cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fd612
title: Data from: Walking like an ant: a quantitative and experimental approach to understanding locomotor mimicry in the jumping spider Myrmarachne formicaria

description: Protective mimicry, in which a palatable species avoids predation by being
 mistaken for an unpalatable model, is a remarkable example of adaptive
 evolution. These complex interactions between mimics, models and predators
 can explain similarities between organisms beyond the often-mechanistic
 constraints typically invoked in studies of convergent evolution. However,
 quantitative studies of protective mimicry typically focus on static
 traits (e.g. colour and shape) rather than on dynamic traits like
 locomotion. Here, we use high-speed cameras and behavioural experiments to
 investigate the role of locomotor behaviour in mimicry by the
 ant-mimicking jumping spider Myrmarachne formicaria, comparing its
 movement to that of ants and non-mimicking spiders. Contrary to previous
 suggestions, we find mimics walk using all eight legs, raising their
 forelegs like ant antennae only when stationary. Mimics exhibited winding
 trajectories (typical wavelength = 5–10 body lengths), which resemble the
 winding patterns of ants specifically engaged in pheromone-trail
 following, although mimics walked on chemically inert surfaces. Mimics
 also make characteristically short (approx. 100 ms) pauses. Our analysis
 suggests that this makes mimics appear ant-like to observers with slow
 visual systems. Finally, behavioural experiments with predatory spiders
 yield results consistent with the protective mimicry hypothesis. These
 findings highlight the importance of dynamic behaviours and observer
 perception in mimicry.
description: General
 READMEThis general README file
 provides an overall description of the other files present in this
 repository.Dryad data repo
 README.txtBehaviorData related to behavior experiments presented in the manuscript.HighSpeedData related to high-speed (limb kinematics) experiments presented in the manuscript.OverallMovementData related to overall movement experiments presented in the manuscript.
DOI: 10.5061/dryad.qp0qv
title: Data from: Developmental changes in hippocampal CA1 single neuron firing and theta activity during associative learning

description: Hippocampal development is thought to play a crucial role in the emergence
 of many forms of learning and memory, but ontogenetic changes in
 hippocampal activity during learning have not been examined thoroughly. We
 examined the ontogeny of hippocampal function by recording theta and
 single neuron activity from the dorsal hippocampal CA1 area while rat pups
 were trained in associative learning. Three different age groups
 [postnatal days (P)17-19, P21-23, and P24-26] were trained over six
 sessions using a tone conditioned stimulus (CS) and a periorbital
 stimulation unconditioned stimulus (US). Learning increased as a function
 of age, with the P21-23 and P24-26 groups learning faster than the P17-19
 group. Age- and learning-related changes in both theta and single neuron
 activity were observed. CA1 pyramidal cells in the older age groups showed
 greater task-related activity than the P17-19 group during CS-US paired
 sessions. The proportion of trials with a significant theta (4–10 Hz)
 power change, the theta/delta ratio, and theta peak frequency also
 increased in an age-dependent manner. Finally, spike/theta phase-locking
 during the CS showed an age-related increase. The findings indicate
 substantial developmental changes in dorsal hippocampal function that may
 play a role in the ontogeny of learning and memory.
description: DevelopmentalHippCA1DataRaw EMG (.rw), LFP (.csc), and pre-processed spike data for the article submitted to PLoSONE. For more details, please contact to Jangjin Kim (kim.jangjin@gmail.com)DevelopmentalCA1Data.zip
DOI: 10.5061/dryad.rh07b
title: Data from: The third dimension: a novel set-up for filming coelacanths in their natural environment

description: Here, we describe a novel design to obtain three-dimensional data on the
 movements of aquatic organisms at depths of up to 140 m. The set-up
 consists of two synchronized high-speed cameras fixed to two articulated
 arms. The set-up was successfully used to film and quantify the locomotion
 of coelacanths Latimeria chalumnae living at a depth of about 120 m in
 Sodwana Bay, South Africa. As an example, the detailed motion of the
 dorsal fin is presented here. This set-up can be used for any underwater
 applications that require synchronized video recordings of medium- to
 large-sized animals.
description: Dorsal
 viewLateral
 viewCoordinates to identify
 the 3D trajectory of pectoral finPectoral fin
 coordinates.txt
DOI: 10.5061/dryad.q530s
title: Data from: Comparative genomics reveals convergent rates of evolution in ant-plant mutualisms

