cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.dvkcqh
title: Occurrence Download

description: A dataset containing 1097 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-1.45946 37.56448,-2.14154 36.97647,-4.75616 36.79462,-5.53296 36.24648,-5.28666 35.97096,-1.42157 36.73391,-0.9858 37.36899,-1.45946 37.56448))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Ziziphus lotus, Periploca angustifolia, Maytenus senegalensis europaeus, Pinus pinaster, Juniperus turbinata, Pancratium maritimum, Ononis talaverae, Ononis ramosissima, Lycium intricatum, Withania frutescens, Malcolmia littorea, Suaeda vera, Sarcocornia fruticosa, Sarcocornia perennis, Crithmum maritimum, Asteriscus maritimus, Cakile maritima, Ruppia maritima, Ammophila arenaria)"
 ]
}

 The dataset includes 1097 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001731-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vn730
title: Data from: Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

description: PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse
 Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher
 plants) represent perhaps the oldest and most diverse lineage of
 carnivorous plants. However, despite numerous studies seeking to elucidate
 their evolutionary relationships, the early-diverging relationships remain
 unresolved. METHODS: To explore the utility of phylogenomic data sets for
 resolving relationships among the carnivorous Caryophyllales, we sequenced
 10 transcriptomes, including all the carnivorous genera except those in
 the rare West African liana family Dioncophyllaceae. We used a variety of
 methods to infer the species tree, examine gene tree conflict, and infer
 paleopolyploidy events. KEY RESULTS: Phylogenomic analyses supported the
 monophyly of the carnivorous Caryophyllales, with a crown age of 68–83
 million years. In contrast to previous analyses, we recovered the
 remaining noncore Caryophyllales as nonmonophyletic, although the node
 supporting this relationship contained a significant amount of gene tree
 discordance. We present evidence that the clade contains at least seven
 independent paleopolyploidy events, previously unresolved nodes from the
 literature have high levels of gene tree conflict, and taxon sampling
 influences topology even in a phylogenomic data set, regardless of the use
 of coalescent or supermatrix methods. CONCLUSIONS: Our data demonstrate
 the importance of carefully considering gene tree conflict and taxon
 sampling in phylogenomic analyses. Moreover, they provide a remarkable
 example of the propensity for paleopolyploidy in angiosperms, with at
 least seven such events in a clade of less than 2500 species.
description: Carnivory
 DataMaterial used in paper
 for analyses and making figuresCarnivoryData.tar.gz
DOI: 10.15468/626e3q
title: University of Central Oklahoma Herbarium - Fungi

description: The fungal collections of CSU emphasize agarics, boletes and related macrofungi mainly from Oklahoma, Texas, Mississippi, Louisiana, Central and South America. There are approximately 4,000 specimens in the herbarium that are pertinent to this project, including vouchers for the studies of Clark Ovrebo and his students (e.g. please site some references). CSU also contains approximately 1000 images of specimens in the living condition, and about 1700 fieldnotes.
DOI: 10.5061/dryad.hb5b0
title: Data from: Origin of land plants revisited in the light of sequence contamination and missing data

