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235 results for “Redundancy”
Supplementary information for: Redundancy analysis, genome-wide association studies, and the pigmentation of brown trout (Salmo trutta L.)
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Data from: Functionally redundant multimodal predator cues elicit changes in prey foraging behavior
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Functional redundancy in natural pico-phytoplankton communities depends on temperature and biogeography
<p><span><span><span><span><span><span><span><span><span><span><span>Biodiversity affects ecosystem function, and how this relationship will change in a warming world is a major and well-examined question in ecology. Yet, it remains understudied for pico-phytoplankton communities, which contribute to carbon cycles and aquatic food webs year-round. Observational studies show a link between phytoplankton community diversity and ecosystem stability, but there is only scarce causal or empirical evidence. Here, we sampled phytoplankton communities from two geographically related regions with distinct thermal and biological properties in the Southern Baltic Sea, and carried out a series of dilution/regrowth experiments across three assay temperatures. This allowed us to investigate the effects of loss of rare taxa and establish causal links in natural communities between species richness and several ecologically relevant traits (e.g. size, biomass production, and oxygen production), depending on sampling location and assay temperature. We found that the samples' bio-geographical origin determined whether and how functional redundancy changed as a function of temperature for all traits under investigation. Samples obtained from the slightly warmer and more thermally variable regions showed overall high functional redundancy. Samples from the slightly cooler, less variable, stations showed little functional redundancy, i.e. function decreased when species were lost from the community. The differences between regions were more pronounced at elevated assay temperatures. Our results imply that the importance of rare species and the amount of species required to maintain ecosystem function even under short-term warming may differ drastically even within geographically closely related regions of the same ecosystem. </span></span></span></span></span></span></span></span></span></span></span></p>
Functional diversity and redundancy of tropical forest mammals over time
Globally, tropical rain forests comprise some of the most diverse and functionally rich ecosystems but are increasingly degraded by human impacts. Protected areas have been shown to conserve species diversity, but their effectiveness at maintaining functional diversity over time is less well known, despite the fact that functional diversity likely reveals more ecological information than taxonomic diversity. By extension, the degree to which species loss decreases functional diversity within protected areas is also unknown; functional redundancy may buffer communities from loss of functional diversity from some local extinctions. Using eight years of camera trap data, we quantified annual functional dispersion of the large mammal community in the Volcán Barva region of Costa Rica and tested for changes in functional dispersion over time in response to environmental and anthropogenic predictors. We quantified functional redundancy based on modeled declines in functional dispersion with species loss. Functional dispersion did not change significantly over time and was not associated with measured environmental or anthropogenic predictors. Quantitative modeling of change in functional traits over time did not identify significant changes. We did however find qualitative trends in relative trait proportions, which could be indicative of functional change in the future. We found high functional redundancy, with average functional dispersion declining significantly only after 9 out of 21 large mammal species were lost from the community. We cautiously suggest that protected tropical rain forests can conserve functional diversity over the course of a decade even in heavily fragmented landscapes.
Taxonomic and functional annotations of the Integrated non-redundant Gene Catalog 9.9
<p>The Integrated non-redundant Gene Catalog (<strong>IGC</strong>) 9.9 is a database of 9.9 million genes from 1267 individual fecal samples together with the Homo sapiens database (MetaHIT project, grant agreement 201052). This repository contains the taxonomic and functional annotation of the IGC database.</p> <p><strong>full_taxonomy_MetaHIT99.tsv </strong>: Taxonomic assignment of proteins from IGC database with the sequence aligner DIAMOND against the non-redundant NCBI database, with an e-value threshold of 10<sup>-4</sup> </p> <p><strong>KEGG89_IGC_hs99.table</strong> : Functional annotation of proteins from IGC database with KEGG resource with an e-value threshold of 10<sup>-5</sup>, a bit-score threshold of 60 and using the sensitive mode of DIAMOND</p>
Data from: Species richness and redundancy promote persistence of exploited mutualisms in yeast
<p>Mutualisms, or reciprocally beneficial interspecific interactions, constitute the foundation of many ecological communities and agricultural systems. Mutualisms come in different forms, from pairwise interactions to extremely diverse communities, and they are continually challenged with exploitation by non-mutualistic community members (exploiters). Thus, understanding how mutualisms persist remains an essential question in ecology. Theory suggests that high species richness and functional redundancy could promote mutualism persistence in complex mutualistic communities. Using a yeast system (<i>Saccharomyces cerevisiae</i>), we experimentally show that communities with the greatest mutualist richness and functional redundancy are nearly two times more likely to survive exploitation than are<b> </b>simple communities. Persistence increased because diverse communities were better able to mitigate the negative effects of competition with exploiters. Thus, large mutualistic networks may be inherently buffered from exploitation.</p>
