Diversity Of Natural Systems Research Articles

In the Memory of Our Teacher

Students, colleagues, and friends of Bella Rafailovna Striganova as well as the Editorial Board of the journal Biology Bulletin, which she headed for many years, dedicate this issue of the journal to her memory. The subjects of the articles represent the most important areas of research for B.R. Striganova: regularities of geographic changes in taxonomic diversity, abundance, and landscape distribution of soil communities; trophic relations of pedobionts and zoomicrobial relationships; functioning of detrital food webs; the importance, conservation, and rational use of the biological diversity of natural systems; soil zoology and problems of the national economy; problems of evolutionary theory.

Bayesian networks for identifying incorrect probabilistic intuitions in a climate trend uncertainty quantification context

Probabilistic thinking can often be unintuitive. This is the case even for simple problems, let alone the more complex ones arising in climate modelling, where disparate information sources need to be combined. The physical models, the natural variability of systems, the measurement errors and their dependence upon the observational period length should be modelled together in order to understand the intricacies of the underlying processes. We use Bayesian networks (BNs) to connect all the above-mentioned pieces in a climate trend uncertainty quantification framework. Inference in such models allows us to observe some seemingly nonsensical outcomes. We argue that they must be pondered rather than discarded until we understand how they arise. We would like to stress that the main focus of this paper is the use of BNs in complex probabilistic settings rather than the application itself.

Indirect interactions between crops and natural vegetation through flower visitors: the importance of temporal as well as spatial spillover

As the Anthropocene advances, understanding the complex web of interactions between species has become a central theme in the maintenance of biodiversity, ecosystem functions, and agricultural systems. Plant-flower visitor networks yield insights into how natural vegetation supports crop pollination. Although crops themselves also support pollinators, the importance of spillover of flower-visiting pollinators from natural vegetation into croplands is increasingly appreciated. Natural vegetation not only provides forage and nesting sites, but can also support crop flower visitors when the crop is not flowering. We evaluated indirect effects between mango (the dominant tropical fruit crop globally) and wild plant species in neighbouring vegetation, and the factors determining these indirect effects, by constructing flower visitor networks. We constructed these networks for transects that included mango fields and neighbouring natural vegetation in north-eastern South Africa. Surveys were conducted before, during and after mango flowering, to allow evaluation of the importance of pollinator support when the crop was not in flower. Network analysis showed that potential indirect effects of other plant species on mango increased with flower abundance of those species, although this increase was less marked for species growing in natural vegetation. The cumulative (total, i.e. indirect effects summed) effect of natural vegetation on mango flower visitation was greater both during mango flowering and when it was not flowering. This is likely because of the greater plant diversity in natural systems, and because the combination of these species provided flowers over a protracted period. These positive indirect effects among plants flowering over extended periods of time have to date rarely been considered in crop pollination studies. Given the rapid expansion of high-intensity, high-yield monoculture plantings, such effects warrant further investigation.

The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish.

The notorious plasticity of gene expression responses and the complexity of environmental gradients complicate the identification of adaptive differences in gene regulation among populations. We combined transcriptome analyses in nature with common-garden and exposure experiments to establish cause-effect relationships between the presence of a physiochemical stressor and expression differences, as well as to test how evolutionary change and plasticity interact to shape gene expression variation in natural systems. We studied two evolutionarily independent population pairs of an extremophile fish (Poecilia mexicana) living in toxic, hydrogen sulphide (H2 S)-rich springs and adjacent nontoxic habitats and assessed genomewide expression patterns of wild-caught and common-garden-raised individuals exposed to different concentrations of H2 S. We found that 7.7% of genes that were differentially expressed between sulphidic and nonsulphidic ecotypes remained differentially expressed in the laboratory, indicating that sources of selection other than H2 S-or plastic responses to other environmental factors-contribute substantially to gene expression patterns observed in the wild. Concordantly differentially expressed genes in the wild and the laboratory were primarily associated with H2 S detoxification, sulphur processing and metabolic physiology. While shared, ancestral plasticity played a minor role in shaping gene expression variation observed in nature, we documented evidence for evolved population differences in the constitutive expression as well as the H2 S inducibility of candidate genes. Mechanisms underlying gene expression variation also varied substantially across the two ecotype pairs. These results provide a springboard for studying evolutionary modifications of gene regulatory mechanisms that underlie expression variation in locally adapted populations.