description: Knowing the closest relatives of land plants is key to understanding the
 complex adaptations to terrestrial life. Unfortunately, multi-gene
 analyses yield highly incongruent results, suggesting for instance
 Charales, Zygnematales, or Coleochaete as the sister-group of land plants.
 Such controversy may result from the real history of life, in particular
 closely spaced speciation events, incomplete lineage sorting, gene
 duplication or horizontal gene transfer. In such cases, the solution
 resides in improved taxon sampling and sophisticated models of evolution.
 However, we will show that the quality of data used to infer the phylogeny
 may also play a major role, creating unnecessary controversy. In
 particular, the inclusion of contaminant sequences from other species, and
 of genes with incomplete taxon sampling explains a large part of the
 discrepancies observed between various studies. The use of a carefully
 checked and almost complete dataset suggests that land plants are closely
 related to a group composed of Zygnematales and Coleochaetales.
description: Figure-S3-54Figures S3-54: Single gene phylogenies used to validate the contamination of the charophyte sequences detected by blast search.FigS3-54-Final.pdfFigure-S55-109Figures S55-109: Single gene phylogenies used for the congruence test.FigS55-109-Final.pdfTable-S2Table S2: Summary of the contaminations detected in the Finet et al. (2010) dataset.Table_S2-Final.pdfTable-S3Table S3: Impact of taxon sampling on the GTR+G and CATGTR+G inferences.Table_S3-Final.pdfComplete-22360NEXUS file: 40 taxa, 119 proteins, 22,360 unambiguously aligned amino acid positions, 11.8% of missing data.Finet-99NEXUS file: 77 ribosomal protein alignments of Finet et al., with 99 sequences deleted. 74 contaminant sequences were detected by the congruence test and a total of 99 sequences were removed because in 25 cases it was impossible to identify the correct sequence.Not-Complete-43300NEXUS file: 40 taxa, 164 proteins, 43,300 unambiguously aligned amino acid positions. Ribosomal dataset (11,571 positions and 4.7 % of missing data) and non-ribosomal dataset (31,729 positions and 24.1 % of missing data).Table-S1Table S1: Contaminations detected in alignments of Finet et al. (2010) by Blast search and by congruence test.Table_S1-Final.pdf164-single-gene-before-SCaFoSNEXUS files: 164 orthologous genes before the use of SCaFoS (selection of sequences, species and genes).FINET-sineContam-TreesThe trees (RAxML and PhyloBayes) are inferred from the cleaned dataset (Finet-99 NEXUS file).PhyloBayes-Trees20 PhyloBayes trees (CATGTR+G) obtained from five different partitions (missing data) with four different taxon samples.Phylobayes-Trees.zipRAxML-Trees20 RAxML Best trees (GTR+G) + 20 Bipartitions (GTR+G) obtained from five different partitions (missing data) with four different taxon samples.
DOI: 10.5061/dryad.dp848
title: Data from: Anolis sex chromosomes are derived from a single ancestral pair

description: To explain the frequency and distribution of heteromorphic sex chromosomes
 in the lizard genus Anolis we compared the relative roles of sex
 chromosome conservation vs. turnover of sex determining mechanisms. We
 used model based comparative methods to reconstruct karyotype evolution
 and the presence of heteromorphic sex chromosomes onto a newly generated
 Anolis phylogeny. We found that heteromorphic sex chromosomes evolved
 multiple times in the genus. Fluorescent in situ hybridization (FISH) of
 repetitive DNA showed variable rates of Y chromosome degeneration among
 Anolis species and identified previously undetected, homomorphic sex
 chromosomes in two species. We confirmed homology of sex chromosomes in
 the genus by performing FISH of an X-linked BAC and qPCR of X-linked genes
 in multiple Anolis species sampled across the phylogeny. Taken together,
 these results are consistent with long-term conservation of sex
 chromosomes in the group. Our results pave the way to address additional
 questions related to Anolis sex chromosome evolution and describe a
 conceptual framework that can be used to evaluate the origins and
 evolution of heteromorphic sex chromosomes in other clades.
description: ND2
 Alignment1510 bp alignment of
 NADH dehydrogenase subunit 2 (ND2) gene, complete cds; tRNA-Trp, tRNA-Ala,
 tRNA-Asx, tRNA-Cys, and tRNA-Tyr genes, complete sequence; and cytochrome
 oxidase subunit I (COI) gene, partial cds for 216 Anolis species plus 3
 outgroup sequencesAnolis_216_species.nexMrBayes consensus treeConsensus tree inferred by MrBayes v3.1.2 including node support in the form of posterior probabilitiesAnolis_216_species.nex.conBEAST MCC treeMaximum clade credibility toplogy inferred using BEAST v1.7.450milBEASTruns_combined_ladderized.treBEAST posterior distibutionA thinned (10,000 samples) and pruned (retaining only taxa for which both chromosome number and sex chromosome complement were known) set of trees from the posterior distribution inferred by BEAST v1.7.4. These data were used as input for BayesTraits analyses.reduced_trees.nex
DOI: 10.15468/dl.ct6a3s
title: Occurrence Download

description: A dataset containing 18787 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is NEON Biorepository Mosquito Collection (Bulk Identified)"
 ]
}

