This book is the second of two volumes in a series on terrestrial and marine comparisons, focusing on the temporal complement of the earlier spatial analysis of patchiness and pattern (Levin et al. 1993). The issue of the relationships among pattern, scale, and patchiness has been framed forcefully in John Steele’s writings of two decades (e.g., Steele 1978). There is no pattern without an observational frame. In the words of Nietzsche, “There are no facts… only interpretations.”

https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.2307/1941447

The Problem of Pattern and Scale in Ecology: The Robert H. MacArthur Award Lecture

▪ Abstract The focus of most ideas on diversity maintenance is species coexistence, which may be stable or unstable. Stable coexistence can be quantified by the long-term rates at which community members recover from low density. Quantification shows that coexistence mechanisms function in two major ways: They may be (a) equalizing because they tend to minimize average fitness differences between species, or (b) stabilizing because they tend to increase negative intraspecific interactions relative to negative interspecific interactions. Stabilizing mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations in population densities and environmental factors in space and time. Equalizing mechanisms contribute to stable coexistence because they reduce large average fitness inequalities which might negate the effects of stabilizing mechanisms. Models of unstable coexitence...

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Mechanisms of Maintenance of Species Diversity

This review summarizes theoretical progress in the field of active matter, placing it in the context of recent experiments. This approach offers a unified framework for the mechanical and statistical properties of living matter: biofilaments and molecular motors in vitro or in vivo, collections of motile microorganisms, animal flocks, and chemical or mechanical imitations. A major goal of this review is to integrate several approaches proposed in the literature, from semimicroscopic to phenomenological. In particular, first considered are ``dry'' systems, defined as those where momentum is not conserved due to friction with a substrate or an embedding porous medium. The differences and similarities between two types of orientationally ordered states, the nematic and the polar, are clarified. Next, the active hydrodynamics of suspensions or ``wet'' systems is discussed and the relation with and difference from the dry case, as well as various large-scale instabilities of these nonequilibrium states of matter, are highlighted. Further highlighted are various large-scale instabilities of these nonequilibrium states of matter. Various semimicroscopic derivations of the continuum theory are discussed and connected, highlighting the unifying and generic nature of the continuum model. Throughout the review, the experimental relevance of these theories for describing bacterial swarms and suspensions, the cytoskeleton of living cells, and vibrated granular material is discussed. Promising extensions toward greater realism in specific contexts from cell biology to animal behavior are suggested, and remarks are given on some exotic active-matter analogs. Last, the outlook for a quantitative understanding of active matter, through the interplay of detailed theory with controlled experiments on simplified systems, with living or artificial constituents, is summarized.

Hydrodynamics of soft active matter

■ Abstract Contributions from the field of population biology hold promise for understanding and managing invasiveness; invasive species also offer excellent opportunities to study basic processes in population biology. Life history studies and demographic models may be valuable for examining the introduction of invasive species and identifying life history stages where management will be most effective. Evolutionary processes may be key features in determining whether invasive species establish and spread. Studies of genetic diversity and evolutionary changes should be useful for

/pdf/the-population-biology-of-invasive-species-bdndjv53b3.pdf

The Population Biology of Invasive Species

Community ecology theory can be used to understand biological invasions by applying recent niche concepts to alien species and the communities that they invade. These ideas lead to the concept of ‘niche opportunity', which defines conditions that promote invasions in terms of resources, natural enemies, the physical environment, interactions between these factors, and the manner in which they vary in time and space. Niche opportunities vary naturally between communities but might be greatly increased by disruption of communities, especially if the original community members are less well adapted to the new conditions. Recent niche theory clarifies the prediction that low niche opportunities (invasion resistance) result from high species diversity. Conflicting empirical patterns of invasion resistance are potentially explained by covarying external factors. These various ideas derived from community ecology provide a predictive framework for invasion ecology.

/pdf/community-ecology-theory-as-a-framework-for-biological-2tep5nf3cd.pdf

Community ecology theory as a framework for biological invasions

Simulation Study of Stratified Diffusion Model

Colonies of bacteria grown on agar plates can display morphological patterns of surprising varieties depending on culture conditions. For instance, B. subtilis shows a dense-branching morphology on a nutrient-poor semi-solid agar medium, while some chemotactic strains of E. coli form a spot pattern on a pseudo-hexagonal lattice. Based on such experimental data, diffusion-reaction models that incorporate cell movements and interactions between bacterial cells and chemical substances have been constructed, and used to explain how the observed patterns are generated.

Modeling Complex Patterns in Bacterial Colonies.

Mathematical models for biological invasions. Competition for open spaces.

In a space environment such as Space Shuttle or Space Station, animal experiments with aquatic species in a closed system pose a crucial problem in maintaining their water quality for a long term. In nature, ammonia as an animal wastes is converted by nitrifying bacteria to nitrite or nitrate compounds, which usually become nitrogen sources for plants. Thus an application of the biological reactor with such bacteria attached on some filters has been suggested and experimentally studied for efficient waste managements of ammonia. Although some successful results were reported (Kozu et al. 1995, Nagaoka et al. 1998, Nakamura et al. 1997, 1998) in the space applications, purely empirical approaches have so far been taken to develop a biological filter having a stable nitrifying activity. In this study, we constructed a mathematical model to deal with the dynamics of the ammonia nitrifying processes in a biological reactor. The model describes population dynamics of the ammonia-oxidizing bacteria and the nitrite-oxidizing bacteria cultivated on the same filter. We estimated parameters involved in the model using the experimental data. The result shows that these estimated parameters could be applied to general cases and that the two bacteria are in a symbiotic relationship; they can better perform when both coexist, as has been empirically recognized. Based on the model analysis, we discuss how to prepare a high performance biological filter.

Nanako Shigesada

Papers

Simulation Study of Stratified Diffusion Model

Modeling Complex Patterns in Bacterial Colonies.

Mathematical models for biological invasions. Competition for open spaces.

Population dynamics of nitrifying bacteria in an aquatic ecosystem.

Modeling Range Expansions in Biological Invasions@@@Biological Invasions: Theory and Practice