Diversity Of Natural Systems Research Articles

Using the Constrained Disorder Principle to Navigate Uncertainties in Biology and Medicine: Refining Fuzzy Algorithms.

Uncertainty in biology refers to situations in which information is imperfect or unknown. Variability, on the other hand, is measured by the frequency distribution of observed data. Biological variability adds to the uncertainty. The Constrained Disorder Principle (CDP) defines all systems in the universe by their inherent variability. According to the CDP, systems exhibit a degree of variability necessary for their proper function, allowing them to adapt to changes in their environments. Per the CDP, while variability differs from uncertainty, it can be viewed as a regulated mechanism for efficient functionality rather than uncertainty. This paper explores the various aspects of un-certainties in biology. It focuses on using CDP-based platforms for refining fuzzy algorithms to address some of the challenges associated with biological and medical uncertainties. Developing a fuzzy decision tree that considers the natural variability of systems can help minimize uncertainty. This method can reveal previously unidentified classes, reduce the number of unknowns, improve the accuracy of modeling results, and generate algorithm outputs that are more biologically and clinically relevant.

Evaluating the feasibility of using plant‐specific metabarcoding to assess forest types from soil eDNA

AbstractQuestionsAn essential aspect of variation in natural systems is that species respond to complex environmental gradients. Recognizing plant composition gradients associated with abiotic factors (ecoclines) can be foundational for defining habitat types, which, in turn, helps map natural variation. Typically, ecoclinal structures are assessed through visual evaluation of above‐ground vegetation and analysis of covarying abiotic factors. However, the correlation between ecological structures detected by soil eDNA plant assessments and those identified by visual assessment remains largely unexplored.LocationHvaler archipelago, southern Norway.MethodsPlant diversity assessments were conducted using metabarcoding of the trnL (UUA) intron p6 loop and ITS2 from 31 soil samples collected across six forest types. These forest types span gradients related to drought risk and calcium richness.ResultsThe barcode amplicons identified 70 plant taxa, primarily vascular plants (67), with most assigned to the species level (59), representing common forest taxa across the sites. Comparisons between soil eDNA compositions and theoretical forest‐type compositions showed a low to medium correspondence (26% to 76%) between the two. Ordinations of soil eDNA compositions revealed two axes without clear ecological interpretation and correlated poorly with the calcium–richness gradient previously identified by visual assessments.ConclusionsOverall, our results emphasize the necessity for comprehensive sequence reference libraries to conduct thorough plant biodiversity assessments. They also highlight the potential of soil eDNA to assess plant composition, which can aid in ecosystem mapping.

Why Is Reducing the Dead Zone in the Gulf of Mexico Such a Complex Goal? Understanding the Structure That Drives Hypoxic Zone Formation via System Dynamics

The Northern Gulf of Mexico hosts a severe dead zone, an oxygen-depleted area spanning 1,618,000 hectares, threatening over 40% of the U.S. fishing industry and causing annual losses of USD 82 million. Using a System Dynamics (SD) approach, this study examined the Mississippi–Atchafalaya River Basin (MARB), a major contributor to hypoxia in the Gulf. A dynamic model, developed with Vensim software version 10.2.1 andexisting data, represented the physical, biological, and chemical processes leading to eutrophication and simulated dead zone formation over time. Various policies were assessed, considering natural system variability. The findings showed that focusing solely on nitrogen control reduced the dead zone but required greater intensity or managing other inputs to meet environmental goals. Runoff control policies delayed nutrient discharge but did not significantly alter long-term outcomes. Extreme condition tests highlighted the critical role of runoff dynamics, dependent on nitrogen load relative to flow volume from upstream. The model suggests interventions should not just reduce eutrophication inputs but enhance factors slowing down the process, allowing natural denitrification to override anthropogenic nitrification.

