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795 results for “fluctuations”
Data from: Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations
In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island Southeast Asia (ISEA). A previous study revealed signatures of inter-specific admixture between these Sus species (Frantz et al. (2013) Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus. Genome biology, 14, R107). However, the timing, directionality and extent of this admixture remain unknown. Here we use a likelihood based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that inter-specific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture.
Data from: Memory and fitness optimization of bacteria under fluctuating environments
Bacteria prudently regulate their metabolic phenotypes by sensing the availability of specific nutrients, expressing the required genes for their metabolism, and repressing them after specific metabolites are depleted. It is unclear, however, how genetic networks maintain and transmit phenotypic states between generations under rapidly fluctuating environments. By subjecting bacteria to fluctuating carbon sources (glucose and lactose) using microfluidics, we discover two types of non-genetic memory in Escherichia coli and analyze their benefits. First, phenotypic memory conferred by transmission of stable intracellular lac proteins dramatically reduces lag phases under cyclical fluctuations with intermediate timescales (1–10 generations). Second, response memory, a hysteretic behavior in which gene expression persists after removal of its external inducer, enhances adaptation when environments fluctuate over short timescales (<1 generation). Using a mathematical model we analyze the benefits of memory across environmental fluctuation timescales. We show that memory mechanisms provide an important class of survival strategies in biology that improve long-term fitness under fluctuating environments. These results can be used to understand how organisms adapt to fluctuating levels of nutrients, antibiotics, and other environmental stresses.
Data from: Both temperature fluctuations and East Asian monsoons have driven plant diversification in the karst ecosystems from southern China
Karst ecosystems in southern China are species-rich and have high levels of endemism, yet little is known regarding the evolutionary processes responsible for the origin and diversification of karst biodiversity. The genus Primulina (Gesneriaceae) comprises ca. 170 species endemic to southern China with high levels of ecological (edaphic) specialization, providing an exceptional model to study the plant diversification in karsts. We used molecular data from nine chloroplast and 11 nuclear regions and macroevolutionary analyses to assess the origin and cause of species diversification due to paleoenvironmental changes and edaphic specialization in Primulina. We found that speciation was positively associated with changes in past temperatures and East Asian monsoons through the evolutionary history of Primulina. Climatic change around the mid-Miocene triggered an early burst followed by a slowdown of diversification rate towards the present with the climate cooling. We detected different speciation rates among edaphic types, and transitions among soil types were infrequently and did not impact the overall speciation rate. Our findings suggest that both global temperature changes and East Asian monsoons have played crucial roles in floristic diversification within the karst ecosystems in southern China, such that speciation was higher when climate was warmer and wetter. This is the first study to directly demonstrate that past monsoon activity is positively correlated with speciation rate in East Asia. This case study could motivate further investigations to assess the impacts of past environmental changes on the origin and diversification of biodiversity in global karst ecosystems, most of which are under threat.
Data from: The ecology of wildlife disease surveillance: demographic and prevalence fluctuations undermine surveillance
Wildlife disease surveillance is the first line of defence against infectious disease. Fluctuations in host populations and disease prevalence are a known feature of wildlife disease systems. However, the impact of such heterogeneities on the performance of surveillance is currently poorly understood. We present the first systematic exploration of the effects of fluctuations' prevalence and host population size on the efficacy of wildlife disease surveillance systems. In this study, efficacy is measured in terms of ability to estimate long-term prevalence and detect disease risk. Our results suggest that for many wildlife disease systems, fluctuations in population size and disease lead to bias in surveillance-based estimates of prevalence and overconfidence in assessments of both the precision of prevalence estimates and the power to detect disease. Neglecting such ecological effects may lead to poorly designed surveillance and ultimately to incorrect assessments of the risks posed by disease in wildlife. This will be most problematic in systems where prevalence fluctuations are large and disease fade-outs occur. Such fluctuations are determined by the interaction of demography and disease dynamics. Although particularly likely in highly fluctuating populations typical of fecund short-lived hosts, such fluctuations cannot be ruled out in more stable populations of longer-lived hosts. Synthesis and applications. Fluctuations in population size and disease prevalence should be considered in the design and implementation of wildlife disease surveillance, and the framework presented here provides a template for conducting suitable power calculations. Ultimately, understanding the impact of fluctuations in demographic and epidemiological processes will enable improvements to wildlife disease surveillance systems leading to better characterization of, and protection against endemic, emerging and re-emerging disease threats.
