cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k282c
title: Data from: Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

description: The marine cyanobacterium Prochlorococcus is the numerically dominant
 photosynthetic organism in the oligotrophic oceans, and a model system in
 marine microbial ecology. Here we report 27 new whole genome sequences (2
 complete and closed; 25 of draft quality) of cultured isolates,
 representing five major phylogenetic clades of Prochlorococcus. The
 sequenced strains were isolated from diverse regions of the oceans,
 facilitating studies of the drivers of microbial diversity—both in the lab
 and in the field. To improve the utility of these genomes for comparative
 genomics, we also define pre-computed clusters of orthologous groups of
 proteins (COGs), indicating how genes are distributed among these and
 other publicly available Prochlorococcus genomes. These data represent a
 significant expansion of Prochlorococcus reference genomes that are useful
 for numerous applications in microbial ecology, evolution and
 oceanography.
description: Prochlorococcus genomes
 and cluster of orthologous groups of proteins (COGs)Cluster assignments and
 annotation metadata for genes in the newly sequenced Prochlorococcus
 genomes described in this work, as well as in previously published
 genomes.Prochlorococcus_COGS_annotations.txtDetailed annotation information for Prochlorococcus genomesSet of tables providing detailed annotation information for each newly sequenced Prochlorococcus genome, as well as re-annotations of previously published genomes.detailed_Prochlorococcus_genome_annotations.zipProchlorococcus genome sequencesSet of nucleotide FASTA-formatted files containing the new Prochlorococcus genome assemblies described in this work.Prochlorococcus_genome_sequences.zipComplete set of initial contig assemblies from non-axenic Prochlorococcus culturesSet of nucleotide FASTA files containing all assembled contigs (&gt;500 bp) from each culture (i.e. both Prochlorococcus and heterotrophs) sequenced in this work. Each file contains the set of contigs assembled from the raw sequencing data, before any filtering to separate Prochlorococcus from heterotroph contigs.Prochlorococcus_cultures_complete_contig_sets.zipAll predicted Prochlorococcus ORFs, nucleotide sequenceSet of nucleotide FASTA files containing the predicted nucleotide sequence for all open reading frames (ORFs) in each genome. This file includes ORFs from both the new genomes presented here as well as the re-annotation of previously released Prochlorococcus genomes.all_Prochlorococcus_ORFs_fna.zipAll predicted Prochlorococcus ORFs, amino acid sequenceSet of protein FASTA files containing the predicted amino acid translation for all ORFs in each genome. This file includes ORFs from both the new genomes presented here as well as the re-annotation of previously released Prochlorococcus genomes.all_Prochlorococcus_ORFs_faa.zip
DOI: 10.5061/dryad.1257p
title: Data from: I meant to do that: determining the intentions of action in the face of disturbances

description: Our actions often do not match our intentions when there are external
 disturbances such as turbulence. We derived a novel modeling approach for
 determining this motor intent from targeted reaching motions that are
 disturbed by an unexpected force. First, we demonstrated how to
 mathematically invert both feedforward (predictive) and feedback controls
 to obtain an intended trajectory. We next examined the model’s sensitivity
 to a realistic range of parameter uncertainties, and found that the
 expected inaccuracy due to all possible parameter mis-estimations was less
 than typical movement-to-movement variations seen when humans reach to
 similar targets. The largest sensitivity arose mainly from uncertainty in
 joint stiffnesses. Humans cannot change their intent until they acquire
 sensory feedback, therefore we tested the hypothesis that a straight-line
 intent should be evident for at least the first 120 milliseconds following
 the onset of a disturbance. As expected, the intended trajectory showed no
 change from undisturbed reaching for more than 150 milliseconds after the
 disturbance onset. Beyond this point, however, we detected a change in
 intent in five out of eight subjects, surprisingly even when the hand is
 already near the target. Knowing such an intent signal is broadly
 applicable: enhanced human-machine interaction, the study of impaired
 intent in neural disorders, the real-time determination (and manipulation)
 of error in training, and complex systems that embody planning such as
 brain machine interfaces, team sports, crowds, or swarms. In addition,
 observing intent as it changes might act as a window into the mechanisms
 of planning, correction, and learning.
description: Horowitz and Patton 2015
 Intent Despite Intermittent DisturbanceData for each of eight
 human subjects is in a MATLAB structure array by trial. Fieldnames are
 descriptive. Experiment consists of targeted reaching with intermittent
 disturbance by large pulses of force or Gaussian noise.horowitzPattonIntent.zip
DOI: 10.5061/dryad.75j0k9c
title: Data from: Coupled land use and ecological models reveal emergence and feedbacks in socio‐ecological systems

