cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mp818
title: Data from: Resolving recent plant radiations: power and robustness of genotyping-by-sequencing

description: Disentangling species boundaries and phylogenetic relationships within
 recent evolutionary radiations is a challenge due to the poor
 morphological differentiation and low genetic divergence between species,
 frequently accompanied by phenotypic convergence, inter-specific gene flow
 and incomplete lineage sorting. Here we employed a
 genotyping-by-sequencing (GBS) approach, in combination with morphometric
 analyses, to investigate a small western Mediterranean clade in the
 flowering plant genus Linaria that radiated in the Quaternary. After
 confirming the morphological and genetic distinctness of eight species, we
 evaluated the relative performances of concatenation and coalescent
 methods to resolve phylogenetic relationships. Specifically, we focused on
 assessing the robustness of both approaches to variations in the parameter
 used to estimate sequence orthology (clustering threshold). Concatenation
 analyses suffered from strong systematic bias, as revealed by the high
 statistical support for multiple alternative topologies depending on
 clustering threshold values. By contrast, topologies produced by two
 coalescent-based methods (NJst, SVDquartets) were robust to variations in
 the clustering threshold. Reticulate evolution may partly explain
 incongruences between NJst, SVDquartets and concatenated trees.
 Integration of morphometric and coalescent-based phylogenetic results
 revealed (1) extensive morphological divergence associated with recent
 splits between geographically close or sympatric sister species, and (2)
 morphological convergence in geographically disjunct species. These
 patterns are particularly true for floral traits related to pollinator
 specialisation, including nectar spur length, tube width and corolla
 colour, suggesting pollinator-driven diversification. Given its relatively
 simple and inexpensive implementation, GBS is a promising technique for
 the phylogenetic and systematic study of recent radiations, but care must
 be taken to evaluate the robustness of results to variation of data
 assembly parameters.
description: Online
 AppendicesOnline Appendices 1 and
 2Supplementary
 FiguresSupplementary Figures
 S1-S9Supplementary
 TablesSupplementary Tables
 S1-S6SNP
 matricesUnlinked SNP matrices
 used in genetic structure analyses. See text for dataset
 nomenclatureSNPs.zipAllele filesSequence datasets used in phylogenetic analyses. Allele files produced by pyRAD are provided. See text for dataset nomenclaturealleles.zip
DOI: 10.5061/dryad.q1cv6
title: Data from: Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds

description: We used genotype data from the caprine 50k Illumina BeadChip for the
 assessment of genetic diversity within and between 10 local Swiss goat
 breeds. Three different cluster methods allowed the goat samples to be
 assigned to the respective breed groups, whilst the samples of Nera
 Verzasca and Tessin Grey goats could not be differentiated from each
 other. The results of the different genetic diversity measures show that
 Appenzell, Toggenburg, Valais and Booted goats should be prioritized in
 future conservation activities. Furthermore, we examined runs of
 homozygosity (ROH) and compared genomic inbreeding coefficients based on
 ROH (FROH) with pedigree-based inbreeding coefficients (FPED). The linear
 relationship between FROH and FPED was confirmed for goats by including
 samples from the three main breeds (Saanen, Chamois and Toggenburg goats).
 FROH appears to be a suitable measure for describing levels of inbreeding
 in goat breeds with missing pedigree information. Finally, we derived
 selection signatures between the breeds. We report a total of 384 putative
 selection signals. The 25 most significant windows contained genes known
 for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2,
 IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative
 genes involved in the formation of populations, which might have been
 selected for adaptation to the alpine environment, are highlighted. The
 results provide a contemporary background for the management of genetic
 diversity in local Swiss goat breeds.
description: goat_data2_dryadGenotypes of 473 Swiss goats and 48'019 SNPs in plink transposed file Format (.tped).goat_data2_dryadthe corresponding tfam file
DOI: 10.5061/dryad.bk0rd
title: Data from: Effects of habitat quality and access management on the density of a recovering grizzly bear population

