cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n40hc
title: Data from: Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis

description: Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic
 regions of yeast and animal genomes play important roles in key biological
 processes. Yet, plant lincRNAs remain poorly characterized and how lincRNA
 biogenesis is regulated is unclear. Using a reproducibility-based
 bioinformatics strategy to analyze 200 Arabidopsis transcriptome datasets,
 we identified 13,230 intergenic transcripts of which 6,480 can be
 classified as lincRNAs. Expression of 2,708 lincRNAs was detected by
 RNA-seq experiments. Transcriptome profiling by custom microarrays
 revealed that the majority of these lincRNAs are expressed at a level
 between those of mRNAs and pri-miRNAs. A subset of lincRNA genes show
 organ-specific expression whereas others are responsive to biotic and/or
 abiotic stresses. Further analysis of transcriptome data in 11 mutants
 uncovered SERRATE, CBP20, and CBP80 as regulators of lincRNA expression
 and biogenesis. RT-PCR experiments confirmed these 3 proteins are also
 needed for splicing of a small group of intron-containing lincRNAs.
description: Supplemental Dataset 1.
 Classification of TAIR9 other RNAsSupplemental Dataset 2.
 Classification of the TUs identifed by ESTsSupplemental Dataset 3.
 Classification of the TUs previously reported by Matsui.A et.al
 2008Supplemental Dataset 4.
 Classification of the TUs previously reported by Okamoto.M et.al
 2010Supplemental Dataset 5.
 Tiling array datasets we used for analysisSupplemental Dataset 6.
 Classification of the TUs identifed by RepTASSupplemental Dataset 7.
 RCTUs identifed by RepTASSupplemental Dataset 8.
 Design of ATH LincRNA v1 ArraySupplemental Dataset 9.
 LincRNAs identified by both RepTAS and RNA-seqSupplemental Dataset 10.
 Summary of assambled transcripts by RNA-seqSupplemental Dataset 11.
 Classification of the TUs identified by RNAseqSupplemental Dataset 12.
 Verfication of organ-preferencially expressed lincRNA by
 qRT-PCRSupplemental Dataset 13.
 Comparison of lincRNAs identifed by mutiple platformsSupplemental Dataset
 13.comparison of lincRNAs identifed by mutiple platforms
 .xlsSupplemental Dataset 14.
 Predicted introns of lincRNAsSupplemental Dataset 15.
 Stresses-responsive lincRNAsSupplemental Dataset 15
 Stresses-responsive lincRNAs.xlsSupplemental Dataset 16.
 LincRNAs associated with smRNAsSupplemental Dataset
 16.LincRNAs associated with
 smRNAs.xlsSupplemental Dataset 17.
 LincRNAs regulated by SERRATE and CBPsSupplemental Dataset 17.
 lincRNAs regulated by SERRATE and
 CBPs.xlsSupplemental Dataset 18.
 Verfication of SE and CBPs regulated lincRNAs by qRT-PCRSupplemental Dataset 19.
 Summary of expression evidence of lincRNASupplemental Dataset 19 Summary
 of expression evidence of lincRNA.xls
DOI: 10.5061/dryad.43160
title: Data from: Chirleja buckii, a new genus and species of lichenized-fungi from Tierra del Fuego, southern South America

description: Chirleja, a new genus of lichenized-fungi, is described to accommodate C.
 buckii, a new species from southern South America with an unusual
 morphology and mode of reproduction. Through an approach that utilizes
 both molecular and non-molecular data, the species is shown to represent a
 previously unknown lineage within the family Icmadophilaceae characterized
 by the production of sporodochia and a sterile dimorphic thallus that
 resembles the unrelated genus Leprocaulon.
description: Chirleja_mtSSUA zipped archive containing the Pertusariales mtSSU nucleotide alignment file analyzed to determine the phylogenetic placement of Chirleja buckii along with various specific input and output files for different types of phylogenetic inference methods.
DOI: 10.5061/dryad.bh581
title: Data from: Multiple capacitors for natural genetic variation in Drosophila melanogaster

