cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5q9q697
title: Data from: Wear, tear and systematic repair: testing models of growth dynamics in conodonts with high-resolution imaging

description: Conodont elements are the earliest mineralised vertebrate dental tools and
 the only ones capable of extensive repair. Two models of conodont growth,
 as well as the presence of a larval stage, have been hypothesised. We
 analysed normally and pathologically developed elements to test these
 hypotheses and identified three ontogenetic stages characterised by
 different anisometric growth and morphology. The distinction of these
 stages is independently corroborated by differences in tissue strontium
 content. The onset of the last stage is marked by the appearance of wear
 resulting from mechanical food digestion. At least five episodes of damage
 and repair could be identified in the normally developed specimen. In the
 pathological element, function was compromised by development of abnormal
 denticles. This development can be reconstructed as addition of new growth
 centres out of the main growth axis during an episode of renewed growth.
 Our findings support the model of periodic retraction of elements and
 addition of new growth centres. Changes in strontium content coincident
 with distinct morphology and lack of wear in the early life stage indicate
 that conodonts might have assumed their mature feeding habit of predators
 or scavengers after an initial larval stage characterised by a different
 feeding mode.
description: (Table 1) Direction of
 GrowthThe data that was used
 to show the preferential growth direction in figure 1 and
 2.(Table 2) Sr
 TransectsData for figure
 3(Table 3) Sr line
 transect dataData for figure
 4(Table 4) Dark and Light
 band thicknessSupplement outlining
 thicknesses of dark and light bands.Fig. 1 Normal
 conodontLarge, high resolution
 image of the normal conodont.Fig. 2 Pathological
 conodontS1Alternative version of
 figure 3 with parallel axes, and the required graphs plotted away from the
 original image.AppendixSupplementary statistical data for the manuscript.
DOI: 10.5061/dryad.626tf4f
title: Data from: Z-DNA and Z-RNA in human disease

description: Left-handed Z-DNA/Z-RNA is bound with high affinity by the Zα domain
 protein family that includes ADAR (a double-stranded RNA editing enzyme),
 ZBP1 and viral orthologues regulating innate immunity. Loss of function
 mutations in ADAR p150 allow persistent activation of the interferon
 system by Alu dsRNAs and are causal for Aicardi-Goutières Syndrome.
 Heterodimers of ADAR and DICER1 regulate the switch from RNA- to
 protein-centric immunity. Loss of DICER1 function produces age related
 macular degeneration, a different type of Alu-mediated disease. The
 overlap of Z-forming sites with those for the signal recognition particle
 likely limits invasion of primate genomes by Alu retrotransposons.
description: Z-Scores &gt;250, All
 Chromosomes (hg19) from ZHUNT3Z-Scores were determined
 using ZHUNT3 Champ, P. C., S. Maurice, et al. (2004). "Distributions
 of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled
 transcriptional regulation." Nucleic acids research 32(22):
 6501-6510. The input was from the hg19 build and only Z-Scores&gt;250 are
 presentZ-DNA.zip
DOI: 10.5061/dryad.40gk7
title: Data from: Accelerometry predicts daily energy expenditure in a bird with high activity levels

