cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6t203
title: Data from: Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre

description: Although metazoan animals in the mesopelagic zone play critical roles in
 deep pelagic food webs and in the attenuation of carbon in midwaters, the
 diversity of these assemblages is not fully known. A metabarcoding survey
 of mesozooplankton diversity across the epipelagic, mesopelagic and upper
 bathypelagic zones (0-1500m) in the North Pacific Subtropical Gyre
 revealed far higher estimates of species richness than expected given
 prior morphology-based studies in the region (4,024 OTUs, 10-fold
 increase), despite conservative bioinformatic processing. OTU richness of
 the full assemblage peaked at lower epipelagic-upper mesopelagic depths
 (100-300m), with slight shoaling of maximal richness at night due to diel
 vertical migration, in contrast to expectations of a deep mesopelagic
 diversity maximum as reported for several plankton groups in early
 systematic and zoogeographic studies. Four distinct depth-stratified
 species assemblages were identified, with faunal transitions occurring at
 100m, 300m, and 500m. Highest diversity occurred in the smallest
 zooplankton size fractions (0.2-0.5mm), which had significantly lower %
 OTUs classified due to poor representation in reference databases,
 suggesting a deep reservoir of poorly understood diversity in the smallest
 metazoan animals. A diverse meroplankton assemblage also was detected (350
 OTUs), including larvae of both shallow and deep living benthic species.
 Our results provide some of the first insights into the hidden diversity
 present in zooplankton assemblages in midwaters, and a molecular
 reappraisal of vertical gradients in species richness, depth
 distributions, and community composition for the full zooplankton
 assemblage across the epipelagic, mesopelagic and upper bathypelagic
 zones.
description: Matthews_et_al_2017.tarArchive containing both raw and processed data files, with a README for both folders and file types.
DOI: 10.5061/dryad.0hr3gk2
title: Data from: The biomechanics of foraging determines face length among kangaroos and their relatives

description: Increasing body size is accompanied by facial elongation across a number
 of mammalian taxa. This trend forms the basis of a proposed evolutionary
 rule, cranial evolutionary allometry (CREA). However, facial length has
 also been widely associated with the varying mechanical resistance of
 foods. Here, we combine geometric morphometric and computational
 biomechanical analyses to determine whether evolutionary allometry or
 feeding ecology have been dominant influences on facial elongation across
 sixteen species of kangaroos and relatives (Macropodiformes). We found no
 support for an allometric trend. Nor was craniofacial morphology strictly
 defined by dietary categories, but rather associated with a combination of
 the mechanical properties of vegetation types and cropping behaviours used
 to access them. Among species examined here, shorter muzzles coincided
 with known diets of tough, resistant plant tissues, accessed via active
 slicing by the anterior dentition. This morphology consistently resulted
 in increased mechanical efficiency and decreased bone deformation during
 incisor biting. Longer muzzles, by contrast, aligned with softer foods or
 feeding behaviours invoking cervical musculature that circumvent the need
 for hard biting. These findings point to a potential for craniofacial
 morphology to predict feeding ecology in macropodiforms, which may be
 useful for species management planning and for inferring palaeoecology.
description: macropodiforms_lmks3D landmarks for shape analysisphylo_mitchelldatesPhylogenetic tree for morphometric analysisMEQcalcCalculations for Mechanical Efficiency Quotient (MEQ)strain dataStrain magnitudes along muzzle for each species during incisor bite simulation.A_rufescensFEM nastran and mandible stlB_penicillataFEM nastran and mandible stlD_dorianusFEM nastran and mandible stlD_lumholtziFEM nastran and mandible stlH_moschatusFEM nastran and mandible stlL_hirsutusFEM nastran and mandible stlM_dorsalisFEM nastran and mandible stlM_giganteusFEM nastran and mandible stlM_robustusFEM nastran and mandible stlM_rufogriseusFEM nastran and mandible stlM_rufusFEM nastran and mandible stlO_fraenataFEM nastran and mandible stlP_penicillataFEM nastran and mandible stlP_tridactylusFEM nastran and mandible stlT_stigmaticaFEM nastran and mandible stlW_bicolorFEM nastran and mandible stl
DOI: 10.5061/dryad.34dt1
title: Data from: Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy

description: RAD-tag is a powerful tool for high-throughput genotyping. It relies on
 PCR amplification of the starting material, following enzymatic digestion
 and sequencing adaptor ligation. Amplification introduces duplicate reads
 into the data, which arise from the same template molecule and are
 statistically nonindependent, potentially introducing errors into genotype
 calling. In shotgun sequencing, data duplicates are removed by filtering
 reads starting at the same position in the alignment. However, restriction
 enzymes target specific locations within the genome, causing reads to
 start in the same place, and making it difficult to estimate the extent of
 PCR duplication. Here, we introduce a slight change to the Illumina
 sequencing adaptor chemistry, appending a unique four-base tag to the
 first index read, which allows duplicate discrimination in aligned data.
 This approach was validated on the Illumina MiSeq platform, using
 double-digest libraries of ants (Wasmannia auropunctata) and yeast
 (Saccharomyces cerevisiae) with known genotypes, producing modest though
 statistically significant gains in the odds of calling a genotype
 accurately. More importantly, removing duplicates also corrected for
 strong sample-to-sample variability of genotype calling accuracy seen in
 the ant samples. For libraries prepared from low-input degraded museum
 bird samples (Mixornis gularis), which had low complexity, having been
 generated from relatively few starting molecules, adaptor tags show that
 virtually all of the genotypes were called with inflated confidence as a
 result of PCR duplicates. Quantification of library complexity by adaptor
 tagging does not significantly increase the difficulty of the overall
 workflow or its cost, but corrects for differences in quality between
 samples and permits analysis of low-input material.
description: Sequence data for
 Mixornis gularisIllumina MiSeq Fastq
 files, including index read sequencesbird.tarwasmannia.tarAlignment files for ant datayeast.tarYeast alignment files
DOI: 10.5061/dryad.3jm3n
title: Data from: "De novo transcriptome assembly and polymorphism detection in ecological important widely distributed Neotropical toads from the Rhinella marina species complex (Anura: Bufonidade)" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014

description: The toads Rhinella marina and R. schneideri are large terrestrial true
 toads widely distributed in the Neotropical region, which can hybridize in
 areas of transition between Amazon rain forest and Cerrado biomes. The
 former is in particular an important ecological species, and a very
 successful invader. Here, we report de novo transcriptome of R. marina and
 R. schneideri and polymorphism SNPs identified between the two species.
 The transcriptome sequencing was performed on an Illumina platform using
 five individuals livers mRNA samples for each specie. A total of
 554,474,410 and 554,276,922 sequencing reads were collected and assembled
 into 199,799 and 172,671 transcripts with N50 lengh of 3106bp and 3106bp
 for R. marina and R. schnedeiri respectively. A total of 709,193 SNPs were
 identified and characterize for both species. This transcriptome and SNPs
 will facilitate studies on hybridization and adaptation of the Rhinella
 complex but also various ecological and evolutionary studies of other
 amphibians as few transcriptome data are available.
description: Rhinella marina
 transcriptome non redundant assemblyassembly_rhin_mar_no_redundancy.fastaRhinella marina transcriptome full assemblyassembly_rhin_mar.fastaRhinella schneideri transcriptome non redundant assemblyassembly_rhin_schn_no_redundancy.fastaRhinella schneideri transcriptome full assemblyassembly_rhin_schn.fastaSNPs data for Rhinella marina and Rhinella schneideriSNPs_mar_schn.vcf
DOI: 10.5061/dryad.gf80t
title: Data from: Identifying metabolic subpopulations from population level mass spectrometry

