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285 results for “evolution models”
Codes and model output supporting Analysis of the Evolution of Parametric Drivers of High-End Sea-Level Hazards
<p>Codes and model output supporting Analysis of the Evolution of Parametric Drivers of High-End Sea-Level Hazards (Advances in Statistical Climatology, Meteorology and Oceanography, May 2022)</p>
Data supporting 'Controls on Greenland moulin geometry and evolution from the Moulin Shape model'
<p>The data included here are MouSh model results generated as part of the following publication: Andrews, L. C., Poinar., K, Trunz, C. (2022). Controls on Greenland moulin geometry and evolution from the Moulin Shape model. The Cryosphere. </p> <p>Nearly all meltwater from glaciers and ice sheets is routed englacially through moulins. Therefore, the geometry and evolution of moulins has the potential to influence subglacial water pressure variations, ice motion, and the runoff hydrograph delivered to the ocean. We develop the Moulin Shape (MouSh) model, a time-evolving model of moulin geometry. MouSh models ice deformation around a moulin using both viscous and elastic rheologies and melting within the moulin through heat dissipation from turbulent water flow, both above and below the water line. We force MouSh with idealized and realistic surface melt inputs. Our results show that variations in surface melt change the geometry of a moulin by approximately 10% daily and over 100% seasonally. These size variations cause observable differences in moulin water storage capacity and moulin water levels compared to a static, cylindrical moulin. Our results suggest that moulins are storage reservoirs for meltwater, with storage capacity and water levels varying over multiple timescales. Representing moulin geometry within subglacial hydrologic models may therefore improve the representation of subglacial pressures, especially over seasonal periods or in regions where overburden pressures are high.</p> <p>These data are also accessible at: https://ubir.buffalo.edu/xmlui/handle/10477/82587</p> <p>The development of the MouSh model was funded by NASA Cryosphere grant 80NSSC19K0054 to Lauren Andrews and Kristin Poinar.</p>
The evolution, complexity and diversity of models of long-term forest dynamics
<p><span>1. To assess the impacts of climate change on vegetation from stand to global scales, models of forest dynamics that include tree demography are needed. Such models are now available for 50 years, but the currently existing diversity of model formulations and its evolution over time are poorly documented. This hampers systematic assessments of structural uncertainties in model-based studies.</span></p> <p><span>2. We conducted a meta-analysis of 28 models, focusing on models that were used in the past five years for climate change studies. We defined 52 model attributes in five groups (basic assumptions, growth, regeneration, mortality and soil moisture) and characterized each model according to these attributes. Analyses of model complexity and diversity included hierarchical cluster analysis and redundancy analysis.</span></p> <p><span>3. Model complexity evolved considerably over the past 50 years. Increases in complexity were largest for growth processes, while complexity of modelled establishment processes increased only moderately. Model diversity was lowest at the global scale, and highest at the landscape scale. We identified five distinct clusters of models, ranging from very simple models to models where specific attribute groups are rendered in a complex manner and models that feature high complexity across all attributes.</span></p> <p><span>4. Most models in use today are not balanced in the level of complexity with which they represent different processes. This is the result of different model purposes, but also reflects legacies in model code, modelers' preferences, and the 'prevailing spirit of the epoch'. The lack of firm theories, laws and 'first principles' in ecology provides high degrees of freedom in model development, but also results in high responsibilities for model developers and the need for rigorous model evaluation.</span></p> <p><span>5. Synthesis. The currently available model diversity is beneficial: convergence in simulations of structurally different models indicates robust projections, while convergence of similar models may convey a false sense of certainty. The existing model diversity – with the exception of global models – can be exploited for improved projections based on multiple models. We strongly recommend balanced further developments of forest models that should particularly focus on establishment and mortality processes, in order to provide robust information for decisions in ecosystem management and policymaking.</span></p>
Reproduction package for the paper "The effects of surface fossil magnetic fields on massive star evolution: IV. Grids of models at Solar, LMC, and SMC metallicities"
<p>This is a reproduction package for the paper "The effects of surface fossil magnetic fields on massive star evolution - IV. Grids of models at Solar, LMC, and SMC metallicities" by <a href="https://doi.org/10.1093/mnras/stac2598">Keszthelyi et al. (2022).</a></p>
