cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0nb2307
title: Data from: Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird

description: The formation of independent evolutionary lineages involves neutral and
 selective factors, and understanding their relative roles in population
 divergence is a fundamental goal of speciation research. Correlations
 between allele frequencies and environmental variability can reveal the
 role of selection, yet the relative contribution of drift can be difficult
 to establish. Recently diversified taxa like the Oregon junco (Aves,
 Passerellidae, Junco hyemalis oreganus) of western North America provide
 ideal scenarios to apply genetic-environment association analyses (GEA)
 while controlling for population structure. Analysis of genome-wide SNP
 loci revealed marked genetic structure consisting of differentiated
 populations in isolated, dry southern mountain ranges, and less divergent,
 recently expanded populations in humid northern latitudes. We used
 correlations between genomic and environmental variance to test for three
 specific modes of evolutionary divergence: (i) drift in geographic
 isolation, (ii) differentiation along continuous selective gradients, and
 (iii) isolation by adaptation. We found evidence of strong drift in
 southern mountains, but also signals of local adaptation driven by
 temperature, precipitation, elevation and vegetation, especially when
 controlling for population history. We identified numerous variants under
 selection scattered across the genome, suggesting that local adaptation
 can promote rapid differentiation when acting over multiple independent
 loci.
description: genolike_map20_q20_snp16_maf002_ind32_430K.beagleInput file of genotype likelihoods in Beagle format (.beagle.gz) for PCANGSD analysis.ORJUSTRUx8_biall_dp450_q40_perpopmiss075_hwe00001_maf002_LD02_neutral01Dataset of 16,858 independent neutral SNPs from 64 samples in vcf format for STRUCTURE analysis.ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_noZ_neutral01Dataset of 15,209 neutral SNPs used in the PCA intended for population structure correction in the redundancy analysis (RDA).ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_noZDataset of 15,252 SNPs used in the redundancy analysis.ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_sel01_BAYESCENVSubset of 49 SNP outliers identified with BayScEnv for the second redundancy analysis in the manuscript.ORJUGEO_coords_ALLSAMPLESTable of sample location and geographic coordinates for all sequenced samples of the study.ORJUGEO_coords_ClimVariablesSample data and WorldClim environmental data (Fick, S.E. and R.J. Hijmans, 2017. Worldclim 2: New 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology.) for each one of the samples included in the genotype-environment association analyses.
DOI: 10.5061/dryad.6f356
title: Data from: Random sequences are an abundant source of bioactive RNAs or peptides

description: It is generally assumed that new genes arise through duplication and/or
 recombination of existing genes. The probability that a new functional
 gene could arise out of random non-coding DNA is so far considered to be
 negligible, as it seems unlikely that such an RNA or protein sequence
 could have an initial function that influences the fitness of an organism.
 Here, we have tested this question systematically, by expressing clones
 with random sequences in Escherichia coli and subjecting them to
 competitive growth. Contrary to expectations, we find that random
 sequences with bioactivity are not rare. In our experiments we find that
 up to 25% of the evaluated clones enhance the growth rate of their cells
 and up to 52% inhibit growth. Testing of individual clones in competition
 assays confirms their activity and provides an indication that their
 activity could be exerted by either the transcribed RNA or the translated
 peptide. This suggests that transcribed and translated random parts of the
 genome could indeed have a high potential to become functional. The
 results also suggest that random sequences may become an effective new
 source of molecules for studying cellular functions, as well as for
 pharmacological activity screening.
description: Results_IPTG_controlTable with read numbers for each clone for experiment plus/minus IPTG control shown in Table 1 of the paper. Further Tabs in the file include the respective DeSeq2 statistics for each sampled timepoint.Results_Exp1Table with read numbers for each clone for experiment 1 shown in Table 1 of the paper. Further Tabs in the file include the respective DeSeq2 statistics for each sampled timepoint.Results_Exp2Table with read numbers for each clone for experiment 2 shown in Table 1 of the paper. Further Tabs in the file include the respective DeSeq2 statistics for each sampled timepoint.Results_Exp3Table with read numbers for each clone for experiment 3 shown in Table 1 of the paper. Further Tabs in the file include the respective DeSeq2 statistics for each sampled timepoint.Results_Exp4Table with read numbers for each clone for experiment 4 shown in Table 1 of the paper. Further Tabs in the file include the respective DeSeq2 statistics for each sampled timepoint.Results_Exp5Table with read numbers for each clone for experiment 5 shown in Table 1 of the paper. Further Tabs in the file include the respective DeSeq2 statistics for each sampled timepoint.Results_Exp6Table with read numbers for each clone for experiment 6 shown in Table 1 of the paper. Further Tabs in the file include the respective DeSeq2 statistics for each sampled timepoint.Results_Exp7Table with read numbers for each clone for experiment 7 shown in Table 1 of the paper. Further Tabs in the file include the respective DeSeq2 statistics for each sampled timepoint.
DOI: 10.5061/dryad.mk067
title: Data from: Mapping wood production in European forests

