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188 results for “time evolution”
Figure 4 in Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies
Figure 4. Phylogenetic relationships among major lineages of the lower Brachycera inferred from the AP12R dataset. Numbers close to the branching points are Bayesian posterior probabilities expressed as percentages. Relevant taxonomic groups and branches have been separated by different colours.
Figure 3 in Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies
Figure 3. Comparison of non-synonymous substitution rate (Ka; for detailed data, see Supporting Information, Table S7). Overall data, including all sampled species, are shown, with infraorder, superfamily or family membership as indicated.
Figure 4. Time-calibrated phylogeny from BEAST2 in Origin and evolution of the Haustoriidae (Amphipoda): a eulogy for the Haustoriidira
Figure 4. Time-calibrated phylogeny from BEAST2. Green diamonds represent calibration points: 1, closure of the Okefenokee Trough (1.75 Mya); 2, proposed migration to Europe by H. arenarius (~5 Mya); 3, Pontocaspian gammarid clade radiation (9–83 Mya); 4,Niphargidae–Pseudoniphargidae split (38–215 Mya); 5, Crangonyctidae-Pseudocrangonyctidae split (38–215 Mya).
Deep-time structural evolution of retroviral and filoviral surface envelope proteins
<p>The retroviral surface envelope protein subunit (SU) mediates receptor binding and triggers membrane fusion by the transmembrane (TM) subunit. SU evolves rapidly under strong selective conditions, resulting in seemingly unrelated SU structures in highly divergent retroviruses. Structural modeling of the SUs of several retroviruses and related endogenous retroviral elements with AlphaFold 2 identifies a TM-proximal SU β-sandwich structure that has been conserved in the orthoretroviruses for at least 110 million years. The SU of orthoretroviruses diversified by the differential expansion of the β-sandwich core to form domains involved in virus-host interactions. The β-sandwich domain is also conserved in the SU equivalent GP1 of Ebola virus although with a significantly different orientation in the trimeric envelope protein structure relative to the β-sandwich of human immunodeficiency virus type 1 gp120, with significant evidence for divergent rather than convergent evolution. The unified structural view of orthoretroviral SU and filoviral GP1 identifies an ancient, structurally conserved, and evolvable domain underlying the structural diversity of orthoretroviral SU and filoviral GP1.</p>
Study on the Evolution Characteristics of the Return Stroke Spectra and Channel Temperatures by Using Two Spectrographs with Different Time Resolution
<p>Temperature is one of the crucial parameters reflecting the energy and current transfer characteristics in the lightning discharge channel. According to the spectra of six lightning return strokes recorded simultaneously by two high-speed slit-less spectrographs with different time resolutions, the spectral intensity and temperature evolution of the return stroke channels over time was quantitatively analyzed. The spectral characteristics show that the ionic line intensity decayed rapidly with time as the current declined, while the atomic line intensity decreased more slowly. Additionally, it is found that ionic lines existed in the spectra of continuing current process for up to hundreds of microseconds. It further indicates that the ionic line intensities are associated with the discharge currents and that their radiation mechanism is closely related to the collision excitation under the action of strong currents. The temperature calculated by the ionic lines can reflect the thermodynamic properties of the current-carrying channel. The temperature calculated using atomic lines is significantly lower than that calculated by the ionic lines in the same spectrum. The radiation mechanism for majority of the atomic lines differs from that of the ionic lines. During the continuing current, the channel temperatures calculated by both ionic lines and atomic lines showed a similar evolution feature which declined slowly or even basically unchanged. This property reflects the persistent heating effect of the current.</p>
