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397 results for “discordance”
Multi-Dimensional Data Viewer (MDV) user manual for data exploration: "Systematic analysis of YFP traps reveals common discordance between mRNA and protein across the nervous system"
<table> <tbody> <tr> <td> <p> Please also see the latest version of the repository:<br> <a href="https://doi.org/10.5281/zenodo.6374011">https://doi.org/10.5281/zenodo.6374011</a> and<br> our website: <a href="https://ilandavis.com/jcb2023-yfp">https://ilandavis.com/jcb2023-yfp</a></p> </td> </tr> </tbody> </table> <p> </p> <p>The explosion in the volume of biological imaging data challenges the available technologies for data interrogation and its intersection with related published bioinformatics data sets. Moreover, intersection of highly rich and complex datasets from different sources provided as flat csv files requires advanced informatics skills, which is time consuming and not accessible to all. Here, we provide a “user manual” to our new paradigm for systematically filtering and analysing a dataset with more than 1300 microscopy data figures using Multi-Dimensional Viewer (MDV) -<a href="https://mdv.molbiol.ox.ac.uk/projects/mdv_project/7012?view=RNA+%2F+Protein+Distribution">link</a>, a solution for interactive multimodal data visualisation and exploration. The primary data we use are derived from our published systematic analysis of 200 YFP traps reveals common discordance between mRNA and protein across the nervous system (<a href="https://doi.org/10.1083/jcb.202205129">eprint link</a>). This manual provides the raw image data together with the expert annotations of the mRNA and protein distribution as well as associated bioinformatics data. We provide an explanation, with specific examples, of how to use MDV to make the multiple data types interoperable and explore them together. We also provide the open-source python code <a href="https://github.com/ilandavislab/Annotate.OMERO.Fig">(github link)</a> used to annotate the figures, which could be adapted to any other kind of data annotation task.</p>
Data from: Discordant patterns of genetic and phenotypic differentiation in five grasshopper species co-distributed across a microreserve network
<p>Conservation plans can be greatly improved when information on the evolutionary and demographic consequences of habitat fragmentation is available for several co-distributed species. Here, we study spatial patterns of phenotypic and genetic variation among five grasshopper species that are co-distributed across a network of microreserves but show remarkable differences in dispersal-related morphology (body size and wing length), degree of habitat specialization and extent of fragmentation of their respective habitats in the study region. In particular, we tested the hypothesis that species with preferences for highly fragmented microhabitats show stronger genetic and phenotypic structure than co-distributed generalist taxa inhabiting a continuous matrix of suitable habitat. We also hypothesized a higher resemblance of spatial patterns of genetic and phenotypic variability among species that have experienced a higher degree of habitat fragmentation due to their more similar responses to the parallel large-scale destruction of their natural habitats. In partial agreement with our first hypothesis, we found that genetic structure, but not phenotypic differentiation, was higher in species linked to highly fragmented habitats. We did not find support for congruent patterns of phenotypic and genetic variability among any studied species, indicating that they show idiosyncratic evolutionary trajectories and distinctive demographic responses to habitat fragmentation across a common landscape. This suggests that conservation practices in networks of protected areas require detailed ecological and evolutionary information on target species in order to focus management efforts on those taxa that are more sensitive to the effects of habitat fragmentation.</p>
On the Helpfulness of Answering Developer Questions on Discord with Similar Conversations and Posts from the Past
<p>Replication Package for "On the Helpfulness of Answering Developer Questions on Discord with Similar Conversations and Posts from the Past".</p>
Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes
<p>Variation in gene tree estimates is widely observed in empirical phylogenomic data and is often assumed to be the result of biological processes. However, a recent study using tetrapod mitochondrial genomes to control for biological sources of variation due to their haploid, uniparentally inherited, and non-recombining nature found that levels of discordance among mitochondrial gene trees were comparable to those found in studies that assume only biological sources of variation. Additionally, they found that several of the models of sequence evolution chosen to infer gene trees were doing an inadequate job of fitting the sequence data. These results indicated that significant amounts of gene tree discordance in empirical data may be due to poor fit of sequence evolution models and that more complex and biologically realistic models may be needed. To test how the fit of sequence evolution models relates to gene tree discordance, we analyzed the same mitochondrial datasets as the previous study using two additional, more complex models of sequence evolution that each model a different biologically realistic aspect of the evolutionary process: a covarion model to incorporate heterotachy, and a model partitioned model to incorporate variable evolutionary patterns by codon position. Our results show that both additional models fit the data better than the models used in the previous study, with the covarion being consistently and strongly preferred as tree size increases. However, even these more preferred models still inferred highly discordant mitochondrial gene trees, thus deepening the mystery around what we label the "Mito-Phylo Paradox" and leading us to ask whether the observed variation could be biological after all.</p>
