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167 results for “Sequence Evolution”
Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes
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Deep sequencing datasets from: RNA-catalyzed evolution of catalytic RNA
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Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
<p>As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suit of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study we show that asymmetric rates of sequence evolution rates lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.</p>
VFTS meeting: animation of main-sequence model evolution
<p>This animation shows the evolution of our binary and single stellar models from 2Myr to 100Myr. We populate 3763 binaries, whose primary mass is in the range of 3Msun to 100Msun, following a Salpeter IMF with an exponent of -2.37. The mass ratio is uniformly distributed from 0.1 to 1. The orbital period logP is uniformly distributed from the minimum value at which the two stars would contact initially to 3.5. Both components rotate at half of their critical velocities initially. </p> <p>Considering a binary fraction of 70%, we populate 1612 single stars with vi=0.5. In addition, we also populate 537 slowly-rotating single stars with vi=0.2 to reproduce the observed blue MS in young star clusters. The number is chosen such that the ratio between the slow and fast rotators is 1/3, which is the same as the ratio of observed blue and red MS stars. </p> <p>Gravity darkening and observational errors are included. Filled circles correspond to single stellar models, while open symbols correspond to binaries with different companions. Single stellar tracks with vi=0.5 are plotted with solid grey lines. The black dotted line represents the ZAMS line of vi=0.2 single stellar models. In the legend, the number in each group outside the parenthesis corresponds to the number of stars whose color and magnitude are in the figure range. While the number in the parenthesis corresponds to the number of stars above the orange dashed line, which is 1.75 mag below the turn-off magnitude. </p>
Supplementary datasets for: Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution
<p>Microalgae are integral primary producers for global ecosystems whose genomes can be mined for ecological insights, but representative genome sequences are lacking for many phyla. We cultured and sequenced 107 microalgae species from 11 different phyla indigenous to varied geographies and climates. This genome collection was used to resolve genomic differences between saltwater and freshwater microalgae. Freshwater species showed domain-centric ontology enrichment for nuclear and nuclear membrane functions, while saltwater species were enriched in organellar and cellular membrane functions. Marine species contained significantly more viral families in their genomes (<span>p-value = 8 x 10(-4))</span>. Viral sequences were identified from Chlorovirus, Coccolithovirus, Pandoravirus, Marseillevirus, Tupanvirus, and others integrated into algal genomes. Algal, viral-origin sequences were found to be expressed and to code for a wide variety of functions. Our results clarify the poorly characterized occurrences of viral elements in algal genomes and define a unified adaptive strategy for algal halotolerance.</p>
A codon model for associating phenotypic traits with altered selective patterns of sequence evolution
<p>Detecting the signature of selection in coding sequences and associating it with shifts in phenotypic states can unveil genes underlying complex traits. Of the various signatures of selection exhibited at the molecular level, changes in the pattern of selection at protein coding genes have been of main interest. To this end, phylogenetic branch-site codon models are routinely applied to detect changes in selective patterns along specific branches of the phylogeny. Many of these methods rely on a pre-specified partition of the phylogeny to branch categories, thus treating the course of trait evolution as fully resolved and assuming that phenotypic transitions have occurred only at speciation events. Here we present TraitRELAX, a new phylogenetic model that alleviates these strong assumptions by explicitly accounting for the uncertainty in the evolution of both trait and coding sequences. This joint statistical framework enables the detection of changes in selection intensity upon repeated trait transitions. We evaluated the performance of TraitRELAX using simulations and then applied it to two case studies. Using TraitRELAX, we found an intensification of selection in the primate SEMG2 gene in polygynandrous species compared to species of other mating forms, as well as changes in the intensity of purifying selection operating on sixteen bacterial genes upon transitioning from a free-living to an endosymbiotic lifestyle.</p>
Data for "Shear Strain Evolution Spanning the 2020 Mw6.8 Elazığ and 2023 Mw7.8/Mw7.6 Kahramanmaraş Earthquake Sequence along the East Anatolian Fault Zone" manuscript
<p>Data necessary to support the analysis presented in "Shear Strain Evolution Spanning the 2020 Mw6.8 Elazığ and 2023 Mw7.8/Mw7.6 Kahramanmaraş Earthquake Sequence along the East Anatolian Fault Zone" manuscript</p>
Metamorphic evolution of the Greater Himalayan Sequence, Bhagirathi Valley (India) through a combination of channel flow and in-sequence shearing
