cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tb700
title: Data from: Genome-wide sequence data suggest the possibility of pollinator sharing by host shift in dioecious figs (Moraceae, Ficus)

description: The obligate mutualism of figs and fig-pollinating wasps has been one of
 the classic models used for testing theories of co-evolution and
 cospeciation due to the high species-specificity of these relationships.
 To investigate the species-specificity between figs and fig pollinators
 and to further understand the speciation process in obligate mutualisms,
 we examined the genetic differentiation and phylogenetic relationships of
 four closely related fig-pollinating wasp species (Blastophaga nipponica,
 Blastophaga taiwanensis, Blastophaga tannoensis and Blastophaga yeni) in
 Japan and Taiwan using genome-wide sequence data, including mitochondrial
 DNA sequences. In addition, population structure was analysed for the fig
 wasps and their host species using microsatellite data. The results
 suggest that the three Taiwanese fig wasp species are a single panmictic
 population that pollinates three dioecious fig species, which are
 sympatrically distributed, have large differences in morphology and
 ecology and are also genetically differentiated. Our results illustrate
 the first case of pollinator sharing by host shift in the subgenus Ficus.
 On the other hand, there are strict genetic codivergences between
 allopatric populations of the two host–pollinator pairs. The possible
 processes that produce these pollinator-sharing events are discussed based
 on the level and pattern of genetic differentiation in these figs and fig
 wasps.
description: Bnip_cytB_140710_cut_name.fasAlignment of haplotypes of cytb sequencesBnip_CO1_2_140710_cut_name.fasAlignment of haplotypes of cox1-cox2 sequencest50Alignment of SNPs from ddRAD-seq loci, read length: 50bpt100Alignment of SNPs from ddRAD-seq loci, read length: 100bp
DOI: 10.5061/dryad.vm525
title: Data from: Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

description: Previous studies had shown that integration of genome wide expression
 profiles, in metabolic tissues, with genetic and phenotypic variance,
 provided valuable insight into the underlying molecular mechanisms. We
 used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred
 strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference
 resource population for cardiovascular and metabolic traits. We report
 numerous novel transcripts supported by proteomic analyses, as well as
 novel non coding RNAs. High resolution genetic mapping of transcript
 levels in HMDP, reveals both local and trans expression Quantitative Trait
 Loci (eQTLs) demonstrating 2 trans eQTL 'hotspots' associated
 with expression of hundreds of genes. We also report thousands of
 alternative splicing events regulated by genetic variants. Finally,
 comparison with about 150 metabolic and cardiovascular traits revealed
 many highly significant associations. Our data provides a rich resource
 for understanding the many physiologic functions mediated by the
 hypothalamus and their genetic regulation.
description: FileS2_ExpressionQTLExpression QTL supplementary file, analyzed in "Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes". Data file that includes all identified expression QTL associations. Includes tracking IDs of the feature and SNP, positions, p value of association, SNP odds ratio and weight, SNP distance to gene and interaction type (local or trans).
DOI: 10.5061/dryad.ck06k75
title: Data from: Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD

description: DUX4 is a transcription factor whose misexpression in skeletal muscle
 causes facioscapulohumeral muscular dystrophy (FSHD). While DUX4's
 transcriptional activity has been extensively characterized, the
 DUX4-induced proteome remains undescribed. Here, we report concurrent
 measurement of RNA and protein levels in DUX4-expressing cells via RNA-seq
 and quantitative mass spectrometry. DUX4 transcriptional targets were
 robustly translated, confirming the likely clinical relevance of proposed
 FSHD biomarkers. However, a multitude of mRNAs and proteins exhibited
 discordant expression changes upon DUX4 expression. Our dataset revealed
 unexpected proteomic, but not transcriptomic, dysregulation of diverse
 molecular pathways, including Golgi apparatus fragmentation, as well as
 extensive post-transcriptional buffering of stress response genes. Key
 components of RNA degradation machineries, including UPF1, UPF3B, and
 XRN1, exhibited suppressed protein, but not mRNA, levels, explaining the
 build-up of aberrant RNAs that characterizes DUX4-expressing cells. Our
 results provide a resource for the FSHD community and illustrate the
 importance of post-transcriptional processes to DUX4-induced pathology.
description: Supp data
 1_psmdata
DOI: 10.5061/dryad.2mn50
title: Data from: Shared genomic regions between derivatives of a large segregating population of maize identified using bulked segregant analysis sequencing and traditional linkage analysis