Frontiers in Ecology and Evolution 01 frontiersin.org Why grazing and soil matter for dry grassland diversity: New insights from multigroup structural equation modeling of micro-patterns
<p>Grazing is recognized as a major process driving the composition of plant<br> communities in grasslands, mostly due to the heterogeneous removal of<br> plant species and soil compaction that results in a mosaic of small patches<br> called micro-patterns. To date, no study has investigated the differences in<br> composition and functioning among these micro-patterns in grasslands in<br> relation to grazing and soil environmental variables at the micro-local scale.<br> In this study, we ask (1) To what extent are micro-patterns different from each<br> other in terms of species composition, species richness, vegetation volume,<br> evenness, and functioning? and (2) based on multigroup structural equation<br> modeling, are those differences directly or indirectly driven by grazing and soil<br> characteristics? We focused on three micro-patterns of the Mediterranean dry<br> grassland of the Crau area, a protected area traditionally grazed in the South-<br> East of France. From 70 plant community relevés carried out in three micro-<br> patterns located in four sites with different soil and grazing characteristics,<br> we performed univariate, multivariate analyses and applied structural equation<br> modeling for the first time to this type of data. Our results show evidence<br> of clear differences among micro-pattern patches in terms of species<br> composition, vegetation volume, species richness, evenness, and functioning<br> at the micro-local scale. These differences are maintained not only by direct<br> and indirect effects of grazing but also by several soil variables such as fine<br> granulometry. Biological crusts appeared mostly driven by these soil variables,<br> whereas reference and edge communities are mostly the result of different<br> levels of grazing pressure revealing three distinct functioning specific to each<br> micro-pattern, all of them coexisting at the micro-local scale in the studied<br> Mediterranean dry grassland. This first overview of the multiple effects of<br> grazing and soil characteristics on communities in micro-patterns is discussed<br> within the scope of the conservation of dry grasslands plant diversity.</p>
Modelling the influence of parental effects on gene network evolution : Data and Program
<p>The C++ software "Simevolv" is a population genetics tool able to simulate the evolution of complex genetic architectures.</p> <p>This version is a development version from which the results of the manuscript "Modelling the influence of parental effects on gene network evolution" (in prep) have been obtained.</p> <p>The "Data" file corresponds to the simulation results used in the above mentioned article.</p>
Dartmouth stellar evolution models
<p>Dartmouth stellar evolution models 2012 version.</p> <p>HST_ACSWF.tgz<br> HST_WFPC2.tgz<br> PanSTARRS.tgz<br> SDSSugriz.tgz<br> UBVRIJHKsKp.tgz</p>
Data from: Stochastic character mapping, Bayesian model selection, and biosynthetic pathways shed new light on the evolution of habitat preference in cyanobacteria
<p>Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis paving the way for complex life. Studying the evolution and ecological niche of cyanobacteria and their ancestors is crucial for understanding the intricate dynamics of biosphere evolution. These organisms frequently deal with environmental stressors such as salinity and drought, and they employ compatible solutes as a mechanism to cope with these challenges. Compatible solutes are small molecules that help maintain cellular osmotic balance in high-salinity environments, such as marine waters. Their production plays a crucial role in salt tolerance, which, in turn, influences habitat preference. Among the five known compatible solutes produced by cyanobacteria (sucrose, trehalose, glucosylglycerol, glucosylglycerate, and glycine betaine), their synthesis varies between individual strains. In this study, we work in a Bayesian stochastic mapping framework, integrating multiple sources of information about compatible solute biosynthesis in order to predict the ancestral habitat preference of Cyanobacteria. Through extensive model selection analyses and statistical tests for correlation, we identify glucosylglycerol and glucosylglycerate as the most significantly correlated with habitat preference, while trehalose exhibits the weakest correlation. Additionally, glucosylglycerol, glucosylglycerate, and glycine betaine show high loss/gain rate ratios, indicating their potential role in adaptability, while sucrose and trehalose are less likely to be lost due to their additional cellular functions. Contrary to previous findings, our analyses predict that the last common ancestor of Cyanobacteria (living at around 3180 Ma) had a 97% probability of a high salinity habitat preference and was likely able to synthesize glucosylglycerol and glucosylglycerate. Nevertheless, cyanobacteria likely colonized low-salinity environments shortly after their origin, with an 89% probability of the first cyanobacterium with low-salinity habitat preference arising prior to the Great Oxygenation Event (2460 Ma). Stochastic mapping analyses provide evidence of cyanobacteria inhabiting early marine habitats, aiding in the interpretation of the geological record. Our age estimate of ~2590 Ma for the divergence of two major cyanobacterial clades (Macro- and Microcyanobacteria) suggests that these were likely significant contributors to primary productivity in marine habitats in the lead-up to the Great Oxygenation Event, and thus played a pivotal role in triggering the sudden increase in atmospheric oxygen.</p>
