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741 results for “Decay”
Decay by ectomycorrhizal fungi couples soil organic matter to nitrogen availability
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Geographical gradient of fungal decay type in Norway spruce logs in Europe and its impact on seedling establishment
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Nitrogen and Phosphorus Content of Decaying Roots on Hog Island, VA 1991-1992
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Rates of Mass Loss During Root Decay on Hog Island, VA 1991-1993
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Reproduction package for the paper "A strongly changing accretion morphology during the outburst decay of the neutron star X-ray binary 4U 1608-52"
<p>This is a basic reproduction package for the paper "A strongly changing accretion morphology during the outburst decay of the neutron star X-ray binary 4U 1608-52" by J. van den Eijnden et al. (2020). It provides reduced data sets, simulation scripts, X-ray spectral fits, and plotting scripts to allow the reproduction of the work performed in this paper. It also lists software used and data archives containing the public observational data. </p> <p>An open access version of the paper can be found at <a href="https://arxiv.org/abs/2002.04003">https://arxiv.org/abs/2002.04003</a>.</p>
How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels
<p>The <em>Mytilus</em> complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.</p>
Data from: Similarity in mycorrhizal communities associating with two widespread terrestrial orchids decays with distance
Aim: Interactions with mycorrhizal fungi are increasingly recognized as an important factor underlying the distribution and abundance of orchid species. However, the geographic distribution of orchid mycorrhizal fungi (OMF) and how their communities vary over large geographical areas are less well understood. Because climatic and environmental similarity may decrease with geographical distance or because some OMF have limited dispersal capabilities, similarities in orchid mycorrhizal communities can be expected to decrease with increasing distances separating orchid populations. However, up till now empirical evidence is largely lacking. Location: Eurasia Taxa: Gymnadenia conopsea (L.) R. Brown and Epipactis helleborine (L.) Crantz Methods: High-throughput sequencing was used to perform a cross-continental comparison of OMF that associate with two widespread Eurasian terrestrial orchids, Epipactis helleborine and Gymnadenia conopsea. Both phylogenetic and non-phylogenetic measures of community dissimilarity and their components were calculated and related to geographic distances using Mantel tests. Results: Our results showed that in both orchid species similarity in mycorrhizal communities decreased significantly with geographical distance. Decomposing the contribution of spatial turnover and nestedness to overall dissimilarity showed that the observed dissimilarity was mainly the result of species replacement between regions, and not of species loss. Similarly, a strong relationship was observed between phylogenetic community dissimilarity and geographic distance. Decomposing PCD values into a nonphylogenetic and phylogenetic component showed that orchid populations located closely next to each other were likely to contain the same OTUs, but that the non-shared taxa came from different phylogenetic clades. Species indicator analyses showed that the majority of OMF OTUs were restricted to particular geographic areas. However, some OTUs occurred in both continents, indicating that some fungi have very wide distributions. Main conclusions: Overall, these results demonstrate that orchid mycorrhizal communities differ substantially across large geographic areas, but that the distribution of orchids is not necessarily restricted by the distribution of particular OMF. Hence, widespread orchid species can be considered mycorrhizal generalists that are flexible in the OMF with which they associate across large geographic areas.
