cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3g092
title: Data from: Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis

description: Identification of residue-residue contacts from primary sequence can be
 used to guide protein structure prediction. Using Escherichia coli CcdB as
 the test case, we describe an experimental method termed
 saturation-suppressor mutagenesis to acquire residue contact information.
 In this methodology, for each of five inactive CcdB mutants, exhaustive
 screens for suppressors were performed. Proximal suppressors were
 accurately discriminated from distal suppressors based on their phenotypes
 when present as single mutants. Experimentally identified putative
 proximal pairs formed spatial constraints to recover &gt;98% of
 native-like models of CcdB from a decoy dataset. Suppressor methodology
 was also applied to the integral membrane protein, diacylglycerol kinase A
 where the structures determined by X-ray crystallography and NMR were
 significantly different. Suppressor as well as sequence co-variation data
 clearly point to the X-ray structure being the functional one adopted in
 vivo. The methodology is applicable to any macromolecular system for which
 a convenient phenotypic assay exists.
description: CcdB_decoy_set.tar
DOI: 10.5061/dryad.5v3d715
title: Data from: How mountains shape biodiversity: the role of the Andes in biogeography, diversification, and reproductive biology in South America's most species‐rich lizard radiation (Squamata: Liolaemidae)

description: Testing hypotheses on the drivers of clade evolution and trait
 diversification provides insight into many aspects of evolutionary
 biology. Often, studies investigate only the intrinsic biological
 properties of organisms as the causes of diversity, however extrinsic
 properties of a clade’s environment, particularly geological history, may
 also offer compelling explanations. The Andes are a young mountain chain
 known to have shaped many aspects of climate and diversity of South
 America. The Liolaemidae are a radiation of South American reptiles with
 over 300 species found across all biomes and with similar numbers of
 egg-laying and live-bearing species. Using the most complete dated
 phylogeny of the family, we tested the role of Andean uplift in the
 biogeography, diversification patterns, and parity mode of the
 Liolaemidae. We find that the Andes has promoted lineage diversification
 and acted as a species pump into surrounding biomes. We also find strong
 support for the role of Andean uplift in boosting the species diversity of
 these lizards via allopatric fragmentation. Finally, we find repeated
 shifts in parity mode associated with changing thermal niches, with
 live-bearing favored in cold climates and egg-laying favoured in warm
 climates. Importantly, we find evidence for possible reversals to
 oviparity, an evolutionary transition believed to be extremely rare.
description: Liolaemidae trees from
 posteriorTrees sampled from
 posterior distribution of Bayesian analysis performed on BEAST
 2LiolaemidaeDec17Combined_green.treesLiolaemidae Maximum Clade Credibility TreeLiolaemidaeDec17Combined_greenMCC.tre
DOI: 10.5061/dryad.4k2t07s
title: Data from: Genomic signatures of parasite-driven natural selection in north European Atlantic salmon (Salmo salar)

description: Understanding the genomic basis of host-parasite adaptation is important
 for predicting the long-term viability of species and developing
 successful management practices. However, in wild populations, identifying
 specific signatures of parasite-driven selection often presents a
 challenge, as it is difficult to unravel the molecular signatures of
 selection driven by different, but correlated, environmental factors.
 Furthermore, separating parasite-mediated selection from similar
 signatures due to genetic drift and population history can also be
 difficult. Populations of Atlantic salmon (Salmo salar L.) from northern
 Europe have pronounced differences in their reactions to the parasitic
 flatworm Gyrodactylus salaris Malmberg 1957 and are therefore a good model
 to search for specific genomic regions underlying inter-population
 differences in pathogen response. We used a dense Atlantic salmon SNP
 array, along with extensive sampling of 43 salmon populations representing
 the two G. salaris response extremes (extreme susceptibility vs
 resistant), to screen the salmon genome for signatures of directional
 selection while attempting to separate the parasite effect from other
 factors. After combining the results from two independent genome scan
 analyses, 57 candidate genes potentially under positive selection were
 identified, out of which 50 were functionally annotated. This candidate
 gene set was shown to be functionally enriched for lymph node development,
 focal adhesion genes and anti-viral response, which suggests that the
 regulation of both innate and acquired immunity might be an important
 mechanism for salmon response to G. salaris. Overall, our results offer
 insights into the apparently complex genetic basis of pathogen
 susceptibility in salmon and highlight methodological challenges for
 separating the effects of various environmental factors
description: Zueva_etal_2018_allelotyping.tarAllelotyping data for 220,000 SNPs (readme file inside package)Zueva_etal_2018_Bayenv2.0_and_Bayescan2.1_data.tarBayenv2.0_and_Bayescan2.1_data (readme file inside package)Zueva_etal_2018_code&files_for_pictures.tarcode&files_for_pictures (readme file inside package)
DOI: 10.5061/dryad.770mc
title: Data from: Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