Data from: Fast mvSLOUCH: Multivariate Ornstein-Uhlenbeck-based models of trait evolution on large phylogenies
<p>The PCMBase R package is a powerful computational tool that enables efficient calculations of likelihoods for a wide range of phylogenetic Gaussian models. Taking advantage of it, we redesigned the R package mvSLOUCH. Here, we demonstrate how the new version of the package can be used to thoroughly examine the evolution and adaptation of traits in a large dataset of 1252 vascular plants through the use of multivariate Ornstein-Uhlenbeck processes. The results of our analysis demonstrate the ability of the modeling framework to distinguish between various alternative hypotheses regarding the evolution of functional traits in angiosperms.</p>
Data for lodubay/galactic-dtd: Multi-Zone Galactic Chemical Evolution Model Outputs and APOGEE Sample
<p>Data for <a href="github.com/lodubay/galactic-dtd">lodubay/galactic-dtd</a>, a project exploring different models for the Type Ia supernova delay-time distribution (DTD) in multi-zone galactic chemical evolution models with the <a href="github.com/giganano/VICE">VICE</a> package. This dataset contains two files: <code>multizone.tar.gz</code> is a compressed archive of all 33 multi-zone outputs (combinations of 8 DTDs x 4 star formation histories, plus one with an alternate stellar migration scheme), and <code>sample.csv</code> contains chemical abundance data from the <a href="https://www.sdss4.org/surveys/apogee/">APOGEE survey</a> (data release 17) and stellar ages from <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.tmp.1191L">Leung et al. (2023)</a>. This project is made reproducible with <code>showyourwork</code>, which will automatically download and extract all data from this deposit when it builds the article.</p> <p>This version contains a minor update to the APOGEE sample file.</p>
Meandering evolution and width variations: a physics-statistics based modeling approach
<p>Coordinates (x,y) of the central bank (field 1 and 2), the distance of the central axis (field 3), coordinates (x,y) of the left bank (fields 4 and 5), coordinates (x,y) of the right bank (fields 6 and 7)</p>
Dataset from Computational modeling of anthocyanin pathway evolution: Biases, hotspots, and trade-offs
<p>This directory contains the scripts used to run simulations, Jupyter notebook with complete analysis, and serialized (pickled) raw simulated dataset from our paper "<em>Computational modeling of anthocyanin pathway evolution: Biases, hotspots, and trade-offs</em>". These materials are referenced in the main text and supplemental text of the publication. The purpose of this repository is to facilitate replication of our analysis by any interested parties. </p>
Sonora 2018: Cloud-free, solar composition, solar C/O substellar evolution models
<p>Tables of the evolution and photometry of brown dwarfs and extrasolar giant planets based on the model described in Marley et al. (2019, in prep.). This publication provides a detailed description of the physics included in the model. The main differences with the previously published tables by Saumon & Marley (2008) are</p> <p>• updated "Sonora 2018" atmosphere models used as the surface boundary conditions, primarily involving improvements in the opacities of H2, CH4 and alkali resonance lines. The new atmosphere models are described in Marley et al. (2019, in prep.).</p> <p>• including metals in the interior equation of state as an additional amount of helium. Currently, the evolution tracks are for solar C/O ratio (defined relative to solar, so C/O=1 here) with cloudless atmospheres.</p> <p>V2.0 adds more photometry tables and evolution for [M/H]=-0.5 and +0.5 to the previous 0.0.</p> <p><a href="/api/files/e3bc80f3-7127-421c-af47-ecfe7e44c40c/tables_m+0.0_2018.tar.gz?versionId=54186e1a-1688-40c5-8405-f289953f134b">tables_m+0.0_2018.tar.gz</a> is now deprecated as V1.0</p> <p><a href="https://zenodo.org/api/files/e3bc80f3-7127-421c-af47-ecfe7e44c40c/Sonora_Bobcat_Tables.tar.gz">Sonora_Bobcat_Tables.tar.gz</a> is current V2.0 and is a superset of V1.0</p> <p>Please cite Marley et al. (2019, in prep.) if you use these in a publication.</p>
FIGURE 3 in Heterochrony in helicoid spiral cones: a computer model for demonstrating heterochronic evolution
FIGURE 3. Modes of heterochronic change. The central simulation has parameters W0=2.5, ΔW=-0.12, D=0, S=0.8, T'0=0.4, ΔT'=0.06, and has six whorls. The other four simulations show the result of one increment of each mode of heterochronic change. The two forms on the left are paedomorphic; the forms on the right are peramorphic. Note that in this case neoteny results in larger size as the ontogenetic decline in whorl expansion is reduced, and acceleration results in a smaller size for the converse reason.
