cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9v46k
title: Data from: Can collective memories shape fish distributions? A test, linking space-time occurrence models and population demographics

description: Social learning can be fundamental to cohesive group living, and schooling
 fishes have proven ideal test subjects for recent work in this field. For
 many species, both demographic factors, and inter- (and intra-)
 generational information exchange are considered vital ingredients in how
 movement decisions are reached. Yet key information is often missing on
 the spatial outcomes of such decisions, and questions concerning how
 migratory traditions are influenced by collective memory,
 density-dependent and density-independent processes remain open. To
 explore these issues, we focused on Atlantic herring (Clupea harengus), a
 long-lived, dense-schooling species of high commercial importance, noted
 for its unpredictable shifts in winter distribution, and developed a
 series of Bayesian space-time occurrence models to investigate wintering
 dynamics over 23 years, using point-referenced fishery and survey records
 from Icelandic waters. We included covariates reflecting local-scale
 environmental factors, temporally-lagged prey biomass and recent fishing
 activity, and through an index capturing distributional persistence over
 time, derived two proxies for spatial memory of past wintering sites. The
 previous winter's occurrence pattern was a strong predictor of the
 present pattern, its influence increasing with adult population size.
 Although the mechanistic underpinnings of this result remain uncertain, we
 suggest that a ‘wisdom of the crowd’ dynamic may be at play, by which
 navigational accuracy towards traditional wintering sites improves in
 larger and/or denser, better synchronized schools. Wintering herring also
 preferred warmer, fresher, moderately stratified waters of lower velocity,
 close to hotspots of summer zooplankton biomass, our results indicative of
 heightened environmental sensitivity in younger cohorts. Incorporating
 spatiotemporal correlation structure and time-varying regression
 coefficients improved model performance, and validation tests on
 independent observations one-year ahead illustrate the potential of
 uniting demographic information and non-stationary models to quantify both
 the strength of collective memory in animal groups and its relevance for
 the spatial management of populations.
description: Spatial similarity
 indexThis folder contains R
 code and data to calculate the spatial similarity index (SSI), and to
 compute and map the ‘distrib(t)’ and ‘counts(t)’ variables, as described
 in Appendix 2 of the paper. See the README file for further information
 and file descriptions.Spatial-similarity-index.zipSpace time modelsThis folder contains R code and data to run all models described in the paper, in addition to model output for plotting Figures. 3-5, A7 and reproducing Tables 2, 3, A1-A3. See the README file for further information and file descriptions.Space-time-models.zip
DOI: 10.5061/dryad.c1j01
title: Data from: A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa

description: Background: Accurate structural annotation depends on well-trained gene
 prediction programs. Training data for gene prediction programs are often
 chosen randomly from a subset of high-quality genes that ideally represent
 the variation found within a genome. One aspect of gene variation is GC
 content, which differs across species and is bimodal in grass genomes.
 When gene prediction programs are trained on a subset of grass genes with
 random GC content, they are effectively being trained on two classes of
 genes at once, and this can be expected to result in poor results when
 genes are predicted in new genome sequences. Results: We find that gene
 prediction programs trained on grass genes with random GC content do not
 completely predict all grass genes with extreme GC content. We show that
 gene prediction programs that are trained with grass genes with high or
 low GC content can make both better and unique gene predictions compared
 to gene prediction programs that are trained on genes with random GC
 content. By separately training gene prediction programs with genes from
 multiple GC ranges and using the programs within the MAKER genome
 annotation pipeline, we were able to improve the annotation of the Oryza
 sativa genome compared to using the standard MAKER annotation protocol.
 Gene structure was improved in over 13% of genes, and 651 novel genes were
 predicted by the GC-specific MAKER protocol. Conclusions: We present a new
 GC-specific MAKER annotation protocol to predict new and improved gene
 models and assess the biological significance of this method in Oryza
 sativa. We expect that this protocol will also be beneficial for gene
 prediction in any organism with bimodal or other unusual gene GC content.
description: 6hmms_makerStandard_noTEs.gff3Genome annotation for Six HMMs gene predictions in rice.6hmms_makerStandard_noTEs_proteins.fastaPredicted proteins from the Six HMMs gene predictions in rice.6hmms_makerStandard_noTEs_transcripts.fastaPredicted transcripts from Six HMMs gene predictions in rice.novel_high_maker_standard_genes.gff3Gene annotations of novel genes predicted by the high GC HMM in rice.novel_high_maker_standard_proteins.fastaPredicted proteins of novel genes predicted by the high GC HMM in rice.novel_high_maker_standard_transcripts.fastaPredicted transcripts of novel genes predicted by the high GC HMM in rice.novel_low_maker_standard_genes.gff3Gene annotations of novel genes predicted by the low GC HMM in rice.novel_low_maker_standard_proteins.fastaPredicted proteins of novel genes predicted by the low GC HMM in rice.novel_low_maker_standard_transcripts.fastaPredicted transcripts of novel genes predicted by the low GC HMM in rice.md5_valuesThe md5 values for the files in this data submission.
DOI: 10.15468/dl.fp4y97
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-123.63560 24.23654,-42.36440 24.23654,-42.36440 56.76346,-123.63560 56.76346,-123.63560 24.23654))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Charadrius melodus melodus"
 ]
}

