cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ts47s
title: Data from: A new ankylosaurine dinosaur from the Judith River Formation of Montana, USA, based on an exceptional skeleton with soft tissue preservation

description: The terrestrial Judith River Formation of northern Montana was deposited
 over an approximately 4 Myr interval during the Campanian (Late
 Cretaceous). Despite having been prospected and collected continuously by
 palaeontologists for over a century, few relatively complete dinosaur
 skeletons have been recovered from this unit to date. Here we describe a
 new genus and species of ankylosaurine dinosaur, Zuul crurivastator, from
 the Coal Ridge Member of the Judith River Formation, based on an
 exceptionally complete and well-preserved skeleton (ROM 75860). This is
 the first ankylosaurin skeleton known with a complete skull and tail club,
 and it is the most complete ankylosaurid ever found in North America. The
 presence of abundant soft tissue preservation across the skeleton,
 including in situ osteoderms, skin impressions and dark films that
 probably represent preserved keratin, make this exceptional skeleton an
 important reference for understanding the evolution of dermal and
 epidermal structures in this clade. Phylogenetic analysis recovers Zuul as
 an ankylosaurin ankylosaurid within a clade of Dyoplosaurus and
 Scolosaurus, with Euoplocephalus being more distantly related within
 Ankylosaurini. The occurrence of Z. crurivastator from the upper Judith
 River Formation fills a gap in the ankylosaurine stratigraphic and
 geographical record in North America, and further highlights that
 Campanian ankylosaurines were undergoing rapid evolution and stratigraphic
 succession of taxa as observed for Laramidian ceratopsids, hadrosaurids,
 pachycephalosaurids and tyrannosaurids.
description: Supplementary Figures
 and Videos of ROM 75860, Zuul crurivastatorSupplementary Figure 1:
 ROM 75860 skull in right lateral view. Supplementary Figure 2: ROM 75860
 skull in left lateral view. Supplementary Figure 3: ROM 75860 skull in
 anterior view. Supplementary Figure 4: ROM 75860 skull in posterior view.
 Supplementary Figure 5: ROM 75860 skull in dorsal view. Supplementary
 Figure 6: ROM 75860 skull in ventral view. Supplementary Figure 7: ROM
 75860 left lower jaw in lateral view. Supplementary Figure 8: ROM 75860
 left lower jaw in medial view. Supplementary Figure 9: ROM 75860 left
 lower jaw in dorsal view. Supplementary Figure 10: ROM 75860 left lower
 jaw in ventral view. Supplementary Figure 11: ROM 75860 right lower jaw in
 lateral view. Supplementary Figure 12: ROM 75860 right lower jaw in medial
 view. Supplementary Figure 13: ROM 75860 right lower jaw in dorsal view.
 Supplementary Figure 14: ROM 75860 right lower jaw in ventral view.
 Supplementary Figure 15: ROM 75860 right lower jaw in anterior view.
 Supplementary Figure 16: ROM 75860 right lower jaw in posterior view.
 Supplementary Figure 17: ROM 75860 tail in dorsal view. Supplementary
 Figure 18: ROM 75860 tail in dorsal view. Supplementary Video:
 Photogrammetric reconstruction of the skull and jaws of ROM
 75860.Zuul
 supplementary files.zip
DOI: 10.5061/dryad.1c3m9
title: Data from: Numerical and experimental study of pyrophoric activated metal Mg surface combustion characteristics

description: The combustion of multi-hole pyrophoric activated metal belongs to solid
 combustion and the combustion mechanism is quite complex, which is a
 difficult problem to be solved. Once the pyrophoric activated metal
 contacting with oxygen, the oxygen diffuses to the interior of the
 activated metal within plenty of holes and reacts with it, which enlarges
 the contact area with oxygen. Consequently, the whole combustion is
 serious and the temperature rises rapidly. To study the combustion
 mechanism of chaff, surface heat balance equation is established in this
 work by taking Mg as the activated metal. To solve this equation, the
 chaff adiabatic wall temperature distribution is computed by computational
 fluid dynamics (CFD) in the presence of high speed airflow. Then, chaff
 surface temperature distribution is obtained by solving the heat balance
 equations. Finally, numerical and experimental results via infrared (IR)
 thermal imager are compared to demonstrate the effectiveness of the
 established equation.
description: Numerical
 dataThe data mainly contain
 the figure data in the manuscript and the temperature distribution of
 chaff in the combustion.Data.rar
DOI: 10.5061/dryad.8bc95
title: Data from: Mechanisms of ovipositor insertion and steering of a parasitic wasp

