Theoretical Ecology

"In archaeology, biotic phenomena (e.g. human behaviour) must be inferred from a-biotic traces, requiring the process model to be conceptually unified. This unification has been prevented by dualistic ontologies that conceive humans and their purported unique traits as epi-phenomena, ontologically separated from their environment. The resulting encapsulation of phenomena within separate theoretical fields is proposed to be the source of our inability to apply evolutionary theory in archaeology.
The symptoms manifest as ontological deletion, isolation or “freezing“ of the organism within  explanatory models, consequently, processes that span the divide for example those that include both biotic and a-biotic components such as technology or culture, have been impossible to integrate with evolutionary theory. "

Plant species vary greatly in their responsiveness to nutritional soil mutualists, such as my- corrhizal fungi and rhizobia, and this responsiveness is associated with a trade-off in alloca- tion to root structures for resource uptake. As a result, the outcome of plant competition can change with the density of mutualists, with microbe-responsive plant species having high competitive ability when mutualists are abundant and non-responsive plants having high competitive ability with low densities of mutualists. When responsive plant species also allow mutualists to grow to greater densities, changes in mutualist density can generate a positive feedback, reinforcing an initial advantage to either plant type. We study a model of mutualist-mediated competition to understand outcomes of plant-plant interactions within a patchy environment. We find that a microbe-responsive plant can exclude a non-responsive plant from some initial conditions, but it must do so across the landscape including in the mi- crobe-free areas where it is a poorer competitor. Otherwise, the non-responsive plant will persist in both mutualist-free and mutualist-rich regions. We apply our general findings to two different biological scenarios: invasion of a non-responsive plant into an established mi- crobe-responsive native population, and successional replacement of non-responders by microbe-responsive species. We find that resistance to invasion is greatest when seed dis- persal by the native plant is modest and dispersal by the invader is greater. Nonetheless, a native plant that relies on microbial mutualists for competitive dominance may be particular- ly vulnerable to invasion because any disturbance that temporarily reduces its density or that of the mutualist creates a window for a non-responsive invader to establish dominance. We further find that the positive feedbacks from associations with beneficial soil microbes create resistance to successional turnover. Our theoretical results constitute an important first step toward developing a general understanding of the interplay between mutualism and competition in patchy landscapes, and generate qualitative predictions that may be tested in future empirical studies.

Mendonca VMD. 1997. Predator-prey interactions in a sandy shore system in the Moray Firth, NE Scotland. PhD Thesis in Zoology (field: Ecology). Univ Aberdeen. Aberdeen, Scotland. 202 pp.