Data from: Accounting for long-term directional trends on year-to-year synchrony in species fluctuations
What determines the stability of communities under environmental fluctuations remains one of the most debated questions in ecology. Scholars generally agree that the similarity in year-to-year fluctuations between species is an important determinant of this stability. Concordant fluctuations in species abundances through time (synchrony) decrease stability while discordance in fluctuations (anti-synchrony) should stabilize communities. Researchers have interpreted the community-wide degree of synchrony in temporal fluctuations as the outcome of different processes. However, existing synchrony measures depend not only on year-to-year species fluctuations, but also on long-term directional trends in species composition, for example due to land-use or climate change. The neglected effect of directional trends in species composition could cause an increase in synchrony that is not due to year-to-year fluctuations, as species that simultaneously increase (or decrease) in abundance over time will appear correlated, even if they fluctuate discordantly from year to year. The opposite pattern is also conceivable, where different species show contrasting trends in their abundances, thus overestimating year-to-year anti-synchrony. Therefore, trends in species composition may limit our understanding of potential ecological mechanisms behind synchrony between species. We propose two easily implementable solutions, with corresponding R functions, for testing and accounting for the effect of trends in species composition on overall synchrony. The first approach is based on computing synchrony over the residuals of fitted species trends over time. The second approach, applicable to already existing indices, is based on three-terms local variance, i.e. computing variance over three-years-long, movable windows. We demonstrate these methods using simulations and data from real plant communities under long-term directional changes, discussing when one approach can be preferred. We show that accounting for long-term temporal trends is both necessary and that separation of effect of trends and year-to-year fluctuation provides a better understanding of ecological mechanisms and their connections with ecological theory.
Data from: Predictability rather than amplitude of temperature fluctuations determines stress resistance in a natural population of Drosophila simulans
The adaptability of organisms to novel environmental conditions depends on the amount of genetic variance present in the population as well as on the ability of individuals to adjust their phenotype through phenotypic plasticity. Here, we investigated the phenotypic plasticity induced by a single generation's exposure to three different temperature regimes with respect to several life-history and stress-resistance traits in a natural population of Drosophila simulans. We studied a constant as well as a predictably and an unpredictably fluctuating temperature regime. We found high levels of phenotypic plasticity among all temperature regimes, suggesting a strong influence of both temperature fluctuations and their predictability. Increased heat tolerance was observed for flies developed in both types of fluctuating thermal environments compared with flies developed in a constant environment. We suggest that this was due to beneficial hardening when developing in either fluctuating temperature environment. To our surprise, flies that developed in constant and predictably changing environments were similar to each other in most traits when compared to flies from the unpredictably fluctuating environment. The unpredictably changing thermal environment imposed the most stressful condition, resulting in the lowest performance for stress-related traits, even though the absolute temperature changes never exceeded that of the predictably fluctuating environment. The overall decreased stress resistance of flies in the unpredictably fluctuating environment may be the consequence of maladaptive phenotypic plasticity in this setting, indicating that the adaptive value of plasticity depends on the predictability of the environment.
Data from: Adaptation to temporally fluctuating environments by the evolution of maternal effects
All organisms live in temporally fluctuating environments. Theory predicts that the evolution of deterministic maternal effects (i.e., anticipatory maternal effects or transgenerational phenotypic plasticity) underlies adaptation to environments that fluctuate in a predictably alternating fashion over maternal-offspring generations. In contrast, randomizing maternal effects (i.e., diversifying and conservative bet-hedging), are expected to evolve in response to unpredictably fluctuating environments. Although maternal effects are common, evidence for their adaptive significance is equivocal since they can easily evolve as a correlated response to maternal selection and may or may not increase the future fitness of offspring. Using the hermaphroditic nematode Caenorhabditis elegans, we here show that the experimental evolution of maternal glycogen provisioning underlies adaptation to a fluctuating normoxia–anoxia hatching environment by increasing embryo survival under anoxia. In strictly alternating environments, we found that hermaphrodites evolved the ability to increase embryo glycogen provisioning when they experienced normoxia and to decrease embryo glycogen provisioning when they experienced anoxia. At odds with existing theory, however, populations facing irregularly fluctuating normoxia–anoxia hatching environments failed to evolve randomizing maternal effects. Instead, adaptation in these populations may have occurred through the evolution of fitness effects that percolate over multiple generations, as they maintained considerably high expected growth rates during experimental evolution despite evolving reduced fecundity and reduced embryo survival under one or two generations of anoxia. We develop theoretical models that explain why adaptation to a wide range of patterns of environmental fluctuations hinges on the existence of deterministic maternal effects, and that such deterministic maternal effects are more likely to contribute to adaptation than randomizing maternal effects.
