cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2bc7c
title: Data from: Cross-platform compatibility of de novo-aligned SNPs in a non-model butterfly genus

description: High-throughput sequencing methods for genotyping genome-wide markers are
 being rapidly adopted for phylogenetics of non-model organisms in
 conservation and biodiversity studies. However, the reproducibility of SNP
 genotyping and degree of marker overlap or compatibility between datasets
 from different methodologies have not been tested in non-model systems.
 Using double-digest restriction site associated DNA sequencing, we
 sequenced a common set of 22 specimens from the butterfly genus Speyeria
 on two different Illumina platforms, using two variations of library
 preparation. We then used a de novo approach to bioinformatic locus
 assembly and SNP discovery for subsequent phylogenetic analyses. We found
 a high rate of locus recovery despite differences in library preparation
 and sequencing platforms, as well as overall high levels of data
 compatibility after data processing and filtering. These results provide
 the first application of NGS methods for phylogenetic reconstruction in
 Speyeria, and support the use and long-term viability of SNP genotyping
 applications in non-model systems.
description: NextSeq_raw_fastqZipped file containing 24 raw fastq files of 11 butterfly species. A ddRAD library was prepared using PstI and MspI restriction enzymes, following the protocol of Peterson et al. 2012, and then sequenced on an Illumina NextSeq 500.HiSeq_raw_fastqZipped file containing 24 raw fastq files of 11 butterfly species. A double enzyme GBS library was prepared using PstI and MspI restriction enzymes, following the protocol of Poland et al. 2012, and then sequenced on an Illumina HiSeq 2000.all_5%_structure_inputInput file for STRUCTURE analysis of the HiSeq + NextSeq dataset filtered with a minor allele frequency of 5%.all_5%.strprocessed nexus input filesZipped file containing all 21 processed nexus files used for phylogenetic analyses
DOI: 10.5061/dryad.0t10j
title: Data from: Image analysis of weaverbird nests reveals signature weave textures

description: In nature, many animals build structures that can be readily measured at
 the scale of their gross morphology (e.g. length, volume and weight).
 Capturing individuality as can be done with the structures designed and
 built by human architects or artists, however, is more challenging. Here,
 we tested whether computer-aided image texture classification approaches
 can be used to describe textural variation in the nests of weaverbirds
 (Ploceus species) in order to attribute nests to the individual weaverbird
 that built them. We found that a computer-aided texture analysis approach
 does allow the assignment of a signature to weaverbirds' nests. We
 suggest that this approach will be a useful tool with which to examine
 individual variation across a range of animal constructions, not just for
 nests.
description: Images of village weaver
 nests- 2008These are the raw images
 used in our texture analysis of weaverbird nests. Images are of the
 completed nests of: six Village weavers (Ploceus cucullatus) collected in
 June and July 2008, from, Laminga Village, Jos, Nigeria. The filename
 indicates which male build the nest (M), which of that males nests the
 image is of (N) and which face of the nest the image is of (e.g. front).
 So an image of the front of Male 1’s, second nest would be:
 M1N2frontVillage-weaver_2008.zipImages of Southern-masked weaver nests -2008These are the raw images used in our texture analysis of weaverbird nests. 15 Southern Masked weavers (P. velatus) from Botswana (Atholl Holme 11-KO, Gaberone) photographed in November and December 2008. The filename indicates which male build the nest (M), which of that males nests the image is of (N) and which face of the nest the image is of (e.g. front). So an image of the front of Male 1’s, second nest would be: M1N2frontSouthern-masked-weaver_2008.zipImages of Southern-masked weaver nests- 2009These are the raw images used in our texture analysis of weaverbird nests. Images are of the completed nests of 7 Southern Masked weavers (P. velatus) from Botswana (Atholl Holme 11-KO, Gaberone) photographed in November and December 2009. The filename indicates which male build the nest (M), which of that males nests the image is of (N) and which face of the nest the image is of (e.g. front). So an image of the front of Male 1’s, second nest would be: M1N2frontSouthern-masked-weaver_2009.zip
DOI: 10.5061/dryad.09q2b
title: Data from: The nature of functional variability in plantar pressure during a range of controlled walking speeds

