cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r4342
title: Data from: Formin is associated with left-right asymmetry in the pond snail and the frog

description: While components of the pathway that establishes left-right asymmetry have
 been identified in diverse animals, from vertebrates to flies, it is
 striking that the genes involved in the first symmetry-breaking step
 remain wholly unknown in the most obviously chiral animals, the gastropod
 snails. Previously, research on snails was used to show that left-right
 signaling of Nodal, downstream of symmetry breaking, may be an ancestral
 feature of the Bilateria. Here, we report that a disabling mutation in one
 copy of a tandemly duplicated, diaphanous-related formin is perfectly
 associated with symmetry breaking in the pond snail. This is supported by
 the observation that an anti-formin drug treatment converts dextral snail
 embryos to a sinistral phenocopy, and in frogs, drug inhibition or
 overexpression by microinjection of formin has a chirality-randomizing
 effect in early (pre-cilia) embryos. Contrary to expectations based on
 existing models, we discovered asymmetric gene expression in 2- and 4-cell
 snail embryos, preceding morphological asymmetry. As the formin-actin
 filament has been shown to be part of an asymmetry-breaking switch in
 vitro, together these results are consistent with the view that animals
 with diverse body plans may derive their asymmetries from the same
 intracellular chiral elements.
description: Alignment of formin
 intron sequences from Euhadra speciesData relates to Figure
 S2d.Euhadra_formin_intron_sequence.fasAlignment of formin intron sequences from Partula speciesData relates to Figure S2ePartula_formin_intron_sequences.fasAlignment of FH2 domain sequencesData relates to Figure S2a. Original alignment kindly provided by Dimitra Chalkia (see Chalkia et al 2008). New accessions were then added manually.FH2_animals.fasAlignment of gastropod FH2 domain sequencesData relates to Figure S2bgastropods_fh2_domain_aligned.fasAlignment of formin gene sequences from Lymnaea stagnalisContains sequences of Ldia1 and Ldia2, derived from dextral and sinistral haplotypesLdia_aligned.fasPredicted gene sequences for candidate genesSequences for sinistral and dextral-derived haplotypesLfry_Ltud_Lprcp_Lmfsd.fasConcatenated alignment of 28S and 18S sequencesConcatenated alignment of 28S (1-3712) and 18S sequences (3716-5448). Data relates to Figure S2c and Figure 1.LSU_SSU.fasTable S1Table S1 from the paper in Excel formatqPCR raw dataThe data in this files relates to Figure 1, Figure S2a and text in the Supplementary Information. Further detail within the file.qPCR_raw_data_relates_to_Fig1_FigS2a.xlsxAssembly of BACsAssembly of the BAC sequences with SPAdes assembler, removing the low coverage scaffolds.BAC_assembly.fasta.gzGenome assembly of Lymnaea stagnalisThe genome of Lymnaea stagnalis assembled with SOAPdenovo using PE and MP libraries.gLs.scaffolds.fa.gz
DOI: 10.5281/zenodo.18380619
title: Tailoring the extraction process and properties of polysaccharides from the lichen Evernia prunastri using natural eutectic solvents following a biorefinery approach
DOI: 10.5281/zenodo.18380620
title: Tailoring the extraction process and properties of polysaccharides from the lichen Evernia prunastri using natural eutectic solvents following a biorefinery approach
DOI: 10.5061/dryad.b1500
title: Data from: Serendipitous meta-transcriptomics: the fungal community of Norway spruce (Picea abies)

description: After performing de novo transcript assembly of &gt;1 billion
 RNA-Sequencing reads obtained from 22 samples of different Norway spruce
 (Picea abies) tissues that were not surface sterilized, we found that
 assembled sequences captured a mix of plant, lichen, and fungal
 transcripts. The latter were likely expressed by endophytic and epiphytic
 symbionts, indicating that these organisms were present, alive, and
 metabolically active. Here, we show that these serendipitously sequenced
 transcripts need not be considered merely as contamination, as is common,
 but that they provide insight into the plant’s phyllosphere. Notably, we
 could classify these transcripts as originating predominantly from
 Dothideomycetes and Leotiomycetes species, with functional annotation of
 gene families indicating active growth and metabolism, with particular
 regards to glucose intake and processing, as well as gene regulation.
description: Supplementary data
 archive for the Delhomme et al., 2015 manuscript.This archive contains
 supplementary data for the Delhomme et al, 2015 manuscript. It contains
 two directories annotation and fasta. The annotation directory contains
 the metadata resulting from several analysis conducted on the
 transcriptome assembly. The fasta directory contains the transcriptome
 assembly and several different subsets of it. The description of the
 methods used to generate: 1) the different fasta sets that can be found in
 the fasta directory 2) the metadata summarized in the annotation tsv file
 can be found in the manuscript method section.Delhomme2015.tgz
DOI: 10.5061/dryad.j0440
title: Data from: Complementary mechanisms for upright balance during walking