Impacts of speciation and extinction measured by an evolutionary decay clock
<p>The hypothesis that destructive mass extinctions enable creative evolutionary radiations (creative destruction) is central to classic concepts of macroevolution[1,2]. However, the relative impacts of extinction and radiation on the co-occurrence of species have not been directly quantitatively compared across the Phanerozoic eon. Here we apply machine learning to generate a spatial embedding (multidimensional ordination) of the temporal co-occurrence structure of the Phanerozoic fossil record, covering 1,273,254 occurrences in the Paleobiology Database for 171,231 embedded species. This facilitates simultaneous comparison of macroevolutionary disruptions, using measures independent of secular diversity trends. Among the 5% most significant periods of disruption, we identify the 'big five' mass extinction events[2], seven additional mass extinctions, two combined mass extinction–radiation events and 15 mass radiations. In contrast to narratives that emphasize post-extinction radiations[1,3], we find that the proportionally most comparable mass radiations and extinctions (such as the Cambrian explosion and the end-Permian mass extinction) are typically decoupled in time, refuting any direct causal relationship between them. Moreover, in addition to extinctions[4], evolutionary radiations themselves cause evolutionary decay (modelled co-occurrence probability and shared fraction of species between times approaching zero), a concept that we describe as destructive creation. A direct test of the time to over-threshold macroevolutionary decay[4] (shared fraction of species between two times ≤ 0.1), counted by the decay clock, reveals saw-toothed fluctuations around a Phanerozoic mean of 18.6 million years. As the Quaternary period began at a below-average decay-clock time of 11 million years, modern extinctions further increase life's decay-clock debt.</p>
Data from: Decay of ecosystem differences and decoupling of tree community-soil environment relationships at ecotones
Ecotones are important landscape features where there is a transition between adjoining ecosystems. However, there are few generalized hypotheses about the response of communities to ecotones, except for a proposed increase in species richness that receives varying empirical support. Based on the assumption that transport of abiotic material and dispersal of organism propagules across ecotones are independent processes, we propose the new hypothesis that ecotones decouple community-environment relationships, increasing the importance of spatial structure that is independent of the environment. We tested this hypothesis by examining the effects of ecotones on relationships between trees and soil properties in a temperate deciduous forest. The study area included different landforms defined by topography, hydrology, and geomorphology, which we designated upland, bottomland, and riparian forests. The site also included a mowed herbaceous corridor. We found that soil properties and tree community composition significantly differed among landforms, and thus they could be treated as differing ecosystem types. However, inclusion of plots near ecotones significantly reduced the variance explained by landform due to introduction of increased noise, increased similarity of ecotone plots in different landforms, or both. To examine tree community-soil environment relationships, factorial kriging analysis was used to decompose variation in soil properties into structures associated with differing spatial scales, which were then used as predictors of tree composition using redundancy analysis. In agreement with the ecotone-decoupling hypothesis, we found that ecotones introduced significant unexplained variation into correlations between tree community composition and soil properties. In addition, spatial variation in tree community composition that was independent of soil properties was only detected when ecotones were included in the analysis, and little variation in tree community composition was attributed to small-scale soil property structures. Together, these results indicate that dispersal limitation and mass effects in the tree community take on increased importance near ecotones. We found no consistent changes in tree species richness associated with ecotones, and suggest that the ecotone-decoupling hypothesis may correspond with a more general community-level pattern that warrants further testing. Decoupling of community-environment relationships near ecotones also has important implications for accuracy of models predicting community distributions from abiotic information.
Data from: Photosynthesis, growth, and decay traits in Sphagnum – a multispecies comparison
Peat mosses (Sphagnum) largely govern carbon sequestration in Northern Hemisphere peatlands. We investigated functional traits related to growth and decomposition in Sphagnum species. We tested the importance of environment and phylogeny in driving species traits and investigated trade-offs among them. We selected 15 globally important Sphagnum species, representing four sections (subgenera) and a range of peatland habitats. We measured rates of photosynthesis and decomposition in standard laboratory conditions as measures of innate growth and decay potential, and related this to realized growth, production, and decomposition in their natural habitats. In general, we found support for a trade-off between measures of growth and decomposition. However, the relationships are not strong, with r ranging between 0.24 and 0.45 for different measures of growth versus decomposition. Using photosynthetic rate to predict decomposition in standard conditions yielded R2 = 0.20. Habitat and section (phylogeny) affected the traits and the trade-offs. In a wet year, species from sections Cuspidata and Sphagnum had the highest production, but in a dry year, differences among species, sections, and habitats evened out. Cuspidata species in general produced easily decomposable litter, but their decay in the field was hampered, probably due to near-surface anoxia in their wet habitats. In a principal components analysis, PCA, photosynthetic capacity, production, and laboratory decomposition acted in the same direction. The species were imperfectly clustered according to vegetation type and phylogeny, so that some species clustered with others in the same section, whereas others clustered more clearly with others from similar vegetation types. Our study includes a wider range of species and habitats than previous trait analyses in Sphagnum and shows that while the previously described growth–decay trade-off exists, it is far from perfect. We therefore suggest that our species-specific trait measures offer opportunities for improvements of peatland ecosystem models. Innate qualities measured in laboratory conditions translate differently to field responses. Most dramatically, fast-growing species could only realize their potential in a wet year. The same species decompose fast in laboratory, but their decomposition was more retarded in the field than that of other species. These relationships are crucial for understanding the long-term dynamics of peatland communities.