description: The genomic causes and effects of divergent ecological selection during
 speciation are still poorly understood. Here we report the discovery and
 detailed characterization of early-stage adaptive divergence of two
 cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater
 lake in Tanzania. The ecomorphs differ in depth preference, male breeding
 color, body shape, diet, and trophic morphology. With whole-genome
 sequences of 146 fish, we identified 98 clearly demarcated genomic
 “islands” of high differentiation and demonstrated the association of
 genotypes across these islands with divergent mate preferences. The
 islands contain candidate adaptive genes enriched for functions in sensory
 perception (including rhodopsin and other twilight-vision–associated
 genes), hormone signaling, and morphogenesis. Our study suggests
 mechanisms and genomic regions that may play a role in the closely related
 mega-radiation of Lake Malawi.
description: SNP chip (Sequenom
 MassARRAY) primersPrimers for the SNP chip
 used in the mate-choice experiments (Figure 4; Table
 S10).I1150_cichlid_design_PCR_primers_sorted_used.txtAll whole-genome variant calls (after BEAGLE genotype refinement)The final product of our variant calling pipeline; obtained as described under: "Variant calling, filtering, and genotype refinement" in Supplementary Methods. This file includes both SNPs and indels. High coverage (15x) Massoko littoral and benthic samples are denoted by "HC" in sample names.Massoko_Dryad_VCF_final.vcf.gzMain whole genome phylogenetic treeFigure 2AMassoko_mainWGtree_forDryad.nexusBootstrap replicates for whole genome phylogenetic treeBootstrap replicates for Figure 2AMassoko_bootstrapReplicates_forDryad.nexus
DOI: 10.5061/dryad.r7q2s
title: Data from: A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.)

description: PREMISE OF THE STUDY: Underutilized crops, such as breadfruit (Artocarpus
 altilis, Moraceae) have the potential to improve global food security.
 Humans have artificially selected many cultivars of breadfruit since its
 domestication began approximately 3,500 years ago. The goal of this
 research is to identify transcriptomic signals of positive selection and
 to develop genomic resources that may facilitate the development of
 improved breadfruit cultivars in the future. METHODS: A reference
 transcriptome of breadfruit was assembled de novo and annotated.
 Twenty-four transcriptomes of breadfruit and its wild relatives were
 generated and analyzed to reveal signals of positive selection that may
 have resulted from local adaptation or natural selection. Emphasis was
 placed on MADS-box genes, which are important because they often regulate
 fruiting timing and structures, and carotenoids biosynthesis genes, which
 can impact the nutritional quality of the fruit. KEY RESULTS: Over 1,000
 genes showed signals of positive selection, and these genes were enriched
 for localization to plastids. Nucleotide sites and individuals under
 positive selection were discovered in MADS-box genes and carotenoid
 biosynthesis genes, with several sites located in cofactor or DNA-binding
 domains. A McDonald-Kreitman test comparing wild to cultivated samples
 revealed selection in one of the carotenoid biosynthesis genes, abscisic
 acid 8'-hydroxylase 3. CONCLUSIONS: This research highlights some of
 the many genes that may have been intentionally or unintentionally
 selected for during the human-mediated dispersal of breadfruit and
 stresses the importance of conserving a varied germplasm collection. It
 has revealed candidate genes for further study and produced new genomic
 resources for breadfruit.
description: XML file for SNAPP
 analysisRandom sample of one SNP
 per locus for Artocarpus camansi and Artocarpus altilis in XML format for
 use in SNAPP analysis.camansi_altilis_snapp.xmlbreadfruit vcfSequences were aligned to Artocarpus camansi draft genome with bwa v0.6.2 mem, called separately for triploids and diploids with GATK v3.2-2 HaplotypeCaller, and hard filtered according to GATK’s recommendations.breadfruit.vcf.gzbreadfruit assembliesAssemblies for nine A. altilis, seven A. camansi, one A. mariannensis, and seven A. altilis × A. mariannensis hybrid samples. Raw reads were trimmed using Trimmomatic v0.30 to remove low quality bases, adapter sequences, and other sequencing artifacts. Poly-A and poly-T tails were removed with Trimest vEMBOSS:6.6.0.0. Trimmed paired and unpaired reads were assembled using Trinity vr2013-02-25 and only the longest isoform per component/subcomponent was retained.breadfruit_assemblies.tar
DOI: 10.5061/dryad.39n4g
title: Data from: Sex differences and allee effects shape the dynamics of sex-structured invasions

