cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6140j
title: Data from: Empirical and Bayesian approaches to fossil-only divergence times: a study across three reptile clades

description: Estimating divergence times on phylogenies is critical in paleontological
 and neontological studies. Chronostratigraphically-constrained fossils are
 the only direct evidence of absolute timing of species divergence. Strict
 temporal calibration of fossil-only phylogenies provides minimum
 divergence estimates, and various methods have been proposed to estimate
 divergences beyond these minimum values. We explore the utility of
 simultaneous estimation of tree topology and divergence times using BEAST
 tip-dating on datasets consisting only of fossils by using relaxed
 morphological clocks and birth-death tree priors that include serial
 sampling (BDSS) at a constant rate through time. We compare BEAST results
 to those from the traditional maximum parsimony (MP) and undated Bayesian
 inference (BI) methods. Three overlapping datasets were used that span 250
 million years of archosauromorph evolution leading to crocodylians. The
 first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on
 early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes
 (101 taxa, 340 chars.). For each dataset three time-calibrated trees
 (timetrees) were calculated: a minimum-age timetree with node ages based
 on earliest occurrences in the fossil record; a 'smoothed'
 timetree using a range of time added to the root that is then averaged
 over zero-length internodes; and a tip-dated timetree. Comparisons within
 datasets show that the smoothed and tip-dated timetrees provide similar
 estimates. Only near the root node do BEAST estimates fall outside the
 smoothed timetree range. The BEAST model is not able to overcome limited
 sampling to correctly estimate divergences considerably older than sampled
 fossil occurrence dates. Conversely, the smoothed timetrees consistently
 provide node-ages far older than the strict dates or BEAST estimates for
 morphologically conservative sister-taxa when they sit on long ghost
 lineages. In this latter case, the relaxed-clock model appears to be
 correctly moderating the node-age estimate based on the limited
 morphological divergence. Topologies are generally similar across
 analyses, but BEAST trees for crocodyliforms differ when clades are deeply
 nested but contain very old taxa. It appears that the constant-rate
 sampling assumption of the BDSS tree prior influences topology inference
 by disfavoring long, unsampled branches.
description: ArchosauriaAnalysis files for the Archosauria dataset including BI, MP, BEAST2, and ghost lineage time scaling.CrocodyliformesAnalysis files for the Crocodyliformes dataset including BI, MP, BEAST2, and ghost lineage time scaling.SauriaAnalysis files for the Sauria dataset including BI, MP, BEAST2, and ghost lineage time scaling.Yule_BEAST1.8Contains tree files from exploratory BEAST1.8 analysis examining Yule tree priors.
DOI: 10.5061/dryad.d2vf8
title: Data from: Acquisition of conditioning between methamphetamine and cues in healthy humans

description: Environmental stimuli repeatedly paired with drugs of abuse can elicit
 conditioned responses that are thought to promote future drug seeking. We
 recently showed that healthy volunteers acquired conditioned responses to
 auditory and visual stimuli after just two pairings with methamphetamine
 (MA, 20 mg, oral). This study extended these findings by systematically
 varying the number of drug-stimuli pairings. We expected that more
 pairings would result in stronger conditioning. Three groups of healthy
 adults were randomly assigned to receive 1, 2 or 4 pairings (Groups P1, P2
 and P4, Ns = 13, 16, 16, respectively) of an auditory-visual stimulus with
 MA, and another stimulus with placebo (PBO). Drug-cue pairings were
 administered in an alternating, counterbalanced order, under double-blind
 conditions, during 4 hr sessions. MA produced prototypic subjective
 effects (mood, ratings of drug effects) and alterations in physiology
 (heart rate, blood pressure). Although subjects did not exhibit increased
 behavioral preference for, or emotional reactivity to, the MA-paired cue
 after conditioning, they did exhibit an increase in attentional bias
 (initial gaze) toward the drug-paired stimulus. Further, subjects who had
 four pairings reported “liking” the MA-paired cue more than the PBO cue
 after conditioning. Thus, the number of drug-stimulus pairings, varying
 from one to four, had only modest effects on the strength of conditioned
 responses. Further studies investigating the parameters under which drug
 conditioning occurs will help to identify risk factors for developing drug
 abuse, and provide new treatment strategies.
description: MAP
 analysisBlood Pressure Raw Data
 SPSS fileHR
 analysisHeart Rate Raw Data SPSS
 fileDEQ_analysisRaw data for DEQ subjective measureEMAC_DEQ_analysis_end of step auc_check.savPOMS_analysisRaw data for POMS subjective measure_ SPSS fileEMAC_POMS_end step 8.savARCI analysisRaw data ARCI subjective measure_SPSS fileEOG_analysisAttention Bias Raw data SPSS fileEMAC_EOG_1.8.16_End_Step_3.savVAS analysisVAS Liking Raw Data SPSS fileEMAC.VAS.1.8.16.minus.outliers.savForced Choice AnalysisBehavioral Preference Raw Data SPSS fileEMAC.FC.1.8.16.savEMG AnalysisFacial EMG Raw Data SPSS fileEMAC.EMG.1.5.16.End.Step.4.savDEQ vs Outcome Measure AnalysisCorrelation Raw Data SPSS fileDEQ vs Outcome measures.savDemographics DataPlease note that sex, height, birth control use, weight, race and ethnicity of grandparents have been removed.
DOI: 10.5061/dryad.68mp3
title: Data from: Spatial variation in climate mediates gene flow across an island archipelago