description: Cryptic genetic variation (CGV) or a standing genetic variation that is
 not ordinarily expressed as a phenotype is released when the robustness of
 organisms is impaired under environmental or genetic perturbations.
 Evolutionary capacitors modulate the amount of genetic variation exposed
 to natural selection and hidden cryptically; they have a fundamental
 effect on the evolvability of traits on evolutionary timescales. In this
 study, I have demonstrated the effects of multiple genomic regions of
 Drosophila melanogaster on CGV in wing shape. I examined the effects of 61
 genomic deficiencies on quantitative and qualitative natural genetic
 variation in the wing shape of D. melanogaster. I have identified 10
 genomic deficiencies that do not encompass a known candidate evolutionary
 capacitor, Hsp90, exposing natural CGV differently depending on the
 location of the deficiencies in the genome. Furthermore, five genomic
 deficiencies uncovered qualitative CGV in wing morphology. These findings
 suggest that CGV in wing shape of wild-type D. melanogaster is regulated
 by multiple capacitors with divergent functions. Future analysis of genes
 encompassed by these genomic regions would help elucidate novel capacitor
 genes and better understand the general features of capacitors regarding
 natural genetic variation.
description: Supplimentary
 dataProcrustes coordinates
 data used for wing morphology analyses. This file contains information
 such as genotype, individual ID, sex and procrustes coordinates for eight
 landmarks.
DOI: 10.5061/dryad.578hr
title: Data from: The genomic trajectory of hybrid swarms: outcomes of repeated crosses between populations of Tigriopus californicus

description: Introgressive hybridization between genetically divergent populations is
 an important evolutionary process. The degree to which repeated
 hybridization events between the same parental taxa lead to similar
 genomic outcomes is unknown. This study addressed this question by
 following genomic trajectories of replicate hybrid swarms of the copepod
 Tigriopus californicus over many generations of free mating. Swarm
 composition was determined both by differential reproductive success of
 founder individuals and subsequent selection on hybrid genotypes. For one
 cross, between two populations showing differential fitness in the
 laboratory and no hybrid breakdown, the genetic trajectory was highly
 repeatable: replicates rapidly became dominated by alleles from the fitter
 parent. In a second cross, between two populations showing similar fitness
 and significant F2 hybrid breakdown, alleles from alternative populations
 dominated different replicates. Swarms exhibited a general temporal trend
 of decreasing cytonuclear mismatch. Some patterns of differential
 introgression across the genome were strikingly congruent amongst swarm
 replicates, both within and between cross types, and reflected patterns of
 segregation distortion previously observed within controlled crosses
 between the same parental populations. Differences in heterozygosity
 between the sexes, and evidence for a previously suspected sex-distortion
 locus, suggest that complex interactions between sex and genotype
 influence hybrid swarm outcome.
description: SNP calls for all T.
 californicus individuals genotyped.SNP genotypes for all T.
 californicus individuals analyzed in the associated study. Genotyping was
 performed using iPLEX Gold on a MassARRAY Compact (Sequenom). SNPs (prefix
 TC) are arranged in map order by linkage group (12 chromosomes plus
 mitochondrion). 'Month 0' indicates individuals collected from
 pure founder populations immediately prior to the establishment of
 experimental swarms. Abbreviations are: f: female; m: male; na: not
 applicable; nc: no call, an unambiguous genotype was not obtained for this
 individual at this SNP.Tig_Paper3_Dryad.xlsMean hybrid indices and cytonuclear mismatch for all simulated populationsSee Readme.txtSimulation_summaries.xls
DOI: 10.5061/dryad.8sc8b
title: Data from: Spatially explicit models of divergence and genome hitchhiking

