The population dynamics of clustered consumer-resource spatial patterns: Insights from the demographics of a Turing mechanism.

In ecology, Alan Turing's proposed activation-inhibition mechanism has been abstracted as corresponding to several ecological interaction types to explain pattern formation in ecosystems. Consumer-resource interactions have strong theoretical arguments linking them to both the Turing mechanism and pattern formation, but there is little empirical support to demonstrate these claims. Here, we connect several lines of evidence to support the proposition that consumer-resource interactions can create empirically observed spatial patterns through a mechanism similar to Turing's theory.

Combining intransitive and higher-order effects in a coupled oscillator framework: A case study of an ant community.

A growing body of literature recognizes that pairwise species interactions are not necessarily an appropriate metaphorical molecule of community ecology. Two examples are intransitive competition and nonlinear higher-order effects. While these two processes have been discussed extensively, the explicit analysis of how the two of them behave when simultaneously part of the same dynamic system has not yet been explored theoretically.

Mycorrhizal feedbacks influence global forest structure and diversity.

One mechanism proposed to explain high species diversity in tropical systems is strong negative conspecific density dependence (CDD), which reduces recruitment of juveniles in proximity to conspecific adult plants. Although evidence shows that plant-specific soil pathogens can drive negative CDD, trees also form key mutualisms with mycorrhizal fungi, which may counteract these effects. Across 43 large-scale forest plots worldwide, we tested whether ectomycorrhizal tree species exhibit weaker negative CDD than arbuscular mycorrhizal tree species.

Coupled Oscillators in an Agroecosystem: Integrating Direct and Indirect Effects.

AbstractAgricultural pests are increasingly appreciated as subjects of ecology. One particular case, a pest in coffee production, is analyzed here using the conceptual framework of complex systems, increasingly acknowledged as having an obvious home in the field of ecology, notorious for its complex structures. The particular case analyzed here arguably falls under the control of the complexity of the ecological system rather than of a simple magic bullet of population regulation.

A multiplexed assay for quantifying immunomodulatory proteins supports correlative studies in immunotherapy clinical trials.

Introduction: Immunotherapy is an effective treatment for a subset of cancer patients, and expanding the benefits of immunotherapy to all cancer patients will require predictive biomarkers of response and immune-related adverse events (irAEs). To support correlative studies in immunotherapy clinical trials, we are developing highly validated assays for quantifying immunomodulatory proteins in human biospecimens.

Methods: Here, we developed a panel of novel monoclonal antibodies and incorporated them into a novel, multiplexed, immuno-multiple reaction monitoring mass spectrometry (MRM-MS)-based proteomic assay targeting 49 proteotypic peptides representing 43 immunomodulatory proteins.

Intransitivity as a dynamic assembly engine of competitive communities.

Historically, those ecological communities thought to be dominated by competitive interactions among their component species have been assumed to exhibit transitive competition, that is, a hierarchy of competitive strength from most dominant to most submissive. A surge of recent literature takes issue with this assumption and notes that some species in some communities are intransitive, where a rock/scissors/paper arrangement characterizes some components of some communities. We here propose a merging of these two ideas, wherein an intransitive subgroup of species connects with a distinct subcomponent that is organized hierarchically, such that the expected eventual takeover by the dominant competitor in the hierarchy is thwarted, and the entire community can be sustained.

Concurrent pembrolizumab with AVD for untreated classic Hodgkin lymphoma.

Concurrent administration of pembrolizumab with chemotherapy in untreated classic Hodgkin lymphoma (CHL) has not been studied previously. To investigate this combination, we conducted a single-arm study of concurrent pembrolizumab with AVD (doxorubicin, vinblastine, and dacarbazine; APVD) for untreated CHL. We enrolled 30 patients and met the primary safety end point with no observed significant treatment delays in the first 2 cycles.

Surprising effects of cascading higher order interactions.

Most species are embedded in multi-interaction networks. Consequently, theories focusing on simple pair-wise interactions cannot predict ecological and/or evolutionary outcomes. This study explores how cascading higher-order interactions (HOIs) would affect the population dynamics of a focal species.

Spatiotemporal Foraging Dynamics of Solenopsis invicta (Hymenoptera: Formicidae) and its Potential Effects on the Spatial Structure of Interspecific Competition.

The ant communities on coffee farms in the West/Central Mountains of Puerto Rico are composed of mainly invasive species, although many have a long history of occupation and are effectively naturalized. The ecological forces that maintain such communities are thus of interest, and are evidently related to the spatial patterns in which they inevitably occur. Furthermore, the spatial patterns in which members of the native ant community forage almost certainly include limitations related to the structure of the networks of subterranean foraging tunnels that extend from the nest mounds of Solenopsis invicta.

Tree Effects on Coffee Leaf Rust at Field and Landscape Scales.

Although integrating trees into agricultural systems (i.e., agroforestry systems) provides many valuable ecosystem services, the trees can also interact with plant diseases.

Distribution of biomass dynamics in relation to tree size in forests across the world.

Tree size shapes forest carbon dynamics and determines how trees interact with their environment, including a changing climate. Here, we conduct the first global analysis of among-site differences in how aboveground biomass stocks and fluxes are distributed with tree size. We analyzed repeat tree censuses from 25 large-scale (4-52 ha) forest plots spanning a broad climatic range over five continents to characterize how aboveground biomass, woody productivity, and woody mortality vary with tree diameter.

