cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1k8738h
title: Data from: Congruent species delimitation of two controversial gold-thread nanmu tree species based on morphological and restriction site-associated DNA sequencing data

description: Species delimitation is fundamental to conservation and sustainable use of
 economically important forest tree species. However, the delimitation of
 two highly valued gold-thread nanmu species (Phoebe bournei and P.
 zhennan) has been confusing and debated. To address this problem, we
 integrated morphology and restriction site-associated DNA sequencing
 (RADseq) to define their species boundaries. We obtained highly consistent
 results from both data sets, supporting two distinct lineages
 corresponding to P. bournei and P. zhennan. In Phoebe bournei, higher
 order leaf venation is more prominent, petioles are thicker and leaf apex
 angle is narrower, compared to P. zhennan. Both data sets also showed that
 putative P. bournei localities from north-eastern Guizhou were P. zhennan.
 The two species have different distributions and only overlap in the
 Wuling Mountains. Phoebe bournei occurs mainly in Central Fujian, southern
 Jiangxi, the Nanling Mountains and the Wuling Mountains, whereas P.
 zhennan is found in the adjoining eastern regions of the Qionglai
 Mountains, the Southern Sichuan Hills and the Wuling Mountains. The
 improved delimitation of P. bournei and P. zhennan and clarification of
 their ranges provide a better guidance for conservation and sustainable
 utilization of these tree species.
description: Supermarix of RADseq
 assemblingSupermarix of RADseq
 assembling for delimitation of Phoebe bournei and Phoebe
 zhennan.c85m16.phyunlinked SNP for structure analysisunlinked_snpsRaw data for the morphological analysis
DOI: 10.5061/dryad.nn8pj
title: Data from: Experiments on torrefied wood pellet: study by gasification and characterization for waste biomass to energy applications

description: Samples of torrefied wood pellet produced by low-temperature microwave
 pyrolysis were tested through a series of experiments relevant to present
 and near future waste to energy conversion technologies. Operational
 performance was assessed using a modern small-scale downdraft gasifier.
 Owing to the pellet's shape and surface hardness, excellent flow
 characteristics were observed. The torrefied pellet had a high energy
 density, and although a beneficial property, this highlighted the present
 inflexibility of downdraft gasifiers in respect of feedstock tolerance due
 to the inability to contain very high temperatures inside the reactor
 during operation. Analyses indicated that the torrefaction process had not
 significantly altered inherent kinetic properties to a great extent;
 however, both activation energy and pre-exponential factor were slightly
 higher than virgin biomass from which the pellet was derived.
 Thermogravimetric analysis-derived reaction kinetics (CO2 gasification),
 bomb calorimetry, proximate and ultimate analyses, and the Bond Work Index
 grindability test provided a more comprehensive characterization of the
 torrefied pellet's suitability as a fuel for gasification and also
 other combustion applications. It exhibited significant improvements in
 grindability energy demand and particle size control compared to other
 non-treated and thermally treated biomass pellets, along with a high
 calorific value, and excellent resistance to water.
description: 150607 Rotawave
 DataTorrefied Pellet
 characterisationBond Index
 SummaryTorrefied pellet
 characterisationGasifier Operational
 DataOperational data on
 product gas outputs and reduction zone temperatures when operating a Power
 Pallet downdraft gasifierGasifier Particulates
 capturedGravimetric particulates
 captured post packed bed filter of a downdraft
 gasifier.Grindability Torrefied
 PelletTorrefied pellet
 characterisationKinetics Corsican
 PineCO2 gasification
 reaction kinetics from TGA for Corsican Pine.Kinetics_European
 LarchCO2 gasification
 reaction kinetics from TGA for European Larch.Kinetics_LTM
 TorrefiedCO2 gasification
 reaction kinetics from TGA for torrefied pellet.Kinetics_Silver
 BirchCO2 gasification
 reaction kinetics from TGA for Silver Birch.Proximate
 TorrefiedTGA proximate analysis
 of torrefied pelletPSIRandom Pore Model,
 torrefied pelletReactivityCO2 gasification reactivity for torrefied pelletWood Chip Moisture and bulk densityDowndraft gasifier feedstock characteristics
DOI: 10.5061/dryad.gk138
title: Data from: Next-Gen phylogeography of rainforest trees: measuring landscape-level cpDNA variation from whole-genome sequencing.