description: Strong barriers to genetic exchange can exist at divergently selected
 loci, whereas alleles at neutral loci flow more readily between
 populations, thus impeding divergence and speciation in the face of gene
 flow. However, ‘divergence hitchhiking’ theory posits that divergent
 selection can generate large regions of differentiation around selected
 loci. ‘Genome hitchhiking’ theory suggests that selection can also cause
 reductions in average genome-wide rates of gene flow, resulting in
 widespread genomic divergence (rather than divergence only around specific
 selected loci). Spatial heterogeneity is ubiquitous in nature, yet
 previous models of genetic barriers to gene flow have explored limited
 combinations of spatial and selective scenarios. Using simulations of
 secondary contact of populations, we explore barriers to gene flow in
 various selective and spatial contexts in continuous, two-dimensional,
 spatially explicit environments. In general, effects of hitchhiking are
 strongest in environments with regular spatial patterning of starkly
 divergent habitat types. When divergent selection is very strong, the
 absence of intermediate habitat types increases the effects of
 hitchhiking. However, when selection is moderate or weak, regular (versus
 random) spatial arrangement of habitat types becomes more important than
 the presence of intermediate habitats per se. We also document
 counterintuitive processes arising from the stochastic interplay of
 selection, gene flow, and drift. Our results indicate that generalization
 of results from two-deme models requires caution and increase
 understanding of the genomic and geographic basis of population
 divergence.
description: Flaxman_Data.zip archive of raw data used in publication figures
DOI: 10.5061/dryad.1bq39
title: Data from: Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms

description: Knowledge about population structure and connectivity of waterfowl
 species, especially mallards (Anas platyrhynchos), is a priority due to
 recent outbreaks of Avian Influenza. Ringing studies that trace
 large-scale movement patterns have to date been unable to detect clearly
 delineated mallard populations. We employed 363 single nucleotide
 polymorphism (SNP) markers in combination with population genetics and
 phylogeographic approaches to conduct a population genomic test of
 panmixia in 801 mallards from 45 locations world-wide. Basic population
 genetic and phylogenetic methods suggest no or very little population
 structure on continental scales. Nor could individual-based structuring
 algorithms discern geographical structuring. Model-based coalescent
 analyses for testing models of population structure pointed to strong
 genetic connectivity among the world’s mallard population. These diverse
 approaches all support the conclusion that there is a lack of clear
 population structure, suggesting that the world’s mallards, perhaps with
 minor exceptions, form a single large, mainly interbreeding population.
description: Mallard SNP
 genotypesPlain text file holding
 genoytpes of all analysed mallards.mallards-SNP-genotypes
DOI: 10.5061/dryad.30932
title: Data from: Positive selection within a diatom species acts on putative protein interactions and transcriptional regulation

description: Diatoms are the most species-rich group of micro-algae, and their
 contribution to marine primary production is important on a global scale.
 Diatoms can form dense blooms through rapid asexual reproduction;
 mutations acquired and propagated during blooms likely provide the
 genetic, and thus phenotypic, variability upon which natural selection may
 act. Positive selection was tested using genome and transcriptome-wide
 pair-wise comparisons of homologs in three genera of diatoms,
 Pseudo-nitzschia, Ditylum, and Thalassiosira that represent decreasing
 phylogenetic distances. The signal of positive selection was greatest
 between two strains of T. pseudonana. Further testing, among seven strains
 of T. pseudonana, yielded 809 candidate genes of positive selection, which
 are 7 % of the protein coding genes. Orphan genes and genes encoding
 protein binding domains and transcriptional regulators were enriched
 within the set of positively selected genes relative to the genome as a
 whole. Positively selected genes were linked to the potential selective
 pressures of nutrient limitation and sea surface temperature based on
 analysis of gene expression profiles and identification of positively
 selected genes in subsets of strains from locations with similar
 environmental conditions. The identification of positively selected genes
 presents an opportunity to test new hypotheses in natural populations and
 the laboratory that integrate selected genotypes in T. pseudonana with
 their associated phenotypes and selective forces.
description: Paustralis_EST_subtraction_libraryPmultistriata_EST
DOI: 10.5061/dryad.88h10
title: Data from: The HypoMethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies)