description: Animal ecology is shaped by energy costs, yet it is difficult to measure
 fine-scale energy expenditure in the wild. Because metabolism is often
 closely correlated with mechanical work, accelerometers have the potential
 to provide detailed information on energy expenditure of wild animals over
 fine temporal scales. Nonetheless, accelerometry needs to be validated on
 wild animals, especially across different locomotory modes. We merged data
 collected on 20 thick-billed murres (Uria lomvia) from miniature
 accelerometers with measurements of daily energy expenditure over 24 h
 using doubly labelled water. Across three different locomotory modes
 (swimming, flying and movement on land), dynamic body acceleration was a
 good predictor of daily energy expenditure as measured independently by
 doubly labelled water (R2 = 0.73). The most parsimonious model suggested
 that different equations were needed to predict energy expenditure from
 accelerometry for flying than for surface swimming or activity on land (R2
 = 0.81). Our results demonstrate that accelerometers can provide an
 accurate integrated measure of energy expenditure in wild animals using
 many different locomotory modes.
description: TDR
 Acc+H2OThese are the time-depth
 recorder files (the .bin files are the binary files from the loggers; the
 .TXT are the converted files provided by the TAGTALK software.) Each
 folder is labelled with the individual ID (the band number) of the murre
 whose doubly-labelled water data appear in the data appendix. After a
 preamble generated by the software, the date-time, pressure (in dbar) and
 temperature are provided.DEE
 calculationsExcel spreadsheet shows
 raw ppm values from blood samples used for measurement of energy
 expenditure using doubly-labelled water and equations used to convert
 those ppm values into energy expenditure. Also shown are calculated PDBA
 (partial dynamic body acceleration) values relative to measured energy
 expenditure. The "ID" is the band number that can be
 cross-referenced with the activity/accelerationd data.Accelerometer
 dataEach bird (ID given by
 five digit band number) can be cross-referenced with TDR and DLW data in
 other files. Each bird has a depth (in m), temperature, X-axis
 acceleration (in g) and Y-axis acceleration (in g) file following a
 preamble describing the time when the logger was started. All data is
 given in 1-s (depth/temperature) or 16 Hz (acceleration)
 increments.
DOI: 10.5061/dryad.7bj0f
title: Data from: Influence of immunogenetics, sex, and body condition on the cutaneous microbial communities of two giant salamanders

description: The complex association between hosts and microbial symbionts requires the
 implementation of multiple approaches to evaluate variation in host
 physiology. Within amphibians, heterogeneity in immunogenetic traits and
 cutaneous microbiota is associated with variation in disease resistance.
 Ozark (Cryptobranchus alleganiensis bishopi) and eastern hellbenders (C.
 a. alleganiensis) provide a model system to assess variation in host
 traits and microbial communities. Ozark hellbenders have experienced
 declines throughout their range, are federally endangered, and experience
 wound retardation that is absent in the eastern subspecies. Previous
 microbial investigations indicate differentiation in the composition of
 the skin microbiota of both hellbender subspecies, but it is not clear if
 these patterns are concurrent with diversity in the major
 histocompatibility complex (MHC) genes. We characterized the MHC IIB and
 the skin microbiota of hellbenders in Missouri, where both subspecies
 co-occur though not sympatric. We compared the microbiota composition and
 MHC diversity between both subspecies and investigated whether
 individual-level MHC diversity, sex, and body condition were associated
 with microbiota composition. Overall MHC IIB diversity was lower in Ozark
 hellbenders compared to the eastern subspecies. Multivariate statistical
 comparisons identified microbiota differentiation between Ozark and
 eastern hellbenders. MHC IIB allele presence/absence, allele divergence,
 body composition, and sex defined grouping of hellbender microbiotas
 within populations. Differentiation of the cutaneous microbiotas and MHC
 IIB genes between eastern and Ozark hellbenders suggest that differences
 exist in immunity between the two subspecies. This study demonstrates how
 simultaneous assessments of host genetic traits and microbiotas can inform
 patterns of microbial community structure in natural systems.
description: hellbender_spleen_contigs
DOI: 10.5061/dryad.r4691
title: Data from: New record of Egertonia (Elopiformes, Phyllodontidae) from the Late Cretaceous of South India

description: We report a new occurrence of the phyllodontid teleost fish Egertonia from
 the Late Cretaceous Kallamedu Formation of the Cauvery Basin, South India.
 This is the oldest occurrence of Phyllodontidae in India, and only the
 second Cretaceous Gondwanan occurrence of this genus, following a
 toothplate previously described from the Late Cretaceous Maevarano
 Formation, Madagascar. The presence of phyllodontid fish supports a
 fluvial–deltaic or brackish environment for the lower part of the
 Kallamedu Formation, a rich deposit including typically Gondwanan taxa,
 such as simosuchid crocodiles, bothremydid turtles and abelisaurid
 dinosaurs, as well as an anomalous troodontid dinosaur. Egertonia adds
 another taxon of primarily Laurasian distribution to the Kallamedu fauna
 and further expands the list of taxa known from the Late Cretaceous of
 both India and Madagascar, strengthening the degree of faunal similarity
 between the two landmasses in the latest Cretaceous.
description: 3D pdfs of
 specimensTwo 3D pdfs, one of
 DGUF-145 and one of DGUF-146. Both images may be rotated, and the bony
 matrix, teeth, and an individual tooth may be viewed
 separately.3D
 pdfs.zipDGUF145DGUF146
DOI: 10.5061/dryad.7205r
title: Data from: De novo assembly and characterization of leaf and floral transcriptomes of the hybridizing bromeliad species (Pitcairnia spp.) adapted to Neotropical Inselbergs

