cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8ff2v
title: Data from: Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms

description: Although the morphological and physiological changes involved in pregnancy
 in live-bearing reptiles are well studied, the genetic mechanisms that
 underlie these changes are not known. We used the viviparous African
 Ocellated Skink, Chalcides ocellatus, as a model to identify a near
 complete gene expression profile associated with pregnancy using RNA-Seq
 analyses of uterine transcriptomes. Pregnancy in C. ocellatus is
 associated with upregulation of uterine genes involved with metabolism,
 cell proliferation and death, and cellular transport. Moreover, there are
 clear parallels between the genetic processes associated with pregnancy in
 mammals and Chalcides in expression of genes related to tissue remodeling,
 angiogenesis, immune system regulation, and nutrient provisioning to the
 embryo. In particular, the pregnant uterine transcriptome is dominated by
 expression of proteolytic enzymes that we speculate are involved both with
 remodeling the chorioallantoic placenta and histotrophy in the
 omphaloplacenta. Elements of the maternal innate immune system are
 downregulated in the pregnant uterus, indicating a potential mechanism to
 avoid rejection of the embryo. We found a downregulation of major
 histocompatability complex loci and estrogen and progesterone receptors in
 the pregnant uterus. This pattern is similar to mammals but cannot be
 explained by the mammalian model. The latter finding provides evidence
 that pregnancy is controlled by different endocrinological mechanisms in
 mammals and reptiles. Finally, 88% of the identified genes are expressed
 in both the pregnant and the nonpregnant uterus, and thus, morphological
 and physiological changes associated with C. ocellatus pregnancy are
 likely a result of regulation of genes continually expressed in the uterus
 rather than the initiation of expression of unique genes.
description: Identified cDNAs from
 combined pregnant and non-pregnant uteri of Chalcides
 ocellatus.Identified cDNAs from
 combined pregnant and non-pregnant uteri of Chalcides ocellatus.
 Identifications by blastx search against multiple vertebrate
 genomes.HQ-FINAL-CONTIGS_replaced.txt.gzChalcides Illumina read filesChalcides.tgz
DOI: 10.5061/dryad.2gp18
title: Data from: Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate

description: Arabidopsis thaliana inhabits diverse climates and exhibits varied
 phenology across its range. Although A. thaliana is an extremely-well
 studied model species, the relationship between geography, growing season
 climate and its genetic variation is poorly characterized. We used
 redundancy analysis (RDA) to quantify the association of genomic variation
 [214,051 single nucleotide polymorphisms (SNPs)] with geography and
 climate among 1,003 accessions collected from 447 locations in Eurasia. We
 identified climate variables most correlated with genomic variation, which
 may be important selective gradients related to local adaptation across
 the species range. Climate variation among sites of origin explained
 slightly more genomic variation than geographical distance. Large-scale
 spatial gradients and early spring temperatures explained the most genomic
 variation, while growing season and summer conditions explained the most
 after controlling for spatial structure. SNP variation in Scandinavia
 showed the greatest climate structure among regions, possibly because of
 relatively consistent phenology and life history of populations in this
 region. Climate variation explained more variation among non-synonymous
 SNPs than expected by chance, suggesting that much of the climatic
 structure of SNP correlations is due to changes in coding sequence that
 may underlie local adaptation.
description: AccessionClimateData_MECThis multiple page spreadsheet contains data giving climate conditions at the site where accessions were collected, the predicted flowering time status of accessions, and RDA SNP scores for the RDA of raw SNP variation, and the partial RDA after removing spatial structure.SNPs_Lasky_MEC.csvSNPs used in analysis. Also used in Horton et al. (2012) Nature Genetics. Column names give ecotype numbers of accessions. Alleles are arbitrarily designated '0' or '1.'grseasRastersCompressed directory with growing season condition rasters. Data sources and calculation details are found in the Molecular Ecology article (Lasky et al. 2012). These rasters can be read into R using the 'raster' function from the 'raster' package. For further details, and a complete list of included files, please see README_growCond.
DOI: 10.5061/dryad.63q27
title: Data from: Three keys to the radiation of angiosperms into freezing environments

