cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nf757
title: Data from: Rapid evolution of adaptive niche construction in experimental microbial populations

description: Many species engage in adaptive niche construction: modification of the
 local environment that increases the modifying organism's competitive
 fitness. Adaptive niche construction provides an alternative pathway to
 higher fitness, shaping the environment rather than conforming to it. Yet,
 experimental evidence for the evolutionary emergence of adaptive niche
 construction is lacking, leaving its role in evolution uncertain. Here we
 report a direct observation of the de novo evolution of adaptive niche
 construction in populations of the bacteria Pseudomonas fluorescens. In a
 laboratory experiment, we allowed several bacterial populations to adapt
 to a novel environment and assessed whether niche construction evolved
 over time. We found that adaptive niche construction emerged rapidly,
 within approximately 100 generations, and became ubiquitous after
 approximately 400 generations. The large fitness effect of this niche
 construction was dominated by the low fitness of evolved strains in the
 ancestrally modified environment: evolved niche constructors were highly
 dependent on their specific environmental modifications. Populations were
 subjected to frequent resetting of environmental conditions and severe
 reduction of spatial habitat structure, both of which are thought to make
 adaptive niche construction difficult to evolve. Our finding that adaptive
 niche construction nevertheless evolved repeatably suggests that it may
 play a more important role in evolution than generally thought.
description: Flow Cytometery Data for
 Figures 2 and 3aFigure2and3.zipFlow Cytometery Data for Figure 5Figure5.zipFlow Cytometery Data for Figures 6 and S11File names are: __.xxxFigure6andS11.zipFlow Cytometery Data for Figure S3FigureS3.zipFlow Cytometery Data for Figure S4FigureS4.zipFlow Cytometery Data for Figure S5FigureS5.zipFlow Cytometery Data for Figure S8Starting ratios for these competitions were X/6, where X is the number in the second slot of the filename (strain_X_time.zzz)FigureS8.zipFlow Cytometery Data for Figure S10FigureS10.zipFlow Cytometery Data for Figure S12FigureS12.zip
DOI: 10.5061/dryad.p1b90
title: Data from: Genetic diversity and population structure in South African, French and Argentinian Angora Goats from genome-wide SNP data

description: The Angora goat populations in Argentina (AR), France (FR) and South
 Africa (SA) have been kept geographically and genetically distinct. Due to
 country-specific selection and breeding strategies, there is a need to
 characterize the populations on a genetic level. In this study we analysed
 genetic variability of Angora goats from three distinct geographical
 regions using the standardized 50k Goat SNP Chip. A total of 104 goats
 (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as
 inbreeding coefficients across all autosomes per population were
 calculated. Diversity, as measured by expected heterozygosity (HE) ranged
 from 0.371 in the SA population to 0.397 in the AR population. The SA
 goats were the only population with a positive average inbreeding
 coefficient value of 0.009. After merging the three datasets, standard QC
 and LD-pruning, 15 105 SNPs remained for further analyses. Principal
 component and clustering analyses were used to visualize individual
 relationships within and between populations. All SA Angora goats were
 separated from the others and formed a well-defined, unique cluster, while
 outliers were identified in the FR and AR breeds. Apparent admixture
 between the AR and FR populations was observed, while both these
 populations showed signs of having some common ancestry with the SA goats.
 LD averaged over adjacent loci within the three populations per chromosome
 were calculated. The highest LD values estimated across populations were
 observed in the shorter intervals across populations. The Ne for the
 Angora breed was estimated to be 149 animals ten generations ago
 indicating a declining trend. Results confirmed that geographic isolation
 and different selection strategies caused genetic distinctiveness between
 the populations.
description: angora_plosGenotyping data of 104 angora goats (30 from Argentina, 26 from France and 48 from South Africa) genotyped with the standardized 50k Goat SNP Chip. Date file is made of 5 colums: 1st Column -&gt; country code (AR -&gt; Argentina, FR -&gt; France, ZA -&gt; South Africa); 2nd column -&gt; Individual ID; 3rd column -&gt; snp name; 4th column -&gt;: allel 1 ; 5th column -&gt; allel 2.
DOI: 10.5061/dryad.k7505mn
title: Data from: A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans

description: Comprising over 15 000 living species, decapods (crabs, shrimp and
 lobsters) are the most instantly recognizable crustaceans, representing a
 considerable global food source. Although decapod systematics have
 received much study, limitations of morphological and Sanger sequence data
 have yet to produce a consensus for higher-level relationships. Here, we
 introduce a new anchored hybrid enrichment kit for decapod phylogenetics
 designed from genomic and transcriptomic sequences that we used to capture
 new high-throughput sequence data from 94 species, including 58 of 179
 extant decapod families, and 11 of 12 major lineages. The enrichment kit
 yields 410 loci (greater than 86 000 bp) conserved across all lineages of
 Decapoda, more clade-specific molecular data than any prior study.
 Phylogenomic analyses recover a robust decapod tree of life strongly
 supporting the monophyly of all infraorders, and monophyly of each of the
 reptant, ‘lobster’ and ‘crab’ groups, with some results supporting
 pleocyemate monophyly. We show that crown decapods diverged in the Late
 Ordovician and most crown lineages diverged in the Triassic–Jurassic,
 highlighting a cryptic Palaeozoic history, and post-extinction
 diversification. New insights into decapod relationships provide a
 phylogenomic window into morphology and behaviour, and a basis to rapidly
 and cheaply expand sampling in this economically and ecologically
 significant invertebrate clade.
description: READMEDescription of all files
 associated with this paper, in all subfolders in this
 repository.dryad_readme.txtBC_Transcriptome_dataThis file contains the assembled transcriptome reads for 4 species (across multiple life stages) used to develop anchored enrichment probes.D_Probe_designThis file contains the probe sequences for each of 6 infraorders (Achelata, Anomura, Astacidea, Brachyura, Caridea, Dendrobranchiata) that were ordered from Agilent, and supporting files related to how the probe sets were constructed.EF_AHE_dataThis file contains the exon-based reference loci from the E. sinensis genome, and the key mapping the final 410 exon-based loci (folder GHI_Data_matrices) to the 352 AHE targets.GHI_Data_matricesThis file contains data matrices used in this study.J_Phylogenetic_treesThis file contains all the phylogenetic trees associated with this study.L_Divergence_time_resultsThis package contains the results of divergence time analyses.
DOI: 10.5061/dryad.k0503c7
title: Data from: Moose movement rates are altered by wolf presence in two ecosystems

description: Predators directly impact prey populations through lethal encounters, but
 understanding non-lethal, indirect effects is also critical because
 foraging animals often face tradeoffs between predator avoidance and
 energy intake. Quantifying these indirect effects can be difficult even
 when it is possible to monitor individuals that regularly interact. Our
 goal was to understand how movement and resource selection o a predator
 (wolves; Canis lupus) influences the movement behavior of a prey species
 (moose; Alces alces). We tested whether moose avoided areas with high
 predicted wolf resource use in two study areas with differing prey
 compositions, whether avoidance patterns varied seasonally, and whether
 daily activity budgets of moose and wolves aligned temporally. We deployed
 GPS-collars on both species at two sites in northern Minnesota. We created
 seasonal resource-selection functions (RSF) for wolves and modeled the
 relationship between moose first-passage time (FPT), a method that
 discerns alterations in movement rates, and wolf RSF values. Larger FPT
 values suggest rest/foraging, whereas shorter FPT values indicate
 travel/fleeing. We found that the movements of moose and wolves peaked at
 similar times of day in both study areas. Moose FPTs were 45% lower in
 areas most selected for by wolves relative to those avoided. The
 relationship between wolf RSF and moose FPT was nonlinear and varied
 seasonally. Differences in FPT between low and high RSF values were
 greatest in winter (-82.1%) and spring (-57.6%) in northeastern Minnesota
 and similar for all seasons in the Voyageurs National Park ecosystem. In
 northeastern Minnesota, where moose comprise a larger percentage of wolf
 diet, the relationship between moose FPT and wolf RSF was more pronounced
 (ave. across seasons: -60.1%) than the Voyageurs National Park ecosystem
 (-30.4%). These findings highlight the role wolves can play in determining
 moose behavior, whereby moose spend less time in areas with higher
 predicted likelihood of wolf resource selection.
description: Wolf movement rate
 dataWolf movement rates from
 GPS-collared wolves in northeastern Minnesota and Voyageurs National Park
 ecosystem. Data also contain other values used in movement rate analysis
 portion of the manuscript.WolfMove_data_Ditmer_070218.csvWolf resource selection function dataData used to create resource selections functions for wolf packs in northern Minnesota.RSF_data_Ditmer_070218.csvMoose first-passage time dataData used to model moose first passage time estimates.MooseFPT_data_Ditmer_070218.csv
DOI: 10.5061/dryad.q1c1j71
title: Data from: Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of the relationship of angiosperms and Gnetales

