cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gf643
title: Data from: Structural mouthpart interaction evolved already in the earliest lineages of insects

description: In butterflies, bees, flies and true bugs specific mouthparts are in close
 contact or even fused to enable piercing, sucking or sponging of
 particular food sources. The common phenomenon behind these mouthpart
 types is a complex composed of several consecutive mouthparts which
 structurally interact during food uptake. The single mouthparts are thus
 only functional in conjunction with other adjacent mouthparts, which is
 fundamentally different to biting–chewing. It is, however, unclear when
 structural mouthpart interaction (SMI) evolved since this principle
 obviously occurred multiple times independently in several extant and
 extinct winged insect groups. Here, we report a new type of SMI in two of
 the earliest wingless hexapod lineages—Diplura and Collembola. We found
 that the mandible and maxilla interact with each other via an articulatory
 stud at the dorsal side of the maxillary stipes, and they are furthermore
 supported by structures of the hypopharynx and head capsule. These
 interactions are crucial stabilizing elements during food uptake. The
 presence of SMI in these ancestrally wingless insects, and its absence in
 those crustacean groups probably ancestral to insects, indicates that SMI
 is a groundplan apomorphy of insects. Our results thus contradict the
 currently established view of insect mouthpart evolution that
 biting–chewing mouthparts without any form of SMI are the ancestral
 configuration. Furthermore, SMIs occur in the earliest insects in a high
 anatomical variety. SMIs in stemgroup representatives of insects may have
 triggered efficient exploitation and fast adaptation to new terrestrial
 food sources much earlier than previously supposed.
description: _Movie_S1a_Diplura_mouthpart_movement_Movie_S1b_Collembole_mouthpart_movementMovie S1b: Video showing the mandible movement in P. flavescens (Collembola) (1st half) and TIFF image stack of the reconstructed microCT dataset of P. flavescens (2nd half). Note the original dataset of the TIFF image stack is 2536x2536 pixel with 2048 single images. The image stack was reduced in size but is available upon request.File_S2_Coll_Diplura_md_mx_details+taxon_samplingFile S2: PDF file with taxon sampling, details of the structural mouthpart interactions in Collembola and Diplura, and a description of their mandibular and maxillary musculature equipment and its function._3D_model_S3_Diplura_Mandible3D model S3: 3D model of the mandible-maxilla-hypopharynx complex of Atlasjapyx cf atlas in .wrl format for import into the program Meshlab or other animation programs._3D_model_S4_Collembola_Mandible3D model S4: 3D model of the mandible-maxilla-hypopharynx complex of Pogonognathellus flavescens in .wrl-format for import into the program Meshlab or other animation programs._3D_model_S5_Protura_Mandible3D model S5: 3D model of the mandible-maxilla-hypopharynx complex of Acerentomon sp. (Protura) in .wrl-format for import into the program Meshlab or other animation programs.
DOI: 10.5281/zenodo.18376587
title: Oopses and Ohs: An Eye-Tracking Study of Human Errors in Virtual Reality

description: This dataset contains longitudinal eye-tracking recordings collected in a virtual reality (VR) experiment investigating human cognitive errors during a mental arithmetic task. Over 18- and 6-month periods, two participants completed repeated VR sessions while solving multiplication problems, yielding more than 60 hours of eye-tracking data sampled at 120 Hz, collected using a Tobii eye tracker integrated into the HTC Vive Pro Eye VR headset.

Each trial is labeled according to task outcome (Correct = 2, Missed = 1, Wrong = 0) and includes a unique trial identifier encoding participant, session, and trial number (UID with format: PX-##-##), as well as the presented question, the participant’s response, pupil diameter, gaze direction, pupil position, and eye openness.

The dataset was designed to support research on cognitive load, error prediction, and human performance modeling in immersive environments, and accompanies the paper “Oopses and Ohs: An Eye-Tracking Study of Human Errors in Virtual Reality” (GEMINI Workshop at IEEE VR).
DOI: 10.5281/zenodo.18376588
title: Oopses and Ohs: An Eye-Tracking Study of Human Errors in Virtual Reality

description: This dataset contains longitudinal eye-tracking recordings collected in a virtual reality (VR) experiment investigating human cognitive errors during a mental arithmetic task. Over 18- and 6-month periods, two participants completed repeated VR sessions while solving multiplication problems, yielding more than 60 hours of eye-tracking data sampled at 120 Hz, collected using a Tobii eye tracker integrated into the HTC Vive Pro Eye VR headset.