description: Standardized phylogeographic studies across co-distributed taxa can
 identify important refugia and biogeographic barriers, and potentially
 uncover how changes in adaptive constraints through space and time impact
 on the distribution of genetic diversity. The combination of Next
 Generation Sequencing and methodologies that enable uncomplicated analysis
 of the full chloroplast genome may provide an invaluable resource for such
 studies. Here we assess the potential of a shotgun-based method across
 twelve non-model rainforest trees sampled from two evolutionary distinct
 regions. Whole genomic shotgun sequencing libraries consisting of pooled
 individuals were used to assemble species-specific chloroplast references
 (in silicio). For each species the pooled libraries allowed for the
 detection of variation within and between datasets (each representing a
 geographic region). The potential use of nuclear rDNA as an additional
 marker from the NGS libraries was investigated by mapping reads against
 available references. We successfully obtained phylogeographically
 informative sequence data from a range of previously unstudied rainforest
 trees. Greater levels of diversity were found in northern refugial
 rainforests than in southern expansion areas. The genetic signatures of
 varying evolutionary histories were detected and interesting associative
 patterns between functional characteristics and genetic diversity were
 identified. This approach can suit a wide range of landscape-level
 studies. As the key laboratory-based steps do not require prior
 species-specific knowledge and can be easily outsourced, the techniques
 described here are even suitable for researchers without access to wet-lab
 facilities, making evolutionary ecology questions increasingly accessible
 to the research community.
description: Next Gen phylogeography
 of rainforest trees van der Merwe et alSee ReadMe file for
 description of contents.Next_Gen_phylogeography_of_rainforest_trees_van_der_Merwe_et_al.zip
DOI: 10.5061/dryad.2f185
title: Data from: Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds

description: BACKGROUND: Modern cattle originate from populations of the wild extinct
 aurochs through a few domestication events which occurred about 8,000
 years ago. Newly domesticated populations subsequently spread worldwide
 following breeder migration routes. The resulting complex historical
 origins associated with both natural and artificial selection have led to
 the differentiation of numerous different cattle breeds displaying a broad
 phenotypic variety over a short period of time. METHODOLOGY/PRINCIPAL
 FINDINGS: This study gives a detailed assessment of cattle genetic
 diversity based on 1,121 individuals sampled in 47 populations from
 different parts of the world (with a special focus on French cattle)
 genotyped for 44,706 autosomal SNPs. The analyzed data set consisted of
 new genotypes for 296 individuals representing 14 French cattle breeds
 which were combined to those available from three previously published
 studies. After characterizing SNP polymorphism in the different
 populations, we performed a detailed analysis of genetic structure at both
 the individual and population levels. We further searched for spatial
 patterns of genetic diversity among 23 European populations, most of them
 being of French origin, under the recently developed spatial Principal
 Component analysis framework. CONCLUSIONS/SIGNIFICANCE: Overall, such high
 throughput genotyping data confirmed a clear partitioning of the cattle
 genetic diversity into distinct breeds. In addition, patterns of
 differentiation among the three main groups of populations—the African
 taurine, the European taurine and zebus—may provide some additional
 support for three distinct domestication centres. Finally, among the
 European cattle breeds investigated, spatial patterns of genetic diversity
 were found in good agreement with the two main migration routes towards
 France, initially postulated based on archeological evidence.
description: Data from Gautier et
 al., 2010 (PLoS ONE 5(9): e13038)See readme
 file.GAUTIER_2010.tar.bz2
DOI: 10.5061/dryad.k83g4
title: Data from: The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization

