cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nm3pq
title: Data from: Assessing strengths and weaknesses of DNA metabarcoding based macroinvertebrate identification for routine stream monitoring

description: 1) DNA metabarcoding holds great promise for the assessment of
 macroinvertebrates in stream ecosystems. However, few large-scale studies
 have compared the performance of DNA metabarcoding with that of routine
 morphological identification. 2) We performed metabarcoding using four
 primer sets on macroinvertebrate samples from 18 stream sites across
 Finland. The samples were collected in 2013 and identified based on
 morphology as part of a Finnish stream monitoring program. Specimens were
 morphologically classified, following standardised protocols, to the
 lowest taxonomic level for which identification was feasible in the
 routine national monitoring. 3) DNA metabarcoding identified more than
 twice the number of taxa than the morphology-based protocol, and also
 yielded a higher taxonomic resolution. For each sample, we detected more
 taxa by metabarcoding than by the morphological method, and all four
 primer sets exhibited comparably good performance. Sequence read abundance
 and the number of specimens per taxon (a proxy for biomass) were
 significantly correlated in each sample, although the adjusted R2 were
 low. With a few exceptions, the ecological status assessment metrics
 calculated from morphological and DNA metabarcoding datasets were similar.
 Given the recent reduction in sequencing costs, metabarcoding is currently
 approximately as expensive as morphology-based identification. 4) Using
 samples obtained in the field, we demonstrated that DNA metabarcoding can
 achieve comparable assessment results to current protocols relying on
 morphological identification. Thus, metabarcoding represents a feasible
 and reliable method to identify macroinvertebrates in stream
 bioassessment, and offers powerful advantage over morphological
 identification in providing identification for taxonomic groups that are
 unfeasible to identify in routine protocols. To unlock the full potential
 of DNA metabarcoding for ecosystem assessment, however, it will be
 necessary to address key problems with current laboratory protocols and
 reference databases.
description: Metabarcoding pipeline
 and scriptsThis folder contains all
 scripts used to process the raw sequence data into OTUs. Additionally, all
 scripts for data analysis and figure generation were
 included.Dryad_Finland_2017.zipDNA extraction and PCR protocolsRaw data on laboratory protocols. Includes gel pictures, PCR sheets and scans of the laboratory protocols as well as pictures of the dried samples.laboratory notes.zipPreprocessed HTS data (144 samples)Sequence data for the 144 sequenced PCR reactions. Files are PE merged, trimmed and quality filtered as described in the manuscript using the scripts also provided on dryad. The sequence files are dereplicated ready to be clustered into OTUs. For OTU sequences and counts see table S4 of the manuscript.6 dereplicate.zip
DOI: 10.5061/dryad.tm47d
title: Data from: Ancient hybridization and genomic stabilization in a swordtail fish

description: A rapidly increasing body of work is revealing that the genomes of
 distinct species often exhibit hybrid ancestry, presumably due to
 postspeciation hybridization between closely related species. Despite the
 growing number of documented cases, we still know relatively little about
 how genomes evolve and stabilize following hybridization, and to what
 extent hybridization is functionally relevant. Here, we examine the case
 of Xiphophorus nezahualcoyotl, a teleost fish whose genome exhibits
 significant hybrid ancestry. We show that hybridization was relatively
 ancient and is unlikely to be ongoing. Strikingly, the genome of X.
 nezahualcoyotl has largely stabilized following hybridization,
 distinguishing it from examples such as human–Neanderthal hybridization.
 Hybridization-derived regions are remarkably distinct from other regions
 of the genome, tending to be enriched in genomic regions with reduced
 constraint. These results suggest that selection has played a role in
 removing hybrid ancestry from certain functionally important regions.
 Combined with findings in other systems, our results raise many questions
 about the process of genomic stabilization and the role of selection in
 shaping patterns of hybrid ancestry in the genome.
description: create_insnp_oneindiv_GATK3_4_v7script to generate insnp file from GATK gVCF files. Must be run on each chromosome separately.5Xipho.fasta.reducedWhole genome alignments used in analysis.RAxML_bestTreeRAxML results fileXiphophorus_maculatus_LG.Xipmac4.4.2.81modified gtf file for the X. maculatus genome used in analysisRAxML_bootstrapbootstrap results for RAxML analysis
DOI: 10.5061/dryad.fp060
title: Data from: A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings

