cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.112dg
title: Data from: The Teleost Anatomy Ontology: anatomical representation for the genomics age

description: The rich knowledge of morphological variation among organisms reported in
 the systematic literature has remained in free-text format, impractical
 for use in large-scale synthetic phylogenetic work. This noncomputable
 format has also precluded linkage to the large knowledgebase of genomic,
 genetic, developmental, and phenotype data in model organism databases. We
 have undertaken an effort to prototype a curated, ontology-based
 evolutionary morphology database that maps to these genetic databases
 (http://kb.phenoscape.org) to facilitate investigation into the
 mechanistic basis and evolution of phenotypic diversity. Among the first
 requirements in establishing this database was the development of a
 multispecies anatomy ontology with the goal of capturing anatomical data
 in a systematic and computable manner. An ontology is a formal
 representation of a set of concepts with defined relationships between
 those concepts. Multispecies anatomy ontologies in particular are an
 efficient way to represent the diversity of morphological structures in a
 clade of organisms, but they present challenges in their development
 relative to single-species anatomy ontologies. Here, we describe the
 Teleost Anatomy Ontology (TAO), a multispecies anatomy ontology for
 teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for
 the purpose of annotating varying morphological features across species.
 To facilitate interoperability with other anatomy ontologies, TAO uses the
 Common Anatomy Reference Ontology as a template for its upper level nodes,
 and TAO and ZFA are synchronized, with zebrafish terms specified as
 subtypes of teleost terms. We found that the details of ontology
 architecture have ramifications for querying, and we present general
 challenges in developing a multispecies anatomy ontology, including
 refinement of definitions, taxon-specific relationships among terms, and
 representation of taxonomically variable developmental pathways.
description: Teleost Anatomy Ontology
 (revision 1.144)This data file contains
 the version (1.144) of the Teleost Anatomy Ontology described in Dahdul et
 al. (2010). It is a text file in OBO format
 (http://www.geneontology.org/GO.format.obo-1_2.shtml).teleost_anatomy_rev1.144.oboTeleost Anatomy Ontology (revision 2012-08-10)Version 2012-08-10 of the Teleost Anatomy Ontology incorporates major changes in its development by importing terms from the Vertebrate Skeletal Anatomy Ontology.tao.obo
DOI: 10.5067/suborbital/firexaq2019/data001
title: Fire Influence on Regional to Global Environments and Air Quality Data
DOI: 10.15468/6hsayw
title: University of South Florida Herbarium - Fungi including lichens

description: The collections of fungi (including lichens) at the USF Herbarium consist of a few hundred specimens. Most specimens were collected in Florida during the 21st century and many include photos of the living specimen. Continuing collections focus on documenting the fungi of Florida.
DOI: 10.5061/dryad.rs39059
title: Data from: Fishing pressure impacts the abundance gradient of European lobsters across the borders of a newly established marine protected area

description: Marine protected areas (MPAs) are considered as viable fisheries
 management tools due to their potential benefits of adult spillover and
 recruitment subsidy to nearby fisheries. However,
 before-after-control-impact (BACI) studies that explore the biological and
 fishery effects of MPAs to surrounding fisheries are scarce. We present
 results from a fine-scale spatial gradient study conducted before and
 after the implementation of a 5km2 lobster MPA in southern Norway. A
 significant non-linear response in lobster abundance, estimated as
 catch-per-unit-effort (CPUE) from experimental fishing, was detected
 within two years of protection. After 4 years, CPUE values inside the MPA
 had increased by a magnitude of 2.6 compared to before-protection values.
 CPUE showed a significant non-linear decline from the center of the MPA,
 with a depression immediately outside the border and a plateau in fished
 areas. Overall fishing pressure almost doubled over the course of the
 study. The highest increase in fishing pressure (by a magnitude of 3) was
 recorded within 1 km of the MPA border, providing a plausible cause for
 the depression in CPUE. Taken together, these results demonstrate the need
 to regulate fishing pressure in surrounding areas when MPAs are
 implemented as fishery management tools.
description: TVEDESTRAND hummer
 2010-2016Raw data file- Nillos
 Kleiven et al.Fishing spots
 2009Fishing spots
 2014Fishing spots
 2015Fishing spots
 2016
DOI: 10.5061/dryad.1bj88
title: Data from: What North America’s skeleton crew of megafauna tells us about community disassembly

