cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1s37q
title: Data from: A MinION™‐based pipeline for fast and cost‐effective DNA barcoding

description: DNA barcodes are useful for species discovery and species identification,
 but obtaining barcodes currently requires a well-equipped molecular
 laboratory, is time-consuming, and/or expensive. We here address these
 issues by developing a barcoding pipeline for Oxford Nanopore MinION™ and
 demonstrate that one flowcell can generate barcodes for ~500 specimens
 despite high base-call error rates of MinION™ reads. The pipeline
 overcomes the errors by first summarizing all reads for the same tagged
 amplicon as a consensus barcode. Consensus barcodes are overall
 mismatch-free but retain indel errors that are concentrated in
 homopolymeric regions. They are addressed with an optional error
 correction pipeline that uses conserved amino-acid motifs from publicly
 available barcodes to correct the indel errors. The effectiveness of this
 pipeline is documented by analysing reads from three MinION™ runs that
 represent different stages of MinION™ development. They generated data for
 (1) 511 specimens of a mixed Diptera sample, (2) 575 specimens of ants,
 and (3) 50 specimens of Chironomidae. The run based on the latest
 chemistry yielded MinION barcodes for 490 of the 511 specimens which were
 assessed against reference Sanger barcodes (N=471). Overall, the MinION
 barcodes have an accuracy of 99.3%-100% and the number of post-correction
 ambiguities ranges from &lt;0.01-1.5% depending on which correction
 pipeline is used. We demonstrate that it requires ~2 hours of sequencing
 to gather all information needed for obtaining reliable barcodes for most
 specimens (&gt;90%). We estimate that up to 1000 barcodes can be
 generated in one flowcell and that the cost per barcode can be
description: READMEDescriptions of files in
 this repositoryfile_descriptionsMinion BarcodesMinion Barcodes generated in the studyBarcodes_results.tgzDataset AFiles for Dataset ADatasetA.tgzDataset BFiles for Dataset BDatasetB.tgzDataset CFiles for Dataset CDatasetC.tgz
DOI: 10.5061/dryad.126k9
title: Data from: Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes

description: High-resolution visualization of short non-repetitive DNA in situ in the
 nuclear genome is essential for studying looping interactions and
 chromatin organization in single cells. Recent advances in fluorescence in
 situ hybridization (FISH) using Oligopaints probes enabled
 super-resolution imaging of genomic domains with a resolution limit of 4.9
 kb. To target shorter elements, we developed a simple FISH method that
 uses only molecular beacon (MB) probes to facilitate the probe-target
 binding, while minimizing non-specific fluorescence. We used
 three-dimensional stochastic optical reconstruction microscopy (3D-STORM)
 and optimized the imaging conditions to efficiently distinguish sparsely
 distributed Alexa-647 from background cellular autofluorescence. Utilizing
 3D-STORM and 29-34 individual MB probes, we observed 3D fine-scale
 nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in
 the human or mouse genome, respectively, demonstrating the capability of
 MB-based FISH in visualizing a so far shortest and non-repetitive genomic
 sequence in 3D at super-resolution.
description: Source data for Figure
 4a-cell IIIRevised2_figure4a_right_raw_data.rarSource data for Figure 4a-cell IIRevised2_figure4a_middle_raw_data.rarSource data for Figure 4a-cell IRevised2_figure4a_left_raw_data.rarSource data for Figure 5d-cell IRevised2_figure5d_cell1_raw_data.rarSource data for Figure 5d-cell IIRevised2_figure5d_cell2_raw_data.rarSource data for Figure 5d-cell IIIRevised2_figure5d_cell3_raw_data.rarSource data for Figure 5d-cell IVRevised2_figure5d_cell4_raw_data.rarSource data for Figure 5d-cell VRevised2_figure5d_cell5_raw_data.rarSource data for Figure 5d-cell VIRevised2_figure5d_cell6_raw_data.rarREADME
DOI: 10.5061/dryad.jv853v1
title: Data from: Evidence of host-associated divergence from coral-eating snails (genus Coralliophila) in the Coral Triangle

