Alternative States Research Articles

Sediment DNA Records the Critical Transition of Bacterial Communities in the Arid Lake

It is necessary to predict the critical transition of lake ecosystems due to their abrupt, non-linear effects on social-economic systems. Given the promising application of paleolimnological archives to tracking the historical changes of lake ecosystems, it is speculated that they can also record the lake’s critical transition. We studied Lake Dali-Nor in the arid region of Inner Mongolia because of the profound shrinking the lake experienced between the 1300 s and the 1600 s. We reconstructed the succession of bacterial communities from a 140-cm-long sediment core at 4-cm intervals and detected the critical transition. Our results showed that the historical trajectory of bacterial communities from the 1200 s to the 2010s was divided into two alternative states: state1 from 1200 to 1300 s and state2 from 1400 to 2010s. Furthermore, in the late 1300 s, the appearance of a tipping point and critical slowing down implied the existence of a critical transition. By using a multi-decadal time series from the sedimentary core, with general Lotka-Volterra model simulations, local stability analysis found that bacterial communities were the most unstable as they approached the critical transition, suggesting that the collapse of stability triggers the community shift from an equilibrium state to another state. Furthermore, the most unstable community harbored the strongest antagonistic and mutualistic interactions, which may imply the detrimental role of interaction strength on community stability. Collectively, our study showed that sediment DNA can be used to detect the critical transition of lake ecosystems.

Threading the Needle: Jacques Maritain’s Defense of a Christian and Liberal Democracy

Some of the key oppositions tearing apart American public life in the early 21st century are related to issues explored in the mid-twentieth century political philosophy of Jacques Maritain. Supporters of liberal democracy, then and now, insist that it is a political system that privatizes religion and all concepts of a common good. Supporters of an integralist alternative demand official state support for religion as the vision underlying political goals. And, of course, arrayed against both are authoritarian movements that threaten democracy altogether. In this context, Maritain’s nuanced political philosophy is far from dated. He thoughtfully defends liberal democracy’s protection of human rights, while also demonstrating that democracy is strengthened by a Catholic vision of the ultimate human good. His political wisdom provides a way through our current impasses and points to a path that will support the survival of this fragile experiment in democracy and the even more fragile hope that democratic processes could be a means to create a more just world.

Exploring tradeoffs in southeast United States marine fisheries management using management strategy evaluation

Recreational fishing is the fastest growing sector in industrialized nations and can have substantial impacts on marine fish populations and ecosystems. Commercial objectives are typically characterized by maximizing yield and fishery stability whereas recreational anglers generally prefer sustained access to fishing and the availability of larger fish. Achieving these objectives while balancing tradeoffs between recreational and commercial fishing is essential to effective recreational and mixed-use fisheries management. Balancing multiple sector objectives is of particular concern in the southeast United States (US), where recreational fishing is the dominant source of mortality for marine fish stocks. We developed and applied a size-structured management strategy evaluation (MSE) tool, individually, to two stocks in southeast US Atlantic waters, black sea bass (Centropristis striata), a sedentary reef fish in overfished condition, and cobia (Rachycentron canadum), a migratory coastal pelagic fish, to evaluate the performance and tradeoffs of mixed management procedures against a variety of objectives. Several recreational and commercial objectives were aligned: fishers sought to conserve the stock and maximize catch, which simplified the evaluation of tradeoffs. We tested management procedures over alternate states of recruitment for black sea bass, and natural mortality for cobia. Management procedures that allowed harvest for black sea bass resulted in or risked an overfished status if the current weak recruitment regime continues, but could rebuild with no fishing regardless of recruitment state. Although results were sensitive to uncertainty in recruitment, no management procedures could achieve historic landings for either sector, and only management procedures that reduced effort consistently resulted in a reduced number of dead discards. No management procedures resulted in an overfished status for cobia. Management procedures for cobia generally achieved objectives and were robust to uncertainty in natural mortality. In both case studies, tradeoffs occurred between maximizing catch and season length and maintaining a stronger size structure in the population. This study resulted in a flexible MSE tool with strong potential utility for scoping management procedures that explicitly consider recreational fishing objectives.