Ecological dynamic regimes: Identification, characterization, and comparison

AbstractUnderstanding ecological dynamics has been a central topic in ecology since its origins. Yet, identifying dynamic regimes remains a research frontier for modern ecology. The concept of ecological dynamic regime (EDR) emerged to emphasize the dynamic property of steady states in nature and refers to the fluctuations of ecosystems around some trend or average. Identifying and characterizing EDRs is of utmost importance in the current context of global change since they form the reference against which post‐disturbance dynamics must be compared to assess ecological resilience. However, the implementation of EDRs in empirical science is still challenging given the high dimensionality and stochasticity of ecological data and the large volume of data required to distinguish stochastic dynamics from general and predictable dynamics. The era of big data and the recent advances in quantitative ecology and data science offer an opportunity to study dynamic regimes using empirical approaches from a new perspective. This paper presents a novel methodological framework to describe EDRs from a set of ecological trajectories defined by the temporal changes of state variables in a multidimensional state space. In our framework, we formally define EDRs and include analytical tools to identify, characterize, and compare EDRs based on their geometric characteristics. More specifically, we propose different ways to identify EDRs from empirical data, develop a new algorithm to identify representative trajectories summarizing the main dynamic patterns, propose a set of metrics to describe the internal distribution of ecological trajectories, and define a dissimilarity index to compare two or more dynamic regimes based on their shape and position in the state space. We used artificial data to illustrate the different elements of our framework and applied our analyses to real data, using permanent sampling plots of Canadian boreal forests as an example. Overall, our framework contributes to filling the gap between theoretical and empirical ecology by providing robust analytical tools to assess ecological resilience and study ecosystem dynamics from a multidimensional perspective and considering the variability of natural systems.

The first arriving virus shapes within-host viral diversity during natural epidemics.

Viral diversity has been discovered across scales from host individuals to populations. However, the drivers of viral community assembly are still largely unknown. Within-host viral communities are formed through co-infections, where the interval between the arrival times of viruses may vary. Priority effects describe the timing and order in which species arrive in an environment, and how early colonizers impact subsequent community assembly. To study the effect of the first-arriving virus on subsequent infection patterns of five focal viruses, we set up a field experiment using naïve Plantago lanceolata plants as sentinels during a seasonal virus epidemic. Using joint species distribution modelling, we find both positive and negative effects of early season viral infection on late season viral colonization patterns. The direction of the effect depends on both the host genotype and which virus colonized the host early in the season. It is well established that co-occurring viruses may change the virulence and transmission of viral infections. However, our results show that priority effects may also play an important, previously unquantified role in viral community assembly. The assessment of these temporal dynamics within a community ecological framework will improve our ability to understand and predict viral diversity in natural systems.

How Strong Sustainability Became Safety

The core commitment of strong sustainability, SS, is that nature really is different: there are strict limits to the substitutability of natural and other kinds of capital. Initially, the threat to sustainability was perceived as human greed and impatience, and the goal of SS to address resource scarcity was to sustain resource stocks, the flow of environmental services, and/or the harvest for human benefit. For landscapes and ecosystems, the SS goal was preservation, often in a gestalt framing: preserved or not. Two developments beginning around the mid-20th century—increasing awareness of the variability of natural systems, and the revolutionary changes in thinking motivated by the study of complex dynamic systems, CDS—re-oriented SS toward Safety, i.e., minimizing exposure to risk defined as threat of harm. Around 2010, the sustainability agenda for CDS shifted from identifying early warning indicators enabling timely interventions to forestall adverse regime change to promoting resilience by expanding scale and encouraging patchwork patterns of systems in various stages of their adaptive cycles. Nevertheless, the need for natural resources to substitute for depleted exhaustibles suggests a continuing role for commercial agriculture, plantation forestry, and managed fisheries. I conclude with a paradox still to be resolved: the need for continued and increased production from renewable resources to replace depleted exhaustibles suggests SS-motivated management practices that seem obsolete from a CDS perspective.

Contrasting coronas: microscale fluid variation deduced from monazite breakdown products in altered metavolcanic rocks associated with the Grängesberg apatite-iron oxide ore, Bergslagen, Sweden

ABSTRACT Three different types of secondary coronas developed around monazite-(Ce) were discovered in altered metavolcanic rocks closely associated with the Palaeoproterozoic apatite-iron oxide ore deposit in Grängesberg, Sweden. All three types of reaction coronas include fluorapatite that is either rimmed by allanite-(Ce), REE-fluorocarbonate(s), or hingganite-(Y). The latter mineral has not been previously observed among monazite breakdown products. A unique feature of the described reaction coronas around monazite is their spatial proximity to each other, not exceeding a few hundreds of micrometres. We infer that the observed, strongly contrasting monazite breakdown assemblages highlight the presence of a heterogeneous fluid that mediated these microscale decomposition reactions. Thus, it is emphasized that metasomatic fluid variability in natural systems may often be too large to be predicted and reproduced experimentally.

