cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6n8kf
title: Data from: Long-term, high frequency in situ measurements of intertidal mussel bed temperatures using biomimetic sensors

description: At a proximal level, the physiological impacts of global climate change on
 ectothermic organisms are manifest as changes in body temperatures.
 Especially for plants and animals exposed to direct solar radiation, body
 temperatures can be substantially different from air temperatures. We
 deployed biomimetic sensors that approximate the thermal characteristics
 of intertidal mussels at 71 sites worldwide, from 1998-present. Loggers
 recorded temperatures at 10–30 min intervals nearly continuously at
 multiple intertidal elevations. Comparisons against direct measurements of
 mussel tissue temperature indicated errors of ~2.0–2.5 °C, during daily
 fluctuations that often exceeded 15°–20 °C. Geographic patterns in thermal
 stress based on biomimetic logger measurements were generally far more
 complex than anticipated based only on ‘habitat-level’ measurements of air
 or sea surface temperature. This unique data set provides an opportunity
 to link physiological measurements with spatially- and temporally-explicit
 field observations of body temperature.
description: Robomussel
 data Robomussel data:
 intertidal biomimic body temperature of mussels deployed at 6 different
 countries. 1913 .txt files in total. Files are categorized by location
 (country, region, site). In addition, metadata files show specific
 information for loggers at each site. robomussel.zip
 
 iButton/Tidbit
 data ibutton/Tidbit data:
 intertidal thermal sensors (aerial and water temperature) deployed at 5
 different countries. 160 .txt files in total. Files are categorized by
 location (country, region, site). In addition, metadata files show
 specific information for loggers at each site. ibutton.zip
DOI: 10.5061/dryad.fg14s2r
title: Data from: Anatomy of the Ediacaran rangeomorph Charnia masoni

description: The Ediacaran macrofossil Charnia masoni Ford is perhaps the most iconic
 member of the Rangeomorpha: a group of seemingly sessile, frondose
 organisms that dominates late Ediacaran benthic, deep‐marine fossil
 assemblages. Despite C. masoni exhibiting broad palaeogeographical and
 stratigraphical ranges, there have been few morphological studies that
 consider the variation observed among populations of specimens derived
 from multiple global localities. We present an analysis of C. masoni that
 evaluates specimens from the UK, Canada and Russia, representing the
 largest morphological study of this taxon to date. We describe substantial
 morphological variation within C. masoni and present a new morphological
 model for this species that has significant implications both for
 interpretation of rangeomorph architecture, and potentially for existing
 taxonomic schemes. Previous reconstructions of Charnia include assumptions
 regarding the presence of structures seen in other rangeomorphs (e.g. an
 internal stalk) and of homogeneity in higher order branch morphology;
 observations that are not borne out by our investigations. We describe
 variation in the morphology of third and fourth order branches, as well as
 variation in gross structure near the base of the frond. The diagnosis of
 Charnia masoni is emended to take account of these new features. These
 findings highlight the need for large‐scale analyses of rangeomorph
 morphology in order to better understand the biology of this
 long‐enigmatic group.
description: Charnia masoni Holotype
 RTISupplementary Figure 1:
 Reflectance transformation image of the Charnia masoni holotype (LEIUG
 2328).
DOI: 10.5061/dryad.qs734tp
title: Data from: Global pairwise RNA interaction landscapes reveal core features of protein recognition