description: During walking, variability in step parameters allows the body to adapt to
 changes in substrate or unexpected perturbations that may occur as the
 feet interface with the environment. Despite a rich literature describing
 biomechanical variability in step parameters, there are as yet no studies
 that consider variability at the body–environment interface. Here, we used
 pedobarographic statistical parametric mapping (pSPM) and two standard
 measures of variability, mean square error (m.s.e.) and the coefficient of
 variation (CV), to assess the magnitude and spatial variability in plantar
 pressure across a range of controlled walking speeds. Results by reduced
 major axis, and pSPM regression, revealed no consistent linear
 relationship between m.s.e. and speed or m.s.e. and Froude number. A
 positive linear relationship, however, was found between CV and walking
 speed and CV and Froude number. The spatial distribution of variability
 was highly disparate when assessed by m.s.e. and CV: relatively high
 variability was consistently confined to the medial and lateral forefoot
 when measured by m.s.e., while the forefoot and heel show high variability
 when measured by CV. In absolute terms, variability by CV was universally
 low (less than 2.5%). From these results, we determined that variability
 as assessed by m.s.e. is independent of speed, but dependent on speed when
 assessed by CV.
description: Subjects1_2Raw pressure data from subjects 1 and 2 collected from 5 different speeds for 5 minutes per speed.Subjects3_4Raw pressure data from subjects 3 and 4 collected from 5 different speeds for 5 minutes per speed.Subjects5_6Raw pressure data from subjects 5 and 6 collected from 5 different speeds for 5 minutes per speed.Subjects7_8Raw pressure data from subjects 7 and 8 collected from 5 different speeds for 5 minutes per speed.Subjects9_10Raw pressure data from subjects 9 and 10 collected from 5 different speeds for 5 minutes per speed.Subjects11_12Raw pressure data from subjects 11 and 12 collected from 5 different speeds for 5 minutes per speed.Subjects13_14Raw pressure data from subjects 13 and 14 collected from 5 different speeds for 5 minutes per speed.Subjects15_16Raw pressure data from subjects 15 and 16 collected from 5 different speeds for 5 minutes per speed.
DOI: 10.5061/dryad.76qd7
title: Data from: Distributions of irritative zones are related to individual alterations of resting-state networks in focal epilepsy

description: Alterations in the connectivity patterns of the fMRI-based resting-state
 networks (RSNs) have been reported in several types of epilepsies.
 Evidence pointed out these alterations might be associated with the
 genesis and propagation of interictal epileptiform discharges (IEDs). IEDs
 also evoke blood-oxygen-level dependent (BOLD) responses, which have been
 used to delineate irritative zones during preoperative work-up. Therefore,
 one may expect a relationship between the topology of the IED-evoked BOLD
 response network and the altered spatial patterns of the RSNs. In this
 study, we used EEG recordings and fMRI data obtained simultaneously from a
 chronic model of focal epilepsy in Wistar rats to verify our hypothesis.
 We found that IED-evoked BOLD response networks comprise both cortical and
 subcortical structures with a rat-dependent topology. In all rats, IEDs
 evoke both activation and deactivation types of BOLD responses. Using a
 Granger causality method, we found that in many cases areas with BOLD
 deactivation have directed influences on areas with activation
 (p&lt;0.05). We were able to predict topological properties (i.e.,
 focal/diffused, unilateral/bilateral) of the IED-evoked BOLD response
 network by performing hierarchical clustering analysis on major spatial
 features of the RSNs. All these results suggest that IEDs and disruptions
 in the RSNs found previously in humans may be different manifestations of
 the same transient events, probably reflecting altered consciousness. In
 our opinion, the shutdown of specific nodes of the default mode network
 may cause uncontrollable excitability in other functionally connected
 brain areas. We conclude that IED-evoked BOLD responses (i.e., activation
 and deactivation) and alterations of RSNs are intrinsically related, and
 speculate that an understanding of their interplay is necessary to
 discriminate focal epileptogenesis and network propagation phenomena
 across different brain modules via hub-based connectivity.
description: EEG-fMRI Data part
 1Rat
 1 - Rat 4EEG-fMRI study part
 1.zipEEG-fMRI study part
 2Rat
 5 - Rat 6
DOI: 10.5061/dryad.rq4b2n6
title: Data from: Does postcranial palaeoneurology provide insight into pterosaur behaviour and lifestyle? New data from the azhdarchoid Vectidraco and the ornithocheirids Coloborhynchus and Anhanguera