description: Lateral balance is a critical factor in keeping the human body upright
 during walking. Two important mechanisms for balance control are the
 stepping strategy, in which the foot placement is changed in the direction
 of a sensed fall to modulate how the gravitational force acts on the body,
 and the lateral ankle strategy, in which the body mass is actively
 accelerated by an ankle torque. Currently, there is minimal evidence about
 how these two strategies complement one another to achieve upright balance
 during locomotion. We use Galvanic vestibular stimulation (GVS) to induce
 the sensation of a fall at heel-off during gait initiation. We found that
 young healthy adults respond to the illusory fall using both the lateral
 ankle strategy and the stepping strategy. The stance foot center of
 pressure (CoP) is shifted in the direction of the perceived fall by ≈2.5
 mm, starting ≈247 ms after stimulus onset. The foot placement of the
 following step is shifted by ≈15 mm in the same direction. The temporal
 delay between these two mechanisms suggests that they independently
 contribute to upright balance during locomotion, potentially in a serially
 coordinated manner. Modeling results indicate that without the lateral
 ankle strategy, a much larger step width is required to maintain upright
 balance, suggesting that the small but early CoP shift induced by the
 lateral ankle strategy is critical for upright stability during
 locomotion. The relative importance of each mechanism and how neurological
 disorders may affect their implementation remain an open question.
description: data
DOI: 10.5061/dryad.t5800
title: Data from: Compensatory selection for roads over natural linear features by wolves in northern Ontario: implications for caribou conservation

description: Woodland caribou (Rangifer tarandus caribou) in Ontario are a threatened
 species that have experienced a substantial retraction of their historic
 range. Part of their decline has been attributed to increasing densities
 of anthropogenic linear features such as trails, roads, railways, and
 hydro lines. These features have been shown to increase the search
 efficiency and kill rate of wolves. However, it is unclear whether
 selection for anthropogenic linear features is additive or compensatory to
 selection for natural (water) linear features which may also be used for
 travel. We studied the selection of water and anthropogenic linear
 features by 52 resident wolves (Canis lupus x lycaon) over four years
 across three study areas in northern Ontario that varied in degrees of
 forestry activity and human disturbance. We used Euclidean distance-based
 resource selection functions (mixed-effects logistic regression) at the
 seasonal range scale with random coefficients for distance to water linear
 features, primary/secondary roads/railways, and hydro lines, and tertiary
 roads to estimate the strength of selection for each linear feature and
 for several habitat types, while accounting for availability of each
 feature. Next, we investigated the trade-off between selection for
 anthropogenic and water linear features. Wolves selected both
 anthropogenic and water linear features; selection for anthropogenic
 features was stronger than for water during the rendezvous season.
 Selection for anthropogenic linear features increased with increasing
 density of these features on the landscape, while selection for natural
 linear features declined, indicating compensatory selection of
 anthropogenic linear features. These results have implications for
 woodland caribou conservation. Prey encounter rates between wolves and
 caribou seem to be strongly influenced by increasing linear feature
 densities. This behavioral mechanism - a compensatory functional response
 to anthropogenic linear feature density resulting in decreased use of
 natural travel corridors - has negative consequences for the viability of
 woodland caribou.
description: Newton et al wolf travel
 on linear features data for rsf modelsThese data provide
 distances from wolf-points ("use" = 1) to available points
 ("use" = 0) within a wolf's ("ID") seasonal
 range. Standardized distances to each habitat feature are provided.
 Availability of each feature type is also provided (Feature_A). These data
 can be used to replicate all figures and tables in the
 study.Newton_LinearFeatures_AllData_Standardized.csvNewton_et_al_Tortuosity_Velocity_NorthernWolvesData underlying Supplementary Figure S1,Season delineation, tortuosity and velocity of resident adult wolves in northern Ontario, Canada, 2010-2014.
DOI: 10.5061/dryad.785sr
title: Data from: Island bat diets: does it matter more who you are or where you live?