Phylogenomics resolves timing and patterns in the evolution of Australasian Cerambycinae (Coleoptera: Cerambycidae), and reveals new insights into the subfamily-level classification and historical biogeography of longhorn beetles
<p><span><span><span><span>Cerambycinae is the second-largest subfamily of longhorn beetles in the Southern Hemisphere. The phylogeny of Cerambycinae is poorly known, resulting in a highly artificial tribal-level classification and a largely speculative evolutionary history. We reconstructed the phylogenetic relationships of Cerambycinae at the generic level using anchored hybrid enrichment data from hundreds of nuclear genes, with a primary focus on the extraordinarily diverse faunas of Australia and New Zealand. We also estimated divergence times by incorporating fossil calibrations in our analyses. We identified two main clades within Cerambycinae, which can also be separated morphologically by a distinct type of antennal foramen. We recovered a Late Jurassic origin of crown Cerambycinae. Dorcasominae, which was newly found to have representatives in Australia, was notably derived from within Cerambycinae. We recovered two independent origins of Australian Cerambycinae: one clade originated in the Early Cretaceous and is likely endemic to the Southern Hemisphere, while the other clade appears to have immigrated to Australia, perhaps from the Northern Hemisphere. Within the Australian lineages were multiple independent origins of New Zealand taxa, all of which are relative host-plant generalists. Tribal relationships and assignments are discussed and, based on our results, the following major nomenclatural acts were made: Dorcasominae Lacordaire, 1868, is downgraded to a tribe Dorcasomini of Cerambycinae Latreille, 1804; Neostenini Lacordaire, 1868 syn. nov. is treated as a junior synonym of Uracanthini Blanchard, 1851.</span></span></span></span></p>
Evolutionary tracks accompanying Stellar Evolution in Real Time II (1/4)
<p>Evolutionary tracks generated with MESA accompanying the project ``Stellar Evolution in Real Time II: R Hydrae and an Open-Source Grid of >3000 Seismic TP-AGB Models Computed with MESA'' ApJ, 2024</p> <p>Due to data volume, this is one of four Zenodo repositories associated to this project. The full list of related dataset DOIs is:</p> <ul> <li>https://doi.org/10.5281/zenodo.11280179</li> <li>https://doi.org/10.5281/zenodo.11282597</li> <li>https://doi.org/10.5281/zenodo.11353933</li> <li>https://doi.org/10.5281/zenodo.11357395</li> </ul> <p><strong>Details on archive files:</strong></p> <p>All phase 1 and phase 2 evolutionary tracks are contained in the files</p> <p>ZAMS_to_TCHeB_y-fixed.tar.gz<br>TCHeB_to_AGB_y-fixed.tar.gz<br>ZAMS_to_TCHeB_y-varied.tar.gz<br>TCHeB_to_AGB_y-varied.tar.gz</p> <p>sorted by whether a varied or static helium assumption was used.</p> <p>To use the smallest number of separate Zenodo listings possible, not all data are grouped in the same way.</p> <p>The tar.gz archive files labeled with a string of the form "AGB_to_end_M1.XX_y-fixed.tar.gz" include all models having a mass beginning with 1 (1.00, 1.10, 1.20, etc) and adopting the fixed helium assumption.</p> <p>Archive files labeled in the form "AGB_to_end_M1.XX_y-varied.tar.gz" include the same, but using the helium-varied assumption. </p> <p>Archive files labeled with a string of the form "AGB_to_end_M3.10_all.tar.gz" include both the fixed-helium and varied-helium tracks for all masses that start with 3 (3.00, 3.10, 3.20, etc).</p> <p> </p> <p><strong>Details on files unpacked from archives:</strong></p> <div>Every unpacked file has a name of the form </div> <div> </div> <div>history_m4.90_z0.0060_y0.261_eta0.01_yi-on_seismic_p3.data</div> <div> </div> <div>Anything that starts with "history" and ends with ".data" is an evolutionary track. Tracks that have "_p3" are the third phase: AGB to end (or failure of the model) and these files are large.</div> <div> </div> <div>Tracks that have "_p1" are the evolution from the zero-age main sequence (ZAMS) to the terminal age core helium burning (TCHeB). Tracks that have "_p2" evolve from TACHeB to the onset of the asymptotic giant branch (AGB).<br><br>In the file name, the two-decimal number after m, four-decimal number after z and 3-decimal number after y encode the evolutionary track's initial mass, initial metallicity (Z) and initial helium abundance (Y), respectively. In cases where there is no y value provided, the helium abundance is fixed as described in the paper. </div> <div> </div> <div>When the file name contains "yi-on" in the name, it means the helium-varied assumption was used. When the file contains "seismic" (should only be the case for p3's), it means the GYRE calculations are included in the output. </div>