Each trial is labeled according to task outcome (Correct = 2, Missed = 1, Wrong = 0) and includes a unique trial identifier encoding participant, session, and trial number (UID with format: PX-##-##), as well as the presented question, the participant’s response, pupil diameter, gaze direction, pupil position, and eye openness.

The dataset was designed to support research on cognitive load, error prediction, and human performance modeling in immersive environments, and accompanies the paper “Oopses and Ohs: An Eye-Tracking Study of Human Errors in Virtual Reality” (GEMINI Workshop at IEEE VR).
DOI: 10.5061/dryad.1q778
title: Data from: Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice

description: Plant genomes contain numerous transposable elements (TEs), and many
 hypotheses on the evolutionary drivers that restrict TE activity have been
 postulated. Few models, however, have focused on the evolutionary
 epigenomic interaction between the plant host and its TE. The host genome
 recruits epigenetic factors, such as methylation, to silence TEs but
 methylation can spread beyond the TE sequence and influence the expression
 of nearby host genes. In this study, we investigated this epigenetic
 trade-off between TE and proximal host gene silencing by studying the
 epigenomic regulation of repressing long terminal repeat (LTR)
 retrotransposons (RTs) in Oryza sativa. Results showed significant
 evidence of methylation spreading originating from the LTR-RT sequences,
 and the extent of spreading was dependent on 5 factors: 1) LTR-RT family,
 2) time since the LTR-RT insertion, 3) recombination rate of the LTR-RT
 region, 4) level of LTR-RT sequence methylation, and 5) chromosomal
 location. Methylation spreading had negative effects by reducing host gene
 expression, but only on host genes with LTR-RT inserted in its introns.
 Our results also suggested high levels of LTR-RT methylation might have a
 role in suppressing TE-mediated deleterious ectopic recombination. In the
 end, despite the methylation spreading, no strong epigenetic trade-off was
 detected and majority of LTR-RT may have only minor epigenetic effects on
 nearby host genes.
description: indica reference
 japonica query genome alignment result in BED formatBED format genome
 alignment results where indica 93-11 was used as reference and japonica
 nipponbare genome was used as query genome. Indica chromosome was named as
 SAI.chromosome_number and japonica chromosome named as
 SAJ.chromosome_number.Osat_indica_9311_REF-Osat_japonica_NPB_QUERY.sorted.bedjaponica reference indica query genome alignment result in BED formatBED format genome alignment results where japonica nipponbare was used as reference and indica 93-11 was used as query genome. Indica chromosome was named as SAI.chromosome_number and japonica chromosome named as SAJ.chromosome_number.Osat_japonica_NPB_REF-Osat_indica_9311_QUERY.sorted.bedjaponica genome LTR-RT and nearby host gene and the host genes' expression valuesjaponica_transcript.txtindica genome LTR-RT and nearby host gene and the host genes' expression valuesindica_transcript.txtjaponica genome LTR-RT methylation levelsjaponica_methyl.txtindica genome LTR-RT methylation levelsindica_methyl.txtjaponica genome LTR-RT up and downstream region methylation levelsjaponica_methyl_updown.txtindica genome LTR-RT up and downstream region methylation levelsindica_methyl_updown.txtMethylation level for LTR-RT and its up or downstream region in japonica genome and its orthologous region in indicajaponica_methyl_updown_ortholog.txtMethylation level for LTR-RT and its up or downstream region in indica genome and its orthologous region in japonicaindica_methyl_updown_ortholog.txt
DOI: 10.5061/dryad.nr780
title: Data from: Evolution of drift robustness in small populations