Summary Statistics from "Genetically regulated gene expression and proteins revealed discordant effects" (LWAS of biomarker)
<p>Summary statistics of 92 blood protein levels. The corresponding publication is currently under revision.</p> <p> The zipped txt file is tab-delimited and contains the following columns:</p> <ul> <li>protein: protein name abbreviation</li> <li>cytoband: genomic region</li> <li>gene: gene name abbreviation</li> <li>setting: either "combined" (adj. for sex & age) or sex-stratified ("males", "females"; adj. for age)</li> <li>variant_id_hg19: SNP ID according to hg19</li> <li>variant_id_hg38: SNP ID according to hg19</li> <li>chr: chromosome</li> <li>pos_hg19: base position according to hg19</li> <li>pos_hg38: base position according to hg19</li> <li>effect_allele: also known as counted allele in additive model</li> <li>other_allele: not-counted allele</li> <li>eaf: effect allele frequency</li> <li>maf: minor allele frequency</li> <li>info: imputation info score</li> <li>n_samples: number of samples</li> <li>beta: effect estimate</li> <li>se: standard error</li> <li>zscore: Z-statistic</li> <li>pvalue: p-value</li> <li>FDR: FDR by gene and setting</li> <li>BBFDR: hierarchical FDR by setting</li> <li>hierFDR: TRUE if SNP is significant after hierarchical FDR</li> </ul>
Discordant population structure among rhizobium divided genomes and their legume hosts
<p>Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprised of multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole-genome resequencing of a hierarchically-structured sample of 191 strains of <em>Sinorhizobium meliloti</em> collected from 21 locations in southern Europe to characterize the population structures of this bacterial symbiont and its host plant <em>Medicago truncatula</em>. <em>Sinorhizobium meliloti</em> genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. The differences in population structure may result from among-replicon differences in the extent of horizontal gene transfer, although given limited recombination of the chromosome, different levels of purifying or positive selection may also contribute to among-replicon differences. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.</p>
Concordance and discordance in the phylogenomics of the wrasses and parrotfishes (Teleostei: Labridae)
<p>Phylogenomic analysis of large genome-wide sequence data sets can resolve phylogenetic tree topologies for large species groups, help test the accuracy of and improve resolution for earlier multilocus studies, and reveal the level of agreement or concordance within partitions of the genome for various tree topologies. Here we used a target-capture approach to sequence more than 1,000 single-copy exons for more than 200 labrid fishes together with more than 100 outgroup taxa to generate a new data-rich phylogeny for the family Labridae. Our time-calibrated phylogenetic analysis of exon-capture data pushes the root node age of the family Labridae back into the Cretaceous to about 79 Ma years ago. The monotypic Centrogenys vaigiensis, and the order Uranoscopiformes (stargazers) are identified as the sister lineages of Labridae. The phylogenetic relationships among major labrid subfamilies and within these clades was largely congruent with prior analyses of select mitochondrial and nuclear datasets. However, the position of the tribe Cirrhilabrini (fairy and flame wrasses) showed discordance, resolving either as the sister to a crown julidine clade or alternatively sister to a group formed by the labrines, cheilines and scarines. Exploration of this pattern using multiple approaches leads to slightly higher support for this latter hypothesis, highlighting the importance of genome-level data sets for resolving short internodes at key phylogenetic positions in large, economically important groups of coral reef fishes.</p>
Meta-analysis of diurnal transcriptomics reveals strong patterns of concordance and discordance in mouse liver: processed data
<p>The accumulation of public transcriptomic timeseries data enables robust meta-analyses that were not possible until recently. To assess the consistency of biological rhythms across studies, 43 public mouse liver tissue timeseries totaling 805 RNA-seq samples were obtained and analyzed. Only the control groups of each study were included, to create comparable data. Technical factors in RNA-seq library preparation were the largest contributors to transcriptome-level differences, beyond biological or experiment-specific factors such as lighting conditions. Core clock genes were remarkably consistent in phase across all studies, while phase distributions of other periodic genes were generally less consistent. Overlap of genes identified as rhythmic across studies was generally low, with around 50% between some of the highest sample count studies. Distributions of phases of significant genes were remarkably inconsistent across studies, but genes consistently identified as rhythmic clustered near ZT0 and ZT12 in acrophase. Data was integrated across studies in a JIVE analysis, which showed that the top two components of joint within-study variation are determined by time of day. A shape-invariant model with random effects was fit to the genes to identify the underlying shape of the rhythms, consistent across all studies. This revealed the extent of asymmetric and multimodal genes.<br> <br> This supplemental file provides preprocessed RNA-seq quantifications of all reviewed datasets, as well as results of multiple analyses.</p>
