cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.48gp0
title: Data from: Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium

description: The analysis of linkage disequilibrium (LD) underpins the development of
 effective genotyping technologies, trait mapping and understanding of
 biological mechanisms such as those driving recombination and the impact
 of selection. We apply the Malécot-Morton model of LD to create additive
 LD maps which describe the high-resolution LD landscape of commercial
 chickens. We investigated LD in chickens (Gallus gallus) at the highest
 resolution to date for broiler, white egg and brown egg layer commercial
 lines. There is minimal concordance between breeds of fine scale LD
 patterns (correlation coefficient &lt; 0.21), and even between
 discrete broiler lines. Regions of LD breakdown, which may align with
 recombination hotspots, are enriched near CpG islands and transcription
 start sites (p &lt; 2.2x10-16), consistent with recent evidence
 described in finches, but concordance in hotspot locations between
 commercial breeds is only marginally greater than random. As in other
 birds functional elements in the chicken genome are associated with
 recombination, but, unlike evidence from other bird species, the LD
 landscape is not stable in the populations studied. The development of
 optimal genotyping panels for genome-led selection programmes will depend
 on careful analysis of the LD structure of each line of interest. Further
 study is required to fully elucidate the mechanisms underlying highly
 divergent LD patterns found in commercial chickens.
description: Genotypes from three
 chicken breedsFiles contain in archive
 Gallus_genotypes.zip contain genotype data from Pengelly et al, 2016.
 'Commercial chicken breeds exhibit highly divergent patterns of
 linkage disequilibrium'. The three breed types are in separate file:
 WEL - white egg layers, BEL - brown egg layers, BRO - broilers. Genotypes
 have been QCed, providing SNPs with an allele frequency &gt; 5%, HWE p
 &gt; 0.001, and having 95% genotyping rate accross the breed. Genotype
 data are provided in the PLINK format, see
 http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml for further details
 including file format specifications.Gallus_genotypes.zip
DOI: 10.5061/dryad.519bm
title: Data from: Genome-wide association study identifies novel loci associated with resistance to bovine tuberculosis

description: Tuberculosis caused by Mycobacterium bovis is a re- emerging disease of
 livestock which is of major economic importance world-wide, as well as
 being a zoonotic risk. There is significant heritability for host
 resistance to bovine tuberculosis (bTB) in dairy cattle. To identify
 resistance loci for bTB, we undertook a genome-wide association study in
 female Holstein-Friesian cattle with 592 cases and 559 age-matched
 controls from case herds. Cases and controls were categorised into
 distinct phenotypes: skin test and lesion positive versus skin test
 negative on multiple occasions, respectively. These animals were genotyped
 with the Illumina Bovine HD 700K bead chip. Genome-wide rapid association
 using linear and logistic mixed models and regression (GRAMMAR), regional
 heritability mapping (RHM) and haplotype-sharing analysis identified two
 novel resistance loci that attained chromosome-wise significance, in
 protein tyrosine phosphatase receptor T (PTPRT; P=4.8 x 10-7) and myosin
 IIIB (MYO3B; P=5.4. x 10-6). We estimated that 21% of the phenotypic
 variance in tuberculosis resistance could be explained by all of the
 informative SNPs, of which the region encompassing the PTPRT gene
 accounted for 6.2% of the variance and a further 3.6% was associated with
 a putative copy number variant (CNV) in MYO3B. The results from this study
 add to our understanding of variation in host control of infection and
 suggest that genetic marker-based selection for resistance to bTB has the
 potential to make a significant contribution to bTB control.
description: Phenotype_forGenABEL2011111.txtCompressed phenotype file in text format for the R GenABEL libraryGenotypes_forGenABEL20111111.raw
DOI: 10.5061/dryad.c0k33vf
title: Data from: Neuroimaging “will to fight” for sacred values: an empirical case study with supporters of an Al Qaeda affiliate