 The dataset includes 96 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000344-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t5r8m
title: Data from: Factors essential for L,D-transpeptidase-mediated peptidoglycan cross-linking and β-lactam resistance in Escherichia coli

description: The target of β-lactam antibiotics is the D,D-transpeptidase activity of
 penicillin-binding proteins (PBPs) for synthesis of 4→3 cross-links in the
 peptidoglycan of bacterial cell walls. Unusual 3→3 cross-links formed by
 L,D-transpeptidases were first detected in Escherichia coli more than four
 decades ago, however no phenotype has previously been associated with
 their synthesis. Here we show that production of the L,D-transpeptidase
 YcbB in combination with elevated synthesis of the (p)ppGpp alarmone by
 RelA lead to full bypass of the D,D-transpeptidase activity of PBPs and to
 broad-spectrum β-lactam resistance. Production of YcbB was therefore
 sufficient to switch the role of (p)ppGpp from antibiotic tolerance to
 high-level β-lactam resistance. This observation identifies a new mode of
 peptidoglycan polymerization in E. coli that relies on an unexpectedly
 small number of enzyme activities comprising the glycosyltransferase
 activity of class A PBP1b and the D,D-carboxypeptidase activity of DacA in
 addition to the L,D-transpeptidase activity of YcbB.
description: GenomeSequencedataofmutant
DOI: 10.15468/dl.d82amw
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is one of (Venezuela (Bolivarian Republic of), Colombia, Ecuador, Panama)",
 "TaxonKey is Lochmias nematura"
 ]
}

 The dataset includes 61 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000347-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cm86089
title: Data from: Gain-of-function experiments in bacteriophage lambda uncover residues under diversifying selection in nature

description: Viral gain-of-function mutations frequently evolve during laboratory
 experiments. Whether the specific mutations that evolve in the lab also
 evolve in nature and whether they have the same impact on evolution in the
 real world is unknown. We studied a model virus, bacteriophage λ, that
 repeatedly evolves to exploit a new host receptor under typical laboratory
 conditions. Here we demonstrate that two residues of λ’s J protein are
 required for the new function. In natural λ variants, these amino acid
 sites are highly diverse and evolve at high rates. Insertions and
 deletions at these locations are associated with phylogenetic patterns
 indicative of ecological diversification. Our results show that viral
 evolution in the laboratory mirrors that in nature and that laboratory
 experiments can be coupled with protein sequence analyses to identify the
 causes of viral evolution in the real world. Furthermore, our results
 provide evidence for widespread host-shift evolution in lambdoid viruses.
description: DRYAD-J-alignment-Evolution
DOI: 10.15468/dl.46z6v3
title: Occurrence Download

description: A dataset containing 419 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Meleagris gallopavo mexicana"
 ]
}

 The dataset includes 419 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000343-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g8h71
title: Data from: Immunohistochemical typing of adenocarcinomas of the pancreatobiliary system improves diagnosis and prognostic stratification

