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244 results for “coalescence”
Contrasting the depths of divergence between gene-tree and coalescent estimates in the North American Racers (Colubridae: Coluber constrictor)
<p>The North American racers (<em>Coluber constrictor</em>) are widely distributed across the Nearctic and numerous studies have demonstrated extensive variation in morphology, ecology, and population genetic structure. Here we take an integrative approach to understand lineage diversification within this taxon by combining genomic sequence capture data, mtDNA sequence data, morphometrics, and ecological niche models. Both the genomic data and mtDNA phylogeographic analyses support five lineages distributed across the range of this species. However, demographic model selection based on these two datasets strongly conflict in both the model of divergence and estimates of timing of lineage divergence. While mtDNA and concatenated genomic data suggest a Miocene origin of these distinct groups, coalescent-based demographic models of sequence capture data suggest lineage diversification occurred at ~33 kya in allopatry without gene flow. Using linear morphological measurements of head shape we demonstrate that lineages distributed largely east and west of the Mississippi River are distinguishable. Furthermore, ecological niche modelling demonstrates that lineages distributed in subtropical habitats have environmental niche space that is significantly differentiated from lineages distributed across the continent. Taken together, these results suggest that ecology is an important axis of lineage divergence within this group and that more fine-scale analyses may find even greater differentiation across the populations identified here.</p>
Observation of Gravitational Waves from the Coalescence of a 2.5-4.5 Msun Compact Object and a Neutron Star --- Data Release
<p>This data release contains the analysis results and data behind the figures of the GW230529 discovery paper (<a href="https://urldefense.com/v3/__https://dcc.ligo.org/LIGO-P2300352/public/__;!!Dq0X2DkFhyF93HkjWTBQKhk!W4i4x3JfGgemcFsnnEYP5qxiknddvrG1LWpTLjs_JGK907kTrEBkS8o6i5T6RUFMX0v04jCPhtTq9K2SLcv_4g$" target="_blank" rel="nofollow noreferrer noopener">https://dcc.ligo.org/LIGO-P2300352/public/</a>). Strain data for this event (the L1:GDS-CALIB_STRAIN_CLEAN_AR channel) can be downloaded on GWOSC (<a href="https://doi.org/10.7935/6k89-7q62" target="_blank" rel="noopener">https://doi.org/10.7935/6k89-7q62</a>).</p> <p>The PESummary metafile containing the parameter estimation posterior samples for all analyses performed in the paper (<strong>posterior_samples.h5</strong>) and skymap fits file (<strong>skymap_combined_PHM_high_spin.fits</strong>) for the preferred parameter estimation analysis (high-spin, combined samples using binary black hole waveforms) can be downloaded directly as individual files.</p> <p>The other analysis results are grouped by type: rates, populations, searches, and tidal. The <strong>figure_scripts.tar.gz</strong> file contains all the paper figures in jpeg format along with a Jupyter notebook to reproduce them and additional required helper scripts. Example code for working with the individual result files is given in the <strong>PaperPlots.ipynb</strong> notebook included in this tar file.</p> <p>In brief, the <strong>rates.tar.gz</strong> file contains two files that each include a subset of the rates probability distributions shown in Fig. 3 of the paper. The <strong>populations.tar.gz</strong> file contains all the data behind Figs. 4-8, with subdirectories for each of the three population analyses considered in the paper: Binned Gaussian Process, NSBH-pop, and Power-Law + Dip + Break. In addition to the data behind the figures, the Power-Law + Dip + Break subdirectory additionally includes two *result.json files for the hyper-parameter posterior samples. These files have the same format as the corresponding NSBH-pop *result.json files and can be manipulated in the same way, as shown in the figures notebook.</p> <p>The <strong>searches.tar.gz</strong> file contains the data behind Figs. 9-11 for each of the three search pipelines whose results are included in the paper. Finally, the <strong>tidal.tar.gz</strong> file contains the four probability distributions plotted in Fig. 14. All other figures are produced only using the posterior_samples.h5 file.</p>
SINGER-inferred targets for exceptional population differentiation in coalescence times in African populations in 1000 Genomes Project