Extracts from Environmental Strains of Pseudomonas spp. Effectively Control Fungal Plant Diseases.

The use of synthetic chemical products in agriculture is causing severe damage to the environment and human health, but agrochemicals are still widely used to protect our crops. To counteract this trend, we have been looking for alternative strategies to control plant diseases without causing harm to the environment or damage to our health. However, these alternatives are still far from completely replacing chemical products. Microorganisms have been widely known as a biological tool to control plant diseases, but their use is still limited due to the high variability in their efficacy, together with issues in product registration. However, the metabolites produced by these microorganisms can represent a novel tool for the environment-friendly management of plant diseases, while reducing the issues mentioned above. In this study, we explore the soil microbial diversity in natural systems to look for microorganisms with the potential to be used in pre- and post-harvest protection against fungal plant pathogens. Using a simple workflow, we isolated 22 bacterial strains that were tested both in vitro and in vivo for their ability to counteract the growth of common plant pathogens. The three best isolates, identified as members of the bacterial genus Pseudomonas, were used to produce a series of alcoholic extracts, which were then tested for their action against plant pathogens in simulated real-world applications. Results show that extracts from these isolates have an exceptional biocontrol activity and can be successfully used to control plant pathogens in operational setups. Thus, this study shows that the environmental microbiome is an important source of microorganisms producing metabolites that might provide an alternative strategy to synthetic chemical products.

Genetic isolation by distance underlies colour pattern divergence in red-eyed treefrogs (Agalychnis callidryas).

Investigating the spatial distribution of genetic and phenotypic variation can provide insights into the evolutionary processes that shape diversity in natural systems. We characterized patterns of genetic and phenotypic diversity to learn about drivers of colour-pattern diversification in red-eyed treefrogs (Agalychnis callidryas) in Costa Rica. Along the Pacific coast, red-eyed treefrogs have conspicuous leg colour patterning that transitions from orange in the north to purple in the south. We measured phenotypic variation of frogs, with increased sampling at sites where the orange-to-purple transition occurs. At the transition zone, we discovered the co-occurrence of multiple colour-pattern morphs. To explore possible causes of this variation, we generated a single nucleotide polymorphism data set to analyse population genetic structure, measure genetic diversity and infer the processes that mediate genotype-phenotype dynamics. We investigated how patterns of genetic relatedness correspond to individual measures of colour pattern along the coast, including testing for the role of hybridization in geographic regions where orange and purple phenotypic groups co-occur. We found no evidence that colour-pattern polymorphism in the transition zone arose through recent hybridization. Instead, a strong pattern of genetic isolation by distance indicates that colour-pattern variation was either retained through other processes such as ancestral colour polymorphisms or ancient secondary contact, or else it was generated by novel mutations. We found that phenotype changes along the Pacific coast more than would be expected based on genetic divergence and geographic distance alone. Combined, our results suggest the possibility of selective pressures acting on colour pattern at a small geographic scale.

Thermodynamics of the evolution of the biosphere

The thermodynamic foundations of the evolution of the biosphere are considered: the variability of natural systems with different dispersion of their components, the alternative ways of development of such systems, the alternative of intermediate stable states of ecosystems depending on fluctuations of external factors, primarily climate. The necessity of developing a system of mutually agreed complex indicators of this process is postulated. The necessity of including the water content of ecosystems in the number of parameters of nonequilibrium thermodynamics is justified. A new section of land hydrology is formulated -the study of thermodynamic aspects of the dynamics of natural waters.

Understanding Drivers of Variation and Predicting Variability Across Levels of Biological Organization.