Data from: Distance-decay differs among vertical strata in a tropical rainforest
1. Assemblage similarity decays with geographic distance—a pattern known as the distance-decay relationship. While this pattern has been investigated for a wide range of organisms, ecosystems, and geographical gradients, whether these changes vary more cryptically across different forest strata (from ground to canopy) remains elusive. 2. Here, we investigated the influence of ground vs arboreal assemblages to the general distance-decay relationship observed in forests. We seek to explain differences in distance-decay relationships between strata in the context of the vertical stratification of assemblage composition, richness, and abundance. 3. We surveyed for a climate sensitive model organism, amphibians, across vertical rainforest strata in Madagascar. For each tree, we defined assemblages of ground-dwelling, understory, or canopy species. We calculated horizontal distance-decay in similarity across all trees, and across assemblages of species found in different forest strata (ground, understory, and canopy). 4. We demonstrate that within stratum comparisons exhibit a classic distance-decay relationship for canopy and understory communities but no distance-decay relationships for ground communities. We suggest that differences in horizontal turnover between strata may be due to local scale habitat and resource heterogeneity in the canopy, or the influence of arboreal traits on species dispersal and distribution. 5. Synthesis: Biodiversity patterns in horizontal space were not consistent across vertical space, suggesting that canopy fauna may not play by the same set of 'rules' as their conspecifics living below them on the ground. Our study provides compelling evidence that the above-ground amphibian assemblage of tropical rainforests is the primary driver of the classical distance-decay relationship.
Substrate quality drives fungal necromass decay and decomposer community structure under contrasting vegetation types
<p>1. Fungal mycelium is increasingly recognized as a central component of soil biogeochemical cycling, yet our current understanding of the ecological controls on fungal necromass decomposition is limited to single sites and vegetation types.</p> <p>2. By deploying common fungal necromass substrates in a temperate oak savannah and hardwood forest in the midwestern USA, we assessed the generality of the rate at which high- and low-quality fungal necromass decomposes; further, we investigated how the decomposer 'necrobiome' varies both across and within sites under vegetation types dominated by either arbuscular (AM) or ectomycorrhizal (EM) plants.</p> <p>3. The effects of necromass quality on decay rate were robust to site and vegetation type differences, with high-quality fungal necromass decomposing, on average, 2.5 times faster during the initial stages of decay. Across vegetation types, bacterial and fungal communities present on decaying necromass differed from bulk soil microbial communities and were influenced by necromass quality. Moulds, yeasts and copiotrophic bacteria consistently dominated the necrobiome of high-quality fungal substrates.</p> <p>4. Synthesis: We show that regardless of differences in decay environments, high-quality fungal substrates decompose faster and support different types of decomposer microorganisms when compared with low-quality fungal tissues. These findings help to refine our theoretical understanding of the dominant factors affecting fast cycling components of soil organic matter (SOM) and the microbial communities associated with rapid decay.</p>
Data from: Neutral and selection-driven decay of sexual traits in asexual stick insects
Environmental shifts and lifestyle changes may result in formerly adaptive traits becoming non-functional or maladaptive. The subsequent decay of such traits highlights the importance of natural selection for adaptations, yet its causes have rarely been investigated. To study the fate of formerly adaptive traits after lifestyle changes, we evaluated sexual traits in five independently derived asexual lineages, including traits that are specific to males and therefore not exposed to selection. At least four of the asexual lineages retained the capacity to produce males that display normal courtship behaviours and are able to fertilize eggs of females from related sexual species. The maintenance of male traits may stem from pleiotropy, or from these traits only regressing via drift, which may require millions of years to generate phenotypic effects. By contrast, we found parallel decay of sexual traits in females. Asexual females produced altered airborne and contact signals, had modified sperm storage organs, and lost the ability to fertilize their eggs, impeding reversals to sexual reproduction. Female sexual traits were decayed even in recently derived asexuals, suggesting that trait changes following the evolution of asexuality, when they occur, proceed rapidly and are driven by selective processes rather than drift.