description: Metabolism underlies many important cellular decisions, such as the
 decisions to proliferate and differentiate, and defects in metabolic
 signaling can lead to disease and aging. In addition, metabolic
 heterogeneity can have biological consequences, such as differences in
 outcomes and drug susceptibilities in cancer and antibiotic treatments.
 Many approaches exist for characterizing the metabolic state of a
 population of cells, but technologies for measuring metabolism at the
 single cell level are in the preliminary stages and are limited. Here, we
 describe novel analysis methodologies that can be applied to established
 experimental methods to measure metabolic variability within a population.
 We use mass spectrometry to analyze amino acid composition in cells grown
 in a mixture of 12C- and 13C-labeled sugars; these measurements allow us
 to quantify the variability in sugar usage and thereby infer information
 about the behavior of cells within the population. The methodologies
 described here can be applied to a large range of metabolites and
 macromolecules and therefore have the potential for broad applications.
description: Raw CDF
 filesCDF files containing raw
 mass spectrometry data for all samples.CDF
 files.zipFF
 filesFiatFlux
 filesModified FiatFlux
 CodeModified version of
 FiatFlux codeFitting code and
 dataZip file contains code
 used to produce amino acid model, perform analysis and produce figures, as
 well as data structures containing fitting information and experimental
 metadataFitting
 code.zip
DOI: 10.5061/dryad.3c0f1
title: Data from: Phylogenomics resolves the timing and pattern of insect evolution

description: Insects are the most speciose group of animals, but the phylogenetic
 relationships of many major lineages remain unresolved. We inferred the
 phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses
 of nucleotide and amino acid sequences, with site-specific nucleotide or
 domain-specific amino acid substitution models, produced statistically
 robust and congruent results resolving previously controversial
 phylogenetic relations hips. We dated the origin of insects to the Early
 Ordovician [~479 million years ago (Ma)], of insect flight to the Early
 Devonian (~406 Ma), of major extant lineages to the Mississippian (~345
 Ma), and the major diversification of holometabolous insects to the Early
 Cretaceous. Our phylogenomic study provides a comprehensive reliable
 scaffold for future comparative analyses of evolutionary innovations among
 insects.
description: Phylogenomics Resolves
 The Timing And Pattern Of Insect Evolution: Supplementary File
 Archives.Phylogenomics Resolves
 The Timing And Pattern Of Insect Evolution: Supplementary File Archives.
 This file includes 14 supplementary archives which are in detail described
 in the README.Misof_et_al_Supplementary_Archives.tar.gz
DOI: 10.5061/dryad.v23v5d2
title: Data from: Dental ontogeny in extinct synapsids reveals a complex evolutionary history of the mammalian tooth attachment system

description: The mammalian dentition is uniquely characterized by a combination of
 precise occlusion, permanent adult teeth, and a unique tooth attachment
 system. Unlike the ankylosed teeth in most reptiles, mammal teeth are
 supported by a ligamentous tissue that suspends each tooth in its socket,
 providing flexible and compliant tooth attachment that prolongs the life
 of each tooth and maintains occlusal relationships. Here we investigate
 dental ontogeny through histological examination of a wide range of
 extinct synapsid lineages to assess whether the ligamentous tooth
 attachment system is unique to mammals and to determine how it evolved.
 This study shows for the first time that the ligamentous tooth attachment
 system is not unique to crown mammals within Synapsida, having arisen in
 several non-mammalian therapsid clades as a result of neoteny and
 progenesis in dental ontogeny. Mammalian tooth attachment is here
 re-interpreted as a paedomorphic condition relative to the ancestral
 synapsid form of tooth attachment.
description: Thrinaxodon adult
 BP/1/7199Images from CT
 reconstruction of the skull of an adult Thrinaxodon (BP/1/7199) used to
 score ontogenetic stages of teeth.Thrinaxodon adult BP 1
 7199.zipThrinaxodon young
 (BP/1/5372)Images from CT
 reconstruction of the skull of a juvenile Thrinaxodon (BP/1/5372) used to
 score ontogenetic stages of teeth.Thrinaxodon young
 5372.zipGalesaurus adult
 BP/1/5064Images from CT
 reconstruction of the skull of an adult Galesaurus (BP/1/5064) used to
 score ontogenetic stages of teeth.Galesaurus adult
 BP-1-5064.zipGalesaurus subadult
 BP/1/4602Images from CT
 reconstruction of the skull of a subadult Galesaurus (BP/1/4602) used to
 score ontogenetic stages of teeth.Galesaurus subadult
 BP-1-4602.zip
DOI: 10.5061/dryad.f7h13
title: Data from: Powerful methods for detecting introgressed regions from population genomic data