Climate variability affects the germination strategies exhibited by arid land plants.

Spatial and temporal environmental variability can lead to variation in selection pressures across a landscape. Strategies for coping with environmental heterogeneity range from specialized phenotypic responses to a narrow range of conditions to generalist strategies that function under a range of conditions. Here, we ask how mean climate and climate variation at individual sites and across a species' range affect the specialist-generalist spectrum of germination strategies exhibited by 10 arid land forbs. We investigated these relationships using climate data for the western United States, occurrence records from herbaria, and germination trials with field-collected seeds, and predicted that generalist strategies would be most common in species that experience a high degree of climate variation or occur over a wide range of conditions. We used two metrics to describe variation in germination strategies: (a) selectivity (did seeds require specific cues to germinate?) and (b) population-level variation (did populations differ in their responses to germination cues?) in germination displayed by each species. Species exhibited distinct germination strategies, with some species demonstrating as much among-population variation as we observed among species. Modeling efforts suggested that generalist strategies evolve in response to higher spatial variation in actual evapotranspiration at a local scale and in available water in the spring and annual precipitation at a range-wide scale. Describing the conditions that lead to variation in early life-history traits is important for understanding the evolution of diversity in natural systems, as well as the possible responses of individual species to global climate change.

Modelling the plankton groups of the deep, peri-alpine Lake Bourget

Predicting phytoplankton succession and variability in natural systems remains to be a grand challenge in aquatic ecosystems research. In this study, we identified six major plankton groups in Lake Bourget (France), based on cell size, taxonomic properties, food-web interactions and occurrence patterns: cyanobacterium Planktothrix rubescens, small and large phytoplankton, mixotrophs, herbivorous and carnivorous zooplankton. We then developed a deterministic dynamic model that describes the dynamics of these groups in terms of carbon and phosphorus fluxes, as well as of particulate organic phosphorus and dissolved inorganic phosphorus. The modular and generic model scheme, implemented as a set of modules under Framework for Aquatic Biogeochemical Models (FABM) enables run-time coupling of the plankton module an arbitrary number of times, each time with a prescribed position across the autotrophy/heterotrophy continuum. Parameters of the plankton groups were mainly determined conjointly by the taxonomic and allometric relationships, based on the species composition and average cellular volume of each group. The biogeochemical model was coupled to the one-dimensional General Ocean Turbulence Model (GOTM) and forced with local meteorological conditions. The coupled model system shows very high skill in predicting the spatiotemporal distributions of water temperature and dissolved inorganic phosphorus for five simulated years within the period 2004 to 2010, and intermediate skill in predicting the plankton succession. We performed a scenario analysis to gain insight into the factors driving the sudden disappearance of P. rubescens in 2010. Our results provide evidence for the hypothesis that the abundance of this species before the onset of stratification is critical for its success later in the growing season, pointing thereby to a priority effect.

Island biodiversity conservation needs palaeoecology.

The discovery and colonization of islands by humans has invariably resulted in their widespread ecological transformation. The small and isolated populations of many island taxa, and their evolution in the absence of humans and their introduced taxa, mean that they are particularly vulnerable to human activities. Consequently, even the most degraded islands are a focus for restoration, eradication, and monitoring programmes to protect the remaining endemic and/or relict populations. Here, we build a framework that incorporates an assessment of the degree of change from multiple baseline reference periods using long-term ecological data. The use of multiple reference points may provide information on both the variability of natural systems and responses to successive waves of cultural transformation of island ecosystems, involving, for example, the alteration of fire and grazing regimes and the introduction of non-native species. We provide exemplification of how such approaches can provide valuable information for biodiversity conservation managers of island ecosystems.

Frequency-dependent selection for rare genotypes promotes genetic diversity of a tropical palm.

