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97 results for “genomic heterogeneity”
Data from: geo-genomic predictors of genetree heterogeneity explain phylogeographic and introgression history: a case study in an Amazonian bird (Thamnophilus aethiops)
<p>Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the biogeographic history of four populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 kya, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered two primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence, and was recovered for the Z chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length, and found that smaller chromosomes experienced higher gene flow. Given that (1) gene-trees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future biogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate biogeographic mechanisms of biotic diversification.</p>
Complementary genomic and epigenomic adaptation to environmental heterogeneity
<p><span>While adaptation is commonly thought to result from selection on DNA sequence-based variation, recent studies have highlighted an analogous epigenetic component as well. However, the relative roles of these mechanisms in facilitating population persistence under environmental heterogeneity remain unclear. To address the underlying genetic and epigenetic mechanisms and their relationship during environmental adaptation, we screened the genomes and epigenomes of nine global populations of a predominately sessile marine invasive tunicate, <em>Botryllus schlosseri</em>. We detected clear population differentiation at the genetic and epigenetic levels. Patterns of genetic and epigenetic structure were significantly influenced by local environmental variables. Among these variables, minimum annual sea surface temperature was simultaneously identified as the top explanatory variable for both genetic and epigenetic variation. However, patterns of population structure driven by genetic and epigenetic variation were somewhat distinct, suggesting possible autonomy of epigenetic variation. We found both shared and specific genes and biological pathways among genetic and epigenetic loci</span><span> associated with environmental factors</span><span>, consistent with complementary and independent contributions of genetic and epigenetic variation to environmental adaptation in this system. Collectively, these mechanisms may facilitate population persistence under environmental change and sustain successful invasions across novel environments.</span></p>
Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability
<p>"Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability", F. Raynaud, M. Mina, D. Tavernari and G. Ciriello</p> <p>These files are necessary to generate the supplementary table containing:</p> <p>#Sample_name #Cancer_type #Cancer_subtype #Mean_reads_per_mutations #Number_of_mutations #Number_of_altered_segments #Number_of_clones #TreeScore #Number_of_mutations_first_clone #Number_of_mutations_other_clones</p> <p>REQUIREMENTS</p> <p>Phylogenies generated by PhyloWGS (PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors](<a href="http://genomebiology.com/2015/16/1/35">http://genomebiology.com/2015/16/1/35</a>), Deshwar et al.)</p> <p>Output files from PhyloWGS for each sample:</p> <ul> <li> <p>top_k_trees which contains the best phylogenies (50 by default) with the label of each clone, the population frequency of each clone, the number of children of each clone, number of mutations in the clone, the labels of the mutations</p> </li> <li> <p>top_k_trees1, top_k_trees2, ... , top_k_treesN output file for the best k trees (50 by default)</p> </li> </ul> <p>FILES</p> <p>*Molecular data for the tumor types: CESC, UCEC, UVM, THCA, KICH, BRCA, SKCM, ACC, CRC, STAD, BLCA, LUAD, KIRP, PRAD, LIHC; has been collected in July 2015 *Molecular data for the tumor types: SARC, PAAD, MESO, LGG, GBM, DLBC, UCS, THYM, TGCT, PCPG, OV, LUSC, LAML, KIRC, HNSC, ESCA, CHOL; has been collected in 2018</p> <p>from the FireHose (<a href="https://gdac.broadinstitute.org/">https://gdac.broadinstitute.org/</a>) and cBioPortal (Cerami et al., 2012) (<a href="http://www.cbioportal.org/">http://www.cbioportal.org/</a>) data repositories for The Cancer Genome Atlas (TCGA). Only TCGA datasets publicly available at that time were used in our study.</p> <p>-Mutation files (MAF format): combined_2015_2018_MAF.maf.bz2</p> <p>-Copy number segmentation files: combined_seg_2015_2018.seg.bz2</p> <p>-analyze_public.py: Python file to generate the Supplementary Table run: python2.7 analyze_public.py</p> <p>- All input data and results from PhyloWGS: PhyloWGS_input_output.tar.bz2 </p>
Prostate Cancer Genomic Heterogeneity
ClinicalTrials.gov study NCT02022371. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus); a dietary-specialist species distributed across heterogeneous environments
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Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments
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Data from: Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin
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Complementary genomic and epigenomic adaptation to environmental heterogeneity
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Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales)