description: Early flowering plants are thought to have been woody species restricted
 to warm habitats1, 2, 3. This lineage has since radiated into almost every
 climate, with manifold growth forms4. As angiosperms spread and climate
 changed, they evolved mechanisms to cope with episodic freezing. To
 explore the evolution of traits underpinning the ability to persist in
 freezing conditions, we assembled a large species-level database of growth
 habit (woody or herbaceous; 49,064 species), as well as leaf phenology
 (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem
 vessels and tracheids) and climate occupancies (exposure to freezing). To
 model the evolution of species’ traits and climate occupancies, we
 combined these data with an unparalleled dated molecular phylogeny (32,223
 species) for land plants. Here we show that woody clades successfully
 moved into freezing-prone environments by either possessing transport
 networks of small safe conduits5 and/or shutting down hydraulic function
 by dropping leaves during freezing. Herbaceous species largely avoided
 freezing periods by senescing cheaply constructed aboveground tissue.
 Growth habit has long been considered labile6, but we find that growth
 habit was less labile than climate occupancy. Additionally, freezing
 environments were largely filled by lineages that had already become herbs
 or, when remaining woody, already had small conduits (that is, the trait
 evolved before the climate occupancy). By contrast, most deciduous woody
 lineages had an evolutionary shift to seasonally shedding their leaves
 only after exposure to freezing (that is, the climate occupancy evolved
 before the trait). For angiosperms to inhabit novel cold environments they
 had to gain new structural and functional trait solutions; our results
 suggest that many of these solutions were probably acquired before their
 foray into the cold.
description: Taxonomic lookup table
 containing clade-level mappings for 15,363 genera of
 Spermatophyta.Spermatophyta_Genera.csvGlobal Woodiness DatabaseGlobalWoodinessDatabase.csvPhylogenetic ResourcesThis archive contains datasets and resulting trees for maximum likelihood phylogeny reconstruction and time-scaling.PhylogeneticResources.zipGlobal Plant Species Freezing Exposure DatabaseThis collection of files documents the processing of the Global Biodiversity Information Facility (GBIF) geographic data and the WorldClim Bioclim data to produce a species freezing exposure datafile which is also included.climate.zipGlobal Leaf Phenology DatabaseGlobalLeafPhenologyDatabase.csv
DOI: 10.15468/dl.nuuctf
title: Occurrence Download

description: A dataset containing 62725 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Aegypius monachus",
 "Year 2021-2026"
 ]
}

 The dataset includes 62725 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001699-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.31159039
title: Temporally Enhanced Cichlid Coloration Dataset (TECCD)

description: One of the datasets used as part of the Animal Boost Net paper.
DOI: 10.6084/m9.figshare.31159039.v1
title: Temporally Enhanced Cichlid Coloration Dataset (TECCD)

description: One of the datasets used as part of the Animal Boost Net paper.
DOI: 10.15468/dl.2qr47q
title: Occurrence Download

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

 The dataset includes 10027 records from 192 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001725-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.93tj942
title: Data from: Effect on electrospun fibers by synthesis of high branching poly-lactic (PLA)

description: Poly-lactic electrospun porous fibers have been widely used in tissue
 engineering scaffolds. However, the application of linear Poly-lactic is
 limited due to its poor hydrophilicity, which leads to phase separation
 and has been seldom used in porous fiber preparation. Instead, using of
 branching Poly-lactic acts as a new effective method to prepare porous
 fibers because it can increase Poly-lactic polar property and make it easy
 to be formulated in the following application. In current study, we
 prepared an ultra-high molecular weight of high branching Poly-lactic with
 glycerol as the initiator by controlling the ring-opening polymerization
 time, adding amount of catalyst and glycerol. The structure, molecular
 weight and thermal properties of copolymers were tested subsequently. The
 result showed that the surface of the high branching Poly-lactic films is
 smooth, hydrophilic and porous. This branching Poly-lactic formed
 electrospun porous fibers, possessed a strong adsorption of silver ion.
 Comparing with the application of linear Poly-lactic and 3-arm Poly-lactic
 materials, our study provided a simple and efficient way to synthesize
 branching Poly-lactic polymer and prepare electrospun porous fibers, which
 may provide potential applications in the field of biomaterials for tissue
 engineering or antibacterial dressing.
description: Effect on electrospun
 fibers by synthesis of high branching PLAThe structure of
 branching PLA was confirmed by IR, 1H-NMR, GPC and DSC.The different
 surface morphology of films was characterized by atomic force microscope
 (AFM), it is found that high branching PLA has higher pores forming
 ability, and its porous nanofibers were prepared by electrospinning (SEM).
 The adsorption of silver ion (Ag+) results showed that porous nanofibers
 of the high branching PLA had a high adsorption of Ag+. The high branching
 PLA has a potential possibility as scaffold for tissue engineering or
 antibacterial dressing
DOI: 10.15468/w78rwb
title: USDA United States National Fungus Collections

