cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7tv21
title: Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure

description: Identification of discrete and unique assemblages of individuals or
 populations is central to the management of exploited species. Advances in
 population genomics provide new opportunities for re-evaluating existing
 conservation units but comparisons among approaches remain rare. We
 compare the utility of RAD-seq, a single nucleotide polymorphism (SNP)
 array and a microsatellite panel to resolve spatial structuring under a
 scenario of possible trans-Atlantic secondary contact in a threatened
 Atlantic Salmon, Salmo salar, population in southern Newfoundland.
 Bayesian clustering indentified two large groups subdividing the existing
 conservation unit and multivariate analyses indicated significant
 similarity in spatial structuring among the three data sets. mtDNA alleles
 diagnostic for European ancestry displayed increased frequency in
 southeastern Newfoundland and were correlated with spatial structure in
 all marker types. Evidence consistent with introgression among these two
 groups was present in both SNP data sets but not the microsatellite data.
 Asymmetry in the degree of introgression was also apparent in SNP data
 sets with evidence of gene flow towards the east or European type. This
 work highlights the utility of RAD-seq based approaches for the resolution
 of complex spatial patterns, resolves a region of trans-Atlantic secondary
 contact in Atlantic Salmon in Newfoundland and demonstrates the utility of
 multiple marker comparisons in identifying dynamics of introgression.
description: Southern Newfoundland
 Atlantic Salmon microsatellite dataAtlantic salmon
 microsatellite data, for 2439 individuals, with an average of 78.7
 individuals per populationMicrosatellite
 data.csvAtlantic salmon RAD-seq
 data VCF formatVCF file for Atlantic
 salmon RAD-seq data from southern Newfoundland
 populations20130820_FOC_Salmon_Bradbury_std.vcfDistance matricesGenetic and geographic distance matricesSNP Array genotype dataSNP array genotypes for 5,568 SNP loci collected with the V2 Atlantic salmon SNP-array developed by the Centre for Integrative Genetics (CIGENE, Norway) using the Illumina infinium assay (Illumina, San Diego, CA, USA) following the manufacturer’s instructions. A total 203 individuals were genotyped from 10 populations, with an average of 20 individuals per population
DOI: 10.5061/dryad.4181f
title: Data from: Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls

description: Understanding relationships among species is a fundamental goal of
 evolutionary biology. Single nucleotide polymorphisms (SNPs) identified
 through next generation sequencing and related technologies enable
 phylogeny reconstruction by providing unprecedented numbers of characters
 for analysis. One approach to SNP-based phylogeny reconstruction is to
 identify SNPs in a subset of individuals, and then to compile SNPs on an
 array that can be used to genotype additional samples at hundreds or
 thousands of sites simultaneously. Although powerful and efficient, this
 method is subject to ascertainment bias because applying variation
 discovered in a representative subset to a larger sample favors
 identification of SNPs with high minor allele frequencies and introduces
 bias against rare alleles. Here, we demonstrate that the use of
 hybridization intensity data, rather than genotype calls, reduces the
 effects of ascertainment bias. Whereas traditional SNP calls assess known
 variants based on diversity housed in the discovery panel, hybridization
 intensity data survey variation in the broader sample pool, regardless of
 whether those variants are present in the initial SNP discovery process.
 We apply SNP genotype and hybridization intensity data derived from the
 Vitis9kSNP array developed for grape to show the effects of ascertainment
 bias and to reconstruct evolutionary relationships among Vitis species. We
 demonstrate that phylogenies constructed using hybridization intensities
 suffer less from the distorting effects of ascertainment bias, and are
 thus more accurate than phylogenies based on genotype calls. Moreover, we
 reconstruct the phylogeny of the genus Vitis using hybridization data,
 show that North American subgenus Vitis species are monophyletic, and
 resolve several previously poorly known relationships among North American
 species. This study builds on earlier work that applied the Vitis9kSNP
 array to evolutionary questions within Vitis vinifera and has general
 implications for addressing ascertainment bias in array-enabled phylogeny
 reconstruction.
description: all_dataA .zip file containing all data required to repeat analyses presented in Miller et al. "Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls" published in PLoS ONE. Includes a ReadMe file.dryad.zip
DOI: 10.5281/zenodo.16943771
title: ICESat-2 Major Activities Table

