cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.53n6n
title: Data from: Late Cenozoic onset of the latitudinal diversity gradient of North American mammals

description: The decline of species richness from equator to pole, or latitudinal
 diversity gradient (LDG), is nearly universal among clades of living
 organisms, yet whether it was such a pervasive pattern in the geologic
 past remains uncertain. Here, we calculate the strength of the LDG for
 terrestrial mammals in North America over the past 65 My, using 27,903
 fossil occurrences of Cenozoic terrestrial mammals from western North
 America downloaded from the Paleobiology Database. Accounting for temporal
 and spatial variation in sampling, the LDG was substantially weaker than
 it is today for most of the Cenozoic and the robust modern LDG of North
 American mammals evolved only over the last 4 My. The strength of the LDG
 correlates negatively with global temperature, suggesting a role of global
 climate patterns in the establishment and maintenance of the LDG for North
 American mammals.
description: Paleobiology Database
 Mammalian Occurrence DataOccurrence data obtained
 from the Paleobiology Database (https://www.paleobiodb.org) on May 21,
 2015 (data were primarily derived from the North American Fossil Mammal
 Systematics Database;
 https://paleobiodb.org/cgi-bin/bridge.pl?page=OSA_3_North_American_mammals).allMammals-20150521-occs.csvR file of results of 10,000 pseudoreplicate analysesThese are the the results of our 10,000 pseudoreplicate analyses described in the paper. They can be loaded into the R environment by placing them into the working directory and using the command: load("ldg_rez_2My_10000_20151023.R")ldg_rez_2My_10000_20151023.RStable Isotope Data from Zachos et al. 2001These include the stable isotope data and dates used to calculate correlation between d18O and fossil slopes. All data are from Zachos J, Pagani M, Sloan L, Thomas E, Billups K (2001) Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292(5517):686–693.zachos2001.csvR-Script: Analysis codeThis contains the code for the analyses described in this paper. All optional settings required for analysis can be set in this script. This file also contains the code to build all the figures.ldg_pub.RR-Script: Supporting FunctionsThis file contains the R code for all of the supporting functions for the complete analysis.ldgSource_pub.R
DOI: 10.5061/dryad.118j2
title: Data from: Force and torque on spherical particles in micro-channel flows using computational fluid dynamics

description: To delineate the influence of hemodynamic force on cell adhesion
 processes, model in vitro fluidic assays that mimic physiological
 conditions are commonly employed. Herein, we offer a framework for
 solution of the three-dimensional Navier–Stokes equations using
 computational fluid dynamics (CFD) to estimate the forces resulting from
 fluid flow near a plane acting on a sphere that is either stationary or in
 free flow, and we compare these results to a widely used theoretical model
 that assumes Stokes flow with a constant shear rate. We find that while
 the full three-dimensional solutions using a parabolic velocity profile in
 CFD simulations yield similar translational velocities to those predicted
 by the theoretical method, the CFD approach results in approximately 50%
 larger rotational velocities over the wall shear stress range of
 0.1–5.0 dynes cm−2. This leads to an approximately 25% difference in force
 and torque calculations between the two methods. When compared with
 experimental measurements of translational and rotational velocities of
 microspheres or cells perfused in microfluidic channels, the CFD
 simulations yield significantly less error. We propose that CFD modelling
 can provide better estimations of hemodynamic force levels acting on
 perfused microspheres and cells in flow fields through microfluidic
 devices used for cell adhesion dynamics analysis.
description: Janus particle perfusion
 foot print data 0.5 dyn/cm^2Footprint data for Janus
 particle perfusion experiments. Used in experimental velocity
 calculations.20150902_JanusFITC particle
 perfusion_short chamber_0p5
 dynpcm2001.avi_footprintdata.txt
DOI: 10.5061/dryad.rb5s1
title: Data from: The ecology of an adaptive radiation of three-spined stickleback from North Uist, Scotland

