cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dq437hf
title: Data from: Encoding of locomotion kinematics in the mouse cerebellum

description: The cerebellum is involved in coordinating motor behaviour, but how the
 cerebellar network regulates locomotion is still not well understood. We
 characterised the activity of putative cerebellar Purkinje cells, Golgi
 cells and mossy fibres in awake mice engaged in an active locomotion task,
 using high-density silicon electrode arrays. Analysis of the activity of
 over 300 neurons in response to locomotion revealed that the majority of
 cells (53%) were significantly modulated by phase of the stepping cycle.
 However, in contrast to studies involving passive locomotion on a
 treadmill, we found that a high proportion of cells (45%) were tuned to
 the speed of locomotion, and 19% were tuned to yaw movements. The activity
 of neurons in the cerebellar vermis provided more information about future
 speed of locomotion than about past or present speed, suggesting a motor,
 rather than purely sensory, role. We were able to accurately decode the
 speed of locomotion with a simple linear algorithm, with only a relatively
 small number of well-chosen cells needed, irrespective of cell class. Our
 observations suggest that behavioural state modulates cerebellar
 sensorimotor integration, and advocate a role for the cerebellar vermis in
 control of high-level locomotor kinematic parameters such as speed and
 yaw.
description: EPhysBehavDataCerebellumMuzzuetalEPhysBehavDataCerebellumMuzzuetal.mat contains 4 fields for each cell: EPhysBehavData{cell#,1} = [ i-th mouse, j-th recording of i-th mouse, Shank_nr, Channel_nr, Unit_ID, depth]; EPhysBehavData{cell#,2} = TimeStamps of spikes in seconds; (sampled at 30 kHz); EPhysBehavData{cell#,3} = EPhysBehavData{cell#,4} = [Pitch, Yaw, sqrt(Pitch.^2 + Yaw.^2), Black screen status, Time in seconds]; Please note that for the animals whose name does not have a T (for trained) the fourth value of EPhysBehavData{cell#,4} does not count as the screen was always black. Please ignore it.
DOI: 10.5061/dryad.1168f
title: Data from: Bayesian hierarchical models suggest oldest known plant-visiting bat was omnivorous

description: The earliest record of plant visiting in bats dates to the Middle Miocene
 of La Venta, the world's most diverse tropical palaeocommunity.
 Palynephyllum antimaster is known from molars that indicate nectarivory.
 Skull length, an important indicator of key traits such as body size, bite
 force and trophic specialization, remains unknown. We developed Bayesian
 models to infer skull length based on dental measurements. These models
 account for variation within and between species, variation between
 clades, and phylogenetic error structure. Models relating skull length to
 trophic level for nectarivorous bats were then used to infer the diet of
 the fossil. The skull length estimate for Palynephyllum places it among
 the larger lonchophylline bats. The inferred diet suggests Palynephyllum
 fed on nectar and insects, similar to its living relatives. Omnivory has
 persisted since the mid-Miocene. This is the first study to corroborate
 with fossil data that highly specialized nectarivory in bats requires an
 omnivorous transition.
description: tooth_fossil
DOI: 10.5061/dryad.p760b
title: Data from: A non-lethal sampling method to obtain, generate and assemble whole-blood transcriptomes from small, wild mammals