description: The USDA-ARS U.S. National Fungus Collections (BPI) currently houses approximately one-million reference specimens. Data associated with over 925,000 specimens have been computerized and are available on-line. In addition reports of fungi on plants provide a comprehensive account of the host range and geographic distribution of fungi on plants throughout the world. Data are continuously added to the databases from herbarium specimens and newly published fungus-host distributions and disease reports. Additional databases contain taxonomic literature references and accurate scientific names of plant pathogenic fungi.
DOI: 10.5061/dryad.76082
title: Data from: Determinants of early survival in marine animal genera

description: Genera by their very nature are expected to be monotypic and
 geographically and environmentally restricted at their origin, and most
 genera do not endure past their stage of first appearance. At the same
 time, those genera that do endure have a capacity to expand greatly in
 geographic range, environmental breadth, and species richness. Here we ask
 what it is that allows some genera and not others to survive past their
 inception. Using occurrence data from the Paleobiology Database, we find
 that initial geographic range has the strongest effect on survival,
 followed by environmental breadth, with the effect of species richness
 weaker on average. The effect of geographic range is strongest if measured
 as the distances spanned by the occurrences of a genus rather than the
 number of distinct areas in which a genus lives. We document substantial
 secular variation in selectivity of early survival. The most striking
 aspect of this variation is that survival is only weakly selective among
 genera that first appear during the Mesozoic. By following genera beyond
 their stage of first appearance, we find that selectivity with respect to
 all factors becomes systematically stronger as cohorts age and genera
 become more differentiated in range, breadth, and richness. This may help
 account for a previously identified statistical effect of genus age on the
 chances of survival.
description: Occurrence data used for
 all analyses in paperThe data for most fields
 come without modification from the Paleobiology Database. In cases where a
 genus name is used in association with more than one higher taxonomic
 name, we attempted to resolve the taxonomic assignments as described in
 our publication. Such assignments are indicated by a hyphenated name in
 the Genus field, for example "Bela-Gastropoda" and
 "Bela-Hexactinellida." These also required modification to the
 Class field in some instances. We assigned collections to our operational
 time intervals using the full spectrum of downloaded stratigraphic fields.
 Most of our assignments to the standard intervals of the Paleobiology
 Database came directly from the downloaded
 "collections.10_my_bin" field, but we consulted other fields if
 this field was blank. Some collections could be assigned to one set of
 time intervals but not the other; these are indicated by "NA" in
 the corresponding field.3Dec2012DryadTable.csv
DOI: 10.5061/dryad.pd40m
title: Data from: Force encoding in muscle spindles during stretch of passive muscle