FIGURE 6. Heterochronic modelling experiment 3 in Heterochrony in helicoid spiral cones: a computer model for demonstrating heterochronic evolution
FIGURE 6. Heterochronic modelling experiment 3. The "ancestor" on the left has parameters W0=2, ΔW=-0.05, D=0, S=0.9, T'0=0.2, ΔT'=0.07, and has eight whorls. As in Figure 4, this is a common general type of gastropod shell shape. The central simulation is a "descendant" derived from this by two increments of neoteny (relative scale x 0.5); the simulation on the right has resulted from two further increments of neoteny (relative scale x 0.39). All three simulations have analogues in the Family Helicidae of the Pulmonata, and this result constitutes a hypothesis for the possible heterochronic evolution of forms with flattened spires (depressed and sub-planispiral).
FIGURE 2 in Heterochrony in helicoid spiral cones: a computer model for demonstrating heterochronic evolution
FIGURE 2. Isometric and allometric gastropods and simulations. 1, An example of a "Raupian" gastropod (Epitonium), showing isometric growth. 2, An example of a "Raupian" simulation with similar shape. 3, An example of an allometric gastropod (Megacochlea); note that there is no straight line that is tangential to the outside of all whorls. 4, A simulation using the program described here with similar shape. (Figures 2.1 and 2.3 © The Trustees of the Natural History Museum, London, reproduced from Anon, 1975, with kind permission.)
FIGURE 1 in Heterochrony in helicoid spiral cones: a computer model for demonstrating heterochronic evolution
FIGURE 1. Raup's definition of the shell dimensions on which the equations for parameters W, D and T are derived. Based on Raup (1966).
FIGURE 5. Heterochronic modelling experiment 2 in Heterochrony in helicoid spiral cones: a computer model for demonstrating heterochronic evolution
FIGURE 5. Heterochronic modelling experiment 2. The "ancestor" on the left has parameters W0=1.1, ΔW=0.05, D=0, S=2.3, T'0=2, ΔT'=-0.03, and has 10 whorls. It has a form, including the slightly concave profile of the spire, which is similar to some members of the Family Volutidae. The next simulations are "descendants" derived from this by successive increments of acceleration (relative scales x 0.5, x 0.225, x 0.0875, respectively). All of these have parallels in the Volutidae, with the final form resembling the giant volutids in the genus Melo. The observation that the simulation predicts the large size of the final form supports the heterochronic hypothesis in the evolution of these gastropods.
FIGURE 4. Heterochronic modelling experiment 1 in Heterochrony in helicoid spiral cones: a computer model for demonstrating heterochronic evolution
FIGURE 4. Heterochronic modelling experiment 1. The "ancestor" on the left has parameters W0=2.5, ΔW=-0.1, D=0, S=1, T'0=0, ΔT'=0.15, and has seven whorls. It has a general shape that is common in gastropods, and especially amongst the subclass Pulmonata. The central simulation is derived from this by one increment of acceleration (relative scale x 1.5) and the simulation on the right by two increments of acceleration (relative scale x 2). The incipient reduction in whorl diameter and incipient loss of whorl-to-whorl contact is typical of some Pulmonata, such as Family Chondrinidae. Note that if Raup's T were used, incipient reduction in whorl diameter (W<1) would lead to reversal of the translation direction, which is nonsensical; using T', this is not the case.
Data: Testing the mating system model of parasite complex life cycle evolution reveals demographically driven mixed mating
<p>Abstract: Many parasite species use multiple host species to complete development; however, empirical tests of models that seek to understand factors impacting evolutionary changes or maintenance of host number in parasite life cycles are scarce. Specifically, Brown et al.’s (2001) mating system model, which posits multi-host life cycles are an adaptation to prevent inbreeding in hermaphroditic parasites and thus, preclude inbreeding depression, remains untested. The model assumes loss of a host results in parasite inbreeding and predicts host loss can only evolve if there is no parasite inbreeding depression. <a name="_Hlk169780726"></a>We provide the first empirical tests of this model using a novel approach we developed for assessing inbreeding depression from field-collected, parasite samples. The method compares genetically-based, selfing-rate estimates to a demographic-based selfing rate, which was derived from the closed mating system experienced by endoparasites. Results from the hermaphroditic trematode <em>Alloglossidium renale</em>, which has a derived 2-host life cycle, supported both the assumption and prediction of the mating system model as this highly inbred species had no indication of inbreeding depression. Additionally, comparisons of genetic and demographic selfing rates revealed <a name="_Hlk169781073"></a>a mixed mating system that could be explained completely by the parasite’s demography, i.e., its infection intensities.</p>
ScienceDex guides
Understand access before you commit
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.