description: Delayed transition from the vegetative stage to the reproductive stage of
 development and increased plant height have been shown to increase biomass
 productivity in grasses. The goal of this project was to detect
 quantitative trait loci using extremes from a large synthetic population,
 as well as a related recombinant inbred line mapping population for these
 two traits. Ten thousand individuals from a B73 × Mo17 noninbred
 population intermated for 14 generations (IBM Syn14) were grown at a
 density of approximately 16,500 plants ha−1. Flowering time and plant
 height were measured within this population. DNA was pooled from the 46
 most extreme individuals from each distributional tail for each of the
 traits measured and used in bulk segregant analysis (BSA) sequencing.
 Allelic divergence at each of the ∼1.1 million SNP loci was estimated as
 the difference in allele frequencies between the selected extremes.
 Additionally, 224 intermated B73 × Mo17 recombinant inbred lines were
 concomitantly grown at a similar density adjacent to the large synthetic
 population and were assessed for flowering time and plant height. Using
 the BSA sequencing method, 14 and 13 genomic regions were identified for
 flowering time and plant height, respectively. Linkage mapping with the
 RIL population identified eight and three regions for flowering time and
 plant height, respectively. Of the regions identified, three colocalized
 between the two populations for flowering time and two colocalized for
 plant height. This study demonstrates the utility of using BSA sequencing
 for the dissection of complex quantitative traits important for production
 of lignocellulosic ethanol.
description: B73_Mo17_extreme_allele_freq_matrix_3301371_SNPs_bias_correct_100bp_0.25_0.75_control_with_headerGenotype counts and frequencies for the filtered SNP set from pooled sequencing data from control plants and selected extremes for flowering time and plant height.
DOI: 10.25345/c5rx93s9z
title: MassIVE MSV000100594 - Single-cell proteomic analysis of 30-week brain organoids indicate sufficient depth for cellular heterogeneity classification
title: Single cell proteomic analysis 293 cells from dissociated human brain organoids.
DOI: 10.5061/dryad.88h1m1h
title: Data from: Energetics and electronic structures of perylene confined in carbon nanotubes

description: The energetics and geometries of perylene encapsulated in carbon nanotubes
 (CNTs) have been investigated employing density functional theory using
 the generalized gradient approximation combined with the van der Waals
 correction. Our calculations show that the encapsulated perylene molecules
 possess two metastable molecular conformations with respect to the CNT
 wall, which are almost degenerate with each other. A standing
 conformation, with respect to the CNT wall, is the ground state
 conformation for a semiconducting (19,0)CNT, while a lying conformation is
 the ground state for a metallic (11,11)CNT. Cooperation and competition
 between perylene-perylene and perylene-CNT interactions cause these
 possible perylene conformations inside CNTs. However, the electronic
 structure of the CNT encapsulating the perylene molecules is found to be
 insensitive to the molecular conformation.
description: Input datas for the
 energetics and electronic structure of perylene-CNTAll input files for the
 calculations on the Energetics and Electronic Structures of Perylene
 Confined in Carbon Nanotubes. The input files are in the format which is
 suitable for the STATE program package.perylene-CNT.zip
DOI: 10.5061/dryad.k58fr
title: Data from: The extra burden of motherhood: reduced dive duration associated with pregnancy status in a deep-diving mammal, the northern elephant seal