description: Differences in body size, echolocation call frequency, and location may
 result in diet partitioning among bat species. Comparisons among island
 populations are one way to evaluate these competing hypotheses. We
 conducted a species-level diet analysis of three Rhinolophus and one
 Hipposideros species on the Philippine islands of Cebu, Bohol, and
 Siquijor. We identified 655 prey (MOTUs) in the guano from 77 individual
 bats. There was a high degree of overlap among species’ diets despite
 differences in body size and call frequency. For example, the diet of the
 3 g-Hipposideros pygmaeus (mean CF = 102 kHz) exhibited a diet overlap
 higher than expected by chance with all three Rhinolophus species, even
 the 13 g-Rhinolophus inops (mean CF = 54 kHz). We observed more
 convergence in diet between Rhinolophus species and H. pygmaeus than
 between Rhinolophus species themselves, which may be explained by the
 broad diet of H. pygmaeus. There was less dietary overlap between
 Rhinolophus virgo from two islands than between R. virgo and congeners
 from Cebu. These data suggest that location causes convergence in diet,
 but specific species characteristics may drive niche specialization. The
 complex interplay between location and the perceptual ability of each
 species leads to a situation where simple explanations, for example, body
 size, do not translate into predictable prey partitioning. In particular,
 our observations raise interesting questions about the foraging strategy
 and adaptability of the tiny H. pygmaeus.
description: Key To FIles Used For
 AnalysisKey to sequence
 titlesMorph and call
 data_Island Bat Diets 2013Unique Haplotypes wtih
 bat IDUnique Haplotypes with
 bat ID redued to those 157bpR_virgo_BLASTR_inops_BLASTR_arcuatus_BLASTPlease see the read me file for details.H_pygmaeus_BLASTPlease see read me file for instructions.
DOI: 10.5061/dryad.vs044
title: Data from: A 3D anatomical atlas of appendage musculature in the chelicerate arthropod Limulus polyphemus

description: Limulus polyphemus, an archetypal chelicerate taxon, has interested both
 biological and paleontological researchers due to its unique suite of
 anatomical features and as a useful modern analogue for fossil arthropod
 groups. To assist the study and documentation of this iconic taxon, we
 present a 3D atlas on the appendage musculature, with specific focus on
 the muscles of the cephalothoracic appendages. As L. polyphemus appendage
 musculature has been the focus of extensive study, depicting the muscles
 in 3D will facilitate a more complete understanding thereof for future
 researchers. A large museum specimen was CT scanned to illustrate the
 major exoskeletal features of L. polyphemus. Micro-CT scans of
 iodine-stained appendages from fresh, non-museum specimens were digitally
 dissected to interactively depict appendage sections and muscles. This
 study has revealed the presence of two new muscles: one within the pushing
 leg, located dorsally relative to all other patella muscles, and the other
 within the male pedipalp, located in the modified tibiotarsus. This atlas
 increases accessibility to important internal and external morphological
 features of L. polyphemus and reduces the need for destructive fresh
 tissue dissection of specimens. Scanning, digitally dissecting, and
 documenting taxa in 3D is a pivotal step towards creating permanent
 digital records of life on Earth.
description: Supplementary Figure
 1Fig.
 S1: 3D interactive model of the complete Limulus polyphemus specimen, as
 modelled from CT-scanning.Fig._S1.pdfSupplementary Figure 2Fig. S2: 3D interactive model of the Limulus polyphemus chelicera, as modelled from iodine staining and micro-CT-scanning.Fig._S2.pdfSupplementary Figure 3Fig. S3: 3D interactive model of the Limulus polyphemus walking leg, as modelled from iodine staining and micro-CT-scanning.Fig._S3.pdfSupplementary Figure 4Fig. S4: 3D interactive model of the Limulus polyphemus male pedipalp, as modelled from iodine staining and micro-CT-scanning.Fig._S4.pdfSupplementary figure 5Fig. S5: 3D interactive model of the Limulus polyphemus pushing leg, as modelled from iodine staining and micro-CT-scanning.Fig._S5.pdfSupplementary Figure 6Fig. S6: 3D interactive model of the Limulus polyphemus chilaria, as modelled from iodine staining and micro-CT-scanning.Fig._S6.pdfSupplementary Figure 7Fig. S7: 3D interactive model of the Limulus polyphemus genital operculum, as modelled from iodine staining and micro-CT-scanning.Fig._S7.pdfSupplementary Figure 8Fig. S8: 3D interactive model of the Limulus polyphemus gill operculum, as modelled from iodine staining and micro-CT-scanning.Fig._S8.pdf
DOI: 10.5061/dryad.cd3hv
title: Data from: Enhancing genomic prediction with genome-wide association studies in multiparental maize populations