description: Wood production is an important forest use, impacting a range of other
 ecosystem services. However, information on the spatial patterns in wood
 production is limited and often available only for larger administrative
 units. In this study, we developed high-resolution wood production maps
 for European forests. We collected wood production statistics for 29
 European countries from 2000 to 2010, as well as comprehensive sets of
 biophysical and socioeconomic location factors. We used regression
 analyses to produce maps indicating the harvest likelihood on a 1 × 1 km2
 grid. These likelihood maps were validated using national forest inventory
 plot data. We then disaggregated wood production statistics from larger
 administrative units to the grid level using the harvest likelihood as
 weights. We verified the resulting wood production maps by correlating
 predicted and observed wood production at the level of smaller
 administrative units not used for generating the wood production maps. We
 conclude that (i) productivity, tree species composition and terrain
 ruggedness are the most important location factors that determine the
 spatial patterns of wood production at the pan-European scale and that
 (ii) incorporating these location factors substantially improves the
 results of disaggregating wood production statistics compared to a
 disaggregation based on forest cover only. Our wood production maps give
 insight into forest ecosystem service provisioning and can be used to
 improve the assessment of potentials and costs of woody biomass supply.
description: Wood production maps for
 EuropeZip folder containing
 maps as TIFF map images.WoodProductionMaps.zip
DOI: 10.5061/dryad.d9c48b6
title: Data from: Disentangling structural genomic and behavioral barriers in a sea of connectivity

description: Genetic divergence among populations arises through natural selection or
 drift and is counteracted by connectivity and gene flow. In sympatric
 populations, isolating mechanisms are thus needed to limit the
 homogenizing effects of gene flow to allow for adaptation and speciation.
 Chromosomal inversions act as an important mechanism maintaining isolating
 barriers, yet their role in sympatric populations and divergence with gene
 flow is not entirely understood. Here, we revisit the question whether
 inversions play a role in the divergence of connected populations of the
 marine fish Atlantic cod, by exploring a unique dataset combining
 whole-genome sequencing data and behavioral data obtained with acoustic
 telemetry. Within a confined fjord environment, we find three genetically
 differentiated Atlantic cod types belonging to the oceanic North Sea
 population, the western Baltic population, and a local fjord-type cod.
 Continuous behavioral tracking over four years revealed temporally stable
 sympatry of these types within the fjord. Despite overall weak genetic
 differentiation consistent with high levels of gene flow, we detected
 significant frequency shifts of three previously identified inversions,
 indicative for an adaptive barrier to gene flow. In addition, behavioral
 data indicated that North Sea cod and individuals homozygous for the LG12
 inversion had lower fitness in the fjord environment. However, North Sea
 and fjord-type cod also occupy different depths, possibly contributing to
 prezygotic reproductive isolation and representing a behavioral barrier to
 gene flow. Our results provide the first insights into a complex interplay
 of genomic and behavioral isolating barriers in Atlantic cod and establish
 a new model system towards an understanding of the role of genomic
 structural variants in adaptation and diversification.
description: Filtered SNP
 datasetThe filtered SNP dataset
 used in Barth et al. as PLINK/MERLIN/Haploview text genotype table (.ped),
 accompanied by a PLINK text fileset variant information file (.map)
 compressed as .zip archive file. Both files are plain text. For usage of
 this format see: https://www.cog-genomics.org/plink2/barth_genotypes.zipSliding window analyses scriptSliding window analyses python3 script used to perform sliding window analyses over a vcf file in Barth et al.barth_sliding_windows.pyIndividual behavioral dataBehavioral data for each specimen as Microsoft Excel spreadsheet (two sheets) used in Barth et al.barth_behavioral_data.xlsx
DOI: 10.15468/yvveam
title: A new species of the surgeonfish genus † Caprovesposus (Acanthuridae) from the Lower to Middle Miocene of the North Caucasus, Russia