Negative frequency-dependent selection among species is a key driver of community diversity in natural systems, but the degree to which negative frequency-dependent selection shapes patterns of survival and genetic diversity within species is poorly understood. In a 5-year field experiment, we show that seedlings of a tropical palm with rare genotypes had a pronounced survival advantage over seedlings with common genotypes, with effect sizes comparable to that of light availability. This 'rare genotype advantage' led to an increase in population-wide genetic diversity among seedlings compared to null expectations, as predicted by negative frequency-dependent selection, and increased reproductive success in adult trees with rare genotypes. These results suggest that within-species negative frequency-dependent selection of genotypes can shape genetic variation on ecologically relevant timescales in natural systems and may be a key, overlooked source of non-random mortality for tropical plants.

First report of a novel multiplexer pumping system coupled to a water quality probe to collect high temporal frequency in situ water chemistry measurements at multiple sites

The increasing availability and use of high-frequency water quality sensors has enabled unprecedented observations of temporal variability in water chemistry in aquatic ecosystems. However, we remain limited by the prohibitive costs of these probes to explore spatial variability in natural systems. To overcome this challenge, we have developed a novel auto-sampler system that sequentially pumps water from up to 12 different sites located within a 12 m radius to a single water quality probe. This system is able to generate high temporal frequency in situ water chemistry data from multiple replicated units during experiments as well as multiple sites and depths within natural aquatic ecosystems. Thus, with one water quality probe, we are able to observe rapid changes in water chemistry concentrations over time and space. Here, we describe the coupled multiplexer-probe system and its performance in two case studies: a mesocosm experiment examining the effects of water current velocity on nitrogen dynamics in constructed wetland sediment cores and a whole-ecosystem manipulation of redox conditions in a reservoir. In both lotic and lentic case studies, we observed minute-scale changes in nutrient concentrations, which provide new insight on the variability of biogeochemical processes. Moreover, in the reservoir, we were able to measure rapid changes in metal concentrations, in addition to those of nutrients, in response to changes in redox. Consequently, we believe that this coupled system holds great promise for measuring biogeochemical fluxes in a diverse suite of aquatic ecosystems and experiments.

The role of competition - colonization tradeoffs and spatial heterogeneity in promoting trematode coexistence.

Competition - colonization tradeoffs occur in many systems, and theory predicts that they can strongly promote species coexistence. However, there is little empirical evidence that observed competition- colonization tradeoffs are strong enough to maintain diversity in natural systems. This is due in part to a mismatch between theoretical assumptions and biological reality in some systems. We tested whether a competition - colonization tradeoff explains how a diverse trematode guild coexists in California horn snail populations, a system that meets the requisite criteria for the tradeoff to promote coexistence. A field experiment showed that subordinate trematode species tended to have higher colonization rates than dominant species. This tradeoff promoted coexistence in parameterized models but did not fully explain trematode diversity and abundance, suggesting a role of additional diversity maintenance mechanisms. Spatial heterogeneity is an alternative way to promote coexistence if it isolates competing species. We used scale transition theory to expand the competition - colonization tradeoff model to include spatial variation. The parameterized model showed that spatial variation in trematode prevalence did not isolate most species sufficiently to explain the overall high diversity, but could benefit some rare species. Together, the results suggest that several mechanisms combine to maintain diversity, even when a competition - colonization tradeoff occurs.

Functional consequences of diversity in natural systems: the effects of succession on the primary productivity of seaweeds

Functional consequences of diversity in natural systems: the effects of succession on the primary productivity of seaweeds

Metamodels to Bridge the Gap Between Modeling and Decision Support.

Insights from process-based models are a mainstay of many groundwater investigations; however, long runtimes often preclude their use in the decision-making process. Screening-level predictions are often needed in areas lacking time or funding for rigorous process-based modeling. The U.S. Geological Survey (USGS) Groundwater Resources and National Water Quality Assessment Programs are addressing these issues by evaluating the “metamodel” to bridge these gaps. A metamodel is a statistical model founded on a computationally expensive model. Although faster, the question remains: Can a statistical model provide similar insights to a numerical model with faster results? Metamodeling was developed to overcome long runtimes for sensitivity analysis (Blanning 1975); our focus is decision support applications. Two representative groundwater applications are: (1) the contribution of surface water to wells in shallow groundwater systems (e.g., Fienen and Plant 2014), and (2) unsaturated zone nitrate flux to groundwater (e.g., Nolan et al. 2012). The first step is to generate a representative sample of input/output combinations from the numerical model over a range of conditions. This variability is especially important when propagating uncertainty to predictions. Variability can be represented by many model runs using different input values or by few model runs with samples scattered in space/time experiencing the range of natural system variability. In the second step, a statistical learning technique is selected with which a predictive model can be “learned” from the data derived from the model. Techniques include

Biogeochemical insights into microbe-mineral-fluid interactions in hydrothermal chimneys using enrichment culture.

