cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f3h72
title: Data from: A combination of transcriptional and microRNA regulation improves the stability of the relative concentrations of target genes

description: It is well known that, under suitable conditions, microRNAs are able to
 fine tune the relative concentration of their targets to any desired
 value. We show that this function is particularly effective when one of
 the targets is a Transcription Factor (TF) which regulates the other
 targets. This combination defines a new class of feed-forward loops (FFLs)
 in which the microRNA plays the role of master regulator. Using both
 deterministic and stochastic equations, we show that these FFLs are indeed
 able not only to fine-tune the TF/target ratio to any desired value as a
 function of the miRNA concentration but also, thanks to the peculiar
 topology of the circuit, to ensure the stability of this ratio against
 stochastic fluctuations. These two effects are due to the interplay
 between the direct transcriptional regulation and the indirect TF/Target
 interaction due to competition of TF and target for miRNA binding (the so
 called “sponge effect”). We then perform a genome wide search of these
 FFLs in the human regulatory network and show that they are characterized
 by a very peculiar enrichment pattern. In particular, they are strongly
 enriched in all the situations in which the TF and its target have to be
 precisely kept at the same concentration notwithstanding the environmental
 noise. As an example we discuss the FFL involving E2F1 as Transcription
 Factor, RB1 as target and miR-17 family as master regulator. These FFLs
 ensure a tight control of the E2F/RB ratio which in turns ensures the
 stability of the transition from the G0/G1 to the S phase in quiescent
 cells.
description: ENCODE_micFFLList of micFFL circuits obtained from ENCODE dataJaspar_micFFLLIst of micFFL circuits obtained from Jaspar PWM
DOI: 10.5061/dryad.5sj852c
title: Data from: Anterior insular cortex plays a critical role in interoceptive attention

description: Accumulating evidence indicates that the anterior insular cortex (AIC)
 mediates interoceptive attention, which refers to attention towards
 physiological signals arising from the body. However, the necessity of the
 AIC in this process has not been demonstrated. Using a novel task that
 directs attention toward breathing rhythm, we assessed the involvement of
 the AIC in interoceptive attention in healthy participants using
 functional magnetic resonance imaging and examined the necessity of the
 AIC in interoceptive attention in patients with AIC lesions. Results
 showed that interoceptive attention was associated with increased AIC
 activation, as well as enhanced coupling between the AIC and somatosensory
 areas along with reduced coupling between the AIC and visual sensory
 areas. In addition, AIC activation was predictive of individual
 differences in interoceptive accuracy. Importantly, AIC lesion patients
 showed disrupted interoceptive discrimination accuracy and sensitivity.
 These results provide compelling evidence that AIC plays a critical role
 in interoceptive attention.
description: behavior
 databehavior
 databehavior.zipfmri_dataThe raw fMRI data are too large, over 100G. Therefore, we upload the contrast maps of each individual, which can be used to reconstruct the figures presented in our manuscript.data_figureData used to reconstruct figures in our manuscript, i.e. bar figure, correlational figure, model selection and parameters, lesion patient results.
DOI: 10.5061/dryad.2rs4k
title: Data from: Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchin Arbacia lixula using RNA-seq