description: Most mutations are deleterious and cause a reduction in population fitness
 known as the mutational load. In small populations, weakened selection
 against slightly-deleterious mutations results in an additional fitness
 reduction. Many studies have established that populations can evolve a
 reduced mutational load by evolving mutational robustness, but it is
 uncertain whether small populations can evolve a reduced susceptibility to
 drift-related fitness declines. Here, using mathematical modeling and
 digital experimental evolution, we show that small populations do evolve a
 reduced vulnerability to drift, or ‘drift robustness’. We find that,
 compared to genotypes from large populations, genotypes from small
 populations have a decreased likelihood of small-effect deleterious
 mutations, thus causing small-population genotypes to be drift-robust. We
 further show that drift robustness is not adaptive, but instead arises
 because small populations can only maintain fitness on drift-robust
 fitness peaks. These results have implications for genome evolution in
 organisms with small effective population sizes.
description: READMEGuide to all of the
 files contained within this directory.rename_detail_filesA Python script that renames Avida detail output files for easier use in Analyze Mode.dr_modelA Mathematica notebook that solves the drift robustness mathematical model.config_filesA folder containing all of the Avida configuration files.create_csv_filesA folder containing all of the Python scripts to create csv files from Avida output.csv_filesA folder containing all of the csv files used to create the figures and perform statistical analyses.data_foldersA folder containing all of the Avida data.sub_filesA folder containing all of the submission scripts for the Avida experiments. These files contain the parameters altered from the main Avida configuration file.figures_statisticsPython script to create the figures and perform statistical analyses.
DOI: 10.5061/dryad.5hq6r
title: Data from: The importance of mechanisms for the evolution of cooperation

description: Studies aimed at explaining the evolution of phenotypic traits have often
 solely focused on fitness considerations, ignoring underlying mechanisms.
 In recent years, there has been an increasing call for integrating
 mechanistic perspectives in evolutionary considerations, but it is not
 clear whether and how mechanisms affect the course and outcome of
 evolution. To study this, we compare four mechanistic implementations of
 two well-studied models for the evolution of cooperation, the Iterated
 Prisoner's Dilemma (IPD) game and the Iterated Snowdrift (ISD) game.
 Behavioural strategies are either implemented by a 1 : 1
 genotype–phenotype mapping or by a simple neural network. Moreover, we
 consider two different scenarios for the effect of mutations. The same set
 of strategies is feasible in all four implementations, but the probability
 that a given strategy arises owing to mutation is largely dependent on the
 behavioural and genetic architecture. Our individual-based simulations
 show that this has major implications for the evolutionary outcome. In the
 ISD, different evolutionarily stable strategies are predominant in the
 four implementations, while in the IPD each implementation creates a
 characteristic dynamical pattern. As a consequence, the evolved average
 level of cooperation is also strongly dependent on the underlying
 mechanism. We argue that our findings are of general relevance for the
 evolution of social behaviour, pleading for the integration of a
 mechanistic perspective in models of social evolution.
description: Simulation
 dataThis file contains the
 output of 100 replicate simulations for each parameter setting of our
 study (both of the results presented in the main text and in the SI). The
 folders are named as follows:
 game_mutationrate_payoffconfiguration_behaviouralimplementation_mutationregime. The abbreviations stand for the following: IPD = Iterated Prioner's Dilemma game, ISD = Iterated Snowdrift game, NN = neural network, TM = 1:1 mapping, GM = entire-genome muation, LM = per-locus mutation. Each folder contains 100 .txt files with simulation output. Time is on the rows (top row is the first generation), the frequencies of the different strategies (in the same order as in table 2 of the main text) are on the columns.simulation_data.rar
DOI: 10.5061/dryad.7990
title: Data from: SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing

description: The western black cottonwood (Populus trichocarpa) was the first tree to
 have its genome fully sequenced and has emerged as the model species for
 the study of secondary growth and wood formation. It is also a good
 candidate species for the production of lignocellulosic biofuels. Here we
 present and make available to the research community the results of the
 sequencing of the transcriptome of developing xylem in 20 accessions with
 high throughput next generation sequencing technology. We found over 0.5
 million putative SNPs in 26,595 genes that are expressed in developing
 secondary xylem. More than two thirds of all SNPs were found in annotated
 exons, with 18% and 14% in regions of the genome annotated as introns and
 intergenic, respectively, where only 3% and 4% of sequence reads mapped.
 This suggests that the current annotation of the poplar genome is
 remarkably incomplete and that there are many transcripts and novel genes
 waiting to be annotated. We hope that this resource will stimulate further
 research in expression profiling, detection of alternative splicing and
 adaptive evolution in poplar.
description: MASTER_REPORT_MER_GERALDES2011
DOI: 10.5061/dryad.5g32f94b
title: Data from: Reference-free transcriptome assembly in non-model animals from next generation sequencing data

