Incorporating Disease and Population Structure into Models of SIR Disease in Contact Networks

We consider the recently introduced edge-based compartmental models (EBCM) for the spread of susceptible-infected-recovered (SIR) diseases in networks. These models differ from standard infectious disease models by focusing on the status of a random partner in the population, rather than a random individual. This change in focus leads to simple analytic models for the spread of SIR diseases in random networks with heterogeneous degree. In this paper we extend this approach to handle deviations of the disease or population from the simplistic assumptions of earlier work. We allow the population to have structure due to effects such as demographic features or multiple types of risk behavior. We allow the disease to have more complicated natural history. Although we introduce these modifications in the static network context, it is straightforward to incorporate them into dynamic network models. We also consider serosorting, which requires using dynamic network models. The basic methods we use to derive these generalizations are widely applicable, and so it is straightforward to introduce many other generalizations not considered here. Our goal is twofold: to provide a number of examples generalizing the EBCM method for various different population or disease structures and to provide insight into how to derive such a model under new sets of assumptions.     

Pan-European Ecological Networks

Pan-European Ecological Networks make a major contribution to the overall effort to protect, maintain and enhance biodiversity; the concept has gained significant political support over the last decade and a half. A platform now exists for: increased integration of ecological networks into the cross-sectoral policy agenda; research into their contribution to ecosystem services and mitigation and adaption for climate change; and an increase in the availability of information about practical delivery. This paper provides an overview of recent policy and research developments in Europe.     

Using Complex Networks to Characterize International Business Cycles

Background

There is a rapidly expanding literature on the application of complex networks in economics that focused mostly on stock markets. In this paper, we discuss an application of complex networks to study international business cycles.

Methodology/Principal Findings

We construct complex networks based on GDP data from two data sets on G7 and OECD economies. Besides the well-known correlation-based networks, we also use a specific tool for presenting causality in economics, the Granger causality. We consider different filtering methods to derive the stationary component of the GDP series for each of the countries in the samples. The networks were found to be sensitive to the detrending method. While the correlation networks provide information on comovement between the national economies, the Granger causality networks can better predict fluctuations in countries’ GDP. By using them, we can obtain directed networks allows us to determine the relative influence of different countries on the global economy network. The US appears as the key player for both the G7 and OECD samples.

Conclusion

The use of complex networks is valuable for understanding the business cycle comovements at an international level.     

Evolving Digital Ecological Networks

“It is hard to realize that the living world as we know it is just one among many possibilities” [1]. Evolving digital ecological networks are webs of interacting, self-replicating, and evolving computer programs (i.e., digital organisms) that experience the same major ecological interactions as biological organisms (e.g., competition, predation, parasitism, and mutualism). Despite being computational, these programs evolve quickly in an open-ended way, and starting from only one or two ancestral organisms, the formation of ecological networks can be observed in real-time by tracking interactions between the constantly evolving organism phenotypes. These phenotypes may be defined by combinations of logical computations (hereafter tasks) that digital organisms perform and by expressed behaviors that have evolved. The types and outcomes of interactions between phenotypes are determined by task overlap for logic-defined phenotypes and by responses to encounters in the case of behavioral phenotypes. Biologists use these evolving networks to study active and fundamental topics within evolutionary ecology (e.g., the extent to which the architecture of multispecies networks shape coevolutionary outcomes, and the processes involved).

This is a “Topic Page” article for PLOS Computational Biology.

     