description: Record of ICESat-2 activities including spacecraft maneuvers, yaw flips, solar array transitions, granule data gaps, safe hold periods, etc., organized by approximate timing of activity. Subset of ICESat-2 Technical References Table.
DOI: 10.5281/zenodo.18378129
title: ICESat-2 Major Activities Table

description: Record of ICESat-2 activities including spacecraft maneuvers, yaw flips, solar array transitions, granule data gaps, safe hold periods, etc., organized by approximate timing of activity. Subset of ICESat-2 Technical References Table.
DOI: 10.5061/dryad.88fm3
title: Data from: Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps

description: Studying patterns of species distributions along elevation gradients is
 frequently used to identify the primary factors that determine the
 distribution, diversity and assembly of species. However, despite their
 crucial role in ecosystem functioning, our understanding of the
 distribution of below-ground fungi is still limited, calling for more
 comprehensive studies of fungal biogeography along environmental gradients
 at various scales (from regional to global). Here, we investigated the
 richness of taxa of soil fungi and their phylogenetic diversity across a
 wide range of grassland types along a 2800 m elevation gradient at a large
 number of sites (213), stratified across a region of the western Swiss
 Alps (700 km2). We used 454 pyro-sequencing to obtain fungal sequences
 that were clustered into operational taxonomic units (OTUs). The OTU
 diversity-area relationship revealed uneven distribution of fungal taxa
 across the study area (i.e. not all taxa are everywhere) and fine-scale
 spatial clustering. Fungal richness and phylogenetic diversity were found
 to be higher in lower temperatures and higher moisture conditions.
 Climatic and soil characteristics as well as plant community composition
 were related to OTU alpha, beta and phylogenetic diversity, with distinct
 fungal lineages suggesting distinct ecological tolerances. Soil fungi,
 thus, show lineage-specific biogeographic patterns, even at a regional
 scale, and follow environmental determinism, mediated by interactions with
 other taxonomic groups, such as plants.
description: Plant and environmental
 dataPlant species (frequency
 estimate) and environmental data in each of the 212 plots used in
 Pellissier et al. (In Review) Mol. Ecol.plant_env_data.txtITS1 sequences from soilITS1 sequences coming from the soil of 204 plots have been obtained with the fungal universal primers ITS1F ITS2. The pyrosequencing outputs of six half 454 runs have been pooled in this unique fasta file. The number of each half of run (R meaning run and H meaning half) and of each MID used are mentionned in the name of each sequence. More information is provided on the information associated to these sequences in the "readme.txt" file454AlpsSoilFungi2009_reads.seqFungal OTUs distribution in plotsFungal OTUs distribution in plotsfungal_OTUs_distribution_in_plots.txt
DOI: 10.5061/dryad.6gh7b
title: Data from: Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish

description: Understanding whether small populations with low genetic diversity can
 respond to rapid environmental change via phenotypic plasticity is an
 outstanding research question in biology. RNA sequencing (RNA-seq) has
 recently provided the opportunity to examine variation in gene expression,
 a surrogate for phenotypic variation, in non-model species. We used a
 comparative RNA-seq approach to assess expression variation within and
 among adaptively divergent populations of a threatened freshwater fish,
 Nannoperca australis, found across a steep hydroclimatic gradient in the
 Murray-Darling Basin, Australia. These populations evolved under
 contrasting selective environments (e.g. dry/hot lowland; wet/cold upland)
 and represent opposite ends of the species’ spectrum of genetic diversity
 and population size. We tested the hypothesis that environmental variation
 among isolated populations has driven the evolution of divergent
 expression at ecologically important genes using differential expression
 (DE) analysis and an ANOVA-based comparative phylogenetic expression
 variance and evolution model framework based on 27,425 de novo assembled
 transcripts. Additionally, we tested whether gene expression variance
 within-populations was correlated with levels of standing genetic
 diversity. We identified 290 DE candidate transcripts, 33 transcripts with
 evidence for high expression plasticity, and 50 candidates for divergent
 selection on gene expression after accounting for phylogenetic structure.
 Variance in gene expression appeared unrelated to levels of genetic
 diversity. Functional annotation of the candidate transcripts revealed
 variation in water quality is an important factor influencing expression
 variation for N. australis. Our findings suggest that gene expression
 variation can contribute to the evolutionary potential of small
 populations.
description: Nannoperca australis
 liver transcriptomeNannoperca australis
 liver transcriptome assembled using Trinity based on RNAseq data from five
 individuals. Assembly contains 201,037 Trinity transcripts clustered into
 96,717 Trinity "genes".Trinity.fastaORF_countsRaw counts data for 27,425 longest open reading framesTMM_ORF_countscross sample normalized counts for 27,425 ORFsSPP_trinotate_annotation_reportannotation information for Trinity.fasta assembly
DOI: 10.5281/zenodo.18380351
title: replicationpackage_theparadoxofSC
DOI: 10.5281/zenodo.18380352
title: replicationpackage_theparadoxofSC
DOI: 10.5061/dryad.tp097
title: Data from: Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians

description: A large fraction of human genes are regulated by genetic variation near
 the transcribed sequence (cis-eQTL, expression quantitative trait locus),
 and many cis-eQTLs have implications for human disease. Less is known
 regarding the effects of genetic variation on expression of distant genes
 (trans-eQTLs) and their biological mechanisms. In this work, we use
 genome-wide data on SNPs and array-based expression measures from
 mononuclear cells obtained from a population-based cohort of 1,799
 Bangladeshi individuals to characterize cis- and trans-eQTLs and determine
 if observed trans-eQTL associations are mediated by expression of
 transcripts in cis with the SNPs showing trans-association, using Sobel
 tests of mediation. We observed 434 independent trans-eQTL associations at
 a false-discovery rate of 0.05, and 189 of these trans-eQTLs were also
 cis-eQTLs (enrichment P&lt;0.0001). Among these 189 trans-eQTL
 associations, 39 were significantly attenuated after adjusting for a
 cis-mediator based on Sobel P&lt;10-5. We attempted to replicate 21 of
 these mediation signals in two European cohorts, and while only 7
 trans-eQTL associations were present in one or both cohorts, 6 showed
 evidence of cis-mediation. Analyses of simulated data show that complete
 mediation will be observed as partial mediation in the presence of
 mediator measurement error or imperfect LD between measured and causal
 variants. Our data demonstrates that trans-associations can become
 significantly stronger or switch directions after adjusting for a
 potential mediator. Using simulated data, we demonstrate that this
 phenomenon is expected in the presence of strong cis-trans confounding and
 when the measured cis-transcript is correlated with the true (unmeasured)
 mediator. In conclusion, by applying mediation analysis to eQTL data, we
 show that a substantial fraction of observed trans-eQTL associations can
 be explained by cis-mediation. Future studies should focus on
 understanding the mechanisms underlying widespread cis-mediation and their
 relevance to disease biology, as well as using mediation analysis to
 improve eQTL discovery.
description: cis_eQTLs_P&lt;0.05cis-eQTLs with p&lt;0.05cis_eQTL_MatrixeQTL_sortp.txttrans_eQTLs_P&lt;0.0001trans-eQTLs with p&lt;0.0001trans_eQTL_MatrixeQTL_sortp.txtmediation_summary_statssummary file for n=781 trans-eQTL associations (p&lt;0.0000001) with a potentially mediating cis-transcript
DOI: 10.5061/dryad.r4b69rg
title: Data from: Suppression of overlearning in independent component analysis used for removal of muscular artifacts from electroencephalographic records