description: The wings of birds and their closest theropod relatives share a uniform
 fundamental architecture, with pinnate flight feathers as the key
 component. Here we report a new scansoriopterygid theropod, Yi qi gen. et
 sp. nov., based on a new specimen from the Middle–Upper Jurassic period
 Tiaojishan Formation of Hebei Province, China. Yi is nested
 phylogenetically among winged theropods but has large stiff filamentous
 feathers of an unusual type on both the forelimb and hindlimb. However,
 the filamentous feathers of Yi resemble pinnate feathers in bearing
 morphologically diverse melanosomes5. Most surprisingly, Yi has a long
 rod-like bone extending from each wrist, and patches of membranous tissue
 preserved between the rod-like bones and the manual digits. Analogous
 features are unknown in any dinosaur but occur in various flying and
 gliding tetrapods, suggesting the intriguing possibility that Yi had
 membranous aerodynamic surfaces totally different from the archetypal
 feathered wings of birds and their closest relatives. Documentation of the
 unique forelimbs of Yi greatly increases the morphological disparity known
 to exist among dinosaurs, and highlights the extraordinary breadth and
 richness of the evolutionary experimentation that took place close to the
 origin of birds.
description: CT data for holotype of
 Yi qiThis data archive
 contains CT slice images in .dcm format for the slab containing the
 holotype specimen (STM, Shandong Tianyu Museum, 31-2) of Yi qi, a
 scansoriopterygid dinosaur from the Middle-Upper Jurassic of Mutoudeng,
 Hebei Province, China. The CT data reveal the 3D structure of the
 specimen, and of the slab itself.Yi_ct_data.rar
DOI: 10.5061/dryad.d45gs
title: Data from: Nonlinear dynamics forecasting of obstructive sleep apnea onsets

description: Recent advances in sensor technologies and predictive analytics are
 fueling the growth in point-of-care (POC) therapies for obstructive sleep
 apnea (OSA) and other sleep disorders. The effectiveness of POC therapies
 can be enhanced by providing personalized and real-time prediction of OSA
 episode onsets. Previous attempts at OSA prediction are limited to
 capturing the nonlinear, nonstationary dynamics of the underlying
 physiological processes. This paper reports an investigation into heart
 rate dynamics aiming to predict in real time the onsets of OSA episode
 before the clinical symptoms appear. A prognosis method based on a
 nonparametric statistical Dirichlet-Process Mixture-Gaussian-Process
 (DPMG) model to estimate the transition from normal states to an anomalous
 (apnea) state is utilized to estimate the remaining time until the onset
 of an impending OSA episode. The approach was tested using three datasets
 including (1) 20 records from 14 OSA subjects in benchmark ECG apnea
 databases (Physionet.org), (2) records of 10 OSA patients from the
 University of Dublin OSA database and (3) records of eight subjects from
 previous work. Validation tests suggest that the model can be used to
 track the time until the onset of an OSA episode with the likelihood of
 correctly predicting apnea onset in 1 min to 5 mins ahead is 83.6 ± 9.3%,
 80 ± 8.1%, 76.2 ± 13.3%, 66.9 ± 15.4%, and 61.1 ± 16.7%, respectively. The
 present prognosis approach can be integrated with wearable devices,
 enhancing proactive treatment of OSA and real-time wearable sensor-based
 of sleep disorders.
description: Obstructive Sleep Apnea
 Prediction DataThe database consists of
 two full datasets. The first dataset is the collection of 20 records
 gathered from 14 OSA patients as part of the Apnea-ECG Database.The second
 dataset consists of 10 records from 10 subjects, who were selected based
 on the quality of the signals, from St. Vincent’s University Hospital/
 University College Dublin (UCD Database) sleep apnea database
 (http://www.physionet.org/pn3/ucddb/). The OSA annotations are in
 minute-wise scored offline by experienced sleep physicians using
 polysomnography (PSG) signals. The PSG signals recorded were EEG, EOG,
 EMG, ECG, nasal airflow, ribcage movements, abdomen movements, oxygen
 saturation (finger pulse oximeter), snoring (tracheal microphone), and
 body position. All subjects have been clinically diagnosed with mild to
 severe OSA.Data.rar
DOI: 10.5061/dryad.37k3n
title: Data from: Object recognition and localization from 3D point clouds by maximum-likelihood estimation