description: Understanding the types and functions of genes that are able to cross
 species boundaries—and those that are not—is an important step in
 understanding the forces maintaining species as largely independent
 lineages across the remainder of the genome. With large next-generation
 sequencing data sets we are now able to ask whether introgression has
 occurred across the genome, and multiple methods have been proposed to
 detect the signature of such events. Here, we introduce a new summary
 statistic that can be used to test for introgression, RNDmin, that makes
 use of the minimum pairwise sequence distance between two population
 samples relative to divergence to an outgroup. We find that our method
 offers a modest increase in power over other, related tests, but that all
 such tests have high power to detect introgressed loci when migration is
 recent and strong. RNDmin is robust to variation in the mutation rate, and
 remains reliable even when estimates of the divergence time between sister
 species are inaccurate. We apply RNDmin to population genomic data from
 the African mosquitoes Anopheles quadriannulatus and A. arabiensis,
 identifying three novel candidate regions for introgression.
 Interestingly, one of the introgressed loci is on the X chromosome, but
 outside of an inversion separating these two species. Our results suggest
 that significant, but rare, sharing of alleles is occurring between
 species that diverged more than 1 million years ago, and that application
 of these methods to additional systems are likely to reveal similar
 results.
description: Whole-genome alignment
 of A. arabiensis and A. quadriannulatus pop. samplesThe data are supplied in
 the Multisample Variant Format (Pease and Rosenzweig, 2015). A complete
 suite of tools for processing MVF files is available on github at
 https://github.com/jbpease/mvftools. Each file contains a full-chromosome
 alignment of computationally phased haplotypes for 23 samples of A.
 arabiensis, A. quadriannulatus, and A. christyi (outgroup); haplotypes are
 identified by ".A" or ".B" appended to the sample ID.
 The sample key (SampleCode.txt) is also included.AarAqu_align.tar.gz
DOI: 10.5061/dryad.kc42g
title: Quantification of endogenous and exogenous protein expressions of Na,K-ATPase with super-resolution PALM/STORM imaging

description: Transient transfection of fluorescent fusion proteins is a key enabling
 technology in fluorescent microscopy to spatio-temporally map cellular
 protein distributions. Transient transfection of proteins may however
 bypass normal regulation of expression, leading to overexpression
 artefacts like misallocations and excess amounts. In this study we
 investigate the use of STORM and PALM microscopy to quantitatively monitor
 endogenous and exogenous protein expression. Through incorporation of an
 N-terminal hemagglutinin epitope to a mMaple3 fused Na,K-ATPase (α1
 isoform), we analyze the spatial and quantitative changes of plasma
 membrane Na,K-ATPase localization during competitive transient expression.
 Quantification of plasma membrane protein density revealed a time
 dependent increase of Na,K-ATPase, but no increase in size of protein
 clusters. Results show that after 41h transfection, the total plasma
 membrane density of Na,K-ATPase increased by 63% while the endogenous
 contribution was reduced by 16 %.
description: PALM localisation
 dataZip archive with PALM
 data. Files are named based on treatment time: 17h or 41h followed by
 experimental day, coverslip and region as:
 TREATMENT.DATE.COVERSLIP#.REGION# Each file contains the processed output
 of SMLM experiments using SMLocalizer and contain all localizations. The
 entries with include flag 1 were used for calculations.PALM.zipSTORM localisation dataZip archive with STORM data. Files are named based on treatment time: control (0h), 17h or 41h followed by experimental day, coverslip and region as: TREATMENT.DATE.COVERSLIP#.REGION# Each file contains the processed output of SMLM experiments using SMLocalizer and contain all localizations. The entries with include flag 1 were used for calculations.STORM.zip
DOI: 10.15468/dl.uw8p7q
title: Occurrence Download