description: High levels of gene flow among partially isolated populations can
 overwhelm selection and limit local adaptation. This process, known as
 “gene swamping,” can homogenize genetic diversity among populations and
 reduce the capacity of a species to withstand rapid environmental change.
 We studied brown anole lizards (Anolis sagrei) distributed across seven
 islands in The Bahamas. We used microsatellite markers to estimate gene
 flow among islands and then examined the correlation between thermal
 performance and island temperature. The thermal optimum for sprint
 performance was correlated with both mean and maximum island temperature
 whereas performance breadth was not correlated with any measure of
 temperature variation. Gene flow between islands decreased as the
 difference between mean island temperatures increased, even when those
 islands were adjacent to one another. These data suggest that phenotypic
 variation is the result of either 1) local genetic adaptation with
 selection against immigrants maintaining variation in the thermal optimum,
 2) irreversible forms of adaptive plasticity such that immigrants have
 reduced fitness, or 3) an interaction between fixed genetic differences
 and plasticity. In general, the patterns of gene flow we observed suggest
 that local thermal environments represent important ecological filters
 that can mediate gene flow on relatively fine geographic scales.
description: MIGRATE
 output_maxLiklihoodThis file contains the
 output from our microsatellite gene flow analyses in the program
 MIGRATE..Sprint
 speedsEstimates of lizard
 sprint speeds at each of six temperatures.Operative temperature
 dataTemperature data from
 iButton data loggers.
DOI: 10.5061/dryad.2kg70
title: Data from: Morphological and taxonomic demarcation of Brachionus asplanchnoidis Charin within the Brachionus plicatilis cryptic species complex (Rotifera, Monogononta)

description: Three well-defined groups, consisting of 15 species, have recently been
 ascribed to organisms historically identified as the Brachionus plicatilis
 species complex. One of these groups, the Large-clade is composed of two
 named species (Brachionus plicatilis s.s. and Brachionus manjavacas) and
 two species identifiers (B. 'Nevada' and B.
 'Austria'). B. 'Austria' has been confirmed to be B.
 asplanchnoidis. As no type specimen exists for this species, and the
 original taxonomic description is lacking in detail, we give a detailed
 account of this species using material from Obere Halbjochlacke in Austria
 where B. 'Austria' was first identified genetically. Our
 analysis of B. asplanchnoidis populations were of global scope; an
 approach that revealed a great degree of morphological variability.
 However, combining aspects of both the dorsal and ventral surfaces clearly
 discriminated B. asplanchnoidis from the rest of the Large type members.
 This approach may prove useful in taxonomic studies of other cryptic
 species with relatively few morphological features. We also observed a
 geographic pattern of genetic divergence within B. asplanchnoidis. Average
 uncorrected COI divergences for a 554-bp fragment of the COI gene ranged
 from 3.9% within species to 17.5% between species of the Large-clade, and
 indicate deep divisions within the cryptic species complex.
description: 1_Alignment2_jModelTest3_MrBayes4_RAxML5_BEAST6_GMYC
DOI: 10.5061/dryad.8g4vp
title: Data from: Stimulation-based control of dynamic brain networks