description: We studied how host-associations and geography shape the genetic structure
 of sister species of marine snails Coralliophila radula (A. Adams, 1853)
 and C. violacea (Kiener, 1836). These obligate ectoparasites prey upon
 corals and are sympatric throughout much of their ranges in coral reefs of
 the tropical and subtropical Indo-Pacific. We tested for population
 genetic structure of snails in relation to geography and their host corals
 using mtDNA (COI) sequences in minimum spanning trees and AMOVAs. We also
 examined the evolutionary relationships of their Porites host coral
 species using maximum likelihood trees of RAD-seq (restriction
 site-associated DNA sequencing) loci mapped to a reference transcriptome.
 A maximum likelihood tree of host corals revealed three distinct clades.
 Coralliophila radula showed a pronounced genetic break across the Sunda
 Shelf (Φ CT = 0.735) but exhibited no genetic structure with respect to
 host. C. violacea exhibited significant geographic structure (Φ CT =
 0.427), with divergence among Hawaiian populations, the Coral Triangle and
 the Indian Ocean. Notably, C. violacea showed evidence of ecological
 divergence; two lineages were associated with different groups of host
 coral species, one widespread found at all sites, and the other restricted
 to the Coral Triangle. Sympatric populations of C. violacea found on
 different suites of coral species were highly divergent (Φ CT = 0.561, d =
 5.13%), suggesting that symbiotic relationships may contribute to lineage
 diversification in the Coral Triangle.
description: RAD-seq data for Porites
 coral species All the demultiplexed
 forward read data files (RADseq) for Porites coral species used in this
 publication. The barcode and parameter files used for processing in iPyrad
 are also included (demultiplexed_forward_reads.zip).
DOI: 10.5061/dryad.r8t2m
title: Data from: Robust DNA isolation and high-throughput sequencing library construction for herbarium specimens

description: Herbaria are an invaluable source of plant material that can be used in a
 variety of biological studies. The use of herbarium specimens is
 associated with a number of challenges including sample preservation
 quality, degraded DNA, and destructive sampling of rare specimens. In
 order to more effectively use herbarium material in large sequencing
 projects, a dependable and scalable method of DNA isolation and library
 preparation is needed. This paper demonstrates a robust, beginning-to-end
 protocol for DNA isolation and high-throughput library construction from
 herbarium specimens that does not require modification for individual
 samples. This protocol is tailored for low quality dried plant material
 and takes advantage of existing methods by optimizing tissue grinding,
 modifying library size selection, and introducing an optional
 reamplification step for low yield libraries. Reamplification of low yield
 DNA libraries can rescue samples derived from irreplaceable and
 potentially valuable herbarium specimens, negating the need for additional
 destructive sampling and without introducing discernible sequencing bias
 for common phylogenetic applications. The protocol has been tested on
 hundreds of grass species, but is expected to be adaptable for use in
 other plant lineages after verification. This protocol can be limited by
 extremely degraded DNA, where fragments do not exist in the desired size
 range, and by secondary metabolites present in some plant material that
 inhibit clean DNA isolation. Overall, this protocol introduces a fast and
 comprehensive method that allows for DNA isolation and library preparation
 of 24 samples in less than 13 hours, with only 8 hours of active hands-on
 time with minimal modifications.
description: Saeidi_etal_Dryad_Submission_REPLACESee README.Saeidi_etal_Dryad_Submission.tar.gz
DOI: 10.5061/dryad.d1s39
title: Data from: Community assembly in Lake Tanganyika cichlid fish: quantifying the contributions of both niche-based and neutral processes