description: The cost of pregnancy is hard to study in marine mammals, particularly in
 species that undergo pregnancy while diving continuously at sea such as
 elephant seals (genus Mirounga). We analyzed the diving behavior of
 confirmed pregnant and non-pregnant northern elephant seals (M.
 angustirostris, n = 172) and showed that after an initial continuous
 increase in dive duration, dives of pregnant females become shorter after
 week 17. The reasons for this reduction in dive duration remain unknown,
 but we hypothesize that increased fetal demand for oxygen could be the
 cause. Our findings reveal an opportunity to explore the use of biologging
 data to investigate pregnancy status of free-ranging marine mammals and
 factors that could affect pregnancy success.
description: NESEDiveDur_V2Northern elephant seal dive metrics and pregnancy statusNESEwithMassNorthern elephant seal deployment and recovery masses with diving data
DOI: 10.5061/dryad.2nh26
title: Data from: Xianella: a new mat-forming calcified cyanobacterium from the Middle–Late Ordovician of North China

description: Xianella hongii gen. et sp. nov. is described from the Middle–Late
 Ordovician of Shaanxi, China and interpreted as a calcified cyanobacterial
 sheath. Xianella filaments formed cable-like strands that constructed
 thick fenestral layers. The specimens occur in metre-sized limestone
 blocks, possibly derived from local collapse of a reefal platform margin.
 In combination with micrite, some of which is intraclastic and peloidal,
 Xianella created thick and extensive stacks of layered calcified fenestral
 fabric that appear to be synsedimentarily calcified open-frame mat
 deposits. The fenestrae range from small, laminose and very irregular, to
 large equidimensional areas ~2 cm across. Fenestrae with rounded outlines
 resemble primary gas bubbles observed in present-day microbial mats. These
 delicate fabrics are comparable in structure and quality of preservation
 with those of some Proterozoic silicified stromatolitic mats.
description: NIGPAS159413Scanned file of NIGPAS159413 (slab)NIGPAS159414Scanned file of NIGPAS159414 (thin section)NIGPAS159415Scanned file of NIGPAS159415 (thin section)NIGPAS159416Scanned file of NIGPAS159416 (thin section)NIGPAS159417Scanned file of NIGPAS159417 (thin section)SCALE for NIGPAS159414-159417SCALE for NIGPAS159414-159417SCALE.jpgPhotomicrograph_XianellaPhotomicrographs of Xianella. File names indicate: NIGPAS15941X(sample number)-XX(photomicrograph number)-X8(scale). Check attached scale file for size of photomicrographs.
DOI: 10.34740/kaggle/dsv/14630467
title: KANPM-DTA Pretrained Models
DOI: 10.5061/dryad.mn46cd6
title: Data from: Hodge decomposition of wall shear stress vector fields characterizing biological flows

description: A discrete boundary-sensitive Hodge decomposition is proposed as a central
 tool for the analysis of wall shear stress (WSS) vector fields in aortic
 blood flows. The method is based on novel results for the smooth and
 discrete Hodge-Morrey-Friedrichs decomposition on manifolds with boundary
 and subdivides the WSS vector field into five components: gradient
 (curl-free), co-gradient (divergence-free), and three harmonic fields
 induced from the boundary, which are called the center, Neumann and
 Dirichlet fields. First, an analysis of WSS in several simulated
 simplified phantom geometries (duct and idealized aorta) was performed in
 order to understand the impact of the five components. It was shown that
 the decomposition is able to distinguish harmonic blood flow arising from
 the inlet from harmonic circulations induced by the interior topology of
 the geometry. Finally, a comparative analysis of 11 patients with
 coarctation of the aorta (CoA) before and after treatment as well as 10
 controls patient was done. The study shows a significant difference
 between the CoA patients and the healthy controls before and after the
 treatment. This means a global difference between aortic shapes of
 diseased and healthy subjects, thus leading to a new type of WSS-based
 analysis and classification of pathological and physiological blood flow.
description: Hodge-Morrey-Friedrich
 decomposition for WSS vector fieldModels and source code
 to decompose a WSS vector field into five components: gradient,
 co-gradient, harmonic center, Neumann, and Dirichlet.HMF_models_and_code.zip
DOI: 10.5061/dryad.hp5h2
title: Data from: Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds

description: Recombination rate is heterogeneous across the genome of various species,
 and so are genetic diversity and differentiation as a consequence of
 linked selection. However, we still lack a clear picture of the underlying
 mechanisms for regulating recombination. Here we estimated fine-scale
 population recombination rate based on the patterns of linkage
 disequilibrium (LD) across the genomes of multiple populations of two
 closely related flycatcher species (Ficedula albicollis and F. hypoleuca).
 This revealed an overall conservation of the recombination landscape
 between these species at the scale of 200-kb, but we also identified
 differences in the local rate of recombination despite their recent
 divergence (&lt;1 million years). Genetic diversity and
 differentiation were associated with recombination rate in a
 lineage-specific manner, indicating differences in the extent of linked
 selection between species. We detected 400-3,085 recombination hotspots
 per population. Location of hotspots was conserved between species, but
 the intensity of hotspot activity varied between species. Recombination
 hotspots were primarily associated with CpG islands (CGIs), regardless of
 whether CGIs were at promoter regions or away from genes. Recombination
 hotspots were also associated with specific transposable elements (TEs),
 but this association appears indirect due to shared preferences of the
 transposition machinery and the recombination machinery for accessible
 open chromatin regions. Our results suggest that CGIs are a major
 determinant of the localization of recombination hotspots, and we propose
 that both the distribution of TEs and fine-scale variation in
 recombination rate may be associated with the evolution of the epigenetic
 landscape.
description: Population scaled
 recombination rate in 8 populations of Ficedula
 flycatchersflycatcher_rho.zip
DOI: 10.5061/dryad.8j88573
title: Data from: Capture enrichment of aquatic environmental DNA: a first proof of concept

description: Environmental DNA (eDNA) sampling – the detection of genetic material in
 the environment to infer species presence – has rapidly grown as a tool
 for sampling aquatic animal communities. A potentially powerful feature of
 environmental sampling is that all taxa within the habitat shed DNA and so
 may be detectable, creating opportunity for whole-community assessments.
 However, animal DNA in the environment tends to be comparatively rare,
 making it necessary to enrich for genetic targets from focal taxa prior to
 sequencing. Current metabarcoding approaches for enrichment rely on bulk
 amplification using conserved primer annealing sites, which can result in
 skewed relative sequence abundance and failure to detect some taxa because
 of PCR bias. Here we test capture enrichment via hybridization as an
 alternative strategy for target enrichment using a series of experiments
 on environmental samples and lab-generated, known-composition DNA
 mixtures. Capture enrichment resulted in detecting multiple species in
 both kinds of samples, and post-capture relative sequence abundance
 accurately reflected initial relative template abundance. However, further
 optimization is needed to permit reliable species detection at the very
 low DNA quantities typical of environmental samples (&lt; 0.1 ng DNA).
 We estimate that our capture protocols are comparable to, but less
 sensitive than, current PCR-based eDNA analyses.
description: FASTQ files for
 Experiments 1 and 2FASTQ files for
 Experiments 1 and 2. List of libraries in Table S4 with the
 manuscript.Exp1_Exp2_fastq_files.zipeDNA-capture-scripts
DOI: 10.5061/dryad.f2g14
title: Data from: Influence of land use and climate on recent forest expansion: a case study in the Eurosiberian-Mediterranean limit of northwest Spain