Evolutionary tracks accompanying Stellar Evolution in Real Time II (4/4)
<p>Evolutionary tracks generated with MESA accompanying the project <br>``Stellar Evolution in Real Time II: R Hydrae and an Open-Source Grid of >3000 Seismic TP-AGB Models Computed with MESA'' ApJ 2024</p> <div> <div> <div> <p>Due to data volume, this is one of four Zenodo repositories associated to this project. The full list of related dataset DOIs is:</p> <ul> <li>https://doi.org/10.5281/zenodo.11280179</li> <li>https://doi.org/10.5281/zenodo.11282597</li> <li>https://doi.org/10.5281/zenodo.11353933</li> <li>https://doi.org/10.5281/zenodo.11357395</li> </ul> <p><strong>Details on archive files:</strong></p> <p>All phase 1 and phase 2 evolutionary tracks are contained in the files</p> <p>ZAMS_to_TCHeB_y-fixed.tar.gz<br>TCHeB_to_AGB_y-fixed.tar.gz<br>ZAMS_to_TCHeB_y-varied.tar.gz<br>TCHeB_to_AGB_y-varied.tar.gz</p> <p>sorted by whether a varied or static helium assumption was used.</p> <p>To use the smallest number of separate Zenodo listings possible, not all data are grouped in the same way.</p> <p>The tar.gz archive files labeled with a string of the form "AGB_to_end_M1.XX_y-fixed.tar.gz" include all models having a mass beginning with 1 (1.00, 1.10, 1.20, etc) and adopting the fixed helium assumption.</p> <p>Archive files labeled in the form "AGB_to_end_M1.XX_y-varied.tar.gz" include the same, but using the helium-varied assumption. </p> <p>Archive files labeled with a string of the form "AGB_to_end_M3.10_all.tar.gz" include both the fixed-helium and varied-helium tracks for all masses that start with 3 (3.00, 3.10, 3.20, etc).</p> <p> </p> <p><strong>Details on files unpacked from archives:</strong></p> <div>Every unpacked file has a name of the form </div> <div> </div> <div>history_m4.90_z0.0060_y0.261_eta0.01_yi-on_seismic_p3.data</div> <div> </div> <div>Anything that starts with "history" and ends with ".data" is an evolutionary track. Tracks that have "_p3" are the third phase: AGB to end (or failure of the model) and these files are large.</div> <div> </div> <div>Tracks that have "_p1" are the evolution from the zero-age main sequence (ZAMS) to the terminal age core helium burning (TCHeB). Tracks that have "_p2" evolve from TACHeB to the onset of the asymptotic giant branch (AGB).<br><br>In the file name, the two-decimal number after m, four-decimal number after z and 3-decimal number after y encode the evolutionary track's initial mass, initial metallicity (Z) and initial helium abundance (Y), respectively. In cases where there is no y value provided, the helium abundance is fixed as described in the paper. </div> <div> </div> <div>When the file name contains "yi-on" in the name, it means the helium-varied assumption was used. When the file contains "seismic" (should only be the case for p3's), it means the GYRE calculations are included in the output. </div> </div> <p> </p> </div> <p> </p> </div>
Evolutionary tracks accompanying Stellar Evolution in Real Time II (3/4)
<p>Evolutionary tracks generated with MESA accompanying the project <br>``Stellar Evolution in Real Time II: R Hydrae and an Open-Source Grid of >3000 Seismic TP-AGB Models Computed with MESA'' ApJ 2024</p> <div> <div> <p>Due to data volume, this is one of four Zenodo repositories associated to this project. The full list of related dataset DOIs is:</p> <ul> <li>https://doi.org/10.5281/zenodo.11280179</li> <li>https://doi.org/10.5281/zenodo.11282597</li> <li>https://doi.org/10.5281/zenodo.11353933</li> <li>https://doi.org/10.5281/zenodo.11357395</li> </ul> <p><strong>Details on archive files:</strong></p> <p>All phase 1 and phase 2 evolutionary tracks are contained in the files</p> <p>ZAMS_to_TCHeB_y-fixed.tar.gz<br>TCHeB_to_AGB_y-fixed.tar.gz<br>ZAMS_to_TCHeB_y-varied.tar.gz<br>TCHeB_to_AGB_y-varied.tar.gz</p> <p>sorted by whether a varied or static helium assumption was used.