description: The cichlid family features some of the most spectacular examples of
 adaptive radiation. Evolutionary studies have highlighted the importance
 of both trophic adaptation and sexual selection in cichlid speciation.
 However, it is poorly understood what processes drive the composition and
 diversity of local cichlid species assemblages on relatively short,
 ecological timescales. Here, we investigate the relative importance of
 niche-based and neutral processes in determining the composition and
 diversity of cichlid communities inhabiting various environmental
 conditions in the littoral zone of Lake Tanganyika, Zambia. We collected
 data on cichlid abundance, morphometrics, and local environments. We
 analyzed relationships between mean trait values, community composition,
 and environmental variation, and used a recently developed modeling
 technique (STEPCAM) to estimate the contributions of niche-based and
 neutral processes to community assembly. Contrary to our expectations, our
 results show that stochastic processes, and not niche-based processes,
 were responsible for the majority of cichlid community assembly. We also
 found that the relative importance of niche-based and neutral processes
 was constant across environments. However, we found significant
 relationships between environmental variation, community trait means, and
 community composition. These relationships were caused by niche-based
 processes, as they disappeared in simulated, purely neutrally assembled
 communities. Importantly, these results can potentially reconcile
 seemingly contrasting findings in the literature about the importance of
 either niche-based or neutral-based processes in community assembly, as we
 show that significant trait relationships can already be found in nearly
 (but not completely) neutrally assembled communities; that is, even a
 small deviation from neutrality can have major effects on community
 patterns.
description: STEPCAM
 outputThe zip file contains
 the raw STEPCAM output for each transect, 3 replicate runs (with different
 seeds) per transect. The zip file is organized as follows: each folder
 (name = fit_transectNo_repl) contains the R files used to run STEPCAM,
 temporary intermediate output ("particles_temp_t=XX.txt"), a
 text file tracking the acceptance rate ("accepted_t=XX.txt") and
 the final posterior distribution (STEPCAM
 Results.zipTransect
 dataThe zip file contains
 the raw pictures taken along each transect. Transects are numbered
 following Table S1. Each folder contains all used pictures. Added are the
 MATLAB scripts used to calculate the relative sand cover within each
 quadrant. Resulting Sand cover estimates are included in the respective
 text files.Transect_data.zip
DOI: 10.5061/dryad.8vp47
title: Data from: Neural correlates of successful and unsuccessful strategical mechanisms involved in uncertain decision-making

description: The ability to develop successful long-term strategies in uncertain
 situations relies on complex neural mechanisms. Although lesion studies
 have shown some of the mechanisms involved, it is still unknown why some
 healthy subjects are able to make the right decision whereas others are
 not. The aim of our study was to investigate neurophysiological
 differences underlying this ability to develop a successful strategy in a
 group of healthy subjects playing a monetary card game called the Iowa
 Gambling Task (IGT). In this task, subjects have to win and earn money by
 choosing between four decks of cards, two were advantageous in the long
 term and two disadvantageous. Twenty healthy right-handed subjects
 performed the IGT while their cerebral activity was recorded by
 electroencephalography. Based on their behavioral performances, two groups
 of subjects could clearly be distinguished: one who selected the good
 decks and thus succeeded in developing a Favorable strategy (9 subjects)
 and one who remained Undecided (11 subjects). No neural difference was
 found between each group before the selection of a deck, but in both
 groups a greater negativity was found emerging from the right superior
 frontal gyrus 600 ms before a disadvantageous selection. During the
 processing of the feedback, an attenuation of the P200 and P300 waveforms
 was found for the Undecided group, and a P300 originating from the medial
 frontal gyrus was found in response to a loss only in the Favorable group.
 Our results suggest that undecided subjects are hyposensitive to the
 valence of the cards during gambling, which affects the feedback
 processing.
description: rawEEG-s1rawEEG-s2rawEEG-s3rawEEG-s4rawEEG-s5rawEEG-s6rawEEG-s7rawEEG-s8rawEEG-s9rawEEG-s10rawEEG-s11rawEEG-s12rawEEG-s13rawEEG-s15rawEEG-s14rawEEG-s16rawEEG-s17rawEEG-s18rawEEG-s19rawEEG-s20behavior_all_subjectsBehavioral data from all 20 participantsreadme
DOI: 10.5061/dryad.79822
title: Data from: Root volume distribution of maturing perennial grasses revealed by correcting for minirhizotron surface effects

