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238 results for “Experimental testing”
Data from: Experimental tests of sex allocation theory with two species of simultaneously hermaphroditic acorn barnacles
Sex allocation theory for simultaneous hermaphrodites predicts increases in relative allocation to male-specific function as competition for fertilizations increases. Theoretical models developed specifically for competing acorn barnacles predict that the proportional allocation to male function increases towards an asymptote of 50% as the number of competitors for fertilizations increases. Experimental manipulations were used to investigate how mate competition affected both relative and absolute allocation to the sex functions for two species of acorn barnacle: Semibalanus balanoides and Balanus glandula. The ratio of male to female allocation did not increase with the number of competitors for either species. However, both species showed increased allocation to male function (estimated as total mass of sex-specific tissues) with increased crowding. Allocation to female function seemed to be limited by other factors and did not vary with mating group size as predicted. Allocation to male and female function were both positively related to body size, but a trade-off between male and female function, a key assumption of prior models, was not observed.
Data from: Experimental design in phylogenetics: testing predictions from expected information
Taxon and character sampling is central to phylogenetic experimental design yet we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman's method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable predictions of which taxon additions would increase information about a particular weakly supported branch of the caecilian phylogeny by the greatest amount. Using mitogenomic and rag1 sequences (some newly determined for this study) from additional caecilian species we studied how information (both expected and observed) and bootstrap support varies as each new taxon is individually added, providing the first empirical test of specific predictions made using Goldman's method for phylogenetic experimental design. Our results empirically validate the top three (more intuitive) taxon addition predictions made in our previous study, but only information results validate unambiguously the fourth (less intuitive) prediction. This highlights a complex relationship between information and support, reflecting that each measures different things: information is related to the ability to estimate branch length accurately, and support to the ability to estimate the tree topology accurately. Thus, an increase in information may be correlated with but does not necessitate an increase in support Our results also provide the first empirical validation of the widely held intuition that additional taxa that join the tree proximal to poorly supported internal branches are more informative and enhance support more than additional taxa that join the tree more distally. Our work supports the view that adding more data for a single (well chosen) taxon may increase phylogenetic resolution and support in weakly supported parts of the tree without adding more characters/genes while illustrating that less well chosen taxon additions can have the opposite effect. Altogether our results corroborate that, although still underexplored, Goldman's method offers a powerful tool for experimental design in molecular phylogenetic studies. However, there are still several drawbacks to overcome, and further assessment of the method is needed in order to make it better understood, more accessible, and able to assess additions of multiple taxa.
Data from: Can plants evolve tolerance mechanisms to heterospecific pollen effects? An experimental test of the adaptive potential in Clarkia species
Flowering plants do not occur alone and often grow in mixed-species communities where pollinator sharing is high and interactions via pollinators can occur at pre- and post-pollination stages. While the causes and consequences of pre-pollination interactions have been well studied little is known about post-pollination interactions via heterospecific pollen (HP) receipt, and even less about the evolutionary implications of these interactions. In particular, the degree to which plants can evolve tolerance mechanisms to the negative effects of HP receipt has received little attention. Here, we aim to fill this gap in our understanding of post-pollination interactions by experimentally testing whether two co-flowering Clarkia species can evolve HP tolerance, and whether tolerance to specific HP 'genotypes' (fine-scale local adaptation to HP) occurs. We find that Clarkia species vary in their tolerance to HP effects. Furthermore, conspecific pollen performance and the magnitude of HP effects were related to the recipient's history of exposure to HP in C. xantiana but not in C. speciosa. Specifically, better conspecific pollen performance and smaller HP effects were observed in populations of C. xantiana plants with previous exposure to HP compared to populations without such exposure. These results suggest that plants may have the potential to evolve tolerance mechanisms to HP effects but that these may occur not from the female (stigma, style) but from the male (pollen) perspective, a possibility that is often overlooked. We find no evidence for fine-scale local adaptation to HP receipt. Studies that evaluate the adaptive potential of plants to the negative effects of HP receipt are an important first step in understanding the evolutionary consequences of plant–plant post-pollination interactions. Such knowledge is in turn crucial for deciphering the role of plant–pollinator interactions in driving floral evolution and the composition of co-flowering communities.