description: RNA–protein interactions permeate biology. Transcription, translation, and
 splicing all hinge on the recognition of structured RNA elements by
 RNA-binding proteins. Models of RNA–protein interactions are generally
 limited to short linear motifs and structures because of the vast sequence
 sampling required to access longer elements. Here, we develop an
 integrated approach that calculates global pairwise interaction scores
 from in vitro selection and high-throughput sequencing. We examine four
 RNA-binding proteins of phage, viral, and human origin. Our approach
 reveals regulatory motifs, discriminates between regulated and
 non-regulated RNAs within their native genomic context, and correctly
 predicts the consequence of mutational events on binding activity. We
 design binding elements that improve binding activity in cells and infer
 mutational pathways that reveal permissive versus disruptive evolutionary
 trajectories between regulated motifs. These coupling landscapes are
 broadly applicable for the discovery and characterization of protein–RNA
 recognition at single nucleotide resolution.
description: RPI_042_bivBIV TAT SEQRS dataRPI_039_GST_bivBIV TAT GST controlRPI_033_lambdaLambda N SEQRS dataRPI_031_GST_lambda_p22Lambda N and P22 N shared with the same GST controlRPI_034_p22P22 N SEQRS data
DOI: 10.17608/k6.auckland.30866705
title: Ultrasound and photoacoustic data of flowing carbon particles in PMMA bone-mimicking phantoms

description: Data acquired from two types of bone-mimicking phantoms with a flowing blood mimic inside the channel. The photoacoustic and ultrasound acquisitions are intertwined, so between each PA image, two sets of plane-wave ultrasound images are obtained with steering angles between +/-10 degrees. There is also single-element US data acquired afterwards to generate a high-quality B-mode image for segmentation of the PMMA layers.We have included a MATLAB file titled "Read_and_organise_data.m" to organise the data into a more usable form. For the PA data, we have corrected the timing jitter, though some initial samples need to be removed to ensure the PA and US images are aligned.
DOI: 10.17608/k6.auckland.30866705.v1
title: Ultrasound and photoacoustic data of flowing carbon particles in PMMA bone-mimicking phantoms

description: Data acquired from two types of bone-mimicking phantoms with a flowing blood mimic inside the channel. The photoacoustic and ultrasound acquisitions are intertwined, so between each PA image, two sets of plane-wave ultrasound images are obtained with steering angles between +/-10 degrees. There is also single-element US data acquired afterwards to generate a high-quality B-mode image for segmentation of the PMMA layers.We have included a MATLAB file titled "Read_and_organise_data.m" to organise the data into a more usable form. For the PA data, we have corrected the timing jitter, though some initial samples need to be removed to ensure the PA and US images are aligned.
DOI: 10.5061/dryad.606ks
title: Data from: Veronica officinalis product authentication using DNA metabarcoding and HPLC-MS reveals widespread adulteration with Veronica chamaedrys

description: Studying herbal products derived from local and traditional knowledge and
 their value chains is one of the main challenges in ethnopharmacology. The
 majority of these products have a long history of use, but non-harmonized
 trade and differences in regulatory policies between countries impact
 their value chains and lead to concerns over product efficacy, safety and
 quality. Veronica officinalis L. (common speedwell), a member of
 Plantaginaceae family, has a long history of use in European traditional
 medicine, mainly in central eastern Europe and the Balkans. However, no
 specified control tests are available either to establish the quality of
 derived herbal products or for the discrimination of its most common
 substitute, V. chamaedrys L. (germander speedwell). In this study, we use
 DNA metabarcoding and high performance liquid chromatography coupled with
 mass spectrometry (HPLC-MS) to authenticate sixteen V. officinalis herbal
 products and compare the potential of the two approaches to detect
 substitution, adulteration and the use of unreported constituents. HPLC-MS
 showed high resolution in detecting phytochemical target compounds, but
 did not enable detection of specific plant species in the products. DNA
 metabarcoding detected V. officinalis in only 15% of the products, whereas
 it detected V. chamaedrys in 62% of the products. The results confirm that
 DNA metabarcoding can be used to test for the presence of Veronica
 species, and detect substitution and/or admixture of other Veronica
 species, as well as simultaneously detect all other species present. Our
 results confirm that none of the herbal products contained exactly the
 species listed on the label, and all included substitutes, contaminants or
 fillers. This study highlights the need for authentication of raw herbals
 along the value chain of these products. An integrative methodology can
 assess both the quality of herbal products in terms of target compound
 concentrations and species composition, as well as admixture and
 substitution with other chemical compounds and plants.
description: Raclariu et
 al_2017_FASTQ Raw
DOI: 10.5061/dryad.7sg58
title: Data from: Deep phylogenetic incongruence in the angiosperm clade Rosidae