 The dataset includes 18787 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001736-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vbyeuk
title: Occurrence Download

description: A dataset containing 20607 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is NEON Biorepository Mosquito Collection (Pinned Vouchers)"
 ]
}

 The dataset includes 20607 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001739-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/rtw4uz
title: University of Cincinnati, Margaret H. Fulford Herbarium - Fungi

description: The herbarium at the University of Cincinnati was founded by Margaret Fulford in 1920s and has grown over the years through the work of prolific collectors and through acquisition of several large and important collections. Today, the herbarium houses around 125,000 specimens of vascular plants, bryophytes, lichens, fungi, and algae, making it the third largest herbarium in Ohio. In addition to the large collection of regional and North American material, it also contains extensive collections from Europe, South America, the Caribbean Basin, Samoa, and China. Particular strengths of the herbarium are North American Sphagnum, South American and Caribbean Hepatics, North American Cladonia, and Trilliaceae.
DOI: 10.5061/dryad.q12c06f
title: Data from: Extreme and rapid bursts of functional adaptations shape bite force in amniotes

description: Adaptation is the fundamental driver of functional and biomechanical
 evolution. Accordingly, the states of biomechanical traits (absolute or
 relative trait values) have long been used as proxies of adaptations in
 response to direct selection. However, ignoring evolutionary history, in
 particular ancestry, passage of time and the rate of evolution, can be
 misleading. Here, we apply a recently developed phylogenetic statistical
 approach using significant rate shifts to detect instances of exceptional
 rates of adaptive changes in bite force, in a large group of terrestrial
 vertebrates, the amniotes. Our results show that bite force in amniotes
 evolved through multiple bursts of exceptional rates of adaptive changes,
 whereby whole groups – including Darwin’s finches, maniraptoran dinosaurs
 (group of non-avian dinosaurs including birds), anthropoids and hominins
 (the group of species including modern humans) – experienced significant
 rate increases compared to the background rate. However, in most parts of
 the amniote tree of life we find no exceptional rate increases, indicating
 that coevolution with body size was primarily responsible for the patterns
 observed in bite force. Our approach represents a template for future
 studies in functional morphology and biomechanics, where exceptional rates
 of adaptative changes can be quantified and potentially linked to specific
 ecological factors underpinning major evolutionary radiations.
description: Movie_S1Movie_S2Data S1 - Data_SpecimenData S2 - Data_TaxonData S3 - Data_5GroupData S4 - Data_5Group_BitePointData S5 - Data_5Group_BiteTypeData S6 - Phylogeny
DOI: 10.5061/dryad.2hv7d
title: Data from: The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing

description: RNA editing by adenosine deamination alters genetic information from the
 genomic blueprint. When it recodes mRNAs, it gives organisms the option to
 express diverse, functionally distinct, protein isoforms. All eumetazoans,
 from cnidarians to humans, express RNA editing enzymes. However,
 transcriptome-wide screens have only uncovered about 25 transcripts
 harboring conserved recoding RNA editing sites in mammals and several
 hundred recoding sites in Drosophila. These studies on few established
 models have led to the general assumption that recoding by RNA editing is
 extremely rare. Here we employ a novel bioinformatic approach with
 extensive validation to show that the squid Doryteuthis pealeii recodes
 proteins by RNA editing to an unprecedented extent. We identify 57,108
 recoding sites in the nervous system, affecting the majority of the
 proteins studied. Recoding is tissue-dependent, and enriched in genes with
 neuronal and cytoskeletal functions, suggesting it plays an important role
 in brain physiology.
description: Supplementary File
 1A
 text file in a fasta format with the constructed squid coding
 sequences.EisenbergSI_Data1.txtSupplementary File 2A spreadsheet with all the A-to-G modification sites detected in the coding regions of the squid, along with their number of supporting reads in all the tissues studied.EisenbergSI_Table1.xlsx
DOI: 10.5061/dryad.cv74242
title: Data from: Conservation of sex-linked markers among conspecific populations of a viviparous skink, Niveoscincus ocellatus, exhibiting genetic and temperature-dependent sex determination

