Negative environmental perturbations may improve species persistence.
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ABSTRACT:
SUBMITTER: Robert A
PROVIDER: S-EPMC1634910 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Epistasis describes the phenomenon that mutations at different loci do not have independent effects with regard to certain phenotypes. Understanding the global epistatic landscape is vital for many genetic and evolutionary theories. Current knowledge for epistatic dynamics under multiple conditions is limited by the technological difficulties in experimentally screening epistatic relations among genes. We explored this issue by applying flux balance analysis to simulate epistatic landscapes under various environmental perturbations. Specifically, we looked at gene-gene epistatic interactions, where the mutations were assumed to occur in different genes. We predicted that epistasis tends to become more positive from glucose-abundant to nutrient-limiting conditions, indicating that selection might be less effective in removing deleterious mutations in the latter. We also observed a stable core of epistatic interactions in all tested conditions, as well as many epistatic interactions unique to each condition. Interestingly, genes in the stable epistatic interaction network are directly linked to most other genes whereas genes with condition-specific epistasis form a scale-free network. Furthermore, genes with stable epistasis tend to have similar evolutionary rates, whereas this co-evolving relationship does not hold for genes with condition-specific epistasis. Our findings provide a novel genome-wide picture about epistatic dynamics under environmental perturbations.
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Project description:Although collectively behaving animal groups often show large-scale order (such as in bird flocks), they need not always (such as in insect swarms). It has been suggested that the signature of collective behaviour in disordered groups is a residual long-range correlation. However, results in the literature have reported contradictory results as to the presence of long-range correlation in insect swarms, with swarms in the wild displaying correlation but those in a controlled laboratory environment not. We resolve these apparently incompatible results by showing that the external perturbations generically induce the emergence of correlations. We apply a range of different external stimuli to laboratory swarms of the non-biting midge Chironomus riparius, and show that in all cases correlations appear when perturbations are introduced. We confirm the generic nature of these results by showing that they can be reproduced in a stochastic model of swarms. Given that swarms in the wild will always have to contend with environmental stimuli, our results thus harmonize previous findings. These findings emphasize that collective behaviour cannot be understood in isolation without considering its environmental context, and that new research is needed to disentangle the distinct roles of intrinsic dynamics and external stimuli.
| S-EPMC7115240 | biostudies-literature
Project description:BackgroundA scarcely studied consequence of urbanization is the effect of temporal stabilization of the environment on bird communities. This alteration is thought to dampen environmental variations between day and night, seasons and years, promoting a temporal persistence of bird composition in urban areas. The aim of this study was to review current evidence of temporal stabilization of biotic and abiotic factors in urban environments and the potential effects of such stabilization on temporal variation of bird species presence at different temporal scales.MethodsI selected the literature by searching published articles and book chapters using Scopus and Google scholar. I only included articles that compared the temporal variation of bird composition or resources between different levels of urbanization.ResultsIn general, there is evidence of temporal stabilization of abiotic and biotic factors at the three time scales considered. At the diurnal scale, the main factor considered was artificial light in the context of light pollution. At the seasonal and interannual scales, several case studies found a smaller temporal variation of primary productivity in urban than in natural and rural areas. Bird species composition showed more stabilization in urban environments at the three temporal scales: (1) several case studies reported bird activity at night, associated with artificial light; (2) studies in urban parks and along urbanization gradients showed smaller seasonal variation of bird composition in the more urbanized areas; and (3) in general, case studies along urbanization gradients showed smaller interannual variation of bird composition in the more urbanized areas, although some studies showed no relationships or opposite trends than expected.DiscussionThe published evidence suggests that urban areas dampen the natural cycles at several temporal scales. The stabilization of biotic and abiotic factors, such as light, temperature, food and habitat structure, is desynchronized from natural diurnal, seasonal and interannual cycles. However, there is a dearth of long-term comparisons of bird composition and studies that simultaneously analyze the relationship between resources and bird composition stabilization at the seasonal and interannual scales. More research is needed in the Southern hemisphere, where there is a lack of studies dealing with the seasonal and interannual variations of primary productivity along urbanization gradients and nocturnal activity of bird species. A future research agenda should include differentiation of spatial and temporal homogenization of avifaunas.
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Project description:Correlation among traits is a fundamental feature of biological systems that remains difficult to study. To address this problem, we developed a flexible approach that allows us to identify factors associated with inter-individual variation in correlation. We use data from three human cohorts to study the effects of genetic and environmental variation on correlations among mRNA transcripts and among NMR metabolites. We first show that environmental exposures (infection and disease) lead to a systematic loss of correlation, which we define as 'decoherence'. Using longitudinal data, we show that decoherent metabolites are better predictors of whether someone will develop metabolic syndrome than metabolites commonly used as biomarkers of this disease. Finally, we demonstrate that correlation itself is under genetic control by mapping hundreds of 'correlation quantitative trait loci (QTLs)'. Together, this work furthers our understanding of how and why coordinated biological processes break down, and points to a potential role for decoherence in disease. This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Project description:BackgroundDifficult temperament in infancy is a risk factor for forms of later internalizing and externalizing psychopathology, including depression and anxiety. A better understanding of the roots of difficult temperament requires assessment of its early development with a genetically informative design. The goal of this study was to estimate genetic and environmental contributions to individual differences in infant negative emotionality, their persistence over time and their influences on stability between 5 and 18 months of age.MethodParticipants were 244 monozygotic and 394 dizygotic twin pairs (49.7% male) recruited from birth. Mothers rated their twins for negative emotionality at 5 and 18 months. Longitudinal analysis of stability and innovation between the two time points was performed in Mplus.ResultsThere were substantial and similar heritability (approximately 31%) and shared environmental (57.3%) contributions to negative emotionality at both 5 and 18 months. The trait's interindividual stability across time was both genetically- and environmentally- mediated. Evidence of innovative effects (i.e., variance at 18 months independent from variance at 5 months) indicated that negative emotionality is developmentally dynamic and affected by persistent and new genetic and environmental factors at 18 months.ConclusionsIn the first two years of life, ongoing genetic and environmental influences support temperamental negative emotionality but new genetic and environmental factors also indicate dynamic change of those factors across time. A better understanding of the source and timing of factors on temperament in early development, and role of sex, could improve efforts to prevent related psychopathology.