description: Drilling into solid substrates with slender beam-like structures is a
 mechanical challenge, but is regularly done by female parasitic wasps. The
 wasp inserts her ovipositor into solid substrates to deposit eggs in
 hosts, and even seems capable of steering the ovipositor while drilling.
 The ovipositor generally consists of three longitudinally connected valves
 that can slide along each other. Alternative valve movements have been
 hypothesized to be involved in ovipositor damage avoidance and steering
 during drilling. However, none of the hypotheses have been tested in vivo.
 We used 3D and 2D motion analysis to quantify the probing behavior of the
 fruit-fly parasitoid Diachasmimorpha longicaudata (Braconidae) at the
 levels of the ovipositor and its individual valves. We show that the wasps
 can steer and curve their ovipositors in any direction relative to their
 body axis. In a soft substrate, the ovipositors can be inserted without
 reciprocal motion of the valves. In a stiff substrate, such motions were
 always observed. This is in agreement with the damage avoidance hypothesis
 of insertion, as they presumably limit the overall net pushing force.
 Steering can be achieved by varying the asymmetry of the distal part of
 the ovipositor by protracting one valve set with respect to the other. Tip
 asymmetry is enhanced by curving of ventral elements in the absence of an
 opposing force, possibly due to pretension. Our findings deepen the
 knowledge of the functioning and evolution of the ovipositor in
 hymenopterans and may help to improve man-made steerable probes.
description: animal spatial probing
 data and rheological dataThis is a matlab file
 containing the rheological measurements of the used substrates (gels) as
 well as the data on spatial probing of all the wasps used in the
 study.waspKinematics_database_forUpload.matexamples of ovipositor insertionsThis matlab file contains data on 3 different insertions in either 2% or 4% gel.waspKinematics_examples_forUpload.mat
DOI: 10.5061/dryad.905sq
title: Data from: Lineage-specific sequence evolution and exon edge conservation partially explain the relationship of evolutionary rate and expression level in A. thaliana

description: Rapidly evolving proteins can aid the identification of genes underlying
 phenotypic adaptation across taxa, but functional and structural elements
 of genes can also affect evolutionary rates. In plants, the ‘edges’ of
 exons, flanking intron junctions, are known to contain splice enhancers
 and to have a higher degree of conservation compared to the remainder of
 the coding region. However, the extent to which these regions may be
 masking indicators of positive selection or account for the relationship
 between dN/dS and other genomic parameters is unclear. We investigate the
 effects of exon edge conservation on the relationship of dN/dS to various
 sequence characteristics and gene expression parameters in the model plant
 Arabidopsis thaliana. We also obtain lineage-specific dN/dS estimates,
 making use of the recently sequenced genome of Thellungiella parvula, the
 second closest sequenced relative after the sister species Arabidopsis
 lyrata. Overall, we find that the effect of exon edge conservation, as
 well as the use of lineage-specific substitution estimates, upon dN/dS
 ratios partly explains the relationship between the rates of protein
 evolution and expression level. Furthermore, the removal of exon edges
 shifts dN/dS estimates upwards, increasing the proportion of genes
 potentially under adaptive selection. We conclude that lineage-specific
 substitutions and exon edge conservation have an important effect on dN/dS
 ratios and should be considered when assessing their relationship with
 other genomic parameters..
description: Alignments and
 evolutionary rate estimatesBoth pairwise and
 multiple sequence alignments, with exon/intron junction trimming
 (tab-separated text files), and associated evolutionary rate estimates
 (Excel spreadsheets).DRYAD_SupplementalData.tar.gz
DOI: 10.5061/dryad.5538k
title: Data from: Optimal nutrient exchange and immune responses operate in partner specificity in the cnidarian-dinoflagellate symbiosis