Single-cell and single-nucleus RNA-sequencing from paired normal-adenocarcinoma lung samples provides both common and discordant biological insights
<p>The datasets generated by <em>Cellranger </em>for all 24 samples (.h5 format).<br><br></p>
STRATIFICATION EFFECTS ON FLOW HYDRODYNAMICS AND MIXING AT A CONFLUENCE WITH A HIGHLY DISCORDANT BED AND A RELATIVELY LOW VELOCITY RATIO
<p>The effects of temperature induced stratification on flow hydrodynamics, thermal mixing and the capacity of the flow to entrain sediment at a medium-size stream confluence with a highly discordant bed are investigated. To isolate the effects due to differences in the temperature/density of the incoming streams, two simulations were conducted with identical flow conditions (mean velocity ratio VR=2.44, temperature difference between the two streams ΔT=4.7<sup>0 </sup>C). In the first case the Richardson number was Ri=0 (no coupling between the temperature and the momentum equations via the Boussinesq approximation), while in the second simulation Ri=0.67. Even in the Ri=0 case the structure of the mixing interface (MI) was different from the one expected for concordant bed confluences with a similar confluence angle and VR. The MI contained only co-rotating eddies shed in the shear layer forming on the fast speed side of the confluence apex. In the Ri = 0.67 case no wake region was present but a large recirculation eddy formed not far from the confluence apex. In both cases, the flow near the upstream part of the MI was found to be highly 3D and to allow the passage of particles from one side of the confluence to the other. While in the Ri = 0 case mixing was driven by the MI eddies, in the Ri = 0.67 case mixing was controlled by large near-bed intrusions of heavier fluid from the tributary containing colder water and also by the fluid advected in and out of the recirculation eddy.</p>
Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids
<p>Supplementary Material accompanying the manuscript titled "Anchored phylogenomics unravels the evolution of spider flies (Acroceridae) and reveals discordance between nucleotides and amino acids", including Supplementary Figures, Tables and Datasets.</p>
Data from: Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies
<p>Rapidly evolving taxa are excellent models for understanding the mechanisms that give rise to biodiversity. However, developing an accurate historical framework for comparative analysis of such lineages remains a challenge due to ubiquitous incomplete lineage sorting and introgression. Here, we use a whole-genome alignment, multiple locus-sampling strategies, and locus-based and SNP-based species-tree methods to infer a species tree for eastern North American <em>Neodiprion</em> species, a clade of pine-feeding sawflies (Order: Hymenopteran; Family: Diprionidae). We recovered a well-supported species tree that—except for three uncertain relationships—is robust to different strategies for analyzing whole-genome data. Despite this consistency, underlying gene-tree discordance is high. To understand this discordance, we use multiple regression to model topological discordance as a function of several genomic features. We find that gene-tree discordance tends to be higher in regions of the genome that may be more prone to gene-tree estimation error, as indicated by a lower density of parsimony-informative sites, a higher density of genes, a higher average pairwise genetic distance, and gene trees with lower average bootstrap support. Also, contrary to the expectation that discordance via incomplete lineage sorting is reduced in low-recombination regions of the genome, we find a <em>negative</em> correlation between recombination rate and topological discordance. We offer potential explanations for this pattern and hypothesize that it may be unique to lineages that have diverged with gene flow. Our analysis also reveals an unexpected discordance hotspot on Chromosome 1, which contains several genes potentially involved in mitochondrial-nuclear interactions and produces a gene-tree that resembles a highly discordant mitochondrial tree. Based on these observations, we hypothesize that our genome-wide scan for topological discordance has identified a nuclear locus involved in a mito-nuclear incompatibility. Together, these results demonstrate how phylogenomic analysis coupled with high-quality, annotated genomes can generate novel hypotheses about the mechanisms that drive divergence and produce variable genealogical histories across genomes.</p>
Data for: Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance
<p>Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic dataset of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a small set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms.</p>
Gene tree discord, simplex plots, and statistical tests under the coalescent
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Data from: Discordant patterns of genetic and phenotypic differentiation in five grasshopper species co-distributed across a microreserve network
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Data for: Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance
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Concordance and discordance in the phylogenomics of the wrasses and parrotfishes (Teleostei: Labridae)
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Data from: Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies
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Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes
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Discordant population structure among rhizobium divided genomes and their legume hosts
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.