description: Next-generation sequencing (NGS) technologies offer the opportunity for
 population genomic study of non-model organisms sampled in the wild. The
 transcriptome is a convenient and popular target for such purposes.
 However, designing genetic markers from NGS transcriptome data requires
 assembling gene-coding sequences out of short reads. This is a complex
 task owing to gene duplications, genetic polymorphism, alternative
 splicing and transcription noise. Typical assembling programmes return
 thousands of predicted contigs, whose connection to the species true gene
 content is unclear, and from which SNP definition is uneasy. Here, the
 transcriptomes of five diverse non-model animal species (hare, turtle,
 ant, oyster and tunicate) were assembled from newly generated 454 and
 Illumina sequence reads. In two species for which a reference genome is
 available, a new procedure was introduced to annotate each predicted
 contig as either a full-length cDNA, fragment, chimera, allele, paralogue,
 genomic sequence or other, based on the number of, and overlap between,
 blast hits to the appropriate reference. Analyses showed that (i) the
 highest quality assemblies are obtained when 454 and Illumina data are
 combined, (ii) typical de novo assemblies include a majority of irrelevant
 cDNA predictions and (iii) assemblies can be appropriately cleaned by
 filtering contigs based on length and coverage. We conclude that robust,
 reference-free assembly of thousands of genes from transcriptomic NGS data
 is possible, opening promising perspectives for transcriptome-based
 population genomics in animals. A Galaxy pipeline implementing our
 best-performing assembling strategy is provided.
description: cahais_al.contigs.tarcontigs files
DOI: 10.5061/dryad.2r4c7
title: Data from: Profiling the immunome of little brown myotis provides a yardstick for measuring the genetic response to white-nose syndrome

description: White-nose syndrome (WNS) has devastated populations of hibernating bats
 in eastern North America, leading to emergency conservation listings for
 several species including the previously ubiquitous little brown myotis
 (Myotis lucifugus). However, some bat populations near the epicenter of
 the white-nose syndrome panzootic appear to be stabilizing after initial
 precipitous declines, which could reflect a selective immunogenetic sweep.
 To investigate the hypothesis that WNS exerts significant selection on the
 immunome of affected bat populations, we developed a novel,
 high-throughput sequence capture assay targeting 138 adaptive, intrinsic,
 and innate immunity genes of putative adaptive significance, as well as
 their respective regulatory regions (~370-kbp of genomic
 sequence/individual). We used the assay to explore baseline immunogenetic
 variation in M. lucifugus and to investigate whether particular immune
 genes/variants are associated with WNS susceptibility. We also used our
 assay to detect 1,038 putatively neutral single-nucleotide polymorphisms
 and characterize contemporary population structure, providing context for
 the identification of local immunogenetic adaptation. Sequence capture
 provided a cost-effective, ‘all-in-one’ assay to test for neutral genetic
 and immunogenetic structure and revealed fine-scale, baseline
 immunogenetic differentiation between sampling sites &lt; 600
 kilometers apart. We identified functional immunogenetic variants in M.
 lucifugus associated with WNS susceptibility. This study lays the
 foundations for future investigations of range-wide immunogenetic
 adaptation to white-nose syndrome in M. lucifugus, and provides a
 blueprint for studies of evolutionary rescue in other host-pathogen
 systems.
description: 92 Myotis lucifugus
 SNPs33,610 GATK
 hard-filtered SNPs from 92 Canadian Myotis lucifugus. Filters to create
 final list included: max-missing=5%; minor allele
 frequency&gt;2%.92_Myotis_lucifugus_SNPs.vcf
DOI: 10.5061/dryad.7j564
title: Data from: Local adaptation when competition depends on phenotypic similarity