description: The relationship between reef-building corals and phototrophic
 dinoflagellates of the genus Symbiodinium is fundamental to the
 functioning of coral reef ecosystems. It has been suggested that reef
 corals may adapt to climate change by changing their dominant symbiont
 type to a more thermally tolerant one, although the capacity for such a
 community shift is potentially hindered by the compatibility of different
 host-symbiont pairings. Here we combined transcriptomic and metabolomic
 analyses to characterize the molecular, cellular, and physiological
 processes that underlie this compatibility, with a particular focus on
 Symbiodinium trenchii, an opportunistic, thermally tolerant symbiont that
 flourishes in coral tissues after bleaching events. Symbiont-free
 individuals of the sea anemone Exaiptasia pallida (commonly referred to as
 Aiptasia), an established model system for the study of the
 cnidarian-dinoflagellate symbiosis, were colonized with the “normal”
 (homologous) symbiont Symbiodinium minutum and the heterologous S.
 trenchii. Analysis of the host gene and metabolite expression profiles
 revealed that heterologous symbionts induced an expression pattern
 intermediate between the typical symbiotic state and the aposymbiotic
 state. Furthermore, integrated pathway analysis revealed that increased
 catabolism of fixed carbon stores, metabolic signaling, and immune
 processes occurred in response to the heterologous symbiont type. Our data
 suggest that both nutritional provisioning and the immune response induced
 by the foreign “invader” are important factors in determining the capacity
 of corals to adapt to climate change through the establishment of novel
 symbioses.
description: Aiptasia and
 Symbiodinium mf105 (clade B) concatenated reference
 transcriptomeConcatenated reference
 transcriptome of both Exaiptasia pallida and Symbiodinium Clade B.
 Assembled using the de novo transcriptome assembler Trinity version 2.0.2
 with default settings.longest_sc_Ap_EM_mf105.fasta
DOI: 10.5061/dryad.2b8f1
title: Data from: Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish

description: Understanding genomic signatures of divergent selection underlying
 long-term adaptation in populations located in heterogeneous environments
 is a key goal in evolutionary biology. In this study, we investigated
 neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31
 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec,
 Canada. Average genetic diversity was low, weakly shared among lakes, and
 positively correlated to lake size, indicating a major role for genetic
 drift subsequent to lake isolation. Putatively deleterious mutations were
 on average at lower frequencies than the other SNPs, and their abundance
 relative to the entire polymorphism in each population was positively
 correlated to inbreeding, suggesting that the effectiveness of purifying
 selection was negatively correlated to inbreeding, as predicted from
 theory. Despite evidence for pronounced genetic drift and inbreeding,
 several outlier loci were associated with temperature and found in or
 close to genes with biologically relevant functions notably related to
 heat-stress and immune responses. Outcomes of gene-temperature
 associations were influenced by the inclusion of the most inbred
 populations, in which allele frequencies deviated the most from model
 predictions. This result illustrates challenge in identifying
 gene-environment associations in cases of high genetic drift and
 restricted gene flow and suggests limited adaptation in populations
 experiencing higher inbreeding. We discuss the relevance of these findings
 for the conservation and management, notably regarding stocking and
 genetic rescue, of Lake Trout populations and other species inhabiting
 highly fragmented habitats.
description: VCF
 fileVCFv4.0 file for the 673
 Lake Trout (Salvelinus namaycush) individuals from 31 populations from
 Quebec, Canada.MEC-17-0449.vcf
DOI: 10.5061/dryad.j5f51
title: Data from: Integrating nonadditive genomic relationship matrices into the study of genetic architecture of complex traits