description: The placement of angiosperms and Gnetales in seed plant phylogeny remains
 one of the most enigmatic problems in plant evolution, with morphological
 analyses (which have usually included fossils) and molecular analyses
 pointing to very distinct topologies. Almost all morphology-based
 phylogenies group angiosperms with Gnetales and certain extinct seed plant
 lineages, while most molecular phylogenies link Gnetales with conifers. In
 this study, we investigate the phylogenetic signal present in published
 seed plant morphological datasets. We use parsimony, Bayesian inference,
 and maximum likelihood approaches, combined with a number of experiments
 with the data, to address the morphological-molecular conflict. First, we
 ask whether the lack of association of Gnetales with conifers in
 morphological analyses is due to an absence of signal or to the presence
 of competing signals, and second, we compare the performance of parsimony
 and model-based approaches with morphological datasets. Our results imply
 that the grouping of Gnetales and angiosperms is largely the result of
 long branch attraction, consistent across a range of methodological
 approaches. Thus, there is a signal for the grouping of Gnetales with
 conifers in morphological matrices, but it was swamped by convergence
 between angiosperms and Gnetales, both situated on long branches. However,
 this effect becomes weaker in more recent analyses, as a result of
 addition and critical reassessment of characters. Even when a clade
 including angiosperms and Gnetales is still weakly supported by parsimony,
 model-based approaches favor a clade of Gnetales and conifers, presumably
 because they are more resistant to long branch attraction. Inclusion of
 fossil taxa weakens rather than strengthens support for a relationship of
 angiosperms and Gnetales. Our analyses finally reconcile morphology with
 molecules in favoring a relationship of Gnetales to conifers, and show
 that morphology may therefore be useful in reconstructing other aspects of
 the phylogenetic history of the seed plants.
description: Supplementary_materialSupportTable with support values for all the experiments.
DOI: 10.15468/dl.fnz3d7
title: Occurrence Download