description: The rate at which a population grows and spreads can depend on individual
 behaviour and interactions with others. In many species with two sexes,
 males and females differ in key life history traits (e.g. growth,
 survival, dispersal), which can scale up to affect population rates of
 growth and spread. In sexually reproducing species, the mechanics of
 locating mates and reproducing successfully introduce further
 complications for predicting the invasion speed (spread rate), as both can
 change nonlinearly with density. Most models of population spread are
 based on one sex, or include limited aspects of sex differences. Here we
 ask whether and how the dynamics of finding mates interact with
 sex-specific life history traits to influence the rate of population
 spread. We present a hybrid approach for modelling invasions of
 populations with two sexes that links individual-level mating behaviour
 (in an individual-based model) to population-level dynamics (in an
 integrodifference equation model). We find that limiting the amount of
 time during which individuals can search for mates causes a demographic
 Allee effect which can slow, delay or even prevent an invasion.
 Furthermore, any sex-based asymmetries in life history or behaviour
 (skewed sex ratio, sex-biased dispersal, sex-specific mating behaviours)
 amplify these effects. In contrast, allowing individuals to mate more than
 once ameliorates these effects, enabling polygynandrous populations to
 invade under conditions where monogamously mating populations would fail
 to establish. We show that details of individuals’ mating behaviour can
 impact the rate of population spread. Based on our results, we propose a
 stricter definition of a mate-finding Allee effect, which is not met by
 the commonly used minimum mating function. Our modelling approach, which
 links individual and population-level dynamics in a single model, may be
 useful for exploring other aspects of individual behaviour that are
 thought to impact the rate of population spread.
description: readmeinstructions for using
 code and simulation data herefiles_plotfiguresContains Matlab code (.m files) for plotting the figures.files_calc_matingfunctionsContains Matlab code (.m files) for calculating the mating functions used in model simulations, and the corresponding data files (matfiles).
DOI: 10.5061/dryad.5302r
title: Data from: In the mood: the dynamics of collective sentiments on Twitter

description: We study the relationship between the sentiment levels of Twitter users
 and the evolving network structure that the users created by @-mentioning
 each other. We use a large dataset of tweets to which we apply three
 sentiment scoring algorithms, including the open source SentiStrength
 program. Specifically we make three contributions. Firstly, we find that
 people who have potentially the largest communication reach (according to
 a dynamic centrality measure) use sentiment differently than the average
 user: for example, they use positive sentiment more often and negative
 sentiment less often. Secondly, we find that when we follow structurally
 stable Twitter communities over a period of months, their sentiment levels
 are also stable, and sudden changes in community sentiment from one day to
 the next can in most cases be traced to external events affecting the
 community. Thirdly, based on our findings, we create and calibrate a
 simple agent-based model that is capable of reproducing measures of
 emotive response comparable with those obtained from our empirical
 dataset.
description: IntheMoodDataThis dataset contains several dynamic mention networks obtained from a sample of UK Twitter users. The content of each individual file is described in ReadMe.
DOI: 10.5061/dryad.sr14q
title: Data from: Population genomic signatures of divergent adaptation, gene flow, and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes

description: Adaptive radiations are an important source of biodiversity, and are often
 characterized by many speciation events in very short succession. It has
 been proposed that the high speciation rates in these radiations may be
 fuelled by novel genetic combinations produced in episodes of
 hybridisation among the young species. The role of such hybridisation
 events in the evolutionary history of a group can be assessed by comparing
 the phylogenetic relationships inferred from different subsets of loci.
 Here, we use a genome-wide sampling of SNPs identified within restriction
 site associated DNA (RAD) tags to investigate the genomic consistency of
 patterns of shared ancestry and adaptive divergence among five sympatric
 cichlid species of two genera, Pundamilia and Mbipia, which form part of
 the massive adaptive radiation of cichlids in the East African Lake
 Victoria. Species pairs differ along several axes: male nuptial
 colouration, feeding ecology, depth distribution, as well as the
 morphological traits that distinguish the two genera and more subtle
 morphological differences. Using outlier scan approaches, we identify
 signals of divergent selection between all species pairs with a number of
 loci showing parallel patterns in replicated contrasts either among genera
 or male colour types. We then create SNP subsets, which we expect to be
 characterised to different extents by selection history and neutral
 processes, and find contrasting population genomic and phylogenomic
 signals among these datasets. In an attempt to resolve the observed
 conflicts, we propose at least two intergeneric hybridisation events
 (between Mbipia spp. and Pundamilia spp.) in the evolutionary history of
 these five species that would have lead to the evolution of novel trait
 combinations and new species.
description: MbipiaPundamilia_M2MbipiaPundamilia_M1MbipiaPundamilia_M4
DOI: 10.5061/dryad.m67r6
title: Data from: A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

description: A prerequisite for the systems biology analysis of tissues is an accurate
 digital three-dimensional reconstruction of tissue structure based on
 images of markers covering multiple scales. Here, we designed a flexible
 pipeline for the multi-scale reconstruction and quantitative morphological
 analysis of tissue architecture from microscopy images. Our pipeline
 includes newly developed algorithms that address specific challenges of
 thick dense tissue reconstruction. Our implementation allows for a
 flexible workflow, scalable to high-throughput analysis and applicable to
 various mammalian tissues. We applied it to the analysis of liver tissue
 and extracted quantitative parameters of sinusoids, bile canaliculi and
 cell shapes, recognizing different liver cell types with high accuracy.
 Using our platform, we uncovered an unexpected zonation pattern of
 hepatocytes with different size, nuclei and DNA content, thus revealing
 new features of liver tissue organization. The pipeline also proved
 effective to analyse lung and kidney tissue, demonstrating its generality
 and robustness.
description: 3D ground truth models
 of liver tissue3D ‘ground truth’ images
 of idealized models of liver tissue ( 0.3 um x 0.3 um x 0.3u m per
 voxel)models.zip3D simulated microscopy images of liver tissue3D simulated microscopy images of liver tissue models with 10:1, 4:1 and 2:1 signal-to-noise ratios.model_image.zipScripts to generate 3D models and simulated imagesMotionTracking scripts to generate 3D ‘ground truth’ voxelated models and simulated microscopy images of mouse liver tissue. A test example is included.scripts_img_generation.zip
DOI: 10.5061/dryad.st7gm24
title: Data from: Distance, elevation, and environment as drivers of diversity and divergence in bumble bees across latitude and altitude

description: Identifying drivers of dispersal limitation and genetic differentiation is
 a key goal in biogeography. We examine patterns of population connectivity
 and genetic diversity using Restriction-site Associated DNA sequencing
 (RADseq) in two bumble bee species, Bombus vosnesenskii and Bombus
 bifarius across latitude and altitude in mountain ranges from California,
 Oregon, and Washington, U.S.A. Bombus vosnesenskii, which occurs across a
 broader elevational range at most latitudes, exhibits little population
 structure while B. bifarius, which occupies a relatively narrow higher
 elevation niche across most latitudes, exhibits much stronger population
 differentiation, although gene flow in both species is best explained by
 isolation with environmental niche resistance. A relationship between
 elevational habitat breadth and genetic diversity is also apparent, with
 B. vosnesenskii exhibiting relatively consistent levels of genetic
 diversity across its range, while B. bifarius has reduced genetic
 diversity at low latitudes, where it is restricted to high elevation
 habitat. The results of this study highlight the importance of the
 intersect between elevational range and habitat suitability in influencing
 population connectivity and suggest that future climate warming will have
 a fragmenting effect even on populations that are presently well
 connected, as they track their thermal niches upward in montane systems.
description: Jackson ME archived
 datadata_uploads.zip
DOI: 10.5061/dryad.vd561
title: Data from: Conventional analysis of trial-by-trial adaptation is biased: empirical and theoretical support using a Bayesian estimator