description: The study of genetic architecture of complex traits has been dramatically
 influenced by implementing genome-wide analytical approaches during recent
 years. Of particular interest are genomic prediction strategies which make
 use of genomic information for predicting phenotypic responses instead of
 detecting trait-associated loci. In this work, we present the results of a
 simulation study to improve our understanding of the statistical
 properties of estimation of genetic variance components of complex traits,
 and of additive, dominance, and genetic effects through best linear
 unbiased prediction methodology. Simulated dense marker information was
 used to construct genomic additive and dominance matrices, and multiple
 alternative pedigree- and marker-based models were compared to determine
 if including a dominance term into the analysis may improve the genetic
 analysis of complex traits. Our results showed that a model containing a
 pedigree- or marker-based additive relationship matrix along with a
 pedigree-based dominance matrix provided the best partitioning of genetic
 variance into its components, especially when some degree of true
 dominance effects was expected to exist. Also, we noted that the use of a
 marker-based additive relationship matrix along with a pedigree-based
 dominance matrix had the best performance in terms of accuracy of
 correlations between true and estimated additive, dominance, and genetic
 effects.
description: 20 simulated datasets
 for 3,000 individuals over different heritability (h2) and dominance ratio
 (d2) conditionsDATA.zip
DOI: 10.5061/dryad.25m10
title: Data from: The FlbA-regulated predicted transcription factor rpnR of Aspergillus niger is involved in stress resistance and protein secretion, in Regulators Controlled by the Sporulation Gene flbA of Aspergillus niger (Ph.D. thesis)

description: Proteins are secreted throughout the mycelium of Aspergillus niger except
 for the sporulating zone. A link between sporulation and repression of
 protein secretion was underlined by the finding that inactivation of the
 sporulation gene flbA results in colonies that secrete proteins throughout
 the colony. This finding is of interest to improve fungi as a cell
 factory. However, ΔflbA hyphae also lyse and have thinner cell walls. This
 pleiotropic phenotype is associated with differential expression of 36
 transcription factor genes, of which rpnR was inactivated in this study.
 Sporulation, biomass, and secretome complexity were not affected in strain
 ΔrpnR. In contrast, ΔrpnR showed decreased resistance to H2O2 and the
 proteotoxic stress-inducing agent dithiothreitol. This was associated with
 reduced ribosomal subunit expression and reduced levels of proteins
 secreted into the medium. Taken together, RpnR of A. niger is involved in
 protein synthesis and proteotoxic stress resistance and is thus an
 interesting target for improving enzyme production capacity.
description: Supplemental Figure 2
 from Chapter 5Hierarchal tree of
 overrepresented GO terms within the set of downregulated genes in ΔrpnR.
 Boxes highlighted in green represent GO terms that are overrepresented, a
 black edge between two nodes means “regulates”, a blue edge “is a”, and a
 light blue edge “is part of”.Supplemental Figure
 2.epsSupplemental Figure 3
 from Chapter 5Hierarchal tree of
 underrepresented GO terms within the set of downregulated genes in ΔrpnR.
 Boxes highlighted in red represent GO terms that are underrepresented. A
 black edge between two nodes means “regulates”, a light blue edge “is part
 of”.Supplemental Figure
 3.epsSupplemental Figure 4
 from Chapter 5Hierarchal tree of
 overrepresented GO terms within the set of upregulated genes in ΔrpnR.
 Boxes highlighted in green represent GO terms that are overrepresented. A
 black edge between two nodes means “regulates”, a light blue edge “is part
 of”.Supplemental Figure
 4.eps
DOI: 10.5061/dryad.tt10r84
title: Data from: How well can we estimate diversity dynamics for clades in diversity decline?

