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70 results for “functional redundancy”
Functional redundancy of non-volant small mammals increases in human-modified habitats
<p>This repository hosts all R codes, data and output supporting the findings of the study "Functional redundancy of non-volant small mammals increases in human-modified habitats", by André L. Luza (UFRGS, BR), Catherine H. Graham (WSL, CH), Sandra M. Hartz (UFRGS, BR), and Dirk, N. Karger (WSL, CH).</p> <p>The only data that are not here are the Ecoregions of WWF. These data can be found in the webpage of WWF.</p>
Data for: Functional redundancy of weed seed predation is reduced by intensified agriculture
<p>Intensive agriculture, a driver of biodiversity loss, can diminish ecosystem functions and their stability. Biodiversity can increase functional redundancy and is expected to stabilize ecosystem functions. Few studies however have explored how agricultural intensity affects functional redundancy and its link with ecosystem function stability. Here, within a continent-wide study, we assess how the functional redundancy of seed predation is affected by agricultural intensity and landscape simplification. By combining carabid abundances with molecular gut content data, functional redundancy of seed predation was quantified for 65 weed genera across 60 fields in four European countries. Across weed genera, functional redundancy was reduced with high field management intensity and simplified crop rotations. Moreover, functional redundancy increased the spatial stability of weed seed predation within fields. We found that ecosystem functions are vulnerable to disturbance in intensively managed agroecosystems, providing empirical evidence of the importance of biodiversity for stable ecosystem functions across space.</p>
Supplementary material: Does functional redundancy determine the ecological severity of a mass extinction event?
<p>Many authors have noted the apparent "decoupling" of the taxonomic and ecological severity of mass extinction events, with no widely accepted mechanistic explanation for this pattern having been offered. Here we test between two key factors that potentially influence ecological severity: biosphere entropy (a measure of functional redundancy), and the degree of functional selectivity (in terms of deviation from a pattern of random extinction with respect to functional entities). While theoretical simulations suggest that the Shannon entropy of a given community prior to an extinction event determines the expected outcome following a perturbation of a given magnitude, actual variation in Shannon entropy between major extinction intervals is insufficient to explain the observed variation in ecological severity. Within this information-theoretic framework, we show that it is the degree of functional selectivity which is expected to primarily determine the ecological impact of a given perturbation when levels of functional redundancy are not substantially different.</p>
Data for: Functional redundancy of weed seed predation is reduced by intensified agriculture
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Supplementary material: Does functional redundancy determine the ecological severity of a mass extinction event?
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Low redundancy and complementarity shape ecosystem functioning in a low-diversity ecosystem
<p>Data used in the publication of "Low redundancy and complementarity shape ecosystem functioning in a low-diversity ecosystem" in the Journal of Animal Ecology.</p>
Mapping trait versus species turnover reveals spatiotemporal variation in functional redundancy and network robustness in a plant‐pollinator community
<p>1. Functional overlap among species (redundancy) is considered important in shaping competitive and mutualistic interactions that determine how communities respond to environmental change. Most studies view functional redundancy as static, yet traits within species – which ultimately shape functional redundancy – can vary over seasonal or spatial gradients. We therefore have limited understanding of how trait turnover within and between species could lead to changes in functional redundancy or how loss of traits could differentially impact mutualistic interactions depending on where and when the interactions occur in space and time.</p> <p>2. Using an Arctic bumblebee community as a case study, and 1,277 individual measures from 14 species over three annual seasons, we quantified how inter- and intraspecific body-size turnover compared to species turnover with elevation and over the season. Coupling every individual and their trait with a plant visitation, we investigated how grouping individuals by a morphological trait or by species identity altered our assessment of network structure and how this differed in space and time. Finally, we tested how the sensitivity of the network in space and time differed when simulating extinction of nodes representing either morphological trait similarity or traditional species groups. This allowed us to explore the degree to which trait-based groups increase or decrease interaction redundancy relative to species-based nodes.</p> <p>3. We found that i) groups of taxonomically and morphologically similar bees turn over in space and time independently from each other, with trait turnover being larger over the season; ii) networks composed of nodes representing species versus morphologically similar bees were structured differently; and iii) simulated loss of bee trait groups caused faster coextinction of bumblebee species and flowering plants than when bee taxonomic groups were lost. Crucially, the magnitude of these effects varied in space and time, highlighting the importance of considering spatiotemporal context when studying the relative importance of taxonomic and trait contributions to interaction network architecture.</p> <p>4. Our finding that functional redundancy varies spatiotemporally demonstrates how considering the traits of individuals within networks is needed to understand the impacts of environmental variation and extinction on ecosystem functioning and resilience.</p>
Data from: Functionally redundant multimodal predator cues elicit changes in prey foraging behavior