<p>Dataset of a manuscript entitled "Metamorphic evolution of the Greater Himalayan Sequence, Bhagirathi Valley (India) through a combination of channel flow and in-sequence shearing " submitted in Tectonics (AGU)</p>
Supplementary Materials from the article Characterization and molecular evolution analysis of Periploca forrestii inferred from its complete chloroplast genome sequence
<p>Table S1. Base composition of chloroplast genome in <em>P. forrestii</em>, Table S2. The lengths of introns and exons for the splitting genes, Table S3. The GC content of the codons from <em>P. forrestii </em>chloroplast genome, Table S4. Preferred codons in chloroplast genome of <em>P. forrestii</em>, Table S5. Long repeat sequences in the <em>P. forrestii </em>chloroplast genome, Figure S1. Codon bias analysis of P. forrestii chloroplast genome. (A) Neutrality plot analysis; (B) Analysis of PR2 bias plot; (C) Analysis on ENC and GC3 relationship.</p>
Evolution models of helium white dwarf-main-sequence star merger remnants: the mass distribution of single low-mass white dwarfs
<p>Inlists and data for "<a href="https://ui.adsabs.harvard.edu/#abs/2018MNRAS.474..427Z/abstract">Evolution models of helium white dwarf-main-sequence star merger remnants: the mass distribution of single low-mass white dwarfs</a>"</p>
Sanger sequencing traces experimental evolution rVSV-SADS
<p>A recombinant vesicular stomatitis virus (VSV) expressing the spike glycoprotein of swine accute diarrhea syndrome virus (SADS) (rVSV-SADS) was serially passaged in three human cell lines (Huh-7, H23, OVCAR-8). The wild-type (WT), initial virus (P0) and final viruses at passage 10 (P10) were sequenced using Sanger sequencing. The seuquence traces are attached.</p>
Supplementary Data for: Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani
<p>Supplementary Data for: Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani</p> <p>This repository contains:</p> <p>SNP call data / VCF file</p> <p>Scripts for all processing steps from mapping up to PCA and phylogenetic analyses (script.ts)<br> Scripts for population genomic analyses with LEA and PopGenome (scripts.SE)<br> All script names are self explanatory.</p>
Stress Drop Catalog for "Spatio-temporal evolution of earthquake static stress drop values in the 2016-2017 Central Italy seismic sequence" - Kemna et al. 2021 JGR - Solid Earth
<p>Catalog with stress drop estimates for "Spatio-temporal evolution of earthquake static stress drop values in the 2016-2017 Central Italy seismic sequence"</p> <p>Kemna et al., 2021, JGR: Solid-Earth, https://doi.org/10.1029/2021JB022566.</p> <p>Description of columns:</p> <p><strong>Earthquake information</strong></p> <ul> <li>ID - INGV Earthquake ID</li> <li>Latitude - Latitude in Degrees</li> <li>Longitude - Longitude in Degrees</li> <li>Depth - Depth in km</li> <li>Magnitude_INGV - Magnitude reported by INGV</li> <li>Origin_UTC - UTC Origin Time in ISO Format</li> <li>Catalog - Catalog source of specific event. See section 2.1 for details</li> <li>Profile_distance_norcia - Distance of earthquake from Norcia Mainshock location projected onto a NW-SE trending line</li> <li>Dayafter_20160101 - Day after start of catalog in float</li> </ul> <p><strong>Single spectra fitting estimates</strong></p> <ul> <li>mw_s_mean - Moment Magnitude averaged over station estimates</li> <li>mw_s_err - 95% error (from delete-one jackknife-mean)</li> <li>m0_s_mean - Seismic Moment in Nm averaged over station estimates</li> <li>m0_s_err - 95 % error(from delete-one jackknife-mean)</li> <li>fc_s_sssa_mean - Corner frequency estimate averaged over station estimates</li> <li>fc_s_sssa_err - 95 % error(from delete-one jackknife-mean)</li> <li>strdrop_s_sssa_mean - Stress drop estimate averaged over station estimates</li> <li>strdrop_s_sssa_err - 95 % error(from delete-one jackknife-mean)</li> <li>sample_size_s_sssa - Number of stations with an estimate</li> <li>azimuthal_gap_s_sssa - Maximum azimuthal gap</li> <li>alpha_vel - P-wave velocity in m/s at Hypocenter</li> <li>beta_vel - S-wave velocity in m/s at Hypocenter</li> </ul> <p><strong>Cluster-event method estimates</strong></p> <ul> <li>fc_s_cema_mean - Corner frequency estimated averaged over clusters</li> <li>fc_s_cema_err - 95 % error(from delete-one jackknife-mean)</li> <li>strdrop_s_cema_mean - Stress drop estimate using Magnitude estimate from single spectra fitting</li> <li>strdrop_s_cema_err - 95 % error</li> </ul> <p><strong>Spectral Ratio fitting estimates</strong></p> <ul> <li>fc1_s_rsta_mean - Target event corner frequency estimate using automatic source spectra fitting averaged over eGfs</li> <li>fc1_s_rsta_err - 95 % error(from delete-one jackknife-mean)</li> <li>strdrop_s_rsta_mean - Stress drop estimate using Magnitude estimate from single spectra fitting</li> <li>strdrop_s_rsta_err - 95 % error</li> <li>egf_number_rsta_s - Number of eGfs for each target event</li> <li>fc1_s_rrta_mean - Target event corner frequency estimate using semi-automatic spectral ratiofitting averaged over eGfs</li> <li>fc1_strdrop_s_rrta_mean - Stress drop estimate using Magnitude estimate from single spectra fitting</li> <li>fc2_s_rrea_mean - eGf event corner frequency estimate using semi-automatic spectral ratiofitting averaged over eGfs</li> <li>fc2_strdrop_s_rrea_mean - Stress drop estimate using Magnitude estimate from single spectra fitting</li> </ul> <p><strong>Magnitude-normalized stress drop</strong></p> <ul> <li>prio_strdrop_s - Which type of estimate is used</li> <li>magbin_s - Magnitude bin to which event is associated</li> <li>prio_strdrop_s_magbinmean - Stress drop mean for specific magnitude bin</li> <li>prio_strdrop_s_magbinstderr - 95 % error(from delete-one jackknife-mean)</li> <li>prio_strdrop_s_magnitude-normalized - Magnitude-normalized stress drop estimate</li> </ul>
