cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.60k68
title: Data from: Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles

description: The genomic basis of adaptation to novel environments is a fundamental
 problem in evolutionary biology that has gained additional importance in
 the light of the recent global change discussion. Here, we combined
 laboratory natural selection (experimental evolution) in Drosophila
 melanogaster with genome-wide next generation sequencing of DNA pools
 (Pool-Seq) to identify alleles that are favourable in a novel laboratory
 environment and traced their trajectories during the adaptive process.
 Already after 15 generations, we identified a pronounced genomic response
 to selection, with almost 5000 single nucleotide polymorphisms (SNP;
 genome-wide false discovery rates &lt; 0.005%) deviating from neutral
 expectation. Importantly, the evolutionary trajectories of the selected
 alleles were heterogeneous, with the alleles falling into two distinct
 classes: (i) alleles that continuously rise in frequency; and (ii) alleles
 that at first increase rapidly but whose frequencies then reach a plateau.
 Our data thus suggest that the genomic response to selection can involve a
 large number of selected SNPs that show unexpectedly complex evolutionary
 trajectories, possibly due to nonadditive effects.
description: Description of
 Bioinformatic Analysis PipelineText file containing
 general remarks and description of the most important tools used in the
 analysis pipelinescriptsZipped folder, which contains the most important python scripts used in the analysis pipelineBF15.vcfTotal set of SNPs identified in the populations used for the comparison of base and generation 15 provided in the *.vcf file formatBF37.vcfTotal set of SNPs identified in the populations used for the comparison of base and generation 37 provided in *.vcf file formatBF15.syncSynchronized pileup file created with PoPoolation2 containing the allelic information of all populations used in the analysis of the comparison between Base and generation 15. P-Values of the Cochran Mantel Haenzel Test are attached to each SNP in the last column. The order of the population is as follows: BR1,BR3,BR2,F15R4,F15R5,F23R1,F27R5,F37R4,F37R5,F37R1BF15.zipBF37.syncSynchronized pileup file created with PoPoolation2 containing the allelic information of all populations used in the analysis of the comparison between Base and generation 37. P-Values of the Cochran Mantel Haenzel Test are attached to each SNP in the last column. The order of the population is as follows: BR1,BR3,BR2,F15R4,F15R5,F23R1,F27R5,F37R4,F37R5,F37R1BF37.zipPairwise Comparisons for CMH testPopulations used for the pairwise CMH tests
DOI: 10.60520/ieda/114294
title: Feldspar composition, zircon U-Pb and Hf isotopic compositions, and whole-rock major and trace element data.

description: Table S1 LA-ICP-MS in-situ feldspar composition data.
Table S2 LA-ICP-MS zircon U-Pb isotopic data.
Table S3 Zircon Hf isotopic compositions of Pucheng quartz monzodiorite.
Table S4 Whole-rock major and trace element data of the Late Cretaceous Pucheng, Shiniushan, and Yunshan in the Daiyunshan volcanic field.
DOI: 10.5061/dryad.sc286
title: Data from: Functional traits in parallel evolutionary radiations and trait-environment associations in the Cape Floristic region of South Africa

description: Evolutionary radiations with extreme levels of diversity present a unique
 opportunity to study the role of the environment in plant evolution. If
 environmental adaptation played an important role in such radiations, we
 expect to find associations between functional traits and key climatic
 variables. Similar trait-environment associations across clades may
 reflect common responses, while contradictory associations may suggest
 lineage-specific adaptations. Here, we explore trait-environment
 relationships in two evolutionary radiations in the fynbos biome of the
 highly biodiverse Cape Floristic Region (CFR) of South Africa. Protea and
 Pelargonium are morphologically and evolutionarily diverse genera that
 typify the CFR yet are substantially different in growth form and
 morphology. Our analytical approach employs a Bayesian multiple-response
 generalized linear mixed-effects model, taking into account covariation
 among traits and controlling for phylogenetic relationships. Of the
 pairwise trait-environment associations tested, 6 out of 24 were in the
 same direction and 2 out of 24 were in opposite directions, with the
 latter apparently reflecting alternative life-history strategies. These
 findings demonstrate that trait diversity within two plant lineages may
 reflect both parallel and idiosyncratic responses to the environment,
 rather than all taxa conforming to a global-scale pattern. Such insights
 are essential for understanding how trait-environment associations arise
 and how they influence species diversification.
description: READMEREADME file for all
 files.Protea_CFR_DATASite and trait data for Protea individuals used in this study.Pel_CFR_2011_2012Site and trait data for Pelargonium individuals used in this study.Protea_Pellie_ClimateClimate data form Wilson & Silander (2014) for both Protea and Pelargonium sites used in this analysis.traits-environment-with-phyloR code for running JAGS model.traits-environment-with-phyloJAGS model code for running analysis.results-2014-03-08-13-25-09Results from Pelargonium analysis in .Rsave format.results-2014-03-06-08-47-40Results from Protea analysis in .txt format.results-2014-03-08-12-23-06Results from Pelargonium analysis in .txt format.results-2014-03-06-09-01-02Ultrametricized tree used in Pelargonium analysis.valentetreeUltrametricized tree used in Protea analysis, from Valente et al. (2010).FINAL_20112012_ultrametricUltrametricized tree used in Pelargonium analysis from Ringelberg et al. (unpublished).posterior-comparisons.pdfContains code, explanation, and results summarized for the posterior comparison.posterior-comparisons.RContains code for running posterior comparisons in R.posterior-comparisons.RtexContains comparisons so that knitr() can run code.posterior-comparisons.texPosterior comparison results in tex format.TreeBASE S11132
DOI: 10.5061/dryad.7717q
title: Data from: Expression of eukaryotic-like protein in the microbiome of sponges