description: Human activities have dramatic effects on the distribution and abundance
 of wildlife. Increased road densities and human presence in wilderness
 areas have elevated human-caused mortality of grizzly bears and reduced
 bears' use. Management agencies frequently attempt to reduce
 human-caused mortality by managing road density and thus human access, but
 the effectiveness of these actions is rarely assessed. We combined
 systematic, DNA-based mark–recapture techniques with spatially explicit
 capture–recapture models to estimate population size of a threatened
 grizzly bear population (Kettle–Granby), following management actions to
 recover this population. We tested the effects of habitat and road density
 on grizzly bear population density. We tested both a linear and
 threshold-based road density metric and investigated the effect of current
 access management (closing roads to the public). We documented an c. 50%
 increase in bear density since 1997 suggesting increased landscape and
 species conservation from management agencies played a significant role in
 that increase. However, bear density was lower where road densities
 exceeded 0.6 km/km2 and higher where motorised vehicle access had been
 restricted. The highest bear densities were in areas with large tracts of
 few or no roads and high habitat quality. Access management bolstered bear
 density in small areas by 27%. Synthesis and applications. Our spatially
 explicit capture–recapture analysis demonstrates that population recovery
 is possible in a multi-use landscape when management actions target
 priority areas. We suggest that road density is a useful surrogate for the
 negative effects of human land use on grizzly bear populations, but
 spatial configuration of roads must still be considered. Reducing roads
 will increase grizzly bear density, but restricting vehicle access can
 also achieve this goal. We demonstrate that a policy target of reducing
 human access by managing road density below 0.6 km/km2, while ensuring
 areas of high habitat quality have no roads, is a reasonable compromise
 between the need for road access and population recovery goals. Targeting
 closures to areas of highest habitat quality would benefit grizzly bear
 population recovery the most.
description: Granby_RNotebook R project for SECR analysis, all scripts and data within project   Read README text file
DOI: 10.5061/dryad.qt48g
title: Sensory feedback and coordinating asymmetrical landing in toads

description: Coordinated landing requires anticipating the timing and magnitude of
 impact, which in turn requires sensory input. To better understand how
 cane toads, well known for coordinated landing, prioritize visual versus
 vestibular feedback during hopping, we recorded forelimb joint angle
 patterns and electromyographic data from five animals hopping under two
 conditions that were designed to force animals to land with one forelimb
 well before the other. In one condition, landing asymmetry was due to
 mid-air rolling, created by an unstable takeoff surface. In this
 condition, visual, vestibular and proprioceptive information could be used
 to predict asymmetric landing. In the other, animals took off normally,
 but landed asymmetrically because of a sloped landing surface. In this
 condition, sensory feedback provided conflicting information, and only
 visual feedback could appropriately predict the asymmetrical landing.
 During the roll treatment, when all sensory feedback could be used to
 predict an asymmetrical landing, pre-landing forelimb muscle activity and
 movement began earlier in the limb that landed first. However, no such
 asymmetries in forelimb preparation were apparent during hops onto sloped
 landings when only visual information could be used to predict landing
 asymmetry. These data suggest that toads prioritize vestibular or
 proprioceptive information over visual feedback to coordinate landing.
description: Kinematic and forleimb
 EMG data of toads landing asymmetricallyAllRollData-3-30 Nov
 2015.csvDigitized points from
 high speed video of toads landing asymmetricallyRollCSVTrigdata10 Mar
 2016.matEMG data from m.anconeus
 of cane toads during hops with asymmetric landingsComplied EMG data for
 each toad for each hop from the m. anconeus muscle of the forelimb during
 hops with asymmetric landings. For further details see the
 readMeemgdataInt28 Nov
 2015.matWhich EMG trace numbers
 correspond to which musclesMuscleDataRoll.csvMatlab file with gui used to do calculationsMatlab file with gui used to complie data, do calculations and provide a user interface to identify hop eventsViewData6.mMatlab file used to compile data from digitized dataReadCSVsTrig.mR markdown file used to do statistics and generate most of the manuscriptRoll2.Rmd
DOI: 10.15468/dl.55sm9w
title: Occurrence Download

description: A dataset containing 239529 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is DFO Arctic Metabarcoding (COI) 2015-2019"
 ]
}