description: Functional trait diversity is increasingly used to model future changes in
 community structure despite a poor understanding of community
 disassembly's effects on functional diversity. By tracking the
 functional diversity of the North American large mammal fauna through the
 End-Pleistocene megafaunal extinction and up to the present, I show that
 contrary to expectations, functionally unique species are no more likely
 to go extinct than functionally redundant species. This makes total
 functional richness loss no worse than expected given similar taxonomic
 richness declines. However, where current species sit in functional space
 relative to pre-anthropogenic baselines is not random and likely explains
 ecosystem functional changes better than total functional richness
 declines. Prehistoric extinctions have left many extant species
 functionally isolated and future extinctions will cause even more rapid
 drops in functional richness.
description: Table
 S1Functional data for
 large North American mammals used in the analysis.Table
 S3Functional data for
 small, extinct North American mammals used in the analysis simulating
 total mammal functional diversity.Appendix
 S2The
 folder contains all the R script files and data used in the paper. Two
 datasets are trimmed .csv versions of Table S1 and S3 and the third is
 functional data for North American mammals from the EltonTraits 1.0
 database. Wilman, H., Belmaker, J., Simpson, J., la Rosa, de, C.,
 Rivadeneira, M. M., & Jetz, W. (2014). EltonTraits 1.0: species-level
 foraging attributes of the world’s birds and mammals. Ecology, 95(7),
 2027. To recreate all analyses and figures used in the paper, open the
 script “Davis Disassembly Main Code Open First.R”, highlight all the text
 and click run. Make sure that all the script files and data .csv files are
 in the same folder and that that folder is set as your working
 directory.Appendix
 S1Supplementary methods,
 results, figures, and tables for the analysis.Davis Megafauna Dissasembly
 Appendix S1.docx
DOI: 10.15468/dl.qcuz8f
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is DEU.16.10_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Psittaciformes"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001757-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.10gh5
title: Data from: Phylogeny of Tetillidae (Porifera, Demospongiae, Spirophorida) based on three molecular markers

description: Tetillidae are spherical to elliptical cosmopolitan demosponges. The
 family comprises eight genera: namely, Acanthotetilla Burton, 1959,
 Amphitethya Lendenfeld, 1907, Cinachyra Sollas, 1886, Cinachyrella Wilson,
 1925, Craniella Schmidt, 1870, Fangophilina Schmidt, 1880, Paratetilla
 Dendy, 1905, and Tetilla Schmidt, 1868. These genera are characterized by
 few conflicting morphological characters, resulting in an ambiguity of
 phylogenetic relationships. The phylogeny of tetillid genera was
 investigated using the cox1, 18S rRNA and 28S rRNA (C1-D2 domains) genes
 in 88 specimens (8 genera, 28 species). Five clades were identified: (i)
 Cinachyrella, Paratetilla and Amphitethya species, (ii) Cinachyrella
 levantinensis, (iii) Tetilla, (iv) Craniella, Cinachyra and Fangophilina
 and (v) Acanthotetilla. Consequently, the phylogenetic analysis supports
 the monophyly of Tetilla, a genus lacking any known morphological
 synapomorphy. Acanthotetilla is also recovered. In contrast, within the
 first clade, species of the genera Paratetilla and Amphitethya were nested
 within Cinachyrella. Similarly, within the fourth clade, species of the
 genera Cinachyra and Fangophilina were nested within Craniella. As
 previously postulated by taxonomists, the loss of ectodermal
 specialization (i.e., a cortex) has occurred several times independently.
 Nevertheless, the presence or absence of a cortex and its features carry a
 phylogenetic signal. Surprisingly, the common view that assumes close
 relationships among sponges with porocalices (i.e., surface depressions)
 is refuted.
description: COI DNA
 alignmentDNA sequence alignment
 of the cox1 gene in Nexus formatcox1.nex18S rDNA alignmentDNA sequence alignment of the 18S rRNA gene in Nexus format18S.nex28S rDNA alignmentDNA sequence alignment of the 28S rRNA gene in Nexus format28S.nexCOI_18SrRNA_28SrRNA_combined_treePhylogenetic tree presented in Figure 1: Bayesian phylogenetic tree reconstructed from a combined dataset of the cox1 gene and the 18S and 28S rRNA sequences. Secondary structures were taken into account in the model. Newick format.FINAL_COMBINED1-consensus.treCOI treePhylogenetic tree presented in Figure 2: Bayesian phylogenetic tree reconstructed from the COI gene, in Nexus format.final_cox1pos1pos2pos3.nex.con.tre
DOI: 10.5061/dryad.8h67t
title: Data from: Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus: implications for gene discovery