Differences within a biological system are ubiquitous, creating variation in nature. Variation underlies all evolutionary processes and allows persistence and resilience in changing environments; thus, uncovering the drivers of variation is critical. The growing recognition that variation is central to biology presents a timely opportunity for determining unifying principles that drive variation across biological levels of organization. Currently, most studies that consider variation are focused at a single biological level and not integrated into a broader perspective. Here we explain what variation is and how it can be measured. We then discuss the importance of variation in natural systems, and briefly describe the biological research that has focused on variation. We outline some of the barriers and solutions to studying variation and its drivers in biological systems. Finally, we detail the challenges and opportunities that may arise when studying the drivers of variation due to the multi-level nature of biological systems. Examining the drivers of variation will lead to a reintegration of biology. It will further forge interdisciplinary collaborations and open opportunities for training diverse quantitative biologists. We anticipate that these insights will inspire new questions and new analytic tools to study the fundamental questions of what drives variation in biological systems and how variation has shaped life.

Advective sorting of silt by currents: A laboratory study

AbstractAccumulations of fine sediments along continental shelf and deep‐sea bathymetric contours, known as contourite drifts, form a sedimentary record that is dependent on oceanographic processes such as ocean–basin‐scale circulation. A tool used to aid in interpretation of such deposits is the sortable silt hypothesis, which suggests that the mean size of the sortable silt (silt from 10 to 63 μm) within a deposit can be used as a proxy for current velocity. While the hypothesis has been applied to numerous drift deposits, it has not been extensively explored. Slow deposition rates of contourite drift systems make it difficult to study in the deep ocean, and past laboratory studies have not tested the full range of conditions or mechanisms that could lead to sorting. This study uses flume experiments and theory to examine how the mean sortable silt in a deposit is related to current velocity under the action of advective depositional sorting. Tests were conducted for a fixed amount of time with four suspended sediment mixtures and current velocities typical of deep‐sea settings (5 to 25 cm s−1). Developed beds were sampled at fixed locations from the entrance and sized. The deposit grain size fined downstream and coarsened with increasing velocity at a particular distance from the inlet. Simple theory was able to capture the observations. Regardless of bed morphology or source sediment mixture, the mean sortable silt in the deposit was related to velocity at a particular flume location across all sediment mixtures. The slope of the relationship between velocity and size was dependent on the distance between the inlet and location of interest. Despite the simplified nature of the study, and the limitations regarding the presumed variability in natural systems, these findings broadly support the validity of mean sortable as a proxy for palaeocurrent velocity at a distance along a depositing current.

Impacts of invasive Amur honeysuckle, Lonicera maackii, leaf litter on multiple trophic levels of detritus‐based experimental wetlands

Abstract Wetlands are especially vulnerable to invasive plants because seasonal movements of sediments, water, nutrients, and debris from adjacent terrestrial habitats create ecological conditions suitable for invasion. Lonicera maackii is a relatively abundant and broadly distributed invasive shrub in the eastern U.S.A., yet few studies have simultaneously tested for effects of its leaf litter on multiple trophic levels within wetland food webs. Hatching success, hatchling survival, and hatchling size of tadpoles (Acris crepitans) were assessed using a laboratory mesocosm experiment with no‐leaf, native‐leaf, and L. maackii‐leaf treatments. In the field, short‐term (c. 3 week) and long‐term (c. 2 years) mesocosm experiments assessed the initial and persistent impacts, respectively, of L. maackii on measures of primary productivity, invertebrate abundance and community structure, and oviposition preference and larval survival of Cope's gray treefrog (Hyla chrysoscelis). Exposure of eggs to L. maackii leaves reduced body size at hatching and larval survival of newly hatched A. crepitans. In short‐term experiments, L. maackii leaves reduced dissolved oxygen levels, filamentous algal biomass, and macroinvertebrate abundance, and altered macroinvertebrate community structure. In long‐term experiments, duckweed cover was 15× times greater in mesocosms with L. maackii leaf additions. Oviposition by a local population of H. chrysoscelis was 10× lower in both short‐ and long‐term mesocosms with L. maackii present. Although ecological impacts of L. maackii have been reported for terrestrial systems, our study is the first to demonstrate the simultaneous effects of its leaves on multiple trophic levels within replicated experimental wetlands. The relatively rapid decomposition of L. maackii leaves, and associated pulse of phenolic compounds, is the most likely proximate mechanism of the bottom‐up effects we observed. The mechanisms, timing, and significance of effects is predicted to vary among natural wetlands. Our study demonstrates multiple ecological impacts of a terrestrial invasive shrub within experimental wetlands. Detailed studies on the specific mechanisms, and their spatial and temporal variability in natural systems, will elucidate management strategies and improve the efficiency of wetland conservation efforts.