<p>This repo saves the gene targets which shows the signal of population differentiation in coalescence times in African populations in 1000 Genomes Project. </p> <p>Here are the detailed explanations for the header of the files:</p> <p>chrom The chromosome where the genomic window is located (e.g., chr1, chrX).<br>window_start The 0-based start position of the genomic window being analyzed.<br>window_end The 1-based end position of the genomic window (exclusive).<br>score Ratio between the overall diversity and the population specific diversity, in the genomic window.<br>transcript_chrom The chromosome where the transcript is located.<br>transcript_start The 0-based start position of the transcript.<br>transcript_end The 1-based end position of the transcript (exclusive).<br>transcript_id The unique identifier for the transcript (e.g., Ensembl or RefSeq ID).<br>strand The strand of the transcript: "+" for forward, "-" for reverse.<br>coding_start The start position of the coding region of the transcript (if applicable).<br>coding_end The end position of the coding region of the transcript (if applicable).<br>RGB The RGB color used for visualization in genome browsers (format: R,G,B).<br>block_count The number of exons in the transcript.<br>block_sizes Comma-separated list of exon lengths (in base pairs).<br>block_starts Comma-separated list of exon start positions relative to transcript_start.</p>
Supplementary material for: Impact of ghost introgression on coalescent-based species tree inference and estimation of divergence time
<p><span>The species studied in any evolutionary investigation generally constitute a small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has rarely been studied and is poorly understood. Here, we use mathematical analysis and simulations to examine the robustness of species tree methods based on the multispecies coalescent model to introgression from a ghost or extant lineage. We found that many results originally obtained for introgression between extant species can easily be extended to ghost introgression, such as the strongly interactive effects of incomplete lineage sorting (ILS) and introgression on the occurrence of anomalous gene trees (AGTs). The relative performance of the summary species tree method (ASTRAL) and the full-likelihood method (*BEAST) varies under different introgression scenarios, with the former being more robust to gene flow between non-sister species whereas the latter performing better under certain conditions of ghost introgression. When an outgroup ghost (defined as a lineage that diverged before the most basal species under investigation) acts as the donor of the introgressed genes, the time of root divergence among the investigated species generally was overestimated, whereas ingroup introgression, as commonly perceived, can only lead to underestimation. In many cases of ingroup introgression that may or may not involve ghost lineages, the stronger the ILS, the higher the accuracy achieved in estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.</span></p>
Formation pathway of Population III coalescing binary black holes through stable mass transfer
<p>MESA inlists associated with <a href="https://ui.adsabs.harvard.edu/?#abs/2017MNRAS.468.5020I">Inayoshi et al. (2017)</a>. MESA version 8845.</p> <p>Publication DOI: <a href="https://doi.org/10.1093/mnras/stx757">10.1093/mnras/stx757</a></p>
The spin of the second-born black hole in coalescing binary black holes
<p>MESA inlists associated with <a href="https://ui.adsabs.harvard.edu/#abs/2018A&A...616A..28Q/abstract">The spin of the second-born black hole in coalescing binary black holes</a></p>
Shock induced Fe0 globules in Chang'E-5 impact melt splash and implication for the coalescence growth of microphase Fe0 in lunar soil
<p>The dataset includes all raw data (Table 1 to Table 3, Table S1 to S8) for the manuscript "Shock induced Fe0 globules in Chang’E-5 impact melt splash and implication for the coalescence growth of microphase Fe0 in lunar soil".</p>
Simulation data for island coalescence
<p>Data from a VPIC simulation of magnetic island coalescence. </p> <p>Read "note.txt" for the details of the data. </p>
Data for the manuscript titled "Solute front shear and coalescence control concentration gradient dynamics in porous micromodel"