description: Violent intergroup conflicts are often motivated by commitments to
 abstract ideals such as god or nation, so-called “sacred” values that are
 relatively insensitive to material incentives or disincentives. There is
 scant knowledge of how the brain processes costly sacrifices for such
 cherished causes. We studied willingness to fight and die for sacred
 values using fMRI among supporters of a radical Islamist group from
 different neighborhoods in and around Barcelona, Spain. We measured brain
 activity in radicalized individuals as they indicated their willingness to
 fight and die for sacred and non-sacred values, and as they reacted to
 peers’ ratings for the same values. We observed diminished activity in
 dorsolateral prefrontal cortex (dlPFC), inferior frontal gyrus, and
 parietal cortex while participants conveyed willingness to fight and die
 for sacred relative to non-sacred values - regions that have previously
 been implicated in calculating costs and consequences. These differences
 could not be attributed to differences between sacred and non-sacred
 values in emotional intensity, familiarity or salience. An overlapping
 region of dlPFC was active when viewing conflicting ratings of sacred
 values from peers, to the extent participants were sensitive to peer
 influence, suggesting that it is possible to induce flexibility in the way
 people defend sacred values. Our results are consistent with a view that
 “devoted actors” motivated by an extreme commitment towards sacred
 in-group values rely on distinctive neurocognitve processes that can be
 identified.
description: WFD Pre and
 PostBehavioral data on
 Willingness to Fight and Die scores from pre and post
 manipulation.pre-post_wfd_clean.savNeuroimaging filesThis package containes individual level contrasts between SV and non-SV. The con-files stand for Contrast 2 (SVs greater than non-SVs) and contrast 3 (non-SV greater than SVs), they are used in second-level/group-level analyses. The spmT files contain the same contrasts, but they are used for visualization purposes.RoyalSociety_pack.zip
DOI: 10.5061/dryad.d3mr7
title: Data from: New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts

description: The nuclei of higher eukaryotic cells display compartmentalization and
 certain nuclear compartments have been shown to follow a degree of spatial
 organization. To date, the study of nuclear organization has often
 involved simple quantitative procedures that struggle with both the
 irregularity of the nuclear boundary and the problem of handling replicate
 images. Such studies typically focus on inter-object distance, rather than
 spatial location within the nucleus. The concern of this paper is the
 spatial preference of nuclear compartments, for which we have developed
 statistical tools to quantitatively study and explore nuclear
 organization. These tools combine replicate images to generate ‘aggregate
 maps' which represent the spatial preferences of nuclear
 compartments. We present two examples of different compartments in
 mammalian fibroblasts (WI-38 and MRC-5) that demonstrate new knowledge of
 spatial preference within the cell nucleus. Specifically, the spatial
 preference of RNA polymerase II is preserved across normal and
 immortalized cells, whereas PML nuclear bodies exhibit a change in spatial
 preference from avoiding the centre in normal cells to exhibiting a
 preference for the centre in immortalized cells. In addition, we show that
 SC35 splicing speckles are excluded from the nuclear boundary and localize
 throughout the nucleoplasm and in the interchromatin space in
 non-transformed WI-38 cells. This new methodology is thus able to reveal
 the effect of large-scale perturbation on spatial architecture and
 preferences that would not be obvious from single cell imaging.
description: OnlineDataForWestonEtALThis zip file contains the 3D spatial location data used in Figures 7 – 12. The data for the figures are separated into subdirectories. All data is stored in R data format (file extension .rda) and an R script (file extension .r) is also provided to show how to extract this data. In addition the full raw image data for Figure 12 is also provided (which can be found in the directory Figure12). The Imagedata zip file contains all the Z-stack images for all the cells used in this analysis. The file format is c_d.TIF. c denotes the cell number, and d denotes the slice, e.g. the file 1_6.TIF is a slice from the first cell, furthermore the first cell has 16 slices (0 to 15). The zip file 2DProjection contains 2D projected images of the full image stack for each of the nuclei. For all the images, the blue channel delineates the nuclear volume, the red channel represents the SC35 splicing speckles and the green channel represents PML bodies (which are not used in the analysis for Figure 12). See the caption of Figure 1 and Supplementary Note 1 for more details.
DOI: 10.5061/dryad.5qs11
title: Data from: Functional diversification of Argonautes in nematodes: an expanding universe