description: Understanding the dynamics of socio‐ecological systems is crucial to the
 development of environmentally sustainable practices. Models of social or
 ecological sub‐systems have greatly enhanced such understanding, but at
 the risk of obscuring important feedbacks and emergent effects. Integrated
 modelling approaches have the potential to address this shortcoming by
 explicitly representing linked socio‐ecological dynamics. We developed a
 socio‐ecological system model by coupling an existing agent‐based model of
 land‐use dynamics and an individual‐based model of demography and
 dispersal. A hypothetical case‐study was established to simulate the
 interaction of crops and their pollinators in a changing agricultural
 landscape, initialised from a spatially random distribution of natural
 assets. The bi‐directional coupled model predicted larger changes in crop
 yield and pollinator populations than a unidirectional uncoupled version.
 The spatial properties of the system also differed, the coupled version
 revealing the emergence of spatial land‐use clusters that neither
 supported nor required pollinators. These findings suggest that important
 dynamics may be missed by uncoupled modelling approaches, but that these
 can be captured through the combination of currently‐available, compatible
 model frameworks. Such model integrations are required to further
 fundamental understanding of socio‐ecological dynamics and thus improve
 management of socio‐ecological systems.
description: All_ResultSummaryData file containing all simulation results. Column "Group" represents the group classification for each value, used to subset data for different analyses. "SimID" uniquely identifies each simulation's parameterisation (represented by the parameters: "Coupled", "NoPolliYield", "Rmax", "CarryingCapacity", "DispersalType").
DOI: 10.5061/dryad.1ck400f
title: Data from: Extreme diversity in the songs of Spitsbergen’s bowhead whales

description: Almost all mammals communicate using sound, but few species produce
 complex songs. Two baleen whales sing complex songs that change annually,
 though only the humpback whale (Megaptera novaeangliae) has received much
 research attention. This study focuses on the other baleen whale singer,
 the bowhead whale (Balaena mysticetus). Members of the Spitsbergen bowhead
 whale population produced 184 different song types over a 3-year period,
 based on duty-cycled recordings from a site in Fram Strait in the NE
 Atlantic. Distinct song types were recorded over short periods, lasting at
 most some months. This song diversity could be the result of a possibly
 increasing population, or immigration of animals from other populations
 that are no longer isolated from each other by heavy sea ice. However,
 this explanation does not account for the within season and annual
 shifting of song types. Other possible explanations, is that the
 extraordinary diversity in songs is the result of weak selection pressure
 for interspecific identification or for maintain song characteristics or,
 alternatively, strong pressure for novelty in a small population.
description: Exemplars of unique
 bowhead whales songs recorded in Fram Strait 2010-11, 2012-13,
 2013-14Bowhead whales produce
 multiple unique songs annually. This dataset provides exemplars of each of
 184 unique songs recorded over three winters in Fram Strait. In 2010-2011,
 38 songs were identified; in 2012-13, 69 songs were identified and in
 2013-14, 76 songs were identified. The zip file contains one exemplar of
 each song type as an mp3 file. The dates and times these were recorded is
 in the README.txt fileSongs-RSBL-2018-0056.zip
DOI: 10.15468/dl.tm88mj
title: Occurrence Download

description: A dataset containing 1663 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Gerrhonotus infernalis"
 ]
}