description: The acquisition of tissue samples from wild populations is a constant
 challenge in conservation biology, especially for endangered species and
 protected species where nonlethal sampling is the only option. Whole blood
 has been suggested as a nonlethal sample type that contains a high
 percentage of bodywide and genomewide transcripts and therefore can be
 used to assess the transcriptional status of an individual, and to infer a
 high percentage of the genome. However, only limited quantities of blood
 can be nonlethally sampled from small species and it is not known if
 enough genetic material is contained in only a few drops of blood, which
 represents the upper limit of sample collection for some small species. In
 this study, we developed a nonlethal sampling method, the laboratory
 protocols and a bioinformatic pipeline to sequence and assemble the whole
 blood transcriptome, using Illumina RNA-Seq, from wild greater mouse-eared
 bats (Myotis myotis). For optimal results, both ribosomal and globin RNAs
 must be removed before library construction. Treatment of DNase is
 recommended but not required enabling the use of smaller amounts of
 starting RNA. A large proportion of protein-coding genes (61%) in the
 genome were expressed in the blood transcriptome, comparable to brain
 (65%), kidney (63%) and liver (58%) transcriptomes, and up to 99% of the
 mitogenome (excluding D-loop) was recovered in the RNA-Seq data. In
 conclusion, this nonlethal blood sampling method provides an opportunity
 for a genomewide transcriptomic study of small, endangered or critically
 protected species, without sacrificing any individuals.
description: A_assembly_RABTThe reference annotation based transcript (RABT) assembly of individual A transcriptomeB_assembly_RABTThe reference annotation based transcript (RABT) assembly of individual B transcriptomeC_assembly_RABTThe reference annotation based transcript (RABT) assembly of individual C transcriptomeD_assembly_RABTThe reference annotation based transcript (RABT) assembly of individual D transcriptomeSuper_assembly_RABTThe reference annotation based transcript (RABT) assembly of pooled libraries (Super transcriptome)Perl ScriptThis Perl script enables you to extract the longest open reading frame (ORF) from nucleatide sequencesGO_AnnotationThe Gene Ontology annotation of the 'Super' transcriptome assembly based on the RABT methodMitochondrial_Site_CoverageThe mitochondrial site coverage by the 'Super' transcriptome dataTranscriptome_comparisons_among_individualsThe unique annotated accessions from each individual for comparisonTranscriptome_comparisons_among_tissuesThe unique annotated accessions from each tissue type for comparisonFPKM_Super_TranscriptomeThe FPKM value for each gene locus from the 'Super' transcriptome based on the RABT method
DOI: 10.5061/dryad.98jj7gk
title: Data from: Generational conservation of composition and diversity of field-acquired midgut microbiota in Anopheles gambiae sensu lato during colonization in the laboratory

description: The gut microbiota is known to play a role in the mosquito vectors’ life
 history, which is a subject of increasing research. Laboratory experiments
 are essential for such studies and require laboratory colonies. In this
 study, the conservation of field-obtained midgut microbiota was evaluated
 in laboratory-reared Anopheles gambiae s.l. mosquitoes continuously
 hatched in water from the field breeding habitats. Pupae and late instars
 were obtained from the field and reared, and the emerged adults were blood
 fed. The eggs obtained from them were hatched in either water from the
 field or in dechlorinated tap water. The mosquito colonies were maintained
 for 10 generations. Midguts of female adults from unfed F0 (emerging from
 field-caught pupae and larvae), F5, and F10 were dissected out and genomic
 DNA were extracted for 16S metagenomic sequencing. The sequences were
 compared to investigate the diversity, and bacteria compositional
 differences using ANCOM and correlation clustering methods. Less than 10%
 of the bacteria families identified had differential relative abundances
 between generational groups and accounted for 46% of the variation
 observed. Although diversity reduced in F10 mosquitoes during lab
 colonization (Shannon-Weaver; p-value&lt; 0.05), 50% of bacteria
 genera were conserved in those bred continuously in field-water compared
 to 38% in those bred in dechlorinated tap water. The study is the first
 report on the assessment of gut bacterial community of mosquitoes during
 laboratory colonization and recommends the use of water from the natural
 breeding habitats if they are intended for microbiota research.
description: Raw bacterial metagenome
 sequences from Illumina MiseqAn.gambiae midgut bacteria
 metagenome_FASTQs.zip
DOI: 10.5061/dryad.v8d05
title: Data from: Evaluation of demographic history and neutral parameterization on the performance of Fst outlier tests