description: The ability to modulate brain states using targeted stimulation is
 increasingly being employed to treat neurological disorders and to enhance
 human performance. Despite the growing interest in brain stimulation as a
 form of neuromodulation, much remains unknown about the network-level
 impact of these focal perturbations. To study the system wide impact of
 regional stimulation, we employ a data-driven computational model of
 nonlinear brain dynamics to systematically explore the effects of targeted
 stimulation. Validating predictions from network control theory, we
 uncover the relationship between regional controllability and the focal
 versus global impact of stimulation, and we relate these findings to
 differences in the underlying network architecture. Finally, by mapping
 brain regions to cognitive systems, we observe that the default mode
 system imparts large global change despite being highly constrained by
 structural connectivity. This work forms an important step towards the
 development of personalized stimulation protocols for medical treatment or
 performance enhancement.
description: connectivity
 matricesMatlab files containing
 the connectivity matrices describing the density of connections between 83
 brain regions as well as the delay time between regions. There are 24
 files (8 subjects and 3 scans per subject), each with 2 variables:
 "connectivity_density_matrix" and "delay_matrix".
 These matrices were used to run the simulations described in the text of
 the manuscript. Please see the Methods section of the manuscript for more
 details.connectivity_matrices.zip
DOI: 10.5061/dryad.877ts
title: Data from: Varying selection differential throughout the climatic range of Norway spruce in Central Europe

description: Predicting species distribution changes in global warming requires an
 understanding of how climatic constraints shape the genetic variation of
 adaptive traits and force local adaptations. To understand the genetic
 capacity of Norway spruce populations in Central Europe, we analyzed
 variation of tree heights at the juvenile stage in common-garden
 experiments established from the species’ warm-dry to cold-moist
 distribution limits. We report the following findings: first, 47 % of the
 total tree-height variation at trial sites is attributable to the tree
 populations irrespective of site climate. Second, tree height variation
 within populations is higher at cold-moist trial sites than at warm-dry
 sites and higher within populations originating from cold-moist habitats
 than from warm-dry habitats. Third, for tree ages of 7 to 15 years, the
 variation within populations increases at cold-moist trial sites, whereas
 it remains constant at warm-dry sites. Fourth, tree-height distributions
 are right-skewed at cold-moist trial sites, whereas they are non-skewed
 but platykurtic at warm-dry sites. Our results suggest that in cold
 environments climatic conditions impose stronger selection and probably
 restrict the distribution of spruce, whereas at the warm distribution
 limit, the species’ realized niche might rather be controlled by external
 drivers, for example forest insects.
description: Austrian Norway spruce
 provenance test 1978 - Individual tree heights at age of 7 to
 15All
 measured tree heights (in cm) from the Austrian Norway spruce provenance
 trial 1978. For details on sites and provenances (i.e., populations) see
 the other two data files with climate data. The trial sites were measured
 in 1983 and 1988, at 5 and 10 years after their establishment. This
 provided height data for the trees at the age of 10 and 15 years. During
 the 1983 measurement, the shoot length for the preceding three years was
 also measured, which provided heights for the trees at the age of 7, 8,
 and 9 years. The trial was established at the Austrian Federal Research
 and Training Centre for Forests, Natural Hazards and Landscape (BFW) by
 Dr. K.Holzer. Measurements by former staff at the BFW.Piceaabies_Treeheights_Age7to15_data.csvAustrian Norway spruce provenance test 1978 - list of trial sites and climatic detailsAll trial sites and according climatic details are given. Climate variables were provided by the Central Institute for Meteorology and Geodynamics, Vienna, Austria. For details see DOI: 10.1016/j.foreco.2012.01.039Climate_trial_sites.csvAustrian Norway spruce provenance test 1978 - list of populations (provenances) and climatic detailsAll tested provenances and according climatic details are given. Climate variables were provided by the Central Institute for Meteorology and Geodynamics, Vienna, Austria. For details see DOI: 10.1016/j.foreco.2012.01.039Climate_provenances.csv
DOI: 10.34740/kaggle/dsv/14638214
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.57826/agimo/ud99gs
title: MATSim Dresden Base Model Output v1.0