 The dataset includes 1663 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000393-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.63j2j
title: Data from: Efficient detection of novel nuclear markers for Brassicaceae by transcriptome sequencing

description: The lack of DNA sequence information for most non-model organisms impairs
 the design of primers that are universally applicable for the study of
 molecular polymorphisms in nuclear markers. Next-generation sequencing
 (NGS) techniques nowadays provide a powerful approach to overcome this
 limitation. We present a flexible and inexpensive method to identify large
 numbers of nuclear primer pairs that amplify in most Brassicaceae species.
 We first obtained and mapped NGS transcriptome sequencing reads from two
 of the distantly related Brassicaceae species, Cardamine hirsuta and
 Arabis alpina, onto the Arabidopsis thaliana reference genome, and then
 identified short conserved sequence motifs among the three species
 bioinformatically. From these, primer pairs to amplify coding regions
 (nuclear protein coding loci, NPCL) and exon-primed intron-crossing
 sequences (EPIC) were developed. We identified 2,334 universally
 applicable primer pairs, targeting 1,164 genes, which provide a large pool
 of markers as readily usable genomic resource that will help addressing
 novel questions in the Brassicaceae family. Testing a subset of the newly
 designed nuclear primer pairs revealed that a great majority yielded a
 single amplicon in all of the 30 investigated Brassicaceae taxa. Sequence
 analysis and phylogenetic reconstruction with a subset of these markers on
 different levels of phylogenetic divergence in the mustard family were
 compared with previous studies. The results corroborate the usefulness of
 the newly developed primer pairs, e.g., for phylogenetic analyses or
 population genetic studies. Thus, our method provides a cost-effective
 approach for designing nuclear loci across a broad range of taxa and is
 compatible with current NGS technologies.
description: Sequence alignments for
 Arabis alpina Cardamine hirsutaWe provide here the
 sequence alignment files of two transcriptome sequencing runs on a Genome
 Sequencer FLX (Roche, Switzerland) for pooled RNA samples of Arabis alpina
 and Cardamine hirsuta mapped to Arabidopsis thaliana (TAIR 9). Each sample
 was sequenced twice on half a picotiter plate. The alignments were used to
 detect conserved regions among the aforementioned species. The reads have
 been mapped against the five chromosomes of Arabidopsis thaliana (TAIR9)
 using samtools (Li et al. 2009).Arabis_alpina_and_Cardamine_hirsuta_mapped.zipConcatenated alignments for all three phylogenetic levels testedConcatenated_alignments.zip
DOI: 10.5061/dryad.553cm8g
title: Data from: Demographic inferences after a range expansion can be biased: the test case of the blacktip reef shark (Carcharhinus melanopterus)

description: The evolutionary history of species is a dynamic process as they modify,
 expand and contract their spatial distributions over time. Range
 expansions (REs) occur through a series of founder events that are
 followed by migration among neighbouring demes. The process usually
 results in structured metapopulations and leaves a distinct signature in
 the genetic variability of species. Explicitly modeling the consequences
 of complex demographic events such as REs is computationally very
 intensive. Here we propose an an alternative approach that requires less
 computational effort than a comprehensive RE model, but that can recover
 the demography of species undergoing a RE, by combining spatially explicit
 modelling with simplified but realistic metapopulation models. We examine
 the demographic and colonization history of Carcharhinus melanopterus, an
 abundant reef-associated shark, as a test case. We first used a population
 genomics approach to statistically confirm the occurrence of a RE in C.
 melanopterus and identify its origin in the Indo-Australian Archipelago.
 Spatial genetic modelling identified two waves of stepping-stone
 colonization: an eastward wave moving through the Pacific and a westward
 one moving through the Indian Ocean. We show that metapopulation models
 best describe the demographic history of this species and that not
 accounting for this may lead to incorrectly interpreting the observed
 genetic variation as signals of widespread population bottlenecks. Our
 study highlights insights that can be gained about demography by coupling
 metapopulation models with spatial modeling and underscores the need for
 cautious interpretation of population genetic data when advancing
 conservation priorities.
description: CM_144samples_MQ40_BQ20_ref200bpNs_exons+introns_12_C50_DP6_SP13_NA0_noMonomorphicSNPs_notriallelic_tag11_dryad.vcfVcf file containing fenotype calls for 144 samples after filtering.cl_cf_co_na_C50_DP6_SP13_merge_144CM.vcfVCF file containing genotype calls for 144 samples (C. melanopterus) and 4 outgroups as described in the readme file.Sample ID and originFile containing sample ID and origin.CM_144samples_MQ40_BQ20_ref200bpNs_exons+introns_12_C50_DP6_SP13_NA0_noMonomorphicSNPs_notriallelic_tag11_dryad_IDsamples
DOI: 10.5061/dryad.316c7h6
title: Data from: A targeted in situ hybridization screen identifies putative seminal fluid proteins in a simultaneously hermaphroditic flatworm