description: FST outlier tests are a potentially powerful way to detect genetic loci
 under spatially divergent selection. Unfortunately, the extent to which
 these tests are robust to non-equilibrium demographic histories has been
 under-studied. We developed a landscape-genetics simulator to test the
 effects of isolation by distance (IBD) and range expansion on FST outlier
 methods. We evaluated the two most commonly used methods for the
 identification of FST outliers (FDIST2 and BayeScan, which assume samples
 are evolutionarily independent) and two recent methods (FLK and Bayenv2,
 which estimate and account for evolutionary non-independence).
 Parameterization with a set of neutral loci (“neutral parameterization”)
 always improved the performance of FLK and Bayenv2, while neutral
 parameterization caused FDIST2 to actually perform worse in the cases of
 IBD or range expansion. BayeScan was improved when the prior odds on
 neutrality was increased, regardless of the true odds in the data. On
 their best performance, however, the widely-used methods had high
 false-positive rates for IBD and range expansion and were outperformed by
 methods that accounted for evolutionary non-independence. In addition,
 default settings in FDIST2 and BayeScan resulted in many false positives
 under balancing selection. However, all methods did very well if a large
 set of neutral loci is available to create empirical p-values. We conclude
 that in species that exhibit IBD or have undergone range expansion, many
 of the published FST outliers based on FDIST2 and BayeScan are probably
 false positives, but FLK and Bayenv2 show great promise for accurately
 identifying loci under spatially-divergent selection.
description: R code for
 simulationsThis .zip file contains
 R code and functions used for the landscape simulator in R and the source
 code for the implementation of FDIST2 in R.Dryad.zip
DOI: 10.5061/dryad.p5dm3
title: Data from: Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

description: Recent advancements in sequencing technology allowed researchers to better
 address the patterns and mechanisms involved in microbial environmental
 adaptation at large spatial scales. Here we investigated the genomic basis
 of adaptation to climate at the continental scale in Suillus brevipes, an
 ectomycorrhizal fungus symbiotically associated with the roots of pine
 trees. We used genomic data from 55 individuals in seven locations across
 North America to perform genome scans to detect signatures of positive
 selection and assess whether temperature and precipitation were associated
 with genetic differentiation. We found that S. brevipes exhibited overall
 strong population differentiation, with potential admixture in Canadian
 populations. This species also displayed genomic signatures of positive
 selection as well as genomic sites significantly associated with distinct
 climatic regimes and abiotic environmental parameters. These genomic
 regions included genes involved in transmembrane transport of substances
 and helicase activity potentially involved in cold stress response. Our
 study sheds light on large-scale environmental adaptation in fungi by
 identifying putative adaptive genes and providing a framework to further
 investigate the genetic basis of fungal adaptation.
description: SNPDataFile containing the SNPs for all the studied populationsAll_Suillus_OUTGROUP.vcf
DOI: 10.5061/dryad.85vn2
title: Data from: Effect of mild thyrotoxicosis on performance and brain activations in a working memory task

description: Aims: Disturbed levels of thyroid hormones are associated with
 neuropsychiatric disorders, including memory impairments. The aim of this
 study was to evaluate effects of mild induced thyrotoxicosis on working
 memory and its neural correlates. Methods: Twenty-nine healthy, male
 subjects with normal thyroid state participated in the study. Functional
 MRI was acquired during a working memory task (n-back task) before and
 after ingesting 250 μg L-thyroxin per day for a period of eight weeks. In
 addition, neuropsychological tests were performed. Results: In the
 hyperthyroid condition the subjects showed slower reaction times, but a
 higher accuracy in the 0-back version of the memory tasks. Fewer
 differences between euthyroid and hyperthyroid state were seen for the
 more difficult conditions of the n-back task. FMRI revealed effects of
 difficulty in the parahippocampal gyrus, supplementary motor area,
 prefrontal cortex, anterior cingulate cortex, posterior cerebellum,
 rolandic operculum and insula (p&lt;0.05, FWE corrected). When
 comparing euthyroid and hyperthyroid condition in relation to task-induced
 activation, differences of activation were found in the right prefrontal
 cortex as well as in the right parahippocampal area. In the psychological
 assessment, the alerting effect in the Attention Network Task (ANT) and
 four out of five parameters of the auditory verbal learning test (AVLT)
 showed an increase from euthyroid to hyperthyroid state. Conclusions: It
 can be concluded that even a short-term intake of thyroid hormones leads
 to an activation of brain areas associated with working memory and to an
 improvement of accuracy of working memory tasks.
description: Data thyroid
 study29 healthy male right
 handed subjects recurited, one excluded due to extensive bodybuilding.
 Imaging data collected on 3.0 Tesla Philips Achieva MR-scanner. High
 resolution structural images with T1-weighted 3D turbo gradient echo
 sequence with SENSE(image matrix 240x240, 180 sliceş 1x1x1 mm3 spatial
 resolution)
DOI: 10.5061/dryad.pk368
title: Data from: The influence of preceding dive cycles on the foraging decisions of Antarctic fur seals