description: The postcranial palaeoneurology of fossil reptiles is understudied, and
 those studies that exist focus predominantly on crocodyliforms and
 dinosaurs. The intervertebral foramina of the spine house nerves that exit
 to innervate surrounding tissues and the extremities. In the heavily fused
 (and typically distorted or poorly preserved) pterosaurian sacrum,
 intervertebral foramina can be difficult to observe and are rarely
 identified. The Early Cretaceous azhdarchoid Vectidraco from the Isle of
 Wight, UK, exhibits large, paired foramina on each sacral vertebra,
 originally identified as pneumatic foramina. Micro‐computed tomography
 imaging reveals these communicate with the neural canal and are
 intervertebral foramina for sacral nerves. The sacral vertebrae of
 Vectidraco are fused, and intervertebral foramina occur dorsolaterally on
 the centra. We identified these structures in other pterosaur sacra,
 including those of the ornithocheiroids Anhanguera and Coloborhynchus. The
 sizes of the sacral and notarial neural canals are compared and considered
 within interpretations of palaeoecology and locomotion, following previous
 studies. The relatively large sacral neural canal of Vectidraco implies a
 sacral enlargement for innervation of the legs and lumbosacral plexus.
 When compared with Anhanguera, this supports indications that azhdarchoids
 were more hindlimb‐proficient than ornithocheiroids. Neural canal size in
 the Coloborhynchus notarium suggests that ornithocheirids spent less time
 on the ground, their brachial enlargement and small sacral region
 indicating enhanced innervation of the wings and poor innervation of the
 sacrum and legs. This is the first study focusing on pterosaur postcranial
 palaeoneurology; more studies on other taxa are needed to reveal patterns
 across Pterosauria as a whole.
description: SMNK PAL 1133
 sacrumCT scans from the sacrum
 of the ornithocheird pterosaurs _Coloborhynchus robust_, SMNK PAL 1133.
 Scans were taken at the u-VIS X-Ray Imaging Centre, University of
 Southampton.20150903_HUTCH_792_EM_Box1_08_SMNK1133_639x620x623x8bit.raw20150903_HUTCH_792_EM_Box2_10_SMNK1133_718x1422x515x8bit20150903_HUTCH_792_EM_Box2_03_SMNK1133_438x325x447x8bitCT scans from cervical vertebra 7 of SMNK PAL 1133, scanned at the u-VIS Imaging Centre, University of Southampton.20150903_HUTCH_792_EM_Box2_04_SMNK1133_338x371x444x8bitCT scans of cervical vertebra 6 from SMNK PAL 1133, _Coloborhynchus robust_, completed at u-VIS Imaging Centre, University of Southampton20150903_HUTCH_792_EM_Box2_05_SMNK1133_330x384x377x8bitCT scans of cervical vertebra 3 from SMNK PAL 1133 _Coloborhynchus robust_, scanned at u-VIS X-Ray Imaging Centre, University of Southampton20150903_HUTCH_792_EM_Box2_12-13-14_SMNK1133_608x716x2258x8bitCT scans of the dorsal vertebrae of SMNK PAL 1133 _Coloborhynchus robust_, scanned at u-VIS X-ray Imaging Centre, University of Southampton.
DOI: 10.5061/dryad.9t740
title: Data from: Human subthalamic nucleus activity during non-motor decision making