Data from: Genetic redundancy fuels polygenic adaptation in Drosophila
The genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic—i.e., result from selection on a large number of genetic loci—but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes (AFCs) across many contributing loci. To resolve this, we use laboratory natural selection to detect signatures for selective sweeps and polygenic adaptation. We exposed 10 replicates of a Drosophila simulans population to a new temperature regime and uncovered a polygenic architecture of an adaptive trait with high genetic redundancy among beneficial alleles. We observed convergent responses for several phenotypes—e.g., fitness, metabolic rate, and fat content—and a strong polygenic response (99 selected alleles; mean s = 0.059). However, each of these selected alleles increased in frequency only in a subset of the evolving replicates. We discerned different evolutionary paradigms based on the heterogeneous genomic patterns among replicates. Redundancy and quantitative trait (QT) paradigms fitted the experimental data better than simulations assuming independent selective sweeps. Our results show that natural D. simulans populations harbor a vast reservoir of adaptive variation facilitating rapid evolutionary responses using multiple alternative genetic pathways converging at a new phenotypic optimum. This key property of beneficial alleles requires the modification of testing strategies in natural populations beyond the search for convergence on the molecular level.
Data from: Massive structural redundancies in species composition patterns of floodplain forest moths
Terrestrial arthropod communities usually consist of very large species numbers. Data from experiments or long time-series would be required to ascertain the functional significance of individual species. Both are largely unavailable for species-rich natural communities. Recognising structural redundancies in species composition allows for an alternative approach to address how strong functional redundancy might be in natural assemblages, if structural and functional redundancies are related to each other. Determining structural redundancies is a regular topic in aquatic ecology, but has rarely been applied to terrestrial communities. We explored the extent of structural redundancy in species-rich terrestrial insect assemblages and whether structural redundancies are contingent to species abundances or functional group affiliations. We used the BVSTEP algorithm to determine structural redundancies in a large data set of moth species (32 181 individuals; 448 species) that had been sampled with light-traps in three different floodplain forests in eastern Austria. We partitioned the moth species into 12 functional types based on larval host-plant affiliations to test if moth species included in reduced subsets represent functional groups in the same proportions as they occur in the entire fauna. We observed far more massive structural redundancies in moth assemblages than previously found in aquatic communities. Subsets containing only 8–15 species (1.8–3.3% of all recorded species) were still highly representative for the overall data. Subsets selected by the BVSTEP procedure performed better than equally small subsets that were defined solely by species abundances or by functional group affiliations. Effective 'surrogate' subsets contained only 6–9 of the 12 functional moth types. High abundance only loosely corresponded with the frequency at which a moth species was included in the subsets. Thus, certain uncommon species contribute importantly to species composition patterns. Our results show unexpectedly extensive structural redundancies in complex floodplain forest moth communities, which may also indicate strong functional redundancies.
Data from: Mouse fitness measures reveal incomplete functional redundancy of Hox paralogous group 1 proteins
Here we assess the fitness consequences of the replacement of the Hoxa1 coding region with its paralog Hoxb1 in mice (Mus musculus) residing in semi-natural enclosures. Previously, this Hoxa1B1 swap was reported as resulting in no discernible embryonic or physiological phenotype (i.e., functionally redundant), despite the 51% amino acid sequence differences between these two Hox proteins. Within heterozygous breeding cages no differences in litter size nor deviations from Mendelian genotypic expectations were observed in the outbred progeny; however, within semi-natural population enclosures mice homozygous for the Hoxa1B1 swap were out-reproduced by controls resulting in the mutant allele being only 87.5% as frequent as the control in offspring born within enclosures. Specifically, Hoxa1B1 founders produced only 77.9% as many offspring relative to controls, as measured by homozygous pups, and a 22.1% deficiency of heterozygous offspring was also observed. These data suggest that Hoxa1 and Hoxb1 have diverged in function through either sub- or neo-functionalization and that the HoxA1 and HoxB1 proteins are not mutually interchangeable when expressed from the Hoxa1 locus. The fitness assays conducted under naturalistic conditions in this study have provided an ultimate-level assessment of the postulated equivalence of competing alleles. Characterization of these differences has provided greater understanding of the forces shaping the maintenance and diversifications of Hox genes as well as other paralogous genes. This fitness assay approach can be applied to any genetic manipulation and often provides the most sensitive way to detect functional differences.