description: Research on human motor adaptation has often focused on how people adapt
 to self-generated or externally-influenced errors. Trial-by-trial
 adaptation is a person’s response to self-generated errors.
 Externally-influenced errors applied as catch-trial perturbations are used
 to calculate a person’s perturbation adaptation rate. Although these
 adaptation rates are sometimes compared to one another, we show through
 simulation and empirical data that the two metrics are distinct. We
 demonstrate that the trial-by-trial adaptation rate, often calculated as a
 coefficient in a linear regression, is biased under typical conditions. We
 tested 12 able-bodied subjects moving a cursor on a screen using a
 computer mouse. Statistically different adaptation rates arise when
 sub-sets of trials from different phases of learning are analyzed from
 within a sequence of movement results. We propose a new approach to
 identify when a person’s learning has stabilized in order to identify
 steady-state movement trials from which to calculate a more reliable
 trial-by-trial adaptation rate. Using a Bayesian model of human movement,
 we show that this analysis approach is more consistent and provides a more
 confident estimate than alternative approaches. Constraining analyses to
 steady-state conditions will allow researchers to better decouple the
 multiple concurrent learning processes that occur while a person makes
 goal-directed movements. Streamlining this analysis may help broaden the
 impact of motor adaptation studies, perhaps even enhancing their clinical
 usefulness.
description: All
 DataAll data associated with
 manuscript. Read the enclosed DataOverview.txt file for a description of
 individual files. CodeOverview.txt (also enclosed) describes the code used
 to generate and analyze the data that are found in the other data
 files.AllData.zipFigure Data and CodeMATLAB code to generate Figures 2-5 and the associated compiled data files. Compiled data extracted from raw data found in 'All Data' data file. Figure 1 simulation and figure generation file is found in the 'KpEstimationToolkit' data file.FigureDataAndCode.zipKp Estimation ToolkitCode to run Kp estimator and run simulations for manuscript. See other data files for more information.KpEstimationToolkit.zipSteady-state analysis toolkitCode to run the steady-state trial identification and analysis.EstimationToolkit.zipManuscript Code & DataDe-identified human subject data, Bayesian learner code and code to generate all figures. Code used to generate the significant difference markings on plots: Rob Campbell (2018). raacampbell/sigstar (https://www.github.com/raacampbell/sigstar), GitHub. Retrieved November 13, 2018. Code used to generate the shaded error bars on plots: Rob Campbell (2018). raacampbell/shadedErrorBar (https://github.com/raacampbell/shadedErrorBar), GitHub. Retrieved November 20, 2018.ManuscriptCode&Data.zip
DOI: 10.5061/dryad.40cd5ps
title: Data from: Screening of cytotoxic or cytostatic flavonoids with quantitative FUCCI-based cell cycle assay

description: The Fluorescence-Ubiquitin Cell Cycle Indicator (FUCCI) system can be used
 not only to study gene expression at a specific cell cycle stage, but also
 to monitor cell cycle transitions in real time. In this study, we used a
 single clone of FUCCI-expressing HeLa cells (FUCCI-HeLa cells) and
 monitored the cell cycle in individual live cells over time by determining
 the ratios between red fluorescence (RF) of RFP-Cdt1 and green
 fluorescence (GF) of GFP-Geminin. Cytotoxic and cytostatic compounds, the
 latter of which induced G2 or mitotic arrest, were identified based on
 periodic cycling of the RF/GF and GF/RF ratios in FUCCI-HeLa cells treated
 with anticancer drugs. With this cell cycle monitoring system, ten
 flavonoids were screened. Of these, apigenin and luteolin, which have a
 flavone backbone, were cytotoxic, whereas kaempferol, which has a flavonol
 backbone, was cytostatic and induced G2 arrest. In summary, we developed a
 system to quantitatively monitor the cell cycle in real time. This system
 can be used to identify novel compounds that modulate the cell cycle and
 to investigate structure–activity relationships.
description: Raw data of all
 figuresFigure raw
 data.zip