ABSTRACT: Culbin Sands is a semi-lagoon system of 1.5 ha of tidal flats, draining to the sea via a tidal gully. It has coarse sandy sediment, experiences an exposed hydrodynamic environment and is protected from the sea by a large sand dune on the seaside and a 28 ha of forest on the landwardside. As a relatively undisturbed area, it provides information useful for conservation biology, habitat management, and for better understanding of the ecology of coastal areas. Areas like Culbin are rich in epibenthic predators that use the shallow and intertidal zones as feeding grounds, as refuge from predators, or both. Many species such as flatfish and gobiids move out to the sea in autumn and return every summer in the breeding season, although the overwintering fish and shrimp that remain may also be important for the ecology of the system. Shorebirds also use the area seasonally, mainly to exploit the high abundance of food, especially during autumn and early winter. This poses the question: ‘are the effects of predation significant for their prey?’ To address this, prey and predators were regularly
sampled over 1994-1996 and the effects of predators (epibenthic fauna and shorebirds) on their invertebrate prey examined using manipulative field experiments. 56 invertebrate species were identified from the sediment at Culbin. There was little evidence of consistent and easily interpretable seasonal cycles for the main invertebrates, but several species tended to have higher abundance during the autumn or early winter. Annual production by invertebrates was 15-23 g ash free dry mass (AFDM) m-2 yr-1. Arenicola marina was the most important in terms of standing stock in the sediment, followed by the bivalve Cerastoderma edule. Production values of cockles were 1.4-3.4 g AFDM m-2 yr-1. The most abundant epibenthic species were the brown shrimp Crangon crangon, the common goby Pomatoschistus microps and plaice Pleuronectes platessa, but other fish (e.g. sandeel Amodytes tobianus, three-spined stickleback Gasterosteus aculeatus, fifteen-spined stickleback Spinachia spinachia, sea scorpion Myoxocephalus scorpio, pipefish Nerophis lumbriciformis, sand goby Pomatoschistus minutus, and flounder Plactichthys flesus), crabs (e.g. shore crab Carcinus maenas and hermit crab Pagurus berhardus) and starfish Asteria rubens were also present. The most important prey were amphipods (mainly Bathyporeia spp.) for the brown shrimp and common goby, and bivalves (siphons of adult individuals) for plaice. Despite the relatively high consumption rates manipulative field experiments showed that none of the predators had significant impact on invertebrate prey densities, although shorebirds had significant size effects on the prey, especially on the larger size classes of the bivalves C. edule and Macoma balthica. These results are in line with others found all around the world such as in the Ythan estuary, Scotland (e.g. Raffaelli & Hall, 1992, Animal. Ecol. 61:551-560), USA (Wilson, 1994, J Exp Mar Biol Ecol 196:15-25), and in New Zealand (Trush et al. 1994, Mar Ecol Prog Ser 107:211-222).


RESULTING PUBLICATIONS:

(5) Mendonca VM, Raffaelli DG, Boyle, PR, Abella E. 2015. The role of the European brown shrimp Crangon crangon in the community ecology of a subarctic food web. Food Webs
https://www.academia.edu/10413497/The_role_of_the_European_brown_shrimp_Crangon_crangon_in_the_community_ecology_of_a_subarctic_food_web

(4) Mendonca VM, Raffaelli DG, Boyle PR, Emes C. 2009. Trophodynamics in a shallow lagoon off NW Europe (Culbin Sands, Moray Firth): Spatial and temporal variability of epibenthic communities, their diets, and consumption efficiency. Zool Stud 48(2): 196-214. http://ualg.academia.edu/VandaMendon%C3%A7a/Papers/662975/Trophodynamics_in_a_Shallow_Lagoon_off_Northwestern_Europe_Culbin_Sands_Moray_Firth_Spatial_and_Temporal_Variability_of_Epibenthic_Communities_Their_

(3) Mendonca VM, Raffaelli,DG, PR Boyle, Hoskins S. 2008. Spatial and temporal characteristics of benthic invertebrate communities at Culbin Sands lagoon, Moray Firth, NE Scotland, and impacts of the disturbance of cockle harvesting. Sci Mar 72(2): 265-278. http://ualg.academia.edu/VandaMendon%C3%A7a/Papers/662982/Spatial_and_temporal_characteristics_of_benthic_invertebrate_communities_at_Culbin_Sands_lagoon_Moray_Firth_NE_Scotland_and_impacts_of_the_disturbance_of_cockle_harvesting

(2) Mendonca VM, Raffaelli DG, Boyle PR, Emes C. 2007. The ecological role of overwintering fish in the food web of the Culbin Sands lagoon ecosystem, NE Scotland: Identifying major trophic links and testing effects of fish Pomatoschistus microps (Pallas) on benthic invertebrates. Sci Mar 71(4): 649-660. http://ualg.academia.edu/VandaMendon%C3%A7a/Papers/662974/The_ecological_role_of_overwintering_fish_in_the_food_web_of_the_Culbin_Sands_lagoon_ecosystem_NE_Scotland_Identifying_major_trophic_links_and_testing_effects_