description: This paper addresses the overlearning problem in the independent component
 analysis (ICA) used for the removal of muscular artifacts from
 electroencephalographic (EEG) records. We note that for short EEG records
 with high number of channels the ICA fails to separate artifact-free EEG
 and muscular artifacts, which has been previously attributed to the
 phenomenon called overlearning. We address this problem by projecting an
 EEG record into several subspaces with a lower dimension, and perform the
 ICA on each subspace separately. Due to a reduced dimension of the
 subspaces, the overlearning is suppressed, and muscular artifacts are
 better separated. Once the muscular artifacts are removed, the signals in
 the individual subspaces are combined to provide an artifact free EEG
 record. We show that for short signals and high number of EEG channels our
 approach outperforms the currently available ICA based algorithms for
 muscular artifact removal. The proposed technique can efficiently suppress
 ICA overlearning for short signal segments of high density EEG signals.
description: EEG and EMG trials,
 features for classification, and estimated PSDsDataFolder.zip
DOI: 10.5061/dryad.11vb2
title: Data from: The evolution of male-biased dispersal under the joint selective forces of inbreeding load, and demographic and environmental stochasticity

description: Sex-biased natal dispersal is widespread, and its significance remains a
 central question in evolutionary biology. However, theory so far fails to
 predict some of the most common patterns found in nature. To address this,
 we present novel results from an individual-based model investigating the
 joint roles of inbreeding load, demographic stochasticity, environmental
 stochasticity, and dispersal costs for the evolution of sex-biased
 dispersal. Most strikingly, we found that male-biased natal dispersal
 evolved in polygynous systems as a result of the interplay between
 inbreeding avoidance and stochasticity, whereas previous theory, in
 contrast to empirical observations, predicted male philopatry and
 female-biased natal dispersal under inbreeding load alone. Furthermore,
 the direction of the bias varied according to the nature of stochasticity.
 Our results therefore provide a unification of previous theory, yielding a
 much better qualitative match with empirical observations of male-biased
 dispersal in mate defense mating systems.
description: main simulation
 filesapp D
 filesSimulation result files
 from the individual based model used in appendix D. Batch file
 included.model src
 codeIndividual based model
 source code in c++. Makefile and parameter files
 included.
DOI: 10.5281/zenodo.18380308
title: Replication Data for "Benchmarks Saturate When The Model Gets Smarter Than The Judge"

description: This repository provides replication data for "Benchmarks Saturate When The Model Gets Smarter Than The Judge". The corresponding code is available at https://github.com/MartheBallon/Benchmarks-saturate-when-the-model-gets-smarter-than-the-judge.
DOI: 10.5281/zenodo.18380309
title: Replication Data for "Benchmarks Saturate When The Model Gets Smarter Than The Judge"

description: This repository provides replication data for "Benchmarks Saturate When The Model Gets Smarter Than The Judge". The corresponding code is available at https://github.com/MartheBallon/Benchmarks-saturate-when-the-model-gets-smarter-than-the-judge.
DOI: 10.5061/dryad.7f138
title: Data from: Combining high-throughput phenotyping and genomic information to increase prediction and selection accuracy in wheat breeding

description: Genomics and phenomics have promised to revolutionize the field of plant
 breeding. The integration of these two fields has just begun and is being
 driven through big data by advances in next-generation sequencing and
 developments of field-based high-throughput phenotyping (HTP) platforms.
 Each year the International Maize and Wheat Improvement Center (CIMMYT)
 evaluates tens-of-thousands of advanced lines for grain yield across
 multiple environments. To evaluate how CIMMYT may utilize dynamic HTP data
 for genomic selection (GS), we evaluated 1170 of these advanced lines in
 two environments, drought (2014, 2015) and heat (2015). A portable
 phenotyping system called ‘Phenocart’ was used to measure normalized
 difference vegetation index and canopy temperature simultaneously while
 tagging each data point with precise GPS coordinates. For genomic
 profiling, genotyping-by-sequencing (GBS) was used for marker discovery
 and genotyping. Several GS models were evaluated utilizing the 2254 GBS
 markers along with over 1.1 million phenotypic observations. The
 physiological measurements collected by HTP, whether used as a response in
 multivariate models or as a covariate in univariate models, resulted in a
 range of 33% below to 7% above the standard univariate model. Continued
 advances in yield prediction models as well as increasing data generating
 capabilities for both genomic and phenomic data will make these selection
 strategies tractable for plant breeders to implement increasing the rate
 of genetic gain.
description: EYT_HTP_GSZip file containing raw data, scripts, and intermediate processing files for the publication Combining High-Throughput Phenotyping and Genomic Information to Increase Prediction and Selection Accuracy in Wheat Breeding. A README file is included in the main directory that provides additional information.
DOI: 10.5281/zenodo.18378112
title: ICESat-2 Technical References Table