description: To evaluate the usefulness of Reduced Representation Libraries (RRL) in
 species with large and highly repetitive genomes such as conifers, we
 employed Hypomethylated Partial Restriction (HMPR) on the genome of Norway
 spruce (Picea abies). The HMPR method preferentially removes the
 repetitive fraction of the genome, which is commonly hypermethylated.
 Hence, RRLs should be enriched for the hypomethylated gene space. For
 comparison a standard shotgun library was constructed and samples of the
 respective libraries were obtained through Sanger sequencing. We obtained
 a nine-fold gene enrichment, a value which is slightly higher than for
 other plant species. The higher relative efficiency of HMPR is probably a
 consequence of the large Norway spruce genome size since the probability
 of finding genes in a standard shotgun library is very small. The amount
 of repetitive DNA was reduced by 45% in the RRLs, demonstrating the
 ability to efficiently remove hypermethylated DNA. Annotating sequences in
 an uncharacterized genome remains challenging and a large number of
 sequences could not be classified as either repetitive DNA or as belonging
 to the gene space. Upon further investigation, we found that some of these
 uncharacterized fragments were expressed, and in most cases the expression
 was spatially differentiated, indicating that they might have a function.
 Full-length transcripts of a subset of expressed fragments also revealed
 that these could be long non-coding RNAs. Long non-coding RNAs have been
 shown to be involved in gene regulation and deserve future attention. In
 conclusion, our study shows that the HMPR method is effective in
 constructing libraries enriched for the genic fraction of the genome,
 while simultaneously reducing the repetitive fraction, in P. abies and may
 prove a valuable tool for the discovery, validation and assessment of
 genetic markers in population studies when combined with next generation
 sequencing technology.
description: Hpa1N_libGenomic DNA sequences in fasta-formatHpa01N_libHpa1S_libHpa01S_libHpy1N_libHpy01N_libHpy1S_libHpy01S_libUF_lib
DOI: 10.5061/dryad.ds2gp
title: Data from: Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms

description: BACKGROUND: A detailed knowledge about spatial and temporal gene
 expression is important for understanding both the function of genes and
 their evolution. For the vast majority of species, transcriptomes are
 still largely uncharacterized and even in those where substantial
 information is available it is often in the form of partially sequenced
 transcriptomes. With the development of next generation sequencing, a
 single experiment can now simultaneously identify the transcribed part of
 a species genome and estimate levels of gene expression. RESULTS: mRNA
 from actively growing needles of Norway spruce (Picea abies) was sequenced
 using next generation sequencing technology. In total, close to 70 million
 fragments with a length of 76 bp were sequenced resulting in 5 Gbp of raw
 data. A de novo assembly of these reads, together with publicly available
 expressed sequence tag (EST) data from Norway spruce, was used to create a
 reference transcriptome. Of the 38,419 PUTs (putative unique transcripts)
 longer than 150 bp in this reference assembly, 83.5% show similarity to
 ESTs from other spruce species and of the remaining PUTs, 3,704 show
 similarity to protein sequences from other plant species, leaving 4,167
 PUTs with limited similarity to currently available plant proteins. By
 predicting coding frames and comparing not only the Norway spruce PUTs,
 but also PUTs from the close relatives Picea glauca and Picea sitchensis
 to both Pinus taeda and Taxus mairei, we obtained estimates of synonymous
 and non-synonymous divergence among conifer species. In addition, we
 detected close to 15,000 SNPs of high quality and estimated gene
 expression differences between samples collected under dark and light
 conditions. CONCLUSIONS: Our study yielded a large number of single
 nucleotide polymorphisms as well as estimates of gene expression on
 transcriptome scale. In agreement with a recent study we find that the
 synonymous substitution rate per year (0.6 x 10-09 and 1.1 x 10-09) is an
 order of magnitude smaller than values reported for angiosperm herbs.
 However, if one takes generation time into account, most of this
 difference disappears. The estimates of the dN/dS ratio (non-synonymous
 over synonymous divergence) reported here are in general much lower than 1
 and only a few genes showed a ratio larger than 1.
description: Picea abies needle
 transcriptsde novo assembly of
 Picea abies needle transcripts sequenced using mRNA-seq
 technologypa_tgicl95_151.faSNP fileThis file describes the single nucleotide polymorphism position, reference and alternative phases in each transcripts.snp_filterQ60AF25.txtPAML tablesIt includes six tables that describe information of orthologous sequences used in pairwise PAML analysis when calculating Ka/Ks ratios.PAML_tables.zip
DOI: 10.5061/dryad.k0d7s
title: Data from: Genotype matching in a parasitoid-host genotypic food web: an approach for measuring effects of environmental change