description: A dataset containing 60727 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation)",
 "Continent is Europe",
 "Issue is one of (Zero coordinate, Coordinate out of range, Coordinate rounded, Geodetic datum invalid, Geodetic datum assumed WGS84, Coordinate reprojected, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate accuracy invalid, Coordinate uncertainty meters invalid, Coordinate precision/uncertainty mismatch, Footprint SRS invalid, Footprint WKT mismatch, Footprint WKT invalid, Country coordinate mismatch, Country mismatch, Country invalid, Country derived from coordinates, Continent coordinate mismatch, Continent country mismatch, Continent invalid, Continent derived from country, Continent derived from coordinates, Presumed negated longitude, Presumed negated latitude, Recorded date mismatch, Recorded date invalid, Recorded date unlikely, Taxon match fuzzy, Taxon match aggregate, The scientific name ID was not used in backbone matching, The taxon concept ID was not used in backbone matching, The taxon ID was not used in backbone matching, The scientific name ID was not found in the checklist, The taxon concept ID was not found in the checklist, The taxon ID was not found in the checklist, The scientific name differs on the record from that found in the checklist, Taxon match none, The backbone match found using the taxon IDs differs from what would be found if using the scientific names, Depth not metric, Depth unlikely, Depth min max swapped, Depth non numeric, Elevation unlikely, Elevation min max swapped, Elevation not metric, Elevation non numeric, Modified date invalid, Modified date unlikely, Identified date unlikely, Identified date invalid, Basis of record invalid, Type status invalid, Multimedia date invalid, Multimedia URI invalid, References URI invalid, Error during interpretation, Individual count invalid, Individual count conflicts with occurrence status, Occurrence status inferred from individual count, Occurrence status inferred from basis of record, Georeferenced date unlikely, Georeferenced date invalid, Ambiguous institution, Ambiguous collection, Institution match none, Collection match none, Institution match fuzzy, Collection match fuzzy, Institution collection mismatch, Possibly on loan, Different owner institution)",
 "OccurrenceStatus is Present",
 "TaxonKey is Orchis militaris",
 "Year 2000-2026"
 ]
}

 The dataset includes 60727 records from 444 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000335-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.92257
title: Data from: Tradeoffs between maize silage yield and nitrate leaching in a Mediterranean nitrate-vulnerable zone under current and projected climate scenarios

description: Future climatic changes may have profound impacts on cropping systems and
 affect the agronomic and environmental sustainability of current N
 management practices. The objectives of this work were to i) evaluate the
 ability of the SALUS crop model to reproduce experimental crop yield and
 soil nitrate dynamics results under different N fertilizer treatments in a
 farmer’s field, ii) use the SALUS model to estimate the impacts of
 different N fertilizer treatments on NO3- leaching under future climate
 scenarios generated by twenty nine different global circulation models,
 and iii) identify the management system that best minimizes NO3- leaching
 and maximizes yield under projected future climate conditions. A field
 experiment (maize-triticale rotation) was conducted in a nitrate
 vulnerable zone on the west coast of Sardinia, Italy to evaluate N
 management strategies that include urea fertilization (NMIN), conventional
 fertilization with dairy slurry and urea (CONV), and no fertilization
 (N0). An ensemble of 29 global circulation models (GCM) was used to
 simulate different climate scenarios for two Representative Circulation
 Pathways (RCP6.0 and RCP8.5) and evaluate potential nitrate leaching and
 biomass production in this region over the next 50 years. Data collected
 from two growing seasons showed that the SALUS model adequately simulated
 both nitrate leaching and crop yield, with a relative error that ranged
 between 0.4% and 13%. Nitrate losses under RCP8.5 were lower than under
 RCP6.0 only for NMIN. Accordingly, levels of plant N uptake, N use
 efficiency and biomass production were higher under RCP8.5 than RCP6.0.
 Simulations under both RCP scenarios indicated that the NMIN treatment
 demonstrated both the highest biomass production and NO3- losses. The
 newly proposed best management practice (BMP), developed from crop N
 uptake data, was identified as the optimal N fertilizer management
 practice since it minimized NO3- leaching and maximized biomass production
 over the long term.
description: Data
 archiveTar archive file that
 contains SALUS model, input and output files.DATA_SIMU_PONE-D-14-21411.tar
DOI: 10.5061/dryad.r32t3
title: Data from: Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency

description: Temporal data on gene expression and context-specific open chromatin
 states can improve identification of key transcription factors (TFs) and
 the gene regulatory networks (GRNs) controlling cellular differentiation.
 However, their integration remains challenging. Here, we delineate a
 general approach for data-driven and unbiased identification of key TFs
 and dynamic GRNs, called EPIC-DREM. We generated time-series
 transcriptomic and epigenomic profiles during differentiation of mouse
 multipotent bone marrow stromal cell line (ST2) toward adipocytes and
 osteoblasts. Using our novel approach we constructed time-resolved GRNs
 for both lineages and identifed the shared TFs involved in both
 differentiation processes. To take an alternative approach to prioritize
 the identified shared regulators, we mapped dynamic super-enhancers in
 both lineages and associated them to target genes with correlated
 expression profiles. The combination of the two approaches identified aryl
 hydrocarbon receptor (AHR) and Glis family zinc finger 1 (GLIS1) as
 mesenchymal key TFs controlled by dynamic cell type-specific
 super-enhancers that become repressed in both lineages. AHR and GLIS1
 control differentiation-induced genes and their overexpression can inhibit
 the lineage commitment of the multipotent bone marrow-derived ST2 cells.
description: Time point-specific gene
 regulatory networks of mesenchymal differentiationThe full matrix of the
 time point-specific TF-target gene interactions for 6 time points of both
 adipocyte and osteoblast differentiation of bone marrow msenchymal stem
 cells as derived and used as input for EPIC-DREM analysis in publication
 by Gerad et al.EPIC-DREM_Input_GRNs-Adipo_Osteo.zip
DOI: 10.5061/dryad.vk775
title: Data from: Automated assembly of a reference taxonomy for phylogenetic data synthesis

description: Taxonomy and nomenclature data are critical for any project that
 synthesizes biodiversity data, as most biodiversity data sets use
 taxonomic names to identify taxa. Open Tree of Life is one such project,
 synthesizing sets of published phylogenetic trees into comprehensive
 summary trees. No single published taxonomy met the taxonomic and
 nomenclatural needs of the project. Here we describe a system for
 reproducibly combining several source taxonomies into a synthetic
 taxonomy, and we discuss the challenges of taxonomic and nomenclatural
 synthesis for downstream biodiversity projects.
description: README file for
 packageDescribes all files in
 package and provides external links to additional
 documentation.SILVA-to-NCBI
 mappingContains a mapping of
 Genbank accession numbers to NCBI taxon ids and names. The accessions are
 those that are the reference sequences for SILVA
 clusters.accessions.tgzOTT amendmentsThe taxonomy amendments used in preparation of OTT. Includes all amendments in https://github.com/OpenTreeOfLife/amendments-1 at the time that we built the version of OTT described in the article. Each amendment is a json file that includes the change being proposed as well as sources that support the change.amendments.tgzmapping of source ids to OTT idsCumulative mapping of identifiers in sources to OTT identifiers. Format of each line is source:sourceid,OTTid.by_qid.tgzOTT version2.10This is the previous version of the Open Tree Taxonomy. It is included because we use the previous version during identifier assignment (ott2.10 required to build ott3.0). See the enclosed README for details on files and formats.ott2.10.tgzOTT version 3.0Version of the Open Tree Taxonomy described in the manuscript. See the enclosed README for details on files and formats.ott3.0.tgzseparation taxonomyThe 'separation taxonomy' described in the manuscript. Contains a list of taxa and a list of synonyms.separation.tgz
DOI: 10.5061/dryad.35qv6
title: Data from: A stochastic neuronal model predicts random search behaviors at multiple spatial scales in C. elegans

description: Random search is a behavioral strategy used by organisms from bacteria to
 humans to locate food that is randomly distributed and undetectable at a
 distance. We investigated this behavior in the nematode Caenorhabditis
 elegans, an organism with a small, well-described nervous system. Here we
 formulate a mathematical model of random search abstracted from the C.
 elegans connectome and fit to a large-scale kinematic analysis of C.
 elegans behavior at submicron resolution. The model predicts behavioral
 effects of neuronal ablations and genetic perturbations, as well as
 unexpected aspects of wild type behavior. The predictive success of the
 model indicates that random search in C. elegans can be understood in
 terms of a neuronal flip-flop circuit involving reciprocal inhibition
 between two populations of stochastic neurons. Our findings establish a
 unified theoretical framework for understanding C. elegans locomotion and
 a testable neuronal model of random search that can be applied to other
 organisms.
description: wormtracks data
 archiveAll raw data, plus the
 main analysis program and spreadsheet.wormtracks
 archive.zip