description: Eukaryotic-like proteins (ELPs) are classes of proteins that are found in
 prokaryotes, but have a likely evolutionary origin in eukaryotes. ELPs
 have been postulated to mediate host-microbiome interactions. Recent work
 has discovered that prokaryotic symbionts of sponges contain abundant and
 diverse genes for ELPs, which could modulate interactions with their
 filter-feeding and phagocytic host. However, the extent to which these ELP
 genes are actually used and expressed by the symbionts is poorly
 understood. Here we use metatranscriptomics to investigate ELP expression
 in the microbiomes of three different sponges (Cymbastella concentrica,
 Scopalina sp. and Tedania anhelens). We developed a workflow with
 optimized rRNA removal and in silico subtraction of host sequences to
 obtain a reliable symbiont metatranscriptome. This showed that between 1.3
 and 2.3% of all symbiont transcripts contain genes for ELPs. Two classes
 of ELPs (cadherin and tetratricopetide repeats) were abundantly expressed
 by in the C. concentrica and Scopalina sp. microbiomes, while ankyrin
 repeat ELPs were predominant in the T. anhelens metatranscriptome.
 Comparison to non-ELP containing transcripts indicated a constitutive
 expression of ELPs across a range of bacterial and archaeal symbionts.
 Expressed ELPs also contained domains involved in protein secretion and/or
 were co-expressed with proteins involved in extra-cellular transport. This
 suggests these ELPs are likely exported, which could allow for direct
 interaction with the sponge. Our study shows that ELP genes in sponge
 symbionts represent actively expressed functions that could mediate
 molecular interaction between symbiosis partners.
description: Eukaryotic
 transcriptomes and prokaryotic metatranscriptomes of three marine
 sponges.Files
 Cym_Euk_165645.fasta, Sco_Euk_90948.fasta, Ted_Euk_113832.fasta are the
 eukaryotic transcriptomes for Cymbastella concentrica, Scopalina sp.,
 Tedania anhelens respectively. Files Meta_Cym_RZ_228060.fasta,
 Meta_Sco_RZ_64649.fasta, Meta_Ted_RZ_56167.fasta are the prokaryotic
 metatranscriptomes of those same sponges. The numbers in the file names
 represent the number of transcripts within the file. See supporting table
 S1 C and D of the manuscript for details.MEC-16-0957.R1.tar.gzEukaryotic transcriptomes and prokaryotic metatranscriptomes of three marine sponges (original assembly files).These six files represent the original de-novo transcriptome assemblies obtained using Trinity software v2.0.6. Files Cym_Euk_184053.fasta, Sco_Euk_103013.fasta, Ted_Euk_129529.fasta are the eukaryotic transcriptomes for Cymbastella concentrica, Scopalina sp., Tedania anhelens respectively. Files Meta_Cym_RZ_383648.fasta, Meta_Sco_RZ_94173.fasta, Meta_Ted_RZ_85440.fasta are the prokaryotic metatranscriptomes of those same sponges. The numbers in the file names represent the number of transcripts within the file. See supplementary table S1 C and D of the manuscript for details.MEC-16-0957.R1_originalFiles.zip
DOI: 10.5061/dryad.446sv
title: Data from: Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the southeastern United States and Caribbean Islands