Data from: Land use alters trophic redundancy and resource flow through stream food webs
1. The changes to physical and chemical ecosystem characteristics as a response to pervasive and intensifying land use have the potential to alter the consumer-resource interactions and to rewire the flow of energy through entire food webs. 2. We investigated these structural and functional properties of food webs in stream ecosystems distributed across woodland, agricultural and urban areas in the Zagreb region of Croatia. We compared resource availability and consumer diet composition using stable isotope mixing models and tested how the isotopic variance of basal resources, primary consumers, macroinvertebrate predators, and other food-web characteristics change with different land use types. 3. Combination of increased loading and altered composition of nutrients, lower water discharge and higher light availability at urban sites likely promoted the contribution of aquatic macrophytes to diets of primary consumers. Macroinvertebrate predators shifted their diet, relying more on active filterers at urban sites relative to woodland and agricultural sites. Urban food webs also had lower trophic redundancy (i.e. fewer species at each trophic level) and a more homogenised energy flow from lower to higher trophic levels. There was no effect of land use on isotopic variation of basal resources, primary consumers or macroinvertebrate predators, but all these trophic groups at urban and agricultural sites were 15N-enriched relative to their counterparts in woodland stream food webs. 4. The physical and chemical ecosystem characteristics associated with intensive land use altered the resource availability, trophic redundancy and the flow of energy to other trophic levels, with potentially negative consequences for community dynamics and ecosystem functioning. These empirical findings indicate that reducing nutrient pollution, agricultural runoffs and maintaining riparian vegetation can mitigate the impacts of land use on structure and function of stream ecosystems.
Data from: Impact of ecological redundancy on the performance of machine learning classifiers in vegetation mapping
Vegetation maps are models of the real vegetation patterns and are considered important tools in conservation and management planning. Maps created through traditional methods can be expensive and time‐consuming, thus, new more efficient approaches are needed. The prediction of vegetation patterns using machine learning shows promise, but many factors may impact on its performance. One important factor is the nature of the vegetation–environment relationship assessed and ecological redundancy. We used two datasets with known ecological redundancy levels (strength of the vegetation–environment relationship) to evaluate the performance of four machine learning (ML) classifiers (classification trees, random forests, support vector machines, and nearest neighbor). These models used climatic and soil variables as environmental predictors with pretreatment of the datasets (principal component analysis and feature selection) and involved three spatial scales. We show that the ML classifiers produced more reliable results in regions where the vegetation–environment relationship is stronger as opposed to regions characterized by redundant vegetation patterns. The pretreatment of datasets and reduction in prediction scale had a substantial influence on the predictive performance of the classifiers. The use of ML classifiers to create potential vegetation maps shows promise as a more efficient way of vegetation modeling. The difference in performance between areas with poorly versus well‐structured vegetation–environment relationships shows that some level of understanding of the ecology of the target region is required prior to their application. Even in areas with poorly structured vegetation–environment relationships, it is possible to improve classifier performance by either pretreating the dataset or reducing the spatial scale of the predictions.