description: This dataset contains the digitized treatments in Plazi based on the original journal article Bannikov, Alexandre F., Tyler, James C., Tyler, Diane M. (2025): A new species of the surgeonfish genus † Caprovesposus (Acanthuridae) from the Lower to Middle Miocene of the North Caucasus, Russia. Zootaxa 5719 (1): 117-125, DOI: 10.11646/zootaxa.5719.1.6, URL: https://doi.org/10.11646/zootaxa.5719.1.6AbstractA new species of fossil surgeonfish, † Caprovesposus daniltshenkoi sp. nov., is described based upon two specimens from the terminal Maikopian (upper Lower to lower Middle Miocene; not less than 15 mya) in the northwestern Caucasus. The specimens were excavated from brownish gray clays in the bank of the Pshekha River in the Krasnodar Region of Apsheronsk District, Russia. Both specimens are in the acronurus presettlement stage of development and are placed within the formerly monotypic genus † Caprovesposus based upon their possession of vertically elongated, needle-like scales on the body. They differ from the Oligocene † Caprovesposus parvus Daniltshenko, 1960 in (1) lacking serrations on the frontal, mesethmoid, preopercle, and basipterygium; and (2) having the vertically elongated, needle-like scales only on the anterior and middle portions of the body, rather than on the entire body. Three additional, previously collected specimens from the Caucasus and Crimea are referred to the new species.
DOI: 10.15139/s3/tunjgi
title: Data Management and Sharing Plan for: Randomized controlled trial of FoRtitude: Targeted eHealth intervention to reduce fear of recurrence among breast cancer survivors in community oncology settings

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.7nb70
title: Data from: Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers

description: Polyploidy is common and an important evolutionary factor in most land
 plant lineages, but it is rare in gymnosperms. Coast redwood (Sequoia
 sempervirens) is one of just two polyploid conifer species and the only
 hexaploid. Evidence from fossil guard cell size suggests that polyploidy
 in Sequoia dates to the Eocene. Numerous hypotheses about the mechanism of
 polyploidy and parental genome donors have been proposed, based primarily
 on morphological and cytological data, but it remains unclear how Sequoia
 became polyploid and why this lineage overcame an apparent gymnosperm
 barrier to whole-genome duplication (WGD). We sequenced transcriptomes and
 used phylogenetic inference, Bayesian concordance analysis and paralog age
 distributions to resolve relationships among gene copies in hexaploid
 coast redwood and close relatives. Our data show that hexaploidy in coast
 redwood is best explained by autopolyploidy or, if there was
 allopolyploidy, it happened within the Californian redwood clade. We found
 that duplicate genes have more similar sequences than expected, given the
 age of the inferred polyploidization. Conflict between molecular and
 fossil estimates of WGD can be explained if diploidization occurred very
 slowly following polyploidization. We extrapolate from this to suggest
 that the rarity of polyploidy in gymnosperms may be due to slow
 diploidization in this clade.
description: Single-copy
 analysesThis file contains
 filtered transcriptome assemblies for S. sempervirens, S. giganteum, M.
 glyptostroboides, and T. occidentalis. These files serve as input for our
 concordance analysis pipleline located at
 https://github.com/nstenz/tocaMulti-copy
 analysesThis directory contains
 .fasta alignments and PAML (codeml) outputs. Files are split between a
 2-copy and 3-copy directory based on the number of putative homeologous
 sequences in hexaploid S. sempervirens.Transcriptome
 assembliesTrinity assemblies for
 four taxa, both with and without EviGene filteringtranscriptomes.zip
DOI: 10.5061/dryad.896cs
title: Data from: Inbreeding effects on gene-specific DNA methylation among tissues of Chinook salmon