description: Genome-wide association mapping using dense marker sets has identified
 some nucleotide variants affecting complex traits that have been validated
 with fine-mapping and functional analysis. However, many sequence variants
 associated with complex traits in maize have small effects and low
 repeatability. In contrast to genome-wide association study (GWAS),
 genomic prediction (GP) is typically based on models incorporating
 information from all available markers, rather than modeling effects of
 individual loci. We considered methods to integrate results of GWASs into
 GP models in the context of multiple interconnected families. We compared
 association tests based on a biallelic additive model constraining the
 effect of a single-nucleotide polymorphism (SNP) to be equal across all
 families in which it segregates to a model in which the effect of a SNP
 can vary across families. Association SNPs were then included as fixed
 effects into a GP model that also included the random effects of the whole
 genome background. Simulation studies revealed that the effectiveness of
 this joint approach depends on the extent of polygenicity of the traits.
 Congruent with this finding, cross-validation studies indicated that GP
 including the fixed effects of the most significantly associated SNPs
 along with the polygenic background was more accurate than the polygenic
 background model alone for moderately complex but not highly polygenic
 traits measured in the maize nested association mapping population.
 Individual SNPs with strong and robust association signals can effectively
 improve GP. Our approach provides a new integrative modeling approach for
 both reliable gene discovery and robust GP.
description: Bian_2016_GWAS_and_Genomic_Prediction_Data_Supplement
DOI: 10.5061/dryad.gp25h48
title: Data from: Genomic insights into the vulnerability of sympatric whitefish species flocks

description: The erosion of habitat heterogeneity can reduce species diversity directly
 but can also lead to the loss of distinctiveness of sympatric species
 through speciation reversal. We know little about changes in genomic
 differentiation during the early stages of these processes, which can be
 mediated by anthropogenic perturbation. Here, we analyse three sympatric
 whitefish species (Coregonus spp) sampled across two neighbouring and
 connected Swiss pre-alpine lakes, which have been differentially affected
 by anthropogenic eutrophication. Our data set comprises 16,173 loci
 genotyped across 138 whitefish using restriction-site associated DNA
 sequencing (RADseq). Our analysis suggests that in each of the two lakes
 the population of a different, but ecologically similar, whitefish species
 declined following a recent period of eutrophication. Genomic signatures
 consistent with hybridisation are more pronounced in the more severely
 impacted lake. Comparisons between sympatric pairs of whitefish species
 with contrasting ecology, where one is shallow benthic and the other one
 more profundal pelagic, reveal genomic differentiation that is largely
 correlated along the genome, while differentiation is uncorrelated between
 pairs of allopatric provenance with similar ecology. We identify four
 genomic loci that provide evidence of parallel divergent adaptation
 between the shallow benthic species and the two different more profundal
 species. Functional annotations available for two of those loci are
 consistent with divergent ecological adaptation. Our genomic analysis
 indicates the action of divergent natural selection between sympatric
 whitefish species in pre-alpine lakes and reveals the vulnerability of
 these species to anthropogenic alterations of the environment and
 associated adaptive landscape.
description: SRP156755Raw read sequencing files (fastq files for all 180 individuals)Denovo reference loci sequences125154 reference loci, denovo assembled from RAD data using stacks and used for mappingCor_denovo_FB.fasta16731 reference loci sequencesreference sequence for 16731 loci used for genotyping in this study16731Loci.fastagenotypes for 20334 position in 141 individualsgenotypes for 20334 position are distributed over 16173 RAD loci; please refer to Table S1 in the manuscript to see details on the 141 samples genotypedfinalLoci.CorZUWL_FB.recode.vcfgenotypes for 16173 position in 141 indivdiualsgenotypes for 16173 position are distributed over 16173 RAD loci; please refer to Table S1 in the manuscript to see details on the 141 samples genotypedfinalSNPs.CorZUWL_FB.recode.vcf
DOI: 10.5061/dryad.43cj7
title: Data from: Evolutionary branching in complex landscapes