description: Muscle spindle proprioceptive receptors play a primary role in encoding
 the effects of external mechanical perturbations to the body. During
 externally-imposed stretches of passive, i.e. electrically-quiescent,
 muscles, the instantaneous firing rates (IFRs) of muscle spindles are
 associated with characteristics of stretch such as length and velocity.
 However, even in passive muscle, there are history-dependent transients of
 muscle spindle firing that are not uniquely related to muscle length and
 velocity, nor reproduced by current muscle spindle models. These include
 acceleration-dependent initial bursts, increased dynamic response to
 stretch velocity if a muscle has been isometric, and rate relaxation,
 i.e., a decrease in tonic IFR when a muscle is held at a constant length
 after being stretched. We collected muscle spindle spike trains across a
 variety of muscle stretch kinematic conditions, including systematic
 changes in peak length, velocity, and acceleration. We demonstrate that
 muscle spindle primary afferents in passive muscle fire in direct
 relationship to muscle force-related variables, rather than length-related
 variables. Linear combinations of whole muscle-tendon force and the first
 time derivative of force (dF/dt) predict the entire time course of
 transient IFRs in muscle spindle Ia afferents during stretch (i.e.,
 lengthening) of passive muscle, including the initial burst, the dynamic
 response to lengthening, and rate relaxation following lengthening.
 Similar to acceleration scaling found previously in postural responses to
 perturbations, initial burst amplitude scaled equally well to initial
 stretch acceleration or dF/dt, though later transients were only described
 by dF/dt. The transient increase in dF/dt at the onset of lengthening
 reflects muscle short-range stiffness due to cross-bridge dynamics. Our
 work demonstrates a critical role of muscle cross-bridge dynamics in
 history-dependent muscle spindle IFRs in passive muscle lengthening
 conditions relevant to the detection and sensorimotor response to
 mechanical perturbations to the body, and to previously-described
 history-dependence in perception of limb position.
description: Muscle Spindle Afferent
 Stretch Recordings from Blum et al. 2017PLoSCompBioData2018-09-14.zip
DOI: 10.5061/dryad.9r161
title: Data from: Genome-wide association study of insect bite hypersensitivity in Swedish-born Icelandic horses

description: Insect bite hypersensitivity (IBH) is the most common allergic skin
 disease in horses and is caused by biting midges, mainly of the genus
 Culicoides. The disease predominantly comprises a type I hypersensitivity
 reaction, causing severe itching and discomfort that reduce the welfare
 and commercial value of the horse. It is a multifactorial disorder
 influenced by both genetic and environmental factors, with heritability
 ranging from 0.16 to 0.27 in various horse breeds. The worldwide
 prevalence in different horse breeds ranges from 3% to 60%; it is more
 than 50% in Icelandic horses exported to the European continent and
 approximately 8% in Swedish-born Icelandic horses. To minimize the
 influence of environmental effects, we analyzed Swedish-born Icelandic
 horses to identify genomic regions that regulate susceptibility to IBH. We
 performed a genome-wide association (GWA) study on 104 affected and 105
 unaffected Icelandic horses genotyped using Illumina® EquineSNP50
 Genotyping BeadChip. Quality control and population stratification
 analyses were performed with the GenABEL package in R (λ = 0.81). The
 association analysis was performed using the Bayesian variable selection
 method, Bayes C, implemented in GenSel software. The highest percentage of
 genetic variance was explained by the windows on X chromosomes (0.51% and
 0.36% by 73 and 74 mb), 17 (0.34% by 77 mb), and 18 (0.34% by 26 mb).
 Overlapping regions with previous GWA studies were observed on chromosomes
 7, 9, and 17. The windows identified in our study on chromosomes 7, 10,
 and 17 harbored immune system genes and are priorities for further
 investigation.
description: Genotypes_for_209_horsesThis file contains genotype information on 54,602 SNPs for 209 horses. The genotypes are from Illumina 50K SNP chip.IBH_swed209.pedSNP informationThis file contains information on SNPs.IBH_swed209.mapInformation on samplesThis file contains information on phenotype, gender, region, age, sire and dam for 209 horses.Sample_information.csv
DOI: 10.5061/dryad.j5r716b
title: Data from: Integration of anatomy ontologies and evo-devo using structured Markov models suggests a new framework for modeling discrete phenotypic traits

