cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ck3g3
title: Data from: Familiarity to a feed additive modulates its effects on brain responses in reward and memory regions in the pig model

description: Brain responses to feed flavors with or without a feed additive (FA) were
 investigated in piglets familiarized or not with this FA. Sixteen piglets
 were allocated to 2 dietary treatments from weaning until d 37: the naive
 group (NAI) received a standard control feed and the familiarized group
 (FAM) received the same feed added with a FA mainly made of orange
 extracts. Animals were subjected to a feed transition at d 16
 post-weaning, and to 2-choice feeding tests at d 16 and d 23. Production
 traits of the piglets were assessed up to d 28 post-weaning. From d 26
 onwards, animals underwent 2 brain imaging sessions (positron emission
 tomography of 18FDG) under anesthesia to investigate the brain activity
 triggered by the exposure to the flavors of the feed with (FA) or without
 (C) the FA. Images were analyzed with SPM8 and a region of interest
 (ROI)-based small volume correction (p &lt; 0.05, k ≥ 25 voxels per
 cluster). The brain ROI were selected upon their role in sensory
 evaluation, cognition and reward, and included the prefrontal cortex,
 insular cortex, fusiform gyrus, limbic system and corpus striatum. The FAM
 animals showed a moderate preference for the novel post-transition FA feed
 compared to the C feed on d 16, i.e., day of the feed transition (67% of
 total feed intake). The presence or absence of the FA in the diet from
 weaning had no impact on body weight, average daily gain, and feed
 efficiency of the animals over the whole experimental period (p ≥ 0.10).
 Familiar feed flavors activated the prefrontal cortex. The amygdala,
 insular cortex, and prepyriform area were only activated in familiarized
 animals exposed to the FA feed flavor. The perception of FA feed flavor in
 the familiarized animals activated the dorsal striatum differently than
 the perception of the C feed flavor in naive animals. Our data
 demonstrated that the perception of FA in familiarized individuals induced
 different brain responses in regions involved in reward anticipation
 and/or perception processes than the familiar control feed flavor in naive
 animals. Chronic exposure to the FA might be necessary for positive
 hedonic effects, but familiarity only cannot explain them.
description: Brain imaging data
 HEDOREXThis data file contains
 brain PET images obtained in growing pigs subjected to different
 olfactogustatory food stimulations.Hedorex_Raw_Data.zip
DOI: 10.5061/dryad.pp551
title: Data from: Bayesian methods for estimating GEBVs of threshold traits

description: Estimation of genomic breeding values is the key step in genomic
 selection. Many methods have been proposed for continuous traits, but
 methods for threshold traits are still scarce. Here we introduced
 threshold model to the framework of genomic selection, and specifically we
 extended the three Bayesian methods BayesA, BayesB and BayesCπ based on
 threshold model for estimating genomic breeding values of threshold
 traits, and the extended methods are correspondingly termed BayesTA,
 BayesTB and BayesTCπ. Computing procedures of the three BayesT methods
 using Markov Chain Monte Carlo (MCMC) algorithm were derived. A simulation
 study was performed to investigate the benefit of the presented methods in
 accuracy of genomic estimated breeding values (GEBVs) for threshold
 traits. Factors affecting the performance of the three BayesT methods were
 addressed. As expected, the three BayesT methods generally performed
 better than the corresponding normal Bayesian methods, in particular when
 the number of phenotypic categories was small. In the standard scenario
 (No. categories = 2, incidence = 30%, No. QTL = 50, h2 = 0.3), the
 accuracies were improved by 30.4, 2.4, and 5.7 percentage points,
 respectively. In most scenarios, BayesTB and BayesTCπ generated similar
 accuracies and both performed better than BayesTA. In conclusion, our work
 proved that threshold model fits well for predicting GEBVs of threshold
 traits, and BayesTCπ is supposed to be the method of choice for genomic
 selection of threshold traits.
description: Data of threshold traits
 with 4 different levels of heritabilityData of threshold traits
 with 4 different levels of heritability (h2) were simulated: 0.05, 0.1,
 0.3 and 0.5. Other parameters: No. categories =2, incidence=30%, No.
 QTL=50h2.rarData of threshold traits with different numbers of QTLData of threshold traits with different numbers of QTL were simulated: 20, 200 and 500. Other parameters: No. categories =2, incidence=30%, h2=0.3qtl.rarData of binary traits with different incidencesData of binary traits with different incidences were simulated: 5%, 15% and 50%. Other parameters: No. categories =2, No. QTL=50, h2=0.3incidences.rarData of threshold traits with different numbers of phenotypic categoriesData of threshold traits with different numbers of phenotypic categories were simulated: 3, 4 and 8. Other parameters: No. QTL=50, h2=0.3categories.rar
DOI: 10.5061/dryad.755b5
title: Data from: Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome

description: Here, we present an adaptation of restriction-site-associated DNA
 sequencing (RAD-seq) to the Illumina HiSeq2000 technology that we used to
 produce SNP markers in very large quantities at low cost per unit in the
 Réunion grey white-eye (Zosterops borbonicus), a nonmodel passerine bird
 species with no reference genome. We sequenced a set of six pools of 18–25
 individuals using a single sequencing lane. This allowed us to build
 around 600 000 contigs, among which at least 386 000 could be mapped to
 the zebra finch (Taeniopygia guttata) genome. This yielded more than 80
 000 SNPs that could be mapped unambiguously and are evenly distributed
 across the genome. Thus, our approach provides a good illustration of the
 high potential of paired-end RAD sequencing of pooled DNA samples combined
 with comparative assembly to the zebra finch genome to build large contigs
 and characterize vast numbers of informative SNPs in nonmodel passerine
 bird species in a very efficient and cost-effective way.
description: SNPs validated with
 different MAC (2 or 3) and a sequencing depth of 10 or
 20XThis archive contains
 three types of files with extensions '.n', '.y' and
 '.alleles'. '.n' files list for each library the
 number of reads associated at each SNP position. '.y' files list
 the number of times a SNP is detected. '.alleles' files give the
 name of the contig displaying a given SNP, then the position of the SNP
 from the restriction site, the total number of reads for the whole
 dataset, the count of the minor allele, the count of the major allele, and
 the two possible nucleotides encountered at this
 positionFiles_with_contigs_names_and_allele_counts_for_several_stringency_criteria.zipFasta file listing contigsconsensus_reads_1_2_UDBA.zip
DOI: 10.5061/dryad.t7r64
title: Data from: Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway

description: The diversity of life on Earth is a result of continual innovations in
 molecular networks influencing morphology and physiology. Plant
 specialized metabolism produces hundreds of thousands of compounds,
 offering striking examples of these innovations. To understand how this
 novelty is generated, we investigated the evolution of the Solanaceae
 family-specific, trichome-localized acylsugar biosynthetic pathway using a
 combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and
 phylogenetics in non-model species. Our results reveal that hundreds of
 acylsugars are produced across the Solanaceae family and even within a
 single plant, revealing this phenotype to be hyper-diverse. The relatively
 short biosynthetic pathway experienced repeated cycles of innovation over
 the last 100 million years that include gene duplication and divergence,
 gene loss, evolution of substrate preference and promiscuity. This study
 provides mechanistic insights into the emergence of plant chemical
 novelty, and offers a template for investigating the ~300,000 non-model
 plant species that remain underexplored.
description: Files obtained from
 RNA-seq analysesTranscript sequence,
 orthologous group and differential expression files obtained from analysis
 of RNA-seq data.RNAseq_related.zip
DOI: 10.5061/dryad.cb4m96b
title: Data from: Effect of hidden relatedness on single-step genetic evaluation in an advanced open-pollinated breeding program