description: Aims: Root architecture drives plant ecology and physiology, but current
 detection methods limit understanding of root placement within soil
 profiles. We developed a statistical model of root volume along depth
 gradients and used it to infer carbon storage potential of land-use
 changes from conventional agriculture to perennial bioenergy grasses.
 Methods: We estimated root volume of maize-soybean rotation and three
 perennial grass systems (Miscanthus × giganteus, Panicum virgatum,
 tallgrass prairie mix) by Bayesian modeling from minirhizotron images,
 correcting for small images and near-surface underdetection. We monitored
 seasonal and inter-annual changes in root volume distribution, then
 validated our estimates against root mass from core samples. Results: The
 model explained 29% of root volume variation and validated well against
 core mass. Seventh-year perennials had greater belowground biomass than
 maize-soybean both in total (11-16×) and throughout the profile (2-17× at
 every depth &lt; 120 cm). Perennials’ relative depth allocations were
 stable over time, while total root volume increased through five years. In
 2012 a historically hot, dry summer damaged maize while perennials
 appeared resilient, suggesting their large-deep root systems aid drought
 resistance. Conclusions: Perennial root systems are large, deep, and
 persistent. Converting row crops to perennial bioenergy grasses likely
 sequesters carbon in a large, potentially very stable, soil pool.
description: READMERaw image
 filesRootvolume_Black_etal_2017_images.zipImage tracing dataFull outputs from the manual image-tracing stage of the analysis. Includes the same data and log files included in the working directory's `rawdata/` folder, plus `.pat` files containing pixel-by-pixel coordinates of every root in each image traced in the experiment... but in an undocumented format :(Rootvolume_Black_etal_2017_tracefiles.zipFull Stan outputFull output (~900 MB) from the Stan models, including saved HMC chains and a lot of diagnostic plots.Rootvolume_Black_etal_2017_stan_output.zipData, analysis scripts, and resultsThis is the main working directory for the project and it contains clean data, all scripts needed to reproduce the analysis, results, figures, notes from the development process, and assorted ancillary files. These files are also available on GitHub (https://github.com/infotroph/efrhizo); this zip file is a snapshot of that repository at revision 8783e81.Rootvolume_Black_etal_2017_scripts_results.zip
DOI: 10.15468/dl.m6q7e6
title: Occurrence Download

description: A dataset containing 121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-180 -60,-70 -60,-70 70,-180 70,-180 -60))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (e9f60bdb-217d-4b4e-a22a-2781321220a1, 28eb1a3f-1c15-4a95-931a-4af90ecb574d, 2538e1c8-ae3c-4812-b6aa-ca9aa53ba277, bf0d80b3-46da-4e60-b1cf-39f2320acb43, c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f, 1928bdf0-f5d2-11dc-8c12-b8a03c50a862)",
 "TaxonKey is Balaenoptera edeni",
 "Year 2000-2026"
 ]
}

 The dataset includes 121 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000443-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m20kh
title: Data from: A double-sided microscope to realize whole-ganglion imaging of membrane potential in the medicinal leech

description: Studies of neuronal network emergence during sensory processing and motor
 control are greatly promoted by technologies that allow us to
 simultaneously record the membrane potential dynamics of a large
 population of neurons in single cell resolution. To achieve whole-brain
 recording with the ability to detect both small synaptic potentials and
 action potentials, we developed a voltage-sensitive dye (VSD) imaging
 technique based on a double-sided microscope that can image two sides of a
 nervous system simultaneously. We applied this system to the segmental
 ganglia of the medicinal leech Hirudo verbana. Double-sided VSD imaging
 enabled simultaneous recording of membrane potential events from almost
 all of the identifiable neurons. Using data obtained from double-sided VSD
 imaging we analyzed neuronal dynamics in both sensory processing and
 generation of behavior and constructed functional maps for identification
 of neurons contributing to these processes.
description: Fig2This archive contains
 the source data and codes for Figures 2b-c.Fig3This archive contains
 the source data and codes for Figures 3c-h.Fig4This archive contains
 the source data and codes for Figures 4a-i.Fig5This archive contains
 the source data and codes for Figures 5a-c.SupplementaryThis archive contains the source data and codes for Supplementary Figures: Fig.1 Supp.1-3, Fig.2 Sup1. and Fig.3 Supp1.functionsAll M-file codes were written in GNU Octave, version 4.0.0 (Free software licensed under the GNU General Public License; https://www.gnu.org/software/octave). You will first need to download octave functions of Wagenaar lab package (https://github.com/wagenadl/octave-wagenaarlab/releases/latest) and Qplot package (https://github.com/wagenadl/qplot/releases/latest) from from GitHub. Then, load packages of 'wagenaarlab', 'qplot', 'signal', 'statistics' before running a code. A manual of M-file functions for analyzing Vscope datasets (by Daniel A. Wagenaar) is available for understanding and using those functions ('vscope_functionNotes.txt' in the folder 'functions').
DOI: 10.5061/dryad.s3015
title: Data from: Extreme climate events counteract the effects of climate and land-use changes in Alpine treelines