<p><span>Many prey species can assess the risk of predation from information acquired through different sensory systems. For many animals, this information is detected with sensory organs specialized for visual (sight) or chemical (smell or taste) stimuli. It is unclear, however, whether information acquired through multiple sensory systems is functionally redundant or interchangeable, especially if the message is the same. Here we assess prey response to unimodal visual and chemical cues as well as multimodal (visual + chemical) cues. We specifically test if a foraging individual shows a stronger behavioral response to risk when they can perceive that risk through multimodal versus unimodal cues. To do this, we measured the functional response (prey abundance-foraging rate relationship) of Tibellus oblongus spiders foraging on midges while exposing them to visual stimuli, chemical stimuli, or a combination of both visual and chemical stimuli from potential predators. We then determined if the spider's functional response for the multimodal treatment differed more strongly from a control treatment than from either unimodal treatment. We found that under any simulated predation risk (multimodal and both unimodal), T. oblongus spiders showed longer handling times than in control groups without risk. </span><span>However, we saw no elevated anti-predator response in the multimodal treatment, suggesting that information from visual and chemical modalities is interchangeable and sufficient to indicate reliably predation risk. </span></p>
Global variation in unique and redundant mammal functional diversity across the daily cycle
<p>(1) Data S1: Excel file consisting of</p> <p>‘1_Data’ Trait data containing both missing values and imputed data, with data sources as a ‘2_Metadata’ sheet in the excel file. Activity patterns were extracted from our recently compiled database for mammals (Cox et al., 2021)<em>.</em> ‘3_Updated activity patterns’: Here, we updated activity patterns for 109 species and provide data sources. We also now consider that the African forest elephant (<em>Loxodonta cyclotis</em>) is a separate species to the African savannah elephant (<em>Loxodonta africana</em>).</p> <p>(2) README.md file describing Data S1</p> <p>(3) Supplementary information in the form of appendixes, figures and tables</p> <p> </p> <p> </p>
Supporting Information: Measuring Functional Redundancy Using Generalized Hill Numbers
<p>A number of metrics for quantifying the amount of functional redundancy in a community have been proposed over the years. Two of the most popular metrics are based on comparing a taxonomic diversity measure with a generalized form of the same measure that accounts for functional dissimilarities between taxa. These two metrics express redundancy as either an absolute or relative difference between the taxonomic diversity measure and its generalized form. Because they express the amount of redundancy in a community in terms of raw diversity values, both redundancy metrics are susceptible to the same issues that complicate the interpretation of most commonly used diversity indices.</p> <p>It is possible to overcome these issues by restating these two indices using a Hill numbers framework. As a growing number of authors have noted, these modified metrics provide a more intuitive quantitative definition of functional redundancy when used to rank communities. Beyond this intuitive definition, measuring redundancy in terms of Hill numbers allows researchers to control the influence of rare taxa on the output value, enabling ecologists to better predict how a community is expected to respond when exposed to an external perturbation that selectively eliminates rare or common taxa.</p> <p>Here I show that, of the two possible Hill number-based redundancy metrics, the form based on a popular absolute redundancy metric is extremely sensitive to differences in taxonomic diversity and can provide a misleading picture of how much redundancy is present in a community. For this reason, I argue that Hill number-based functional redundancy should be quantified using a relative metric that explicitly accounts for differences in effective taxonomic diversity. The proposed Hill number-based relative redundancy measure is shown to provide a much more complete picture of the distribution of redundant taxa within a community, highlighting subtle patterns that are completely missed by the Hill number-based absolute redundancy metric.</p>
Supporting Information: Measuring Functional Redundancy Using Generalized Hill Numbers
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Mapping trait versus species turnover reveals spatiotemporal variation in functional redundancy and network robustness in a plant‐pollinator community
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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: 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 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>
Supplement: Functional strain redundancy and persistent phage infection in a Swiss hard cheese starter culture
<p>Undefined starter cultures are bacterial communities used in cheese making. They are phenotypically stable and propagated under constant conditions in milk. This makes them interesting to understand the eco-evolutionary dynamics of microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to analyze historical samples spanning 22 years and continuous propagation for 123 generations of an important Swiss cheese starter culture. We found that the bacterial community is highly stable and dominated by two species, Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Each species is represented by a few coexisting strains. Genome sequencing, metabolomics analysis, and co-culturing experiments show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large diversity of matching CRISPR spacers. Our findings provide novel insights into strain-level diversity in domesticated microbial communities and highlight an important role of bacteria-phage interactions in cheese starter cultures. </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)
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.