cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.854j2
title: Data from: Dynamic structure of locomotor behavior in walking fruit flies

description: The function of the brain is unlikely to be understood without an accurate
 description of its output, yet the nature of movement elements and their
 organization remains an open problem. Here, movement elements are
 identified from dynamics of walking in flies, using unbiased criteria. On
 one time scale, dynamics of walking are consistent over hundreds of
 milliseconds, allowing elementary features to be defined. Over longer
 periods, walking is well described by a stochastic process composed of
 these elementary features, and a generative model of this process
 reproduces individual behavior sequences accurately over seconds or
 longer. Within elementary features, velocities diverge, suggesting that
 dynamical stability of movement elements is a weak behavioral constraint.
 Rather, long-term instability can be limited by the finite memory between
 these elementary features. This structure suggests how complex dynamics
 may arise in biological systems from elements whose combination need not
 be tuned for dynamic stability.
description: dataset_SVelocity trajectories and segmentation annotation.dataset_LVelocity trajectories and segmentation annotation.dataset_AVelocity trajectories and segmentation annotation.classify_submodes_cmsec_degsec_30fpsMATLAB script to classify behavior elements (submodes, modes) in velocity time series of walking fruit flies. Requires parameter file classification_params_r.mat.classification_params_rParameter file for script classify_submodes_cmsec_degsec_30fps.mmode_data_scriptsScripts, parameter files, and data structures operating on segmented trajectoriessegmented_data_scripts.zip
DOI: 10.5061/dryad.tr2f1
title: Data from: Collagen network strengthening following cyclic tensile loading

description: The bulk mechanical properties of tissues are highly tuned to the
 physiological loads they experience and reflect the hierarchical structure
 and mechanical properties of their constituent parts. A thorough
 understanding of the processes involved in tissue adaptation is required
 to develop multi-scale computational models of tissue remodelling. While
 extracellular matrix (ECM) remodelling is partly due to the changing
 cellular metabolic activity, there may also be mechanically directed
 changes in ECM nano/microscale organization which lead to mechanical
 tuning. The thermal and enzymatic stability of collagen, which is the
 principal load-bearing biopolymer in vertebrates, have been shown to be
 enhanced by force suggesting that collagen has an active role in ECM
 mechanical properties. Here, we ask how changes in the mechanical
 properties of a collagen-based material are reflected by alterations in
 the micro/nanoscale collagen network following cyclic loading.
 Surprisingly, we observed significantly higher tensile stiffness and
 ultimate tensile strength, roughly analogous to the effect of work
 hardening, in the absence of network realignment and alterations to the
 fibril area fraction. The data suggest that mechanical loading induces
 stabilizing changes internal to the fibrils themselves or in the
 fibril–fibril interactions. If such a cell-independent strengthening
 effect is operational in vivo, then it would be an important consideration
 in any multiscale computational approach to ECM growth and remodelling.
description: MechanicalTestingDataCompressed file containing raw force data of the cyclic loading experiments.TEM ImagesCompressed file containing TEM images of en face and transverse section of dense disorganized collagen substrate after cyclic loading
DOI: 10.5061/dryad.5tp6r
title: Data from: The dynamic role of genetics on cortical patterning during childhood and adolescence