description: Sex determination systems are exceptionally diverse and have undergone
 multiple and independent evolutionary transitions among species,
 particularly reptiles. However, the mechanisms underlying these
 transitions have not been established. Here we tested for differences in
 sex-linked markers in the only known reptile that is polymorphic for sex
 determination system, the spotted snow skink, Niveoscincus ocellatus, to
 quantify the genomic differences that have accompanied this transition. In
 a highland population, sex is determined genetically, whilst in a lowland
 population, offspring sex ratio is influenced by temperature. We found a
 similar number of sex-linked loci in each population, including shared
 loci, with genotypes consistent with male heterogamety (XY). However,
 population-specific linkage disequilibrium suggests greater
 differentiation of sex chromosomes in the highland population. Our results
 suggest that transitions between sex determination systems can be
 facilitated by subtle genetic differences.
description: Readme_SexMarkersInSkink_Hilletal2018FASTA_SexMarkersInSkink_Hilletal2018SNPs_SexMarkersInSkink_Hilletal2018PA_SexMarkersInSkink_Hilletal2018
DOI: 10.5061/dryad.68s40
title: Data from: Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus)

description: Species are a fundamental unit for biological studies, yet no uniform
 guidelines exist for determining species limits in an objective manner.
 Given the large number of species concepts available, defining species can
 be both highly subjective and biased. Although morphology has been
 commonly used to determine species boundaries, the availability and
 prevalence of genetic data has allowed researchers to use such data to
 make inferences regarding species limits. Genetic data also have been used
 in the detection of cryptic species, where other lines of evidence
 (morphology in particular) may underestimate species diversity. In this
 study, we investigate species limits in a complex of morphologically
 conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from
 California. Multiple approaches were used to determine species boundaries
 in this highly genetically fragmented group, including both multilocus
 discovery and validation approaches (plus a chimeric approach).
 Additionally, we introduce a novel tree-based discovery approach using
 species trees. Results suggest that this complex includes multiple cryptic
 species, with two groupings consistently recovered across analyses. Due to
 incongruence across analyses for the remaining samples, we take a
 conservative approach and recognize a three species complex, and formally
 describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus
 starretti, sp. nov.). This study helps to clarify species limits in a
 genetically fragmented group and provides a framework for identifying and
 defining the cryptic lineage diversity that prevails in many organismal
 groups.
description: Nexus files for all six
 lociDNA sequences for
 individuals used in all multilocus analyses.NexusFiles.zipComplete COI mtDNA nexus fileContain mtDNA sequences for all individuals used in this study.COI_complete.nexTables S1-3Supplementary tables 1-3TablesS1-3_revised.docxSupplemental MaterialSupplemental material file.SupplementalMaterial_R2.docxFigures S1-10Supplemental Figures 1 - 10.FiguresS1-10_R2.pdfSupplemental Figure LegendsSupplemental figure legendsSupplementalFigureLegends.pdf
DOI: 10.5061/dryad.7r7n7
title: Data from: Spike-triggered covariance analysis reveals phenomenological diversity of contrast adaptation in the retina

description: When visual contrast changes, retinal ganglion cells adapt by adjusting
 their sensitivity as well as their temporal filtering characteristics. The
 latter has classically been described by contrast-induced gain changes
 that depend on temporal frequency. Here, we explored a new perspective on
 contrast-induced changes in temporal filtering by using spike-triggered
 covariance analysis to extract multiple parallel temporal filters for
 individual ganglion cells. Based on multielectrode-array recordings from
 ganglion cells in the isolated salamander retina, we found that contrast
 adaptation of temporal filtering can largely be captured by
 contrast-invariant sets of filters with contrast-dependent weights.
 Moreover, differences among the ganglion cells in the filter sets and
 their contrast-dependent contributions allowed us to phenomenologically
 distinguish three types of filter changes. The first type is characterized
 by newly emerging features at higher contrast, which can be reproduced by
 computational models that contain response-triggered gain-control
 mechanisms. The second type follows from stronger adaptation in the Off
 pathway as compared to the On pathway in On-Off-type ganglion cells.
 Finally, we found that, in a subset of neurons, contrast-induced filter
 changes are governed by particularly strong spike-timing dynamics, in
 particular by pronounced stimulus-dependent latency shifts that can be
 observed in these cells. Together, our results show that the contrast
 dependence of temporal filtering in retinal ganglion cells has a
 multifaceted phenomenology and that a multi-filter analysis can provide a
 useful basis for capturing the underlying signal-processing dynamics.
description: Spike and Stimulus
 DataData.zip
DOI: 10.15468/ytj8rh
title: University of Florida Herbarium - Fungi