(1) Mendonca VM, Raffaelli DG, Boyle PR. 2007. Interactions between shorebirds and benthic invertebrates at Culbin Sands lagoon, NE Scotland: Effects of avian predation on their prey community density and structure. Sci Mar 71(3): 579-591. http://ualg.academia.edu/VandaMendon%C3%A7a/Papers/662973/Interactions_between_shorebirds_and_benthic_invertebrates_at_Culbin_Sands_lagoon_NE_Scotland_Effects_of_avian_predation_on_their_prey_community_density_and_"""

To better understand and manage complex systems like ecosystems it is critical to know the relative contribution of the system components to the system function. Ecologists and social scientists have described a diversity of ways that individuals can be important; This paper makes two key contributions to this research area. First, it shows that throughflow (Tj), the total energy or matter entering or exiting a system component, is a global indicator of the relative contribution of the component to the whole system activity. It is global because it includes the direct and indirect exchanges among community members.  Further, throughflow is a special case of Hubbell status or centrality as defined in social science. This recognition effectively joins the concepts, enabling ecologists to use and build on the broader centrality research in network science. Second, I characterize the distribution of throughflow in 45 empirically-based trophic ecosystem models. Consistent with theoretical expectations, this analysis shows that a small fraction of the system components are responsible for the majority of the system activity. In 73% of the ecosystem models, 20% or less of the nodes generate 80% or more of the total system through flow. Four or fewer nodes are required to account for 50% of the total system activity and are thus defined as community dominants. 121 of the 130 dominant nodes in the 45 ecosystem models could be classified as primary producers, dead organic matter, or bacteria. Thus, throughflow centrality indicates the rank power of the ecosystems components and shows the concentration of power in the primary production and decomposition cycle. Although these results are specific to ecosystems, these techniques build on flow analysis based on economic input–output analysis. Therefore these results should be useful for ecosystem ecology, industrial ecology, the study of urban metabolism, as well as other domains using input–output analysis.

As indicated early by Charles Darwin, languages behave and change very much like living species. They display high diversity, differentiate in space and time, emerge and disappear. A large body of literature has explored the role of information exchanges and communicative constraints in groups of agents under selective scenarios. These models have been very helpful in providing a rationale on how complex forms of communication emerge under evolutionary pressures. However, other patterns of large-scale organization can be described using math- ematical methods ignoring communicative traits. These approaches consider shorter time scales and have been developed by exploiting both theoretical ecology and statistical physics methods. The models are reviewed here and include extinction, invasion, origination, spatial organization, coexistence and diversity as key concepts and are very simple in their defining rules. Such simplicity is used in order to catch the most fundamental laws of organization and those universal ingredients responsible for qualitative traits. The similarities between observed and predicted patterns indicate that an ecological theory of language is emerging, supporting (on a quantitative basis) its ecological nature, although key differences are also present. Here, we critically review some recent advances and outline their implications and limitations as well as highlight problems for future research.

Theoretical models of predator–prey systems predict that sufficient enrichment of prey can generate large amplitude limit cycles, paradoxically causing a high risk of extinction (the paradox of enrichment). Although real ecological communities contain many gregarious species, whose foraging behaviour should be influenced by socially transmitted information, few theoretical studies have examined the possibility that social foraging might resolve this paradox. I considered a predator population in which individuals play the producer–scrounger foraging game in one-prey-one-predator and two-prey-one-predator systems. I analysed the stability of a coexisting equilibrium point in the one-prey system and that of non-equilibrium dynamics in the two-prey system. The results revealed that social foraging could stabilize both systems, and thereby resolve the paradox of enrichment when scrounging behaviour (i.e. kleptoparasitism) is prevalent in predators. This suggests a previously neglected mechanism underlying a powerful effect of group-living animals on the sustainability of ecological communities.