description: The sea urchin Arbacia lixula is a keystone species in Mediterranean
 ecosystems that drive landscape changes in littoral communities. However,
 genomic information available for the whole order Arbacioida is very
 limited. Using RNA-seq techniques, we have characterized the transcriptome
 of four different tissue types in A. lixula: the ‘somatic’ tissues
 (coelomocytes and digestive tissue) and the ‘reproductive’ tissues (ovary
 and testis), from two replicated cDNA libraries for each sample.
 Additionally, we performed a de novo assembly to build the ‘reference’
 transcriptome, pooling reads of the four tissues, to analyse the
 differential expression (DE) in pairwise comparisons between tissues. The
 complete de novo assembly yielded 186 084 transcripts, with a sequence
 size limit of 100 nt, being 31% of them spliced isoforms. Approximately
 21% of the transcripts had blast hits against proteins of metazoans (E
 &lt; 10−5), being less than 2.2% functionally annotated. Between
 coelomocytes and digestive, 30 794 transcripts showed DE (~11.8% of them
 with blast hit), and 19 567 transcripts did so between testis and ovary
 (~28.5% of them with blast hit). Major GO-term categories upregulated in
 somatic tissues were those related to muscle contraction and energy
 generation in digestive, and lipid metabolism associated with immune
 response in coelomocytes. Between reproductive tissues, the major
 upregulated GO categories were related to energy generation in testis, and
 negative regulation of nucleotide metabolism in ovary. We particularly
 screened for a collection of target genes in each tissue because of their
 relevance for further studies on evolution and adaptation of echinoids.
description: RSEM_files from four
 different tissues and 8 librariesRSEM files from 4
 different tissues of Arbacia lixula, the black sea urchin, and two
 replicates per tissue (8 libraries in total)DESeq_resultsDEseq results of the comparison of two somatic (Coelomocytes vs Digestive) and two reproductive tissues (Ovary vs Testis) in the black sea urchin Arbacia lixulaArbacia lixula_Assemblies_TissuesDe novo assemblies of the transcriptomes of four different tissues (Coelomocytes, Digestive, Ovary and Testis) in the black sea urchin Arbacia lixulaArbacia lixula_Annotation_tissuesAnnotations for the transcriptomes of four different tissues (Coelomocytes, Digestive, Ovary and Testis) in the black sea urchin Arbacia lixulaArbacia_lixula_Reference_Assembly_TrinityDe novo assembly of the Reference transcriptome of the black sea urchin Arbacia lixula. The reference transcriptome includes transcritps from coelomocytes, digestive, ovary and testisArbacila_lixula_Reference_annotAnnotations of the reference transcriptome of the black sea urchin Arbacia lixula
DOI: 10.5061/dryad.m4vh4
title: Data from: A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods

description: Genomic selection (GS) potentially offers an unparalleled advantage over
 traditional pedigree-based selection (TS) methods by reducing the time
 commitment required to carry out a single cycle of tree improvement. This
 quality is particularly appealing to tree breeders, where lengthy
 improvement cycles are the norm. We explored the prospect of implementing
 GS for interior spruce (Picea engelmannii × glauca) utilizing a genotyped
 population of 769 trees belonging to 25 open-pollinated families. A series
 of repeated tree height measurements through ages 3–40 years permitted the
 testing of GS methods temporally. The genotyping-by-sequencing (GBS)
 platform was used for single nucleotide polymorphism (SNP) discovery in
 conjunction with three unordered imputation methods applied to a data set
 with 60% missing information. Further, three diverse GS models were
 evaluated based on predictive accuracy (PA), and their marker effects.
 Moderate levels of PA (0.31–0.55) were observed and were of sufficient
 capacity to deliver improved selection response over TS. Additionally, PA
 varied substantially through time accordingly with spatial competition
 among trees. As expected, temporal PA was well correlated with age-age
 genetic correlation (r=0.99), and decreased substantially with increasing
 difference in age between the training and validation populations
 (0.04–0.47). Moreover, our imputation comparisons indicate that k-nearest
 neighbor and singular value decomposition yielded a greater number of SNPs
 and gave higher predictive accuracies than imputing with the mean.
 Furthermore, the ridge regression (rrBLUP) and BayesCπ (BCπ) models both
 yielded equal, and better PA than the generalized ridge regression
 heteroscedastic effect model for the traits evaluated.
description: phenotypephenotype and experimental designphen mask dryad.txtSVD genotype imputationmarker matrix for SVD imputation methodSVDimp dryad.txtMean genotype imputationmarker matrix for mean imputation methodMeanImp dryad.txtKNN genotype imputationmarker matrix for KNN imputation methodKNNimp dryad.txt
DOI: 10.5061/dryad.ms52b
title: Data from: Evolution of quantitative traits under a migration-selection balance: when does skew matter?