description: Background & Aims: Adenocarcinomas of the pancreatobiliary system
 are currently classified by their primary anatomical location. In
 particular, the pathological diagnosis of intrahepatic cholangiocarcinoma
 is still considered as a diagnosis of exclusion of metastatic
 adenocarcinoma. Periampullary cancers have been previously classified
 according to the histological type of differentiation (pancreatobiliary,
 intestinal), but overlapping morphological features hinder their
 differential diagnosis. We performed an integrative immunohistochemical
 analysis of pancreato-biliary tumors to improve their diagnosis and
 prediction of outcome. Methods: This was a retrospective observational
 cohort study on patients with adenocarcinoma of the pancreatobiliary
 system who underwent diagnostic core needle biopsy or surgical resection
 at a tertiary referral center. 409 tumor samples were analyzed with up to
 27 conventional antibodies used in diagnostic pathology.
 Immunohistochemical scoring system was the percentage of stained tumor
 cells. Bioinformatic analysis, internal validation, and survival analysis
 were performed. Results: Hierarchical clustering and differential
 expression analysis identified three immunohistochemical tumor types
 (extrahepatic pancreatobiliary, intestinal, and intrahepatic
 cholangiocarcinoma) and the discriminant markers between them. Among
 patients who underwent surgical resection of their primary tumor with
 curative intent, the intestinal type showed an adjusted hazard ratio of
 0.19 for overall survival (95% confidence interval 0.05–0.72; p value =
 0.014) compared to the extrahepatic pancreatobiliary type. Conclusions:
 Integrative immunohistochemical classification of adenocarcinomas of the
 pancreatobiliary system results in a characteristic immunohistochemical
 profile for intrahepatic cholangiocarcinoma and intestinal type
 adenocarcinoma, which helps in distinguishing them from metastatic and
 pancreatobiliary type adenocarcinoma, respectively. A diagnostic
 immunohistochemical panel and additional extended panels of discriminant
 markers are proposed as guidance for their pathological diagnosis.
description: Immunohistochemical
 typing of adenocarcinomas of the pancreatobiliary system - data and
 analysis codeData and analysis code
 for study "Immunohistochemical Typing of Adenocarcinomas of the
 Pancreatobiliary System Improves Diagnosis and Prognostic
 Stratification"PCBIL_data_and_code.zipImmunohistochemical typing of adenocarcinomas of the pancreatobiliary system - Reproducible computer environmentReproducible computer environment as Docker image for study "Immunohistochemical Typing of Adenocarcinomas of the Pancreatobiliary System Improves Diagnosis and Prognostic Stratification"pcbil_docker_image.tar.gz
DOI: 10.5061/dryad.7rm34
title: Data from: On the optimal trimming of high-throughput mRNA sequence data

description: The widespread and rapid adoption of high-throughput sequencing
 technologies has afforded researchers the opportunity to gain a deep
 understanding of genome level processes that underlie evolutionary change,
 and perhaps more importantly, the links between genotype and phenotype. In
 particular, researchers interested in functional biology and adaptation
 have used these technologies to sequence mRNA transcriptomes of specific
 tissues, which in turn are often compared to other tissues, or other
 individuals with different phenotypes. While these techniques are
 extremely powerful, careful attention to data quality is required. In
 particular, because high-throughput sequencing is more error-prone than
 traditional Sanger sequencing, quality trimming of sequence reads should
 be an important step in all data processing pipelines. While several
 software packages for quality trimming exist, no general guidelines for
 the specifics of trimming have been developed. Here, using empirically
 derived sequence data, I provide general recommendations regarding the
 optimal strength of trimming, specifically in mRNA-Seq studies. Although
 very aggressive quality trimming is common, this study suggests that a
 more gentle trimming, specifically of those nucleotides whose Phred score
 &lt; 2 or &lt; 5, is optimal for most studies across a wide
 variety of metrics.
description: Assembly
 FilesThese files correspond
 to the assemblies described in the manuscript.assemblies.zip
DOI: 10.15468/dl.huu34h
title: Occurrence Download

description: A dataset containing 142 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pampatherium humboldtii"
 ]
}

 The dataset includes 142 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000346-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.057b7
title: Data from: Gene expression profiling in the hibernating primate, Cheirogaleus Medius

description: Hibernation is a complex physiological response that some mammalian
 species employ to evade energetic demands. Previous work in mammalian
 hibernators suggests that hibernation is activated not by a set of genes
 unique to hibernators, but by differential expression of genes that are
 present in all mammals. This question of universal genetic mechanisms
 requires further investigation and can only be tested through additional
 investigations of phylogenetically dispersed species. To explore this
 question, we use RNA-Seq to investigate gene expression dynamics as they
 relate to the varying physiological states experienced throughout the year
 in a group of primate hibernators—Madagascar’s dwarf lemurs (genus
 Cheirogaleus). In a novel experimental approach, we use longitudinal
 sampling of biological tissues as a method for capturing gene expression
 profiles from the same individuals throughout their annual hibernation
 cycle. We identify 90 candidate genes that have variable expression
 patterns when comparing two active states (Active 1 and Active 2) with a
 torpor state. These include genes that are involved in metabolic pathways,
 feeding behavior, and circadian rhythms, as might be expected to correlate
 with seasonal physiological state changes. The identified genes appear to
 be critical for maintaining the health of an animal that undergoes
 prolonged periods of metabolic depression concurrent with the hibernation
 phenotype. By focusing on these differentially expressed genes in dwarf
 lemurs, we compare gene expression patterns in previously studied
 mammalian hibernators. Additionally, by employing evolutionary rate
 analysis, we find that hibernation-related genes do not evolve under
 positive selection in hibernating species relative to nonhibernators.
description: Trinity
 assemblyTrinity assembly of
 filtered paired-end reads (phred score &gt;30, both pairs passed QC
 control) pooling all samples.Trinity.fasta.tar.gzblastx table for all reconstructed transcriptsBlastx table against human for all reconstructed transcripts. Includes the perecentage of the human protein covered by the lemur transcript.blastx.outfmt6.w_pct_hit_length.sorted.tar.gzGTEx rpkm tableGTEX rpkm table for the 2 human adipose tissue samples analyzed: GTEX9N7MS903269SM94E3K2 and GTEX9NFK9903269SM93MJGV)GTEx_Analysis_2014-01-17_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct.tar.gzTable of counts at the gene levelTable of counts at the gene level generated with RSEM and used for calling Differentially exrpressed genes with EdgeR. Towhee samples removed.gene.counts.matrix.sorted_towhee_out.tar.gz
DOI: 10.5061/dryad.pj44k
title: Data from: Selection against recombinant hybrids maintains reproductive isolation in hybridizing Populus species despite F1 fertility and recurrent gene flow