Data from: Exploring an alternative explanation for the second phase of viral decay: infection of short-lived cells in a drug-limited compartment during HAART
Most HIV-infected patients who initiate combination antiretroviral therapy experience a viral load decline in several phases. These phases are characterized by different rates of viral load decay that decrease when transitioning from one phase to the next. There is no consensus as to the origin of these phases. One hypothesis put forward is that short- and long-lived infected cells are responsible for the first and second phases of decay, respectively. However, significant differences in drug concentrations are observed in monocytes from various tissues, suggesting the first two phases of decay in viral loads could instead be attributed to short-lived cells being differently exposed to drugs. Compared to a well-exposed compartment, new cell infection can be expected in a compartment with limited drug exposure, thus leading to a slower viral load decay with potential virologic failure and drug resistance. In the current study, the latter hypothesis was investigated using a model of viral kinetics. Empirical datasets were involved in model elaboration and parameter estimation. In particular, susceptibility assay data was used for an in vitro to in vivo extrapolation based on the expected drug concentrations inside physiological compartments. Results from numerical experiments of the short-term evolution of viral loads can reproduce the first two phases of viral decay when allowing new short-lived cell infections in an unidentified drug-limited compartment. Model long-term predictions are however less consistent with clinical observations. For the hypothesis to hold, efavirenz, tenofovir and emtricitabine drug exposure in the drug-limited compartment would have to be very low compared to exposure in peripheral blood. This would lead to significant long-term viral growth and the frequent development of resistant strains, a prediction not supported by clinical observations. This suggests that the existence of a drug-limited anatomical compartment is unlikely, by itself, to explain the second phase of viral load decay.
Data from: Gauging scale effects and biogeographical signals in similarity distance decay analyses: an Early Jurassic ammonite case study
In biogeography, the similarity distance decay (SDD) relationship refers to the decrease in compositional similarity between communities with geographical distance. Although representing one of the most widely used relationships in biogeography, a review of the literature reveals that: (1) SDD is influenced by both spatial extent and sample size; (2) the potential effect of the phylogenetic level has yet to be tested; (3) the effect of a marked biogeographical structuring upon SDD patterns is largely unknown; and (4) the SDD relationship is usually explored with modern, mainly terrestrial organisms, whereas fossil taxa are seldom used in that perspective. Using this relationship, we explore the long-distance dispersal of the Early Jurassic (early Pliensbachian, c. 190.8 Ma to 187.6 Ma) ammonites of the western Tethys and adjacent areas, in a context of marked provincialism. We show that the long-distance dispersal of these ammonites is not related to shell size and shape, but rather to the environmental characteristics of the province to which they belong. This suggests that their long-distance dispersal may have been essentially driven by passive planktonic drift during early juvenile, post-hatching stages. Furthermore, it seems that the SDD relationship is not always an appropriate method to characterize the existence of a biogeographical structuring. We conducted SDD analyses at various spatial, sampling and phylogenetic scales in order to evaluate their sensitivity to scale effects. This multi-scale approach indicates that the sampling scale may influence SDD rates in an unpredictable way and that the phylogenetic level has a major impact on SDD patterns.
Data from: Exclusion of invertebrates influences saprotrophic fungal community and wood decay rate in an experimental field study
1. Decomposer communities perform an essential ecosystem function by recycling nutrients. However, the effect of higher trophic levels on microbial decomposer communities and rate of decomposition is poorly understood. We therefore conducted an exclusion experiment to test the effect of invertebrates on fungal decomposer communities in dead wood, repeated at 30 sites in two landscapes, and measured wood density to assess effect on decay rate. 2. Invertebrates were excluded from recently cut logs by cages with a 1 mm mesh net, and fungal communities in caged logs were compared to logs accessible to invertebrates by DNA metabarcoding analyses. Accessible logs included control logs, cage control logs and positive control logs. 3. We found that exclusion of invertebrates had a significant effect on fungal community composition. For example, the wood decay fungi Trametes versicolor and T. ochracea were significantly more abundant in accessible logs than in caged logs. The strongest effect on fungal community composition, however, was attributed to differing baseline conditions in the individual trees. When accounting for these baseline differences, caged logs had significantly higher wood density than control logs after two years, indicating lower rates of wood decay in caged logs. 4. Further studies, spanning several years, are required to fully understand the influence of invertebrates on fungi and wood decay. However, our results indicate that invertebrates influence both the composition of saprotrophic communities in dead wood and their decomposition function, which is vital to forest ecosystems.