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Project description:Progress in systems biology depends on accurate descriptions of biological networks. Connections in a regulatory network are identified as correlations of gene expression across a set of environmental or genetic perturbations. To use this information to predict system behavior, we must test how the nature of perturbations affects topologies of networks they reveal. To probe this question, we focused on metabolism of Drosophila melanogaster. Our source of perturbations is a set of crosses among 92 wild-derived lines from five populations, replicated in a manner permitting separate assessment of the effects of genetic variation and environmental fluctuation. We directly assayed activities of enzymes and levels of metabolites. Using a multivariate Bayesian model, we estimated covariance among metabolic parameters and built fine-grained probabilistic models of network topology. The environmental and genetic co-regulation networks are substantially the same among five populations. However, genetic and environmental perturbations reveal qualitative differences in metabolic regulation, suggesting that environmental shifts, such as diet modifications, produce different systemic effects than genetic changes, even if the primary targets are the same.
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Project description:Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession.
| S-EPMC3948316 | biostudies-literature
Project description:BackgroundCoral reefs are facing unprecedented pressure on local and global scales. Sensitive and rapid markers for ecosystem stress are urgently needed to underpin effective management and restoration strategies. Although the fundamental contribution of microbes to the stability and functioning of coral reefs is widely recognised, it remains unclear how different reef microbiomes respond to environmental perturbations and whether microbiomes are sensitive enough to predict environmental anomalies that can lead to ecosystem stress. However, the lack of coral reef microbial baselines hinders our ability to study the link between shifts in microbiomes and ecosystem stress. In this study, we established a comprehensive microbial reference database for selected Great Barrier Reef sites to assess the diagnostic value of multiple free-living and host-associated reef microbiomes to infer the environmental state of coral reef ecosystems.ResultsA comprehensive microbial reference database, originating from multiple coral reef microbiomes (i.e. seawater, sediment, corals, sponges and macroalgae), was generated by 16S rRNA gene sequencing for 381 samples collected over the course of 16 months. By coupling this database to environmental parameters, we showed that the seawater microbiome has the greatest diagnostic value to infer shifts in the surrounding reef environment. In fact, 56% of the observed compositional variation in the microbiome was explained by environmental parameters, and temporal successions in the seawater microbiome were characterised by uniform community assembly patterns. Host-associated microbiomes, in contrast, were five-times less responsive to the environment and their community assembly patterns were generally less uniform. By applying a suite of indicator value and machine learning approaches, we further showed that seawater microbial community data provide an accurate prediction of temperature and eutrophication state (i.e. chlorophyll concentration and turbidity).ConclusionOur results reveal that free-living microbial communities have a high potential to infer environmental parameters due to their environmental sensitivity and predictability. This highlights the diagnostic value of microorganisms and illustrates how long-term coral reef monitoring initiatives could be enhanced by incorporating assessments of microbial communities in seawater. We therefore recommend timely integration of microbial sampling into current coral reef monitoring initiatives.
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Project description:The ability to respond quickly and accurately to an external perturbation with a stepping response is critical to avoid falls and this ability is impaired in older, compared to young adults. However, little is known about whether young and older adults improve compensatory stepping responses similarly with practice. This study compares the extent to which young and older adults can improve, retain, and generalize postural compensatory steps in response to external perturbations. Centre of mass displacement, step characteristics and lower leg muscle activation latencies were measured during one training session of compensatory stepping in response to large surface translations in 13 young and 12 older adults. Retention was tested 24 h later. Older adults decreased their center of mass displacements over repeated exposure to large surface translations in both the anterior and posterior directions and retained these improvements. In contrast, young adults only showed adaptation and retention of forward stepping responses. Neither group was able to generalize improvements in stepping responses across directions. These results suggest step training may be beneficial for older adults, however additional, multidirectional training may be necessary to facilitate generalization of postural stepping responses for any direction of a slip or trip.
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Project description:Environmental perturbations have large effects on both organismal and cellular traits, including gene expression, but the extent to which the environment affects RNA processing remains largely uncharacterized. Recent studies have identified a large number of genetic variants associated with variation in RNA processing that also have an important role in complex traits; yet we do not know in which contexts the different underlying isoforms are used. Here, we comprehensively characterized changes in RNA processing events across 89 environments in five human cell types and identified 15,300 event shifts (FDR = 15%) comprised of eight event types in over 4,000 genes. Many of these changes occur consistently in the same direction across conditions, indicative of global regulation by trans factors. Accordingly, we demonstrate that environmental modulation of splicing factor binding predicts shifts in intron retention, and that binding of transcription factors predicts shifts in alternative first exon (AFE) usage in response to specific treatments. We validated the mechanism hypothesized for AFE in two independent datasets. Using ATAC-seq, we found altered binding of 64 factors in response to selenium at sites of AFE shift, including ELF2 and other factors in the ETS family. We also performed AFE QTL mapping in 373 individuals and found an enrichment for SNPs predicted to disrupt binding of the ELF2 factor. Together, these results demonstrate that RNA processing is dramatically changed in response to environmental perturbations through specific mechanisms regulated by trans factors.
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