description: Background: Along with sperm, in many taxa ejaculates also contain large
 numbers of seminal fluid proteins (SFPs). SFPs and sperm are transferred
 to the mating partner, where they are thought to play key roles in
 mediating post-mating sexual selection. They modulate the partner's
 behavior and physiology in ways that influence the reproductive success of
 both partners, thus potentially leading to sexual conflict. Despite the
 presumed general functional and evolutionary significance of SFPs, their
 identification and characterization has to date focused on just a few
 animal groups, predominantly insects and mammals. Moreover, until now
 seminal fluid profiling has mainly focused on species with separate sexes.
 Here we report a comprehensive screen for putative SFPs in the
 simultaneously hermaphroditic flatworm Macrostomum lignano. Results: Based
 on existing transcriptomic data, we selected 150 transcripts known to be
 (a) predominantly expressed in the tail region of the worms, where the
 seminal fluid-producing prostate gland cells are located, and (b)
 differentially expressed in social environments differing in sperm
 competition level, strongly implying that they represent a phenotypically
 plastic aspect of male reproductive allocation in this species. For these
 SFP candidates, we then performed whole mount in situ hybridization (ISH)
 experiments to characterize tissue-specific expression. In total, we
 identified 98 transcripts that exhibited prostate-specific expression, 76
 of which we found to be expressed exclusively in the prostate gland cells;
 additional sites of expression for the remaining 22 included the testis or
 other gland cells. Bioinformatics analyses of the prostate-limited
 candidates revealed that at least 64 are predicted to be secretory
 proteins, making these especially strong candidates to be SFPs that are
 transferred during copulation. Conclusions: Our study represents a first
 comprehensive analysis using a combination of transcriptomic and
 whole-mount ISH screen data to identify SFPs based on transcript
 expression in seminal fluid-producing tissues. We thereby extend the range
 of taxa for which seminal fluid has been characterized to a flatworm
 species with a sequenced genome and for which several methods such as
 antibody staining, transgenesis and RNA interference have been
 established. Our data provide a basis for testing the functional and
 evolutionary significance of SFPs.
description: in situ hybridization
 picturesA collection of 3-5 ISH
 pictures for each transcript.ISH pictures
 supplementary.zip
DOI: 10.15468/dl.3ushun
title: Occurrence Download

description: A dataset containing 10044 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "Geometry POLYGON((-137.45999 -8.83352,-14.25295 -8.83352,-14.25295 40.50910,-137.45999 40.50910,-137.45999 -8.83352))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ctenosaura similis",
 "Year 2020-2026"
 ]
}

 The dataset includes 10044 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000391-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jc3ht
title: Data from: Genome-environment associations in sorghum landraces predict adaptive traits

description: Improving environmental adaptation in crops is essential for food security
 under global change, but phenotyping adaptive traits remains a major
 bottleneck. If associations between single-nucleotide polymorphism (SNP)
 alleles and environment of origin in crop landraces reflect adaptation,
 then these could be used to predict phenotypic variation for adaptive
 traits. We tested this proposition in the global food crop Sorghum
 bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and
 quantifying allelic associations with bioclimatic and soil gradients.
 Environment explained a substantial portion of SNP variation, independent
 of geographical distance, and genic SNPs were enriched for environmental
 associations. Further, environment-associated SNPs predicted
 genotype-by-environment interactions under experimental drought stress and
 aluminum toxicity. Our results suggest that genomic signatures of
 environmental adaptation may be useful for crop improvement, enhancing
 germplasm identification and marker-assisted selection. Together,
 genome-environment associations and phenotypic analyses may reveal the
 basis of environmental adaptation.
description: snpsLaskySciAdv_dryad.tar
DOI: 10.5061/dryad.n55r8
title: Data from: Incubator-independent cell-culture perfusion platform for continuous long-term microelectrode array electrophysiology and time-lapse imaging