description: Modeling discrete phenotypic traits for either ancestral character state
 reconstruction or morphology-based phylogenetic inference suffers from
 ambiguities of character coding, homology assessment, dependencies, and
 selection of adequate models. These drawbacks occur because trait
 evolution is driven by two key processes – hierarchical and hidden – which
 are not accommodated simultaneously by the available phylogenetic methods.
 The hierarchical process refers to the dependencies between anatomical
 body parts, while the hidden process refers to the evolution of gene
 regulatory networks underlying trait development. Herein, I demonstrate
 that these processes can be efficiently modeled using structured Markov
 models equipped with hidden states, which resolves the majority of the
 problems associated with discrete traits. Integration of structured Markov
 models with anatomy ontologies can adequately incorporate the hierarchical
 dependencies, while the use of the hidden states accommodates hidden
 evolution of gene regulatory networks and substitution rate heterogeneity.
 I assess the new models using simulations and theoretical synthesis. The
 new approach solves the long-standing "tail color problem," in
 which the trait is scored for species with tails of different colors or no
 tails. It also presents a previously unknown issue called the
 "two-scientist paradox," in which the nature of coding the trait
 and the hidden processes driving the trait's evolution are
 confounded; failing to account for the hidden process may result in a
 bias, which can be avoided by using hidden state models. All this provides
 a clear guideline for coding traits into characters. This paper gives
 practical examples of using the new framework for phylogenetic inference
 and comparative analysis.
description: Supplementary
 MaterialsThis file contains the
 scripts of simulations used in the study, and R functions for the
 construction of structured Markov models.Supplementary_materials.zipSupplementary AppendixThis file explains the math described in the paper.Supplementary_Appendix_Tarasov.pdf
DOI: 10.5061/dryad.p660m
title: Data from: Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight and crown birds

description: Branch lengths—measured in character changes—are an essential requirement
 of clock-based divergence estimation, regardless of whether the fossil
 calibrations used represent nodes or tips. However, a separate set of
 divergence time approaches are typically used to date palaeontological
 trees, which may lack such branch lengths. Among these methods,
 sophisticated probabilistic approaches have recently emerged, in contrast
 with simpler algorithms relying on minimum node ages. Here, using a novel
 phylogenetic hypothesis for Mesozoic dinosaurs, we apply two such
 approaches to estimate divergence times for: (i) Dinosauria, (ii) Avialae
 (the earliest birds) and (iii) Neornithes (crown birds). We find: (i) the
 plausibility of a Permian origin for dinosaurs to be dependent on whether
 Nyasasaurus is the oldest dinosaur, (ii) a Middle to Late Jurassic origin
 of avian flight regardless of whether Archaeopteryx or Aurornis is
 considered the first bird and (iii) a Late Cretaceous origin for
 Neornithes that is broadly congruent with other node- and tip-dating
 estimates. Demonstrating the feasibility of probabilistic time-scaling
 further opens up divergence estimation to the rich histories of extinct
 biodiversity in the fossil record, even in the absence of detailed
 character data.
description: dinosaur_MRP.tntThe MRP matrix submitted to TNT (Goloboff et al. 2008) for performing tree searches; in Hennig86/TNT format.dinosaur_tnt_1000_mpts.tre.zipThe 1,000 MPTs returned from the TNT tree searches; in Newick format (and zipped).dinosaur_str_1000_mpts.tre.zipThe 1,000 MPTs returned from the TNT tree searches with STR taxa reinserted; in Newick format (and zipped).dinosaur_dating_100_mpts.treThe 100 trees randomly sampled and taken forward for dating; in Newick format.consensus.treStrict consensus of the 1,000 MPTs of dinosaur_str_1000_mpts.tre.zip in Newick format.dinosaur_occurrences.xlsxThe dinosaur occurrences used for dating; in MS Excel format.dinosaur_occurrences.txtThe dinosaur occurrences used for dating; in plain text format.dinosaur_tipages.txtThe tip ages (hard lower bounds) used for dating; in plain text format.dinosaur_timelist.txtThe time list data used to generate the three rates used in the cal3 function; in plain text format.cal3_rates_code.RThe R code used to generate the three rates used in the cal3 dating code; in R code format.cal3_rates_code_11-11-16.Rcal3_dating_code.RThe R code used to perform the cal3 dating; in R code format.Hedman_code.RThe R code used to perform the Hedman dating; in R code format.Hedman_code.rcal3_dates.txtThe cal3 dates output from R; in plain text format.Hedman_dates.txtThe Hedman dates output from R; in plain text format.