Transmission Networks and Population Turnover of Echovirus 30

Globally, echovirus 30 (E30) is one of the most frequently identified enteroviruses and a major cause of meningitis. Despite its wide distribution, little is known about its transmission networks or the dynamics of its recombination and geographical spread. To address this, we have conducted an extensive molecular epidemiology and evolutionary study of E30 isolates collected over 8 years from a geographically wide sample base (11 European countries, Asia, and Australia). 3Dpol sequences fell into several distinct phylogenetic groups, interspersed with other species B serotypes, enabling E30 isolates to be classified into 38 recombinant forms (RFs). Substitutions in VP1 and 3Dpol regions occurred predominantly at synonymous sites (ratio of nonsynonymous to synonymous substitutions, 0.05) with VP1 showing a rapid substitution rate of 8.3 × 10⁻³ substitutions per site per year. Recombination frequency was tightly correlated with VP1 divergence; viruses differing by evolutionary distances of >0.1 (or 6 years divergent evolution) almost invariably (>97%) had different 3Dpol groups. Frequencies of shared 3Dpol groups additionally correlated with geographical distances, with Europe and South Asia showing turnover of entirely distinct virus populations. Population turnover of E30 was characterized by repeated cycles of emergence, dominance, and disappearance of individual RFs over periods of 3 to 5 years, although the existence and nature of evolutionary selection underlying these population replacements remain unclear. The occurrence of frequent “sporadic” recombinants embedded within VP1 groupings of other RFs and the much greater number of 3Dpol groups than separately identifiable VP1 lineages suggest frequent recombination with an external diverse reservoir of non-E30 viruses.The genus Enterovirus in the family Picornaviridae is a group of nonenveloped RNA viruses that cause a wide range of diseases in humans and other mammals. Enteroviruses contain a positive-sense RNA genome of approximately 7,500 nucleotides encoding a polyprotein that after cleavage yields structural (capsid proteins VP1 to VP4) and nonstructural (2A to 3D) proteins. Primary infection with an enterovirus leads to viral replication in the tissue around the gastrointestinal tract, followed by a transient viremia and sometimes migration into other tissues (6, 44). Although infection in immunocompetent individuals is often asymptomatic or causes mild febrile illness, enteroviruses are a common etiological agent in aseptic meningitis, encephalitis, and paralysis in individuals of all ages, with persistent and/or widely disseminated systemic infection in immunosuppressed individuals and neonates (12, 19, 23).Enteroviruses were originally classified as polioviruses, coxsackie virus type A or B viruses, or echoviruses (enteric cytopathic human orphan viruses), depending upon the infectious properties of the virus such as pathogenicity in mice (reviewed in reference 22). From the 1960s onwards, enteroviruses within these groups were further differentiated into serotypes originally by using panels of specific neutralizing antisera and, more recently, by sequence comparisons of structural gene regions such as VP1 (9, 34, 38, 43). There are currently over 100 recognized human enterovirus serotypes that fall into four main species (designated A to D) using phylogenetic analysis (54). The Enterovirus genus additionally contains several other species infecting primates, cattle, and pigs and has recently been expanded to include the genetically related human rhinovirus A and B (54).The species B serotype, echovirus 30 (E30), is a major cause of meningitis in both children and adults. Among the many serotypes associated with this disease presentation, E30 is generally the most commonly isolated in Europe (8, 31, 49), the United States (10, 37), Asia (1, 60), and South America (33). E30 infections typically occur as a series of outbreaks every 3 to 5 years, frequently over large geographical areas. For example, high frequencies of E30 detection in meningitis cases and surveillance programs were reported for 2000 to 2001 throughout Europe, including Denmark (58), Belgium (57), Cyprus (45), Germany (46), and France (3, 5), and again in 2005 to 2006 (8). Similarly, in the United States, long-term surveillance by the Centers for Disease Control and Prevention revealed peaks of E30 isolation in 1981, 1991 to 1993, 1997, and 2003 (10, 37). The underlying basis for this periodicity in E30 infections and the possible association of different genetic variants of E30 with outbreaks are currently poorly understood.At any one time point, a range of different species B enterovirus serotypes circulate in human populations. The evolution of enteroviruses occurs through genetic drift and, over much longer periods, antigenic diversification in the structural gene region encoding the virus capsid (7, 14, 25, 30, 51, 55); it may also occur by recombination between the capsid and nonstructural coding parts of the genome and the 5′ untranslated region (2, 13, 16, 20, 26, 28, 29, 35, 39, 41, 47, 48, 53). To date, almost all documented examples of recombination have been limited to members of the same species (e.g., between species B serotypes), with the exception of the 5′ untranslated region, where only a single genetic group can be identified within human species A and B and a second with species C and D (48).In this study, we have carried out an extensive investigation of VP1 sequence divergence and recombination through sequencing the 3Dpol region of E30 isolates and samples collected from several European countries, Southeast Asia, and Australia over a combined 8-year observation period. Using this geographically diverse sample collection, our aims were to document the time span and geographical extent of different E30 variants as they emerged and spread during the observation period. The identification of individual recombinants of E30 provides the means to document in detail the dynamics of E30 population turnover, geographical ranges of enterovirus transmission networks, and, ultimately, the relationship between the emergence of new variants of E30 and longer-term changes in disease associations and pathogenicity.     