description: Longitudinal imaging and quantitative genetic studies have both provided
 important insights into the nature of human brain development. In the
 present study we combine these modalities to obtain dynamic anatomical
 maps of the genetic contributions to cortical thickness through childhood
 and adolescence. A total of 1,748 anatomic MRI scans from 792 healthy
 twins and siblings were studied with up to eight time points per subject.
 Using genetically informative latent growth curve modeling of 81,924
 measures of cortical thickness, changes in the genetic contributions to
 cortical development could be visualized across the age range at high
 resolution. There was highly statistically significant (P &lt; 0.0001)
 genetic variance throughout the majority of the cerebral cortex, with the
 regions of highest heritability including the most evolutionarily novel
 regions of the brain. Dynamic modeling of changes in heritability over
 time demonstrated that the heritability of cortical thickness increases
 gradually throughout late childhood and adolescence, with sequential
 emergence of three large regions of high heritability in the temporal
 poles, the inferior parietal lobes, and the superior and dorsolateral
 frontal cortices.
description: Twin and Family
 Longitudinal Measures of Cortical Thickness.RData file containing
 demographic information and vertex-level longitudinal measures of cortical
 thickness. Users will need to install the free software package R at
 http://http://cran.us.r-project.org. The readme object within the .RData
 file contains descriptions of individual variables. Vectors of
 vertex-level results can be visualized using brain-view2; see
 https://wiki.mouseimaging.ca/display/MICePub/brain-view to access
 information on how to download brainview. Further details on cortical
 thickness measures and zygosity determination can be found in the original
 manuscript.DynamicHeritability2.RData
DOI: 10.6084/m9.figshare.31151329
title: Supporting Data for the following paper, published in Current Biology:

description: Average neural responses in three conditions in a [neuron x orientation x time] format.
DOI: 10.6084/m9.figshare.31151329.v1
title: Supporting Data for the following paper:

description: Average neural responses in three conditions in a [neuron x orientation x time] format.
DOI: 10.6084/m9.figshare.31151329.v2
title: Supporting Data for the following paper, published in Current Biology:

description: Average neural responses in three conditions in a [neuron x orientation x time] format.
DOI: 10.15468/dl.g4e28b
title: Occurrence Download

description: A dataset containing 33 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.hascoordinate = TRUE
 AND occurrence.hasgeospatialissues = FALSE
 AND occurrence.occurrencestatus = 'PRESENT'
 AND GBIF_STRINGARRAYCONTAINS(occurrence.classifications['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c'], '4377502', TRUE)
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 33 records were derived from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000314-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5k56c
title: Data from: A complex evolutionary history in a remote archipelago: phylogeography and morphometrics of the Hawaiian endemic Ligia isopods

description: Compared to the striking diversification and levels of endemism observed
 in many terrestrial groups within the Hawaiian Archipelago, marine
 invertebrates exhibit remarkably lower rates of endemism and
 diversification. Supralittoral invertebrates restricted to specific
 coastal patchy habitats, however, have the potential for high levels of
 allopatric diversification. This is the case of Ligia isopods endemic to
 the Hawaiian Archipelago, which most likely arose from a rocky
 supralittoral ancestor that colonized the archipelago via rafting, and
 diversified into rocky supralittoral and inland lineages. A previous study
 on populations of this isopod from Oʻahu and Kauaʻi revealed high levels
 of allopatric differentiation, and suggested inter-island historical
 dispersal events have been rare. To gain a better understanding on the
 diversity and evolution of this group, we expanded prior phylogeographic
 work by incorporating populations from unsampled main Hawaiian Islands
 (Maui, Molokaʻi, Lanaʻi, and Hawaiʻi), increasing the number of gene
 markers (four mitochondrial and two nuclear genes), and conducting Maximum
 likelihood and Bayesian phylogenetic analyses. Our study revealed new
 lineages and expanded the distribution range of several lineages. The
 phylogeographic patterns of Ligia in the study area are complex, with
 Hawaiʻi, Oʻahu, and the Maui-Nui islands sharing major lineages, implying
 multiple inter-island historical dispersal events. In contrast, the oldest
 and most geographically distant of the major islands (Kauaʻi) shares no
 lineages with the other islands. Our results did not support the monophyly
 of all the supralittoral lineages (currently grouped into L. hawaiensis),
 or the monophyly of the terrestrial lineages (currently grouped into L.
 perkinsi), implying more than one evolutionary transition between coastal
 and inland forms. Geometric-morphometric analyses of three supralittoral
 clades revealed significant body shape differences among them. A taxonomic
 revision of Hawaiian Ligia is warranted. Our results are relevant for the
 protection of biodiversity found in an environment subject to high
 pressure from disturbances.
description: Hawaiian Ligia
 DataIncludes all
 morphometrics and molecular data used in the
 publication.
DOI: 10.5061/dryad.pr078
title: Data from: Demographic history and adaptation account for clock gene diversity in humans