Changing structures, changing paradigms: NELF helps regulate paused or elongating RNA polymerase II

Using cryo-EM and biochemical methods, Su and Vos1 discover an alternative NELF structural state that enables transcription and switches NELF-RNA polymerase II (RNAPII) compatibility with other RNAPII-associated factors that regulate pausing, elongation, termination, and transcription-coupled DNA repair.

Foundation species stabilize an alternative eutrophic state in nutrient-disturbed ponds via selection on microbial community.

Eutrophication due to nutrient addition can result in major alterations in aquatic ecosystem productivity. Foundation species, individually and interactively, whether present as invasive species or as instruments of ecosystem management and restoration, can have unwanted effects like stabilizing turbid eutrophic states. In this study, we used whole-pond experimental manipulations to investigate the impacts of disturbance by nutrient additions in the presence and absence of two foundation species: Dreissena polymorpha (a freshwater mussel) and Myriophyllum spicatum (a macrophyte). We tracked how nutrient additions to ponds changed the prokaryotic and eukaryotic communities, using 16S, 18S, and COI amplicon sequencing. The nutrient disturbance and foundation species imposed strong selection on the prokaryotic communities, but not on the microbial eukaryotic communities. The prokaryotic communities changed increasingly over time as the nutrient disturbance intensified. Post-disturbance, the foundation species stabilized the prokaryotic communities as observed by the reduced rate of change in community composition. Our analysis suggests that prokaryotic community change contributed both directly and indirectly to major changes in ecosystem properties, including pH and dissolved oxygen. Our work shows that nutrient disturbance and foundation species strongly affect the prokaryotic community composition and stability, and that the presence of foundation species can, in some cases, promote the emergence and persistence of a turbid eutrophic ecosystem state.

Evaluating impacts of environmental stress and bioactive chemicals on the North Carolina blue crab population: An individual‐based model

AbstractObjectiveRecent estimates of the North Carolina blue crab Callinectes sapidus stock found that the stock is overfished and overfishing is occurring. Threats outlined in the 2018 stock assessment include climate change and estrogenic endocrine‐disrupting chemicals (EEDCs). The objective of this study was to use an individual‐based modeling approach to simulate the long‐term effects of climate change and EEDCs on the North Carolina blue crab stock.MethodsTo do this, we built an individual‐based model that simulated the life history of individual blue crabs, including but not limited to growth, reproduction, and mortality. We then tested our population of blue crabs against 30 different combinations of temperature and EEDC scenarios over 50 years to determine the long‐term effects on the population.ResultOur simulations suggested that the North Carolina blue crab population may be relatively resilient to climate change‐related temperature shifts but that there may be significant impacts at the population level as summer temperatures become more extreme. Endocrine‐disrupting chemical effects resulted in an alternative stable state of lower catch or the total extinction of the population.ConclusionThese results suggest that management strategy changes may be necessary as temperatures become more extreme in the region. In addition, more research is necessary to fully understand the effects of EEDCs on blue crabs and other crustaceans at the individual and population level.

The puzzling ecology of African Marantaceae forests.

Marantaceae forests are tropical rainforests characterized by a continuous understory layer of perennial giant herbs and a near absence of tree regeneration. Although widespread in West-Central Africa, Marantaceae forests have rarely been considered in the international literature. Yet, they pose key challenges and opportunities for theoretical ecology that transcend the borders of the continent. Specifically, we ask in this review whether open Marantaceae forests and dense closed-canopy forests can be considered as one of the few documented examples of alternative stable states in tropical forests. First, we introduce the different ecological factors that have been posited to drive Marantaceae forests (climate, soil, historical and recent anthropogenic pressures, herbivores) and develop the different hypotheses that have been suggested to explain how Marantaceae forests establish in relation with other vegetation types (understory invasion, early succession after disturbance, and intermediate successional stage). Then, we review the underlying ecological mechanisms that can explain the stability of Marantaceae forests in the long term (tree recruitment inhibition, promotion of and resilience to fire, adaptive reproduction, maintenance by megaherbivores). Although some uncertainties remain and call for further empirical and theoretical research, we found converging evidence that Marantaceae forests are associated with an ecological succession that has been deflected or arrested. If verified, Marantaceae forests may provide a useful model to understand critical transitions in forest ecosystems, which is of particular relevance to achieve sustainable forest management and mitigate global climate change.