description: See Metadata→Related Publication
DOI: 10.5061/dryad.pm354
title: Data from: Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon

description: Farmed Atlantic salmon (Salmo salar) is a globally important production
 species, including in Australia where breeding and selection has been in
 progress since the 1960s. The recent development of SNP genotyping
 platforms means genome-wide association and genomic prediction can now be
 implemented to speed genetic gain. As a precursor, this study collected
 genotypes at 218 132 SNPs in 777 fish from a Tasmanian breeding population
 to assess levels of genetic diversity, the strength of linkage
 disequilibrium (LD) and imputation accuracy. Genetic diversity in
 Tasmanian Atlantic salmon was lower than observed within European
 populations when compared using four diversity metrics. The distribution
 of allele frequencies also showed a clear difference, with the Tasmanian
 animals carrying an excess of low minor allele frequency variants. The
 strength of observed LD was high at short distances (&lt;25 kb) and
 remained above background for marker pairs separated by large chromosomal
 distances (hundreds of kb), in sharp contrast to the European Atlantic
 salmon tested. Genotypes were used to evaluate the accuracy of imputation
 from low density (0.5 to 5 K) up to increased density SNP sets (78 K).
 This revealed high imputation accuracies (0.89–0.97), suggesting that the
 use of low density SNP sets will be a successful approach for genomic
 prediction in this population. The long-range LD, comparatively low
 genetic diversity and high imputation accuracy in Tasmanian salmon is
 consistent with known aspects of their population history, which involved
 a small founding population and an absence of subsequent introgression.
 The findings of this study represent an important first step towards the
 design of methods to apply genomics in this economically important
 population.
description: SNP
 genotypesGenotypes from 106,492
 SNP collected in 777 Atlantic Salmon. Contains a bed, bim and fam file
 formatted for analysis using Plinkv1.9.Salmon_SNP.zip
DOI: 10.5061/dryad.v15v0
title: Data from: ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

description: We present an r package, ggtree, which provides programmable visualization
 and annotation of phylogenetic trees. ggtree can read more tree file
 formats than other softwares, including newick, nexus, NHX, phylip and
 jplace formats, and support visualization of phylo, multiphylo, phylo4,
 phylo4d, obkdata and phyloseq tree objects defined in other r packages. It
 can also extract the tree/branch/node-specific and other data from the
 analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml
 and revbayes software, and allows using these data to annotate the tree.
 The package allows colouring and annotation of a tree by
 numerical/categorical node attributes, manipulating a tree by rotating,
 collapsing and zooming out clades, highlighting user selected clades or
 operational taxonomic units and exploration of a large tree by zooming
 into a selected portion. A two-dimensional tree can be drawn by scaling
 the tree width based on an attribute of the nodes. A tree can be annotated
 with an associated numerical matrix (as a heat map), multiple sequence
 alignment, subplots or silhouette images. The package ggtree is released
 under the artistic-2.0 license. The source code and documents are freely
 available through bioconductor
 (http://www.bioconductor.org/packages/ggtree).
description: MCC_FluA_H3Time-scaled phylogenetic tree of H3 influenza viruses inferred by BEAST using molecular clock model.rstOutput file of CODEML inferring ancestral sequences of H3 influenza viruses using codon model.mlcOutput file of CODEML estimating selection pressure using codon model.NAG_inHA1The predicted number of N-linked glycosylation sites in the hemagglutinin proteins of H3 influenza viruses.sitesThe sequence sites selected to display amino acid substitutions on the phylogenetic tree of H3 influenza viruses.GenotypeGenotype table of the H3 influenza viruses.
DOI: 10.5061/dryad.2g8j2
title: Data from: Sumakuru, a deeply-diverging new genus of lyssomanine jumping spiders from Ecuador (Araneae: Salticidae)