</p> <p>To use the smallest number of separate Zenodo listings possible, not all data are grouped in the same way.</p> <p>The tar.gz archive files labeled with a string of the form "AGB_to_end_M1.XX_y-fixed.tar.gz" include all models having a mass beginning with 1 (1.00, 1.10, 1.20, etc) and adopting the fixed helium assumption.</p> <p>Archive files labeled in the form "AGB_to_end_M1.XX_y-varied.tar.gz" include the same, but using the helium-varied assumption. </p> <p>Archive files labeled with a string of the form "AGB_to_end_M3.10_all.tar.gz" include both the fixed-helium and varied-helium tracks for all masses that start with 3 (3.00, 3.10, 3.20, etc).</p> <p> </p> <p><strong>Details on files unpacked from archives:</strong></p> <div>Every unpacked file has a name of the form </div> <div> </div> <div>history_m4.90_z0.0060_y0.261_eta0.01_yi-on_seismic_p3.data</div> <div> </div> <div>Anything that starts with "history" and ends with ".data" is an evolutionary track. Tracks that have "_p3" are the third phase: AGB to end (or failure of the model) and these files are large.</div> <div> </div> <div>Tracks that have "_p1" are the evolution from the zero-age main sequence (ZAMS) to the terminal age core helium burning (TCHeB). Tracks that have "_p2" evolve from TACHeB to the onset of the asymptotic giant branch (AGB).<br><br>In the file name, the two-decimal number after m, four-decimal number after z and 3-decimal number after y encode the evolutionary track's initial mass, initial metallicity (Z) and initial helium abundance (Y), respectively. In cases where there is no y value provided, the helium abundance is fixed as described in the paper. </div> <div> </div> <div>When the file name contains "yi-on" in the name, it means the helium-varied assumption was used. When the file contains "seismic" (should only be the case for p3's), it means the GYRE calculations are included in the output. </div> </div> <p> </p> </div>
Evolutionary tracks accompanying Stellar Evolution in Real Time II (2/4)
<p>Evolutionary tracks generated with MESA accompanying the project <br>``Stellar Evolution in Real Time II: R Hydrae and an Open-Source Grid of >3000 Seismic TP-AGB Models Computed with MESA'' ApJ 2024</p> <div> <p>Due to data volume, this is one of four Zenodo repositories associated to this project. The full list of related dataset DOIs is:</p> <ul> <li>https://doi.org/10.5281/zenodo.11280179</li> <li>https://doi.org/10.5281/zenodo.11282597</li> <li>https://doi.org/10.5281/zenodo.11353933</li> <li>https://doi.org/10.5281/zenodo.11357395</li> </ul> <p><strong>Details on archive files:</strong></p> <p>All phase 1 and phase 2 evolutionary tracks are contained in the files</p> <p>ZAMS_to_TCHeB_y-fixed.tar.gz<br>TCHeB_to_AGB_y-fixed.tar.gz<br>ZAMS_to_TCHeB_y-varied.tar.gz<br>TCHeB_to_AGB_y-varied.tar.gz</p> <p>sorted by whether a varied or static helium assumption was used.</p> <p>To use the smallest number of separate Zenodo listings possible, not all data are grouped in the same way.</p> <p>The tar.gz archive files labeled with a string of the form "AGB_to_end_M1.XX_y-fixed.tar.gz" include all models having a mass beginning with 1 (1.00, 1.10, 1.20, etc) and adopting the fixed helium assumption.</p> <p>Archive files labeled in the form "AGB_to_end_M1.XX_y-varied.tar.gz" include the same, but using the helium-varied assumption. </p> <p>Archive files labeled with a string of the form "AGB_to_end_M3.10_all.tar.gz" include both the fixed-helium and varied-helium tracks for all masses that start with 3 (3.00, 3.10, 3.20, etc).</p> <p> </p> <p><strong>Details on files unpacked from archives:</strong></p> <div>Every unpacked file has a name of the form </div> <div> </div> <div>history_m4.90_z0.0060_y0.261_eta0.01_yi-on_seismic_p3.data</div> <div> </div> <div>Anything that starts with "history" and ends with ".data" is an evolutionary track. Tracks that have "_p3" are the third phase: AGB to end (or failure of the model) and these files are large.