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Data Testing
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Data from: Using probability modelling and genetic parentage assignment to test the role of local mate availability in mating system variation.
The formal testing of mating system theories with empirical data is important for evaluating the relative importance of different processes in shaping mating systems in wild populations. Here we present a generally applicable probability modelling framework to test the role of local mate availability in determining a population's level of genetic monogamy. We provide a significance test for detecting departures in observed mating patterns from model expectations based on mate availability alone, allowing the presence and direction of behavioural effects to be inferred. The assessment of mate availability can be flexible and in this study it was based on population density, sex ratio and spatial arrangement. This approach provides a useful tool for (1) isolating the effect of mate availability in variable mating systems and (2) in combination with genetic parentage analyses, gaining insights into the nature of mating behaviours in elusive species. To illustrate this modelling approach, we have applied it to investigate the variable mating system of the mountain brushtail possum (Trichosurus cunninghami) and compared the model expectations with the outcomes of genetic parentage analysis over an 18 year study. The observed level of monogamy was higher than predicted under the model. Thus, behavioural traits, such as mate guarding or selective mate choice, may increase the population level of monogamy. We show that combining genetic parentage data with probability modelling can facilitate an improved understanding of the complex interactions between behavioural adaptations and demographic dynamics in driving mating system variation.
Data from: Testing for universal common ancestry
A phylogenetic model selection test to quantify the evidence for the Universal Common Ancestry (UCA) of life forms was proposed recently (Theobald 2010a), based on the comparison of the statistical support, using likelihoods, the Akaike Information Criterion (AIC), or Bayes factors, for two different phylogenetic models representing the UCA and the independent origins (IOs) hypotheses (Sober and Steel 2002). In this test, the former is represented by a single phylogeny connecting all sequences, whereas the latter is depicted by several, independent phylogenetic trees (Fig. 1). Importantly, in the original UCA test, the same alignment was used to represent both hypotheses. When applied to a particular data set of 23 universally conserved proteins, the test strongly favored a UCA scenario.
Data from: A geographic test of species selection using planktonic foraminifera during the Cretaceous/Paleogene mass extinction
Species selection has received a great deal of theoretical attention but it has rarely been empirically tested. It is important to determine the level of selection that operated during a particular extinction event because it can help distinguish between traits that were actually responsible for extinction and those that were merely correlated with it. Here, we present a test that can help distinguish between organismal and species-level selection, which we demonstrate using the high-resolution fossil record of planktonic foraminifera species recorded in deep-sea sediment cores. Our test examines the fate of survivors and victims during the Cretaceous/Paleogene (K/Pg) mass extinction within single geographic regions, where all individuals experience the same selection pressures. Selection at the organismal level implies that individual members of surviving species are more fit than those of victimized species, and therefore should be more likely to survive in affected areas; conversely, selection at the species level implies individuals will suffer equally within an affected area. We find that survivors of the mass extinction suffered very high extirpation rates in cores where the overall extinction rate was high, indicating that individual members of the surviving species were generally no more fit than individual members of extinct species. Rather, these species were able to survive because they possessed advantageous species-level traits, such as larger geographic ranges and greater abundances than victimized species. This geographic pattern of extirpation suggests that selection operated at the species, rather than organismal, level during the K/Pg mass extinction of planktonic foraminifera.
Data from: Testing convergence versus history: convergence dominates phenotypic evolution for over 150 million years in frogs
Striking evolutionary convergence can lead to similar sets of species in different locations, such as in cichlid fishes and Anolis lizards, and suggests that evolution can be repeatable and predictable across clades. Yet, most examples of convergence involve relatively small temporal and/or spatial scales. Some authors have speculated that at larger scales (e.g., across continents), differing evolutionary histories will prevent convergence. However, few studies have compared the contrasting roles of convergence and history, and none have done so at large scales. Here we develop a two-part approach to test the scale over which convergence can occur, comparing the relative importance of convergence and history in macroevolution using phylogenetic models of adaptive evolution. We apply this approach to data from morphology, ecology, and phylogeny from 167 species of anuran amphibians (frogs) from 10 local sites across the world, spanning ∼160 myr of evolution. Mapping ecology on the phylogeny revealed that similar microhabitat specialists (e.g., aquatic, arboreal) have evolved repeatedly across clades and regions, producing many evolutionary replicates for testing for morphological convergence. By comparing morphological optima for clades and microhabitat types (our first test), we find that convergence associated with microhabitat use dominates frog morphological evolution, producing recurrent ecomorphs that together encompass all sampled species in each community in each region. However, our second test, which examines whether and how much species differ from their inferred optima, shows that convergence is incomplete: that is, phenotypes of most species are still somewhat distant from the estimated optimum for each microhabitat, seemingly because of insufficient time for more complete adaptation (an effect of history). Yet, these effects of history are related to past ecologies, and not clade membership. Overall, our study elucidates the dominant drivers of morphological evolution across a major vertebrate clade and shows that evolution can be repeatable at much greater temporal and spatial scales than commonly thought. It also provides an analytical framework for testing other potential examples of large-scale convergence.