A taxonomy of multiple stable states in complex ecological communities.

Natural systems are built from multiple interconnected units, making their dynamics, functioning and fragility notoriously hard to predict. A fragility scenario of particular relevance concerns so-called regime shifts: abrupt transitions from healthy to degraded ecosystem states. An explanation for these shifts is that they arise as transitions between alternative stable states, a process that is well-understood in few-species models. However, how multistability upscales with system complexity remains a debated question. Here, we identify that four different multistability regimes generically emerge in models of species-rich communities and other archetypical complex biological systems assuming random interactions. Across the studied models, each regime consistently emerges under a specific interaction scheme and leaves a distinct set of fingerprints in terms of the number of observed states, their species richness and their response to perturbations. Our results help clarify the conditions and types of multistability that can be expected to occur in complex ecological communities.

SeaTE: Subjective ex ante Treatment Effect of Health on Retirement

The paper studies the effect of health on work among older workers by eliciting two- and four-year-ahead subjective probabilities of working under alternative health states. These measures predict work outcomes. Person-specific differences in working probabilities across health states can be interpreted as Subjective ex ante Treatment Effects (SeaTEs) in a potential outcomes framework and as taste for work within a discrete choice dynamic programming framework. There is substantial heterogeneity in expectations of work conditional on health. The paper shows how heterogeneity in taste for work correlated with health can bias regression estimates of the effect of health on retirement. (JEL D84, I12, J14, J22, J26)

Carbon Dynamics of a Coastal Wetland Transitioning to Mangrove Forest

AbstractCoastal wetlands play a vital role in the global carbon cycle and are under pressure from multiple anthropogenic influences. Altered hydrology and land use change increase susceptibility of wetlands to sea‐level rise, saltwater intrusion, tidal flood events, and storm surges. Flooding from perigean spring tides and storm surges rapidly inundates coastal wetlands with saline waters, quickly surpassing vegetation tolerances, leading to shifts in soil microbial respiration, peat collapse, and plant mortality, followed by establishment of salt‐tolerant vegetation. The Southeast Saline Everglades (SESE) is facing many of these pressures, making it a model system to examine the impacts of ecosystem state transitions and their carbon dynamics. Saltwater flooding from Hurricane Irma (2017) initiated a transitional state, where less salt‐tolerant vegetation (e.g., Cladium jamaicense) is declining, allowing halophytic species such as Rhizophora mangle to colonize, altering the ecosystem's biogeochemistry. We utilized eddy covariance techniques in the SESE to measure ecosystem fluxes of CO2 and CH4 in an area that is transitioning to an alternative state. The landward expansion of mangroves is increasing leaf area, leading to greater physiological activity and higher biomass. Our site was presented initially as a small C source (47.0 g C m−2) in 2020, and by 2022 was a sink (−84.24 g C m−2), with annual greenhouse carbon balance ranging from −0.04 to 0.18. Net radiative forcing ranged from 2.04 to 2.27 W m−2 d−1. As the mangrove landward margin expands, this may lead the area to become a greater carbon sink and a potential offset to increasing atmospheric CO2 concentrations.

FLEXR GUI: a graphical user interface for multi-conformer modeling of proteins.

Proteins are well known 'shapeshifters' which change conformation to function. In crystallography, multiple conformational states are often present within the crystal and the resulting electron-density map. Yet, explicitly incorporating alternative states into models to disentangle multi-conformer ensembles is challenging. We previously reported the tool FLEXR, which, within a few minutes, automatically separates conformational signal from noise and builds the corresponding, often missing, structural features into a multi-conformer model. To make the method widely accessible for routine multi-conformer building as part of the computational toolkit for macromolecular crystallography, we present a graphical user interface (GUI) for FLEXR, designed as a plugin for Coot 1. The GUI implementation seamlessly connects FLEXR models with the existing suite of validation and modeling tools available in Coot. We envision that FLEXR will aid crystallographers by increasing access to a multi-conformer modeling method that will ultimately lead to a better representation of protein conformational heterogeneity in the Protein Data Bank. In turn, deeper insights into the protein conformational landscape may inform biology or provide new opportunities for ligand design. The code is open source and freely available on GitHub at https://github.com/TheFischerLab/FLEXR-GUI.