description: The University of Florida Herbarium is a unit of the Department of Natural History of the Florida Museum of Natural History. The herbarium is affiliated with the Institute of Food and Agricultural Sciences, Florida Agricultural Experiment Station, Florida Cooperative Extension Service, Department of Biology and the Department of Plant Pathology. The FLAS acronym is the standard international abbreviation for the University of Florida Herbarium. It is derived from the herbarium's early association with the Florida Agricultural Experiment Station. Our mission focuses in plant collections acquisition and care, research based on the collections, education and public service.
DOI: 10.5061/dryad.k84c3k8j
title: Data from: Early evolutionary trends in ammonoid embryonic development

description: During the Devonian Nekton Revolution, ammonoids show a progressive
 coiling of their shell just like many other pelagic mollusk groups. These
 now extinct, externally shelled cephalopods derived from bactritoid
 cephalopods with a straight shell in the Early Devonian. During the
 Devonian, evolutionary trends toward tighter coiling and a size reduction
 occurred in ammonoid embryonic shells. In at least three lineages,
 descendants with a closed umbilicus evolved convergently from forms with
 an opening in the first whorl (umbilical window). Other lineages having
 representatives with open umbilici became extinct around important
 Devonian events while only those with more tightly coiled embryonic shells
 survived. This change was accompanied by an evolutionary trend in shape of
 the initial chamber, but no clear trend in its size. The fact that several
 ammonoid lineages independently reduced and closed the umbilical window
 more or less synchronously indicates that common driving factors were
 involved. A trend in size decrease of the embryos as well as the
 concurrent increase in adult size in some lineages likely reflects a
 fundamental change in reproductive strategies toward a higher fecundity
 early in the evolutionary history of ammonoids. This must have played an
 important role in their subsequent success as well as in their demise.
description: Table S1: Embryonic
 shell measurements of Devonian ammonoidsDeBaets_etal_Appendix1_new.xlsTable S2: Embryonic shell measurements of Carboniferous-Cretaceous ammonoidsDeBaets_etal_Appendix2_new.xlsTable S3: Compilation of egg sizes and fecundities of Recent cephalopodsDeBaets_etal_Appendix3_corrected_dryad.xlsTable S4: Compilation of adult size conch measurements, calculated body chamber and egg volumes and egg number estimatesDeBaets_etal_Appendix4.xlsFigure S1: Changes in coiling and initial chamber size through time(A) Diversity from the early Emsian to the late Eifelian with proportion of forms with openly coiled adult whorls and umbilical window (open + enclosed). The embryonic and post-embryonic whorls of representative taxa are shown of each category are shown (respectively Erbenoceras, Mimagoniatites and Agoniatites). (B-C) Boxplots showing the distribution and fluctuations of initial chamber size (initial chamber diameter PD in mm) within the Devonian (B) and in the Phanerozoic (C) from the Devonian until the Cretaceous (whiskers = minima and maxima excluding outliers, boxes = middle two quartiles, horizontal stripe = median value, dots = outliers). Abbreviations: E. Dev = Early Devonian, M. Dev. = Middle Devonian, L. Dev. = Late Devonian, Dev. = Devonian, Carb. = Carboniferous, Perm. = Permian, Tria = Triassic, Jura. = Jurassic, Cret. = Cretaceous. Histograms were produced in the freely available statistical environment R (http://www.r-project.org/).DeBaets_etal_Supplementary_Fig_01_UmbilicalWindowGeneraSolo_New.tif