description: There has been a large focus on the genetics of traits involved in
 adaptation, but knowledge of the environmental variables leading to
 adaptive changes is surprisingly poor. Combined use of environmental data
 with morphological and genomic data should allow us to understand the
 extent to which patterns of phenotypic and genetic diversity within a
 species can be explained by the structure of the environment. Here, we
 analyse the variation of populations of three-spined stickleback from 27
 freshwater lakes on North Uist, Scotland, that vary greatly in their
 environment, to understand how environmental and genetic constraints
 contribute to phenotypic divergence. We collected 35 individuals per
 population and 30 abiotic and biotic environmental parameters to
 characterize variation across lakes and analyse phenotype–environment
 associations. Additionally, we used RAD sequencing to estimate the genetic
 relationships among a subset of these populations. We found a large amount
 of phenotypic variation among populations, most prominently in armour and
 spine traits. Despite large variation in the abiotic environment, namely
 in ion composition, depth and dissolved organic Carbon, more phenotypic
 variation was explained by the biotic variables (presence of predators and
 density of predator and competitors), than by associated abiotic
 variables. Genetic structure among populations was partly geographic, with
 closer populations being more similar. Altogether, our results suggest
 that differences in body shape among stickleback populations are the
 result of both canalized genetic and plastic responses to environmental
 factors, which shape fish morphology in a predictable direction regardless
 of their genetic starting point.
description: depth_coordinatesGPS coordinates and depth of points used to calculate average depth and maximum depth for each lochGenomic_PCsindividual PC scores from the PCA performed on SNPsNUist_phenotypesIndividual phenotypic databatch_4_fresh.plinkInput file for fastStructure (file1 of 3)batch_4_fresh.plinkInput file for fastStructure (file 2 of 3)batch_4_fresh.plinkInput file for fastStructure (file 3 of 3)
DOI: 10.5061/dryad.sg1hs
title: Data from: Social behaviours and networks of vervet monkeys are influenced by gastrointestinal parasites

description: Substantial research has shown that while some parasite infections can be
 fatal to hosts, most infections are sub-clinical and non-lethal. Such
 sub-clinical infections can nonetheless have negative consequences for the
 long-term fitness of the host such as reducing juvenile growth and the
 host’s ability to compete for food and mates. With such effects, infected
 individuals are expected to exhibit behavioural changes. Here we use a
 parasite removal experiment to quantify how gastrointestinal parasite
 infections affect the behaviour of vervet monkeys (Chlorocebus aethiops)
 at Lake Nabugabo, Uganda. Behavioural profiles and the structure of
 nearest neighbour relationships varied significantly. As predicted, after
 deworming the duration of the resting events decreased, which is
 consistent with the idea that parasite infections are energetically
 costly. In contrast to what was predicted, we could not reject the null
 hypothesis and we observed no change in either the frequency or duration
 of grooming, but we found that the duration of travel events increased. A
 network analysis revealed that after deworming, individuals tended to have
 more nearest neighbours and hence probably more frequent interactions,
 with this effect being particularly marked for juveniles. The heightened
 response by juveniles may indicate that they are avoiding infected
 individuals more than other age classes because it is too costly to move
 energy away from growth. We consider that populations with high parasite
 burden may have difficulties developing social networks and behaviours
 that could have cascading effects that impact the population in general.
description: Nabugabo vervet
 observationsObservational data
 collected in the field at Lake Nabugabo, Uganda of Vervet monkeys
 (Chlorocebus aethiops) between June 2011 and April 2014. The data is
 stored created using excel and stored as a .xlsx. The column names are
 kept intuitive. Further codes used in the file can be found in the
 "Read Me" file.Nab_VT_Act_Master_forDryad.xlsx
DOI: 10.5061/dryad.db0r1
title: Data from: Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice

description: Phylogenetic trees can reveal the origins of endosymbiotic lineages of
 bacteria and detect patterns of co-evolution with their hosts. Although
 taxon sampling can greatly affect phylogenetic and co-evolutionary
 inference, most hypotheses of endosymbiont relationships are based on few
 available bacterial sequences. Here we examined how different sampling
 strategies of Gammaproteobacteria sequences affect estimates of the number
 of endosymbiont lineages in parasitic sucking lice (Insecta:
 Phthirapatera: Anoplura). We estimated the number of louse endosymbiont
 lineages using both newly obtained and previously sequenced 16S rDNA
 bacterial sequences and more than 42,000 16S rDNA sequences from other
 Gammaproteobacteria. We also performed parametric and nonparametric
 bootstrapping experiments to examine the effects of phylogenetic error and
 uncertainty on these estimates. Sampling of 16S rDNA sequences affects the
 estimates of endosymbiont diversity in sucking lice until we reach a
 threshold of genetic diversity, the size of which depends on the sampling
 strategy. Sampling by maximizing the diversity of 16S rDNA sequences is
 more efficient than randomly sampling available 16S rDNA sequences.
 Although simulation results validate estimates of multiple endosymbiont
 lineages in sucking lice, the bootstrap results suggest that the precise
 number of endosymbiont origins is still uncertain.
description: Alignment and
 Phylogenetic TreesThe Alignment consists
 of the masked 42,626 16SrDNA sequences sampled from Genbank
 Gammaproteobacteria as well as all known endosymbionts from lice including
 the newly sequenced taxa for this study: KX146199-KX146216. The tree files
 consists of 6 phylogenetic trees taken from different samples of the
 42,626 taxa. The reduced trees are consensus trees of sampled sequence
 from a clustering algorithm, selected to represent sequence diversity.
 Numbers on the names of these datasets indicate the stringency of
 clustering. For example Ribo.70.con.tre indicates the sequences were
 selected from clusters were each sequence in the cluster had to be at
 least 70% or more similar to each other. Ribo.80.con.tre means the tree
 was built from sequences clustered with 80% similarity or more. Finally
 Ribo.100.con.tre indicates 100% of the sequences were used in this
 tree.Alignment_and_Trees.zip
DOI: 10.6084/m9.figshare.30162868
title: EEG dataset of consumer- and research-grade systems

description: This dataset contains electroencephalography (EEG) recordings from 30 participants acquired using four consumer-grade devices (BrainLink Pro, NeuroNicle FX2, MindWave Mobile 2, Muse 2) and one research-grade device (DSI-24). Each participant completed four experimental paradigms: (1) eye blinks, (2) jaw clenching, (3) head movements with eyes open, and (4) head movements with eyes closed. All paradigms included pre-task resting-state EEG, task execution (20 repetitions at 3-second intervals), and post-task resting-state EEG.The dataset is intended to facilitate the evaluation of consumer-grade EEG devices in comparison with a research-grade system. It provides recordings suitable for assessing signal quality, validating the detection of neural features (e.g., alpha-band power), and examining the robustness of devices to movement-induced artifacts.Raw data are organized by participant in the sourcedata directory. A subset of noisy recordings excluded from analysis is not included in this release.
DOI: 10.6084/m9.figshare.30162868.v1
title: EEG dataset of consumer- and research-grade systems

description: This dataset contains electroencephalography (EEG) recordings from 30 participants acquired using four consumer-grade devices (BrainLink Pro, NeuroNicle FX2, MindWave Mobile 2, Muse 2) and one research-grade device (DSI-24). Each participant completed four experimental paradigms: (1) eye blinks, (2) jaw clenching, (3) head movements with eyes open, and (4) head movements with eyes closed. All paradigms included pre-task resting-state EEG, task execution (20 repetitions at 3-second intervals), and post-task resting-state EEG.The dataset is intended to facilitate the evaluation of consumer-grade EEG devices in comparison with a research-grade system. It provides recordings suitable for assessing signal quality, validating the detection of neural features (e.g., alpha-band power), and examining the robustness of devices to movement-induced artifacts.Raw data are organized by participant in the sourcedata directory. A subset of noisy recordings excluded from analysis is not included in this release.
DOI: 10.5061/dryad.96hr3
title: Data from: Adaptation to warmer climates by parallel functional evolution of CBF genes in Arabidopsis thaliana

