cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.47v40
title: Data from: Selecting question-specific genes to reduce incongruence in phylogenomics: a case study of jawed vertebrate backbone phylogeny

description: Incongruence between different phylogenomic analyses is the main challenge
 faced by phylogeneticists in the genomic era. To reduce incongruence,
 phylogenomic studies normally adopt some data filtering approaches, such
 as reducing missing data or using slowly evolving genes, to improve the
 signal quality of data. Here, we assembled a phylogenomic data set of 58
 jawed vertebrate taxa and 4682 genes to investigate the backbone phylogeny
 of jawed vertebrates under both concatenation and coalescent-based
 frameworks. To evaluate the efficiency of extracting phylogenetic signals
 among different data filtering methods, we chose six highly intractable
 internodes within the backbone phylogeny of jawed vertebrates as our test
 questions. We found that our phylogenomic data set exhibits substantial
 conflicting signal among genes for these questions. Our analyses showed
 that non-specific data sets that are generated without bias toward
 specific questions are not sufficient to produce consistent results when
 there are several difficult nodes within a phylogeny. Moreover,
 phylogenetic accuracy based on non-specific data is considerably
 influenced by the size of data and the choice of tree inference methods.
 To address such incongruences, we selected genes that resolve a given
 internode but not the entire phylogeny. Notably, not only can this
 strategy yield correct relationships for the question, but it also reduces
 inconsistency associated with data sizes and inference methods. Our study
 highlights the importance of gene selection in phylogenomic analyses,
 suggesting that simply using a large amount of data cannot guarantee
 correct results. Constructing question-specific data sets may be more
 powerful for resolving problematic nodes.
description: tree_nexThese are trees generated from different data sets.Names were refered as corresponding data setsdata_nex_newThese data sets were generated from genomic and transcriptomic data of jawed vertebrate. The compressed file contains data sets generated by different filtering approach,including data filtered by data completeness,alignment quality, gene informative, evolutionary rate,resolution of gene and specific data sets designed for neoaves,eutheria,teleostei questions.data_nex.zippython_scriptsCustom python_scripts used in the analysis, including mutual best hit analysis, pairwise_p_distance calculator, gene_average_bootstrap_value calculator, parse_gene_tree_topology. All scripts call module of Biopython. Please install Biopython before use.python_script.zipSupplementary File ArchivesThese are supplementary tables and figures related to the paper.Supplementary_files.zip
DOI: 10.5061/dryad.2vm47
title: Data from: How animals follow the stars

description: Throughout history, the stars have provided humans with ever more
 information about our world, enabling increasingly accurate systems of
 navigation in addition to fuelling some of the greatest scientific
 controversies. What information animals have evolved to extract from a
 starry sky and how they do so, is a topic of study that combines the
 practical and theoretical challenges faced by both astronomers and field
 biologists. While a number of animal species have been demonstrated to use
 the stars as a source of directional information, the strategies that
 these animals use to convert this complex and variable pattern of dim
 light-points into a reliable “stellar orientation” cue have been more
 difficult to ascertain. In this review, we assess the stars as a visual
 stimulus that conveys directional information, and compare the bodies of
 evidence available for the different stellar orientation strategies
 proposed to date. In this context, we also introduce new technologies that
 may aid in the study of stellar orientation, and suggest how field
 experiments may be used to characterise the mechanisms underlying stellar
 orientation.
description: Figure 2 Raw
 dataSpectral radiance data
 for the Milky Way recorded under clear skies.HAFS-Fig2.zipFigure 3 Raw dataSpectral radiance of the starry sky recorded under different atmospheric conditions.HAFS-Fig3.zipFigure S2 Raw dataSpectral radiance recorded in planetaria displaying conditions from Dacke et al 2013.HAFS-FigS2.zip
DOI: 10.5061/dryad.nn77p
title: Data from: How mechanisms of habitat preference evolve and promote divergence with gene flow