description: The foraging strategy of many animals is thought to be determined by their
 past experiences. However, few empirical studies have investigated whether
 this is true in diving animals. We recorded three-dimensional movements
 and mouth-opening events from three Antarctic fur seals during their
 foraging trips to examine how they adapt their behaviour based on past
 experience—continuing to search for prey in the same area or moving to
 search in a different place. Each dive cycle was divided into a transit
 phase and a feeding phase. The linear horizontal distance travelled after
 feeding phases in each dive was affected by the mouth-opening rate during
 the previous 244 s, which typically covered two to three dive cycles. The
 linear distance travelled tended to be shorter when the mouth-opening rate
 in the previous 244 s was higher, i.e. seals tended to stay in the same
 areas with high prey-encounter rates. These results indicate that
 Antarctic fur seals follow decision-making strategies based on the past
 foraging experience over time periods longer than the immediately
 preceding dive.
description: Foraging decision of fur
 sealsThree axis acceleration,
 three axis magnetism, depth, temperature and speed data from 3MPD3GT
 (attached body). Two axis acceleration, depth and temperature data from
 D2GT (attached jaw). GPS data.Foraging decision of Fur
 seal.zip
DOI: 10.5061/dryad.n8f30
title: Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

description: Copepods of the genus Calanus are key zooplankton species in temperate to
 arctic marine ecosystems. Despite their ecological importance, species
 identification remains challenging. Furthermore, the recent report of
 hybrids among Calanus species highlights the need for diagnostic nuclear
 markers in order to efficiently identify parental species and hybrids.
 Using Next Generation Sequencing analysis of both the genome and
 transcriptome from two sibling species, C. finmarchichus and C. glacialis,
 we developed a panel of 12 nuclear insertion/deletion markers. All the
 markers showed species specific amplicon length. Furthermore most of the
 markers were successfully amplified in other Calanus species allowing the
 molecular identification of C. helgolandicus, C hyperboreus and C.
 marshallae.
description: C. finmarchicus genome
 (contigs)Contigs of C.
 finmarchicus genome assembled with Geneious 6.1.6. Sequencing technology:
 Ion Torrent, 200 bp. File contain consensus sequences in fastq
 file.Cfin_Genome_Contigs.fastaC. glacialis genome (contigs)Contigs of C. glacialis genome assembled with Geneious 6.1.6. Sequencing technology: Ion Torrent, 200 bp. File contain consensus sequences in fastq file.Cgla_Genome_Contigs.fastaC. finmarchicus transcriptome (contigs)Contigs of C. finmarchicus transcriptome assembled with Geneious 6.1.6. Sequencing technology: Ion Torrent, 200 bp. File contain consensus sequences in fastq file.Cfin_Transcriptome_Contigs.fastaC. glacialis transcriptome (contigs)Contigs of C. glacialis transcriptome assembled with Geneious 6.1.6. Sequencing technology: Ion Torrent, 200 bp. File contain consensus sequences in fastq file.Cgla_Transcriptome_Contigs.fastaMicrosatellites_GenotypesTable of microsatellite genotyping for species identification of Calanus finmarchicus and C. glacialisMsat_Genotypes_SuppInfo.xlsx
DOI: 10.5061/dryad.pp7qj1s
title: Data from: Cytotaxonomy of Piptatherum kuoi (Stipeae, Poaceae)

description: The generic placement of Piptatherum kuoi (Poaceae, Stipeae) has long been
 a controversial matter. Recent molecular phylogenetic analyses indicate
 that Piptatherum kuoi should be transferred to Patis. Here, we present
 cytological evidence for this transfer. Piptatherum kuoi has a chromosome
 number of 2n = 46 with the chromosomes varying in length between 1.1 – 3.1
 μm, and a symmetrical karyotype 2n = 26m + 16sm + 4st (2sat). Karyological
 characters of Piptatherum kuoi, including chromosome number, size, and
 karyotype asymmetry, all agree remarkably with those in Patis, but are
 distinct from those in other species of Piptatherum. The transference of
 Piptatherum kuoi to Patis is corroborated.
description: chromosome number of
 PatisThe zip document
 includes mitotic metaphase chromosome photographs of three species. It
 includes 7 items for Patis coreana var. coreana, 9 items for Patis
 racemosa, and 23 items for Piptatherum kuoi.
DOI: 10.5061/dryad.h79q4
title: Data from: Sound exposure in harbour seals during the installation of an offshore wind farm: predictions of auditory damage