description: The evolutionary processes and genetics underlying local adaptation at a
 specieswide level are largely unknown. Recent work has indicated that a
 frameshift mutation in a member of a family of transcription factors,
 C-repeat binding factors or CBFs, underlies local adaptation and freezing
 tolerance divergence between two European populations of Arabidopsis
 thaliana. To ask whether the specieswide evolution of CBF genes in
 Arabidopsis is consistent with local adaptation, we surveyed CBF variation
 from 477 wild accessions collected across the species’ range. We found
 that CBF sequence variation is strongly associated with winter temperature
 variables. Looking specifically at the minimum temperature experienced
 during the coldest month, we found that Arabidopsis from warmer climates
 exhibit a significant excess of nonsynonymous polymorphisms in CBF genes
 and revealed a CBF haplotype network whose structure points to multiple
 independent transitions to warmer climates. We also identified a number of
 newly described mutations of significant functional effect in CBF genes,
 similar to the frameshift mutation previously indicated to be locally
 adaptive in Italy, and find that they are significantly associated with
 warm winters. Lastly, we uncover relationships between climate and the
 position of significant functional effect mutations between and within CBF
 paralogs, suggesting variation in adaptive function of different
 mutations. Cumulatively, these findings support the hypothesis that
 disruption of CBF gene function is adaptive in warmer climates, and
 illustrate how parallel evolution in a transcription factor can underlie
 adaptation to climate.
description: complete_coding_at4g25470Coding region sequence for at4g25470 (CBF2) for all accessions used in this study.complete_coding_at4g25480Coding region sequence for at4g25470 (CBF3) for all accessions used in this study.complete_coding_at4g25490Coding region sequence for at4g25470 (CBF1) for all accessions used in this study.
DOI: 10.5061/dryad.s7r47
title: Data from: Faster and farther: wolf movement on linear features and implications for hunting behaviour

description: Predation by grey wolves Canis lupus has been identified as an important
 cause of boreal woodland caribou Rangifer tarandus caribou mortality, and
 it has been hypothesized that wolf use of human-created linear features
 such as seismic lines, pipelines and roads increases movement, resulting
 in higher kill rates. We tested if wolves select linear features and
 whether movement rates increased while travelling on linear features in
 north-eastern Alberta and north-western Saskatchewan using 5-min GPS
 (Global Positioning System) locations from twenty-two wolves in six packs.
 Wolves selected all but two linear feature classes, with the magnitude of
 selection depending on feature class and season. Wolves travelled two to
 three times faster on linear features compared to the natural forest.
 Increased average daily travelling speed while on linear features and
 increased proportion of steps spent travelling on linear features
 increased net daily movement rates, suggesting that wolf use of linear
 features can increase their search rate. Synthesis and applications. Our
 findings that wolves move faster and farther on human-created linear
 features can inform mitigation strategies intended to decrease predation
 on woodland caribou, a threatened species. Of the features that can
 realistically be restored, mitigation strategies such as silviculture and
 linear deactivation (i.e. tree-felling and fencing) should prioritize
 conventional seismic lines (i.e. cleared lines used for traditional oil
 and gas exploration) and pipelines, as they were selected by wolves and
 increased travelling speed, before low-impact seismic lines.
description: Zip file of RSF Data and
 Step DataData collected using GPS
 collars. RSF data includes 10 random/GPS location. Step data are lines
 connecting sequential 5 minute locations. RSF data: Data collected using
 GPS collars. Fields include a unique ID field (SEQID), animal identifier
 field (DEVICE_ID), season, year, if the GPS location is on (1) or off (0)
 a linear feature (LF), what type of feature (LF_TYPE), landcover(HABITAT),
 if its a use (1) or random (0) location (USE) and the conditional point ID
 (PNTID). Additionally elevation (ELEV) and linear feature density
 (LINE_DENSE) are included fields, but were not used in these analyses.
 Step Data: a unique identifier (Unique_ID), animal identifier (DEVICE_ID),
 datatime field (DT_GMT), year, season, if the location is on (1) or off
 (0) a linear feature (LF), location linear feature class (PT_LF_TYPE),
 location landcover (PT_HABITAT), Northing (X) and Easting (Y) of the
 location, length between successive locations (Shape_Leng), speed
 (STEPLENGTH), if the path is on (1) or off (0) a linear feature (PATH_LF),
 the linear feature class (PATH_LFTYP), and the proportion of the path
 within each landcover class (PTH_ **) where ** is the
 landcover.Dryad_Data.zip
DOI: 10.15468/dl.wq7q9f
title: Occurrence Download