description: Open-pollinated (OP) mating is frequently used in forest tree breeding due
 to the relative temporal and financial efficiency of the approach. The
 trade-off is the lower precision of the estimated genetic parameters.
 Pedigree/sib-ship reconstruction has been proven as a tool to correct and
 complete pedigree information and to improve the precision of genetic
 parameter estimates. Our study analyzed an advanced generation Eucalyptus
 population from an OP breeding program using single-step genetic
 evaluation. The relationship matrix inferred from sib-ship reconstruction
 was used to rescale the marker-based relationship matrix (G matrix). This
 was compared with a second scenario that used rescaling based on the
 documented pedigree. The proposed single-step model performed better with
 respect to both model fit and the theoretical accuracy of breeding values.
 We found that the prediction accuracy was superior when using the pedigree
 information only when compared with using a combination of the pedigree
 and genomic information. This pattern appeared to be mainly a result of
 accumulated unrecognized relatedness over several breeding cycles,
 resulting in breeding values being shrunk toward the population mean.
 Using biased, pedigree-based breeding values as the base with which to
 correlate predicted GEBVs, resulted in the underestimation of prediction
 accuracies. Using breeding values estimated on the basis of sib-ship
 reconstruction resulted in increased prediction accuracies of the
 genotyped individuals. Therefore, selection of the correct base for
 estimation of prediction accuracy is critical. The beneficial impact of
 sib-ship reconstruction using G matrix rescaling was profound, especially
 in traits with inbreeding depression, such as stem diameter.
description: Markers_for_publicationMarker data used in the study coded -1, 0 and 1 refering reference allele homozygote, heterozygote and alternative allele homozygotePedigree_for_publicationDocumented pedigree tracking relatedness from the base population of the New Zealand E. nitens breeding programPhenotypes_for_publicationPhenotypic data and design terms used in the mixed modelSib-ship_reconstruction_relationship_matrixRelationship matrix constructed on the basis of information from sib-ship reconstruction analysis performed in our previous study (Klapste et al., 2017)
DOI: 10.5061/dryad.1525t
title: Data from: An equation to predict the accuracy of genomic values by combining data from multiple traits, populations, or environments

description: Predicting the accuracy of estimated genomic values using genome-wide
 marker information is an important step in designing training populations.
 Currently, different deterministic equations are available to predict
 accuracy within populations, but not for multipopulation scenarios where
 data from multiple breeds, lines or environments are combined. Therefore,
 our objective was to develop and validate a deterministic equation to
 predict the accuracy of genomic values when different populations are
 combined in one training population. The input parameters of the derived
 prediction equation are the number of individuals and the heritability
 from each of the populations in the training population; the genetic
 correlations between the populations, i.e., the correlation between allele
 substitution effects of quantitative trait loci; the effective number of
 chromosome segments across predicted and training populations; and the
 proportion of the genetic variance in the predicted population captured by
 the markers in each of the training populations. Validation was performed
 based on real genotype information of 1033 Holstein–Friesian cows that
 were divided into three different populations by combining half-sib
 families in the same population. Phenotypes were simulated for multiple
 scenarios, differing in heritability within populations and in genetic
 correlations between the populations. Results showed that the derived
 equation can accurately predict the accuracy of estimating genomic values
 for different scenarios of multipopulation genomic prediction. Therefore,
 the derived equation can be used to investigate the potential accuracy of
 different multipopulation genomic prediction scenarios and to decide on
 the most optimal design of training populations.
description: Genotypes_422405SNPsGenotypes for 1033 animals and 422405 SNPsPedigreePedigree of 1033 animalsID_PopulationDivision of the 1033 animals over the three populationsPhenotypes_QTL_RANDOMPhenotypes for all 1033 animals when QTL are randomly sampled for all seven scenarios and 100 replicates per scenarios. The phenotype files contains: animal number, population number, ID, and phenotype.Phenotypes_QTL_LowMAFPhenotypes for all 1033 animals when QTL are sampled with a low Minor Allele Frequency for all seven scenarios and 100 replicates per scenarios. The phenotype files contains: animal number, population number, ID, and phenotype.
DOI: 10.5061/dryad.rh04m
title: Data from: Compartment-specific transcriptomics in a reef-building coral exposed to elevated temperatures