 The dataset includes 239529 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000400-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7842r
title: Data from: Population connectivity and genetic structure of burbot (Lota lota) populations in the Wind River Basin, Wyoming

description: Burbot (Lota lota) occur in the Wind River Basin in central Wyoming, USA,
 at the southwestern extreme of the species’ native range in North America.
 The most stable and successful of these populations occur in six glacially
 carved mountain lakes on three different tributary streams and one large
 main stem impoundment (Boysen Reservoir) downstream from the tributary
 populations. Burbot are rarely found in connecting streams and rivers,
 which are relatively small and high gradient, with a variety of potential
 barriers to upstream movement of fish. We used high-throughput genomic
 sequence data for 11,197 SNPs to characterize the genetic diversity,
 population structure, and connectivity among burbot populations on the
 Wind River system. Fish from Boysen Reservoir and lower basin tributary
 populations were genetically differentiated from those in the upper basin
 tributary populations. In addition, fish within the same tributary streams
 fell within the same genetic clusters, suggesting there is movement of
 fish between lakes on the same tributaries but that populations within
 each tributary system are isolated and genetically distinct from other
 populations. Observed genetic differentiation corresponded to natural and
 anthropogenic barriers, highlighting the importance of barriers to fish
 population connectivity and gene flow in human-altered linked lake-stream
 habitats.
description: VCF
 fileThis is a .vcf file
 produced by calling variant genetic sites using samtools and bcftools. For
 each variant site identified, we required that &gt;60% of all individuals
 had 1 or more read at that locus.variants_0.6.vcfentropy_variants0.6Input file for analysis with the "entropy" model. This file is a filtered version of the VCF file, including genotype likelihoods for loci with MAF&gt;1%. Additionally, we randomly selected 1 SNP per contig for contigs with multiple variant sites, to ensure independence of SNPs.split_scaffold_burbot_ref_long_94Because there are no existing genomic resources for burbot, we constructed an artificial reference genome using smng (Seq- Man NGen, DNAstar), using 25 million reads. This artificial reference genome contains 53,789 contigs. We used this assembly as a template to for a reference-based assembly with bwa.
DOI: 10.5061/dryad.tg8fq3c
title: Data from: DNA metabarcoding reveals changes in the contents of carnivorous plants along an elevation gradient

description: Resource variation along abiotic gradients influences subsequent trophic
 interactions and these effects can be transmitted through entire food
 webs. Interactions along abiotic gradients can provide clues as to how
 organisms will face changing environmental conditions, such as future
 range shifts. However, it is challenging to find replicated systems to
 study these effects. Phytotelmata, such as those found in carnivorous
 plants, are isolated aquatic communities and thus form a good model for
 the study of replicated food webs. Due to the degraded nature of the prey,
 molecular techniques provide a useful tool to study these communities. We
 studied the pitcher plant Sarracenia purpurea L. in allochthonous
 populations along an elevational gradient in the Alps and Jura. We
 predicted that invertebrate richness in the contents of the pitcher plants
 would decrease with increasing elevation, reflecting harsher environmental
 conditions. Using metabarcoding of the COI gene, we sequenced the
 invertebrate contents of these pitcher plants. We assigned Molecular
 Operational Taxonomic Units at ordinal level as well as recovering
 species-level data. We found small but significant changes in community
 composition with elevation. These recovered sequences could belong to
 invertebrate prey, rotifer inquilines, pollinators and other animals
 possibly living inside the pitchers. However, we found no directional
 trend or site-based differences in MOTU richness with elevational
 gradient. Use of molecular techniques for dietary or contents analysis is
 a powerful way to examine numerous degraded samples, although factors such
 as DNA persistence and the relationship to species presence still have to
 be completely determined.
description: CB_600mFasta file of MOTU from plants at 600mFR_800mFasta file of MOTU from plants at 800mLE_1000mFasta file of MOTU from plants at 1000mLT_1200mFasta file of MOTU from plants at 1200mLM_1450mFasta file of MOTU from plants at 1450mall_motuBinary datasheet of denovo MOTU by plant. This was used as the input datasheet for the mantel test and linear model in the manuscript.
DOI: 10.5061/dryad.r34k1
title: Data from: The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific manner