description: In the last decade, many diverse RNAi (RNA interference) pathways have
 been discovered that mediate gene silencing at epigenetic, transcriptional
 and post-transcriptional levels. The diversity of RNAi pathways is
 inherently linked to the evolution of Ago (Argonaute) proteins, the
 central protein component of RISCs (RNAinduced silencing complexes). An
 increasing number of diverse Agos are have been identified in different
 species. The functions of most of these proteins are not yet known, but
 they are generally assumed to play roles in development, genome stability
 and/or protection against pathogens. Recent research in the nematode
 Caenorhabditis elegans has expanded the breadth of RNAi functions to
 include transgenerational epigenetic memory and, possibly, environmental
 sensing. These functions are inherently linked to the production of
 secondary siRNAs (small interfering RNAs) that bind to members of a clade
 of WAGOs (wormspecific Agos). In the present article, we review briefly
 what is known about the evolution and function of Ago proteins in
 eukaryotes, including the expansion of WAGOs in nematodes. We postulate
 that the rapid evolution of WAGOs enables the exceptional functional
 plasticity of nematodes, including their capacity for parasitism.
description: Compressed repository of
 Nematode Argonaute phylogenetic analysesThe repository contains
 a NEXUS format protein alignment, the outputs from MrBayes analyses of
 this alignment, and a figure describing the analyses.AGO_Buck_Blaxter_Dryad_2013.zip
DOI: 10.5061/dryad.1f1rc
title: Data from: Error-robust modes of the retinal population code

description: Across the nervous system, certain population spiking patterns are
 observed far more frequently than others. A hypothesis about this
 structure is that these collective activity patterns function as
 population codewords–collective modes–carrying information distinct from
 that of any single cell. We investigate this phenomenon in recordings of
 ∼150 retinal ganglion cells, the retina’s output. We develop a novel
 statistical model that decomposes the population response into modes; it
 predicts the distribution of spiking activity in the ganglion cell
 population with high accuracy. We found that the modes represent localized
 features of the visual stimulus that are distinct from the features
 represented by single neurons. Modes form clusters of activity states that
 are readily discriminated from one another. When we repeated the same
 visual stimulus, we found that the same mode was robustly elicited. These
 results suggest that retinal ganglion cells’ collective signaling is
 endowed with a form of error-correcting code–a principle that may hold in
 brain areas beyond retina.
description: Multi-electrode retinal
 ganglion cell population spiking dataThe file contains spike
 time data from multi-electrode array recordings of salamander retinal
 ganglion cells under four stimulus conditions: a white noise checkerboard,
 a repeated natural movie, a non-repeated natural movie, and a bar
 exhibiting random one-dimensional motion. For each experiment, spike time
 data is provided in the file 'data.mat' and information
 necessary to reconstruct the stimulus and align to spike times is
 contained in 'aux_data' where relevant. All recordings were
 sampled at 10 kHz. Data is in Matlab .mat format.error_robust_mode_data.zip
DOI: 10.5061/dryad.d3k37
title: Data from: Parasitism overrides herbivore identity allowing hyperparasitoids to locate their parasitoid host by using herbivore-induced plant volatiles

