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427 results for “modularity”
Data from: Cope's Rule in a modular organism: directional evolution without an overarching macroevolutionary trend
Cope's Rule describes increasing body size in evolutionary lineages through geological time. This pattern has been documented in unitary organisms but does it also apply to module size in colonial organisms? We address this using 1169 cheilostome bryozoans ranging through the entire 150 million years of their evolutionary history. The temporal pattern evident in cheilostomes as a whole shows no overall change in zooid (module) size. However, individual subclades show size increases: within a genus, younger species often have larger zooids than older species. Analyses of (paleo)latitudinal shifts show that this pattern cannot be explained by latitudinal effects (Bergmann's Rule) coupled with younger species occupying higher latitudes than older species (an 'out of the tropics' hypothesis). While it is plausible that size increase was linked to the advantages of large zooids in feeding, competition for trophic resources and living space, other proposed mechanisms for Cope's Rule in unitary organisms are either inapplicable to cheilostome zooid size or cannot be easily evaluated. Patterns and mechanisms in colonial organisms cannot and should not be extrapolated from the better-studied unitary organisms. And even if macroevolution simply comprises repeated rounds of microevolution, evolutionary processes occurring with lineages are not always detectable from macroevolutionary patterns.
Data from: Pleiotropic jaw morphology links the evolution of mechanical modularity and functional feeding convergence in Lake Malawi Cichlids
Complexity in how mechanistic variation translates into ecological novelty could be critical to organismal diversification. For instance, when multiple distinct morphologies can generate the same mechanical or functional phenotype this could mitigate tradeoffs and/or provide alternative ways to meet the same ecological challenge. To investigate how this type of complexity shapes diversity in a classic adaptive radiation, we tested several evolutionary consequences of the anterior jaw four-bar linkage for Lake Malawi cichlid trophic diversification. Using a novel phylogenetic framework, we demonstrated that different mechanical outputs of the same four jaw elements are evolutionarily associated with both jaw protrusion distance and jaw protrusion angle. However, these two functional aspects of jaw protrusion have evolved independently. Additionally, although four-bar morphology showed little evidence for attraction to optima, there was substantial evidence of adaptive peaks for emergent four-bar linkage mechanics and jaw protrusion abilities among Malawi feeding guilds. Finally, we highlighted a clear case of "cryptic convergence" in which two cichlid species that have independently evolved to graze algae in less than two million years, have converged on similar jaw protrusion abilities as well as four-bar linkage mechanics, but have evolved these similarities via non-convergent four-bar morphologies.
Data from: Mosaic heterochrony and evolutionary modularity: the trilobite genus Zacanthopsis as a case study
Logical connections exist between evolutionary modularity and heterochrony, two unifying and structuring themes in the expanding field of evolutionary developmental biology. The former sees complex phenotypes as being made up of semi-independent units of evolutionary transformation; the latter requires such a modular organization of phenotypes to occur in a localized or mosaic fashion. This conceptual relationship is illustrated here by analyzing the evolutionary changes in the cranidial ontogeny of two related species of Cambrian trilobites. With arguments from comparative developmental genetics and functional morphology, we delineate putative evolutionary modules within the cranidium and examine patterns of evolutionary changes in ontogeny at both global and local scales. Results support a case of mosaic heterochrony, i.e. a combination of local heterochronies affecting the different parts individuated in the cranidium, leading to the complex pattern of allometric repatterning observed at the global scale. Through this example, we show that recasting morphological analyses of complex phenotypes with a priori knowledge or hypotheses about their organizational and variational properties can significantly improve our interpretation and understanding of evolutionary changes among related taxa, fossil and extant. Such considerations open avenues to investigate the large-scale dynamics of modularity and its role in phenotypic evolution.
Data from: Constraint and opportunity: the genetic basis and evolution of modularity in the cichlid mandible
Modular variation, whereby the relative degree of connectivity varies within a system, is sometimes thought to evolve through natural selection. In this way, modularity may facilitate evolution. Alternatively, conserved patterns of modularity may act to constrain evolution by preventing certain functions from evolving. A comprehensive understanding of the interplay between these phenomena will require knowledge of both the inheritance and genetic basis of modularity. Here we explore these ideas in the cichlid mandible by investigating modularity at the genus, species, and through a new approach, the individual level. Specifically, we assessed patterns of covariation in Lake Malawi cichlid species that employ alternate 'biting' and 'suction-feeding' modes of feeding, and in a hybrid cross between these two ecotypes. Across the suction-feeding genus, patterns of modularity were conserved and reflected function. In contrast, the 'biting' species displayed a pattern of modularity that closely matched developmental modules. The modularity pattern present in our F2 population was similar to the pattern exhibited by our biter, suggesting a role for dominance. We also demonstrated that our individual-level metrics of modularity (IMM) were a valid quantitative traits and used them to map modularity QTL. In all, our findings suggest that modularity is both a constraining and evolvable force in cichlid evolution, with distinct patterns between species and variation among individuals.
Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates
We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.
Data from: Ontogenetic changes in the phenotypic integration and modularity of leaf functional traits
1.Changes in resource availability, functional demands, hormonal regulation and developmental constraints can promote differences in the expression of leaf traits during plant development and foster changes in the targets of natural selection. As a consequence, the pattern and magnitude of covariation among traits, and therefore their phenotypic integration and modularity are equally expected to change throughout ontogeny. However, these changes have not been described yet. 2.We measured leaf economic, defensive and morphological traits in plants of Turnera velutina and estimated the magnitude and pattern of foliar integration and modularity for juvenile and reproductive individuals. In addition, we assessed the relationship between plant biomass and foliar integration within and among ontogenetic stages. 3.Both the pattern and magnitude of foliar integration changed across plant ontogeny. Foliar integration was lower in juvenile than in reproductive plants, and the pattern of phenotypic integration and modularity was different between ontogenetic stages: whereas leaves from juvenile plants showed two functional modules related to plant defence and leaf economy, traits from reproductive plants had greater interconnectivity and hence lower modularity. 4.The relationship between plant biomass and foliar integration was negative within each ontogenetic stage but positive between ontogenetic stages, suggesting that processes intrinsic to plant development influenced the magnitude of foliar integration to a greater extent than plant size. 5.Our findings indicate that plants can change the patterns of covariation among leaf traits during their development. Whereas a lower foliar integration in juvenile plants could allow for greater lability to explore a multi-trait phenotypic space, canalization of leaf attributes along ontogeny should promote greater phenotypic integration, constraining the number of multi-trait combinations that plants can express. Hence, we suggest that ontogenetic changes in foliar integration allow plants to deal with changing selective dynamics and physiological priorities along their development.
Data from: Analysis and visualization of H7 influenza using genomic, evolutionary and geographic information in a modular web service
We have reported previously on use of a web-based application, Supramap (http://supramap.org) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug-resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonotic pathogen, H7 influenza, and provide an update on the implementation of Supramap as a web service. We find that the emergence of pathogenic strains of H7 is labile with many transitions from high to low pathogenicity, and from low to high pathogenicity. We use Supramap to put these events in a temporal and geospatial context. We identify several lineages of H7 influenza with biomarkers of high pathogenicity in regions that have not been reported in the scientific literature. The original implementation of Supramap was built with tightly coupled client and server software. Now we have decoupled the components to provide a modular web service for POY (http://poyws.org) that can be consumed by a data provider to create a novel application. To demonstrate the web service, we have produced an application, Geogenes (http://geogenes.org). Unlike in Supramap, in which the user is required to create and upload data files, in Geogenes the user works from a graphical interface to query an underlying dataset. Geogenes demonstrates how the web service can provide underlying processing for any sequence and metadata database.
Comparing the strength of modular signal, and evaluating alternative modular hypotheses, using covariance ratio effect sizes with morphometric data
<p>The study of modularity is paramount for understanding trends of phenotypic evolution, and for determining the extent to which covariation patterns are conserved across taxa and levels of biological organization. However, biologists currently lack quantitative methods for statistically comparing the strength of modular signal across datasets, and a robust approach for evaluating alternative modular hypotheses for the same dataset. As a solution to these challenges, we propose an effect size measure (Z_CR) derived from the covariance ratio, and develop hypothesis-testing procedures for their comparison. Computer simulations demonstrate that Z_CR displays appropriate statistical properties and low levels of misspecification, implying that it correctly identifies modular signal, when present. By contrast, alternative methods based on likelihood (EMMLi) and goodness of fit (MINT) suffer from high false positive rates and high model misspecification rates. An empirical example in sigmodontine rodent mandibles is provided to illustrate the utility of Z_CR for comparing modular hypotheses. Overall, we find that covariance ratio effect sizes are useful for comparing patterns of modular signal across datasets or for evaluating alternative modular hypotheses for the same dataset. Finally, the statistical philosophy for pairwise model comparisons using effect sizes should accommodate any future analytical developments for characterizing modular signal.</p>
Lowpoly Stylized Modular Village
Source: Objaverse 1.0 / Sketchfab