description: Inbreeding depression is the loss of fitness resulting from the mating of
 genetically related individuals. Traditionally, the study of inbreeding
 depression focused on genetic effects, although recent research has
 identified DNA methylation as also having a role in inbreeding effects.
 Since inbreeding depression and DNA methylation change with age and
 environmental stress, DNA methylation is a likely candidate for the
 regulation of genes associated with inbreeding depression. Here, we use a
 targeted, multigene approach to assess methylation at 22 growth-,
 metabolic-, immune- and stress-related genes. We developed PCR-based DNA
 methylation assays to test the effects of intense inbreeding on intragenic
 gene-specific methylation in inbred and outbred Chinook salmon. Inbred
 fish had altered methylation at three genes, CK-1, GTIIBS and hsp70,
 suggesting that methylation changes associated with inbreeding depression
 are targeted to specific genes and are not whole-genome effects. While we
 did not find a significant inbreeding by age interaction, we found that
 DNA methylation generally increases with age, although methylation
 decreased with age in five genes, CK-1, IFN-ɣ, HNRNPL, hsc71 and FSHb,
 potentially due to environmental context and sexual maturation. As
 expected, we found methylation patterns differed among tissue types,
 highlighting the need for careful selection of target tissue for
 methylation studies. This study provides insight into the role of
 epigenetic effects on ageing, environmental response and tissue function
 in Chinook salmon and shows that methylation is a targeted and regulated
 cellular process. We provide the first evidence of epigenetically based
 inbreeding depression in vertebrates.
description: Venney_et_al_inbreeding_fastqFastq files for each tissue in each individual split using mothur. File name includes the population (H=inbred, P=outbred), individual number (fry: P1-10, H1-11, yearling: P11-20, H12-21), and the tissue denoted by the first letter of each word (Fin, Gill, Liver, Spleen).Venney_final_pct_meth_dataFinal percent methylation data after outlier exclusion and quality control.Venney_et_al_geneseqs_bwamethGene sequences used for bwa-meth alignment and methylation analysis.
DOI: 10.5061/dryad.1v2s7
title: Data from: The walking dead: blender as a tool for palaeontologists with a case study on extinct arachnids

description: This paper serves two roles. First, it acts as an introduction to Blender,
 an open-source computer graphics program, which can be of utility to
 paleontologists. To lessen the software's otherwise steep learning
 curve, a step-by-step guide to create an idealized reconstruction of a
 fossil in the form of a three-dimensional model in Blender, or to use the
 software to render results from ‘virtual paleontology' techniques, is
 provided as an online supplemental data file. Second, here we demonstrate
 the use of Blender with a case study on the extinct trigonotarbid
 arachnids. We report the limb articulations of members of the Devonian
 genus Palaeocharinus on the basis of exceptionally preserved fossils from
 the Rhynie Cherts of Scotland. We use these newly reported articulations
 to create a Blender model, and draw comparisons with the gait of extant
 arachnids to produce as accurate a representation of the trigonotarbid
 flexing its limbs and walking as possible, presented in additional online
 supplemental data files. Knowledge of the limb articulations of
 trigonotarbid arachnids also allows us to discuss their functional
 morphology: trigonotarbids' limbs and gait were likely comparable to
 extant cursorial spiders, but lacked some innovations seen in more derived
 arachnids.
description: Supplemental Data File
 1An
 introductory guide to using Blender for scientific visualisation in
 paleontology.Garwood_and_Dunlop_Supplemental_Data_1_An_introductory_guide_to_Blender.pdfSupplemental Data File 2A video showing the model of Palaeocharinus spp. created for the current study. Created, animated and edited in Blender, this shows first the model flexing its legs from a rest position to beneath the body, and then back again. Subsequently the video shows the model walking from a variety of angles. All limb movement is constrained by the findings reported herein.Garwood_and_Dunlop_Supplemental_Data_File_2_Palaeocharinus_video.aviSupplemental Data File 3The Blender file containing this model animated to show Palaeocharinus spp. walking. Tested on Blender releases 2.65 - 2.70 on Windows and Ubuntu.Garwood_and_Dunlop_Supplemental_Data_File_3_Palaeocharinus_walking.blendSupplemental Data File 4The Blender file containing this model animated to show Palaeocharinus spp. flexing its limbs. Tested on Blender releases 2.65 - 2.70 on Windows and Ubuntu.Garwood_and_Dunlop_Supplemental_Data_File_4_Palaeocharinus_leg_flex.blend
DOI: 10.5061/dryad.r62f0
title: Data from: Proximal methylation features associated with nonrandom changes in gene body methylation