description: Quantitative-genetic models of differentiation under migration-selection
 balance often rely on the assumption of normally distributed genotypic and
 phenotypic values. When a population is subdivided into demes with
 selection toward different local optima, migration between demes may
 result in asymmetric, or skewed, local distributions. Using a simplified
 two-habitat model, we derive formulas without a priori assuming a Gaussian
 distribution of genotypic values, and we find expressions that naturally
 incorporate higher moments, such as skew. These formulas yield predictions
 of the expected divergence under migration-selection balance that are more
 accurate than models assuming Gaussian distributions, which illustrates
 the importance of incorporating these higher moments to assess the
 response to selection in heterogeneous environments. We further show with
 simulations that traits with loci of large effect display the largest skew
 in their distribution at migration-selection balance.
description: Folder to reproduce the
 figures of the articleR scripts to plot the
 figures of the article, and output of the individual-based simulations run
 with the software Nemo.scripts-Debarre-Yeaman-Guillaume_2015.zip
DOI: 10.5061/dryad.gt413
title: Data from: Simultaneously uncovering the patterns of the brain regions involved in different story reading subprocesses

description: Story understanding involves many perceptual and cognitive subprocesses,
 from perceiving individual words, to parsing sentences, to understanding
 the relationships among the story characters. We present an integrated
 computational model of reading that incorporates these and additional
 subprocesses, simultaneously discovering their fMRI signatures. Our model
 predicts the fMRI activity associated with reading arbitrary text
 passages, well enough to distinguish which of two story segments is being
 read with 74% accuracy. This approach is the first to simultaneously track
 diverse reading subprocesses during complex story processing and predict
 the detailed neural representation of diverse story features, ranging from
 visual word properties to the mention of different story characters and
 different actions they perform. We construct brain representation maps
 that replicate many results from a wide range of classical studies that
 focus each on one aspect of language processing and offer new insights on
 which type of information is processed by different areas involved in
 language processing. Additionally, this approach is promising for studying
 individual differences: it can be used to create single subject maps that
 may potentially be used to measure reading comprehension and diagnose
 reading disorders.
description: subject_1subject_2subject_3subject_4subject_5subject_6subject_7subject_8descriptionmethodsAppendix_A.pdfstory_features
DOI: 10.5061/dryad.n9r3h
title: Data from: SATé-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees

description: Highly accurate estimation of phylogenetic trees for large datasets is
 difficult, in part because multiple sequence alignments must be accurate
 for phylogeny estimation methods to be accurate. Co-estimation of
 alignments and trees has been attempted, but currently only SATé estimates
 reasonably accurate trees and alignments for large datasets in practical
 time frames (Liu et al., 2009b). Here, we present a modification to the
 original SATé algorithm that improves upon SATé (which we now call SATé-I)
 in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses
 a different divide-and-conquer strategy than SATé-I, and so produces
 smaller, more closely related subsets than SATé-I; as a result, SATé-II
 produces more accurate alignments and trees, can analyze larger datasets,
 and runs more efficiently than SATé-I. SATé-II is a meta-method that takes
 an existing multiple sequence alignment method as an input parameter and
 boosts the quality of that alignment method. SATé-II-boosted alignment
 methods are significantly more accurate than their unboosted versions, and
 trees based upon these improved alignments are more accurate than trees
 based upon the original alignments. Finally, because SATé-I used maximum
 likelihood methods that treat gaps as missing data to estimate trees, and
 because we found a correlation between the quality of tree/alignment pairs
 and maximum likelihood scores, we explored the degree to which SATé’s
 performance depends on using maximum likelihood with gaps treated as
 missing data to determine the best tree/alignment pair. We present two
 lines of evidence that using maximum likelihood with gaps treated as
 missing data to optimize the alignment and tree produces very poor
 results. First, we show that the optimization problem where a set of
 unaligned DNA sequences is given and the output is the tree and alignment
 of those sequences that maximize likelihood under the Jukes-Cantor model
 is uninformative in the worst possible sense: for all inputs, all trees
 optimize the likelihood score. Second, we show that a greedy heuristic
 that uses GTR+Gamma maximum likelihood to optimize the alignment and the
 tree can produce very poor alignments and trees. Therefore, the excellent
 performance of SATé-II and SATé-I is not because maximum likelihood is
 used as an optimization criterion for choosing the best tree/alignment
 pair, but rather due to the particular divide-and-conquer re-alignment
 techniques employed.
description: 16S.B.ALLThis zip file contains the data files for all of the analyses reported in our paper for the 16S.B.ALL dataset. Set the readme file for additional details.16S.TThis zip file contains the alignments and trees reported in our paper for the 16S.T dataset from Robin Gutell. Please see the readme.txt file for additional information on individual alignments and trees.
DOI: 10.5061/dryad.5n882
title: Data from: Genomic analysis of a cardinalfish with larval homing potential reveals genetic admixture in the Okinawa Islands