<p>Concentration images and data for plots for the manuscript "Solute front shear and coalescence control concentration gradient dynamics in porous micromodel" submitted for publication in Geophysical Research Letters.</p> <p>See the README file for explanations on the data file.</p> <p><strong>Movie captions:</strong></p> <p><strong>Movie S1:</strong> Concentration field for the Péclet Pe = 33 experiment. Solid pillars are represented by the gray discs, and the colormap corresponds to the rescaled concentration <span class="math-tex">\(c/c_\mathrm{max}\)</span>. The black line represents the solute front, which is the boundary of the continuous <span class="math-tex">\(c/c_\mathrm{max} < 0.5\)</span> region within the porous medium. The x- and y-coordinates of the porous medium length and width (respectively) are rescaled by the average pore diameter <span class="math-tex">\(\lambda\)</span>.</p> <p><strong>Movie S2:</strong> Concentration gradient field for the Pe = 33 experiment. Solid pillars are represented by the gray discs, and the colormap corresponds to the rescaled gradient <span class="math-tex">\( a \nabla c / c_\mathrm{max}\)</span>. The x- and y-coordinates of the porous medium length and width (respectively) are rescaled by the average pore diameter <span class="math-tex">\(\lambda\)</span>.</p> <p><strong>Movie S3:</strong> Concentration field for the Pe = 1104 experiment. Solid pillars are represented by the gray discs, and the colormap corresponds to the rescaled concentration <span class="math-tex">\(c/c_\mathrm{max}\)</span>. The black line represents the solute front, which is the boundary of the continuous <span class="math-tex">\(c/c_\mathrm{max} < 0.5\)</span> region within the porous medium. The x- and y-coordinates of the porous medium length and width (respectively) are rescaled by the average pore diameter <span class="math-tex">\(\lambda\)</span>.</p> <p><strong>Movie S4:</strong> Concentration gradients field for the Pe = 1104 experiment. Solid pillars are represented by the gray discs, and the colormap corresponds to the rescaled gradient <span class="math-tex">\( a \nabla c / c_\mathrm{max}\)</span>. The x- and y-coordinates of the porous medium length and width (respectively) are rescaled by the average pore diameter <span class="math-tex">\(\lambda\)</span>.</p>
Biotic and abiotic drivers of coalescence asymmetry between soil and manure microbiomes
<p>The dataset includes bacterial and fungal OTU tables for all soil and manure samples after 180 days incubation, bacterial and fungal OTU abundance tables, the data for variance partitioning analysis, and the phylogenetic trees for calculating MNTD.</p>
The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic
<p>A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019, with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489–422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.</p>
CARDIOMYOCYTE RYANODINE RECEPTOR CLUSTERS EXPAND AND COALESCE AFTER APPLICATION OF ISOPROTERENOL
<p>This is data that was used to generate the figures and tables for the Journal of General Physiology paper<br> CARDIOMYOCYTE RYANODINE RECEPTOR CLUSTERS EXPAND AND COALESCE AFTER APPLICATION OF ISOPROTERENOL</p> <p>The data is in two parts: i) Blink data that records the positions of blinks collected from fluorescently labelled ryanodine receptors on the surface of rat ventricular myocytes. ii) Cluster data that records parameters from each of the clusters created by the blink data. </p> <p>The blink data was used to generate Figs. 1 to 4, S3 to S5, while cluster data was used to generate the tables<br> and Figs. 5 to 9. More detailed explanations of the data are in the files blinkinfo.html and clustinfo.html in their respective<br> directories.</p>
Data from: Limitations of separate cloud and rain categories in parameterizing collision-coalescence for bulk microphysics schemes
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The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic
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Data from: Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent
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The power of coalescent methods for inferring recent and ancient gene flow in endangered Bactrian camels
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Hybrid zone analysis using coalescent-based estimates of introgression and migration in plateau fence lizards (Sceloporus tristichus)
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Bayesian inference under the multispecies coalescent with ancient DNA sequences
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Data for: Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo River
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Data from: The multilocus multispecies coalescent: a flexible new model of gene family evolution
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