Initial abundance and stochasticity influence competitive outcome in communities.

Predicting competitive outcomes in communities frequently involves inferences based on deterministic population models since these provide clear criteria for exclusion (e.g. R* rule) or long-term coexistence (e.g. mutual invasibility). However, incorporating stochasticity into population- or community-level processes into models is necessary if the goal is to explain variation in natural systems, which are inherently stochastic. Similarly, in systems with demographic or environmental stochasticity, weaker competitors have the potential to exclude superior competitors, contributing to what is known as 'competitive indeterminacy'. The importance of such effects for natural communities is unknown, in part because it is difficult to demonstrate that multiple forms of stochasticity are present in these communities. Moreover, the effects of multiple forms of stochasticity on competitive outcomes are largely untested, even in theory. Here, we address these issues by examining the role of stochasticity in replicated communities of flour beetles (Tribolium sp.). To do so, we developed a set of two-species stochastic Ricker models incorporating four distinct forms of stochasticity: environmental stochasticity, demographic stochasticity, demographic heterogeneity and stochastic sex determination. By fitting models to experimental data, and simulating fit models to examine long- term behaviour, we found that both the duration of transient coexistence and the degree of competitive indeterminacy were sensitive to the forms of stochasticity included in our models. These findings suggest the current estimates of extinction risk, coexistence and time until competitive exclusion in communities may not be accurate when based on models that exclude relevant forms of stochasticity.

Long-term Exposure to Predation Threat Can Modulate the Expression of Sexually Selected Traits in Male Guppy (Poecilia reticulata)

The expression of sexual traits can be affected by different environmental factors among which predation may be particularly important life-history traits. This study investigated the effects of predation risk on courtship behavior, growth and sexual color patterns in male guppy (Poecilia reticulata). In the study, juvenile male guppies were randomly assigned to two treatments, namely T1 (predation threat) and T2 (no predation threat). The courtship performances were visually observed and recorded, while color patterns and morphological traits were measured by using the ImageJ software from the captured photos. The courtship behavioral trials revealed that predation threatened males performed significantly lower number of sigmoid displays than those of no-predation group. Further, the predation scared group had significantly shorter standard length, body area and a reduced number and area of orange spots than their counter group. However, the predation threat did not affect significantly the gonopodial thrusts, and black and iridescent color components (spot number and area). The reduction of costly traits (e.g. behavior, color patterns and body size) is common anti-predator response which presumably reduces predation risks. Male guppies are probably using this form of defence in response to the increased predation risk. The overall result suggests that growth and sexually selected trait expression are sensitive to predation risk and thereby aid in our understanding to predict the evolution of phenotypic variation in natural systems.

Reprogramming Substrate and Catalytic Promiscuity of Tryptophan Prenyltransferases

Prenylation is a process widely prevalent in primary and secondary metabolism, contributing to functionality and chemical diversity in natural systems. Due to their high regio- and chemoselectivities, prenyltransferases are also valuable tools for creation of new compounds by chemoenzymatic synthesis and synthetic biology. Over the last ten years, biochemical and structural investigations shed light on the mechanism and key residues that control the catalytic process, but to date crucial information on how certain prenyltransferases control regioselectivity and chemoselectivity is still lacking. Here, we advance a general understanding of the enzyme family by contributing the first structure of a tryptophan C5-prenyltransferase 5-DMATS. Additinally, the structure of a bacterial tryptophan C6-prenyltransferase 6-DMATS was solved. Analysis and comparison of both substrate-bound complexes led to the identification of key residues for catalysis. Next, site-directed mutagenesis was successfully implemented to not only modify the prenyl donor specificity but also to redirect the prenylation, thereby switching the regioselectivity of 6-DMATS to that of 5-DMATS. The general strategy of structure-guided protein engineering should be applicable to other related prenyltransferases, thus enabling the production of novel prenylated compounds.