description: Recent work incorporating demographic–genetic interactions indicates the
 importance of population size, gene flow, and selection in influencing
 local adaptation. This work typically assumes that density-dependent
 survival affects individuals equally, but individuals in natural
 population rarely compete equally. Among-individual differences in
 resource use generate stronger competition between more similar phenotypes
 (frequency-dependent competition) but it remains unclear how this
 additional form of selection changes the interactions between population
 size, gene flow, and local stabilizing selection. Here, we integrate
 migration–selection dynamics with frequency-dependent competition. We
 developed a coupled demographic-quantitative genetic model consisting of
 two patches connected by dispersal and subject to local stabilizing
 selection and competition. Our model shows that frequency-dependent
 competition slightly increases local adaptation, greatly increases genetic
 variance within patches, and reduces the amount that migration depresses
 population size, despite the increased genetic variance load. The effects
 of frequency-dependence depend on the strength of divergent selection,
 trait heritability, and when mortality occurs in the life cycle in
 relation to migration and reproduction. Essentially, frequency-dependent
 competition reduces the density-dependent interactions between migrants
 and residents, the extent to which depends on how different and common
 immigrants are compared to residents. Our results add new dynamics that
 illustrate how competition can alter the effects of gene flow and
 divergent selection on local adaptation and population carrying
 capacities.
description: ExecuteCode.RExecuteCode.R is the code used to run the model. Use this file to change parameters, run the model, and get outputs. It calls on PDDDModel_V2.R, SetupModel.R, and Functions.R. It produces various model outputs in a list and saves as an R object file, called output.Rdat, which can then be read back into R at a later date using the function ‘load’.ExecuteModel.RPDDDModel_V2.RPDDDModel_V2.R contains the actual code for the model. The model is contained inside a function called RunModel, which is called upon in ExecuteCode.R.SetupModel.RSetupModel.R contains code to define all the default parameters, vectors, and matrices used in the main code.Functions.RFunctions.R contains the customized functions used throughout.output.Rdatoutput.Rdat is the output file used to create Figure 2, S1, and S2.Figure_2.RFigure_2.R contains the code used to produce Figure 2 in the paper.ReadMe
DOI: 10.5061/dryad.29374n2
title: Data from: Trade-offs and synergies between bird conservation and wildfire suppression in the face of global change

description: 1. The combined effects of climate change and other factors, such as land
 use change or fire disturbance, pose daunting challenges for biodiversity
 conservation worldwide. 2. In this study, we predicted the future
 effectiveness of the Natura 2000 (N2000), the current network of protected
 areas (PA) in Europe, at maintaining and representing suitable
 environmental conditions for a set of 79 bird species between 2000 and
 2050 in a fire-prone area strongly affected by land abandonment processes
 in NE Spain. We then compared PA performance against a set of alternative
 priority areas for conservation, which take into account fire–vegetation
 dynamics, selected by using a conservation planning tool (MARXAN).
 Fire–vegetation dynamics were modelled using a process-based model
 (MEDFIRE MODEL) under alternative fire management and climate change
 scenarios. Bird assemblage distributions were predicted using the
 spatially-explicit species assemblage modelling frameworkSESAMusing
 distribution models from individual species that hierarchically integrate
 climate change and wildfire–vegetation dynamics. 3. The amount of suitable
 environmental conditions within the N2000 network was predicted to fall by
 around 15%, on average, over the next decades in relation to the initial
 conditions, but could be partially modulated by fire management policies
 in the near future. The efficiency of the current PA system was predicted
 to decrease from 17.4 to 15% over the next decades. However, a more
 efficient PA system could be achieved with a conservation planning
 approach that explicitly considers fire–vegetation dynamics and their
 management. 4. Synthesis and applications: Our findings shed light on: (1)
 how the current Natura 2000 might still hold an important bird
 conservation value by 2050; (2) how the relocation of some protected areas
 could be considered along the next decades to substantially increase bird
 conservation effectiveness; and (3) how the integration of fire-vegetation
 dynamics, fire management policies and their objectives within
 conservation planning can provide ‘win-win’ solutions for bird
 conservation and fire prevention in fire-prone abandoned landscapes.
description: Data files from Regos et
 al. (2018)These data files include
 the environmental suitability predicted from the SESAM framework for each
 bird species, under each run simulation and management scenario. It also
 includes the Natura 2000 network at 100 m and all remaining files required
 to run MARXAN simulations.Datafiles.zip