description: Symbiosis—the close and often long-term interaction of species—is
 predicted to drive genome evolution in a variety of ways. For example,
 parasitic interactions have been shown to increase rates of molecular
 evolution, a trend generally attributed to the Red Queen Hypothesis.
 However, it is much less clear how mutualisms impact the genome, as both
 increased and reduced rates of change have been predicted. Here we
 sequence the genomes of seven species of ants, three that have
 convergently evolved obligate plant–ant mutualism and four closely related
 species of non-mutualists. Comparing these sequences, we investigate how
 genome evolution is shaped by mutualistic behaviour. We find that rates of
 molecular evolution are higher in the mutualists genome wide, a
 characteristic apparently not the result of demography. Our results
 suggest that the intimate relationships of obligate mutualists may lead to
 selective pressures similar to those seen in parasites, thereby increasing
 rates of evolution.
description: pgra_genome_v1.0pgra_OGSv1.0_CDSCDS from annotation version 1.0.pgra_OGSv1.0_pepProtein sequences from version 1.0 of the annotation.pgra_OGSv1.0_genesGFF from version 1.0 of the annotation.aligned_pseudomyrmex_genomes.tarSix species of Pseudomyrmex were assembled based on alignments to the P. gracilis reference.aligned_pseudomyrmex_genes.tarGene alignments for the seven Pseudomyrmex species sequenced. Genes that did not pass quality controls are not included.
DOI: 10.5061/dryad.216tp
title: Data from: Substantial compositional turnover of fungal communities in an alpine ridge-to-snowbed gradient

description: The main gradient in vascular plant, bryophyte and lichen species
 composition in alpine areas, structured by the topographic gradient from
 wind-exposed ridges to snowbeds, has been extensively studied. Tolerance
 to environmental stress, resulting from wind abrasion and desiccation
 towards windswept ridges or reduced growing season due to prolonged snow
 cover towards snowbeds, is an important ecological mechanism in this
 gradient. The extent to which belowground fungal communities are
 structured by the same topographic gradient, and the eventual mechanisms
 involved, are less well known. In this study, we analyzed variation in
 fungal diversity and community composition associated with roots of the
 ectomycorrhizal plant Bistorta vivipara along the ridge-to-snowbed
 gradient. We collected root samples from fifty B. vivipara plants in ten
 plots in an alpine area in central Norway. The fungal communities were
 analyzed using 454 pyrosequencing analyses of tag encoded ITS1 amplicons.
 A distinct gradient in the fungal community composition was found that
 coincided with variation from ridge to snowbeds. This gradient was
 paralleled by change in soil content of carbon, nitrogen and phosphorus. A
 large proportion (66%) of the detected 801 non-singleton operational
 taxonomic units (OTUs) were ascomycetes, while basidiomycetes dominated
 quantitatively (i.e., with respect to number of reads). Numerous fungal
 OTUs, many with taxonomic affinity to Sebacinales, Cortinarius and
 Meliniomyces, showed distinct affinities either to ridge or to snowbed
 plots, indicating habitat specialization. The compositional turnover of
 fungal communities along the gradient was not paralleled by a gradient in
 species richness.
description: L1.sff.SFF file for lane one
 run on the 454 platform. A mapping file is added.SBFY1.734.sffL2.sffSBFY2.735.sffL3.sff.SFF file, lane 3SBFY3.736.sffL4.sffSBFY4.737.sffOTU tableOTU table used in analyses.otu_table.from_biom_.txtRAW OTU table with taxonomyRaw otu-table with taxonomy form NCBI-blast.RAW_OTU_table w tax.xlsxVegetation of the sampled plotsThe vegetation recorded in the 10 sampled plots.veg_.txtGNMDSScript for GNMDS ordinationsAccumulation curves and species diversity estimatesR script for accumulation curves and species diversity estimatesAccum&Spec_div_.RVariablesEnvironmental and plant variables for the 10 sampled plots.variables.txt
DOI: 10.5061/dryad.45pv2
title: Data from: Low host specificity among arctic root-assosiated fungi