Active hydrothermal chimneys host diverse microbial communities exhibiting various metabolisms including those involved in various biogeochemical cycles. To investigate microbe-mineral-fluid interactions in hydrothermal chimney and the driver of microbial diversity, a cultural approach using a gas-lift bioreactor was chosen. An enrichment culture was performed using crushed active chimney sample as inoculum and diluted hydrothermal fluid from the same vent as culture medium. Daily sampling provided time-series access to active microbial diversity and medium composition. Active archaeal and bacterial communities consisted mainly of sulfur, sulfate and iron reducers and hydrogen oxidizers with the detection of Thermococcus, Archaeoglobus, Geoglobus, Sulfurimonas and Thermotoga sequences. The simultaneous presence of active Geoglobus sp. and Archaeoglobus sp. argues against competition for available carbon sources and electron donors between sulfate and iron reducers at high temperature. This approach allowed the cultivation of microbial populations that were under-represented in the initial environmental sample. The microbial communities are heterogeneously distributed within the gas-lift bioreactor; it is unlikely that bulk mineralogy or fluid chemistry is the drivers of microbial community structure. Instead, we propose that micro-environmental niche characteristics, created by the interaction between the mineral grains and the fluid chemistry, are the main drivers of microbial diversity in natural systems.

Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment.

Methanogenic archaea are genotypically and phenotypically diverse organisms that are integral to carbon cycling in anaerobic environments. Owing to their genetic tractability and ability to be readily cultivated, Methanosarcina spp. have become a powerful model system for understanding methanogen biology at the cellular systems level. However, relatively little is known of how genotypic and phenotypic variation is partitioned in Methanosarcina populations inhabiting natural environments and the possible ecological and evolutionary implications of such variation. Here, we have identified how genomic and phenotypic diversity is partitioned within and between Methanosarcina mazei populations obtained from two different sediment environments in the Columbia River Estuary (Oregon, USA). Population genomic analysis of 56 M. mazei isolates averaging <1% nucleotide divergence revealed two distinct clades, which we refer to as 'mazei-T' and 'mazei-WC'. Genomic analyses showed that these clades differed in gene content and fixation of allelic variants, which point to potential differences in primary metabolism and also interactions with foreign genetic elements. This hypothesis of niche partitioning was supported by laboratory growth experiments that revealed significant differences in trimethylamine utilization. These findings improve our understanding of the ecologically relevant scales of genomic variation in natural systems and demonstrate interactions between genetic and ecological diversity in these easily cultivable and genetically tractable model methanogens.

Elemental signature of terrigenous sediment runoff as recorded in coastal salt ponds: US Virgin Islands

A high-resolution, multi-proxy approach is utilized on mm- to cm-scale laminated coastal salt pond sediments from St. John, U.S. Virgin Islands, to determine: (1) the sedimentological signature of depositional events/processes, (2) link this sedimentological signature with known depositional events/processes in the historical (past ∼100years) record; and, (3) project back into the recent geologic past (past ∼1400years) to investigate the natural variability of depositional events/processes. High-resolution, short-lived radioisotope geochronology (210Pb, 137Cs, 7Be) combined with high-resolution elemental scanning techniques (scanning XRF and scanning LA-ICP-MS) allows for the direct comparison of well-preserved salt pond deposits to historical records of depositional events (e.g., runoff/rainfall, tropical cyclones, tsunamis) to identify the sedimentary signature of each type of event. There is a robust sedimentary record of terrigenous sediment runoff linked to the frequency of rainfall events that exceed a threshold of ∼12mm/day (minimum to mobilize and transport sediment) for study sites. This is manifested in the sedimentary record as increases in terrigenous indicator elements (%Al, %Fe, %Ti, %Si), which agree well with rainfall records over the past ∼50years. Variability in the sedimentary record over the past ∼100years reflects decadal-scale fluctuations between periods of increased frequency of rainfall events, and decreased frequency of rainfall events. Dm-scale variability in terrigenous indicator elements over the past ∼1400years represents the natural system variability on a decadal–centennial scale, and provides a high-resolution, long-term baseline of natural variability of rainfall/runoff events. A period of increased terrigenous sediment delivery during the 1700s and 1800s likely indicates increased erosion in response to anthropogenic activities associated with the island’s plantation era, and perhaps increased frequency of rainfall events.