Data from: Synergism and antagonism of proximate mechanisms enable and constrain the response to simultaneous selection on body size and development time: an empirical test using experimental evolution
Natural selection acts on multiple traits simultaneously. How mechanisms underlying such traits enable or constrain their response to simultaneous selection is poorly understood. We show how antagonism and synergism among three traits at the developmental level enable or constrain evolutionary change in response to simultaneous selection on two focal traits at the phenotypic level. After 10 generations of 25% simultaneous directional selection on all four combinations of body size and development time in Manduca sexta (Sphingidae), the changes in the three developmental traits predict 93% of the response of development time and 100% of the response of body size. When the two focal traits were under synergistic selection, the response to simultaneous selection was enabled by juvenile hormone and ecdysteroids and constrained by growth rate. When the two focal traits were under antagonistic selection, the response to selection was due primarily to change in growth rate and constrained by the two hormonal traits. The approach used here reduces the complexity of the developmental and endocrine mechanisms to three proxy traits. This generates explicit predictions for the evolutionary response to selection that are based on biologically informed mechanisms. This approach has broad applicability to a diverse range of taxa, including algae, plants, amphibians, mammals, and insects.
Data from: An experimental test of the transmission−virulence trade-off hypothesis in a plant virus
The transmission–virulence trade-off hypothesis is one of the few adaptive explanations of virulence evolution, and assumes that there is an overall positive correlation between parasite transmission and virulence. The shape of the transmission–virulence relationship predicts whether virulence should evolve toward either a maximum or to an intermediate optimum. A positive correlation between each of these traits and within-host growth is often suggested to underlie the relationship between virulence and transmission. There are few experimental tests of this hypothesis; this study reports on the first empirical test on a plant pathogen. We infected Brassica rapa plants with nine natural isolates of Cauliflower mosaic virus and then estimated three traits: transmission, virulence, and within-host viral accumulation. As predicted by the trade-off hypothesis, we observed a positive correlation between transmission and virulence, suggestive of the existence of an intermediate optimum. We discovered the unexpected existence of two groups of within-host accumulation, differing by at least an order of magnitude. When accumulation groups were not accounted for, within-host accumulation was correlated neither to virulence nor transmission, although our results suggest that within each group these correlations exist.
Data from: Replaying evolution to test the cause of extinction of one ecotype in an experimentally evolved population
In a long-term evolution experiment with Escherichia coli, bacteria in one of twelve populations evolved the ability to consume citrate, a previously unexploited resource in a glucose-limited medium. This innovation led to the frequency-dependent coexistence of citrate-consuming (Cit+) and non-consuming (Cit–) ecotypes, with Cit−bacteria persisting on the exogenously supplied glucose as well as other carbon molecules released by the Cit+ bacteria. After more than 10,000 generations of coexistence, however, the Cit−lineage went extinct; cells with the Cit−phenotype dropped to levels below detection, and the Cit−clade could not be detected by molecular assays based on its unique genotype. We hypothesized that this extinction was a deterministic outcome of evolutionary change within the population, specifically the appearance of a more-fit Cit+ ecotype that competitively excluded the Cit−ecotype. We tested this hypothesis by re-evolving the population from a frozen population sample taken within 500 generations of the extinction and from another sample taken several thousand generations earlier, in each case for 500 generations and with 20-fold replication. To our surprise, the Cit−type did not go extinct in any of these replays, and Cit−cells also persisted in a single replicate that was propagated for 2,500 generations. Even more unexpectedly, we showed that the Cit−ecotype could reinvade the Cit+ population after its extinction. Taken together, these results indicate that the extinction of the Cit−ecotype was not a deterministic outcome driven by competitive exclusion by the Cit+ ecotype. The extinction also cannot be explained by demographic stochasticity alone, as the population size of the Cit−ecotype should have been many thousands of cells even during the daily transfer events. Instead, we infer that the extinction must have been caused by a rare chance event in which some aspect of the experimental conditions was inadvertently perturbed.