description: In High Arctic ecosystems, plant growth and reproduction are limited by
 low soil moisture and nutrient availability, low soil and air
 temperatures, and a short growing season. Mycorrhizal associations
 facilitate plant nutrient acquisition and water uptake and may therefore
 be particularly ecologically important in nutrition-poor and dry
 environments, such as parts of the Arctic. Similarly, endophytic root
 associates are thought to play a protective role, increasing plants'
 stress tolerance, and likely have an important ecosystem function. Despite
 the importance of these root-associated fungi, little is known about their
 host specificity in the Arctic. We investigated the host specificity of
 root-associated fungi in the common, widely distributed arctic plant
 species Bistorta vivipara, Salix polaris and Dryas octopetala in the High
 Arctic archipelago Svalbard. High-throughput sequencing of the internal
 transcribed spacer 1 (ITS1) amplified from whole root systems generated no
 evidence of host specificity and no spatial autocorrelation within two 3 m
 × 3 m sample plots. The lack of spatial structure at small spatial scales
 indicates that Common Mycelial Networks (CMNs) are rare in marginal arctic
 environments. Moreover, no significant differences in fungal OTU richness
 were observed across the three plant species, although their root system
 characteristics (size, biomass) differed considerably. Reasons for lack of
 host specificity could be that association with generalist fungi may allow
 arctic plants to more rapidly and easily colonize newly available
 habitats, and it may be favourable to establish symbiotic relationships
 with fungi possessing different physiological attributes.
description: L1.sff.SFF file for lane one
 run on the 454 platform. A mapping file is addedSBFY1.734.sffL2.sffSBFY2.735.sffL3.sffSBFY3.736.sffL4.sffSBFY4.737.sffAccum&estR script for accumulation curves and species diversity estimatesGNMDSandDCAR scripts for DCA and GNMDS ordinationsotu_table_hellingerOTU table used in analyses.
DOI: 10.13140/rg.2.2.14722.54722
title: Moluscos ibéricos. Material docente: Lutraria lutraria
DOI: 10.5061/dryad.s9v06
title: Data from: The crested newt Triturus cristatus recolonized temperate Eurasia from an extra-Mediterranean glacial refugium

description: We assess the role of the Carpathians as an extra-Mediterranean glacial
 refugium for the crested newt Triturus cristatus. We combine a multilocus
 phylogeography (one mitochondrial protein-coding gene, three nuclear
 introns, and one major histocompatibility complex gene) with species
 distribution modelling (projected on current and Last Glacial Maximum
 climate layers). All genetic markers consistently show extensive genetic
 variation within and genetic depletion outside the Carpathians. The
 species distribution model suggests that most of the current range was
 unsuitable at the Last Glacial Maximum, but a small suitable area remained
 in the Carpathians. Triturus cristatus dramatically expanded its
 postglacial range, colonizing much of temperate Eurasia from a glacial
 refugium in the Carpathians. Within the Carpathians, T. cristatus
 persisted in multiple geographically discrete regions, providing further
 support for a Carpathian ‘refugia within refugia’ scenario.
description: Raw Ion Torrent reads in
 FASTQ formatRaw Ion Torrent reads in
 FASTQ formatMHC_Ion
 torrent_fastq.zipDecoding table and an
 alignment of the MHC class II DAB haplotypesDecoding table and an
 alignment of the MHC class II DAB haplotypesMHC_decoding_table_alignment.zipInput files for MrBayes, BEAST, Newhybrids, and BAPSInput files for MrBayes, BEAST, Newhybrids, and BAPSInput_files_genetics.zipBioclimatic layers used for species distribution modellingBioclimatic layers used for species distribution modellingMaxent_climate_layers.zip
DOI: 10.5061/dryad.1nt24m0
title: Data from: Step-to-step variations in human running reveal how humans run without falling

