures, supplemental
 v2.pdf
DOI: 10.5061/dryad.nc4k0
title: Data from: There is no general model for occlusal kinematics in conodonts

description: Knowledge of conodont element function is based largely on analysis of
 morphologically similar P1 elements of few comparatively closely related
 species known from abundant articulated remains. From these, a
 stereotypical pattern of rotational occlusion has been inferred, leading
 to the suggestion that this may represent a general model for ozarkodinin
 P1 elements at the very least. We test the generality of this occlusal
 model through functional analysis of Pseudofurnishius murcianus P1
 elements which, though superficially similar to homologous elements in
 gnathodids, evolved their platform morphology independently, through a
 different mode of morphogenesis, and in a different topological position
 within the element. Our integrated functional analysis of several
 articulated clusters of P1 elements encompassed physical and virtual
 occlusal analyses, constrained by microwear and sharpness analyses. All of
 the evidence supports an occlusal model in which the Pseudofurnishius P1
 elements occluded with the dextral blade located between the rostral face
 of the sinistral blade and the first cusp of the rostral primary process.
 In achieving this, the dorsal and ventral blades guided the opposing
 elements, and the rostral processes of both elements guided the final
 stages of precise occlusion. Spalling and microwear on the non-occlusal
 side of the element evidence malocclusion, requiring the complete
 separation of elements within the occlusal cycle. This occlusal cycle is
 entirely linear, orthogonal to the plane of attachment of the elements.
 Evidently, the rotational occlusal model is not general for P1 elements,
 even for ozarkodinins, and it is likely that among conodonts occlusal
 kinematics are as disparate as element morphologies. Attempts to elucidate
 the diversity of occlusal kinematics and, therefore, feeding ecologies of
 conodonts will be repaid by an understanding of the role of this important
 abundant and diverse clade in Palaeozoic and Mesozoic marine ecosystems.
description: murcianus_cluster_dextralstl file of a Pseudofurnishius murcianus dextral P1 element from a fused pair of elements from a single individual.murcianus_cluster_sinistralstl file of a Pseudofurnishius murcianus sinistral P1 element from a fused pair of elements from a single individual.
DOI: 10.5061/dryad.t6k57
title: Data from: Cooperative breeding favours maternal investment in size over number of eggs in spiders

description: The transition to cooperative breeding may alter maternal investment
 strategies depending on density of breeders, extent of reproductive skew
 and allo-maternal care. Change in optimal investment from solitary to
 cooperative breeding can be investigated by comparing social species with
 non-social congeners. We tested two hypotheses in a mainly semelparous
 system: that social, cooperative breeders, compared to subsocial,
 solitarily breeding congeners, 1) lay fewer and larger eggs because larger
 offspring compete better for limited resources and become reproducers; 2)
 induce egg size variation within clutches as a bet-hedging strategy to
 ensure that some offspring become reproducers. Within two spider genera,
 Anelosimus and Stegodyphus, we compared species from similar habitats and
 augmented the results with a mini-meta-analysis of egg numbers depicted in
 phylogenies. We found that social species indeed laid fewer, larger eggs
 than subsocials, while egg size variation was low overall, giving no
 support for bet-hedging. We propose that the transition to cooperative
 breeding selects for producing few, large offspring because reproductive
 skew and high density of breeders and young create competition for
 resources and reproduction. Convergent evolution has shaped maternal
 strategies similarly in phylogenetically distant species and directed
 cooperatively breeding spiders to invest in quality rather than quantity
 of offspring.
description: Grinsted et al. 2014
 EvolutionEgg data from social and
 subsocial spidersGrinsted et al. 2014
 data.xlsx
DOI: 10.7927/swb0-vr02
title: IPCC AR6 Synthesis Report LR Figure 4.5: Potential synergies and trade-offs between the portfolio of climate change mitigation and adaptation options and the Sustainable Development Goals

description: This figure presents a high-level summary of potential synergies and trade-offs based on the qualitative and quantitative assessment of each individual mitigation or option. The Sustainable Development Goals (SDGs) serve as an analytical framework for the assessment of different sustainable development dimensions, which extend beyond the time frame of 2030 SDG targets. Synergies and trade-offs across all individual options within a sector/system are aggregated into sector/system potentials for the whole mitigation or adaptation portfolio. The length of each bar represents the total number of mitigation or adaptation options under each system/sector. The number of adaptation and mitigation options vary across system/sector, and have been normalised to 100% so that bars are comparable across mitigation, adaptation, system/sector, and SDGs.