Охрана окружающей среды кажется главным образом предметом практическим. СМИ, популяризаторы науки да и сами исследователи, обсуждая экологические проблемы, подают их как неотложные нужды, чьë решение важно, но развитие собственно науки происходит где-то. Этот устойчивый стереотип при преподавании надо развенчивать: именно природоохранная практика очень много даёт развитию фундаментальной науки. Ею обусловлена смена парадигм в экологии и теории эволюции-переход от описания видимого к пониманию скрытого, утверждение одновременности экологических и (микро)эволюционных процессов-раньше считали, что они следуют друг за другом и т.д.. Поднятые ею проблемы интеллектуально сложны, как всякий анализ реакции сложных систем с их контринтуитивностью ответов на воздействие, почему будут особенно интересны учащимся. Увы, эта "фундаментальная" сторона чаще всего игнорируется, что снижает интерес учащихся к предмету (особенно у мотивированных стать биологом, хотя им он особенно необходим), исключает сопряжение природоохранных знаний со знаниями фундаментальных биологических дисциплин-притом что оно безусловно необходимо для понимания. Как писал наш великий философ Эвальд Ильенков, школа должна учить мыслить, и стоит назвать самые явные способы это делать в преподавании охраны природы.

HERE: http://www.sciencedirect.com/science/article/pii/S1369848616300723

AND HERE: http://authors.elsevier.com/a/1Twba4tTwyAx2p

                            The world’s leading environmental advisory institutions look to ecological theory and research as an objective guide for policy and resource management decision-making.  In addition to the theoretical and broadly philosophical merits of doing so, it is therefore practically significant to clear up confusions about ecology’s conceptual foundations and to clarify the basic workings of inferential methods used in the science.  Through discussion of key moments in the genesis of the theoretical branch of ecology, this essay elucidates a general heuristic role of teleological metaphors in ecological research and defuses certain enduring confusions about work in ecology.

One of the most popular approaches for investigating the roles of niche and neutral processes driving metacommunity patterns consists of partitioning variation in species data into environmental and spatial components. The logic is that the distance decay of similarity in communities is expected under neutral models. However, because environmental variation is often spatially structured, the decay could also be attributed to environmental factors that are missing from the analysis. Here, we use a spatial autocorrelation analysis protocol, previously developed to detect isolation-by-distance in allele frequencies, to evaluate patterns of species abundances under neutral dynamics. We show that this protocol can be linked with variation partitioning analyses. Moreover, in an attempt to test the neutral model, we derive three predictions to be applied both to original species abundances and to abundances predicted by a pure spatial model species abundances will be uncorrelated; Moran's I correlograms will reveal similar short-distance autocorrelation patterns; an increasing degree of non-neutrality will tend to generate patterns of correlation among abundances within groups of species with similar correlograms (i.e. within species with neutral and non-neutral dynamics). We illustrate our protocol by analyzing spatial patterns in abundance of 28 terrestrially breeding anuran species from Central Amazonia. We recommend that researchers should investigate spatial autocorrelation patterns of abundances predicted by pure spatial models to identify similar patterns of spatial autocorrelation at short distances and lack of correlation between species abundances. Therefore, the hypothesis that spatial patterns in abundances are primarily due to pure neutral dynamics (rather than to missing spatiallystructured environmental factors) can be confirmed after taking environmental variables into account.

Diferentes métodos han sido propuestos para evaluar el grado de señal filogenética (autocorrelación) en los rasgos macroecológicos. Estos métodos son útiles para desarrollar maneras alternativas de evitar el problema de la falta de independencia entre especies y, actualmente, han demostrado ser importantes para inferir la velocidad de evolución de un rasgo al compararlo con modelos evolutivos alternativos, tales como el movimiento Browniano o el proceso Ornstein-Uhlenbeck (OU). Recientemente, desarrollamos un método llamado Curva de Señal-Representación Filogenética (PSR, por sus siglas en inglés), una expansión de la regresión de autovectores filogenéticos (PVR, por sus siglas en inglés) propuesto en 1998, que consiste en estimar diferentes coeficientes de determinación mediante la regresión de un rasgo de interés contra los autovectores extraídos de una matriz de distancias filogenéticas. El primer modelo únicamente utiliza los primeros de estos autovectores como variable explicativa, el segundo modelo utiliza tanto los primeros como los segundos autovectores y así sucesivamente. Posteriormente, los coeficientes de determinación resultantes son graficados contra los autovalores acumulados y la forma de esta curva es relacionada con modelos evolutivos determinando la variación del rasgo (i.e. un patrón lineal es esperado bajo movimiento Browniano). Aquí, aplicamos la curva PSR para estudiar los patrones de variación interespecífica en la talla corporal y tamaño de área de distribución de los carnívoros a nivel mundial y comparamos dichas curvas con aquellas simuladas bajo diferentes modelos de evolución. Nuestros resultados apoyan inequívocamente nuestras expectativas basadas en estudios previos acerca de la talla corporal presentando una fuerte señal filogenética, aproximada por un patrón OU con baja restricción, mientras el tamaño de área de distribución es más variable y mejor ajustado por un modelo nulo sugiriendo la ausencia de señal filogenética.