description: We present an algorithm based on maximum-likelihood analysis for the
 automated recognition of objects, and estimation of their pose, from 3D
 point clouds. Surfaces segmented from depth images are used as the
 features, unlike ‘interest point’-based algorithms which normally discard
 such data. Compared to the 6D Hough transform, it has negligible memory
 requirements, and is computationally efficient compared to iterative
 closest point algorithms. The same method is applicable to both the
 initial recognition/pose estimation problem as well as subsequent pose
 refinement through appropriate choice of the dispersion of the probability
 density functions. This single unified approach therefore avoids the usual
 requirement for different algorithms for these two tasks. In addition to
 the theoretical description, a simple 2 degrees of freedom (d.f.) example
 is given, followed by a full 6 d.f. analysis of 3D point cloud data from a
 cluttered scene acquired by a projected fringe-based scanner, which
 demonstrated an RMS alignment error as low as 0.3 mm.
description: CRT monitor model raw
 dataContains 7 views of a
 CRT monitor that were used to create the gold standard
 modelCRT_model_raw_data.matBike helmet model raw dataBike helmet model raw data containing 9 views of the gold standard model.Bike_helmet_model_raw_data.matSonotrode model raw dataContains 9 views of the sonotrode (conical transducer) gold standard modelSonotrode_model_raw_data.matCRT Bike helmet Sonotrode scenes3 scenes containing the CRT monitor, one scene each containing a bike helmet and a sonotrode (conical transducer)CRT_Bike_helmet_Sonotrode_scenes.mat
DOI: 10.5061/dryad.006bf
title: Data from: Genome sequences reveal cryptic speciation in the human pathogen Histoplasma capsulatum

description: Histoplasma capsulatum is a pathogenic fungus that causes life-threatening
 lung infections. About 500,000 people are exposed to H. capsulatum each
 year in the United States, and over 60% of the U.S. population has been
 exposed to the fungus at some point in their life. We performed
 genome-wide population genetics and phylogenetic analyses with 30
 Histoplasma isolates representing four recognized areas where
 histoplasmosis is endemic and show that the Histoplasma genus is composed
 of at least four species that are genetically isolated and rarely
 interbreed. Therefore, we propose a taxonomic rearrangement of the genus.
 IMPORTANCE: The evolutionary processes that give rise to new pathogen
 lineages are critical to our understanding of how they adapt to new
 environments and how frequently they exchange genes with each other. The
 fungal pathogen Histoplasma capsulatum provides opportunities to precisely
 test hypotheses about the origin of new genetic variation. We find that H.
 capsulatum is composed of at least four different cryptic species that
 differ genetically and also in virulence. These results have implications
 for the epidemiology of histoplasmosis because not all Histoplasma species
 are equivalent in their geographic range and ability to cause disease.
description: Histoplasma Raw
 DataHistoplasmaData.tgzSupplementary Tables: S1-S6 (Sepulveda et al. mBio 2017)supplement_proofs.docxHistoplasma H88: Reference genomehistoplasma_h88_ref.fastaHistoplasma BAM filesbams_histoplasma.zip
DOI: 10.5061/dryad.2c220
title: Data from: High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements

description: Sample availability limits population genetics research on many species,
 especially taxa from regions with high diversity. However, many such
 species are well represented in museum collections assembled before the
 molecular era. Development of techniques to recover genetic data from
 these invaluable specimens will benefit biodiversity science. Using a
 mixture of freshly preserved and historical tissue samples, and a sequence
 capture probe set targeting &gt;5000 loci, we produced high-confidence
 genotype calls on thousands of single nucleotide polymorphisms (SNPs) in
 each of five South-East Asian bird species and their close relatives (N =
 27–43). On average, 66.2% of the reads mapped to the pseudo-reference
 genome of each species. Of these mapped reads, an average of 52.7% was
 identified as PCR or optical duplicates. We achieved deeper effective
 sequencing for historical samples (122.7×) compared to modern samples
 (23.5×). The number of nucleotide sites with at least 8× sequencing depth
 was high, with averages ranging from 0.89 × 106 bp (Arachnothera, modern
 samples) to 1.98 × 106 bp (Stachyris, modern samples). Linear regression
 revealed that the amount of sequence data obtained from each historical
 sample (represented by per cent of the pseudo-reference genome recovered
 with ≥8× sequencing depth) was positively and significantly (P ≤ 0.013)
 related to how recently the sample was collected. We observed
 characteristic post-mortem damage in the DNA of historical samples.
 However, we were able to reduce the error rate significantly by truncating
 ends of reads during read mapping (local alignment) and conducting
 stringent SNP and genotype filtering.
description: arachnothera.bam.tar.gzBam and index files of Arachnothera reads mapped to pseudo-reference genomeirena.bam.tar.gzBam and index files of Irena reads mapped to pseudo-reference genomearach.uce.mar17.csPseudo-reference genome for Arachnotherairena.uce.mar20.csPseudo-reference genome for Irena.niltava.bam.tar.gzBam and index files of Niltava reads mapped to pseudo-reference genomeniltava.uce.apr30.csPseudo-reference genome for Niltava.pycnonotus.bam.tar.gzBam and index files of Pycnonotus reads mapped to pseudo-reference genomepyc.uce.may5.csPseudo-reference genome for Pycnonotus.stachyris.bam.tar.gzBam and index files of Stachyris reads mapped to pseudo-reference genome.stachyris.uce.mar19.csPseudo-reference genome for Stachyris.
DOI: 10.5061/dryad.f5q4f
title: Data from: The large-X effect in plants: increased species divergence and reduced gene flow on the Silene X-chromosome

description: The disproportionately large involvement of the X-chromosome in the
 isolation of closely related species (the large-X effect) has been
 reported for many animals, where X-linked genes are mostly hemizygous in
 the heterogametic sex. The expression of deleterious recessive mutations
 is thought to drive the frequent involvement of the X-chromosome in hybrid
 sterility, as well as to reduce interspecific gene flow for X-linked
 genes. Here, we evaluate the role of the X-chromosome in the speciation of
 two closely related plant species – the white and red campions (Silene
 latifolia and S. dioica) – that hybridize widely across Europe. The two
 species evolved separate sexes and sex chromosomes relatively recently
 (~107 years), and unlike most animal species, most X-linked genes have
 intact Y-linked homologs. We demonstrate that the X-linked genes show a
 very small and insignificant amount of interspecific gene flow, while gene
 flow involving autosomal loci is significant and sufficient to homogenise
 the gene pools of the two species. These findings are consistent with the
 hypothesis of the large-X effect in Silene and comprise the first report
 of this effect in plants. Non-hemizygosity of many X-linked genes in
 Silene males indicates that exposure of recessive mutations to selection
 may not be essential for the occurrence of the large-X effect. Several
 possible causes of the large-X effect in Silene are discussed.
description: data used to generate
 Figure 1The zip-compressed
 archive contains text files used as input files to generate figure 1 in
 R.dataForFig1.zipsequence alignmentszip-compressed archive containing sequence alignments in fasta format. These sequences were used throughout the paper.alignments.fasta.zip
DOI: 10.5061/dryad.63h33
title: Data from: Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