Abstract 6600: Investigating molecular regulators of a dual identity state in lung adenocarcinoma

Abstract Lung adenocarcinoma (LUAD) is the largest subtype of lung cancer and is the most common cause of cancer related death. LUAD progression is driven by both genetic alterations and epigenetic changes that confer increased lineage plasticity and heterogeneity, but underlying mechanisms dictating cell identity in LUAD remain incompletely understood. The lineage defining transcription factors, NKX2-1 and FoxA1/2, coordinately maintain a pulmonary identity in LUAD. Recent work suggests that NKX2-1-positive (NKX2-1+) LUAD evolves from an alveolar-like state and adopts various disparate cell fates that drive progression, including “dual-identity” states, characterized by acquisition of gastrointestinal (GI) and pulmonary-like states in the same cell. Using sophisticated genetically engineered mouse models and 3D organoid cultures, we demonstrated that the gastrointestinal transcription factor HNF4α, which robustly marks the dual-identity state, is critical for growth in NKX2-1+ LUAD. We performed bulk RNA-seq and single cell RNA-seq in vitro and in vivo, and we found that loss of HNF4α alters the differentiation state of NKX2-1+ LUAD, causing cells to shed elements of their gastric identity in favor of alternate differentiation states. Using paired chromatin immunoprecipitation sequencing and RNA-seq in dual-identity organoids, we found that HNF4α can access and activate many of its canonical gastrointestinal target genes despite being aberrantly expressed in the lung, where it is typically epigenetically silenced early in development. Surprisingly, HNF4α also colocalizes with NKX2-1 and FoxA1/2 and binds at novel sites, suggesting that HNF4α acquires expanded activity in this state beyond its canonical roles. Together, our work unveils key insights into the mechanisms by which lineage defining transcription factors regulate cellular identity and growth in LUAD. Citation Format: Gabriela Fort, Soledad Camolotto, Rushmeen Tariq, Pengshu Fang, Katherine L. Gillis, Chris Stubben, Eric L. Snyder. Investigating molecular regulators of a dual identity state in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6600.

A historical contingency hypothesis for population ecology

Assessments of historical contingency have advanced our understanding of adaptive radiation and community ecology, but little attention has been given to assessing the importance of historical contingency in population ecology. An obstacle has been the unmet need to conceptualize historical contingencies for populations in a manner that allows for their explanatory power to be assessed and quantified so that it can be directly compared with the explanatory power of statistical models representing other hypotheses or theory-based explanations. Here we conceptualize historical contingencies as a series of random events characterized by (1) significant legacy effects that are comparable in length to the waiting time between such events, and (2) the disparate nature of individual events in the series. From that conceptualization, we present a simple quantitative framework for assessing the explanatory power of historical contingencies in population ecology and apply it to an existing long-term dataset on the predator-prey system in Isle Royale National Park. The population-level phenomenon that we focused on was predation rate because it is a synthesis of three basic elements in population ecology (predator abundance, prey abundance and kill rate). We also compared the explanatory power of models of the historical contingency hypothesis to a wide-range of alternative, theory-based, statistical models used to assess underlying mechanisms or forecast future dynamics. Models of the historical contingency hypothesis explained over half of the interannual variation in predation rate and performed similarly, or better than, the vast majority of alternative, theory-based, models. Those findings highlight the potential value of reconsidering the way that population ecologists traditionally attempt to explain phenomena. We also discuss how this new conceptualization of the historical contingency hypothesis can also be valuable for synthesizing several other important ecological concepts of broad significance, especially reddened spectra, tipping points, alternative stable states, and ecological surprises. If the historical contingency hypothesis were found to be broadly applicable, then it would likely explain why ecologists are conspicuously poor at forecasting future dynamics.