Data from: Is saltmarsh restoration success constrained by matching natural environments or altered succession? a test using niche models
1.Restored habitats, such as saltmarsh created through managed realignment, sometimes fail to meet targets for biological equivalence with natural reference sites. Understanding why this happens is important in order to improve restoration outcomes. 2.Elevation in the tidal frame and sediment redox potential are major controls on the distribution of saltmarsh plants. We use niche models to characterize ten species' responses to these, and test whether differences in species occurrence between restored and natural saltmarshes in the UK result from failure to recreate adequate environmental conditions. 3.Six species occurred less frequently in recently restored marshes than natural marshes. Failure of restored marshes to achieve the elevation and redox conditions of natural marshes partially explained the underrepresentation of five of these species, but did not explain patterns of occurrence on older (> 50 years) restored marshes. 4.For all species, an effect of marsh age remained after controlling for differences in environmental conditions. This could be due to differences in successional mechanism between restored and natural marshes. In recently restored marshes, high-marsh species occurred lower in the tidal frame and low-marsh species occurred at higher elevations than in natural marshes. This supports the hypothesis that competition is initially weaker in restored marshes, because of the availability of bare sediment across the whole tidal frame. Species that establish outside their normal realized niche, such as Atriplex portulacoides, may inhibit subsequent colonization of other species that occurred less frequently than expected on older restored marshes. 5.Synthesis and applications. Niche models can be used to test whether abiotic differences between restored sites and their natural counterparts are responsible for discrepancies in species occurrence. In saltmarshes, simply replicating environmental conditions will not result in equivalent species occurrence.
Data from: Multiple data sets, congruence, and hypothesis testing for the phylogeny of basal groups of the lizard genus Sceloporus (Squamata, Phrynosomatidae)
Several data partitions, including nuclear and mitochondrial gene sequences, chromosomes, isozymes, and morphological characters, were used to propose a new phylogeny and to test previously published hypotheses about the phylogenetic positions of basal clades of the lizard genus Sceloporus and the relationship of Sceloporus to the former genus "Sator". In accord with earlier studies, our results grouped "Sator" internal to Sceloporus, and both support a hypothesis of transgulfian vicariance for the origin of the former genus "Sator" on islands in the Sea of Cortez. Robustness of support for internal nodes in our best tree was established though widely used indices (bootstrap proportions, decay values) but also through congruence among independent data partitions. Several deep nodes in the tree recovered by a number of methods, including equally weighted and differentially weighted parsimony, and maximum likelihood models, are only weakly supported by the traditional indices, and this methodological concordance is taken as evidence for insensitivity of the deep structure of the topology to alternate assumptions.
Data from: Testing for Depéret's rule (body size increase) in mammals using combined extinct and extant data
Whether or not evolutionary lineages in general show a tendency to increase in body size has often been discussed. This tendency has been dubbed "Cope's rule" but because Cope never hypothesized it, we suggest renaming it after Depéret, who formulated it clearly in 1907. Depéret's rule has traditionally been studied using fossil data, but more recently a number of studies have used present-day species. While several paleontological studies of Cenozoic placental mammals have found support for increasing body size, most studies of extant placentals have failed to detect such a trend. Here, we present a method to combine information from present-day species with fossil data in a Bayesian phylogenetic framework. We apply the method to body mass estimates of a large number of extant and extinct mammal species, and find strong support for Depéret's rule. The tendency for size increase appears to be driven not by evolution toward larger size in established species, but by processes related to the emergence of new species. Our analysis shows that complementary data from extant and extinct species can greatly improve inference of macroevolutionary processes.