description: Humans can run without falling down, usually despite uneven terrain or
 occasional pushes. Even without such external perturbations, intrinsic
 sources like sensorimotor noise perturb the running motion incessantly,
 making each step variable. Here, using simple and generalizable models, we
 show that even such small step-to-step variability contains considerable
 information about strategies used to run stably. Deviations in the center
 of mass motion predict the corrective strategies during the next stance,
 well in advance of foot touchdown. Horizontal motion is stabilized by
 total leg impulse modulations, whereas the vertical motion is stabilized
 by differentially modulating the impulse within stance. We implement these
 human-derived control strategies on a simple computational biped, showing
 that it runs stably for hundreds of steps despite incessant noise-like
 perturbations or larger discrete perturbations. This running controller
 derived from natural variability echoes behaviors observed in previous
 animal and robot studies.
description: Data for: Step-to-step
 variations in human running reveal how humans run without
 fallingData for: Step-to-step
 variations in human running reveal how humans run without
 fallingRunningData_Seethapathi2018.zip
DOI: 10.5061/dryad.jb10510
title: Data from: Synergy between RecBCD subunits is essential for efficient DNA unwinding

description: The subunits of the bacterial RecBCD act in coordination, rapidly and
 processively unwinding DNA at the site of a double strand break. RecBCD is
 able to displace DNA binding proteins, suggesting that it generates high
 forces, but the specific role of each subunit in the force generation is
 unclear. Here, we present a novel optical tweezers assay that allows
 monitoring the activity of RecBCD's individual subunits, when they
 are part of an intact full complex. We show that RecBCD and its subunits
 are able to generate forces up to 25-40 pN without a significant effect on
 their velocity. Moreover, the isolated RecD translocates fast, but is a
 weak helicase with limited processivity. Experiments at a broad range of
 [ATP] and forces suggest that RecD unwinds DNA as a Brownian ratchet,
 rectified by ATP binding, and that the presence of the other subunits
 shifts the ratchet equilibrium towards the post-translocation state.
description: DatasetThe dataset includes a Matlab (“.mat”) file for each experimental trace measured in the optical tweezers. Each file contains a single structure with the name “Data” that has the following fields: Data.time – An array containing the time (in seconds, at 2.5 kHz) Data.contour – An array containing the measured contour length (in bps, at 2.5 kHz) Data.force – An array containing the measured force (in pN, at 2.5 kHz) Data.Protein – A string with the name of the protein used Data.DNAconstruct – A string with the type of construct (Hairpin, symmetric, RecB, and RecD) Data.ATP – The ATP concentration (uM) Data.ProteinConcentration – The protein concentration(nM)
DOI: 10.5061/dryad.52582
title: Data from: A lower jaw of Palaeoxonodon from the Middle Jurassic of the Isle of Skye, Scotland, sheds new light on the diversity of British stem therians

description: The Middle Jurassic was a key interval of mammalian evolutionary history
 that witnessed the diversification of the therian stem-group. Great
 Britain has yielded a significant record of mammalian fossils from this
 interval, represented by numerous isolated jaws and teeth from the
 Bathonian of Oxfordshire and the Isle of Skye. This record captures a key
 period in early cladotherian evolution, with amphitheriids, peramurans and
 “stem zatherians” displaying intermediate talonid morphologies that
 document the evolutionary assembly of tribosphenic molars. We present a
 mandible with near-complete dentition from the late Bathonian (ca.
 167.4–166.5 Ma) Kilmaluag Formation, near Elgol, Skye, representing the
 amphitheriid Palaeoxonodon ooliticus, previously known only from isolated
 teeth. The specimen sheds new light on the taxonomic diversity of British
 Middle Jurassic stem therians, as the morphological variation within the
 preserved tooth row encompasses that previously ascribed to three distinct
 species within two genera: Palaeoxonodon ooliticus, P. freemani, and
 Kennetheridium leesi. Thus, both P. freemani and Kennetheridium leesi are
 subjective junior synonyms of P. ooliticus. The dental formula of P.
 ooliticus (i4:c1:p5:m5) is intermediate between the primitively larger
 postcanine count (p5:m6-7) of Amphitherium and the reduced number in
 peramurans and tribosphenidans (p5:m3). Phylogenetic analyses of P.
 ooliticus generally confirm a close affinity with Amphitherium, but
 highlight the lack of strong empirical support for hypothesized patterns
 of divergences among early cladotherians.
description: Palaeoxonodon ooliticus
 NMS G.2015.17.10 movie renderingMovie rendering of
 Palaeoxonodon ooliticus NMS G. 2015.17.10.Palaeoxonodon_ooliticus_movie_rendering.movPalaeoxonodon ooliticus NMS G.2015.17.10 PLY file3D surface file of Palaeoxonodon ooliticus NMS G.2015.17.10 in PLY format.Palaeoxonodon_ooliticus_NMS_G.2015.17.10.plyPalaeoxonodon ooliticus NMS G.2015.17.10 PLY (dentary only)3D surface file of Palaeoxonodon ooliticus NMS G.2015.17.10 in PLY format (dentary only)Palaeoxonodon_ooliticus_NMS_G.2015.17.10_dentary.plyPalaeoxonodon ooliticus NMS G.2015.17.10 PLY (dentition only)3D surface file of Palaeoxonodon ooliticus NMS G.2015.17.10 in PLY format (dentition only)Palaeoxonodon_ooliticus_NMS_G.2015.17.10_dentition.plyClose et al. TNT input and output filesInput and output files for phylogenetic analyses using TNTClose et al. TNT Files.zipCT scan of Palaeoxonodon ooliticus NMS G. 2015.17.10X-Ray Computed Tomographic (CT) Scan of Palaeonxonodon ooliticus NMS G. 2015.17.10 in DICOM formatDICOM.zip
DOI: 10.5061/dryad.8231nj1
title: Data from: Developmental 'awakening' of primary motor cortex to the sensory consequences of movement