description: Record of ICESat-2 activities including spacecraft maneuvers, on-board algorithm updates, yaw flips, solar array transitions, granule data gaps, safe hold periods, etc., organized by mission cycle (every ~91 days) and approximate timing of activity.
DOI: 10.5281/zenodo.16283560
title: ICESat-2 Technical References Table

description: Record of ICESat-2 activities including spacecraft maneuvers, on-board algorithm updates, yaw flips, solar array transitions, granule data gaps, safe hold periods, etc., organized by mission cycle (every ~91 days) and approximate timing of activity.
DOI: 10.5281/zenodo.18371747
title: Slow Quasiparticle Dynamics and Anyonic Statistics in a Fractional Quantum Hall Fabry-Perot Interferometer
DOI: 10.5281/zenodo.18371748
title: Slow Quasiparticle Dynamics and Anyonic Statistics in a Fractional Quantum Hall Fabry-Perot Interferometer
DOI: 10.5061/dryad.dm132
title: Spatio-temporal dynamics of impulse responses to figure motion in optic flow neurons

description: White noise techniques have been used widely to investigate sensory
 systems in both vertebrates and invertebrates. White noise stimuli are
 powerful in their ability to rapidly generate data that help the
 experimenter decipher the spatio-temporal dynamics of neural and
 behavioral responses. One type of white noise stimuli, maximal length
 shift register sequences (m-sequences), have recently become particularly
 popular for extracting response kernels in insect motion vision. We here
 use such m-sequences to extract the impulse responses to figure motion in
 hoverfly lobula plate tangential cells (LPTCs). Figure motion is
 behaviorally important and many visually guided animals orient towards
 salient features in the surroundings. We show that LPTCs respond robustly
 to figure motion in the receptive field. The impulse response is scaled
 down in amplitude when the figure size is reduced, but its time course
 remains unaltered. However, a low-contrast stimulus generates a slower
 response with a significantly longer time-to-peak and half-width. Impulse
 responses in females have a slower time-to-peak than males but are
 otherwise similar. Finally, we show that the shapes of the impulse
 response to a figure and a widefield stimulus are very similar, suggesting
 that the figure response could be coded by the same input as the widefield
 response.
description: # Spatio-temporal dynamics of impulse responses to figure motion in optic
 flow neurons
 [https://doi.org/10.5061/dryad.dm132](https://doi.org/10.5061/dryad.dm132)
 #### LeePlosOne2015 The data are organized in the same way as in the
 figures of the paper. They are all in Matlab format.
DOI: 10.5061/dryad.g928q
title: Data from: Differential phasing between circadian clocks in the brain and peripheral organs in humans

description: The daily timing of mammalian physiology is coordinated by circadian
 clocks throughout the body. Although measurements of clock gene expression
 indicate that these clocks in mice are normally in phase with each other,
 the situation in humans remains unclear. We used publicly available data
 from five studies, comprising over 1000 samples, to compare the phasing of
 circadian gene expression in human brain and human blood. Surprisingly,
 after controlling for age, clock gene expression in brain was
 phase-delayed by ~8.5 h relative to that of blood. We then examined clock
 gene expression in two additional human organs and in organs from nine
 other mammalian species, as well as in the suprachiasmatic nucleus (SCN).
 In most tissues outside the SCN, the expression of clock gene orthologs
 showed a phase difference of ~12 h between diurnal and nocturnal species.
 The exception to this pattern was human brain, whose phasing resembled
 that of the SCN. Our results highlight the value of a multi-tissue,
 multi-species meta-analysis, and have implications for our understanding
 of the human circadian system.
description: Data, code, results, and
 figures for the paper.The zip file contains
 everything necessary to reproduce the entire analysis. See the readme.txt
 for instructions.circadian_multispecies.zip