description: We present the leaf and floral transcriptomes of two hybridizing bromeliad
 species that differ in their major pollinator systems. Here we identified
 candidate genes responsible for pollinator attraction and reproductive
 isolation in these two species. We searched for candidate genes involved
 in floral traits, such as color. Approximately 34 Gbp of cDNA sequence
 data were produced from both tissues and species, resulting in a total of
 424,506,914 raw reads. The de novo-assembled transcriptomes consisted of a
 total of 263,955 contigs, further clustered into 110,977 unigenes. Over
 58% of the unigenes were functionally annotated and assigned to one or
 more Gene Ontology terms. The transcriptomes revealed 144 unique
 transcripts that encode key enzymes in the flavonoid and anthocyanin
 biosynthesis pathways. The domain/family annotation and phylogenetic
 analysis allowed us to infer, by homology, potential functions of the
 genes encoding MYB, HD-ZIP, and bZIP-HY5 transcription factors, as well as
 WD40 protein, which may be involved in anthocyanin and flavonoid
 regulation in these species. These candidate genes are associated with
 natural regulation in flower color in other plant species and will
 facilitate future studies aimed at elucidating the molecular basis of
 adaptive differentiation and the evolution of mechanisms of
 pollinator-mediated reproductive isolation in these two bromeliads. In
 addition, we identified a total of 49,439 microsatellite loci. These
 resources will assist future research into adaptation and speciation
 events in bromeliad species, thus providing a starting point for
 investigation of the molecular mechanisms of the traits responsible for
 their reproductive isolation.
description: SSR primers
 designedMicrosatellite loci
 identifed for Pitcairnia staminea and P. albiflos leaf and floral
 transcriptomesTable SSR Primers
 designed.xlsTable S3_List of
 candidate genesAnnotation of candidate
 genes of anthocyanin and flavonoid biosynthetic pathway, including FPKM
 (fragments per kilobase of transcript per million fragments sequenced) for
 each transcript.Table S1_The GOs
 classifcation all leavesGO classification of the
 assembled sequences into three main categories (biological function,
 cellular component and molecular function) at all levels (1–17). Columns
 list the number of transcripts corresponding to the individual species and
 tissues separatelyTable S2_Keeg
 pathwaysList of all KEGG
 pathways with the number of annotated ECsPhylogeny
 alignmentsAlignments of MYB, HY5,
 WD40, HD-ZIP genesContigs of each
 transcriptomeFiles with assembled
 contigs of each transcriptomeFPKM values for each
 transcriptomeExcel files containing
 FPKM values for each contig
DOI: 10.5061/dryad.071p0
title: Data from: Soil microbiome responses to the short-term effects of Amazonian deforestation