description: Divergent adaptation to different environments can promote speciation, and
 it is thus important to consider spatial structure in models of
 speciation. Earlier theoretical work, however, has been limited to
 particularly simple types of spatial structure (linear environmental
 gradients and spatially discrete metapopulations), leaving unaddressed the
 effects of more realistic patterns of landscape heterogeneity, such as
 nonlinear gradients and spatially continuous patchiness. To elucidate the
 consequences of such complex landscapes, we adapt an established spatially
 explicit individual-based model of evolutionary branching. We show that
 branching is most probable at intermediate levels of various types of
 heterogeneity and that different types of heterogeneity have, to some
 extent, additive effects in promoting branching. In contrast to such
 additivity, we find a novel refugium effect in which refugia in hostile
 environments provide opportunities for colonization, thus increasing the
 probability of branching in patchy landscapes. Effects of patchiness
 depend on the scale of patches relative to dispersal. Providing a needed
 connection to empirical research on biodiversity and conservation policy,
 we introduce empirically accessible spatial environmental metrics that
 quantitatively predict a landscape’s branching propensity.
description: Model
 videoa video of one model
 realizationHMD2012_video.aviAbsorbing boundary condition dataHMD2012_absorbing.csvReflecting boundary condition dataHMD2012_reflecting.csvReprising boundary condition dataHMD2012_reprising.csvStopping boundary condition dataHMD2012_stopping.csvReprising boundary condition data (replicate dataset)HMD2012_reprising_replicate.csvR script to produce fitted GAMs from the datasetsHMD2012_GAM_fits.RA readme file describing the files in this archive
DOI: 10.15468/dl.z7zatk
title: Occurrence Download

description: A dataset containing 882005 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Acanthocyclops americanus, Acartia tonsa, Amphibalanus amphitrite, Amphibalanus eburneus, Amphibalanus improvisus, Apionsoma misakianum, Aporrectodea trapezoides, Arcuatula senhousia, Armadillidium nasatum, Ascidiella aspersa, Asparagopsis armata, Asparagopsis taxiformis, Aurelia solida, Austrominius modestus, Balanus trigonus, Boccardia proboscidea, Bonnemaisonia hamifera, Botrylloides violaceus, Bugula neritina, Caprella mutica, Caprella scaura, Celleporaria brunnea, Cephalothrix simula, Cercopagis pengoi, Corambe obscura, Cordylophora caspia, Corella eumyota, Crepidula fornicata, Cutleria multifida, Dasysiphonia japonica, Ensis directus, Eucheilota menoni, Euphysa tentaculata, Evadne anonyx, Fenestrulina delicia, Fibrocapsa japonica, Ficopomatus enigmaticus, Gammarus tigrinus, Gonionemus vertens, Haloa japonica, Halothrix lumbricalis, Haminella solitaria, Hemigrapsus takanoi, Herdmania momus, Hydroides elegans, Juxtacribrilina mutabilis, Leptosiphonia fibrillosa, Marenzelleria arctia, Marenzelleria neglecta, Marenzelleria viridis, Mawia benovici, Melanothamnus harveyi, Mnemiopsis leidyi, Monocorophium acherusicum, Monocorophium sextonae, Mytilicola orientalis, Neogobius melanostomus, Nitokra hibernica, Oithona davisae, Ostreopsis ovata, Palaemon elegans, Paracerceis sculpta, Paranthura japonica, Parathalestris harpactoides, Perophora japonica, Petricolaria pholadiformis, Pleurosira laevis, Polycerella emertoni, Polydora cornuta, Polydora websteri, Polysiphonia brodiei, Potamopyrgus antipodarum, Pseudocalanus acuspes, Pseudocalanus mimus, Pseudodiaptomus marinus, Rangia cuneata, Rhithropanopeus harrisii, Rhodochorton tenue, Schizoporella japonica, Sinelobus vanhaareni, Smittoidea prolifica, Streblospio benedicti, Stylochus ellipticus, Telmatogeton japonicus, Thalassiosira punctigera, Tharyx setigera, Torquigener flavimaculosus, Xenostrobus securis)"
 ]
}

 The dataset includes 882005 records from 2089 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000169-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.