description: Most in vitro electrophysiology studies extract information and draw
 conclusions from representative, temporally limited snapshot experiments.
 This approach bears the risk of missing decisive moments that may make a
 difference in our understanding of physiological events. This feasibility
 study presents a simple benchtop cell-culture perfusion system adapted to
 commercial microelectrode arrays (MEAs), multichannel electrophysiology
 equipment and common inverted microscopy stages for simultaneous and
 uninterrupted extracellular electrophysiology and time-lapse imaging at
 ambient CO2 levels. The concept relies on a transparent, replica-casted
 polydimethylsiloxane perfusion cap, gravity- or syringe-pump-driven
 perfusion and preconditioning of pH-buffered serum-free cell-culture
 medium to ambient CO2 levels at physiological temperatures. The low-cost
 microfluidic in vitro enabling platform, which allows us to image cultures
 immediately after cell plating, is easy to reproduce and is adaptable to
 the geometries of different cell-culture containers. It permits the
 continuous and simultaneous multimodal long-term acquisition or
 manipulation of optical and electrophysiological parameter sets, thereby
 considerably widening the range of experimental possibilities. Two
 exemplary proof-of-concept long-term MEA studies on hippocampal networks
 illustrate system performance. Continuous extracellular recordings over a
 period of up to 70 days revealed details on both sudden and gradual neural
 activity changes in maturing cell ensembles with large intra-day
 fluctuations. Correlated time-lapse imaging unveiled rather static
 macroscopic network architectures with previously unreported local
 morphological oscillations on the timescale of minutes.
description: RSOS-150031 data
 filesData files accompanying
 manuscript 'Incubator-independent cell culture perfusion platform for
 continuous long-term microelectrode array electrophysiology and time-lapse
 imaging' by irk Saalfrank, Anil Krishna Konduri, Shahrzad Latifi,
 Rouhollah Habibey, Asiyeh Golabchi, Aurel Vasile Martiniuc, Alois Knoll,
 Sven Ingebrandt, and Axel BlauRSOS-150031data
 files.zip
DOI: 10.5061/dryad.4pf96
title: Data from: RNA-Seq reveals virus–virus and virus–plant interactions in nature

description: As research on plant viruses has focused mainly on crop diseases, little
 is known about these viruses in natural environments. To understand the
 ecology of viruses in natural systems, comprehensive information on
 virus–virus and virus–host interactions is required. We applied RNA-Seq to
 plants from a natural population of Arabidopsis halleri subsp. gemmifera
 to simultaneously determine the presence/absence of all sequence-reported
 viruses, identify novel viruses, and quantify the host transcriptome. By
 introducing the criteria of read number and genome coverage, we detected
 infections by Turnip mosaic virus (TuMV), Cucumber mosaic virus, and
 Brassica yellows virus. Active TuMV replication was observed by
 ultramicroscopy. De novo assembly further identified a novel partitivirus,
 Arabidopsis halleri partitivirus 1. Interestingly, virus reads reached a
 maximum level that was equivalent to that of the host's total mRNA,
 although asymptomatic infection was common. AhgAGO2, a key gene in host
 defence systems, was upregulated in TuMV-infected plants. Multiple
 infection was frequent in TuMV-infected leaves, suggesting that TuMV
 facilitates multiple infection, probably by suppressing host RNA
 silencing. Revealing hidden plant–virus interactions in nature can enhance
 our understanding of biological interactions and may have agricultural
 applications.
description: halleri_transcript_modified_lyrataJGI_ERCC_2_CBF2_Virus3981_AhgThe reference transcriptome sequences file of Arabidopsis halleri subsp. gemmifera