description: Foraging success of predators profoundly depends on reliable and
 detectable cues indicating the presence of their often inconspicuous prey.
 Carnivorous insects rely on chemical cues to optimize foraging efficiency.
 Hyperparasitoids that lay their eggs in the larvae or pupae of parasitic
 wasps may find their parasitoid hosts developing in different herbivores.
 They can use herbivore-induced plant volatiles (HIPVs) to locate
 parasitized caterpillars. Because different herbivore species induce
 different HIPV emission from plants, hyperparasitoids may have to deal
 with large variation in volatile information that indicates host presence.
 In this study, we used an ecogenomics approach to first address whether
 parasitized caterpillars of two herbivore species (Pieris rapae and P.
 brassicae) induce similar transcriptional and metabolomic responses in
 wild Brassica oleracea plants and, second, whether hyperparasitoids
 Lysibia nana are able to discriminate between these induced plant
 responses to locate their parasitoid host in different herbivores under
 both laboratory and field conditions. Our study revealed that both
 herbivore identity and parasitism affect plant transcriptional and
 metabolic responses to herbivory. We also found that hyperparasitoids are
 able to respond to HIPVs released by wild B. oleracea under both
 laboratory and field conditions. In addition, we observed stronger
 attraction of hyperparasitoids to HIPVs when plants were infested with
 parasitized caterpillars. However, hyperparasitoids were equally attracted
 to plants infested by either herbivore species. Our results indicate that
 parasitism plays a major role in HIPV-mediated plant–hyperparasitoid
 interactions. Furthermore, these findings also indicate that plant
 trait-mediated indirect interaction networks play important roles in
 community-wide species interactions.
description: Microarray raw
 dataPlant volatile
 analysisY-tube
 bioassayField
 dataqPCR raw
 data
DOI: 10.5061/dryad.8p984
title: Data from: Evidence of land-sea transfer of the zoonotic pathogen Campylobacter to a wildlife marine sentinel species

description: Environmental pollution often accompanies the expansion and urbanization
 of human populations where sewage and wastewaters commonly have an impact
 on the marine environments. Here, we explored the potential for faecal
 bacterial pathogens, of anthropic origin, to spread to marine wildlife in
 coastal areas. The common zoonotic bacterium Campylobacter was isolated
 from grey seals (Halichoerus grypus), an important sentinel species for
 environmental pollution, and compared to isolates from wild birds,
 agricultural sources and clinical samples to characterize possible
 transmission routes. Campylobacter jejuni was present in half of all grey
 seal pups sampled (24/50 dead and 46/90 live pups) in the breeding colony
 on the Isle of May (Scotland), where it was frequently associated with
 histological evidence of disease. Returning yearling animals (19/19) were
 negative for C. jejuni suggesting clearance of infection while away from
 the localized colony infection source. The genomes of 90 isolates from
 seals were sequenced and characterized using a whole-genome multilocus
 sequence typing (MLST) approach and compared to 192 published genomes from
 multiple sources using population genetic approaches and a probabilistic
 genetic attribution model to infer the source of infection from MLST data.
 The strong genotype-host association has enabled the application of source
 attribution models in epidemiological studies of human campylobacteriosis,
 and here assignment analyses consistently grouped seal isolates with those
 from human clinical samples. These findings are consistent with either a
 common infection source or direct transmission of human campylobacter to
 grey seals, raising concerns about the spread of human pathogens to
 wildlife marine sentinel species in coastal areas.
description: 88 assembled whole
 genome sequences from Campylobacter jejuni and Campylobacter coli isolated
 from grey seals (Halichoerus grypus)88 assembled whole
 genome sequences from Campylobacter jejuni and Campylobacter coli isolated
 from grey seals (Halichoerus grypus). Please refer to the full text
 publication for full description.Baily_et_al_88_wgs_Cj_Cc_from_grey_seals.zipCore genome alignment for isolates used in this studyMulti-FASTA file of core genes concatenated and aligned using MUSCLE, from Campylobacter coli and C. jejuni isolates used and sequenced in this study.278_genomes_core_alignment.fasAdditional histopathology and immunohistochemistry figuresAdditional information about those is available from corresponding authors on request.Additional figures.rarSeal data associated with bacterial isolationDetailed data about animal hosts from which strains sequenced in this study were isolated (animal weight, length to tail, sex, GPS location of isolation, date of isolation).Seal data associated with bacterial isolation (updated)Isolation information for strains of which genomes are available in Dryad accession: doi:10.5061/dryad.8p984
DOI: 10.5061/dryad.622h6
title: Data from: Multilocus phylogenetic analyses of Hispaniolan and Bahamian trunk anoles (distichus species group)