Reduced rainfall and resistant varieties mediate a critical transition in the coffee rust disease.

Critical transitions, sudden responses to slow changes in environmental drivers, are inherent in many dynamic processes, prompting a search for early warning signals. We apply this framework to understanding the coffee rust disease, which experienced an unprecedented outbreak in Mesoamerica in 2012-2013, likely a critical transition. Based on monthly infection data from 128 study quadrats in a 45-ha plot in southern Mexico from 2014 to 2020, we find that the persistent seasonal epidemic following the initial outbreak collapses in an evident subsequent critical transition.

Can Conflicting Selection from Pollinators and Nectar-Robbing Antagonists Drive Adaptive Pollen Limitation? A Conceptual Model and Empirical Test.

AbstractPollen limitation is widespread, despite predictions that it should not be. We propose a novel mechanism generating pollen limitation: conflicting selection by pollinators and antagonists on pollinator attraction traits. We introduce a heuristic model demonstrating antagonist-induced adaptive pollen limitation and present a field study illustrating its occurrence in a wild population.

New forms of structure in ecosystems revealed with the Kuramoto model.

Ecological systems, as is often noted, are complex. Equally notable is the generalization that complex systems tend to be oscillatory, whether Huygens' simple patterns of pendulum entrainment or the twisted chaotic orbits of Lorenz' convection rolls. The analytics of oscillators may thus provide insight into the structure of ecological systems.

The assembly and importance of a novel ecosystem: The ant community of coffee farms in Puerto Rico.

Agricultural ecosystems are by their very nature novel and by definition the more general biodiversity associated with them must likewise constitute a novel community. Here, we examine the community of arboreally foraging ants in the coffee agroecosystem of Puerto Rico. We surveyed 20 coffee plants in 25 farms three times in a period of one year.

Light availability influences the intensity of nectar robbery and its effects on reproduction in a tropical shrub via multiple pathways.

Premise: The multiple exogenous pathways by which light availability affects plant reproduction (e.g., via influence on attraction of mutualists and antagonists) remain surprisingly understudied.

Endogenous spatial pattern formation from two intersecting ecological mechanisms: the dynamic coexistence of two noxious invasive ant species in Puerto Rico.

Endogenous (or autonomous, or emergent) spatial pattern formation is a subject transcending a variety of sciences. In ecology, there is growing interest in how spatial patterns can 'emerge' from internal system processes and simultaneously affect those very processes. A classic situation emerges when a predator's focus on a dominant competitor releases competitive pressure on a subdominant competitor, allowing coexistence of the two.

Response of Coffee Farms to Hurricane Maria: Resistance and Resilience from an Extreme Climatic Event.

Resistance and resilience have become important concepts in the evaluation of disturbance events, providing a framework that is useful in light of the expected increase in frequency and occurrences of hurricanes as a consequence of climate change. Hurricane Maria landed on Puerto Rico as a category 4 storm in September of 2017. Among the affected elements were agricultural systems, including coffee agroecosystems.

Hysteresis and critical transitions in a coffee agroecosystem.

Seeking to employ ecological principles in agricultural management, a classical ecological debate provides a useful framing. Whether ecosystems are controlled from above (predators are the limiting force over herbivores) or from below (overutilization of plant resources is the limiting force over herbivores) is a debate that has motivated much research. The dichotomous nature of the debate (above or below) has been criticized as too limiting, especially in light of contemporary appreciation of ecological complexity-control is more likely from a panoply of direct and indirect interactions.

Huffaker revisited: spatial heterogeneity and the coupling of ineffective agents in biological control.

In a classic study, Huffaker demonstrated that abiotic forms of spatial heterogeneity could induce stability in predator-prey interactions. Recent theories suggest that space can also act to destabilize predator-prey systems and that stability can arise from coupling of unstable units. Here, using Huffaker's classic experimental design refitted with modern empirical and statistical techniques, we reassess the effect of space on predator-prey interactions when the prey are pests of agriculture, and when predators must compete with pathogens for shared prey resources.

Scale and strength oak-mesophyte interactions in a transitional oak-hickory forest.

Forests in eastern North America are undergoing rapid compositional changes as they experience novel climate, disturbance, and pest conditions. One striking pattern is the replacement of canopy oaks spp.) by mesic, fire-sensitive, shade-tolerant species like red maple .

Effect of coffee agriculture management on the population structure of a forest dwelling rodent ().

Most of the natural habitat in tropical regions exists as scattered fragments embedded in a matrix of different agricultural uses. As a result of this agricultural expansion, habitat loss and fragmentation have become the main drivers of biodiversity loss. Understanding the long-term effects of agricultural management on populations is of great importance for the development of successful conservation strategies.

Anolis lizards as biocontrol agents in mainland and island agroecosystems.

Our knowledge of ecological interactions that bolster ecosystem function and productivity has broad applications to the management of agricultural systems. Studies suggest that the presence of generalist predators in agricultural landscapes leads to a decrease in the abundance of herbivorous pests, but our understanding of how these interactions vary across taxa and along gradients of management intensity and eco-geographic space remains incomplete. In this study, we assessed the functional response and biocontrol potential of a highly ubiquitous insectivore (lizards in the genus ) on the world's most important coffee pest, the coffee berry borer ().