Why species richness of plants and herbivorous insects do or do not correlate

AbstractUnraveling the determinants of herbivorous insect diversity has been a significant challenge in ecology. Despite the strong association between insect and plant species, previous studies conducted in natural systems have shown great variation in the strength of the correlation between their species richness. Such variation could be attributed to the proportion of generalist insect species (generality). However, both higher and lower generality may weaken the correlation because (a) generalist insect species are less dependent on the number of plant species, and (b) specialist insect species utilize only a proportion of the total plant species. To explore these contradictory effects, we studied plant and herbivorous insect communities in seminatural grasslands in Japan. Plant–insect interactions were evaluated in a unique way with a particular focus on the staying and herbivory behaviors of insects, which reflect their habitat use as well as host use. We found that lower generality of insect communities strengthened the correlation between species richness of plants and insects, but this was not the case when plant species that had no interaction with insect species were also considered. This was because lower generality increased the number of plant species that did not interact with insects. The results indicate that insect generality has contradictory effects on the plant–insect diversity relationship, which emphasizes the importance of distinguishing the effects to understand the variation in the relationship between plant and insect diversity in natural systems.

Getting a Grip on Variability.

Because science is a modeling enterprise, a key question for educators is: What kind of repertoire can initiate students into the practice of generating, revising, and critiquing models of the natural world? Based on our 20years of work with teachers and students, we nominate variability as a set of connected key ideas that bridge mathematics and science and are fundamental for equipping youngsters for the posing and pursuit of questions about science. Accordingly, we describe a sequence for helping young students begin to reason productively about variability. Students first participate in random processes, such as repeated measure of a person's outstretched arms, that generate variable outcomes. Importantly, these processes have readily discernable sources of variability, so that relations between alterations in processes and changes in the collection of outcomes can be easily established and interpreted by young students. Following these initial steps, students invent and critique ways of visualizing and measuring distributions of the outcomes of these processes. Visualization and measure of variability are then employed as conceptual supports for modeling chance variation in components of the processes. Ultimately, students reimagine samples and inference in ways that support reasoning about variability in natural systems.

Genome-wide epigenetic isolation by environment in a widespread Anolis lizard.

Epigenetic changes can provide a pathway for organisms to respond to local environmental conditions by influencing gene expression. However, we still know little about the spatial distribution of epigenetic variation in natural systems, how it relates to the distribution of genetic variation and the environmental structure of the landscape, and the processes that generate and maintain it. Studies examining spatial patterns of genetic and epigenetic variation can provide valuable insights into how ecological and population processes contribute to epigenetic divergence across heterogeneous landscapes. Here, we perform a comparative analysis of spatial genetic and epigenetic variation based on 8,459 single nucleotide polymorphisms (SNPs) and 8,580 single methylation variants (SMVs) from eight populations of the Puerto Rican crested anole, Anolis cristatellus, an abundant lizard in the adaptive radiations of anoles on the Greater Antilles that occupies a diverse range of habitats. Using generalized dissimilarity modelling and multiple matrix regression, we found that genome-wide epigenetic differentiation is strongly correlated with environmental divergence, even after controlling for the underlying genetic structure. We also detected significant associations between key environmental variables and 96 SMVs, including 42 located in promoter regions or gene bodies. Our results suggest an environmental basis for population-level epigenetic differentiation in this system and contribute to better understanding how environmental gradients structure epigenetic variation in nature.

Controlling cell-to-cell variability with synthetic gene circuits.

Cell-to-cell variability originating, for example, from the intrinsic stochasticity of gene expression, presents challenges for designing synthetic gene circuits that perform robustly. Conversely, synthetic biology approaches are instrumental in uncovering mechanisms underlying variability in natural systems. With a focus on reducing noise in individual genes, the field has established a broad synthetic toolset. This includes noise control by engineering of transcription and translation mechanisms either individually, or in combination to achieve independent regulation of mean expression and its variability. Synthetic feedback circuits use these components to establish more robust operation in closed-loop, either by drawing on, but also by extending traditional engineering concepts. In this perspective, we argue that major conceptual advances will require new theory of control adapted to biology, extensions from single genes to networks, more systematic considerations of origins of variability other than intrinsic noise, and an exploration of how noise shaping, instead of noise reduction, could establish new synthetic functions or help understanding natural functions.