description: 1. In Mediterranean mountainous areas, forests have expanded in recent
 decades because traditional management practices have been abandoned or
 reduced. However, understanding the ecological mechanism behind landscape
 change is a complex undertaking as the effects of land use may be
 influenced (reinforced or constrained) by other factors such as climate.
 2. We used orthorectified aerial photographs to monitor changes in forest
 distribution in a set of 20 head-water basins (located in the Cantabrian
 Mountains of northwest Spain, at the Eurosiberian-Mediterranean limit)
 during the second half of the 20th century (1956, 1974, 1983, 1990 and
 2004). In particular, we evaluated the combined effects of both land use
 history (comparing natural vs. anthropic basins) and microclimate
 (comparing shaded vs. sunny aspects) for assessing gain/loss rates and
 spatial distribution shifts of forests. Finally, in the stated scenarios
 of land use history and microclimate, we applied Species Distribution
 Modeling techniques (MaxEnt and BIOMOD) for defining forest expansion both
 spatially and statistically on the basis of topography, soil properties
 and mesoclimatic variables. 3. On average, forest cover increased from
 10.72% in 1956 to 27.67% in 2004. The rate of expansion was significantly
 higher in natural basins and, particularly, on shaded slopes in recent
 decades. In all cases, the mean elevation of new forest patches increased
 during the study period, this trend being more evident on natural sunny
 slopes. The performance of the models and the magnitude of the effects
 varied across land use history, microclimatic conditions and biogeographic
 origin of forests. The main drivers of forest expansion were temperature
 and precipitation in late spring and early summer and soil properties,
 although land use history and plant diversity primarily controlled forest
 expansion rates and upward altitudinal shifts. 4. Synthesis. The
 combination of monitoring and modeling used in this work contributes to
 the understanding of forest dynamics in cultural systems, indicating that
 ecological succession is not a homogeneous process, but varies spatially
 due to human and abiotic constraints since historical times.
description: On-line data
 support_monitoring and modelling forest expansion
DOI: 10.5061/dryad.2sv13
title: Data from: Vulnerability mapping as a tool to manage the environmental impacts of oil and gas extraction

description: Various biophysical and socio-economic impacts may be associated with
 unconventional oil and gas (UOG) extraction. A vulnerability map may
 assist governments during environmental assessments, spatial planning and
 the regulation of UOG extraction, as well as decision-making around UOG
 extraction in fragile areas. A regional interactive vulnerability map was
 developed for UOG extraction in South Africa. This map covers groundwater,
 surface water, vegetation, socio-economics and seismicity as mapping
 themes, based on impacts that may emanate from UOG extraction. The mapping
 themes were developed using a normative approach, where expert input
 during the identification and classification of vulnerability indicators
 may increase the acceptability of the resultant map. This article
 describes the development of the interactive vulnerability map for South
 Africa, where UOG extraction is not yet allowed and where regulations are
 still being developed to manage this activity. The importance and policy
 implications of using vulnerability maps for managing UOG extraction
 impacts in countries where UOG extraction is planned are highlighted in
 this article.
description: Interactive
 vulnerability map dataThe zip file contains
 shapefile data that was used in the interactive vulnerability map for UOG
 extraction as described in the article.
DOI: 10.5061/dryad.p610q
title: Data from: The chimerical genome of Isla del Coco feral pigs (Costa Rica), an isolated population since 1793 but with remarkable levels of diversity

description: The history of domestic species and of their wild ancestors is not a
 simple one, and feral processes can clarify key aspects of this history,
 including the adaptive processes triggered by new environments. Here, we
 provide a comprehensive genomic study of Isla del Coco (Costa Rica) feral
 pigs, a unique population that was allegedly founded by two individuals
 and has remained isolated since 1793. Using SNP arrays and genome
 sequencing, we show that Cocos pigs are hybrids between Asian and European
 pigs, as are modern international pig breeds. This conclusively shows
 that, as early as the 18th century, British vessels were loading crossbred
 pigs in Great Britain and transporting them overseas. We find that the Y
 chromosome has Asian origin, which has not been reported in any
 international pig breed. Chinese haplotypes seem to have been transmitted
 independently between Cocos and other pig breeds, suggesting independent
 introgression events and a complex pattern of admixing. Although data are
 compatible with a founder population of N = 2, variability levels are as
 high in Cocos pigs as in international pig breeds (~1.9 SNPs/kb) and
 higher than in European wild boars or local breeds (~1.7 SNPs/kb).
 Nevertheless, we also report a 10-Mb region with a marked decrease in
 variability across all samples that contains four genes (CPE, H3F3C,
 SC4MOL and KHL2) previously identified as highly differentiated between
 wild and domestic pigs. This work therefore illustrates how feral
 population genomic studies can help to resolve the history of domestic
 species and associated admixture events.
description: READMEDescription of
 filesME-15-0114Tar file containing all relevant files plus README file