description: Although rising ocean temperatures threaten scleractinian corals and the
 reefs they construct, certain reef corals can acclimate to elevated
 temperatures to which they are rarely exposed in situ. Specimens of the
 Indo-Pacific reef coral Pocillopora damicornis collected from upwelling
 reefs of Southern Taiwan were previously found to have survived a 36-week
 exposure to 30°C, a temperature they encounter infrequently and one that
 elicits the breakdown of the coral-dinoflagellate (genus Symbiodinium)
 endosymbiosis in many corals of the Pacific Ocean. In order to gain
 insight into the sub-cellular pathways utilized by both the coral hosts
 and their mutualistic Symbiodinium populations to acclimate to this
 temperature, mRNAs from both control (27°C) and high (30°C) temperature
 samples were sequenced on an Illumina platform and assembled into a
 236,435-contig transcriptome. These P. damicornis specimens were found to
 be ~60% anthozoan and 40% microbe (Symbiodinium, other eukaryotic
 microbes, and bacteria), from an mRNA-perspective. Furthermore, a
 significantly higher proportion of genes from the Symbiodinium compartment
 were differentially expressed after two weeks of exposure. Specifically,
 at elevated temperatures Symbiodinium populations residing within the
 coral gastrodermal tissues were more likely to up-regulate the expression
 of genes encoding proteins involved in metabolism than their coral hosts.
 Collectively, these transcriptome-scale data suggest that the two members
 of this endosymbiosis have distinct strategies for acclimating to elevated
 temperatures that are expected to characterize many of Earth's coral
 reefs in the coming decades.
description: big_tabletable file that combines all information of each contig, including annotation, taxonomy and FPKMcontig.fnaAssembly from multiple assemble procedure, read fastq files can be downloaded from NCBI SRA center by link to http://www.ncbi.nlm.nih.gov/sra/SRX378204NCBI SRA deposit3 ILLUMINA (Illumina Genome Analyzer IIx) runs: 134.4M spots, 27.1G bases, 16.3Gb downloads
DOI: 10.5061/dryad.n5rd6
title: Data from: Mating system plasticity promotes persistence and adaptation of colonizing populations of hermaphroditic angiosperms

description: Persistence and adaptation in novel environments are limited by small
 population size, strong selection, and maladaptive gene flow. Mating
 system plasticity is common in angiosperms and may provide both
 demographic and genetic benefits that promote niche evolution, including
 reproductive assurance and isolation from maladaptive gene flow. Yet
 increased self-fertilization may also cause inbreeding depression,
 accumulation of deleterious mutations, and reduced adaptive potential.
 Here we use individual-based simulations to examine the consequences of
 mating system plasticity for persistence and adaptation in a novel
 environment that imposes selection on a quantitative trait. We examine the
 joint evolution of local adaptation, inbreeding depression, and genetic
 load. We find that a plastic shift to a mixed mating system generally
 promotes niche evolution by decreasing the risk of extinction, providing
 isolation from maladaptive gene flow, and temporarily increasing genetic
 variance in the trait under selection, whereas obligate self-fertilization
 reduces adaptive potential. These effects are most pronounced under
 conditions of mate limitation, strong selection, or maladaptive gene flow.
 Our results highlight the diverse demographic and genetic consequences of
 self-fertilization and support the potential role for plastic shifts in
 mating system to promote niche evolution in flowering plants.
description: Simulation Raw
 OutputCodeScripts used to simulate
 data in R v.3.1.0. Contains two R scripts. Peterson&Kay_Prior
 Selfing.R simulates prior self-fertilization, and Peterson&Kay_Delayed
 Selfing.R simulates delayed self-fertilization. See article for
 details.
DOI: 10.5061/dryad.m5b784h
title: Data from: In that vein: inflated wing veins contribute to butterfly hearing

description: Insects have evolved a diversity of hearing organs specialized to detect
 sounds critical for survival. We report on a unique structure on butterfly
 wings that enhances hearing. The Satyrini are a diverse group of
 butterflies occurring throughout the world. One of their distinguishing
 features is a conspicuous swelling of their forewing vein, but the
 functional significance of this structure is unknown. Here we show that
 wing vein inflations function in hearing. Using the Common Wood-Nymph,
 Cercyonis pegala, as a model, we show that (1) these butterflies have ears
 on their forewings that are most sensitive to low frequency sounds
 (&lt;5 kHz); (2) inflated wing veins are directly connected to the
 ears; (3) when vein inflations are ablated, sensitivity to low frequency
 sounds is impaired. We propose that inflated veins contribute to low
 frequency hearing by impedance matching.
description: Repository data
 Butterfly_YackThese data files include
 measurements taken from hearing organs of Cercyonis pegala butterflies.
 There are two file types: excel spreadsheets as well as .svd files that
 include morphology and laser vibrometry measurements that are included in
 the figures of the manuscript. Laser vibrometer software to view the .svd
 files can be found at:
 https://www.polytec.com/eu/vibrometry/products/software/scanviewer/
DOI: 10.5061/dryad.77428
title: Data from: The evolution of annelids reveals two adaptive routes to the interstitial realm