A paleoecological context for forest distribution and restoration in Grootbos Nature Reserve, Agulhas Plain, South Africa

Grootbos Nature Reserve falls within the Cape Floristic Region of South Africa and comprises fynbos and forest vegetation elements, which exist as alternate stable states and are naturally maintained by feedbacks between vegetation, fire, topography and climate. The objective of this study was to investigate changes in forest extent in the Baviaansfontein valley in Grootbos Nature Reserve in order to understand whether current forest coverage was greater or lesser prior to colonial settlement. Incorporating paleoecology has the potential to define historical ranges of landscape variability that can guide forest restoration programs that are aligned to historical forest occurrence. Not all landscapes are suited for tree planting initiatives as they harbor indigenous open vegetation, which is of conservation value. Historical and palaeoecological information is especially valuable as tree planting initiatives and reforestation programs are becoming more popular. Here we present a combined palynological (pollen, spores, charcoal) and geochemical approach (X-ray fluorescence elemental ratios, Loss-on-ignition), to evaluate the historic extent and distribution of forest and fynbos vegetation for the past ~250 years at Baviaansfontein in the Grootbos Nature Reserve. The start of the record was dominated by pollen typical of asteraceous fynbos, with evidence of forest elements also present, though in low abundance. After 200 years (c.1750 CE–1950 CE) of increased input of micro- and macrocharcoal, the subsequent decline in charcoal indicates a decrease in fire occurrence. This decline coincides with increased input of forest pollen taxa, suggesting that fire suppression most likely triggered forest expansion and perhaps initiated the beginning of a biome boundary shift. The continued decline in fire promoted the development of the present-day proteoid fynbos type around ~1980 CE and was responsible for the replacement of the previously more asteraceous-dominated fynbos type. The results show that changes in fire occurrence have driven compositional changes over time within fynbos but also contributed to the expansion of forest at the expense of fynbos. Considering the palaeoecological record and the expected warmer climate with more fires, forest expansion at Baviaansfontein is not recommended. The proteoid-dominated fynbos biome might be similarly negatively affected by warmer climate and a shift to an asteraceous fynbos community could occur in the future.

Rotational fishery closures could enhance coral recovery in systems with alternative states

AbstractRotational closures have potential fisheries benefits, yet their impact on coral cover is unknown. Research has shown that permanent closures can protect herbivorous fish, indirectly benefiting corals, but these observations may not apply when closed periods alternate with fishing. Here, we examine how rotational closures affect coral, focusing on systems with the potential to switch between alternative stable states, a context in which temporary closures may have persistent effects. We show that rotational closures can trigger coral recovery, and in some contexts lead to better coral recovery than fixed closures of similar size. Such benthic effects are only possible if closures last long enough for change to occur. We also note that very large fixed or rotating closures may concentrate fishing effort in areas where fishing remains permitted, leading to lower overall coral cover. Our findings offer crucial guidance to managers regarding rotational closures’ potential advantages and drawbacks.

Ecosystem function associated with soil organic carbon declines with tropical dry forest degradation

AbstractForest degradation is increasingly recognized as a major threat to global biodiversity and the multiple ecosystem services forests provide. This study examined the impacts of forest degradation on soil quality and function in a seasonally dry tropical forest (SDTF) of Ecuador. Previous studies of SDTFs have focused on the impacts of land‐use conversion on soils, while this study assessed the less visible but pervasive effects of degradation. We compared soil physical–chemical properties, enzymatic activity, particulate organic carbon (POC) and mineral‐associated organic carbon (MAOC) along a gradient of SDTF degradation in both the dry and rainy season. Our findings showed a consistent and steady reduction in soil quality (total C and N) and function (dehydrogenase and β‐glucosidase activity) that paralleled the loss of vegetative structure and diversity along the degradation gradient. Soil physical–chemical properties were less variable and enzymatic activity was generally higher in the dry season compared to the rainy season. We also showed for the first time a significant and uniform decrease in POC and MAOC with degradation in SDTF. The relative proportion of these two components was constant along the gradient except in the most degraded state (arid land), where POC was higher in proportion to MAOC, suggesting that extreme forest degradation may cause this ecosystem to cross a functional tipping point. These findings address an important knowledge gap for SDTFs by showing a consistent loss of soil quality and functionality with degradation, and suggest that extreme degradation can result in an alternate state with compromised resilience.