description: Habitat preference may promote adaptive divergence and speciation, yet the
 conditions under which this is likely are insufficiently explored. We use
 individual-based simulations to study the evolution and consequence of
 habitat preference during divergence with gene flow, considering four
 different underlying genetically-based behavioral mechanisms: natal
 habitat imprinting, phenotype-dependent, competition-dependent, and direct
 genetic habitat preference. We find that the evolution of habitat
 preference generally requires initially high dispersal, is facilitated by
 asymmetry in population sizes between habitats, and is hindered by an
 increasing number of underlying genetic loci. Moreover, the probability of
 habitat preference to emerge and promote divergence differs greatly among
 the underlying mechanisms. Natal habitat imprinting evolves most easily
 and can allow full divergence in parameter ranges where no divergence is
 possible in the absence of habitat preference. The reason is that
 imprinting represents a one-allele mechanism of assortative mating linking
 dispersal behavior very effectively to local selection. At the other
 extreme, direct genetic habitat preference, a two-allele mechanism,
 evolves under restricted conditions only, and even then facilitates
 divergence weakly. Overall, our results indicate that habitat preference
 can be a strong reproductive barrier promoting divergence with gene flow,
 but that this is highly contingent on the underlying preference mechanism.
description: Online data
 browserThis package contains
 supplementary material for the paper "How mechanisms of habitat
 preference evolve and promote divergence with gene flow" in Journal
 of Evolutionary Biology. An interactive version of this material can also
 be found at http://xavier.thibert-plante.com/habitatPref . Download this
 package habPrefSupp.tar.bz2 into a directory of your choice. We will call
 this directory . Unload the package using for example: tar -xjf
 habPrefSupp.tar.bz2 (UNIX) http://www.7-zip.org/download.html (MS Windows)
 Using your favorite web browser "open file":
 /DIR.bernerThibert-Plante/index.html and you can start browsing
 the supplementary material.habPrefSupp.tar.bz2
DOI: 10.5061/dryad.ph37b2q
title: Data from: Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map

description: Identifying the sources of natural variation underlying metabolic
 differences between plants will enable a better understanding of plant
 metabolism and provide insights into the regulatory networks that govern
 plant growth and morphology. So far, however, the contribution of
 epigenetic variation to metabolic diversity has been largely ignored. In
 the present study, we utilized a panel of Arabidopsis thaliana epigenetic
 recombinant inbred lines (epiRILs) to assess the impact of epigenetic
 variation on the metabolic composition. Thirty epigenetic QTL (QTLepi)
 were detected, which partly overlap with QTLepi linked to growth and
 morphology. In an effort to identify causal candidate genes in the QTLepi
 regions or their putative trans-targets we performed in silico small RNA
 and qPCR analyses. Differentially expressed genes were further studied by
 phenotypic and metabolic analyses of knockout mutants. Three genes were
 detected that recapitulated the detected QTLepi effects, providing
 evidence for epigenetic regulation in cis and in trans. These results
 indicate that epigenetic mechanisms impact metabolic diversity, possibly
 via small RNAs, and thus aid in further disentangling the complex
 epigenotype-phenotype map.
description: EpiRILsand
 parentsQTL-mapping_rawLCMScdfsEpiRILs and parents
 QTL-mapping raw LCMS dataEpiRILs and parents
 QTL-mapping_raw LCMS cdfs.zipMutantsSupplTable7_rawLCMscdfsMutants Suppl Table 7_raw LCMs cdfs.zipsamplecodes_rawLCMScdfssample codes _raw LCMS cdfs.xlsx
DOI: 10.5061/dryad.4fn70
title: Data from: The effect of Speed of Processing training on microsaccade magnitude

