Predicting Avian Influenza Co-Infection with H5N1 and H9N2 in Northern Egypt.

Human outbreaks with avian influenza have been, so far, constrained by poor viral adaptation to non-avian hosts. This could be overcome via co-infection, whereby two strains share genetic material, allowing new hybrid strains to emerge. Identifying areas where co-infection is most likely can help target spaces for increased surveillance. Ecological niche modeling using remotely-sensed data can be used for this purpose. H5N1 and H9N2 influenza subtypes are endemic in Egyptian poultry. From 2006 to 2015, over 20,000 poultry and wild birds were tested at farms and live bird markets. Using ecological niche modeling we identified environmental, behavioral, and population characteristics of H5N1 and H9N2 niches within Egypt. Niches differed markedly by subtype. The subtype niches were combined to model co-infection potential with known occurrences used for validation. The distance to live bird markets was a strong predictor of co-infection. Using only single-subtype influenza outbreaks and publicly available ecological data, we identified areas of co-infection potential with high accuracy (area under the receiver operating characteristic (ROC) curve (AUC) 0.991)

Niche divergence and limits to expansion in the high polyploid Dianthus broteri complex

Niche evolution in plant polyploids remains controversial and evidence for alternative patterns has been reported. Using the autopolyploid Dianthus broteri complex (2×, 4×, 6× and 12×) as a model, we aimed to integrate three scenarios – competitive exclusion, recurrent origins of cytotypes and niche filling – into a single framework of polyploid niche evolution. We hypothesized that high polyploids would tend to evolve towards extreme niches when low ploidy cytotypes have nearly filled the niche space. We used several ecoinformatics and phylogenetic comparative analyses to quantify differences in the ecological niche of each cytotype and to evaluate alternative models of niche evolution. Each cytotype in this complex occupied a distinct ecological niche. The distributions were mainly constrained by soil characteristics, temperature and drought stress imposed by the Mediterranean climate. Tetraploids had the highest niche breadth and overlap due to their multiple origins, whereas the higher ploidy cytotypes were found in different, restricted, nonoverlapping niches. Niche evolution analyses suggested a scenario with one niche optimum for each ploidy, including the two independent tetraploid lineages.Our results suggest that the fate of nascent polyploids could not be predicted without accounting for phylogenetic relatedness, recurrent origins or the niche occupied by ancestors.Aridos La Melera S.L. (FIUS project 2234/0724

Mechanistic and Correlative Models of Ecological Niches

The suite of factors that drives where and under what conditions a species occurs has become the focus of intense research interest. Three general categories of methods have emerged by which researchers address questions in this area: mechanistic models of species’ requirements in terms of environmental conditions that are based on first principles of biophysics and physiology, correlational models based on environmental associations derived from analyses of geographic occurrences of species, and process-based simulations that estimate occupied distributional areas and associated environments from assumptions about niche dimensions and dispersal abilities. We review strengths and weaknesses of these sets of approaches, and identify significant advantages and disadvantages of each. Rather than identifying one or the other as ‘better,’ we suggest that researchers take great care to use the method best-suited to each specific research question, and be conscious of the weaknesses of any method, such that inappropriate interpretations are avoided

A conceptual map of invasion biology: Integrating hypotheses into a consensus network

Background and aims Since its emergence in the mid‐20th century, invasion biology has matured into a productive research field addressing questions of fundamental and applied importance. Not only has the number of empirical studies increased through time, but also has the number of competing, overlapping and, in some cases, contradictory hypotheses about biological invasions. To make these contradictions and redundancies explicit, and to gain insight into the field’s current theoretical structure, we developed and applied a Delphi approach to create a consensus network of 39 existing invasion hypotheses. Results The resulting network was analysed with a link‐clustering algorithm that revealed five concept clusters (resource availability, biotic interaction, propagule, trait and Darwin’s clusters) representing complementary areas in the theory of invasion biology. The network also displays hypotheses that link two or more clusters, called connecting hypotheses, which are important in determining network structure. The network indicates hypotheses that are logically linked either positively (77 connections of support) or negatively (that is, they contradict each other; 6 connections). Significance The network visually synthesizes how invasion biology’s predominant hypotheses are conceptually related to each other, and thus, reveals an emergent structure – a conceptual map – that can serve as a navigation tool for scholars, practitioners and students, both inside and outside of the field of invasion biology, and guide the development of a more coherent foundation of theory. Additionally, the outlined approach can be more widely applied to create a conceptual map for the larger fields of ecology and biogeography

Modelling Socio-Technical Transition Patterns and Pathways

We report on research that is developing a simulation model for assessing systemic innovations, or 'transitions', of societal systems towards a more sustainable development. Our overall aim is to outline design principles for models that can offer new insights into tackling persistent problems in large-scale systems, such as the European road transport system or the regional management of water resources. The systemic nature of these problems is associated with them being complex, uncertain and cutting across a number of sectors, and indicates a need for radical technological and behavioural solutions that address changes at the systems level rather than offering incremental changes within sub-systems. Model design is inspired by recent research into transitions, an emerging paradigm which provides a framework for tackling persistent problems. We use concepts from the literature on transitions to develop a prototype of a generic 'transition model'. Our prototype aims to capture different types of transition pathways, using historical examples such as the transition from horse-drawn carriages to cars or that from sailing ships to steam ships. The model combines agent-based modelling techniques and system dynamics, and includes interactions of individual agents and sub-systems, as well as cumulative effects on system structures. We show success in simulating different historical transition pathways by adapting the model's parameters and rules for each example. Finally, we discuss the improvements necessary for systematically exploring and detailing transition pathways in empirical case-study applications to current and future transitions such as the transition to a sustainable transport system in Europe.Complex Systems, Agent-Based Modelling, Social Simulation, Transitions, Transition Theory

Ecological Modelling with the Calculus of Wrapped Compartments

The Calculus of Wrapped Compartments is a framework based on stochastic multiset rewriting in a compartmentalised setting originally developed for the modelling and analysis of biological interactions. In this paper, we propose to use this calculus for the description of ecological systems and we provide the modelling guidelines to encode within the calculus some of the main interactions leading ecosystems evolution. As a case study, we model the distribution of height of Croton wagneri, a shrub constituting the endemic predominant species of the dry ecosystem in southern Ecuador. In particular, we consider the plant at different altitude gradients (i.e. at different temperature conditions), to study how it adapts under the effects of global climate change.Comment: A preliminary version of this paper has been presented in CMC13 (LNCS 7762, pp 358-377, 2013

Ecological theory as a foundation to control pathogenic invasion in aquaculture

Detrimental host-pathogen interactions are a normal phenomenon in aquaculture animal production, and have been counteracted by prophylactic use of antibiotics. Especially, the youngest life stages of cultivated aquatic animals are susceptible to pathogen invasion, resulting in disease and mortality. To establish a more sustainable aquatic food production, there is a need for new microbial management strategies that focus on 'join them' and not the traditional 'beat them' approaches. We argue that ecological theory could serve as a foundation for developing sustainable microbial management methods that prevent pathogenic disease in larviculture. Management of the water microbiota in aquaculture systems according to ecological selection principles has been shown to decrease opportunistic pathogen pressure and to result in an improved performance of the cultured animals. We hypothesize that manipulation of the biodiversity of the gut microbiota can increase the host's resistance against pathogenic invasion and infection. However, substantial barriers need to be overcome before active management of the intestinal microbiota can effectively be applied in larviculture