</div> <div> </div> <div>Tracks that have "_p1" are the evolution from the zero-age main sequence (ZAMS) to the terminal age core helium burning (TCHeB). Tracks that have "_p2" evolve from TACHeB to the onset of the asymptotic giant branch (AGB).<br><br>In the file name, the two-decimal number after m, four-decimal number after z and 3-decimal number after y encode the evolutionary track's initial mass, initial metallicity (Z) and initial helium abundance (Y), respectively. In cases where there is no y value provided, the helium abundance is fixed as described in the paper. </div> <div> </div> <div>When the file name contains "yi-on" in the name, it means the helium-varied assumption was used. When the file contains "seismic" (should only be the case for p3's), it means the GYRE calculations are included in the output. </div> </div>
Dataset for time evolution of classical contact process with 100 sites
Open the record for dataset details and reuse information.
Supplemental Online Material for "Comparing the Effects of Euclidean Distance Matching and Dynamic Time Warping in the Clustering of COVID-19 Evolution": Interactive Figures
<p>This repository contains the interactive figures accompanying the manuscript "<em>Comparing the Effects of Euclidean Distance Matching and Dynamic Time Warping in the Clustering of COVID-19 Evolution</em>". These interactive visualizations provide a dynamic exploration of some of the data and results discussed in the paper. The following interactive figures are included:</p> <ul> <li><code>Figure-1.html</code>: Interactive version of Figure 1 from the paper, showing a time series heatmap of the 14-day simple moving average of reported COVID-19 cases for each of Europe's 298 NUTS 2 regions, from 02/10/2020 - 07/12/2020.</li> <li><code>Figure-2.html</code>: Interactive version of Figure 2, which visualizes two heatmap dendrograms showcasing the pairwise distance matrices and hierarchical clustering results for (a) the Euclidean distance and (b) the Dynamic Time Warping distance.</li> <li><code>cluster_maps.html</code>: Interactive cluster maps, allowing for detailed exploration of the clusters discussed in the paper. Users can select between different distance metrics (Euclidean or Dynamic Time Warping) and adjust the number of clusters to visualize, providing greater flexibility in exploring the clustering patterns. This figure is not included as a static figure in the paper but is provided merely as supplemental online material.</li> </ul> <p>These interactive figures are best viewed using a modern web browser (e.g., Chrome, Firefox ...). For all visualizations, upon hovering over the figure, a label appears displaying the NUTS 2 region and the country it is in, providing additional geographic context.</p>
Data from: Including fossils in phylogenetic climate reconstructions: a deep time perspective on the climatic niche evolution and diversification of spiny lizards (Sceloporus)
Fossils and other paleontological information can improve phylogenetic comparative method estimates of phenotypic evolution and generate hypotheses related to species diversification. Here, we use fossil information to calibrate ancestral reconstructions of suitable climate for Sceloporus lizards in North America. Integrating data from the fossil record, general circulation models of paleoclimate during the Miocene, climate envelope modeling, and phylogenetic comparative methods provides a geographically and temporally explicit species distribution model of Sceloporus-suitable habitat through time. We provide evidence to support the historic biogeographic hypothesis of Sceloporus diversification in warm North American deserts and suggest a relatively recent Sceloporus invasion into Mexico around 6 Ma. We use a physiological model to map extinction risk. We suggest that the number of hours of restriction to a thermal refuge limited Sceloporus from inhabiting Mexico until the climate cooled enough to provide suitable habitat at approximately 6 Ma. If the future climate returns to the hotter climates of the past, Mexico, the place of highest modern Sceloporus richness, will no longer provide suitable habitats for Sceloporus to survive and reproduce.