description: Type 2 diabetes is typified by insulin-resistance in adipose tissue,
 skeletal muscle, and liver, leading to chronic hyperglycemia.
 Additionally, obesity and type 2 diabetes are characterized by chronic
 low-grade inflammation. Membrane-associated RING-CH-1 (MARCH1) is an E3
 ubiquitin ligase best known for suppression of antigen presentation by
 dendritic and B cells. MARCH1 was recently found to negatively regulate
 the cell surface levels of the insulin receptor via ubiquitination. This,
 in turn, impaired insulin sensitivity in mouse models. Here, we report
 that MARCH1-deficient (knockout; KO) female mice exhibit excessive weight
 gain and excessive visceral adiposity when reared on standard chow diet,
 without increased inflammatory cell infiltration of adipose tissue. By
 contrast, male MARCH1 KO mice had similar weight gain and visceral
 adiposity to wildtype (WT) male mice. MARCH1 KO mice of both sexes were
 more glucose tolerant than WT mice. The levels of insulin receptor were
 generally higher in insulin-responsive tissues (especially the liver) from
 female MARCH1 KO mice compared to males, with the potential to account in
 part for the differences between male and female MARCH1 KO mice. We also
 explored a potential role for MARCH1 in human type 2 diabetes risk through
 genetic association testing in publicly-available datasets, and found
 evidence suggestive of association. Collectively, our data indicate an
 additional link between immune function and diabetes, specifically
 implicating MARCH1 as a regulator of lipid metabolism and glucose
 tolerance, whose function is modified by sex-specific factors.
description: Data from Figure 1: The
 E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage
 in a sex-specific mannerFigure1_data.xlsxData from Figure 2: The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific mannerFigure2_data.xlsxData from Figure 3: The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific mannerFigure3_data.xlsxData from Figure 4 (part 1 of 4): The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific mannerOriginal immunoblot images of liver samplesAdipose blots.tifData from Figure 4 (part 2 of 4): The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific mannerOriginal immunoblot images of muscle samplesMuscle blots.tifData from Figure 4 (part 3 of 4): The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific mannerOriginal immunoblot images of liver samplesLiver blots.tifData from Figure 4 (part 4 of 4): The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific mannerData for quantification of immunoblotsQuantification InsR blots.xlsx
DOI: 10.5061/dryad.13qh4
title: Data from: Do cost functions for tracking error generalize across tasks with different noise levels?

description: Control of human-machine interfaces are well modeled by computational
 control models, which take into account the behavioral decisions people
 make in estimating task dynamics and state for a given control law. This
 control law is optimized according to a cost function, which for the sake
 of mathematical tractability is typically represented as a series of
 quadratic terms. Recent studies have found that people actually use cost
 functions for reaching tasks that are slightly different than a quadratic
 function, but it is unclear which of several cost functions best explain
 human behavior and if these cost functions generalize across tasks of
 similar nature but different scale. In this study, we used an
 inverse-decision-theory technique to reconstruct the cost function from
 empirical data collected on 24 able-bodied subjects controlling a
 myoelectric interface. Compared with previous studies, this experimental
 paradigm involved a different control source (myoelectric control, which
 has inherently large multiplicative noise), a different control interface
 (control signal was mapped to cursor velocity), and a different task (the
 tracking position dynamically moved on the screen throughout each trial).
 Several cost functions, including a linear-quadratic; an inverted
 Gaussian, and a power function, accurately described the behavior of
 subjects throughout this experiment better than a quadratic cost function
 or other explored candidate cost functions (p&lt;0.05). Importantly,
 despite the differences in the experimental paradigm and a substantially
 larger scale of error, we found only one candidate cost function whose
 parameter was consistent with the previous studies: a power function (cost
 ∝ errorα) with a parameter value of α = 1.69 (1.53–1.78 interquartile
 range). This result suggests that a power-function is a representative
 function of user’s error cost over a range of noise amplitudes for
 pointing and tracking tasks.
description: dataPlease see the
 Readme.txt file for a description of the data.
DOI: 10.5061/dryad.c3q5c
title: Data from: Asynchronous demographic responses to Pleistocene climate change in Eastern Nearctic vertebrates