description: Slash-and-burn clearing of forest typically results in increase in soil
 nutrient availability. However, the impact of these nutrients on the soil
 microbiome is not known. Using next generation sequencing of 16S rRNA gene
 and shotgun metagenomic DNA, we compared the structure and the potential
 functions of bacterial community in forest soils to deforested soils in
 the Amazon region and related the differences to soil chemical factors.
 Deforestation decreased soil organic matter content and factors linked to
 soil acidity and raised soil pH, base saturation and exchangeable bases.
 Concomitant to expected changes in soil chemical factors, we observed an
 increase in the alpha diversity of the bacterial microbiota and relative
 abundances of putative copiotrophic bacteria such as Actinomycetales and a
 decrease in the relative abundances of bacterial taxa such as Chlamydiae,
 Planctomycetes and Verrucomicrobia in the deforested soils. We did not
 observe an increase in genes related to microbial nutrient metabolism in
 deforested soils. However, we did observe changes in community functions
 such as increases in DNA repair, protein processing, modification,
 degradation and folding functions, and these functions might reflect
 adaptation to changes in soil characteristics due to forest clear-cutting
 and burning. In addition, there were changes in the composition of the
 bacterial groups associated with metabolism-related functions.
 Co-occurrence microbial network analysis identified distinct phylogenetic
 patterns for forest and deforested soils and suggested relationships
 between Planctomycetes and aluminium content, and Actinobacteria and
 nitrogen sources in Amazon soils. The results support taxonomic and
 functional adaptations in the soil bacterial community following
 deforestation. We hypothesize that these microbial adaptations may serve
 as a buffer to drastic changes in soil fertility after slash-and-burning
 deforestation in the Amazon region.
description: SEED_STAMP_input_fileInput file used for SEED/STAMP analysis.sequences_input_otu_pickingOTU tabledeforestation.qiimeotutableOTU reference sequencesOTU_references.fastaqPCR resultsqPCR_results.xls
DOI: 10.5061/dryad.3pb86
title: Data from: Flight paths of seabirds soaring over the ocean surface enable measurement of fine-scale wind speed and direction

description: Monitoring ocean surface winds is essential for understanding ocean and
 atmosphere interactions and weather forecasts. However, wind measured by
 satellite scatterometers and buoys are spatially and temporally coarse,
 particularly in coastal areas. We deployed small global positioning system
 units on soaring seabirds to record their tracks. Seabirds were
 accelerated by tail winds or slowed down by head winds during flight, so
 their flight speed changed in relation to wind speed and direction. Taking
 advantage of these changes in flight speed, we reliably estimated wind
 speed and direction experienced by the seabirds. The wind observed by
 soaring seabird’s tracks complemented the conventional observation gaps in
 terms of both time and space, suggesting the possibility of using soaring
 seabirds as a living anemometer.
description: streaked_shearwater_no1time series of latitude and longitudestreaked_shearwater_no2time series of latitude and longitudestreaked_shearwater_no3time series of latitude and longitudestreaked_shearwater_no4time series of latitude and longitudestreaked_shearwater_no5time series of latitude and longitudestreaked_shearwater_no6time series of latitude and longitudestreaked_shearwater_no7time series of latitude and longitudestreaked_shearwater_no11time series of latitude and longitudestreaked_shearwater_no12time series of latitude and longitudestreaked_shearwater_no13time series of latitude and longitudestreaked_shearwater_no14time series of latitude and longitudestreaked_shearwater_no15time series of latitude and longitudestreaked_shearwater_no16time series of latitude and longitudeLaysan_albatross_no1time series of latitude and longitudeLaysan_albatross_no2time series of latitude and longitudewandering_albatross_no1time series of latitude and longitudewandering_albatross_no2time series of latitude and longitudewandering_albatross_no3time series of latitude and longitudewandering_albatross_no4time series of latitude and longitude
DOI: 10.5061/dryad.35k67
title: Data from: Molecular resources from transcriptomes in the Brassicaceae family

description: The rapidly falling costs and the increasing availability of large DNA
 sequence data sets facilitate the fast and affordable mining of large
 molecular markers data sets for comprehensive evolutionary studies. The
 Brassicaceae (mustards) are an important species-rich family in the plant
 kingdom with taxa distributed worldwide and a complex evolutionary
 history. We performed Simple Sequence Repeats (SSRs) mining using de novo
 assembled transcriptomes from 19 species across the Brassicaceae in order
 to study SSR evolution and provide comprehensive sets of molecular markers
 for genetic studies within the family. Moreover, we selected the genus
 Cochlearia to test the transferability and polymorphism of these markers
 among species. Additionally, we annotated Cochlearia pyrenaica
 transcriptome in order to identify the position of each of the mined SSRs.
 While we introduce a new set of tools that will further enable
 evolutionary studies across the Brassicaceae, we also discuss some broader
 aspects of SSR evolution. Overall, we developed 2012 ready-to-use SSR
 markers with their respective primers in 19 Brassicaceae species and a
 high quality annotated transcriptome for C. pyrenaica. As indicated by our
 transferability test with the genus Cochlearia these SSRs are transferable
 to species within the genus increasing exponentially the number of
 targeted species. Also, our polymorphism results showed substantial levels
 of variability for these markers. Finally, despite its complex
 evolutionary history, SSR evolution across the Brassicaceae family is
 highly conserved and we found no deviation from patterns reported in other
 Angiosperms.
description: Molecular resources for
 the Brassicaceae family.MolRes_for_Brassicaceae.zip
DOI: 10.5061/dryad.cv1f50m
title: Data from: Invasion complexity at large spatial scales is an emergent property of interactions among landscape characteristics and invader traits