description: A dataset listing the 108 species recorded in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Especies silvestres de nopales mexicanos",
 "Geometry POLYGON((-133.86069 11.27208,-70.13931 11.27208,-70.13931 36.72792,-133.86069 36.72792,-133.86069 11.27208))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 108 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000324-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2r79q
title: Data from: A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells

description: Technological advances have enabled the analysis of cellular protein and
 RNA levels with unprecedented depth and sensitivity, allowing for an
 unbiased re-evaluation of gene regulation during fundamental biological
 processes. Here, we have chronicled the dynamics of protein and mRNA
 expression levels across a minimally perturbed cell cycle in human myeloid
 leukemia cells using centrifugal elutriation combined with mass
 spectrometry-based proteomics and RNA-Seq, avoiding artificial
 synchronization procedures. We identify myeloid-specific gene expression
 and variations in protein abundance, isoform expression and
 phosphorylation at different cell cycle stages. We dissect the
 relationship between protein and mRNA levels for both bulk gene expression
 and for over ∼6000 genes individually across the cell cycle, revealing
 complex, gene-specific patterns. This data set, one of the deepest surveys
 to date of gene expression in human cells, is presented in an online,
 searchable database, the Encyclopedia of Proteome Dynamics
 (http://www.peptracker.com/epd/).
description: Peptide
 EvidenceThis compressed file
 contains a tab-delimited table listing the peptide evidence generated by
 processing the raw MS and MS/MS data using the MaxQuant software package,
 which includes a built-in database search engine called Andromeda. The
 spectra were searched against the UniProt Human Reference Proteome,
 accessed on August 2012. The table includes all instances of peptide
 identifications and quantitations, and their database search scores and
 posterior error probabilities.combined_evidence.zip
DOI: 10.5061/dryad.m2821
title: Data from: Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing

description: The molecular mechanisms and genetic architecture that facilitate adaptive
 radiation of lineages remain elusive. Polymorphic chromosomal inversions,
 due to their recombination-reducing effect, are proposed instruments of
 ecotypic differentiation. Here we study an ecologically diversifying
 lineage of An. gambiae, known as the Bamako chromosomal form based on its
 unique complement of three chromosomal inversions, to explore the impact
 of these inversions on ecotypic differentiation. We used pooled and
 individual genome sequencing of Bamako, typical (non-Bamako) An. gambiae,
 and the sister species An. coluzzii to investigate evolutionary
 relationships and genome-wide patterns of nucleotide diversity and
 differentiation among lineages. Despite extensive shared polymorphism and
 limited differentiation from the other taxa, Bamako clusters apart from
 the other taxa, and forms a maximally supported clade in neighbor-joining
 trees based on whole genome data (including inversions) or solely on
 collinear regions. Nevertheless, FST outlier analysis reveals that the
 majority of differentiated regions between Bamako and typical An. gambiae
 are located inside chromosomal inversions, consistent with their role in
 the ecological isolation of Bamako. Exceptionally differentiated genomic
 regions were enriched for genes implicated in nervous system development
 and signaling. Candidate genes associated with a selective sweep unique to
 Bamako contain substitutions not observed in sympatric samples of the
 other taxa, and several insecticide resistance gene alleles shared between
 Bamako and other taxa segregate at sharply different frequencies in these
 samples. Bamako represents a useful window into the initial stages of
 ecological and genomic differentiation from sympatric populations in this
 important group of malaria vectors.
description: VCF of all
 SNPsSNPs from 38 members of
 An. gambiae and An. coluzziiall.Bamakoset.2.recode.vcf.gzVCF of Bamako SNPsSNPs retained and filtered for the Bamako population onlyBamakoset.2.recode.vcf.gz