description: Background: Simple Sequence Repeats (SSRs) are widely used in population
 genetic studies but their classical development is costly and
 time-consuming. The ever-increasing available DNA datasets generated by
 high-throughput techniques offer an inexpensive alternative for SSRs
 discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR
 source for plants of economic relevance but their application to non-model
 species is still modest. Methods: Here, we explored the use of publicly
 available ESTs (GenBank at the National Center for Biotechnology
 Information-NCBI) for SSRs development in non-model plants, focusing on
 genera listed by the International Union for the Conservation of Nature
 (IUCN). We also search two model genera with fully annotated genomes for
 EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome
 distribution analyses. Overall, we downloaded 16 031 555 sequences for 258
 plant genera which were mined for SSRsand their primers with the help of
 QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by
 blasting the sequences with SSR against the Oryza sativa and Arabidopsis
 thaliana reference genomes implemented in the Basal Local Alignment Tool
 (BLAST) of the NCBI website. Finally, we performed an empirical test to
 determine the performance of our EST-SSRs in a few individuals from four
 species of two eudicot genera, Trifolium and Centaurea. Results: We
 explored a total of 14 498 726 EST sequences from the dbEST database
 (NCBI) in 257 plant genera from the IUCN Red List. We identify a very
 large number (17 102) of ready-to-test EST-SSRs in most plant genera (193)
 at no cost. Overall, dinucleotide and trinucleotide repeats were the
 prevalent types but the abundance of the various types of repeat differed
 between taxonomic groups. Control genomes revealed that trinucleotide
 repeats were mostly located in coding regions while dinucleotide repeats
 were largely associated with untranslated regions. Our results from the
 empirical test revealed considerable amplification success and
 transferability between congenerics. Conclusions: The present work
 represents the first large-scale study developing SSRs by utilizing
 publicly accessible EST databases in threatened plants. Here we provide a
 very large number of ready-to-test EST-SSR (17 102) for 193 genera. The
 cross-species transferability suggests that the number of possible target
 species would be large. Since trinucleotide repeats are abundant and
 mainly linked to exons they might be useful in evolutionary and
 conservation studies. Altogether, our study highly supports the use of EST
 databases as an extremely affordable and fast alternative for SSR
 developing in threatened plants.
description: Type I
 EST_SSRZip file containing 194
 excel file with the EST-SSR and primers information for the 193 IUCN plant
 genera and one file for Arabidopsis.
DOI: 10.5061/dryad.5hq56
title: Data from: Macroevolution of leaf defenses and secondary metabolites across the genus Helianthus

description: Leaf defenses are widely recognized as key adaptations and drivers of
 plant evolution. Across environmentally diverse habitats, the
 macroevolution of leaf defenses can be predicted by the univariate
 trade-off model, which predicts that defenses are functionally redundant
 and thus trade off, and the resource availability hypothesis, which
 predicts that defense investment is determined by inherent growth rate and
 that higher defense will evolve in lower resource environments. Here, we
 examined the evolution of leaf physical and chemical defenses and
 secondary metabolites in relation to environmental characteristics and
 leaf economic strategy across 28 species of Helianthus (the sunflowers).
 Using a phylogenetic comparative approach, we found few evolutionary
 trade-offs among defenses and no evidence for defense syndromes. We also
 found that leaf defenses are strongly related to leaf economic strategy,
 with higher defense in more resource-conservative species, although there
 is little support for the evolution of higher defense in low-resource
 habitats. A wide variety of physical and chemical defenses predict
 resistance to different insect herbivores, fungal pathogens, and a
 parasitic plant, suggesting that most sunflower defenses are not redundant
 in function and that wild Helianthus represents a rich source of variation
 for the improvement of crop sunflower.
description: Notes S1 - Population
 Sources, Defense Trait Data, and Aggregated Literature
 DataPopulation source and
 locality data. Population least squares means for all leaf defense traits,
 secondary metabolite metrics, and environmental characteristics. Species
 means for all leaf defense traits and secondary metabolite metrics.
 Aggregated species-level data on plant interactions with herbivores and
 pathogens from the literature.Notes
 S1.xlsxNotes S2 - HeliaMet
 DatabaseHeliaMet database of
 normalized peak areas for individuals of all detected compounds via
 HPLC-MS, with m/z ratios and retention times.Notes
 S2.xlsx