description: A dataset containing 97 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Salix arbutifolia"
 ]
}

 The dataset includes 97 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001457-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9rp2b
title: Data from: A chromosome-level genome assembly of the Asian arowana, Scleropages formosus

description: Asian arowana (Scleropages formosus), an ancient teleost belonging to the
 Order Osteoglossomorpha, has been a valuable ornamental fish with some
 varieties. However, its biological studies and breeding germplasm have
 been remarkably limited by the lack of a reference genome. To solve these
 problems, here we report high-quality genome sequences of three common
 varieties of Asian arowana (the golden, red and green arowana). We firstly
 generated a chromosome-level genome assembly of the golden arowana, on
 basis of the genetic linkage map constructed with the restriction
 site-associated DNA sequencing (RAD-seq). In addition, we obtained draft
 genome assemblies of the red and green varieties. Finally, we annotated
 22,016, 21,256 and 21,524 protein-coding genes in the genome assemblies of
 golden, red and green varieties respectively. Our data were deposited in
 publicly accessible repositories to promote biological research and
 molecular breeding of Asian arowana.
description: Three_varieties_of_arowana_gene_annotation_gffThis '.zip' file contains the three "gff" format annotation files of the genome assemblies of golden, red and green arowana varieties, respectively.Three_varieties_of_arowana_gene_annotation_proteinThis ".zip" file contains the three "fasta" format protein files of the genome assemblies of golden, red and green arowana varieties, respectively.Golden_arowana_chromosomes_gene_annotationThis "gff" format file contains the gene annotation of golden arowana chromosomes.
DOI: 10.5061/dryad.1v5d3
title: Data from: Dietary breadth is positively correlated with venom complexity in cone snails

description: Although diet is believed to be a major factor underlying the evolution of
 venom, few comparative studies examine both venom composition and diet
 across a radiation of venomous species. Cone snails within the family,
 Conidae, comprise more than 700 species of carnivorous marine snails that
 capture their prey by using a cocktail of venomous neurotoxins (conotoxins
 or conopeptides). Venom composition across species has been previously
 hypothesized to be shaped by (a) prey taxonomic class (i.e., worms,
 molluscs, or fish) and (b) dietary breadth. We tested these hypotheses
 under a comparative phylogenetic framework using ecological data from past
 studies in conjunction with venom duct transcriptomes sequenced from 12
 phylogenetically disparate cone snail species, including 10 vermivores
 (worm-eating), one molluscivore, and one generalist.
description: all_extractedseq_renamedAll transcripts categorized as venom from all species. The headers are sequence ID, species, gene superfamily, and coverage.conus_phylogenynexus file used for phylogenetic analysisscriptsscripts and readme files used in processing of all data. Same directory structure kept.expression_resultsExpression result output from RSEM for all species.