description: Circadian clocks give rise to daily oscillations in behavior and
 physiological functions that often anticipate upcoming environmental
 changes generated by the Earth rotation. In model organisms a relationship
 exists between several genes affecting the circadian rhythms and latitude.
 We investigated the allele distributions at 116 000 single-nucleotide
 polymorphisms (SNPs) of 25 human clock and clock-related genes from the
 1000Genomes Project, and at a reference data set of putatively neutral
 polymorphisms. The global genetic structure at the clock genes did not
 differ from that observed at the reference data set. We then tested for
 evidence of local adaptation searching for FST outliers under both an
 island and a hierarchical model, and for significant association between
 allele frequencies and environmental variables by a Bayesian approach. A
 total of 230 SNPs in 23 genes, or 84 SNPs in 19 genes, depending on the
 significance thresholds chosen, showed signs of local adaptation, whereas
 a maximum of 190 SNPs in 23 genes had significant covariance with one or
 more environmental variables. Only two SNPs from two genes (NPAS2 and
 AANAT) exhibit both elevated population differentiation and covariance
 with at least one environmental variable. We then checked whether the SNPs
 emerging from these analyses fall within a set of candidate SNPs
 associated with different chronotypes or sleep disorders. Correlation of
 five such SNPs with environmental variables supports a selective role of
 latitude or photoperiod, but certainly not a major one.
description: candidate.maf.005_mapplink map file for Bayescan, Arlequin and Bayenv - candidate datasetcandidate.maf.005.mapcandidate.maf.005_pedplink ped file for Bayescan, Arlequin and Bayenv - candidate datasetcandidate.maf.005.pedreference.maf.005_mapplink map file for Bayescan and Bayenv - reference datasetreference.maf.005.mapreference.maf.005_pedplink ped file for Bayescan and Bayenv - reference datasetreference.maf.005.pedreference_thinned_mapplink map file for Arlequin - reference datasetreference_thinned.mapreference_thinned_pedplink ped file for Arlequin - reference datasetreference_thinned.pedcandidate_005_arpInput file for Arlequin - candidate datasetcandidate_005.arpreference_thinned_arpInput file for Arlequin - reference datasetreference_thinned.arpcandidate.maf.005_bayescanInput file for BayeScan - candidate datasetcandidate.maf.005reference.maf.005_bayescanInput file for BayeScan - reference datasetreference.maf.005EnvVar_phase3Values of the environmental variables used as input for Bayenvcandidate.maf.005_bayenvInput file for Bayenv - candidate datasetcandidate.maf.005.bayenvreference.maf.005_bayenvInput file for Bayenv - reference datasetreference.maf.005.bayenvEnvironmentalVariables_phase3.xlsDetails of the environmental variabes used in Bayenv
DOI: 10.5061/dryad.r578p
title: Data from: Postcrania of the most primitive euprimate and implications for primate origins