Thresholds and Alternative States in a Neotropical Dry Forest in Response to Fire Severity

Thresholds and Alternative States in a Neotropical Dry Forest in Response to Fire Severity

First Passage Times of Long Transient Dynamics in Ecology.

Long transient dynamics in ecological models are characterized by extended periods in one state or regime before an eventual, and often abrupt, transition. One mechanism leading to long transient dynamics is the presence of ghost attractors, states where system dynamics slow down and the system lingers before eventually transitioning to the true attractor. This transition results solely from system dynamics rather than external factors. This paper investigates the dynamics of a classical herbivore-grazer model with the potential for ghost attractors or alternative stable states. We propose an intuitive threshold for first passage time analysis applicable to both bistable and ghost attractor regimes. By formulating the first passage time problem as a backward Kolmogorov equation, we examine how the mean first passage time changes as parameters are varied from the ghost attractor regime to the bistable one, through a saddle-node bifurcation. Our results reveal that the mean and variance of first passage times vary smoothly across the bifurcation threshold, eliminating the deterministic distinction between ghost attractors and bistable regimes. This work suggests that first passage time analysis can be an informative way to classify the length of a long transient. A better understanding of the duration of long transients may contribute to greater ecological understanding and more effective environmental management.

О ВОЗМОЖНОСТИ ФОРМИРОВАНИЯ ОБНОВЛЕННОЙ ПАРАДИГМЫ ТЕОРИЙ ИНДИВИДУАЛЬНОГО И ГРУППОВОГО ВЫБОРА

It is proposed to make adjustments to V. Pareto’s theory of utility, recognizing the category of individual utility as primary in relation to the category of individual preferences. With this approach, the properties of preferences become derivatives of the properties of the utility function, and the latter turns out to be uniquely determined up to linear transformations. Attention is drawn to the fact that when analyzing the problem of group choice, researchers relying both on maximizing the group utility function and on binary comparisons of alternative social states traditionally strive to ensure that the social optimum meets the requirements of Pareto efficiency. The failure of such attempts in the article is associated with ignoring the peculiarities of the choice made in hierarchical and network groups. A two-tier model is proposed as a starting point. First, the collective welfare function «constructed» by the members of society is maximized, and then the redistribution of the received benefits through horizontal interaction leads to the consistency of their interests. It is shown why, in practice, making a choice is accompanied by the use of an aggregated social utility function, delegation of the functions of a large group to specially created small groups. The need to pay attention to the formation of adequate motivation in small groups is particularly justified.

Consequences of kelp forest ecosystem shifts and predictors of persistence through multiple stressors.

Ecological communities can be stable over multiple generations, or rapidly shift into structurally and functionally different configurations. In kelp forest ecosystems, overgrazing by sea urchins can abruptly shift forests into alternative states that are void of macroalgae and primarily dominated by actively grazing sea urchins. Beginning in 2014, a sea urchin outbreak along the central coast of California resulted in a patchy mosaic of remnant forests interspersed with sea urchin barrens. In this study, we used a 14-year subtidal monitoring dataset of invertebrates, algae, and fishes to explore changes in community structure associated with the loss of forests. We found that the spatial mosaic of barrens and forests resulted in a region-wide shift in community structure. However, the magnitude of kelp forest loss and taxonomic-level consequences were spatially heterogeneous. Taxonomic diversity declined across the region, but there were no declines in richness for any group, suggesting compositional redistribution. Baseline ecological and environmental conditions, and sea urchin behaviour, explained the persistence of forests through multiple stressors. These results indicate that spatial heterogeneity in preexisting ecological and environmental conditions can explain patterns of community change.