description: The distichus species group includes six species and 21 subspecies of
 trunk ecomorph anoles distributed across Hispaniola and its satellite
 islands as well as the northern Bahamas. Although this group has long
 served as a model system for studies of reproductive character
 displacement, adaptation, behavior and speciation, it has never been the
 subject of a comprehensive phylogenetic analysis. Our goal here is to
 generate a multilocus phylogenetic dataset (one mitochondrial and seven
 nuclear loci) and to use this dataset to infer phylogenetic relationships
 among the majority of the taxa assigned to the distichus species group. We
 use these phylogenetic trees to address three topics about the group’s
 evolution. First, we consider longstanding taxonomic controversies about
 the status of several species and subspecies assigned to the distichus
 species group. Second, we investigate the biogeographic history of the
 group and specifically test the hypotheses that historical division of
 Hispaniola into two paleo-islands contributed to the group’s
 diversification and that Bahamian and Hispaniolan satellite island
 populations are derived from colonists from the main Hispaniolan landmass.
 Finally, third, we use comparative phylogenetic analyses to test the
 hypothesis that divergence between pale yellow and darkly pigmented orange
 or red dewlap coloration has occurred repeatedly across the distichus
 species group.
description: distichus species group
 DNA alignmentConcatenated multilocus
 DNA sequence alignment of the distichus species group and outgroups.
 Alignment consists of 58 taxa and eight genes - seven nuclear loci (RAG1,
 R35, BDNF, NT3, B108, B127, and GJA) and one mitochondrial locus (ND2).
 File includes mrbayes block used for analysis.concatenated_by_gene.nex*BEAST posterior distribution of treesPosterior distribution of phylogenetic trees estimated using the coalescent species tree software *BEAST (v1.7.5).StarBEAST_posterior.species.trees*BEAST MCC treeMaximum clade credibility species tree inferred using the coalescent species tree software *BEAST v1.7.5.StarBEAST_MCC.species.treMrBayes consensus treeMajority rule consensus tree inferred using MrBayes. Node support values are posterior probabilities.concatenated_by_gene.nex.con.treBEAST MCC treeMaximum clade credibility tree inferred from analysis of concatenated dataset using BEAST v1.7.5.dist_BEAST_combined.tre
DOI: 10.5061/dryad.3kd4134
title: Data from: Distance-dependent defensive coloration in the poison frog Dendrobates tinctorius, Dendrobatidae

description: Poison dart frogs provide classic examples of warning signals: potent
 toxins signaled by distinctive, conspicuous coloration. We show that,
 counterintuitively, the bright yellow and blue-black color of Dendrobates
 tinctorius (Dendrobatidae) also provides camouflage. Through computational
 modeling of predator vision, and a screen-based detection experiment
 presenting frogs at different spatial resolutions, we demonstrate that at
 close range the frog is highly detectable, but from a distance the colors
 blend together, forming effective camouflage. This result was corroborated
 with an in situ experiment, which found survival to be
 background-dependent, a feature more associated with camouflage than
 aposematism. Our results suggest that in D. tinctorius the distribution of
 pattern elements, and the particular colors expressed, act as a highly
 salient close range aposematic signal, while simultaneously minimizing
 detectability to distant observers.
description: image_dataImage data associated with Barnett, J.B. et al. "Distance dependent defensive coloration in the poison frog Dendrobates tinctorius, Dendrobatidae"detection_dataDetection data associated with Barnett, J.B. et al. "Distance dependent defensive coloration in the poison frog Dendrobates tinctorius, Dendrobatidae"survival_dataSurvival data associated with Barnett, J.B. et al. "Distance dependent defensive coloration in the poison frog Dendrobates tinctorius, Dendrobatidae"