description: 1. With ambitious renewable energy targets, pile driving associated with
 offshore wind farm construction will become widespread in the marine
 environment. Many proposed wind farms overlap with the distribution of
 seals, and sound from pile driving has the potential to cause auditory
 damage. 2. We report on a behavioural study during the construction of a
 wind farm using data from GPS/GSM tags on 24 harbour seals Phoca vitulina
 L. Pile driving data and acoustic propagation models, together with seal
 movement and dive data, allowed the prediction of auditory damage in each
 seal. 3. Growth and recovery functions for auditory damage were combined
 to predict temporary auditory threshold shifts in each seal. Further,
 M-weighted cumulative sound exposure levels [cSELs(Mpw)] were calculated
 and compared to permanent auditory threshold shift exposure criteria for
 pinnipeds in water exposed to pulsed sounds. 4. The closest distance of
 each seal to pile driving varied from 4·7 to 40·5 km, and predicted
 maximum cSELs(Mpw) ranged from 170·7 to 195·3 dB re 1μPa2-s for individual
 seals. Comparison to exposure criteria suggests that half of the seals
 exceeded estimated permanent auditory damage thresholds. 5. Prediction of
 auditory damage in marine mammals is a rapidly evolving field and has a
 number of key uncertainties associated with it. These include how sound
 propagates in shallow water environments and the effects of pulsed sounds
 on seal hearing; as such, our predictions should be viewed in this
 context. 6. Policy implications. We predicted that half of the tagged
 seals received sound levels from pile driving that exceeded auditory
 damage thresholds for pinnipeds. These results have implications for
 offshore industry and will be important for policymakers developing
 guidance for pile driving. Developing engineering solutions to reduce
 sound levels at source or methods to deter animals from damage risk zones,
 or changing temporal patterns of piling could potentially reduce auditory
 damage risk. Future work should focus on validating these predictions by
 collecting auditory threshold information pre- and post-exposure to pile
 driving. Ultimately, information on population-level impacts of exposure
 to pile driving is required to ensure that offshore industry is developed
 in an environmentally sustainable manner.
description: pv42_data
DOI: 10.5061/dryad.b42h2
title: Data from: First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics

description: The giant panda (Ailuropoda melanoleuca) is one of the most famous
 flagship species for conservation, and its draft genome has recently been
 assembled. However, the transcriptome is not yet available. In this study,
 the blood transcriptomes of three pandas were characterized and about 160
 million sequencing reads were generated using Illumina HiSeq 2000
 paired-end sequencing technology. The assembly yielded 92 598 transcripts
 with an average length of 1626 bp and N50 length of 2842 bp. Based on a
 sequence similarity search against nonredundant (nr) protein database, a
 total of 38 522 (41.6%) transcripts were annotated. Of these annotated
 transcripts, 25 142 and 8272 transcripts were assigned to gene ontology
 terms and clusters of orthologous group, respectively. A search against
 the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG)
 indicated that 9098 (9.83%) transcripts mapped to 324 KEGG pathways, and
 the best represented functional categories of pathways were signal
 transduction and immune system. We have also identified 23 460
 microsatellites, 43 560 SNPs as well as 21 456 alternative splicing events
 in the assembly. Additionally, a total of 24 341 complete open reading
 frames (ORFs) were detected from the assembly where 1492 ORFs were found
 to be novel gene loci as these have not been annotated so far in any
 public database.
description: assembled
 transcriptsTotal assembled
 transcriptsAM_PASA_assembly_transcripts.faSSRs from giant panda transcriptomemicrosatellites identified in giant panda blood transcriptomeSSRs.xlsnovel gene idthe ids of novel genenovol_gene.txttranscript expression value FPKM and TPMall transcripts expression value FPKM and TPMtranscript_expression.txtSNP sitesgiant_panda_blood_transcriptome_snps.gff