description: Invasion potential should be part of the evaluation of candidate species
 for any species introduction. However, estimating invasion risks remains a
 challenging problem, particularly in complex landscapes. Certain plant
 traits are generally considered to increase invasive potential and there
 is an understanding that landscapes influence invasions dynamics, but
 little research has been done to explore how those drivers of invasions
 interact. We evaluate the relative roles of, and potential interactions
 between, plant invasiveness traits and landscape characteristics on
 invasions with a case study using a model parameterized for the
 potentially invasive biomass crop, Miscanthus × giganteus. Using that
 model we simulate invasions on 1000 real landscapes to evaluate how
 landscape characteristics, including both composition and spatial
 structure, effect invasion outcomes. We conducted replicate simulations
 with differing strengths of plant invasiveness traits (dispersal ability,
 establishment ability, population growth rate, and the ability to utilize
 dispersal corridors) to evaluate how the importance of landscape
 characteristics for predicting invasion patterns changes depending on the
 invader details. Analysis of simultations showed that the presence of
 highly suitable habitat (e.g., grasslands) is generally the strongest
 determinant of invasion dynamics but that there are also more subtle
 interactions between landscapes and invader traits. These effects can also
 vary between different aspects of invasion dynamics (short vs long time
 scales and population size vs spatial extent). These results illustrate
 that invasions are complex emergent processes with multiple drivers and
 effective management needs to reflect the ecology of the species of
 interest and the particular goals or risks for which efforts need to be
 optimized.
description: Data_archiveThis compressed archive includes multiple other files including data files (in .csv format for tabular data, .Rdata files for data from higher dimensional arrays, and .tif files for landscape grids) and R scripts for running invasion simulations and to read and evaluate data files. Specific descriptions of each file are supplied in the ReadMe.txt file.
DOI: 10.5061/dryad.sn69s
title: Data from: Image based modelling of lateral magma flow: the Basement Sill, Antarctica

description: The McMurdo Dry Valleys magmatic system, Antarctica, provides a
 world-class example of pervasive lateral magma flow on a continental
 scale. The lowermost intrusion (Basement Sill) offers detailed sections
 through the now frozen particle microstructure of a congested magma
 slurry. We simulated the flow regime in two and three dimensions using
 numerical models built on a finite-element mesh derived from field data.
 The model captures the flow behaviour of the Basement Sill magma over a
 viscosity range of 1–104 Pa s where the higher end (greater than or equal
 to 102 Pa s) corresponds to a magmatic slurry with crystal fractions
 varying between 30 and 70%. A novel feature of the model is the discovery
 of transient, low viscosity (less than or equal to 50 Pa s) high Reynolds
 number eddies formed along undulating contacts at the floor and roof of
 the intrusion. Numerical tracing of particle orbits implies crystals
 trapped in eddies segregate according to their mass density. Recovered
 shear strain rates (10−3–10−5 s−1) at viscosities equating to high
 particle concentrations (around more than 40%) in the Sill interior point
 to shear-thinning as an explanation for some types of magmatic layering
 there. Model transport rates for the Sill magmas imply a maximum
 emplacement time of ca 105 years, consistent with geochemical evidence for
 long-range lateral flow. It is a theoretically possibility that
 fast-flowing magma on a continental scale will be susceptible to
 planetary-scale rotational forces.
description: Supplementary
 MaterialsAdditional data on model
 runs. This folder contains supplementary figures in ppt and video clips of
 model test runs and of particle circulation paths. Data include 2 and 3D
 visualisations, calculations of shear rate and Reynolds numbers and other
 parameters arising from the model simulations.Supplementary_Materials.zip