Data and code for the article " Dissimilarity of vertebrate trophic interactions reveals spatial uniqueness but functional redundancy across Europe"
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Post-drought community turnover and functional redundancy in a tropical forest understorey
<p>Drought events are increasingly frequent, threatening the biodiversity of tropical forests. The understorey comprises a large fraction of the total plant species richness of these systems with the presence of Individual plants of some highly diverse Angiosperm families are patchily organized in the understorey of these communities. Here we quantified the effects of a drought on abundance and functional structures and on the ecosystem functioning of these patches Rubiaceae assemblages along a topographic gradient. We show that swarms of species can maintain biological diversity and stability in ecosystem functioning under drought in the understorey of a tropical forest. (Published in Journal Vegetation Science; Funded by Fundação de Amparo à Pesquisa e Inovação do Espírito Santo, FAPES).</p> <p>If you have any query, write to: karinnasantos0@gmail.com</p>
Phenotype data for: Pleiotropic and non-redundant effects of an auxin importer in Setaria and maize
<p>Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in <i>Setaria viridis </i>and maize, we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, and glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of <i>ZmAUX1</i> also affect vegetative development. A GFP-tagged construct of <i>Spp1</i> under its native promoter showed that the SPP1 protein localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis finds that most gene expression modules are conserved between mutant and wildtype plants, with only a few hundred genes differentially expressed in <i>spp1</i> inflorescences. Using CRISPR-Cas9 technology, we disrupted <i>SPP1</i> and the other four <i>AUX1</i> homologs in <i>S. viridis</i>. SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, leaf, and root development. The AUX1 importers are thus not fully redundant in <i>S. viridis</i>. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.</p>
Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: viruses, plasmids, and more
<p>Supplementary Table 2-1. Samples and assembly summary <br> Supplementary Table 2-2. CRISPR-targeted TR sequence summary</p>
SSR and SNP profiles obtained for 40 non-redundant grapevine genotypes found in the living collection of Ain Taoujdate (Morocco)
<p>This dataset includes the genetic profiles (13 SSR and 240 SNP markers) of 40 grapevine genotypes identified in the living collection of Ain Taoujdate (Morocco)</p>
Dataset for Unique and redundant roles of mouse BCMA, TACI, BAFF, APRIL and IL-6 in supporting antibody-producing cells in different tissues
<p>This dataset is related to "Unique and redundant roles of mouse BCMA, TACI, BAFF, APRIL and IL-6 in supporting antibody-producing cells in different tissues" (Eslami M, Schuepbach-Mallpell S, Diana D, Willen L, Kowalczyk-Quintas C, Desponds C, Peter B, Vigolo M, Renevey F, Donzé O, Lüther SA, Yalkinoglu Ö, Alouche N, Schneider P).</p>
Replication Package for: "Redundancy-free Analysis of Multi-revision Software Artifacts"
<p>Researchers often analyze several revisions of a software project to obtain historical data about its evolution. For example, they statically analyze the source code and monitor the evolution of certain metrics over multiple revisions. The time and resource requirements for running these analyses often make it necessary to limit the number of analyzed revisions, e.g. by only selecting major revisions or by using a coarse-grained sampling strategy, which could remove significant details of the evolution. Most existing analysis techniques are not designed for the analysis of multi-revision artifacts and they treat each revision individually. However, the actual difference between two subsequent revisions is typically very small. Thus, tools tailored for the analysis of multiple revisions should only analyze these differences, thereby preventing re-computation and storage of redundant data, improving scalability and enabling the study of a larger number of revisions. In this work, we propose the Lean Language-Independent Software Analyzer (LISA), a generic framework for representing and analyzing multi-revisioned software artifacts. It employs a redundancy-free, multi-revision representation for artifacts and avoids re-computation by only analyzing changed artifact fragments across thousands of revisions. The evaluation of our approach consists of measuring the effect of each individual technique incorporated, an in-depth study of LISA's resource requirements and a large-scale analysis over 7 million program revisions of 4,000 software projects written in four languages. We show that the time and space requirements for multi-revision analyses can be reduced by multiple orders of magnitude, when compared to traditional, sequential approaches.</p>
FIGURE 2. Individual hypothetical area cladograms and matrix creation through BuM 2.0. A. Individual area cladogram with a redundant Area E. B. Individual area cladogram with a redundant Area D. C. Individual area cladogram with a in BuM 2.0: Software for online generation of matrices for Brooks Parsimony Analysis
FIGURE 2. Individual hypothetical area cladograms and matrix creation through BuM 2.0. A. Individual area cladogram with a redundant Area E. B. Individual area cladogram with a redundant Area D. C. Individual area cladogram with a MAST (D#E). D. Combined MRP-matrix after BuM 2.0 (option Modified BPA); og: outgroup. E. General area cladogram after the parsimony analysis of the combined matrix. The resulting pattern converges with the actual pattern of fragmentation of ancestral Area 0.
FIGURE 6. Redundancy Analysis biplot ordination diagram, obtain from a in The recognition of infraspecific taxa in Juniperus brevifolia (Cupressaceae)
FIGURE 6. Redundancy Analysis biplot ordination diagram, obtain from a matrix of 12 populations and 10 abiotic variables (not all variables are shown) (Abbreviations: see Table 1) (adapted from Elias 2007).
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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.