description: Food webs typically quantify interactions between species, whereas
 evolution operates through the success of alleles within populations of a
 single species. To bridge this gap, we quantify genotypic interaction
 networks among individuals of a single specialized parasitoid species and
 its obligately to cyclically parthenogenetic aphid host along a climatic
 gradient. As a case study for the kinds of questions genotype food webs
 could be used to answer, we show that genetically-similar parasitoids
 became more likely to attack genetically-similar hosts in warmer sites
 (i.e. there was network-wide congruence between the within-species shared
 allelic distance of the parasitoid and that of its host). Narrowing of
 host-genotype-niche breadth by parasitoids could reduce resilience of the
 network to changes in host genetic structure or invasion by novel host
 genotypes, and inhibit biological control. Thus, our approach can be
 easily used to detect changes to sub-species-level food webs, which may
 have important ecological and evolutionary implications, such as promoting
 host-race specialisation or the accelerated loss of functional diversity
 following extinctions of closely-related genotypes.
description: aphelinusDAC_popGenotypes and Shared allelic distances-parasitoid-aphid, interaction matrix and distance matricesdata.zipDAC_eriosoma_popaphid dataDistance_matricesdistances between individualsInteraction_matricesgenotypes Eriosomalist of aphid genotypes including individual code number, name of microsatellite loci and sampling populationgenotypes Aphelinus malilist of parasitoid genotypes including individual code number, name of microsatellite loci and sampling population
DOI: 10.5061/dryad.6d86v
title: Data from: Rapid, habitat-related evolution of land snail colour morphs on reclaimed land

description: I made use of the known dates of reclamation (and of afforestations) in
 the IJsselmeerpolders in The Netherlands to assess evolutionary adaptation
 in Cepaea nemoralis. At 12 localities (three in each polder), I sampled a
 total of 4390 adult individuals in paired open and shaded habitats, on
 average 233 m apart, and scored these for genetic shell colour
 polymorphisms. The results show (highly) significant differentiation at
 most localities, although the genes involved differed per locality.
 Overall, though, populations in shaded habitats had evolved towards darker
 shells than those in adjacent open habitats, whereas a ‘Cain &
 Sheppard’ diagram (proportion yellow shells plotted against ‘effectively
 unbanded’ shells) failed to reveal a clear pattern. This might suggest
 that thermal selection is more important than visual selection in
 generating this pattern. Trait differentiation, regardless of whether they
 were plotted against polder age or habitat age, showed a linear increase
 of differentiation with time, corresponding to a mean rate of trait
 evolution of 15–31 kilodarwin. In conclusion, C. nemoralis is capable of
 rapid and considerable evolutionary differentiation over 1–25 snail
 generations, though equilibrium may be reached only at longer time scales.
description: Schilthuizen
 ALLRaw data for each of the
 sample sites, with absolute and relative frequencies of morph categories
 (as well as bar and pie graphs of the same), photographs of the habitat
 and maps of the exact locations of the study sites, summaries of the
 vegetation, sampling dates, coordinates, and other field
 notes.
DOI: 10.21227/afdq-7e30
title: "BOB bamboo scaffolding dataset"

description: "The dataset was collected at multiple construction sites, including Smithfield Gardens on Lung Wah Street, Wing Shing Building on Davis Street, and Man Fat Building on Belcher Street. Data acquisition was performed using an iPhone 12 camera in automatic zoom mode to ensure high-definition imaging. A total of 226 photographs of bamboo scaffolding were captured to form the dataset for training deep learning models. The images were recorded at a resolution of 4032 \u00d7 3024 pixels. An overlap of approximately 30% was maintained between successive images, achieved by adjusting the camera\u2019s pitch angle and horizontal position. The photographs were taken under diverse weather and lighting conditions, including sunny, cloudy, and rainy days, and the scaffolding was in a natural, unaltered state\u2014reflecting real construction environments without any cleaning or arrangement."