Deep sequencing datasets from: Witnessing the structural evolution of an RNA enzyme
<p>An RNA polymerase ribozyme that has been the subject of extensive directed evolution efforts has attained the ability to synthesize complex functional RNAs, including a full-length copy of its own evolutionary ancestor. During the course of evolution, the catalytic core of the ribozyme has undergone a major structural rearrangement, resulting in a novel tertiary structural element that lies in close proximity to the active site. Through a combination of site-directed mutagenesis, structural probing, and deep sequencing analysis, the trajectory of evolution was seen to involve the progressive stabilization of the new structure, which provides the basis for improved catalytic activity of the ribozyme. Multiple paths to the new structure were explored by the evolving population, converging upon a common solution. Tertiary structural remodeling of RNA is known to occur in nature, as evidenced by the phylogenetic analysis of extant organisms, but this type of structural innovation had not previously been observed in an experimental setting. Despite prior speculation that the catalytic core of the ribozyme had become trapped in a narrow local fitness optimum, the evolving population has broken through to a new fitness locale, raising the possibility that further improvement of polymerase activity may be achievable.</p> <p> </p>
Perianth evolution and implications for generic delimitation in the Eucalypts (Myrtaceae): DNA sequences, morphological data
<p><em>Eucalyptus</em> was traditionally defined by the operculate perianth—hence the generic name (Latin, meaning "well-covered"). But after previous phylogenetic analysis placed <em>Angophora</em>, which has free sepals and petals, as sister to the bloodwood eucalypts, the latter were segregated into a new genus, <em>Corymbia</em>. We made a targeted capture of 101 low-copy nuclear exons from 392 samples representing 329 species-level taxa. The phylogeny was estimated using maximum likelihood (IQtree and RAxML) and the multi-species coalescent (Astral). We tested alternative relationships between four genera within Eucalypteae (<em>Arillastrum</em>, <em>Angophora</em>, <em>Eucalyptus</em>, <em>Corymbia</em>) at each of two nodes critical to generic delimitation using Shimodaira's Approximately Unbiased (AU) test. Monophyly of <em>Arillastrum</em> + (<em>Corymbia</em> + <em>Angophora</em>) relative to <em>Eucalyptus</em> sensu stricto was supported whereas monophyly of <em>Corymbia</em> relative to <em>Angophora</em> was decisively rejected. These results indicate that either <em>Eucalyptus</em> should be expanded to include all four genera or <em>Corymbia</em> should be split into two. All of the alternative relationships among the four currently recognised genera imply homoplasy in perianth evolution, specifically with respect to origins of the bud cap (operculum or calyptra), which has been traditionally used to define <em>Eucalyptus</em>. Inferred evolutionary transitions in perianth traits are generally congruent with divergences between major clades with a single exception: expression of separate sepals and petals in <em>Angophora</em>, which is nested within the operculate genus <em>Corymbia</em>, appears prima facie to be a reversal to the plesiomorphic perianth structure. Strictly, this is not a reversal because the petals of <em>Angophora</em> and <em>Corymbia</em> have a novel compound keel-and-limb structure that is absent in the outgroups. This structure is evident in early development, irrespective of whether the petals remain free or later become part of an operculum. Many of the currently recognised infrageneric taxa down to sectional level (and below in some cases) are well-supported by the sequence data and definable by morphological traits. Inclusion of <em>Angophora</em> within <em>Eucalyptus</em> was formally proposed two decades ago but did not gain acceptance. Here instead, we formally raise <em>Corymbia</em> subg. <em>Blakella</em> to genus rank and make the relevant new combinations.</p>
Study of Ibrutinib in Patients With Symptomatic, Previously Untreated Waldenstrom's Macroglobulinemia, and Impact on Tumor Genomic Evolution Using Whole Genome Sequencing
ClinicalTrials.gov study NCT02604511. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
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Perianth evolution and implications for generic delimitation in the Eucalypts (Myrtaceae): DNA sequences, morphological data
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Supplementary datasets for: Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution
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Data from: Genomic sequence capture of haemosporidian parasites: methods and prospects for enhanced study of host-parasite evolution
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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.