description: Older adults experience cognitive deficits that can lead to driving errors
 and a loss of mobility. Fortunately, some of these deficits can be
 ameliorated with targeted interventions which improve the speed and
 accuracy of simultaneous attention to a central and a peripheral stimulus
 called Speed of Processing training. To date, the mechanisms behind this
 effective training are unknown. We hypothesized that one potential
 mechanism underlying this training is a change in distribution of eye
 movements of different amplitudes. Microsaccades are small amplitude eye
 movements made when fixating on a stimulus, and are thought to counteract
 the “visual fading” that occurs when static stimuli are presented. Due to
 retinal anatomy, larger microsaccadic eye movements are needed to move a
 peripheral stimulus between receptive fields and counteract visual fading.
 Alternatively, larger microsaccades may decrease performance due to neural
 suppression. Because larger microsaccades could aid or hinder peripheral
 vision, we examine the distribution of microsaccades during stimulus
 presentation. Our results indicate that there is no statistically
 significant change in the proportion of large amplitude microsaccades
 during a Useful Field of View-like task after training in a small sample
 of older adults. Speed of Processing training does not appear to result in
 changes in microsaccade amplitude, suggesting that the mechanism
 underlying Speed of Processing training is unlikely to rely on
 microsaccades.
description: Eyetracking data for
 UFOV-like taskThis file contains
 behavioral and eyetracking data collected from participants in the
 experiment. It also contains the MATLAB codes used to analyze this
 data.PLoSData.zip
DOI: 10.5061/dryad.qf83q
title: Data from: Surface-water dynamics and land use influence landscape connectivity across a major dryland region

description: Landscape connectivity is important for the long-term persistence of
 species inhabiting dryland freshwater ecosystems, with spatiotemporal
 surface-water dynamics (e.g., flooding) maintaining connectivity by both
 creating temporary habitats and providing transient opportunities for
 dispersal. Improving our understanding of how landscape connectivity
 varies with respect to surface-water dynamics and land use is an important
 step to maintaining biodiversity in dynamic dryland environments. Using a
 newly available validated Landsat TM and ETM+ surface-water time series,
 we modelled landscape connectivity between dynamic surface-water habitats
 within Australia's 1 million km2 semi-arid Murray Darling Basin
 across a 25-year period (1987 to 2011). We identified key habitats that
 serve as well-connected ‘hubs’, or ‘stepping-stones’ that allow
 long-distance movements through surface-water habitat networks. We
 compared distributions of these habitats for short- and long-distance
 dispersal species during dry, average and wet seasons, and across land-use
 types. The distribution of stepping-stones and hubs varied both spatially
 and temporally, with temporal changes driven by drought and flooding
 dynamics. Conservation areas and natural environments contained higher
 than expected proportions of both stepping-stones and hubs throughout the
 time series; however, highly modified agricultural landscapes increased in
 importance during wet seasons. Irrigated landscapes contained particularly
 high proportions of well-connected hubs for long-distance dispersers, but
 remained relatively disconnected for less vagile organisms. The habitats
 identified by our study may serve as ideal high-priority targets for
 land-use specific management aimed at maintaining or improving dispersal
 between surface-water habitats, potentially providing benefits to
 biodiversity beyond the immediate site scale. Our results also highlight
 the importance of accounting for the influence of spatial and temporal
 surface-water dynamics when studying landscape connectivity within highly
 variable dryland environments.
description: Local graph theory
 connectivity metrics from Bishop-Taylor et al. 2017Graph theory local
 connectivity metrics data for two dispersal distances and each seasonal
 time-step in the 1987-2011 Landsat-derived surface-water time series
 (Tulbure et al. 2016). Betweenness and degree centrality results were used
 to assess the distribution of important “stepping-stone” and “hub”
 habitats across Australia’s Murray-Darling Basin.Bishop-Taylor_et_al_2017_localmetrics.txt
DOI: 10.5061/dryad.cp723
title: Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives

description: Although the Compositae harbours only two major food crops, sunflower and
 lettuce, many other species in this family are utilized by humans and have
 experienced various levels of domestication. Here we have used next
 generation sequencing technology to develop 15 reference transcriptome
 assemblies for Compositae crops or their wild relatives. These data allow
 us to gain insight into the evolutionary and genomic consequences of plant
 domestication. Specifically, we performed Illumina sequencing of Cichorium
 endivia, Cichorium intybus, Echinacea angustifolia, Iva annua, Helianthus
 tuberosus, Dahlia hybrida, Leontodon taraxacoides and Glebionis segetum,
 as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium
 argentatum and Smallanthus sonchifolius. Illumina reads were assembled
 using Trinity, and 454 reads were assembled using MIRA and CAP3. We
 evaluated the coverage of the transcriptomes using BLASTX analysis of a
 set of ultra-conserved orthologs (UCOs) and recovered most of these genes
 (88-98%). We found a correlation between contig length and read length for
 the 454 assemblies, and greater contig lengths for the 454 compared to the
 Illumina assemblies. This suggests that longer reads can aid in the
 assembly of more complete transcripts. Finally, we compared the divergence
 of orthologs at synonymous sites (Ks) between Compositae crops and their
 wild relatives and found greater divergence when the progenitors were
 self-incompatible. We also found greater divergence between pairs of taxa
 that had some evidence of post-zygotic isolation. For several more
 distantly related congeners, such as chicory and endive, we identified a
 signature of introgression in the distribution of Ks values.
description: The 15 reference
 transcriptome assemblies of Compositae crops and their wild
 relativesdryad_submission.tar
DOI: 10.5061/dryad.654sm
title: Data from: Mortality risk and social network position in resident killer whales: sex differences and the importance of resource abundance

description: An individual’s ecological environment affects their mortality risk, which
 in turn has fundamental consequences for life history evolution. In many
 species social relationships are likely to be an important component of an
 individual’s environment, and therefore their mortality risk. Here we
 examine the relationship between social position and mortality risk in
 resident killer whales (Orcinus orca) using over three decades of social
 and demographic data. We find that the social position of male, but not
 female, killer whales in their social unit predicts their mortality risk.
 More socially integrated males have a significantly lower risk of
 mortality than socially peripheral males, particularly in years of low
 prey abundance, suggesting that social position mediates access to
 resources. Male killer whales are larger and require more resources than
 females, increasing their vulnerability to starvation in years of low
 salmon abundance. More socially integrated males are likely to have better
 access to social information and food sharing opportunities which may
 enhance their survival in years of low salmon. Our results show that
 observable variation in the social environment is linked to variation in
 mortality risk, and highlight how sex differences in social effects on
 survival may be linked to sex differences in life-history evolution.
description: Permutations- within
 community closeness10 000 permutations of
 within community closeness centrality10000communitycloseness.permutations.csvPermutations - within community degree10 000 permutations of within community degree10000communitydegree.permutations.csvPermutations - whole population measures10 000 permutations of whole population measures degree and closeness10000permutations_ofwholenetworkmeasures.csvCensus data giving births and deaths of whalesNOTE: IDs relate to those in other uploaded filesAnonomised.census.data.csv
DOI: 10.5061/dryad.r6t26
title: Data from: The ‘heritability’ of domestication and its functional partitioning in the pig

description: We propose to estimate the proportion of variance explained by regression
 on genome-wide markers (or genomic heritability) when wild/domestic status
 is considered the phenotype of interest. This approach differs from the
 standard Fst in that it can accommodate genetic similarity between
 individuals in a general form. We apply this strategy to complete genome
 data from 47 wild and domestic pigs from Asia and Europe. When we
 partitioned the total genomic variance into components associated to
 subsets of single nucleotide polymorphisms (SNPs) defined in terms of
 their annotation, we found that potentially deleterious non-synonymous
 mutations (9566 SNPs) explained as much genetic variance as the whole set
 of 25 million SNPs. This suggests that domestication may have affected
 protein sequence to a larger extent than regulatory or other kinds of
 mutations. A pathway-guided analysis revealed ovarian steroidogenesis and
 leptin signaling as highly relevant in domestication. The genomic
 regression approach proposed in this study revealed molecular processes
 not apparent through typical differentiation statistics. We propose that
 at least some of these processes are likely new discoveries because
 domestication is a dynamic process of genetic selection, which may not be
 completely characterized by a static metric like Fst. Nevertheless, and
 despite some particularly influential mutation types or pathways, our
 analyses tend to rule out a simplistic genetic basis for the domestication
 process: neither a single pathway nor a unique set of SNPs can explain the
 process as a whole.
description: Imputed and non imputed
 genotypesSample list and
 characteristics, imputed and non imputed vcf files.
 "h2dom.tar.gz" contains 3 files: sample.txt contains sample
 description (also below); countries are ISO codes. all.gt.vcf.gz contains
 vcf file with all and phased imputed SNPs. all.vcf.gz contains merged vcf
 file with all non imputed SNPs as missing (./.)h2dom.tar.gzsample.txtSRP074357
DOI: 10.5061/dryad.612jm
title: Data from: Validation of network communicability metrics for the analysis of brain structural networks.