Data from: Mutation accumulation in selfing populations under fluctuating selection
Selfing species are prone to extinction, possibly because highly selfing populations can suffer from a continuous accumulation of deleterious mutations, a process analogous to Muller's ratchet in asexual populations. However, current theory provides little insight into which types of genes are most likely to accumulate deleterious alleles and what environmental circumstances may accelerate genomic degradation. Here we investigate temporal changes in the environment that cause fluctuations in the strength of purifying selection. We simulate selfing populations with genomes containing a mixture of loci experiencing constant selection and loci experiencing selection that fluctuates in strength (but not direction). Even when both types of loci experience the same average strength of selection, loci under fluctuating selection contribute disproportionately more to deleterious mutation accumulation. Moreover, the presence of loci experiencing fluctuating selection in the genome increases the deleterious fixation rate at loci under constant selection; under most realistic scenarios this effect of linked selection can be attributed to a reduction in N¬e. Fluctuating selection is particularly injurious when selective environments are strongly autocorrelated over time and when selection is concentrated into rare bouts of strong selection. These results imply that loci under fluctuating selection are likely important drivers of extinction in selfing species.
Data from: Do larger individuals cope with resource fluctuations better? An artificial selection approach
Size determines the rate at which organisms acquire and use resources but it is unclear what size should be favoured under unpredictable resource regimes. Some theories claim smaller organisms can grow faster following a resource pulse, whereas others argue larger species can accumulate more resources and maintain growth for longer periods between resource pulses. Testing these theories has relied on interspecific comparisons, which tend to confound body size with other life-history traits. As a more direct approach, we used 280 generations of artificial selection to evolve a 10-fold difference in mean body size between small- and large-selected phytoplankton lineages of the green microalga Dunaliella tertiolecta, while controlling for biotic and abiotic variables. We then quantified how body size affected the ability of this species to grow at nutrient-replete conditions and following periods of nitrogen or phosphorous deprivation. Overall, smaller cells showed slower growth, lower storage capacity and poorer recovery from phosphorous depletion, as predicted by the "fasting endurance hypothesis". However, recovery from nitrogen limitation was independent of size – a finding unanticipated by current theories. Phytoplankton species are responsible for much of the global carbon fixation and projected trends of cell size decline could reduce primary productivity by lowering the ability of a cell to store resources.
Figure 2 from: Blanckenhorn WU (2021) A fungal parasite selects against body size but not fluctuating asymmetry in Swiss subalpine yellow dung flies. Alpine Entomology 5: 27-35. https://doi.org/10.3897/alpento.5.65653
Figure 2 Body size (top; here exemplified by wing length) and mean percentage of fluctuating asymmetry (FA; bottom) of all traits for unpaired (filled squares) and paired males (open squares) over the season.
Figure 3 from: Blanckenhorn WU (2021) A fungal parasite selects against body size but not fluctuating asymmetry in Swiss subalpine yellow dung flies. Alpine Entomology 5: 27-35. https://doi.org/10.3897/alpento.5.65653
Figure 3 Body size (here exemplified by hind tibia length) of unpaired (filled squares) and paired males (open squares) when they were infected by the fungus or not (all seasonal samples combined).
Figure 1 from: Blanckenhorn WU (2021) A fungal parasite selects against body size but not fluctuating asymmetry in Swiss subalpine yellow dung flies. Alpine Entomology 5: 27-35. https://doi.org/10.3897/alpento.5.65653
Figure 1 Proportion of male (filled squares) and female (open circles) flies infected by the fungus Entomophthora over the season 2002, with an infected specimen inset (photo Peter Jann).