description: Recent studies have implicated the subthalamic nucleus (STN) in decisions
 that involve inhibiting movements. Many of the decisions that we make in
 our daily lives, however, do not involve any motor actions. We studied
 non-motor decision making by recording intraoperative STN and prefrontal
 cortex (PFC) electrophysiology as participants perform a novel task that
 required them to decide whether to encode items into working memory.
 During all encoding trials, beta band (15-30 Hz) activity decreased in the
 STN and PFC, and this decrease was progressively enhanced as more items
 were stored into working memory. Crucially, the STN and lateral PFC beta
 decrease was significantly attenuated during the trials in which
 participants were instructed not to encode the presented stimulus. These
 changes were associated with increase lateral PFC-STN coherence and
 altered STN neuronal spiking. Our results shed light on why states of
 altered basal ganglia activity disrupt both motor function and cognition.
description: Human subthalamic
 nucleus activity during non-motor decision makingBehavioral and
 electrophysiology data during memory encoding task. See
 Readme.rtfSeqMemRawdata.zip
DOI: 10.5061/dryad.5j129
title: Data from: Coevolutionary feedbacks between family interactions and life history

description: Families with parental care show a parent–offspring conflict over the
 amount of parental investment. To date, the resolution of this conflict
 was modeled as being driven by either purely within-brood or between-brood
 competition. In reality the partitioning of parental resources within-
 versus between-broods is an evolving life history trait, which can be
 affected by parent–offspring interactions. This coevolutionary feedback
 between life history and family interactions may influence the
 evolutionary process and outcome of parent–offspring coadaptation. We used
 a genetic framework for a simulation model where we allowed parental
 parity to coevolve with traits that determine parental investment. The
 model included unlinked loci for clutch size, parental sensitivity,
 baseline provisioning, and offspring begging. The simulation showed that
 tight coadaptation of parent and offspring traits only occurred in
 iteroparous outcomes whereas semelparous outcomes were characterized by
 weak coadaptation. When genetic variation in clutch size was unrestricted
 in the ancestral population, semelparity and maximal begging with poor
 coadaptation evolved throughout. Conversely, when genetic variation was
 limited to iteroparous conditions, and/or when parental sensitivity was
 treated as an evolutionarily fixed sensory bias, coadapted outcomes were
 more likely. Our findings show the influence of a feedback between parity,
 coadaptation, and conflict on the evolution of parent–offspring
 interactions.
description: Data_CoEvolutionary_FeedbacksThe folder contains all data simulated for the experimental set-ups described in the article as well as the specific Java source code used for each set-up. Further a fully commented version of the source code is included.
DOI: 10.5061/dryad.bv989
title: Data from: Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching

description: Antibody class switching is a feature of the adaptive immune system which
 enables diversification of the effector properties of antibodies. Even
 though class switching is essential for mounting a protective response to
 pathogens, the in vivo patterns and lineage characteristics of antibody
 class switching have remained uncharacterized in living humans. Here we
 comprehensively measured the landscape of antibody class switching in
 human adult twins using antibody repertoire sequencing. The map identifies
 how antibodies of every class are created and delineates a two-tiered
 hierarchy of class switch pathways. Using somatic hypermutations as a
 molecular clock, we discovered that closely related B cells often switch
 to the same class, but lose coherence as somatic mutations accumulate.
 Such correlations between closely related cells exist when purified B
 cells class switch in vitro, suggesting that class switch recombination is
 directed toward specific isotypes by a cell-autonomous imprinted state.
description: Data from Lineage
 Tracing of Human B Cells Reveals the In Vivo Landscape of Human Antibody
 Class SwitchingHorns_Elife_2016_data.zipBCellClassSwitchingScripts associated with Horns et al. Elife 2016. Available in GitHub at https://github.com/felixhorns/BCellClassSwitching
DOI: 10.5061/dryad.8h95q
title: Data from: Potential and pitfalls of eukaryotic metagenome skimming: A test case for lichens