description: Climate change and extreme events, such as drought, threaten ecosystems
 world-wide and in particular mountain ecosystems, where species often live
 at their environmental tolerance limits. In the European Alps, plant
 communities are also influenced by land-use abandonment leading to woody
 encroachment of subalpine and alpine grasslands. In this study, we
 explored how the forest–grassland ecotone of Alpine tree lines will
 respond to gradual climate warming, drought events and land-use change in
 terms of forest expansion rates, taxonomic diversity and functional
 composition. We used a previously validated dynamic vegetation model,
 FATE-HD, parameterized for plant communities in the Ecrins National Park
 in the French Alps. Our results showed that intense drought counteracted
 the forest expansion at higher elevations driven by land-use abandonment
 and climate change, especially when combined with high drought frequency
 (occurring every 2 or less than 2 years). Furthermore, intense and
 frequent drought accelerated the rates of taxonomic change and resulted in
 overall higher taxonomic spatial heterogeneity of the ecotone than would
 be expected under gradual climate and land-use changes only. Synthesis and
 applications. The results from our model show that intense and frequent
 drought counteracts forest expansion driven by climate and land-use
 changes in the forest–grassland ecotone of Alpine tree lines. We argue
 that land-use planning must consider the effects of extreme events, such
 as drought, as well as climate and land-use changes, since extreme events
 might interfere with trends predicted under gradual climate warming and
 agricultural abandonment.
description: Data files and Rscripts
 - part1Rates of
 shrubland/forest expansion, temporal and spatial ecotone beta-diversity
 and changes in Community soil moisture values + R scripts - part1. See
 README file for further detailsDrought1.zipData files and Rscripts - part2Rates of shrubland/forest expansion, temporal and spatial ecotone beta-diversity and changes in Community soil moisture values + R scripts - part2. See README file for further detailsDrought2.zipData files and Rscripts - part3Rates of shrubland/forest expansion, temporal and spatial ecotone beta-diversity and changes in Community soil moisture values + R scripts - part3. See README file for further detailsDrought3.zipData files and Rscripts - part4Rates of shrubland/forest expansion, temporal and spatial ecotone beta-diversity and changes in Community soil moisture values + R scripts - part4. See README file for further detailsDrought4.zip
DOI: 10.5061/dryad.4tr2v
title: Data from: Mutation accumulation and the formation of range limits

description: The dynamics of range formation are important for understanding and
 predicting species distributions. Here, we focus on a process that has
 thus far been overlooked in the context of range formation; the
 accumulation of mutation load. We find that mutation accumulation severely
 reduces the extent of a range across an environmental gradient, especially
 when dispersal is limited, growth rate is low and mutations are of
 intermediate deleterious effect. Our results illustrate the important role
 deleterious mutations can play in range formation. We highlight this as a
 necessary focus for further work, noting particularly the potentially
 conflicting effects dispersal may have in reducing mutation load and
 simultaneously increasing migration load in marginal populations.
description: Raw data file
 1The
 raw data files were first zipped before being split so they could be
 uploaded to Dryad. The data files contain information for each patch on
 the simulated landscape through time. Files contain self explanatory
 column headings. Data used and presented in the paper are contained in the
 folders named, 'mut_load_10.10' and
 'varying_static_K'. Other folders contain data used to test the
 effect of selfing and back mutations in the simulations. These data were
 used to answer referee questions but were not presented or discussed in
 the results.xaaRaw data file 2xabRaw data file 3xacRaw data file 4xad