description: Analysis of large data sets can help resolve difficult nodes in the tree
 of life and also reveal complex evolutionary histories. The placement of
 the Celastrales-Oxalidales-Malpighiales (COM) clade within Rosidae remains
 one of the most confounding phylogenetic questions in angiosperms, with
 previous analyses placing it with either Fabidae or Malvidae. To elucidate
 the position of COM, we assembled multi-gene matrices of chloroplast,
 mitochondrial, and nuclear sequences, as well as large single- and
 multi-copy nuclear gene data sets. Analyses of multi-gene data sets
 demonstrate conflict between the chloroplast and both nuclear and
 mitochondrial data sets, and the results are robust to various
 character-coding and data-exclusion treatments. Analyses of single- and
 multi-copy nuclear loci indicate that most loci support the placement of
 COM with Malvidae, fewer loci support COM with Fabidae, and almost no loci
 support COM outside a clade of Fabidae and Malvidae. Although incomplete
 lineage sorting and ancient introgressive hybridization remain as
 plausible explanations for the conflict among loci, more complete sampling
 is necessary to evaluate these hypotheses fully. Our results emphasize the
 importance of genomic data sets for revealing deep incongruence and
 complex patterns of evolution.
description: single-copy nuclear gene
 analysisCollection of 8,445
 potentially informative ortholog sets extracted from Lee at al. (2011) for
 single-copy nuclear gene analysis.SingleCopyGenes From Lee et al.
 2011 Data.rarMulti-copy nuclear gene
 analysisCollection of 3,748 gene
 family alignments from 22 plant taxa for multi-copy nuclear gene
 analysis.MultiCopyGenes.rarAnalysis of multi-gene matrices from chloroplast, mitochondrial, and nuclear sequences1. Files from the 82-taxon, 78-gene cpDNA analysis. This compressed file includes: 82-taxon, 78-gene cpDNA nucleotide, AA, and RY-coding , and 1st & 2nd condon only alignments; associated AA tree, RY-coding tree,78 individual gene trees, and tree of 78-gene 1st & 2nd condon positions only; trees and sorted matrices from method to remove highly variable sites. 2. Files from the 79-taxon, 4-gene mtDNA analysis. This compressed file includes: 79-taxon, 4-gene mtDNA nucleotide, AA, RY-coding and 1st & 2nd condon only alignments; associated AA tree, RY-coding tree, 4 individual gene trees, and tree of 4-gene 1st & 2nd condon positions only; trees and sorting matrices method to remove highly variable sites. 3. Files from the 92-taxon, 5-gene nuDNA analysis. This compressed file includes: 92-taxon, 5-gene nuDNA nucleotide, AA, RY-coding, and 1st & 2nd condon only alignments; associated AA tree, RY-coding tree, 5 individual gene trees, and tree of 5-gene 1st & 2nd condon positions only; sorting matrices and trees from method to remove highly variable sites.Analysis of multi-gene matrices CP_MT_NU_updated.rar
DOI: 10.5061/dryad.dq87d
title: Data from: A modelling framework to assess the effect of pressures on river abiotic habitat conditions and biota