description: The fossil record shows that the vast majority of all species that ever
 existed are extinct and that most lineages go through an expansion and
 decline in diversity. However, macroevolutionary analyses based upon
 molecular phylogenies have difficulty inferring extinction dynamics,
 raising questions about whether the neontological record can contribute to
 an understanding of the decline phenomenon. Two recently developed
 diversification methods for molecular phylogenies (RPANDA and BAMM)
 incorporate models that theoretically have the capacity to capture decline
 dynamics by allowing extinction to be higher than speciation. However, the
 performance of these frameworks over a wide range of decline scenarios has
 not been studied. Here we investigate the behavior of these methods under
 decline scenarios caused by decreasing speciation and increasing
 extinction through time on simulated trees at fixed intervals over
 diversity trajectories with expansion and decline phases. We also compared
 method performance over a comprehensive dataset of 214 empirical trees.
 Our results show that both methods perform equally well when varying
 speciation rates control decline. When decline was only caused by an
 increase in extinction rates both methods wrongly assign the variation in
 net diversification to a drop in speciation, even though the positive
 gamma values of those trees would suggest otherwise. We also found a
 tendency for RPANDA to favor increasing extinction and BAMM to favor
 decreasing speciation as the most common cause of decline in empirical
 trees. Overall our results shed light on the limitations of both methods,
 encouraging researchers to carefully interpret the results from
 diversification studies.
description: Burin_et_al_suppmat
DOI: 10.5061/dryad.6q738
title: Data from: Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

description: Colugos are one of the most poorly studied mammals despite their
 centrality to resolving supraordinal primate relationships. Two described
 species of these gliding mammals are the sole living members of the order
 Dermoptera, distributed throughout Southeast Asia. We generated a draft
 genome sequence for a Sunda colugo and a Philippine colugo reference
 alignment, and used these to identify colugo-specific genetic changes that
 were enriched in sensory and musculo-skeletal related genes that likely
 underlie their nocturnal and gliding adaptations. Phylogenomic analysis
 and catalogs of rare genomic changes overwhelmingly support the contested
 hypothesis that colugos are the sister group to primates (Primatomorpha),
 to the exclusion of treeshrews. We captured ~140-kb of orthologous
 sequence data from colugo museum specimens sampled across their range, and
 identified large genetic differences between many geographically isolated
 populations that may result in a 300% increase in the number of recognized
 colugo species. Our results identify conservation units to mitigate future
 losses of this enigmatic mammalian order.
description: ColguoGenomePaper2016This file contains 1) files for divergence time estimation, 2) Sequence matrices used for phylogenetic analysis, 3) Files for the BPP analyses, and 4) 21 mammal orthologous alignments
DOI: 10.5061/dryad.7ns5c
title: Data from: Admixture mapping in two Mexican samples identifies significant associations of locus ancestry with triglyceride levels in the BUD13/ZNF259/APOA5 region and fine mapping points to rs964184 as the main driver of the association signal

description: We carried out an admixture mapping study of lipid traits in two samples
 from Mexico City. Native American locus ancestry was significantly
 associated with triglyceride levels in a broad region of chromosome 11
 overlapping the BUD13, ZNF259 and APOA5 genes. In our fine-mapping
 analysis of this region using dense genome-wide data, rs964184 is the only
 marker included in the 99% credible set of SNPs, providing strong support
 for rs964184 as the causal variant within this region. The frequency of
 the allele associated with increased triglyceride concentrations
 (rs964184-G) is between 30-40% higher in Native American populations from
 Mexico than in European populations. The evidence currently available for
 this variant indicates that it may be exerting its effect through three
 potential mechanisms: 1) modification of enhancer activity, 2) regulation
 of the expression of several genes in cis and/or trans, or 3) modification
 of the methylation patterns of the promoter of the APOA5 gene.
description: MC-sample1-HDL-AMAdmixture Mapping results for HDL-cholesterol: Mexico City sample 1MC-sample1-LDL-AMAdmixture Mapping results for LDL-cholesterol: Mexico City sample 1MC-sample1-TCHOL-AMAdmixture Mapping results for Total-cholesterol: Mexico City sample 1MC-sample1-TG-AMAdmixture Mapping results for triglycerides: Mexico City sample 1MC-sample2-HDL-AMAdmixture Mapping results for HDL-cholesterol: Mexico City sample 2MC-sample2-LDL-AMAdmixture Mapping results for LDL-cholesterol: Mexico City sample 2MC-sample2-TCHOL-AMAdmixture Mapping results for Total-cholesterol: Mexico City sample 2MC-sample2-TG-AMAdmixture Mapping results for triglycerides: Mexico City sample 2Mexico-City-AM-signalsAdmixture Mapping signals identified in both Mexico City samples for all the lipid traits.