description: Natural hybrid zones have proven to be precious tools for understanding
 the origin and maintenance of reproductive isolation (RI) and therefore
 species. Most available genomic studies of hybrid zones using whole- or
 partial-genome resequencing approaches have focused on comparisons of the
 parental source populations involved in genome admixture, rather than
 exploring fine-scale patterns of chromosomal ancestry across the full
 admixture gradient present between hybridizing species. We have studied
 three well-known European ‘replicate’ hybrid zones of Populus alba and P.
 tremula, two widespread, ecologically divergent forest trees, using up to
 432 505 single-nucleotide polymorphisms (SNPs) from restriction
 site-associated DNA (RAD) sequencing. Estimates of fine-scale chromosomal
 ancestry, genomic divergence and differentiation across all 19 poplar
 chromosomes revealed strikingly contrasting results, including an
 unexpected preponderance of F1 hybrids in the centre of genomic clines on
 the one hand, and genomically localized, spatially variable shared
 variants consistent with ancient introgression between the parental
 species on the other. Genetic ancestry had a significant effect on
 survivorship of hybrid seedlings in a common garden trial, pointing to
 selection against early-generation recombinants. Our results indicate a
 role for selection against recombinant genotypes in maintaining RI in the
 face of apparent F1 fertility, consistent with the intragenomic
 ‘coadaptation’ model of barriers to introgression upon secondary contact.
 Whole-genome resequencing of hybridizing populations will clarify the
 roles of specific genetic pathways in RI between these model forest trees
 and may reveal which loci are affected most strongly by its cyclic
 breakdown.
description: RADseq vcf
 fileRADseq vcf file
 individuals described in table S1 in Supporting
 InformationALL_ALL_dryad.recode.vcf.tar.gzchloro_alba_trem_can_7snpPlastid DNA for RADseq for 256 individuals from P. alba, P. tremula and P. x canescens
DOI: 10.15468/dl.n3pqmq
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Curculio davidi"
 ]
}

 The dataset includes 14 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000345-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gf07m
title: Data from: Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution.

description: Most laboratory evolution studies that characterize evolutionary
 adaptation genomically focus on genetically simple traits that can be
 altered by one or few mutations. Such traits are important, but they are
 few compared with complex, polygenic traits influenced by many genes. We
 know much less about complex traits, and about the changes that occur in
 the genome and in gene expression during their evolutionary adaptation.
 Salt stress tolerance is such a trait. It is especially attractive for
 evolutionary studies, because the physiological response to salt stress is
 well-characterized on the molecular and transcriptome level. This provides
 a unique opportunity to compare evolutionary adaptation and physiological
 adaptation to salt stress. The yeast Saccharomyces cerevisiae is a good
 model system to study salt stress tolerance, because it contains several
 highly conserved pathways that mediate the salt stress response. We
 evolved three replicate lines of yeast under continuous salt (NaCl) stress
 for 300 generations. All three lines evolved faster growth rate in high
 salt conditions than their ancestor. In these lines, we studied gene
 expression changes through microarray analysis and genetic changes through
 next generation population sequencing. We found two principal kinds of
 gene expression changes, changes in basal expression (82 genes) and
 changes in regulation (62 genes). The genes that change their expression
 involve several well-known physiological stress-response genes, including
 CTT1, MSN4 and HLR1. Next generation sequencing revealed only one
 high-frequency single-nucleotide change, in the gene MOT2, that caused
 increased fitness when introduced into the ancestral strain. Analysis of
 DNA content per cell revealed ploidy increases in all the three lines. Our
 observations suggest that evolutionary adaptation of yeast to salt stress
 is associated with genome size increase and modest expression changes in
 several genes.
description: 454 sequencing
 data454 sequencing data from
 ancestral(ANC) and evolved yeast populations - base sequences in fasta
 format along with corresponding base quality scoresSequencing_Data_Dhar.tar.gz