Seasonal forcing in a host-macroparasite system.

Seasonal forcing represents a pervasive source of environmental variability in natural systems. Whilst it is reasonably well understood in interacting populations and host-microparasite systems, it has not been studied in detail for host-macroparasite systems. In this paper we analyse the effect of seasonal forcing in a general host-macroparasite system with explicit inclusion of the parasite larval stage and seasonal forcing applied to the birth rate of the host. We emphasise the importance of the period of the limit cycles in the unforced system on the resulting dynamics in the forced system. In particular, when subject to seasonal forcing host-macroparasite systems are capable of multi-year cycles, multiple solution behaviour, quasi-periodicity and chaos. The host-macroparasite systems show a larger potential for multiple solution behaviour and a wider range of periodic solutions compared to similar interacting population and microparasite systems. By examining the system for parameters that represent red grouse and the macroparasite nematode Trichostrongylus tenuis we highlight how seasonality could be an important factor in explaining the wide range of seemingly uncorrelated cycle periods observed in grouse abundance in England and Scotland.

Conceptual aspects of the biosphere-balanced use of ecological and biological systems

This article covers the dynamics of the current state of natural ecosystems under the influence of rapid increase in recent decades of anthropogenic impact on them, with negative effects on the environment and normal reproduction and survival of the biota in it as a resource and most crucial basic integral part of the biosphere. It is noted, particularly, that the current anthropogenic influence has become a powerful factor in the evolution of the biosphere in which biological systems began to function in anthropogenically transformed circulation of substances, often severely impaired harmonization of processes of their self-recovery, often leading to the need for society to revise its behavior in the "man-nature-economy - living environment" system. At the same time the conceptual aspects of strategic environmental and anthropogenic using of ecological and biological systems are presented. Against the background of the above-mentioned changes of the necessity of the transition from the unitary-consumptive use of biotic systems to the system(biosphere)-balanced, in which their component parts - the soil, plant, animals or other forms of terrestrial and aquatic ecosystems are considered not only as a source of obtaining the necessary and usefull for human products or basic production resoursed and objects of application of labor, but are as inseparable parts of a whole, functionally interacting entities of nature, beyond which, development and existence is impossible. According to tasks, assessment of the ecological and biological formations and optimization of their use can be carried out on 1) a globally-biosphere 2) landscape-ecological, 3) elementary biogeocenotical levels of the organization of natural and anthropogenically transformed systems. In the article the methodological principles of assessment of the ecological and biological systems in the biosphere-balanced use of them. It is stated that the main focus of their learning and assessment is a systematic approach to the wide range of applications in addition to traditional methods of identifying of structurally elementary indicators and functionally-group-biomorphological, environmental, rhythmic and many other features, the fundamental properties of the study of nonlinear dynamics of processes as complex open ecosystems with determinant-chaotic type of development and the appearance in them of high degree of random factors in the formation. The high appropriateness of accounting hemerobility of representatives of biota is mentioned. that is, their genetic and physiological responses to disturbance of edaphotopes or cultivated land for establishing the degree of degradation of natural ecosystems and acceptable thresholds of anthropogenic load on them. It is noted, that the implementation of a balanced use of natural resources of the biosphere requires changes in traditional thinking and developing of skills of innovative systemic approach and analysis of the surrounding material world, the ability to see the invisible on the basis of visible phenomena of nature, that is, the so-called invisible matter and its powerful energy - intra- and intersystem communication, laws of present and future development of ecological systems, and on this foundation to build properly a model of effective use. It is noted that human disturbance of balance in one or more parts of the system, due to the action intra - and intersystem balance masses, inevitably leads to a change in the entire system and puts it into new functioning modes, which are not always desirable. The task is to prevent the release of anthropogenic variability of natural systems beyond their adaptive stability.

