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285 results for “evolution models”
Figure 7 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 7. The relative force output at the upper canine [(I(Tf(cos Q))/Oca) where I, inlever moment arm; Tf, theoretical force output from the muscle fibre; Q, angle between the effective (rotational) torque about the temporomandibular joint and T; O, outlever moment arm to the centre of C1] at gape angles from occlusion to maximal inferred gape in: A, deep f ca masseter + zygomaticomandibularis fibre 1; B, deep masseter + zygomaticomandibularis fibre 2; C, deep masseter + zygomaticomandibularis fibre 3; D, deep masseter + zygomaticomandibularis fibre 4; E, deep masseter + zygomaticomandibularis fibre 5; F, superficial masseter. Negative values imply that an adductor has shifted to becoming an abductor at this gape angle.
Figure 3 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 3. The angle (Q) between the effective (rotational) torque about the temporomandibular joint (Te) and the theoretical force output from the muscle fibre (Tf) at gape angles from occlusion to maximal inferred gape in: A, deep masseter + zygomaticomandibularis fibre 1; B, deep masseter + zygomaticomandibularis fibre 2; C, deep masseter + zygomaticomandibularis fibre 3; D, deep masseter + zygomaticomandibularis fibre 4; E, deep masseter + zygomaticomandibularis fibre 5; F, superficial masseter.
Figure 2 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 2. The angle (Q) between the effective (rotational) torque about the temporomandibular joint (Te) and the theoretical force output from the muscle fibre (Tf) at gape angles from occlusion to maximal inferred gape in: A, temporalis fibre 1; B, temporalis fibre 3; C, temporalis fibre 5; D, temporalis fibre 7; E, temporalis fibre 8; F, temporalis fibre 10.
Figure 5 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 5. The relative ability of individual muscle fibres to generate rotational torque about the temporomandibular joint (TMJ) [effective (rotational) torque about the TMJ divided by the theoretical force output from the muscle fibre (Te/Tf)] at gape angles from occlusion to maximal inferred gape in: A, deep masseter + zygomaticomandibularis fibre 1; B, deep masseter + zygomaticomandibularis fibre 2; C, deep masseter + zygomaticomandibularis fibre 3; D, deep masseter + zygomaticomandibularis fibre 4; E, deep masseter + zygomaticomandibularis fibre 5; F, superficial masseter.
Figure 4 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 4. The relative ability of individual muscle fibres to generate rotational torque about the temporomandibular joint (TMJ) [effective (rotational) torque about the TMJ divided by the theoretical force output from the muscle fibre (Te/Tf)] at gape angles from occlusion to maximal inferred gape in: A, temporalis fibre 1; B, temporalis fibre 3; C, temporalis fibre 5; D, temporalis fibre 7; E, temporalis fibre 8; F, temporalis fibre 10.
Figure 6 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 6. The relative force output at the upper canine [(I(Tf(cos Q))/Oca) where I, inlever moment arm; Tf, theoretical force output from the muscle fibre; Q, angle between the effective (rotational) torque about the temporomandibular joint and T; O, outlever moment arm to the centre of C1] at gape angles from occlusion to maximal inferred gape in: A, f ca temporalis fibre 1; B, temporalis fibre 3; C, temporalis fibre 5; D, temporalis fibre 7; E, temporalis fibre 8; F, temporalis fibre 10. Negative values imply that an adductor has shifted to becoming an abductor at this gape angle.
Figure 1 in A dynamic model for the evolution of sabrecat predatory bite mechanics
Figure 1. The ability of the mandibular adductors to generate torque about the temporomandibular joint (TMJ) was estimated at ten regularly spaced intervals of the M. temporalis (T1–T10); at five regularly spaced intervals of the M. masseter profunda + M. zygomaticomandibularis (M1–M5); and the anterior-most insertion of the M. masseter superficialis. A, lion (Panthera leo; CN3503; ♂), with mandible at occlusion and at estimated maximal gape, illustrating torque about the TMJ at T1 (green vectors); B, Smilodon fatalis [LACMHC2001-173 (cranium) and LACMHC2001-4543 (mandible)] with mandible at occlusion and at estimated maximal gape, illustrating torque about the TMJ at M2 (blue vectors), and at SM (red vectors). Abbreviations: Im, inlever moment arm for masseter muscle fibre torque about the TMJ; I, inlever moment arm for temporalis muscle fibre torque about the TMJ; O, outlever moment arm to the carnassial (P4) t c paracone apex; O, outlever moment arm to the centre of C1; T, effective (rotational) torque about the TMJ; T, theoretical ca e f force output from the muscle fibre; Q, angle between Te and Tf. Scale bars = 10 cm.