Data underlying "EVE is an open modular data analysis software for event-based localization microscopy"
<p>Data underlying the manuscript "EVE is an open modular data analysis software for event-based localization microscopy"</p> <p>Contains raw EBS-recorded SMLM (eveSMLM) data of DNA-PAINT nanoruler, E.coli cell, and aTubulin network in Cos-7 cells (3D and high density acquisitions).</p>
ROS 2 Bag acquired from AgRob Modular-e during the V SCORPION Integration (Quinta do Seixo, Portugal)
<p>ROS 2 Bag acquired with the AgRob Modular-e robot during the V SCORPION Integration in Quinta do Seixo (Valença do Douro, Portugal), on October 26, 2023.<br><br>Dataset description:<br>rosbag2_2023_10_26-16_22_30 - Robot navigating across four crop rows in a steep slope vineyard, returning to the main road.<br><br>Main topics available include:<br>- Redshift UM7 IMU data (/eut_sensors/imu/data)<br>- RS-LIDAR 3D scans (/rslidar_points)<br>- U-Blox GNSS coordinates with RTK precision (/base/fix)<br>- U-Blox heading data from moving baseline setup (/rover/navheading)<br> </p>
A Stable Software Architecture Modularity Metric
<p>Anonymous Replication Package for A Stable Software Architecture Modularity Metric</p>
Data for "MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0"
<p>This data set contains reanalyzed data from the "MS2 500 ms" and "MS2 750 ms" workflow <a href="https://doi.org/10.1016/j.mcpro.2022.100219">originally published by Furtwängler et al. 2022</a>. </p><p>The full data set is available on ProteomeXchange via the PRIDE partner repository using ID <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD029320">PXD029320</a>. <br> </p><p>This data set contains, for both workflows </p><ul><li>mzML files</li><li>Output files from analysis with MS Amanda + settings file</li><li>Output files from analysis with MS Amanda in combination with Percolator + settings file</li><li>Percolator pin files</li><li>Output files from analysis with MS²Rescore</li></ul>
A tunable family of CAAC-ruthenium olefin metathesis catalysts modularly derived from a large-scale produced ibuprofen intermediate
<p>Data confirming the structure of the new compounds obtained within the project, published in <br><i><strong>Chem. Sci.</strong></i>, 2023,<strong>14</strong>, 10744-10755</p><p>The research was supported by the National Science Centre, Poland (OPUS grant DEC-2017/27/B/ST5/02563).</p>
Modular Bunker
Some modular bunker parts with a lamp and a bench Source: Objaverse 1.0 / Sketchfab
Origami-inspired modular electro-ribbon actuator for multi-DoF motion
<p>This upload contains the dataset for the paper: Origami-inspired modular electro-ribbon actuator for multi-DoF motion. The description of the data can be found in the ReadMe file in the folder.</p>
Five thousand randomly generated modular biosynthetic pathways visualised by RAIChU
<p>We randomly generated 5000 modular biosynthetic pathways to test our visualisation software RAIChU: Reaction Analysis through Illustration of Chemical Units.</p>
Thread-Modular Abstract Interpretation: The Local Perspective
<div> <h1>Thread-Modular Abstract Interpretation: The Local Perspective</h1> <br> <div><strong>This artifact contains the software and data necessary to reproduce the results described in the chapter entitled </strong><strong><em>Experimental Evaluation</em> of the manuscript <em>Thread-Modular Abstract Interpretation: The Local Perspective</em> by </strong><strong>Michael Schwarz.</strong></div> <br> <div>It is structured as follows:</div> <br> <div>- The folder <em>analyzer</em> contains the Goblint analyzer in the version used for the experiments (Branch <em>michael-schwarz-dissertation</em>).</div> <div>- The folder <em>bench</em> contains the Goblint benchmark repository in the version used for the experiments which also contains scripts to run the experiments (Branch <em>michael-schwarz-dissertation</em>).</div> <div>- The archive <em>bench_raw.tar.xz</em> contains the raw benchmark results.</div> <div>- The folder <em>data</em> contains spreadsheets, CSV files, and scripts necessary to extract relevant information from the raw benchmark results.</div> <br> <div>This artifact is unfortunately documented relatively poorly at the moment. A good starting point for understanding the various scripts etc. are our previous artifacts on which this evaluation builds and their rather comprehensive READMEs.</div> <br> <div>- ESOP '23: https://zenodo.org/records/7767778</div> <div>- SAS '21: https://zenodo.org/records/5148608</div> <br> <div>If you want to reproduce these results but have trouble getting started, you are very much encouraged to bother me, e.g., by emailing me at `m DOT schwarz AT tum DOT de`</div> <br> <div>The contents of `analyzer` and `bench` all are published under the respective licenses mentioned in folders or individual files.</div> </div>
Data for "Heuristic algorithms in Evolutionary Computations and modular organization of biological macromolecules: applications to in vitro evolution"
<p>This publication contains data for the construction of the figures and tables for the paper "Heuristic algorithms in Evolutionary Computations and modular organization of biological macromolecules: applications to in vitro evolution" accepted to publication in PLOS ONE.</p>
Dataset: Modular Piezoresistive Smart Textile for State Estimation of Cloths
<p>This set contains data obtained using the smart textile featured in "Modular Piezoresistive Smart Textile for State Estimation of Cloths", R. Proesmans et al., MDPI Sensors.<br> </p>
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.