description: Pleistocene climatic cycles altered species distributions in the Eastern
 Nearctic of North America, yet the degree of congruent demographic
 response to the Pleistocene among codistributed taxa remains unknown. We
 use a hierarchical approximate Bayesian computational approach to test if
 population sizes across lineages of snakes, lizards, turtles, mammals,
 birds, salamanders and frogs in this region expanded synchronously to Late
 Pleistocene climate changes. Expansion occurred in 75% of 74 lineages, and
 of these, population size trajectories across the community were partially
 synchronous, with coexpansion found in at least 50% of lineages in each
 taxonomic group. For those taxa expanding outside of these synchronous
 pulses, factors related to when they entered the community, ecological
 thresholds or biotic interactions likely condition their timing of
 response to Pleistocene climate change. Unified timing of population size
 change across communities in response to Pleistocene climate cycles is
 likely rare in North America.
description: Fasta files for each
 taxon.Fasta files for each
 taxon used to generate Bayesian Skyline Plots and population genetic
 summary statistics.Fasta_Files.zipBayesian Skyline PlotsExcel sheet containing tabs for each lineage/taxon showing time, median, mean, and CI of Ne*t used to construct Bayesian Skyline Plots.Total_BSP.xlsxPrior and Posterior SamplesThe prior and posterior samples (and column headers) used for the hABC coexpansion models for each tetrapod grouphABC_Prior_Posterior_Samples.zipSupporting Material; Table S1Table S1: Columns show species used for demographic reconstruction, citations for original studies, Bayesian Skyline Plot profiles and slopes, mutation rate priors (low and high locus mutation rate) used in hABC analyses, Ne priors (low and high Ne) used in hABC analyses, generation times with citations, and genetic summary statistics used in the hABC models. This file is a CSV file and can be opened for viewing in Excel, Google Sheets, or any other spreadsheet software.Table_S1.xlsx
DOI: 10.5061/dryad.4h76d
title: Data from: Biophysically inspired model for functionalized nanocarrier adhesion to cell surface: roles of protein expression and mechanical factors

description: In order to achieve selective targeting of affinity–ligand coated
 nanoparticles to the target tissue, it is essential to understand the key
 mechanisms that govern their capture by the target cell. Next-generation
 pharmacokinetic (PK) models that systematically account for proteomic and
 mechanical factors can accelerate the design, validation and translation
 of targeted nanocarriers (NCs) in the clinic. Towards this objective, we
 have developed a computational model to delineate the roles played by
 target protein expression and mechanical factors of the target cell
 membrane in determining the avidity of functionalized NCs to live cells.
 Model results show quantitative agreement with in vivo experiments when
 specific and non-specific contributions to NC binding are taken into
 account. The specific contributions are accounted for through extensive
 simulations of multivalent receptor–ligand interactions, membrane
 mechanics and entropic factors such as membrane undulations and receptor
 translation. The computed NC avidity is strongly dependent on ligand
 density, receptor expression, bending mechanics of the target cell
 membrane, as well as entropic factors associated with the membrane and the
 receptor motion. Our computational model can predict the in vivo targeting
 levels of the intracellular adhesion molecule-1 (ICAM1)-coated NCs
 targeted to the lung, heart, kidney, liver and spleen of mouse, when the
 contributions due to endothelial capture are accounted for. The effect of
 other cells (such as monocytes, etc.) do not improve the model predictions
 at steady state. We demonstrate the predictive utility of our model by
 predicting partitioning coefficients of functionalized NCs in mice and
 human tissues and report the statistical accuracy of our model predictions
 under different scenarios.
description: SI-Draft-6Apr16Sections S1 to S4 and Figures S1 to S10SI-MoviesMovies M1 to M7