description: Many animals permanently inhabit the marine interstitium, the space
 between sand grains [ 1, 2 ]. Different evolutionary scenarios may explain
 the existence of interstitial animals [ 3, 4 ]. These scenarios include
 (1) that the interstitial realm is the ancestral habitat of bilaterians [
 5, 6 ], (2) that interstitial taxa evolved from larger ancestors by
 miniaturization, or (3) progenesis [ 3 ]. The first view mirrors the
 former hypothesis that interstitial annelids, called archiannelids, were
 at the base of the annelid radiation [ 7 ]. Based on morphological data,
 however, progenesis is generally favored for interstitial annelids today [
 3, 4, 8 ]. Herein, our phylogenomic approach revealed that interstitial
 archiannelids are robustly placed into two groups nested within the
 annelid tree. Evolution of the first group comprising among others
 Dinophilidae is best explained by progenesis. In contrast, the second
 group comprising Protodrilida and Polygordiidae appears to have evolved by
 stepwise miniaturization adapting from coarser to finer sediments. Thus,
 in addition to progenesis [ 3, 4 ], miniaturization, thought to be too
 slow for an adaptation to the interstitium [ 3 ], is an important second
 route allowing adaptation to interstitial environments. Both progenesis
 and miniaturization should be considered when investigating evolution of
 interstitial taxa [ 1, 3 ].
description: Struck2015_CurrentBiology_InterstitialAnnelidahis file contains the concatenated datasets used for phylogenetic analyses in phylip-format in the folder „Datasets“and additional results in the pdf-file „ExtraResults“ with an explanation of the results. The datasets are named in correspondence to the numbers in Table 1 of the manuscript in Current Biology by Struck and co-authors entitled „The evolution of annelids reveals two adaptive routes to the interstitial realm“. The names of the dataset files are as follows: Dataset_1.phy Dataset_2.phy Dataset_3.phy Dataset_4.phy Dataset_5.phy Dataset_6.phy Dataset_7.phy Dataset_8.phy Dataset_9.phy Dataset_10.phy Dataset_11.phy Dataset_12.phy Dataset_13.phy Dataset_14.phy Dataset_15.phy Dataset_16.phy Dataset_17.phy Dataset_18.phy Dataset_19.phy Dataset_20.phy Dataset_21.phy Dataset_22.phy Dataset_23.phy Dataset_24.phy
DOI: 10.5061/dryad.qv145
title: Data from: Accounting for female space sharing in St. Kilda Soay sheep (Ovis aries) results in little change in heritability estimates

description: When estimating heritability in free-living populations, it is common
 practice to account for common environment effects, because of their
 potential to generate phenotypic covariance among relatives thereby
 biasing heritability estimates. In quantitative genetic studies of natural
 populations, however, philopatry, which results in relatives being
 clustered in space, is rarely accounted for. The two studies to have done
 so suggest absolute declines in heritability estimates of up to 43% when
 accounting for space sharing by relatives. However, due to methodological
 limitations these estimates may not be representative. We used data from
 the St. Kilda Soay sheep population to estimate heritabilities with and
 without accounting for space sharing for five traits for which there is
 evidence for additive genetic variance (birth weight, birth date, lamb
 August weight, and female post mortem jaw and metacarpal length). We
 accounted for space sharing by related females by separately incorporating
 spatial autocorrelation, and a home range similarity matrix. Although
 these terms accounted for up to 17% of the variance in these traits,
 heritability estimates were only reduced by up to 7%. Our results suggest
 that the bias caused by not accounting for space sharing may be lower than
 previously thought. This suggests that philopatry does not inevitably lead
 to a large bias if space sharing by relatives is not accounted for. We
 hope our work stimulates researchers to model shared space when relatives
 in their study population share space, as doing so will enable us to
 better understand when bias may be of particular concern.
description: Genomic relatedness
 matricesFolder containing
 genomic relatedness matrices for all traitsPhenotypic
 dataFolder containing
 phenotypic data for all traitsS
 matricesFolder containing S
 matrices for all traits