Effects of marine reserves in the context of spatial and temporal variation: an analysis using Bayesian zero-inflated mixed models

Evaluating the effects of marine reserves on exploited species can be challenging because they occur within a context of natural spatial and temporal variation at many scales. For rigorous inferences to be made, such evaluations require monitoring programmes that are repli- cated at appropriate scales. We analysed monitoring data of snapper Pagrus auratus (Sparidae) in northeastern New Zealand, comprised of counts from baited-underwater-video surveys from inside and outside 3 marine reserves. Surveys were replicated at many levels, including areas inside and outside of marine reserves at 3 locations in 2 seasons, over a period of up to 14 yr, in an unbalanced design. The Bayesian modelling approach allowed the use of some familiar aspects of ANOVA, including mixed models of fixed and random effects, hierarchically nested structures, and variance decomposition, while allowing for overdispersion and excess zeros in the counts. Model selection and estimates of variance components revealed that protection by marine reserves was by far the strongest measured source of variation for relative densities of legal-sized snapper. The size of the effect varied across years among the 3 reserves, with relative densities between 7 and 20 times greater in reserves than in nearby areas. Other than the reserve effect, the temporal factors of season and year were generally more important than the spatial factors at explaining variation in counts. In particular, overall relative densities were ~2 to 3 times greater in autumn than in spring for legal-sized snapper, although the seasonal effect was also variable among locations and years. We consider that the Bayesian generalised linear mixed modelling approach, as used here, provides an extremely useful and flexible tool for estimating the effects of management actions and comparing them directly with other sources of spatial and temporal variation in natural systems.

Does Deming’s “System of Profound Knowledge” Apply to Leaders of Biodiversity Conservation?

The challenges of ecological and environmental change are significant and solutions remain largely under the influence of people and the decisions of governments, interest groups, national and local communities and individuals. Evidence suggests that despite 20 years of effort, conservation initiatives have failed to achieve the targets set for protecting biodiversity in the UN Convention on Biological Diversity 2010. A common factor influencing effectiveness of conservation work undertaken by the diverse mix of government, non-government and civil organisations is leadership. A command-and-control approach to leadership is commonly encountered in conservation and previous reviews suggest this as a major factor in ineffective conservation initiatives. This suggests that conservation leaders should consider a fundamentally different approach to leadership. We examine whether an alternative paradigm, Deming’s System of Profound Knowledge, offers a suitable new basis for leadership in biodiversity conservation. This “Systems Thinking” approach should encompass (i) an understanding of natural systems, (ii) a sense of how human behaviour is influenced, (iii) an understanding of how knowledge should inform decision-making and problem solving, and (iv) an understanding of variation in natural systems. Current paradigms of conservation management fail to address these four fundamentals and therefore do not represent the most effective way to manage conservation. Conversely, challenges and opportunities encountered in biodiversity conservation are well-aligned to a Systems Thinking approach. Leadership approaches defined in Deming’s “System of Profound Knowledge” offer significant positive impacts on biodiversity conservation achievement and provide lessons for leaders in other areas of human activity.

Quantification of Modeling-Induced Uncertainties in Simulation-Based Analyses

Traditional uncertainty quantification in simulation-based analyses typically focuses upon the quantification of parametric uncertainties: the uncertainties inherent to the input parameters of the simulation. This type of uncertainty often represents the inherent variability of natural systems due to incomplete information or implicit variations in the system itself. However, when simulation-based models are used to evaluate the performance of a system, an additional level of uncertainty is introduced (one often not rigorously considered in probabilistic design): modeling-induced uncertainty. This work adapts uncertainty quantification for the multiple forms of uncertainties into a single framework to quantify the uncertainty in an analysis from not only the inherent variability of the parameters but also the uncertainties induced by the modeling process itself. By using Bayesian statistics, a stochastic representation of model results can be constructed in the presence of given data. These data can then be used to drive rigorous reduction and selection of models among a model set that most accurately represent the given physical scenario. The utility and application of such an approach will be demonstrated on a transonic aeroelastic flutter analysis for the Advisory Group for Aerospace Research and Development 445.6 wing.