Data from: Evaluation of demographic history and neutral parameterization on the performance of Fst outlier tests
FST outlier tests are a potentially powerful way to detect genetic loci under spatially divergent selection. Unfortunately, the extent to which these tests are robust to non-equilibrium demographic histories has been under-studied. We developed a landscape-genetics simulator to test the effects of isolation by distance (IBD) and range expansion on FST outlier methods. We evaluated the two most commonly used methods for the identification of FST outliers (FDIST2 and BayeScan, which assume samples are evolutionarily independent) and two recent methods (FLK and Bayenv2, which estimate and account for evolutionary non-independence). Parameterization with a set of neutral loci ("neutral parameterization") always improved the performance of FLK and Bayenv2, while neutral parameterization caused FDIST2 to actually perform worse in the cases of IBD or range expansion. BayeScan was improved when the prior odds on neutrality was increased, regardless of the true odds in the data. On their best performance, however, the widely-used methods had high false-positive rates for IBD and range expansion and were outperformed by methods that accounted for evolutionary non-independence. In addition, default settings in FDIST2 and BayeScan resulted in many false positives under balancing selection. However, all methods did very well if a large set of neutral loci is available to create empirical p-values. We conclude that in species that exhibit IBD or have undergone range expansion, many of the published FST outliers based on FDIST2 and BayeScan are probably false positives, but FLK and Bayenv2 show great promise for accurately identifying loci under spatially-divergent selection.
Data from: Demographic inferences after a range expansion can be biased: the test case of the blacktip reef shark (Carcharhinus melanopterus)
The evolutionary history of species is a dynamic process as they modify, expand and contract their spatial distributions over time. Range expansions (REs) occur through a series of founder events that are followed by migration among neighbouring demes. The process usually results in structured metapopulations and leaves a distinct signature in the genetic variability of species. Explicitly modeling the consequences of complex demographic events such as REs is computationally very intensive. Here we propose an an alternative approach that requires less computational effort than a comprehensive RE model, but that can recover the demography of species undergoing a RE, by combining spatially explicit modelling with simplified but realistic metapopulation models. We examine the demographic and colonization history of Carcharhinus melanopterus, an abundant reef-associated shark, as a test case. We first used a population genomics approach to statistically confirm the occurrence of a RE in C. melanopterus and identify its origin in the Indo-Australian Archipelago. Spatial genetic modelling identified two waves of stepping-stone colonization: an eastward wave moving through the Pacific and a westward one moving through the Indian Ocean. We show that metapopulation models best describe the demographic history of this species and that not accounting for this may lead to incorrectly interpreting the observed genetic variation as signals of widespread population bottlenecks. Our study highlights insights that can be gained about demography by coupling metapopulation models with spatial modeling and underscores the need for cautious interpretation of population genetic data when advancing conservation priorities.
Transparent experiments: releasing data from mechanical tests on three dimensional hydrogel sphere packings
<p>We describe here experiments on the mechanics of hydrogel particle packings from the Behringer lab, performed between 2012 and 2015. These experiments quantify the evolution of all contact forces inside soft particle packings exposed to compression, shear, and the intrusion of a large intruder. The experimental set-ups and processes are presented and the data are concomitantly published in a repository.</p>
Data for Stool Studies Don't Pass the Sniff Test
<p>Data for manuscript "Stool Studies Don't Pass the Sniff Test".</p>
Original data of compression test for cracked specimen