description: To investigate the phenomic and genomic traits that allow green algae to
 survive in deserts, we characterized a ubiquitous species, Chloroidium sp.
 UTEX 3007, which we isolated from multiple locations in the United Arab
 Emirates (UAE). Metabolomic analyses of Chloroidium sp. UTEX 3007
 indicated that the alga accumulates a broad range of carbon sources,
 including several desiccation tolerance-promoting sugars and unusually
 large stores of palmitate. Growth assays revealed capacities to grow in
 salinities from zero to 60 g/L and to grow heterotrophically on &gt;40
 distinct carbon sources. Assembly and annotation of genomic reads yielded
 a 52.5 Mbp genome with 8153 functionally annotated genes. Comparison with
 other sequenced green algae revealed unique protein families involved in
 osmotic stress tolerance and saccharide metabolism that support phenomic
 studies. Our results reveal the robust and flexible biology utilized by a
 green alga to successfully inhabit a desert coastline.
description: Dataset
 1-genomicsDataset containing files
 related to sequencing and annotation as a compressed .zip
 archive.Dataset
 2-phenomicsDataset containing files
 related to phenomic studies including GC-FID, GC/MS, HPLC, and phenotype
 microarrays.Dataset
 2.zipDataset_3Interactive Venn diagram displaying shared and unique protein families (Pfams) among 6 different algae. File can be uploaded to interactivenn.net.
DOI: 10.5061/dryad.nf591
title: Data from: Neutral biogeography and the evolution of climatic niches

description: Recent debate on whether climatic niches are conserved through time has
 focused on how phylogenetic niche conservatism can be measured by
 deviations from a Brownian motion model of evolutionary change. However,
 there has been no evaluation of this methodological approach. In
 particular, the fact that climatic niches are usually obtained from
 distribution data and are thus heavily influenced by biogeographic factors
 has largely been overlooked. Our main objective here was to test whether
 patterns of climatic niche evolution that are frequently observed might
 arise from neutral dynamics rather than adaptive scenarios. We develop a
 model inspired by Neutral Biodiversity Theory, where individuals disperse,
 compete, and undergo speciation independently of climate. We then sample
 the climatic niches of species according to their geographic position and
 show that even when species evolved independently of climate, their niches
 can nonetheless exhibit evolutionary patterns strongly differing from
 Brownian motion. Indeed, climatic niche evolution is better captured by a
 model of punctuated evolution with constraints due to landscape
 boundaries, two features that are traditionally interpreted as evidence
 for selective processes acting on the niche. We therefore suggest that
 deviation from Brownian motion alone should not be used as evidence for
 phylogenetic niche conservatism, but that information on phenotypic traits
 directly linked to physiology is required to demonstrate that climatic
 niches have been conserved through time.
description: Simulated
 metacommunitiesFor each speciation
 scenario, each folder contains characteristics of each metacommunity
 simulated. Each file is a R binary object stored as a list with 5
 elements: $tree: the phylogenetic tree of extant species in
 'phylo' format ; $land: a raster map of the climatic variable;
 $niche: the mean niche of each species ; $meta: an array that identifies
 the species each individual in the metacommunity belongs to (NAs are empty
 slots), which dimensions are (landscape length, landscape width, carrying
 capacity in each pixel) ; $Res gives the parameter used to simulate each
 metacommunity.
DOI: 10.5061/dryad.124hj21
title: Data from: The systematic position of the stonefly †culonga Sinitshenkova, 2011 (Plecoptera: Leuctrida) reassessed using Reflectance Transforming Imaging and cladistic analysis

description: The phylogenetic position of the insect species †culonga Sinitshenkova,
 2011, recovered from the Khasurty locality (Transbaikalia, Russia; Early
 Cretaceous), is re-investigated. This fossil needle stonefly has been
 considered an Exeleuctrida nec Mioleuctrida & Eleuctrida based on
 the organization of the hind wing venation opposite the arculus. We
 reconsidered this interpretation based on a direct observation,
 complemented by a Reflectance Transforming Imaging file. Our investigation
 indicates that the species displays the defining character state of
 Eleuctrida while it lacks the defining character state of Mioleuctrida.
 Due to inconsistencies in the character state combination displayed by the
 species, we carried out a cladistics analysis. The species †culonga is
 recovered as an Eleuctrida nec Mioleuctrida, and therefore represents a
 suitable calibration point for a node more recent than previously assumed,
 and incidentally demonstrates that Mioleuctrida belongs to Eleuctrida.
description: RTI
DOI: 10.5061/dryad.n0hk7
title: Data from: Neutral and adaptive genomic signatures of rapid poleward range expansion