description: The fossil record of early primates is largely comprised of dentitions.
 While teeth can indicate phylogenetic relationships and dietary
 preferences, they say little about hypotheses pertaining to the positional
 behavior or substrate preference of the ancestral crown primate. Here we
 report the discovery of a talus bone of the dentally primitive fossil
 euprimate Donrussellia provincialis. Our comparisons and analyses indicate
 that this talus is more primitive than that of other euprimates. It lacks
 features exclusive to strepsirrhines, like a large medial tibial facet and
 a sloping fibular facet. It also lacks the medially positioned
 flexor-fibularis groove of extant haplorhines. In these respects, the
 talus of D. provincialis comes surprisingly close to that of the
 pen-tailed treeshrew, Ptilocercus lowii, and extinct plesiadapiforms for
 which tali are known. However, it differs from P. lowii and is more like
 other early euprimates in exhibiting an expanded posterior trochlear shelf
 and deep talar body. In overall form, the bone approximates more leaping
 reliant euprimates. The phylogenetically basal signal from the new fossil
 is confirmed with cladistic analyses of two different character matrices,
 which place D. provincialis as the most basal strepsirrhine when the new
 tarsal data are included. Interpreting our results in the context of other
 recent discoveries, we conclude that the lineage leading to the ancestral
 euprimate had already become somewhat leaping specialized, while certain
 specializations for the small branch niche came after crown primates began
 to radiate.
description: RTI_dataset_RI428This file contains five *.rti files of the specimen MNHN RI 428 of Donrussellia provincialis in different orientation views (dorsal, lateral, medial, plantar and posterior). This specimen has been described and analyzed in the associated paper "Postcrania of the most primitive euprimate and implications for primate origins". This right talus is the first discovery of non-dental skeletal material of Donrussellia provincialis, the most primitive fossil species belonging to the order Euprimates at present time. These RTI files enable a visualisation of the specimen in a high resolution photographic quality, for five orientations, with interactive re-lighting capturing surface, shape and color.
DOI: 10.5061/dryad.mr0v3
title: Data from: Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans

description: Genetic diversity is maintained by continuing generation and removal of
 variants. While examining over 800,000 DNA variants in wild isolates of
 Caenorhabditis elegans, we made a discovery that the proportions of
 variant types are not constant across the C. elegans genome. The variant
 proportion is defined as the fraction of a specific variant type (e.g.
 single nucleotide polymorphism (SNP) or indel) within a broader set of
 variants (e.g. all variants or all non-SNPs). The proportions of most
 variant types show a correlation with the recombination rate. These
 correlations can be explained as a result of a concerted action of two
 mutation mechanisms, which we named Morgan and Sanger mechanisms. The two
 proposed mechanisms act according to the distinct components of
 recombination rate, specifically the genetic and physical distance.
 Regression analysis was used to explore the characteristics and
 contributions of the two mutation mechanisms. According to our model,
 ~20–40% of all mutations in C. elegans wild populations are derived from
 programmed meiotic double strand breaks, which precede chromosomal
 crossovers and thus may be the point of origin for the Morgan mechanism. A
 substantial part of the known correlation between the recombination rate
 and variant distribution appears to be caused by the mutations generated
 by the Morgan mechanism. Mathematically integrating the mutation model
 with background selection model gives a more complete depiction of how the
 variant landscape is shaped in C. elegans. Similar analysis should be
 possible in other species by examining the correlation between the
 recombination rate and variant landscape within the context of our
 mutation model.
description: HwangWangPLOScomp.tarContains R scripts used for the analysis presented in the associated manuscript along with the source files needed to run the scripts.
DOI: 10.5061/dryad.f6qb7c5
title: Data from: Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea)

description: Gene flow is thought to impede genetic divergence and speciation by
 homogenizing genomes. Recent theory and research suggests that strong
 enough divergent selection can overpower gene flow, leading to islands of
 divergence. However, there are alternative explanations for these
 patterns. Independent evidence that islands of divergence are due to
 divergent selection would allow these explanations to be distinguished,
 but such evidence is scarce. Here we present multiple lines of evidence
 that islands of divergence in a pair of sister morning glory species,
 Ipomoea cordatotriloba and I. lacunosa, are the outcome of divergent
 selection in the face of gene flow. We analyzed a SNP dataset across the
 genome to assess the amount of gene flow, resistance to introgression, and
 patterns of selection on genes resistant to introgression. We show that
 differentiation between the two species is much lower in sympatry than in
 allopatry, consistent with gene flow between the species in sympatry. In
 addition, highly differentiated SNPs were subject to divergent selection.
 Finally, despite gene flow in sympatry, SNPs that are highly
 differentiated in allopatry are resistant to homogenization in sympatry.
 Our investigation reveals the complex interplay between selection and gene
 flow that can occur during the early stages of speciation.
description: APL Pipeline
 IIIAPL analysis
 scripts.I. lacunosa draft
 assemblyThe I. lacunosa draft
 genome assembly, generated from PacBio assembled with CANU and polished
 with Illumina using Pilon.lacunosa_genome_070416.fastaJG_LacRef_QD_DP_XTOME_SNPS
DOI: 10.26021/canterburynz.31129912
title: Taxonomy and conservation genomic project of the Senecio matatini complex using GBS data