<p>To explore the crack propagation and failure process of surrounding rock with deep cracks under external stress adjustment, the failure of cracked specimens under external load was studied. The required test pieces were prepared by using a self-developed mold and using cement mortar as a similar material. Through the uniaxial compression test, the basic mechanical properties of the material and the specimen were obtained, and the crack propagation process and the failure evolution mechanism of the specimen under different crack inclination angles and loading rates were revealed. The test results show that the presence of cracks can significantly affect the overall strength of the specimen, and the strength and failure mechanism of the specimen vary with the change in the crack angle and rate of loading. The larger the crack inclination angle, the lower the strength of the specimen, and the two are linearly related. With the increase in the loading rate, the failure mode of the specimen gradually changes, the dynamic effect is enhanced, and typical characteristics of a rockburst appear. Furthermore, the reasons for the modes of failure and changes in strength of the specimens were analyzed from the energy point of view, and the non-contact full-field strain measurement system (DIC) was used to explain the macroscopic failure modes of the specimens from a meso-level perspective. Combining this with the failure behavior of the specimen, reasonable suggestions are proposed for the smooth construction of the actual project in the later stage.</p>
Tests of General Relativity with Binary Black Holes from the second LIGO–Virgo Gravitational-Wave Transient Catalog - Full Posterior Sample Data Release
<p>Data release containing full posterior samples of the following analyses reported in the paper "Tests of General Relativity with Binary Black Holes from the second LIGO–Virgo Gravitational-Wave Transient Catalog" from the LIGO Scientific Collaboration and Virgo Collaboration (<a href="https://doi.org/10.1103/PhysRevD.103.122002">Phys. Rev. D 103, 122002</a>, also available at <a href="https://arxiv.org/abs/2010.14529">arxiv.org:2010.14529</a> and <a href="https://dcc.ligo.org/LIGO-P2000091/public">https://dcc.ligo.org/LIGO-P2000091/public</a>):</p> <ul> <li>Echoes (Sec VII B): ech.zip</li> <li>Inspiral-merger-ringdown consistency test (Sec IV B): imr.zip</li> <li>Lorentz invariance violation test (Sec V I): liv.zip</li> <li>Parametrized tests of general relativity (Sec V A): par.zip</li> <li>Ringdown test (Sec VII A): rin.zip</li> <li>Spin-induced quadrupole moment test (Sec V B): sim.zip</li> </ul> <p>Each zip file contains HDF5 files that can either be read directly with standard HDF5 tools, or using PESummary (<a href="https://docs.ligo.org/lscsoft/pesummary/">https://docs.ligo.org/lscsoft/pesummary/</a>)</p> <p> </p>
Observation, simulation and sensitivity test data of peroxy radical in October 2018
<p>Observation, simulation and sensitivity test data of peroxy radical in October 2018</p>
Data set IDA tests for activity A 3.3.1 MeDDII
<p>Data set IDA tests for activity A 3.3.1 MeDDII</p>
Supporting Data for Generating Realistic and Diverse Tests for LiDAR-Based Perception Systems
<p>Supporting data for ICSE 2023 paper "Generating Realistic and Diverse Tests for LiDAR-Based Perception Systems".</p> <p> </p> <p>The "selected_data.tar.xz" file contains a small subsample of the <a href="http://www.semantic-kitti.org">SemanticKITTI data set</a> for use in demonstration of the capabilities of the research prototype tool used in the evaluation. The SemanticKITTI data set is released under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License, which permits redistribution under the same terms.</p> <p>The "study_data_compressed.tar.xz" file contains the intermediate results obtained during the study conducted in the paper. We provide scripts to generate the figures and tables from the paper given this data.</p> <p> </p> <p>The</p>
Test data for hdl_graph_slam
<p>Test data for hdl_graph_slam</p>
Data from: When scientific experts come to be media stars: an evolutionary model tested by analysing coronavirus media coverage across Italian newspapers
<p>This dataset includes metadata of the newspaper articles used for the paper "When scientific experts come to be media stars: an evolutionary model tested by analysing coronavirus media coverage across Italian newspapers". The dataset is in JSON format. The metadata includes: "uuid" (unique identifier we associated to an article), "URLs" (the URLs where the article was published), "sources" (newspaper and feed/section where the article was published), "datesPublished" (dates when the article was published/updated).</p> <p>License: Attribution-ShareAlike 4.0 International (<a href="https://creativecommons.org/licenses/by-sa/4.0/legalcode">https://creativecommons.org/licenses/by-sa/4.0/legalcode</a>)</p> <p> </p>
Experimental data for chloride diffusion coefficient of concrete by rapid chloride migration test
<p>This database collects the chloride ion diffusion coefficient measured by RCM method (including the method adopted by the Nordic standard NT Build 492, the IBAC method of Germany's Anchen University of technology, as well as the methods adopted by China's GB/T 50082-2009 and JTG/T B07-01-2006); The curing method is standard curing.</p>
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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.