description: The lyssomanine jumping spider genus Sumakuru gen. n. is here described
 for Sumakuru bigal sp. n., from the Bigal River Biological Reserve in
 Ecuador. Known from a single male, the embolus of the palp takes the form
 of a smoothly arching curve, and appears fully mobile, being connected to
 the tegulum by a thin sclerite and a twisted hematodocha. Data from four
 gene regions (28S, 16SND1, CO1, wingless) indicate that Sumakuru is the
 sister group to all other sampled lyssomanines, diverging deeply on the
 stem lineage of the clade of other known lyssomanines. Unlike previous
 molecular results, the sampled species of Lyssomanes Hentz, 1845 are
 supported as monophyletic, with Chinoscopus Simon, 1900 as the sister to
 Lyssomanes.
description: Alignments and trees for
 Sumakuru study (Salticidae)Alignments for 28S,
 16SND1, CO1, wingless, and maximum likelihood trees from analysis of
 salticid spider phylogeny, showing placement of Sumakuru within the
 lyssomanines.Sumakuru-Maddison2016-ForDryad04.nex
DOI: 10.5061/dryad.21sj8
title: Data from: Future ecosystem services from European mountain forests under climate change

description: Ecosystem services (ES) from mountain forests are highly relevant for
 human societies. ES with a direct economic support function (e.g. timber
 production), regulatory services (e.g. protection from natural hazards)
 and cultural services (e.g. recreation) are likely to be affected strongly
 by a rapidly changing climate. To evaluate whether adverse climate change
 effects on ES can be counteracted by adapting management, dynamic models
 and indicator-based assessments are needed. We applied a forest dynamic
 model in case study areas of four European mountain regions and evaluated
 the future supply of four ES – timber production, carbon sequestration,
 biodiversity and protection against natural hazards – using
 state-of-the-art ES indicators. Forest dynamics were simulated under three
 management scenarios (no management, business-as-usual and alternative
 management) and five climate change projections for selected
 representative stand types in each region. We analysed potential
 trade-offs and synergies between ES and evaluated future changes among
 regions, forest stands, climate and management scenarios. Impacts of
 climate change on the provision of multiple ES were found to be highly
 heterogeneous and to depend on the region, site and future climate. In the
 absence of large-scale natural disturbance (not considered), protection
 services, carbon stock and deadwood abundance (proxy for biodiversity)
 benefitted from no management in all regions. Negative impacts of climate
 change were evident for the provision of multiple ES but limited to the
 most severe climate scenarios and low-elevation stands. Synergies and
 trade-offs between the majority of ES were found to be sensitive to the
 choice of management strategy and – in some regions – to climate change.
 Synthesis and applications. Management regimes in European mountain
 forests should be regionally adapted to stand and site conditions.
 Although in some cases alternative management regimes may be more suitable
 than current management for supporting multiple ecosystem services,
 adaptation options should be evaluated carefully at the local scale due to
 the highly different magnitude of the impacts of climate change in
 different regions and along elevation gradients.
description: Simulated ecosystem
 services indicators with the ForClim modelList of ecosystem
 service indicator values for each simulated year (2010-2100/2150) for
 representative stand types (RST) in the four case study areas (CSA). The
 data were generated with the climate-sensitive forest succession model
 FORCLIM, an open-access software which is available for download through
 the Chair of Forest Ecology at ETH Zürich
 (https://uwis-server102.ethz.ch/openaccess/). Column headings are
 described in the associated ReadMe file.ES_ForClim_Mina-JAPP.csv
DOI: 10.5061/dryad.4mv7h
title: Data from: Taxonomic resolution is a determinant of biodiversity effects in arbuscular mycorrhizal fungal communities

description: Arbuscular mycorrhizal fungi (AMF) are key regulators of ecosystem
 processes, yet how their biodiversity works in ecosystems remains poorly
 understood. We documented the extent to which taxonomic resolution
 influenced the effect of biodiversity of AMF taxa on plant performance
 (growth, nutrient uptake and stress tolerance) in a meta-analysis of 902
 articles. We found that the effect of biodiversity of AMF taxa depended on
 taxonomic resolution. Plant performance was positively promoted by AMF
 family richness, while no effect was found for fungal species richness. In
 addition, negative effect was found between AMF phylogenetic diversity and
 plant growth. This pattern can be explained by functional conservatism
 within AMF families and functional differentiation among AMF families.
 Synthesis. Conservation of AMF communities to maintain a full complement
 of ecosystem functions requires the presence of diverse families and not
 simply diverse species within a family. This finding may be of key
 importance for the function of ecosystems under various environmental
 perturbations to which AMF families may respond differently.
description: AMF
 functionAdditional file 2-Appendix
 S2-Database.xls