Supplementary material 1 from: Blanckenhorn WU (2021) A fungal parasite selects against body size but not fluctuating asymmetry in Swiss subalpine yellow dung flies. Alpine Entomology 5: 27-35. https://doi.org/10.3897/alpento.5.65653
Table S1
Data from: Fluctuating selection strength and intense male competition underlie variation and exaggeration of a water strider's male weapon
Sexually selected traits can reach high degrees of expression and variation under directional selection. A growing number of studies suggest that such selection can vary in space, time and form within and between populations. However, the impact of these fluctuations on sexual trait expression is poorly understood. The water strider Microvelia longipes displays a striking case of exaggeration and phenotypic variation where males display extreme differences in the size of their rear legs. To study the origin and maintenance of this exaggerated trait, we conducted comparative behavioral and morphometric experiments in a sample of Microvelia species. We uncovered differences both in the mating behavior and the degree of sexual dimorphism across these species. Interestingly, M. longipes evolved a specific mating behavior where males compete for egg-laying sites, consisting of small floating objects, to intercept and copulate with gravid females. Through male-male competition assays, we demonstrated that male rear legs are used as weapons to dominate egg-laying sites and that intense competition is associated with the evolution of rear leg length exaggeration. Field observations revealed rapid fluctuation in M. longipes habitat stability and the abundance of egg-laying sites. Paternity tests using genetic markers demonstrated that small males could only fertilize about 5% of the eggs when egg-laying sites are limiting, whereas this proportion increased to about 20% when egg-laying sites become abundant. Furthermore, diet manipulation and artificial selection experiments also showed that the exaggerated leg length in M. longipes males is influenced by both genetic and nutritional factors. Collectively, our results highlight how fluctuation in the strength of directional sexual selection, through changes in the intensity of male competition, can drive the exaggeration and phenotypic variation in this weapon trait.
Data from: Selection in a fluctuating environment leads to decreased genetic variation and facilitates the evolution of phenotypic plasticity
Changes in the environment are expected to induce changes in the quantitative genetic variation, which influences the ability of a population to adapt to environmental change. Furthermore, environmental changes are not constant in time, but fluctuate. Here we investigate the effect of rapid, continuous and/or fluctuating temperature changes in the seed beetle Callosobruchus maculatus, using an evolution experiment followed by a split brood experiment. In line with expectations, individuals responded in a plastic way and had an overall higher potential to respond to selection after a rapid change in the environment. After selection in an environment with increasing temperature, plasticity remained unchanged (or decreased) and environmental variation decreased, especially when fluctuations were added; these results were unexpected. As expected, the genetic variation decreased after fluctuating selection. Our results suggest that fluctuations in the environment have major impact on the response of a population to environmental change; in a highly variable environment with low predictability a plastic response might not be beneficial and the response is genetically and environmentally canalized resulting in a low potential to respond to selection and low environmental sensitivity. Interestingly, we found greater variation for phenotypic plasticity after selection, suggesting that the potential for plasticity to evolve is facilitated after exposure to environmental fluctuations. Our study highlights that environmental fluctuations should be considered when investigating the response of a population to environmental change.
Data from: Variation in species light acquisition traits under fluctuating light regimes: implications for non‐equilibrium coexistence
Resource distribution heterogeneity offers niche opportunities for species with different functional traits to develop and potentially coexist. Available light (photosynthetically active radiation or PAR) for suspended algae (phytoplankton) may fluctuate greatly over time and space. Species-specific light acquisition traits capture important aspects of the ecophysiology of phytoplankton and characterize species growth at either limiting or saturating daily PAR supply. Efforts have been made to explain phytoplankton coexistence using species-specific light acquisition traits under constant light conditions, but not under fluctuating light regimes that should facilitate non-equilibrium coexistence. In the well-mixed, hypertrophic Lake TaiHu (China), we incubated the phytoplankton community in bottles placed either at fixed depths or moved vertically through the water column to mimic vertical mixing. Incubations at constant depths received only the diurnal changes in light, while the moving bottles received rapidly fluctuating light. Species-specific light acquisition traits of dominant cyanobacteria (Anabaena flos-aquae, Microcystis spp.) and diatom (Aulacoseira granulata, Cyclotella pseudostelligera) species were characterized from their growth-light relationships that could explain relative biomasses along the daily PAR gradient under both constant and fluctuating light. Our study demonstrates the importance of interspecific differences in affinities to limiting and saturating light for the coexistence of phytoplankton species in spatially heterogeneous light conditions. Furthermore, we observed strong intraspecific differences in light acquisition traits between incubation under constant and fluctuating light – leading to the reversal of light utilization strategies of species. This increased the niche space for acclimated species, precluding competitive exclusion. These observations could enhance our understanding of the mechanisms behind the Paradox of the Plankton.