description: Genomic studies have been used to identify genes underlying many important
 plant secondary metabolic pathways. However, genes for salicinoid phenolic
 glycosides (SPGs)—ecologically important compounds with significant
 commercial, cultural, and medicinal applications—remain largely
 undescribed. We used a linkage map derived from a full‐sib population of
 hybrid cottonwoods (Populus spp.) to search for quantitative trait loci
 (QTL) for the SPGs salicortin and HCH‐salicortin. SSR markers and primer
 sequences were used to anchor the map to the V3.0 P. trichocarpa genome.
 We discovered 21 QTL for the two traits, including a major QTL for
 HCH‐salicortin (R2 = .52) that colocated with a QTL for salicortin on
 chr12. Using the V3.0 Populus genome sequence, we identified 2,983
 annotated genes and 1,480 genes of unknown function within our QTL
 intervals. We note ten candidate genes of interest, including a BAHD‐type
 acyltransferase that has been potentially linked to PopulusSPGs. Our
 results complement other recent studies in Populus with implications for
 gene discovery and the evolution of defensive chemistry in a model genus.
 To our knowledge, this is the first study to use a full‐sib mapping
 population to identify QTL intervals and gene lists associated with SPGs.
description: Table S1. Candidate gene
 lists for Populus salicinoid phenolic glycosidesAn Excel file of
 candidate genes from QTL intervals for the salicinoid phenolic glycosides,
 salicortin and HCH-salicortin in a backcross population of hybrid
 cottonwoods (Populus fremontii x P. angustifolia. Each worksheet in the
 file contains the gene lists for a particular interval. In cases where QTL
 intervals overlapped on the same chromosome, the +/- 1.3Mb interval
 pertains to the furthest/nearest point from the chromosome start (i.e.
 co-occurring peaks at 1Mb and 2Mb would have an interval ranging from 0Mb
 to 3.3Mb). Each table includes gene name, start and end positions in bp,
 description. QTL peaks from our study, shared SSR makers from Caseys et
 al. (2015), and candidate genes are all shown in red
 text.Table
 S1.xlsxTable S2. Proposed SPG
 candidate genesThe table summarizes
 gene information for fourteen candidate genes that stand out with regard
 to their potential roles in SPG synthesis or regulation. Data are arranged
 by transcript name, gene name, gene start and end positions in bp, and a
 general description.Table
 S2.xlsx
DOI: 10.5061/dryad.pc5n9
title: Data from: The molecular evolution of spiggin nesting glue in sticklebacks

description: Gene duplication and subsequent divergence can lead to the evolution of
 new functions and lineage-specific traits. In sticklebacks, the successive
 duplication of a mucin gene (MUC19) into a tandemly arrayed, multigene
 family has enabled the production of copious amounts of ‘spiggin’, a
 secreted adhesive protein essential for nest construction. Here, we
 examine divergence between spiggin genes among three-spined sticklebacks
 (Gasterosteus aculeatus) from ancestral marine and derived freshwater
 populations, and propose underpinning gene duplication mechanisms. Sanger
 sequencing revealed substantial diversity among spiggin transcripts,
 including alternatively spliced variants and interchromosomal spiggin
 chimeric genes. Comparative analysis of the sequenced transcripts and all
 other spiggin genes in the public domain support the presence of three
 main spiggin lineages (spiggin A, spiggin B and spiggin C) with further
 subdivisions within spiggin B (B1, B2) and spiggin C (C1, C2). Spiggin A
 had diverged least from the ancestral MUC19, while the spiggin C
 duplicates had diversified most substantially. In silico translations of
 the spiggin gene open reading frames predicted that spiggins A and B are
 secreted as long mucin-like polymers, while spiggins C1 and C2 are
 secreted as short monomers, with putative antimicrobial properties. We
 propose that diversification of duplicated spiggin genes has facilitated
 local adaptation of spiggin to a range of aquatic habitats.
description: Spiggin EST alignment
 for internal RACE-PCR primer designA nucleotide alignment
 of spiggin ESTs generated in an earlier study (Seear et al, 2014, Ecology
 and Evolution 4(8) 1233-1242) used to design internal reverse RACE-PCR
 primers.Intrachromosomal spiggin
 alignment for verification PCRA nucleotide alignment
 of spiggin B/C1 and spiggin B/C2 intrachromosomal genes used to design
 additional internal reverse primers to verify the original
 intrachromosomal PCR products.Full spiggin gene
 alignmentA nucleotide alignment
 of all unique spiggin sequences produced in this study with spiggin
 sequences from the public domain (including all published spiggin cDNAs
 and representatives from each of the six Ensembl gene predictions from the
 2006 draft assembly of G. aculeatus).Working alignment of
 accessions from tables S2 and S3Working alignment of
 MUC19/Spiggin sequence accessions listed in tables S2 and S3 from Seear et
 al. Molecular Ecology 2015, with an additional line for excluded/alignment
 ambiguous regions; note that AB243103 has been duplicated for comparison
 of both forms of spiggin in this accession.working_alignment_of_accessions_from_tables_S2_and_S3.nex
DOI: 10.5061/dryad.g7t04
title: Data from: Impact of caesarean section on mode of delivery, pregnancy-induced and pregnancy-associated disorders, and complications in the subsequent pregnancy in Germany