Data from: Edge-mediated compositional and functional decay of tree assemblages in Amazonian forest islands after 26 years of isolation
1.Islands formed upstream of mega hydroelectric dams are excellent experimental landscapes to assess the impacts of habitat fragmentation on biodiversity. We examined the effects of plot-, patch- and landscape-scale variables on the patterns of floristic diversity across 34 forest islands that had experienced 26 years of isolation since the creation of the 4,437 km2 Balbina Hydroelectric Reservoir of central Brazilian Amazonia. In addition, three undisturbed continuous forest sites in neighbouring mainland areas were also sampled across a comparable elevational gradient. 2.We identified all live trees ≥10 cm DBH at species level within a total of 87 quarter-hectare forest plots and conducted a comprehensive compilation of functional attributes of each tree species. We then examined species-area relationships (SARs) and the additional effects of patch and landscape scale metrics on patterns of tree assemblage heterogeneity, both in terms of taxonomic and functional diversity. 3.Despite a clearly positive SAR, edge-mediated forest disturbance was the single most important driver of species composition and abundance within islands. Our results suggest that non-random floristic transitions within island plots followed a predictable pattern, with different life-history traits either penalizing or rewarding local persistence of different functional groups. Distance to edges mediated the probability of tree mortality induced by windfalls and episodic surface fires, clearly resulting in faster species turnover and unidirectional changes in guild structure within small islands where light-wooded fast-growing pioneers largely replaced heavy-wooded species of the old-growth flora. 3.Synthesis ─ Following a simultaneous 26-year post-isolation history, we disentangle the effects of habitat loss and insularization on tree assemblages within a large set of Amazonian 'true' forest islands, of variable sizes, sharing a uniform open-water matrix. Area effects are expressed via a response to edge effects, with trees in smaller islands being more vulnerable to edge-related surface fires and windthrows. Additionally, forest edge effects can be a powerful driver of non-random floristic transitions across islands within the Balbina archipelago via a process of rapid pioneer proliferation, drastically affecting both the taxonomic and functional composition of insular tree communities. Finally, our results indicate that detrimental effects of forest fragmentation induced by hydroelectric dams are considerably stronger than those of forest patches embedded within a terrestrial vegetation matrix.
Data from: Horizontal gene acquisitions, mobile element proliferation, and genome decay in the host - restricted plant pathogen Erwinia tracheiphila
Modern industrial agriculture depends on high density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared to ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, Kentucky, and Michigan. These genomes exhibit a high proportion of recent horizontal gene acquisitions, invasion and remarkable amplification of mobile genetic elements, and pseudogenization of ~20% of the coding sequences. These genome attributes indicate that E. tracheiphila recently emerged as a host-restricted pathogen. Furthermore, chromosomal rearrangements associated with phage and transposable element proliferation contributes to substantial differences in gene content and genetic architecture between the six E. tracheiphila strains and other Erwinia species. Together, these data lead us to hypothesize that E. tracheiphila has undergone recent evolution via both genome decay (pseudogenization) and genome expansion (horizontal gene transfer and mobile element amplification). Despite evidence of dramatic genomic changes, the six strains are genetically monomorphic, suggesting a recent population bottleneck and emergence into E. tracheiphila's current ecological niche.
Data from: Untangling phylogenetical, geometrical and ornamental imprints on Early Triassic ammonoid biogeography: a similarity-distance decay study.
Ammonoids are diverse and widespread fossil shelly cephalopods that flourished in the world ocean during more than 300 million years before their total extinction, 65 million years ago. In spite of two centuries of intensive scientific studies, their mode(s) of life, and most particularly long-distance dispersal abilities remain poorly known. Here we address this question by looking at the latitudinal distribution of Early Triassic (~250 Myr) ammonoids through similarity-distance decay analyses. We examine and compare how rates of similarity-distance decay differ between various systematic, shell geometry and ornamentation groups, during the same ~3.5 myr Early Triassic time interval, in order to untangle phylogenetical, geometrical and ornamental imprints on the observed biogeographical pattern. Our data do not support any phylogenetical and shell ornamentation control on the similarity-distance decay, but rather evidence a significant effect of (sub-)adult shell geometry: most evolute morphs tend to have been more endemic than most involute ones. This result contrasts with the classical hypothesis that long-distance ammonoid dispersal mainly occurred during the earliest planktonic young stages, and thus that (sub-)adult morphological characteristics should not constrain large-scale biogeographical patterns of ammonoids. While a direct control by Sea Surface Temperature can be discarded, this result may indicate that at least some adult Triassic ammonoid morphs were good active swimmers able to achieve long-distance migrations, as observed for some present-day coleoid cephalopods.
EOS-DATA-2016-01: Monte Carlo Pseudo Events for the Decays Bbar -> P mu X_nubar, P = D,pi
<p>This archive EOS-DATA-2016-01 contains pseudo events of the decays</p> <p> Bbar -> P mu X_nubar</p> <p>where X_nubar is either nubar or (nubar nu nubar), and P = D or pi. The archive<br /> complements the publication EOS-2016-01. The events are stored as binary files<br /> in the HDF5 format.</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.