An Automated, Experimenter-Free Method for the Standardised, Operant Cognitive Testing of Rats __ Data supplementing __
<p>These data supplement the article:</p> <p><strong>An Automated, Experimenter-Free Method for the Standardised, Operant Cognitive Testing of Rats</strong></p> <p><em>Marion Rivalan, Humaira Munawar, Anna Fuchs, York Winter (2017)</em></p> <ul> <li>Published: January 6, 2017</li> <li>http://dx.doi.org/10.1371/journal.pone.0169476</li> </ul> <p>Use is free for academic purposes, provided the aforementioned article is appropriately cited.</p> <p>The directory contains the following file: Pone_2016_DataSupplement-Zenodo.xlsx</p> <p>Explanations are within the document.</p>
Raw data of eDNA quantities from an experimental study testing temperature, water masses, and fish species
<p>Environmental DNA (eDNA) is a very promising approach to facilitate and improve the aquatic species monitoring, which is crucial for their management and conservation. In comparison with the plethora of monitoring studies in the fields, relatively few studies have focused on experimentally investigating the "ecology" of eDNA, in particular pertaining to processes influencing the detection of eDNA. The paucity of knowledge about its ecology hampers the use of eDNA analysis to its full potential. In this study, we experimentally evaluated the impact of several biotic and abiotic factors on the rate of production and degradation of eDNA. Individuals of three freshwater fish species (brown bullhead, tench, and yellow perch) with distinct ecology were placed in two types of water from the St. Lawrence River (Québec, Canada) with very distinct physicochemical characteristics and at three different temperatures. Water samples were then filtered at predetermined time intervals, and quantitative PCR was used to quantify the eDNA in each sample. We found that temperature, species, water types, and some interactions between these factors had a strong effect on the production and degradation of eDNA. The results of this study enhance our knowledge about the ecology of eDNA, thus improving eDNA data interpretation.</p>
FIGURE 2 in The effects of lithification on fossil assemblage biodiversity and composition: An experimental test
FIGURE 2. Classical (A) and coverage-based (B) rarefaction of the Bermont Formation samples. In each panel, the red curve marks the lithified sample, and the blue curve marks the corresponding unlithified replicate sample. The gray curves mark other unlithified samples taken from different horizons of the same formation at the same outcrop. The red and blue bands mark 95% confidence intervals.
FIGURE 8 in The effects of lithification on fossil assemblage biodiversity and composition: An experimental test
FIGURE 8. Hypothetical rarefaction curves illustrating the potential effects of lithification or other diagenetic processes on the observed biodiversity of a fossil assemblage. The rarefaction curves are shown in blue for unlithified, unaltered assemblages and in red for the lithified, altered assemblages. A-C, Total species richness is the same in the pristine and altered samples. D-F, Total species richness is lower in the altered samples. A,D, Evenness is lower in the altered samples. B,E Evenness is the same. C,F, Evenness is higher in the altered samples.
FIGURE 1 in The effects of lithification on fossil assemblage biodiversity and composition: An experimental test
FIGURE 1. Photographs of the outcrop and fossil samples. A. Outcrop at Caloosa Shell Quarry, Hillsborough County, Florida, USA. B. Close-up of outcrop showing sampling scheme. Pairs of replicate samples were taken immediately adjacent to each other at 30 cm vertical increments. C. Fossil sample prior to either sieving or cementation. D. Artificially cemented sample.
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>
Test on a New Experimental Mouth Rinse for Relieving Tooth Sensitivity
ClinicalTrials.gov study NCT02113579. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Test on a New Experimental Mouth Rinse for Relieving Tooth Sensitivity
ClinicalTrials.gov study NCT01727258. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: An experimental test of the mutation-selection balance model for the maintenance of genetic variance in fitness components
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Data from: Experimental tests of sex allocation theory with two species of simultaneously hermaphroditic acorn barnacles
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Data from: Evolutionary change in testes tissue competition among experimental populations of house mice
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Data from: An experimental test of whether cheating is context dependent
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Data from: An experimental test of the relationship between yolk testosterone and the social environment in a colonial passerine
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Data from: The regulation of behavioral plasticity by performance-based feedback and an experimental test with avian egg production
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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.