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>
Fitting and evaluating univariate and multivariate models of within-lineage evolution
<p><span>The nature of phenotypic evolution within lineages is central to many unresolved questions in paleontology and evolutionary biology. Analyses of evolutionary time-series of ancestor-descendant populations in the fossil record are likely to make important contributions to many of these debates. However, the limited number of models that have been applied to these types of data may restrict our ability to interpret phenotypic evolution in the fossil record. </span>Using uni- and multivariate models of trait evolution <span>that make different assumptions regarding</span> <span>the </span>dynamic<span>s of the</span> adaptive landscape, I evaluate contrasting hypotheses to explain evolution of size in the radiolarian <em><span>Eucyrtidium calvertense</span></em> and armor in the stickleback <em>Gaserosteus doryssus</em>. Body size evolution in <span><em>E. calvertense</em> </span><span>is best explained by a model where the lineage evolves as a consequence of a shift in the adaptive landscape that coincides with the initiation of neosympatry with its sister lineage. Multivariate evolution of armor traits in a stickleback lineage (<em>Gasterosteus</em> <em>doryssus</em>) shows evidence of adaptation towards independent optima on the adaptive landscape at the same time as traits change in a correlated fashion. The fitted models are available in an R package evoTS, which builds on the commonly used paleoTS framework.</span></p>
Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution
<p>The archives uploaded here include the code used to perform the evolutionary simulations as described in <em>Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution </em>authors: Martin,R. Tate, A. as well as the data that was used in the generation of the figures for that paper. Code requires the Julia programming language and necessary packages to run.</p>
Numerical results data of 'Impact of Injection Pressure and Polyaxial Stress on Hydraulic Fracture Propagation and Permeability Evolution in Greywacke: Insights from Discrete Element Models of a Laboratory Test'
<p>Numerical results data of '<strong>Impact of Injection Pressure and Polyaxial Stress on Hydraulic Fracture Propagation and Permeability Evolution in Greywacke: Insights from Discrete Element Models of a Laboratory Test</strong>'</p>
Model aversiveness and the evolution of imperfect Batesian mimics
<p>There are numerous examples in the natural world of Batesian mimics that only imperfectly resemble their models. Given that inaccurate mimics are known to be predated more frequently than accurate ones, imperfect mimicry therefore poses something of a conundrum. One putative explanation, the relaxed selection hypothesis, predicts that when the cost of attacking a model is high relative to the benefit of consuming a mimic, selection against imperfect mimics will be relaxed, allowing mimics to be more imperfect for a given level of fitness. However, empirical support for this hypothesis is equivocal. Here we report an experimental test of the relaxed selection hypothesis, in which human participants were tasked with discriminating between artificial stimuli representing models and mimics. In response to 'attacking' a model (i.e., misclassifying it as palatable, or non-aversive) they received either a mild electric shock (high cost) or vibratory feedback (low cost). Consistent with the predictions of this hypothesis, we found that when the cost of attacking a model was high, mimetic phenotype could deviate more from the model (i.e., be more imperfect) for a given level of fitness than when the cost of attacking a model was low. Moreover, when the cost of attacking a model was high, participants showed an increased latency to attack. This finding shows that given sufficient costs, the relaxed selection hypothesis is a plausible explanation for the evolution of imperfect mimicry within certain ecological contexts.</p>
Data from: Exploring the possible role of hybridization in the evolution of photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4 photosynthesis evolution
<p><em>Flaveria</em> (Asteraceae) is the prime model for the study of C<sub>4</sub> photosynthesis evolution and seems to support a stepwise acquisition of the pathway through C<sub>3</sub>-C<sub>4</sub> intermediate phenotypes, still existing in <em>Flaveria</em> today. Molecular phylogenies of <em>Flaveria</em> based on concatenated data matrices are currently used to reconstruct the complex sequence of trait shifts during C<sub>4</sub> evolution. To assess the possible role of hybridization in C<sub>4</sub> evolution in <em>Flaveria</em>, we re-analyzed transcriptome data of 17 <em>Flaveria</em> species to infer the extent of gene tree discordance and possible reticulation events. We found massive gene tree discordance as well as reticulation along the backbone and within clades containing C<sub>3</sub>-C<sub>4</sub> intermediate and C<sub>4</sub>-like species. An early hybridization event between two C<sub>3</sub> species might have triggered C<sub>4 </sub>evolution in the genus. The clade containing all C<sub>4</sub> species plus the C<sub>4</sub>-like species F. vaginata and<em> F. palmeri </em>is highly supported in our phylogenetic analyses, but it might be of hybrid origin involving <em>F. angustifolia</em> and<em> F. sonorensis</em> (both C<sub>3</sub>-C<sub>4</sub> intermediate) as parental lineages. Hybridization seems to be a driver of C<sub>4</sub> evolution in<em> Flaveria</em> and likely promoted the fast acquisition of C<sub>4</sub> traits. This new insight can be used in further exploring C<sub>4</sub> evolution and can inform C<sub>4</sub> bioengineering efforts.</p>
"Predictive Models of the Morphological Evolution of the Human Body to Improve Adherence and Motivation in Dietetic-nutritional Treatments of Overweight and Obesity" [Modelos Predictivos de Evolución
ClinicalTrials.gov study NCT07205029. IPD Sharing: NO. Countries: 1. Publications: 6.
Data from: A test of the "flexible stem" model of evolution: ancestral plasticity, genetic accommodation, and morphological divergence in the threespine stickleback radiation
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Data from: A two-state model of tree evolution and its applications to alu retrotransposition
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Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments
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Data from: Deep learning on butterfly phenotypes tests evolution’s oldest mathematical model
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Data from: Epistatic contributions promote the unification of incompatible models of neutral molecular evolution
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Data from: Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system
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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.