description: Computational network analysis provides new methods to analyze the
 brain's structural organization based on diffusion imaging
 tractography data. Networks are characterized by global and local metrics
 that have recently given promising insights into diagnosis and the further
 understanding of psychiatric and neurologic disorders. Most of these
 metrics are based on the idea that information in a network flows along
 the shortest paths. In contrast to this notion, communicability is a
 broader measure of connectivity which assumes that information could flow
 along all possible paths between two nodes. In our work, the features of
 network metrics related to communicability were explored for the first
 time in the healthy structural brain network. In addition, the sensitivity
 of such metrics was analysed using simulated lesions to specific nodes and
 network connections. Results showed advantages of communicability over
 conventional metrics in detecting densely connected nodes as well as
 subsets of nodes vulnerable to lesions. In addition, communicability
 centrality was shown to be widely affected by the lesions and the changes
 were negatively correlated with the distance from lesion site. In summary,
 our analysis suggests that communicability metrics that may provide an
 insight into the integrative properties of the structural brain network
 and that these metrics may be useful for the analysis of brain networks in
 the presence of lesions. Nevertheless, the interpretation of
 communicability is not straightforward; hence these metrics should be used
 as a supplement to the more standard connectivity network metrics.
description: ConnectMatrix files of
 the subjectsThese are structures
 files storing the connectivity matrices of the
 subjects.Data_ConnectMatrix.rarSimulated lesions filesThese files summarize the network properties in the case of different lesion types.Lesions.zip
DOI: 10.5061/dryad.8bj97
title: Data from: The extracellular domains of IgG1 and T cell-derived IL-4/IL-13 are critical for the polyclonal memory IgE response in vivo

description: IgE-mediated activation of mast cells and basophils contributes to
 protective immunity against helminths but also causes allergic responses.
 The development and persistence of IgE responses are poorly understood,
 which is in part due to the low number of IgE-producing cells. Here, we
 used next generation sequencing to uncover a striking overlap between the
 IgE and IgG1 repertoires in helminth-infected or OVA/alum-immunized
 wild-type BALB/c mice. The memory IgE response after secondary infection
 induced a strong increase of IgE+ plasma cells in spleen and lymph nodes.
 In contrast, germinal center B cells did not increase during secondary
 infection. Unexpectedly, the memory IgE response was lost in mice where
 the extracellular part of IgG1 had been replaced with IgE sequences.
 Adoptive transfer studies revealed that IgG1+ B cells were required and
 sufficient to constitute the memory IgE response in recipient mice. T
 cell-derived IL-4/IL-13 was required for the memory IgE response but not
 for expansion of B cells from memory mice. Together, our results reveal a
 close relationship between the IgE and IgG1 repertoires in vivo and
 demonstrate that the memory IgE response is mainly conserved at the level
 of memory IgG1+ B cells. Therefore, targeting the generation and survival
 of allergen-specific IgG1+ B cells could lead to development of new
 therapeutic strategies to treat chronic allergic disorders.
description: sequences related to
 Figures 2, 3 and 6sequences.zip