Sensitivity analysis, the study of how ecological variables of interest respond to changes in external conditions, is a theoretically well-developed and widely applied approach in population ecology. Though the application of sensitivity analysis to predicting the response of species-rich communities to disturbances also has a long history, derivation of a mathematical framework for understanding the factors leading to robust coexistence has only been a recent undertaking. Here we suggest that this development opens up a new perspective, providing advances ranging from the applied to the theoretical. First, it yields a framework to be applied in specific cases for assessing the extinction risk of community modules in the face of environmental change. Second, it can be used to determine trait combinations allowing for coexistence that is robust to environmental variation, and limits to diversity in the presence of environmental variation, for specific community types. Third, it offer...

Intergroup violence is assumed to play a key role in establishing and maintaining gang competitive dominance. However , it is not clear how competitive ability, gang size and reciprocal violence interact. Does competitive dominance lead to larger gangs, or allow them to remain small? Does competitive dominance lead gangs to mount more attacks against rivals, or expose them to more attacks? We explore a model developed in theoretical ecology to understand communities arranged in strict competitive hierarchies. The model is extended to generate expectations about gang size distributions and the directionality of gang violence. Model expectations are explored with twenty-three years of data on gang homicides from Los Angeles. Gangs may mitigate competitive pressure by quickly finding gaps in the spatial coverage of superior competitors. Competitively superior gangs can be larger or smaller than competitively inferior gangs and a disproportionate source or target of directional violence, depending upon where exactly they fall in the competitive hierarchy. A model specifying the mechanism of competitive dominance is needed to correctly interpret gang size and violence patterns.

13 In this work we propose an ecological model, which is a modified version of the Bazykin 14 model. This model of predator–prey interaction emphasizes predator pairing that yields 15 steady state, periodic and extinction stable solutions. Moreover, we find attractor coex-16 istence between limit cycles, steady states, and the extinction solution, which is always a 17 stable attractor. We also study this model as a spatially extended system in one and two 18 dimensions and obtain Turing patterns such as stripes and spots as well as the so-called 19 black-eye patterns, and, as in the homogeneous case, the spatial patterns coexist with 20 the homogeneous extinction solution.

Scientists have used Richard Dawkins’ ideas of the extended
phenotype to postulate levels of selection higher than an individual in evolution. Dawkins rejects this extension and insists
that there must be a reproductive bottleneck for the extended
phenotype, and thus, higher levels of selection to exist. In
this research, a model is presented that shows levels of selection higher than the individual, without the reproductive bottleneck insisted upon by Dawkins. A 2-dimensional cellular automata Daisyworld model is extended with a gene that controls the rate of albedo mutation. A large number of runs of the model are performed with a variety of different parameters, and the statistics for the runs are analyzed. The results show that contrary to expectations, the mutation rate does not stay low but instead rises to high levels. The reasons for this are analyzed and it is shown that patch level selection pressures are acting upon the individuals. It is concluded that selection pressures higher than the individual can exist, mimicking the extended phenotype, without the need for a reproductive bottleneck.