description: Drosophila melanogaster is postulated to have colonized North America in
 the past several 100 years in two waves. Flies from Europe colonized the
 east coast United States while flies from Africa inhabited the Caribbean,
 which if true, make the south-east US and Caribbean Islands a secondary
 contact zone for African and European D. melanogaster. This scenario has
 been proposed based on phenotypes and limited genetic data. In our study,
 we have sequenced individual whole genomes of flies from populations in
 the south-east US and Caribbean Islands and examined these populations in
 conjunction with population sequences from the west coast US, Africa, and
 Europe. We find that west coast US populations are closely related to the
 European population, likely reflecting a rapid westward expansion upon
 first settlements into North America. We also find genomic evidence of
 African and European admixture in south-east US and Caribbean populations,
 with a clinal pattern of decreasing proportions of African ancestry with
 higher latitude. Our genomic analysis of D. melanogaster populations from
 the south-east US and Caribbean Islands provides more evidence for the
 Caribbean Islands as the source of previously reported novel African
 alleles found in other east coast US populations. We also find the border
 between the south-east US and the Caribbean island to be the admixture hot
 zone where distinctly African-like Caribbean flies become genomically more
 similar to European-like south-east US flies. Our findings have important
 implications for previous studies examining the generation of east coast
 US clines via selection.
description: Chromopainter files
 zippedZipped folder containing
 scripts, input files, and README for running Chromopainter
 analysisChromopainter.zipSNPRelate_admixtureR script to run PCA analysisVCFtools_Fst_LDScript to us VCFTools for generating Fst and LD valuesADMIXTURE files zippedZipped folder that contains scripts, input files, and README for performing ADMIXTURE analysisADMIXTURE.zipDxy analysis filesDxy.tar.gzvcf SNP file for Fst, LD, and PCA analysesglobal.pop.GATK.SNP.hard.filters.V3.phased_all.pop.maf.05.recode.vcf.gzvcf SNP file from SNP calling pipeline with no additional filtersglobal.pop.GATK.SNP.hard.filters.V3.vcf.gz
DOI: 10.5061/dryad.10877
title: Data from: Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants

description: Gene expression profiling studies are usually performed on pooled samples
 grown under tightly controlled experimental conditions to suppress
 variability among individuals and increase experimental reproducibility.
 In addition, to mask unwanted residual effects, the samples are often
 subjected to relatively harsh treatments that are unrealistic in a natural
 context. Here, we show that expression variations among individual
 wild-type Arabidopsis thaliana plants grown under the same macroscopic
 growth conditions contain as much information on the underlying gene
 network structure as expression profiles of pooled plant samples under
 controlled experimental perturbations. We advocate the use of subtle
 uncontrolled variations in gene expression between individuals to uncover
 functional links between genes and unravel regulatory influences. As a
 case study, we use this approach to identify ILL6 as a new regulatory
 component of the jasmonate response pathway.
description: Supplemental Dataset
 1Module figures for all
 modules learned from the residuals dataset.Supplemental Dataset
 2Excel file containing
 predicted GO annotations for all modules in Supplemental Data Set
 1.tpc112268SupplementalDS2.xlsxSupplemental Dataset 3Module figures for all modules learned from the original dataset, without removing lab and accession effects.Supplemental Dataset 4Excel file containing predicted GO annotations for all modules in Supplemental Data Set 3.tpc112268SupplementalDS4.xlsxSupplemental Dataset 5Excel file with gene counts in the residuals and sample networks for all GO processes with at least 10 nodes in the residuals network.tpc112268SupplementalDS5.xlsxSupplemental Dataset 6Category-specific function prediction performance figures for all GO categories scored in Supplemental Figure 5.tpc112268SupplementalDS6.pdf
DOI: 10.15468/dl.yvf9qd
title: Occurrence Download

description: A dataset containing 2624 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Codium tomentosum"
 ]
}

 The dataset includes 2624 records from 165 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001726-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25431/11380_1270618
title: Database elaborated in the paper "Agents and artefacts in the emerging electric vehicle space"

description: DATABASE elaborated in the paper 
Agents and artefacts in the emerging electric vehicle space published in Int. J. Automotive Technology and Management, 2022
DOI: 10.6084/m9.figshare.31160689
title: Visual Dataset: Conceptual Models of Reality Drift and Synthetic Systems

description: This dataset contains a collection of visual conceptual models used to analyze epistemic degradation, semantic collapse, and recursive symbolic systems in modern cognitive, organizational, and AI-mediated environments.The images represent formal structural patterns observed in synthetic systems, including cognitive compression, semantic fidelity loss, optimization traps, filter fatigue, performativity drift, and recursive symbolic feedback loops.The dataset is intended to support research and analysis in systems theory, AI governance, institutional epistemology, and human–machine cognition. The models function as analytical tools for reasoning about how symbolic systems evolve when internal representations increasingly replace external reality as the primary reference point for decision-making.
DOI: 10.6084/m9.figshare.31160689.v1
title: Visual Dataset: Conceptual Models of Reality Drift and Synthetic Systems