description: Background: Gene body methylation at CG dinucleotides is a widely
 conserved feature of methylated genomes but remains poorly understood. The
 Arabidopsis thaliana strain Cvi has depleted gene body methylation
 relative to the reference strain Col. Here, we leverage this natural
 epigenetic difference to investigate gene body methylation stability.
 Results: Recombinant inbred lines derived from Col and Cvi were used to
 examine the transmission of distinct gene body methylation states. The
 vast majority of genic CG methylation patterns are faithfully transmitted
 over nine generations according to parental genotype, with only 1–4% of
 CGs either losing or gaining methylation relative to the parent. Genic CGs
 that fail to maintain the parental methylation state are shared among
 independent lines, suggesting that these are not random occurrences. We
 use a logistic regression framework to identify features that best predict
 sites that fail to maintain parental methylation state. Intermediate
 levels of CG methylation around a dynamic CG site and high methylation
 variability across many A. thaliana strains at that site are the strongest
 predictors. These data suggest that the dynamic CGs we identify are not
 specific to the Col–Cvi recombinant inbred lines but have an epigenetic
 state that is inherently less stable within the A. thaliana species.
 Extending this, variably methylated genic CGs in maize and Brachypodium
 distachyon are also associated with intermediate local CG methylation.
 Conclusions: These results provide new insights into the features
 determining the inheritance of gene body methylation and demonstrate that
 two different methylation equilibria can be maintained within single
 individuals.
description: Genome_Biol_2017_datasetsZip archive containing four .txt files: 3 tab-delimited datasets and a README (readme also uploaded separately). full_dataset.txt contains methylation and other information from A. thaliana generated as part of this study, full_distachyon_Bd1_1_data.txt contains data from B. distachyon generated by Eichten et al. 2016 (Genome Res.), and full_maize_B73_data.txt contains data from Z. mays generated by Li et al. 2015 (Plant Physiol.). Datasets contain all data used to generate Fig. 5 and Fig. S11. Details on each field in each file found in README.
DOI: 10.5061/dryad.3ts56
title: Data from: Smaller is better: drift in gaze measurements due to pupil dynamics

description: Camera-based eye trackers are the mainstay of eye movement research and
 countless practical applications of eye tracking. Recently, a significant
 impact of changes in pupil size on gaze position as measured by
 camera-based eye trackers has been reported. In an attempt to improve the
 understanding of the magnitude and population-wise distribution of the
 pupil-size dependent shift in reported gaze position, we present the first
 collection of binocular pupil drift measurements recorded from 39
 subjects. The pupil-size dependent shift varied greatly between subjects
 (from 0.3 to 5.2 deg of deviation, mean 2.6 deg), but also between the
 eyes of individual subjects (0.1 to 3.0 deg difference, mean difference
 1.0 deg). We observed a wide range of drift direction, mostly downward and
 nasal. We demonstrate two methods to partially compensate the pupil-based
 shift using separate calibrations in pupil-constricted and pupil-dilated
 conditions, and evaluate an improved method of compensation based on
 individual look-up-tables, achieving up to 74% of compensation.
description: Eye tracking data from
 Drewes et al, PlosONE 2014A tar/zipped matlab
 datafile (.mat), containing structured dataDrewesEtAl_PlosONE_2014.tar.gz