description: River biota are affected by global reach-scale pressures, but most
 approaches for predicting biota of rivers focus on river reach or segment
 scale processes and habitats. Moreover, these approaches do not consider
 long-term morphological changes that affect habitat conditions. In this
 study, a modelling framework was further developed and tested to assess
 the effect of pressures at different spatial scales on reach-scale habitat
 conditions and biota. Ecohydrological and 1D hydrodynamic models were used
 to predict discharge and water quality at the catchment scale and the
 resulting water level at the downstream end of a study reach. Long-term
 reach morphology was modelled using empirical regime equations, meander
 migration and 2D morphodynamic models. The respective flow and substrate
 conditions in the study reach were predicted using a 2D hydrodynamic
 model, and the suitability of these habitats was assessed with novel
 habitat models. In addition, dispersal models for fish and
 macroinvertebrates were developed to assess the re-colonization potential
 and to finally compare habitat suitability and the availability / ability
 of species to colonize these habitats. Applicability was tested and model
 performance was assessed by comparing observed and predicted conditions in
 the lowland Treene River in northern Germany. Technically, it was possible
 to link the different models, but future applications would benefit from
 the development of open source software for all modelling steps to enable
 fully automated model runs. Future research needs concern the physical
 modelling of long-term morphodynamics, feedback of biota (e.g.,
 macrophytes) on abiotic habitat conditions, species interactions, and
 empirical data on the hydraulic habitat suitability and dispersal
 abilities of macroinvertebrates. The modelling framework is flexible and
 allows for including additional models and investigating different
 research and management questions, e.g., in climate impact research as
 well as river restoration and management.
description: Kail_etal_2015_PlosOne_DataZip-file containing all data provided for the publication. It includes (i) a read-me file (Word document) with a detailed description of the data files, and (ii) five folders with input data and result data of the different models. TIFF files included in this archive are GeoTIFF files and may be viewed in GIS software such as ESRI ArcGIS or GRASS-GIS.
DOI: 10.5061/dryad.ck2cm
title: Data from: Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae

description: The genetic architecture of adaptive traits can reflect the evolutionary
 history of populations and also shape divergence among populations.
 Despite this central role in evolution, relatively little is known
 regarding the genetic architecture of adaptive traits in nature,
 particularly for traits subject to known selection intensities. Here we
 quantitatively describe the genetic architecture of traits that are
 subject to known intensities of differential selection between host plant
 species in Timema cristinae stick insects. Specifically, we used
 phenotypic measurements of 10 traits and 211,004 single-nucleotide
 polymorphisms (SNPs) to conduct multilocus genome-wide association
 mapping. We identified a modest number of SNPs that were associated with
 traits and sometimes explained a large proportion of trait variation.
 These SNPs varied in their strength of association with traits, and both
 major and minor effect loci were discovered. However, we found no
 relationship between variation in levels of divergence among traits in
 nature and variation in parameters describing the genetic architecture of
 those same traits. Our results provide a first step toward identifying
 loci underlying adaptation in T. cristinae. Future studies will examine
 the genomic location, population differentiation, and response to
 selection of the trait-associated SNPs described here.
description: Phenotypic measurements
 of Timema cristinaeFile contains all the
 raw phenotypic measurements for all individuals included in the
 genome-wide association mapping analyses ("individual" begins
 with "FHA") and the same measurements for individuals collected
 from two additional populations ("individual" begins with
 "VPC" or "HVA").Tcris_FHA_phenotypes.txtTcris_fin_mod_snpcntII.txtFile contains variant counts (snp calling) for each individual. This file was used to estimate genotype probabilities that were ultimately used to generate the composite genotypes (see "Tcris_pimass_composite_genotypes.txt" file for these) use in GWAS analyses carried out in piMASS.Tcris_pimass_composite_genotypes.txtInput genotype file for piMASS. Contains composite genotypic values for each individual.Tcris_pimass_FHA_hiPIP_snpFile contains all snps (snp_id) with Rao-Blackwell posterior inclusion probabilities (PIP_rb) greater than 0.01 and includes the trait a given snp was associated with (trait) and the estimate of beta given by piMASS (B_rb).
DOI: 10.5061/dryad.7c99f
title: Data from: De novo transcriptomic analyses for non-model organisms: an evaluation of methods across a multi-species data set