description: This dataset contains a collection of visual conceptual models used to analyze epistemic degradation, semantic collapse, and recursive symbolic systems in modern cognitive, organizational, and AI-mediated environments.The images represent formal structural patterns observed in synthetic systems, including cognitive compression, semantic fidelity loss, optimization traps, filter fatigue, performativity drift, and recursive symbolic feedback loops.The dataset is intended to support research and analysis in systems theory, AI governance, institutional epistemology, and human–machine cognition. The models function as analytical tools for reasoning about how symbolic systems evolve when internal representations increasingly replace external reality as the primary reference point for decision-making.
DOI: 10.5061/dryad.3gq12
title: Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

description: The study of parallel evolution facilitates the discovery of common rules
 of diversification. Here, we examine the repeated evolution of thick lips
 in Midas cichlid fishes (the Amphilophus citrinellus species complex)—from
 two Great Lakes and two crater lakes in Nicaragua—to assess whether
 similar changes in ecology, phenotypic trophic traits and gene expression
 accompany parallel trait evolution. Using next-generation sequencing
 technology, we characterize transcriptome-wide differential gene
 expression in the lips of wild-caught sympatric thick- and thin-lipped
 cichlids from all four instances of repeated thick-lip evolution. Six
 genes (apolipoprotein D, myelin-associated glycoprotein precursor,
 four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member
 8-like and one hypothetical protein) are significantly underexpressed in
 the thick-lipped morph across all four lakes. However, other aspects of
 lips' gene expression in sympatric morphs differ in a lake-specific
 pattern, including the magnitude of differentially expressed genes
 (97-510). Generally, fewer genes are differentially expressed among morphs
 in the younger crater lakes than in those from the older Great Lakes. Body
 shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and
 δ15N) differ between all sympatric morphs, with the greatest
 differentiation in the Great Lake Nicaragua. Some ecological traits evolve
 in parallel (those related to foraging ecology; e.g. lip size, body and
 head shape) but others, somewhat surprisingly, do not (those related to
 diet and food processing; e.g. jaw size and shape, stable isotopes). Taken
 together, this case of parallelism among thick- and thin-lipped cichlids
 shows a mosaic pattern of parallel and nonparallel evolution.
description: Manousakietal_transcriptsTranscripts built from assembling raw reads (with oases v0.1.22) that have significant similarity with known vertebrate proteins.LippyProject_Ecological_dataEcological datalippy vs non lippy body shapeA tps file that contains the raw landmark coordinates and associated ID's for all 777 specimens used for body shape analysis.lippy vs non lippy_FINAL.TPS
DOI: 10.15468/dl.4xnxju
title: Occurrence Download

description: A dataset containing 4998 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Ohio State University Tetrapod Division - Amphibian Collection (OSUM)"
 ]
}

 The dataset includes 4998 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001727-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b42pxu
title: Occurrence Download

description: A dataset containing 460 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Grampus griseus"
 ]
}

 The dataset includes 460 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001724-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6169b
title: Data from: Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3

description: We describe new methods for characterizing gene tree discordance in
 phylogenomic datasets, which screen for deviations from neutral
 expectations, summarize variation in statistical support among gene trees,
 and allow comparison of the patterns of discordance induced by various
 analysis choices. Using an exceptionally complete set of genome sequences
 for the short arm of chromosome 3 in Oryza (rice) species, we applied
 these methods to identify the causes and consequences of differing
 patterns of discordance in the sets of gene trees inferred using a panel
 of 20 distinct analysis pipelines. We found that discordance patterns were
 strongly affected by aspects of data selection, alignment, and alignment
 masking. Unusual patterns of discordance evident when using certain
 pipelines were reduced or eliminated by using alternative pipelines,
 suggesting that they were the product of methodological biases rather than
 evolutionary processes. In some cases, once such biases were eliminated,
 evolutionary processes such as introgression could be implicated.
 Additionally, patterns of gene tree discordance had significant downstream
 impacts on species tree inference. For example, inference from
 supermatrices was positively misleading when pipelines that led to biased
 gene trees were used. Several results may generalize to other data sets:
 we found that gene tree and species tree inference gave more reasonable
 results when intron sequence was included during sequence alignment and/or
 tree inference, the alignment software PRANK was used, and/or detectable
 "block-shift" alignment artifacts were removed. We discuss our
 findings in the context of well-established relationships in Oryza and
 continuing controversies regarding the domestication history of O. sativa.
description: SupplementaryFigures1-5onlineAppendicescollectedAlignmentsForPosting.tarAbout 26,000 alignments used in study, in nexus format.annotationGffsForPosting.targff formatted files describing gene annotations not available from other sources. Coordinates correspond to sequence assemblies deposited in Dryad, which may differ from versions in Genbank.SupplementaryTables1-3seqAssembliesForPostingSequence assemblies in fasta format for all taxa except O. sativa. Some differ from assemblies deposited in Genbank.