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Data from: Heterogeneous genomic differentiation in marine threespine sticklebacks: adaptation along an environmental gradient
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Data from: Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia: genomic heterogeneity and temporal stability
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Data from: The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: threespine sticklebacks in divergent environments
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A population-genomic approach for estimating selection on polygenic traits in heterogeneous environments
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Data from: On the roles of landscape heterogeneity and environmental variation in determining population genomic structure in a dendritic system
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Data from: geo-genomic predictors of genetree heterogeneity explain phylogeographic and introgression history: a case study in an Amazonian bird (Thamnophilus aethiops)
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Data from: Sun skink landscape genomics: assessing how microevolutionary processes shape genetic and phenotypic diversity across a heterogeneous and fragmented landscape
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Data from: Demographic history and genomic diversity and divergence in blue tit populations across heterogeneous environments
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Data from: Genome-wide association analysis for blood lipid traits measured in three pig populations revealed a substantial level of genetic heterogeneity
Serum lipids are associated with myocardial infarction and cardiovascular disease in humans. Here we dissected the genetic architecture of blood lipid traits by applying genome-wide association studies (GWAS) in 1,256 pigs from Laiwu, Erhualian and Duroc × (Landrace × Yorkshire) populations, and a meta-analysis of GWAS in more than 2,400 pigs from five diverse populations. A total of 22 genomic loci surpassing the suggestive significance level were detected on 11 pig chromosomes (SSC) for six blood lipid traits. Meta-analysis of GWAS identified 5 novel loci associated with blood lipid traits. Comparison of GWAS loci across the tested populations revealed a substantial level of genetic heterogeneity for porcine blood lipid levels. We further evaluated the causality of nine polymorphisms nearby or within the APOB gene on SSC3 for serum LDL-C and TC levels. Of the 9 polymorphisms, an indel showed the most significant association with LDL-C and TC in Laiwu pigs. But the significant association was not identified in the White Duroc × Erhualian F2 resource population, in which the QTL for LDL-C and TC was also detected on SSC3. This indicates that population-specific signals may exist for the SSC3 QTL. Further investigations are warranted to validate this assumption.
Data from: Genomic heterogeneity of historical gene flow between two species of newts inferred from transcriptome data
The role of gene flow in species formation is a major unresolved issue in speciation biology. Progress in this area requires information on the long-term patterns of gene flow between diverging species. Here, we used thousands of single-nucleotide polymorphisms derived from transcriptome resequencing and a method modeling the joint frequency spectrum of these polymorphisms to reconstruct patterns of historical gene flow between two Lissotriton newts: L. vulgaris (Lv) and L. montandoni (Lm). We tested several models of divergence including complete isolation and various scenarios of historical gene flow. The model of secondary contact received the highest support. According to this model, the species split from their common ancestor ca. 5.5 million years (MY) ago, evolved in isolation for ca. 2 MY, and have been exchanging genes for the last 3.5 MY Demographic changes have been inferred in both species, with the current effective population size of ca. 0.7 million in Lv and 0.2 million in Lm. The postdivergence gene flow resulted in two-directional introgression which affected the genomes of both species, but was more pronounced from Lv to Lm. Interestingly, we found evidence for genomic heterogeneity of interspecific gene flow. This study demonstrates the complexity of long-term gene flow between distinct but incompletely reproductively isolated taxa which divergence was initiated millions of years ago.
Data from: Ribosomal DNA sequence heterogeneity reflects intra-species phylogenies and predicts genome structure in two contrasting yeast species
The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the ITS region, frequently used in plant phylogenetics, is now recognised as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analysed datasets from the Saccharomyces Genome Resequencing Project, characterising rDNA sequence variation within multiple strains of the baker's yeast <i>Saccharomyces cerevisiae</i> and its nearest wild relative <i>Saccharomyces paradoxus</i> in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterisation of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intra-species phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridisation events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multi-locus rDNA systems.
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.