description: Discrepancies between potential and observed dispersal distances of reef
 fish indicate the need for a better understanding of the influence of
 larval behaviour on recruitment and dispersal. Population genetic studies
 can provide insight on the degree to which populations are connected, and
 the development of restriction site-associated sequencing (RAD-Seq)
 methods has made such studies of nonmodel organisms more accessible. We
 applied double-digest RAD-Seq methods to test for population
 differentiation in the coral reef-dwelling cardinalfish, Siphamia tubifer,
 which based on behavioural studies, have the potential to use navigational
 cues to return to natal reefs. Analysis of 11,836 SNPs from fish collected
 at coral reefs in Okinawa, Japan, from eleven locations over 3 years
 reveals little genetic differentiation between groups of S. tubifer at
 spatial scales from 2 to 140 km and between years at one location:
 pairwise FST values were between 0.0116 and 0.0214. These results suggest
 that the Kuroshio Current largely influences larval dispersal in the
 region, and in contrast to expectations based on studies of other
 cardinalfishes, there is no evidence of population structure for S.
 tubifer at the spatial scales examined. However, analyses of outlier loci
 putatively under selection reveal patterns of temporal differentiation
 that indicate high population turnover and variable larval supply from
 divergent source populations between years. These findings highlight the
 need for more studies of fishes across various geographic regions that
 also examine temporal patterns of genetic differentiation to better
 understand the potential connections between early life-history traits and
 connectivity of reef fish populations.
description: Stacks catalog (m=3,
 M=2, n=3)Stacks catalog for the
 main assembly (m=3, M=2, n=3)stacks_catalog.txtSNP callsSNP calls from main assembly in Stackssnp_calls.vcf2013 STRUCTURE fileSTRUCTURE input file for 2013 dataset2013.stru2014 STRUCTURE fileSTRUCTURE input file for 2014 dataset2014.struSesoko STRUCTURE fileSTRUCTURE input file for Sesoko datasetsesoko.stru
DOI: 10.5061/dryad.gr732
title: Data from: Phylogenetic evidence for cladogenetic polyploidization in land plants

description: Premise of the study: Polyploidization is a common and recurring
 phenomenon in plants and is often thought to be a mechanism of
 "instant speciation." Whether polyploidization is associated
 with the formation of new species ("cladogenesis") or simply
 occurs over time within a lineage ("anagenesis") has never,
 however, been assessed systematically. Methods: Here, we tested this
 hypothesis using phylogenetic and karyotypic information from 235 plant
 genera (mostly angiosperms). We first constructed a large database of
 combined sequence and chromosome number data sets using an automated
 procedure. We then applied likelihood models (ClaSSE) that estimate the
 degree of synchronization between polyploidization and speciation events
 in maximum likelihood and Bayesian frameworks. Key results: Our maximum
 likelihood analysis indicated that 35 genera supported a model that
 includes cladogenetic transitions over a model with only anagenetic
 transitions, whereas three genera supported a model that incorporates
 anagenetic transitions over one with only cladogenetic transitions.
 Furthermore, the Bayesian analysis supported a preponderance of
 cladogenetic change in four genera but did not support a preponderance of
 anagenetic change in any genus. Conclusions: Overall, these phylogenetic
 analyses provide the first broad confirmation that polyploidization is
 temporally associated with speciation events, suggesting that it is indeed
 a major speciation mechanism in plants, at least in some genera.
description: PloiDBPhylogenetic trees
 inferred using MrBayes, ploidy estimates using ChromEvol, and TPL-based
 genus species diversity estimates for 223 genera.ploidb_dryad.tar.gz
DOI: 10.5061/dryad.pb787
title: Data from: New insights into New World biogeography: an integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies

description: Understanding the biogeographic origins and temporal sequencing of groups
 within a region or of lineages within an ecosystem can yield important
 insights into evolutionary dynamics and ecological processes. Fifty years
 ago, Ernst Mayr generated comprehensive—if limited—inferences about the
 origins of the New World avifaunas, including the importance of
 pre-Isthmian dispersal between North and South America. Since then,
 methodological advances have improved our ability to address many of the
 same questions, but the phylogenies upon which such analyses should be
 based have been incompletely sampled or fragmentary. Here, we report a
 near-species-level phylogeny of the diverse (~832 species) New World clade
 Emberizoidea—the group that includes the familiar sparrows, cardinals,
 blackbirds, wood-warblers, tanagers, and their close relatives—to our
 knowledge the largest essentially complete (≥95%) phylogenetic hypothesis
 for any group of organisms. Biogeographic analyses based on this tree
 suggest initial dispersal into the New World via Beringia, with rapid
 subsequent diversification, including early dispersal of 1 lineage (the
 tanagers, Thraupidae) into South America. We found substantial dispersal
 between North and South America prior to closure of the Isthmus of Panama,
 but with a notable increase afterward, with a directional bias from north
 to south. With much greater detail and historical rigor, these analyses
 largely confirm Mayr's speculations based on taxonomy, resolving
 outstanding ambiguity regarding the continental origins of some groups
 such as the Emberizidae and Icteridae. The phylogeny reported here will be
 a resource of broad utility for addressing additional evolutionary and
 ecological questions with this diverse group.
description: Emberizoid
 Pseudoposterior TreesA zipped folder
 containing emberizoid pseudoposterior and maximum clade credibility
 trees.Emberizoid_trees.zipEmberizoid R WorkspaceThis is an R workspace containing backbone and subclade trees and code for generation of pseudoposterior trees.emberizoid.supertrees.RDataR Code for Pseudoposterior GenerationContains functions and example code for generation of emberizoid pseudoposterior trees.output.posterior.rTaxon TranslationsA tab-delimited text file containing a translation table for taxon names used by trees in Emberizoid_trees.zip to the standardized taxonomy of The Clements Checklist of Birds of the World, 6th Edition.taxon_translations.txt
DOI: 10.5061/dryad.9r816
title: Data from: The Sphagnum microbiome supports greatly bog ecosystem functioning under extreme conditions

description: Sphagnum-dominated bogs represent a unique yet widely distributed type of
 terrestrial ecosystem, and strongly contribute to global biosphere
 functioning. Sphagnum is colonised by highly diverse microbial
 communities, but less is known about their function. We identified a high
 functional diversity within the Sphagnum microbiome applying an
 Illumina-based metagenomic approach followed by de novo assembly and
 MG-RAST annotation. An inter-environmental comparison revealed that the
 Sphagnum microbiome harbours specific genetic features that distinguish it
 significantly from microbiomes of higher plants and peat soils. The
 differential traits especially support ecosystem functioning by a
 symbiotic life style under poikilohydric and ombrotrophic conditions. To
 realise a plasticity-stability balance, we found abundant subsystems
 responsible to cope with oxidative and drought stresses, to exchange
 (mobile) genetic elements, and genes that encode for resistance to
 detrimental environmental factors, repair, and self-controlling
 mechanisms. Multiple microbe-microbe and plant-microbe interactions were
 also found to play a crucial role as indicated by diverse genes necessary
 for biofilm formation, interaction via quorum sensing and nutrient
 exchange. A high proportion of genes involved in nitrogen cycle and
 recycling of organic material supported the role of bacteria for nutrient
 supply. 16S rDNA analysis indicated a higher structural diversity than
 that which had been previously detected using PCR-dependent techniques.
 Altogether, the diverse Sphagnum microbiome has the ability to support the
 life of the host plant and the entire ecosystem under changing
 environmental conditions. Beyond this, the moss microbiome presents a
 promising bio-resource for environmental biotechnology – with respect to
 novel enzymes or stress-protecting bacteria.
description: 4533611.3_M2_retainMode_16SPartial 16S rRNA gene sequences from the complete Sphagnum magellanicum metagenome4533611.3_M2_retianMode_NmetabolismPartial gene sequences encoding for nitrogen metabolism from the complete Sphagnum magellanicum metagenome.4516652.3_M2norm_L008_R1_paired_de_novo_assembly_NmetabolismPartial gene sequences encoding for nitrogen metabolism from the normalised Sphagnum magellanicum metagenome.