description: Before primary motor cortex (M1) develops its motor functions, it
 functions like a somatosensory area. Here, by recording from neurons in
 the forelimb representation of M1 in postnatal day (P) 8-12 rats, we
 demonstrate a rapid shift in its sensory responses. At P8-10, M1 neurons
 respond overwhelmingly to feedback from sleep-related twitches of the
 forelimb, but the same neurons do not respond to wake-related movements.
 By P12, M1 neurons suddenly respond to wake movements, a transition that
 results from opening the sensory gate in the external cuneate nucleus.
 Also at P12, fewer M1 neurons respond to individual twitches, but the full
 complement of twitch-related feedback observed at P8 is unmasked through
 local disinhibition. Finally, through P12, M1 sensory responses originate
 in the deep thalamorecipient layers, not primary somatosensory cortex.
 These findings demonstrate that M1 initially establishes a sensory
 framework upon which its later-emerging role in motor control is built.
description: Matlab Structure of Raw
 Timeseries dataeLifeData.mat
DOI: 10.5061/dryad.c5p1f
title: Data from: Transcriptome profiling of ontogeny in the acridid grasshopper Chorthippus biguttulus

description: Acridid grasshoppers (Orthoptera:Acrididae) are widely used model
 organisms for developmental, evolutionary, and neurobiological research.
 Although there has been recent influx of orthopteran transcriptomic
 resources, many use pooled ontogenetic stages obscuring information about
 changes in gene expression during development. Here we developed a de novo
 transcriptome spanning 7 stages in the life cycle of the acridid
 grasshopper Chorthippus biguttulus. Samples from different stages
 encompassing embryonic development through adults were used for
 transcriptomic profiling, revealing patterns of differential gene
 expression that highlight processes in the different life stages. These
 patterns were validated with semi-quantitative RT-PCR. Embryonic
 development showed a strongly differentiated expression pattern compared
 to all of the other stages and genes upregulated in this stage were
 involved in signaling, cellular differentiation, and organ development.
 Our study is one of the first to examine gene expression during
 post-embryonic development in a hemimetabolous insect and we found that
 only the fourth and fifth instars had clusters of genes upregulated during
 these stages. These genes are involved in various processes ranging from
 synthesis of biogenic amines to chitin binding. These observations
 indicate that post-embryonic ontogeny is not a continuous process and that
 some instars are differentiated. Finally, genes upregulated in the imago
 were generally involved in aging and immunity. Our study highlights the
 importance of looking at ontogeny as a whole and indicates promising
 directions for future research in orthopteran development.
description: Unfiltered
 transcriptomeRaw output from the
 trinity assemblyall6_larval.fastaFiltered transcriptomeTranscriptome filtered (Isopct ≥ 51, FPKM ≥ 0.1, length ≥ 600 bp)all6_larva_fpkm0.1_minLen600.fastaDESeq2 Input fileCount matrixlarval_and_erl_adults.counts.matrixSample IDssample_IDs.xlsx