description: High-throughput sequencing (HTS) is revolutionizing biological research by
 enabling scientists to quickly and cheaply query variation at a genomic
 scale. Despite the increasing ease of obtaining such data, using these
 data effectively still poses notable challenges, especially for those
 working with organisms without a high-quality reference genome. For every
 stage of analysis – from assembly to annotation to variant discovery –
 researchers have to distinguish technical artefacts from the biological
 realities of their data before they can make inference. In this work, I
 explore these challenges by generating a large de novo comparative
 transcriptomic data set data for a clade of lizards and constructing a
 pipeline to analyse these data. Then, using a combination of novel metrics
 and an externally validated variant data set, I test the efficacy of my
 approach, identify areas of improvement, and propose ways to minimize
 these errors. I find that with careful data curation, HTS can be a
 powerful tool for generating genomic data for non-model organisms.
description: AssembliesTranscriptome assemblies for each of the 7 lineages studied in this paper.assemblies.tar.gzPipelineR and Perl scripts used in this work.pipeline.tar.gz
DOI: 10.15468/dl.tkguky
title: Occurrence Download

description: A dataset containing 425 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abies fraseri",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is United States of America",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 425 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000398-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.nt461
title: Data from: Evolved genetic and phenotypic differences due to mitochondrial-nuclear interactions

description: The oxidative phosphorylation (OxPhos) pathway is responsible for most
 aerobic ATP production and is the only pathway with both nuclear and
 mitochondrial encoded proteins. The importance of the interactions between
 these two genomes has recently received more attention because of their
 potential evolutionary effects and how they may affect human health and
 disease. In many different organisms, healthy nuclear and mitochondrial
 genome hybrids between species or among distant populations within a
 species affect fitness and OxPhos functions. However, what is less
 understood is whether these interactions impact individuals within a
 single natural population. The significance of this impact depends on the
 strength of selection for mito-nuclear interactions. We examined whether
 mito-nuclear interactions alter allele frequencies for ~11,000 nuclear
 SNPs within a single, natural Fundulus heteroclitus population containing
 two divergent mitochondrial haplotypes (mt-haplotypes). Between the two
 mt-haplotypes, there are significant nuclear allele frequency differences
 for 349 SNPs with a p-value of 1% (236 with 10% FDR). Unlike the rest of
 the genome, these 349 outlier SNPs form two groups associated with each
 mt-haplotype, with a minority of individuals having mixed ancestry. We use
 this mixed ancestry in combination with mt-haplotype as a polygenic factor
 to explain a significant fraction of the individual OxPhos variation.
 These data suggest that mito-nuclear interactions affect cardiac OxPhos
 function. The 349 outlier SNPs occur in genes involved in regulating
 metabolic processes but are not directly associated with the 79 nuclear
 OxPhos proteins. Therefore, we postulate that the evolution of
 mito-nuclear interactions affects OxPhos function by acting upstream of
 OxPhos.
description: Unfiltered
 hapmapAn unfiltered hapmap
 including all SNPs and individuals from genotyping by sequencing pipeline.
 "N" or "S" prior to individual number refers to
 northern or southern mt-haplotype. "12" or "28" after
 individual refers to acclimation temperature of
 individual.unfiltered_hapmap_180individuals.hmp.txtFiltered hapmapFiltered hapmap with 155 individuals and 11,705 SNPs. Data was filtered so that each SNP was found in at least 70% of individuals, and each individual had at least 50% of all SNPs. "N" or "S" prior to individual number refers to northern or southern mt-haplotype. "12" or "28" after individual refers to acclimation temperature of individual.filtered_hapmap.hmp.txtSequence TagsChromosome and start site of 64bp tags from genotyping by sequencing pipeline.Chr_StartTags.txtNJ_OxPhos_DataOxPhos data for individuals in filtered hapmap. Includes State 2, State 3, Complex I, Complex II, Complex IV and E State.
DOI: 10.15468/dl.wdxxrw
title: Occurrence Download

description: A dataset containing 439785 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Global distribution of marine forests [literature records]"
 ]
}

 The dataset includes 439785 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000367-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.