Data from: Clock gene evolution: seasonal timing, phylogenetic signal, or functional constraint?
Genetic determinants of seasonal reproduction are not fully understood, but may be important predictors of organism responses to climate change. We used a comparative approach to study the evolution of seasonal timing within a fish community in a natural common garden setting. We tested the hypothesis that allelic length variation in the PolyQ domain of a circadian rhythm gene, Clock1a, corresponded to interspecific differences in seasonal reproductive timing across five native and one introduced cyprinid fishes (n = 425 individuals) that co-occur in the Rio Grande, New Mexico, USA. Most common allele lengths were longer in native species that initiated reproduction earlier (Spearman's r = -0.70, p = 0.23). Clock1a allele length exhibited strong phylogenetic signal and earlier spawners were evolutionarily derived. Aside from length variation in Clock1a, all other amino acids were identical across native species, suggesting functional constraint over evolutionary time. Interestingly, the endangered Rio Grande silvery minnow (Hybognathus amarus) exhibited less allelic variation in Clock1a and observed heterozygosity was 2- to 6-fold lower than the five other (non-imperiled) species. Reduced genetic variation in this functionally important gene may impede this species' capacity to respond to ongoing environmental change.
Data for: Sex-specific ornament evolution is a consistent feature of climatic adaptation across space and time in dragonflies
<p><span>Adaptation to different climates fuels the origins and maintenance of biodiversity. Detailing how organisms optimize fitness for their local climate is therefore an essential goal in biology. Although we increasingly understand how survival-related traits evolve as organisms adapt to climatic conditions, it is unclear if organisms also optimize traits that coordinate </span><span><span>mating</span></span><span> between the sexes. Here, we show that dragonflies consistently adapt to warmer climates across space and time by evolving less male melanin ornamentation—a mating-related trait that also absorbs solar radiation and heats individuals above ambient temperatures. Continent-wide macroevolutionary analyses reveal that species inhabiting warmer climates evolve less male ornamentation. Community-science observations across ten species indicate that populations adapt to warmer parts of species' ranges </span><span><span>through microevolution of</span></span><span> smaller male ornaments. Observations from 2005-2019 detail that contemporary selective pressures oppose male ornaments in warmer years; and our climate-warming projections predict further decreases by 2070. Conversely, our analyses show that female ornamentation responds idiosyncratically to temperature across space and time, indicating the sexes evolve in different ways to meet the demands of the local climate. Overall, these macro- and microevolutionary findings demonstrate that organisms predictably optimize their mating-related traits for the climate just as they do their survival-related traits.</span></p>
Data from: Alteration of (frequency-dependent) fitness in time-shift experiments reveals cryptic co-evolution and uncoordinated stasis in a virtual Jurassic Park
Digital evolution is a computer-based instantiation of Darwinian evolution in which short self-replicating computer programs compete, mutate, and evolve. It is an excellent experimental platform for addressing topics in both short-term and long-term evolution, such as whether co-evolving multispecies communities are dominated more by biotic or abiotic factors, and whether evolutionary stasis affects performance as well as ecological profile. We evolved model communities with ecological interdependence among community members, which were subjected to two principal types of mass extinction: a pulse extinction that killed randomly, and a selective press extinction involving an alteration of the abiotic environment to which the communities had to adapt. These treatments were applied at two different strengths (Strong and Weak), along with unperturbed Control experiments. We performed several kinds of competition experiments using simplified versions of these communities to see whether long-term stability that was implied previously by ecological and