description: Whole genome shotgun sequencing of multi species communities using only a
 single library layout is commonly used to assess taxonomic and functional
 diversity of microbial assemblages. Here we investigate to what extent
 such metagenome skimming approaches are applicable for in-depth genomic
 characterizations of eukaryotic communities, e.g. lichens. We address how
 to best assemble a particular eukaryotic metagenome skimming data, what
 pitfalls can occur, and what genome quality can be expected from this
 data. To facilitate a project specific benchmarking, we introduce the
 concept of twin sets, simulated data resembling the outcome of a
 particular metagenome sequencing study. We show that the quality of genome
 reconstructions depends essentially on assembler choice. Individual tools,
 including the metagenome assemblers Omega and MetaVelvet, are surprisingly
 sensitive to low and uneven coverages. In combination with the routine of
 assembly parameter choice to optimize the assembly N50 size, these tools
 can preclude an entire genome from the assembly. In contrast, MIRA, an
 all-purpose overlap assembler, and SPAdes, a multi-sized de Bruijn graph
 assembler, facilitate a comprehensive view on the individual genomes
 across a wide range of coverage ratios. Testing assemblers on a real-world
 metagenome skimming data from the lichen Lasallia pustulata demonstrates
 the applicability of twin sets for guiding method selection. Furthermore,
 it reveals that the assembly outcome for the photobiont Trebouxia sp.
 falls behind the a-priori expectation given the simulations. Although the
 underlying reasons remain still unclear this highlights that further
 studies on this organism require special attention during sequence data
 generation and downstream analysis.
description: AssemblyResultsThe assemblies generated by the 6 different assemblers for the 11 data sets.AsterochlorisPseudogenomeThe pseudogenome used for simulating the reads.CladoniaPseudogenomeThe pseudogenome used for simulating the Cladonia reads.lasallia_assembliesThe 6 different assemblies generated from the real Lasallia pustulata data set.
DOI: 10.5061/dryad.36775
title: Data from: Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform

description: Next-generation sequencing is a fast and cost-effective way to obtain
 sequence data for non-model organisms for many markers and for many
 individuals. We describe a protocol through which we obtain orthologous
 markers for the crested newts (Amphibia: Salamandridae: Triturus),
 suitable for analysis of interspecific hybridization. We use transcriptome
 data of a single Triturus species and design 96 primer pairs that amplify
 c. 180 bp fragments positioned in 3-prime untranslated regions. Next these
 markers are tested with uniplex PCR for a set of species spanning the
 taxonomical width of the genus Triturus. The 52 markers that consistently
 show a single band of expected length at gel electrophoreses for all
 tested crested newt species are then amplified in five multiplex PCRs
 (with a plexity of ten or eleven) for 132 individual newts: a set of 84
 representing the seven (candidate) species and a set of 48 from a presumed
 hybrid population. After pooling multiplexes per individual, unique tags
 are ligated to link amplicons to individuals. Subsequently individuals are
 pooled equimolar and sequenced on the Ion Torrent next-generation
 sequencing platform. A bioinformatics pipeline identifies the alleles and
 recodes these to a genotypic format. Next we test the utility of our
 markers. BAPS allocates the 84 crested newt individuals representing
 (candidate) species to their expected (candidate) species, confirming the
 markers are suitable for species delineation. NewHybrids, a hybrid index
 and HIest confirm the 48 individuals from the presumed hybrid population
 to be genetically admixed, illustrating the potential of the markers to
 identify interspecific hybridization. We expect the set of markers we
 designed to provide a high resolving power for analysis of hybridization
 in Triturus.
description: Triturus
 transcriptome-based gene models in FASTA formatTriturus
 transcriptome-based gene models in FASTA formatTriturus_transcriptome_contigs_sorted_to_length.fasExcel sheet and macro to compose multiplexesExcel sheet and macro to compose multiplexesExcel_multiplex_check.zipRaw Ion Torrent reads in FASTQ formatRaw Ion Torrent reads in FASTQ formatFASTQ_IonTorrent.zipBWA alignments in SAM formatBWA alignments in SAM formatSAM_alignments.zipRaw SNP reports in VCF formatRaw SNP reports in VCF formatVCF_raw_SNP_reports.zipFASTA files of reconstructed sequencesFASTA files of reconstructed sequencesReconstructed_sequences_FASTA.zipInput files for the BAPS analysis (in GENEPOP format), NewHybrids and HIest.Input files for the BAPS analysis (in GENEPOP format), NewHybrids and HIest.input_files.zipScript associated with the bioinformatics pipelineScript associated with the bioinformatics pipeline. The first script strings the programs together (used in Linux environment). The second script determines the SNPs and allelic variants. The third script creates the consensus sequences.Scripts.zip