description: Many species are expanding their range polewards and this has been
 associated with rapid phenotypic change. Yet, it is unclear to what extent
 this reflects rapid genetic adaptation or neutral processes associated
 with range expansion, or selection linked to the new thermal conditions
 encountered. To disentangle these alternatives, we studied the genomic
 signature of range expansion in the damselfly Coenagrion scitulum using
 4950 newly developed genomic SNPs and linked this to the rapidly evolved
 phenotypic differences between core and (newly established) edge
 populations. Most edge populations were genetically clearly differentiated
 from the core populations and all were differentiated from each other
 indicating independent range expansion events. In addition, evidence for
 genetic drift in the edge populations, and strong evidence for adaptive
 genetic variation in association with the range expansion was detected. We
 identified one SNP under consistent selection in four of the five edge
 populations and showed that the allele increasing in frequency is
 associated with increased flight performance. This indicates collateral,
 non-neutral evolutionary changes in independent edge populations driven by
 the range expansion process. We also detected a genomic signature of
 adaptation to the newly encountered thermal regimes, reflecting a pattern
 of countergradient variation. The latter signature was identified at a
 single SNP as well as in a set of covarying SNPs using a polygenic
 multilocus approach to detect selection. Overall, this study highlights
 how a strategic geographic sampling design and the integration of genomic,
 phenotypic and environmental data can identify and disentangle the neutral
 and adaptive processes that are simultaneously operating during range
 expansions.
description: SNP_dataset_Coenagrion_scitulumPhenotype_dataset_Coenagrion_scitulumSingle_locus_outlier_detection_LFMM_parallelSingle_locus_outlier_detection_LFMM_thermalPolygenic_multilocus_outlier_detection_parallelPolygenic_multilocus_outlier_detection_thermalClimate_dataset_Coenagrion_scitulum
DOI: 10.5061/dryad.43vc3c6
title: Data from: Paraneoplastic neuronal intermediate filament autoimmunity

description: Objective: To describe paraneoplastic neuronal intermediate filament (NIF)
 autoimmunity. Methods: Archived patient and control serum and CSF
 specimens were evaluated by tissue-based indirect immunofluorescence assay
 (IFA). Autoantigens were identified by western blot and mass spectrometry.
 NIF specificity was confirmed by dual tissue section staining and 5
 recombinant NIF-specific HEK293 cell based assays (CBAs, for alpha
 internexin, neurofilament light [NF-L], medium, or heavy chain, and
 peripherin). NIF-IgGs were correlated with neurological syndromes and
 cancers. Results: Among 65 patients, NIF-IgG positive by IFA and CBAs, 33
 were female (51%). Median symptom-onset age was 62 years (range, 18-88).
 Patients fell into 2 groups, defined by the presence of NF-L-IgG (21
 patients, who mostly had ≥4 NIF-IgGs detected) or its absence (44
 patients, who mostly had ≤2 NIF-IgGs detected). Among NF-L-IgG positive
 patients, 19/21 had ≥1 subacute onset CNS disorders: cerebellar ataxia
 (11), encephalopathy (11); myelopathy (2). Cancers were detected in 16 of
 21 patients (77%): carcinomas of neuroendocrine lineage (10) being most
 common (small cell [5], Merkel cell [3], other neuroendocrine [2]). Two of
 257 controls (0.8%, both with small cell carcinoma) were positive by both
 IFA and CBA. Five of 7 patients with immunotherapy data improved. By
 comparison, the 44 NF-L-IgG negative patients had findings of unclear
 significance: diverse nervous system disorders (p=0.006), as well as
 limited (p=0.003) and more diverse (p&lt;0.0001) cancer
 accompaniments. Conclusions: NIF-IgG detection by IFA, with confirmatory
 CBA testing that yields a profile including NF-L-IgG, defines a
 paraneoplastic CNS disorder (usually ataxia or encephalopathy)
 accompanying neuroendocrine lineage neoplasia.
description: Appendix
 e-1Appendix containing
 detailed research methodsFigure
 e-1Figure
 e-2Figure e-3, part
 1Figure e-3, part
 2Figure
 e-4Figure
 e-5Tables e-1, e-2,
 e-3
DOI: 10.5061/dryad.bc598
title: Data from: Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression

description: [No abstract entered]
description: Genotyping 50kSNPs East
 African Shorthorn ZebuPlink files with no
 QC50kSNPs.ped
DOI: 10.5061/dryad.vb76b45
title: Data from: Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: the monophyly of characiform fishes

description: Phylogenomic studies using genome‐wide datasets are quickly becoming the
 state of the art for systematics and comparative studies, but in many
 cases, they result in strongly supported incongruent results. The extent
 to which this conflict is real depends on different sources of error
 potentially affecting big datasets (assembly, stochastic, and systematic
 error). Here, we apply a recently developed methodology (GGI or gene
 genealogy interrogation) and data curation to new and published datasets
 with more than 1000 exons, 500 ultraconserved element (UCE) loci, and
 transcriptomic sequences that support incongruent hypotheses. The
 contentious non‐monophyly of the order Characiformes proposed by two
 studies is shown to be a spurious outcome induced by sample contamination
 in the transcriptomic dataset and an ambiguous result due to poor
 taxonomic sampling in the UCE dataset. By exploring the effects of number
 of taxa and loci used for analysis, we show that the power of GGI to
 discriminate among competing hypotheses is diminished by limited taxonomic
 sampling, but not equally sensitive to gene sampling. Taken together, our
 results reinforce the notion that merely increasing the number of genetic
 loci for a few representative taxa is not a robust strategy to advance
 phylogenetic knowledge of recalcitrant groups. We leverage the expanded
 exon capture dataset generated here for Characiformes (206 species in 23
 out of 24 families) to produce a comprehensive phylogeny and a revised
 classification of the order.
description: Database
 S1GGI
 genes trees and species trees analyses using ASTRAL-2Database1Database S4Subsets of exon captureDatabase4.txtDatabase S3Gene and multi-locus treesDataset3.txtDatabaseS2DNA sequence alignments
DOI: 10.5061/dryad.84mh3
title: Data from: An early chondrichthyan and the evolutionary assembly of a shark body plan

description: Although relationships among the major groups of living gnathostomes are
 well established, the relatedness of early jawed vertebrates to modern
 clades is intensely debated. Here, we provide a new description of
 Gladbachus, a Middle Devonian (Givetian ~385-million-year-old) stem
 chondrichthyan from Germany, and one of the very few early chondrichthyans
 in which substantial portions of the endoskeleton are preserved.
 Tomographic and histological techniques reveal new details of the gill
 skeleton, hyoid arch and jaws, neurocranium, cartilage, scales and teeth.
 Despite many features resembling placoderm or osteichthyan conditions,
 phylogenetic analysis confirms Gladbachus as a stem chondrichthyan and
 corroborates hypotheses that all acanthodians are stem chondrichthyans.
 The unfamiliar character combination displayed by Gladbachus, alongside
 conditions observed in acanthodians, implies that pre-Devonian
 stem-chondrichthyans are severely under-sampled and strongly supports
 indications from isolated scales that the gnathostome crown group
 originated at the latest by the early Silurian (~440 mya). Moreover,
 phylogenetic results highlight the likely convergent evolution of
 conventional chondrichthyan conditions among earliest members of this
 primary gnathostome division, while skeletal morphology points towards the
 likely suspension feeding habits of Gladbachus, suggesting a functional
 origin of the gill slit condition characteristic of the vast majority of
 living and fossil chondrichthyans.
description: Gladbachus Complete
 SpecimenBraincase, jaws, gill
 arches, pectoral girdle and associated scales as preserved. File format
 .stl.GladFlat.STLGladbachus Gill SkeletonReconstructed hyoid arch and gill arches. File format .stl.GladGills.STLGladbachus matrixNexus file for phylogenetic analysis.