description: GBS data from Samiksha Patel's MSc project on the taxonomy and conservation genomics of the Senecio matatini complex.
DOI: 10.26021/canterburynz.31129912.v1
title: Taxonomy and conservation genomic project of the Senecio matatini complex using GBS data

description: GBS data from Samiksha Patel's MSc project on the taxonomy and conservation genomics of the Senecio matatini complex.
DOI: 10.5061/dryad.3kc345s
title: Data from: The role of metalloproteases in fertilisation in the ascidian Ciona robusta

description: In the ascidian Ciona robusta (formerly C. intestinalis type A), the
 mechanism underlying sperm penetration through the egg investment remains
 unknown. We previously reported that proteins containing both an astacin
 metalloprotease domain and thrombospondin type 1 repeats are abundant in
 the sperm surface protein-enriched fraction of C. robusta. Here we
 investigated the involvement of those proteins in fertilisation. We
 refined the sequences of astacin metalloproteases, confirmed that five of
 them are present in the sperm, and labelled them as tunicate astacin and
 thrombospondin type 1 repeat-containing (Tast) proteins. Fertilisation of
 C. robusta eggs was potently inhibited by a metalloprotease inhibitor
 GM6001. The eggs cleaved normally when they were vitelline coat-free or
 the inhibitor was added after insemination. Furthermore, vitelline coat
 proteins were degraded after incubation with intact sperm. These results
 suggest that sperm metalloproteases are indispensable for fertilisation,
 probably owing to direct or indirect mediation of vitelline-coat digestion
 during sperm penetration. TALEN-mediated knockout of Tast genes and the
 presence of GM6001 impaired larval development at the metamorphic stage,
 suggesting that Tast gene products play a key role in late development.
description: SREP-18-29283B_mass_spectraThe raw mass spectra (ThermoFisher RAW files) and the spectra converted to mascot generic format acquired from vitelline coat protein bands shown in Fig. 2.
DOI: 10.5061/dryad.qp499
title: Data from: The application of optical coherence tomography to image subsurface tissue structure of Antarctic krill Euphausia superba

description: Many small open ocean animals, such as Antarctic krill, are an important
 part of marine ecosystems. To discover what will happen to animals such as
 krill in a changing ocean, experiments are run in aquaria where conditions
 can be controlled to simulate water characteristics predicted to occur in
 the future. The response of individual animals to changing water
 conditions can be hard to observe, and with current observation techniques
 it is very difficult to follow the progress of an individual animal
 through its life. Optical coherence tomography (OCT) is an optical imaging
 technique that allows images at high resolution to be obtained from depths
 up to a few millimeters inside biological specimens. It is compatible with
 in vivo imaging and can be used repeatedly on the same specimens. In this
 work, we show how OCT may be applied to post mortem krill samples and how
 important physiological data such as shell thickness and estimates of
 organ volume can be obtained. Using OCT we find an average value for the
 thickness of krill exoskeleton to be (30±4) µm along a 1 cm length of the
 animal body. We also show that the technique may be used to provide
 detailed imagery of the internal structure of a pleopod joint and provide
 an estimate for the heart volume of (0.73±0.03) mm3.
description: Archive of data of OCT
 on Euphasia superbaThis .zip file contains
 the OCT data used to obtain quantitative measurements and to produce 3D
 images. The MATLAB cods used to rescale the data, produce movies and
 obtain automated estimates for physiological features are also
 provided.OCT Euphausia
 superba.zip