description: Objectives: To analyze the impact of caesarean section (CS) on mode of
 delivery, pregnancy-induced and pregnancy-associated disorders, as well as
 complications in the subsequent pregnancy within German gynecological
 practices. Methods: 1,801 women with CS and 1,801 matched women with
 vaginal delivery (VD) from the IMS Disease Analyzer database were
 included. The impact of previous CS on the mode of delivery and
 pregnancy-associated disorders as well as complications prior to or during
 birth in the subsequent pregnancy were analyzed. Cox regressions were used
 to determine the influence of CS with regard to these outcomes. Results:
 Medical abortion and single spontaneous delivery were significantly less
 frequent in women with a history of CS compared to VD (OR equal to 0.52
 and 0.04 respectively), whereas CS after CS was the significantly more
 common mode of delivery (79.0% versus 9.3%, OR=36.47). Gestational
 hypertension without significant proteinuria, gestational hypertension
 with significant proteinuria, and polyhydramnios were more frequent in
 women with CS than in women with VD (OR equal to 6.80, 1.71, and 2.29).
 Hemorrhage and maternal care for known or suspected disproportion were
 more common in the CS group than in the VD group (OR equal to 1.34 and
 3.75). Prolonged pregnancy, preterm labor, abnormalities arising from
 forces of labor, and perineal laceration during delivery were
 significantly less frequent in women with CS than in women with VD (OR
 between 0.32 and 0.75), whereas long labor was more common (OR=2.09).
 Conclusion: Women with CS were more likely to undergo further CS and to
 develop major pregnancy-associated diseases in the following pregnancy
 compared to women with VD.
description: caesarean_section1,801 women with caesarean section (CS) and 1,801 matched women with vaginal delivery (VD) from gynecological practices in Germany. Data set includes the patient-id, age, obesity, mode of delivery (CS versus VD) in the first pregnancy and in the second pregnancy, the most common pregnancy-induced diseases, pregnancy-associated disorders and complications prior to or during birth in the subsequent pregnancy. The index date (Indexdate) relates to the physician visit.
DOI: 10.5061/dryad.16nt8
title: Data from: Historical biogeography using species geographical ranges

description: Spatial variation in biodiversity is the result of complex interactions
 between evolutionary history and ecological factors. Methods in historical
 biogeography combine phylogenetic information with current species
 locations to infer the evolutionary history of a clade through space and
 time. A major limitation of most methods for historical biogeographic
 inference is the requirement of single locations for terminal lineages,
 reducing contemporary species geographical ranges to a point in
 two-dimensional space. In reality, geographic ranges usually show complex
 geographic patterns, irregular shapes, or discontinuities. In this
 article, we describe a method for phylogeographic analysis using polygonal
 species geographic ranges of arbitrary complexity. By integrating the
 geographic diversification process across species ranges, we provide a
 method to infer the geographic location of ancestors in a Bayesian
 framework. By modeling migration conditioned on a phylogenetic tree, this
 approach permits reconstructing the geographic location of ancestors
 through time. We apply this new method to the diversification of two
 neotropical bird genera, Trumpeters (Psophia) and Cinclodes ovenbirds. We
 demonstrate the usefulness of our method (called rase) in phylogeographic
 reconstruction of species ancestral locations and contrast our results
 with previous methods that compel researchers to reduce the distribution
 of species to one point in space. We discuss model extensions to enable a
 more general, spatially explicit framework for historical biogeographic
 analysis.
description: rase_0.2-1.tarRange ancestral state estimation (rase) R package used for the analyses. The most up to date version can be found on https://bitbucket.org/ignacioq/rase.Online Appendix about Monte Carlo ErrorMathematical derivations for the Monte Carlo sampling routine used and analyses of Monte Carlo error for approximating the likelihood of a domain.online_appendix.pdf
DOI: 10.15468/dl.bfpa66
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((66.78874 10.88715,134.78520 10.88715,134.78520 38.07288,66.78874 38.07288,66.78874 10.88715))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Leucomeris decora"
 ]
}

 The dataset includes 49 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001756-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xcncdt
title: Occurrence Download

description: A dataset containing 45695 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "GadmGid is ITA.10_1",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Nymphalidae, Papilionidae, Pieridae, Lycaenidae, Hesperiidae, Riodinidae, Hedylidae)"
 ]
}

 The dataset includes 45695 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001758-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.975ecg
title: Occurrence Download

description: A dataset containing 6745 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation)",
 "Country is Kenya",
 "TaxonKey is Giraffa"
 ]
}

 The dataset includes 6745 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001755-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.