Data from: Environmental fluctuations restrict eco-evolutionary dynamics in predator-prey system
Environmental fluctuations, species interactions and rapid evolution are all predicted to affect community structure and their temporal dynamics. Although the effects of the abiotic environment and prey evolution on ecological community dynamics have been studied separately, these factors can also have interactive effects. Here we used bacteria–ciliate microcosm experiments to test for eco-evolutionary dynamics in fluctuating environments. Specifically, we followed population dynamics and a prey defence trait over time when populations were exposed to regular changes of bottom-up or top-down stressors, or combinations of these. We found that the rate of evolution of a defence trait was significantly lower in fluctuating compared with stable environments, and that the defence trait evolved to lower levels when two environmental stressors changed recurrently. The latter suggests that top-down and bottom-up changes can have additive effects constraining evolutionary response within populations. The differences in evolutionary trajectories are explained by fluctuations in population sizes of the prey and the predator, which continuously alter the supply of mutations in the prey and strength of selection through predation. Thus, it may be necessary to adopt an eco-evolutionary perspective on studies concerning the evolution of traits mediating species interactions.
Data from: Escherichia coli populations adapt to complex, unpredictable fluctuations by minimizing trade-offs across environments
In nature, organisms are simultaneously exposed to multiple stresses (i.e. complex environments) that often fluctuate unpredictably. Although both these factors have been studied in isolation, the interaction of the two remains poorly explored. To address this issue, we selected laboratory populations of Escherichia coli under complex (i.e. stressful combinations of pH, H2O2 and NaCl) unpredictably fluctuating environments for ~900 generations. We compared the growth rates and the corresponding trade-off patterns of these populations to those that were selected under constant values of the component stresses (i.e. pH, H2O2 and NaCl) for the same duration. The fluctuation-selected populations had greater mean growth rate and lower variation for growth rate over all the selection environments experienced. However, whereas the populations selected under constant stresses experienced trade-offs in the environments other than those in which they were selected, the fluctuation-selected populations could bypass the across-environment trade-offs almost entirely. Interestingly, trade-offs were found between growth rates and carrying capacities. The results suggest that complexity and fluctuations can strongly affect the underlying trade-off structure in evolving populations.
Data from: Multiple benefits of alloparental care in a fluctuating environment
Although cooperatively breeding vertebrates occur disproportionately in unpredictable environments, the underlying mechanism shaping this biogeographic pattern remains unclear. Cooperative breeding may buffer against harsh conditions (hard life hypothesis), or additionally allow for sustained breeding under benign conditions (temporal variability hypothesis). To distinguish between the hard life and temporal variability hypotheses, we investigated whether the number of alloparents at a nest increased reproductive success or load-lightening in superb starlings (Lamprotornis superbus), and whether these two types of benefits varied in harsh and benign years. We found that mothers experienced both types of benefits consistent with the temporal variability hypothesis, as larger contingents of alloparents increased the number of young fledged while simultaneously allowing mothers to reduce their provisioning rates under both harsh and benign rainfall conditions. In contrast, fathers experienced load-lightening only under benign rainfall conditions, suggesting that cooperative breeding may serve to take advantage of unpredictable benign breeding seasons when they do occur. Cooperative breeding in unpredictable environments may thus promote flexibility in offspring care behaviour, which could mitigate variability in the cost of raising young. Our results highlight the importance of considering how offspring care decisions vary among breeding roles and across fluctuating environmental conditions.
Data from: Effects of cell-cycle-dependent expression on random fluctuations in protein levels
Expression of many genes varies as a cell transitions through different cell-cycle stages. How coupling between stochastic expression and cell cycle impacts cell-to-cell variability (noise) in the level of protein is not well understood. We analyse a model where a stable protein is synthesized in random bursts, and the frequency with which bursts occur varies within the cell cycle. Formulae quantifying the extent of fluctuations in the protein copy number are derived and decomposed into components arising from the cell cycle and stochastic processes. The latter stochastic component represents contributions from bursty expression and errors incurred during partitioning of molecules between daughter cells. These formulae reveal an interesting trade-off: cell-cycle dependencies that amplify the noise contribution from bursty expression also attenuate the contribution from partitioning errors. We investigate the existence of optimum strategies for coupling expression to the cell cycle that minimize the stochastic component. Intriguingly, results show that a zero production rate throughout the cell cycle, with expression only occurring just before cell division, minimizes noise from bursty expression for a fixed mean protein level. By contrast, the optimal strategy in the case of partitioning errors is to make the protein just after cell division. We provide examples of regulatory proteins that are expressed only towards the end of the cell cycle, and argue that such strategies enhance robustness of cell-cycle decisions to the intrinsic stochasticity of gene expression.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.