phylogenetic metrics was also reflected in terms of performance, i.e. whether fitness was static over long periods of time. Results from Control and Weak treatment communities revealed almost completely transitive evolution, while Strong treatment communities showed higher incidences of intransitivity, with pre-treatment ecotypes often able to displace some of their post-recovery successors. However, pre-treatment carryovers more often had lower fitness in mixed communities than in their own fully native conditions. Replacement and invasion experiments pitting single ecotypes against pre-treatment reference communities showed that many of the invading ecotypes could measurably alter the fitnesses of one or more residents, usually with depressive effects, and that the strength of these effects increased over time even in the most stable communities. However, invaders taken from Strong treatment communities often had little to no effect on resident performance. While we detected periods of time when the fitness of a particular evolving ecotype remained static, this stasis was not permanent and was uncoordinated, never affecting an entire community at once. Our results lend support to the fitness-deterioration interpretation of the Red Queen hypothesis, and highlight community context-dependence in determining fitness, the shaping of communities by both biotic factors and abiotic forcing, and the illusory nature of evolutionary stasis. Our results also demonstrate the potential of digital evolution studies to illuminate many aspects of evolution in interacting multispecies communities.
Modeling pulsed evolution and time-independent variation improves the confidence level of ancestral and hidden state predictions
<p><span><span><span><span><span><span><span><span><span><span>Ancestral state reconstruction is not only a fundamental tool for studying trait evolution, but also very useful for predicting the unknown trait values (hidden states) of extant species. A well-known problem in ancestral and hidden state predictions is that the uncertainty associated with predictions can be so large that predictions themselves are of little use. Therefore, for meaningful interpretation of predicted traits and hypothesis testing, it is prudent to accurately assess the uncertainty of the predictions. Commonly used constant-rate Brownian motion (BM) model fails to capture the complexity of tempo and mode of trait evolution in nature, making predictions under the BM model vulnerable to lack-of-fit errors from model misspecification. Using empirical data (mammalian body size and bacterial genome size), we show that the distribution of residual Z-scores under the BM model is neither homoscedastic nor normal as expected. Consequently, the 95% confidence intervals (CIs) of predicted traits are so unreliable that the actual coverage probability ranges from 33% (strongly permissive) to 100% (strongly conservative). Alternative methods such as BayesTraits and StableTraits that allow variable rates in evolution improve the predictions but are computationally expensive. Here we develop RasperGade, a method of ancestral and hidden state prediction that uses the Levy process to explicitly model gradual evolution, pulsed evolution and time-independent variation. Using the same empirical data, we show that RasperGade outperforms both BayesTraits and StableTraits and is orders-of-magnitude faster. Our results suggest that, when predicting the ancestral and hidden states of continuous traits, the tempo and mode of evolution should always be assessed and the quality of confidence estimates should always be examined.</span></span></span></span></span></span></span></span></span></span></p>
Effects of a Manual Therapy Program to Reduce the Evolution Time of Axillary Web Syndrome
ClinicalTrials.gov study NCT05115799. IPD Sharing: YES. Countries: 1. Publications: 32.
Canadian Study of Prediction of Risk and Evolution to Dialysis, Death and Interim Cardiovascular Events Over Time
ClinicalTrials.gov study NCT00826319. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Contemporary evolution of sea urchin gamete-recognition proteins: experimental evidence of density-dependent gamete performance predicts shifts in allele frequencies over time
Open the record for dataset details and reuse information.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.