Parasitic and Infectious Disease Responses to Changing Global Nutrient Cycles

Parasitic and infectious diseases (PIDs) are a significant threat to human, livestock, and wildlife health and are changing dramatically in the face of human-induced environmental changes such as those in climate and land use. In this article we explore the little-studied but potentially important response of PIDs to another major environmental change, that in the global nutrient cycles. Humans have now altered the nitrogen (N) cycle to an astonishing degree, and those changes are causing a remarkable diversity of environmental and ecological responses. Since most PIDs are strongly regulated by ecological interactions, changes in nutrients are likely to affect their dynamics in a diversity of environments. We show that while direct tests of the links between nutrients and disease are rare, there is mounting evidence that higher nutrient levels frequently lead to an increased risk of disease. This trend occurs across multiple pathogen types, including helminths, insect-vectored diseases, myxozoa, and bacterial and fungal diseases. The mechanistic responses to increased nutrients are often complex and frequently involve indirect responses that are regulated by intermediate or vector hosts involved in disease transmission. We also show that rapid changes in the N cycle of tropical regions combined with the high diversity of human PIDs in these regions will markedly increase the potential for N to alter the dynamics of disease. Finally, we stress that progress on understanding the effects of nutrients on disease ecology requires a sustained effort to conduct manipulative experiments that can reveal underlying mechanisms on a species-specific basis.     

Development and Infectious Disease in Hosts with Complex Life Cycles

Metamorphosis is often characterized by profound changes in morphology and physiology that can affect the dynamics of species interactions. For example, the interaction between a pathogen and its host may differ depending on the life stage of the host or pathogen. One pathogen that infects hosts with complex life cycles is the emerging fungal pathogen of amphibians, Batrachochytrium dendrobatidis (Bd). We sought to determine how conditions at the larval stage can affect variation in development and patterns of Bd infection across amphibian life stages. We used outdoor experimental mesocosms to simulate natural pond habitats and manipulated the presence of Bd, the larval density, and the number of host species in larvae of two co-occurring amphibian species (Rana cascadae and Pseudacris regilla). We found that infection differed between species throughout development; P. regilla consistently had higher infection severity compared to R. cascadae. Additionally, while up to 100% of larvae were infected, only 18.2% of R. cascadae and 81.5% of P. regilla were infected after metamorphosis. This indicates that amphibians have the ability to recover from Bd infection as they undergo metamorphosis. Higher larval densities in P. regilla led to a shorter larval period, and individuals with a shorter larval period had lower infection severity. This led to a trend where P. regilla larvae reared at high densities tended to have lower infection prevalence after metamorphosis. We also found that exposure to Bd increased larval mortality and prolonged the larval period in P. regilla, indicating that P. regilla are susceptible to the negative effects of Bd as larvae. This study demonstrates that host density, species composition, and pathogen exposure may all interact to influence development and infection in hosts with complex life cycles.     

Correlation between Thermodynamic Efficiency and Ecological Cyclicity for Thermodynamic Power Cycles

A sustainable global community requires the successful integration of environment and engineering. In the public and private sectors, designing cyclical (“closed loop”) resource networks increasingly appears as a strategy employed to improve resource efficiency and reduce environmental impacts. Patterning industrial networks on ecological ones has been shown to provide significant improvements at multiple levels. Here, we apply the biological metric cyclicity to 28 familiar thermodynamic power cycles of increasing complexity. These cycles, composed of turbines and the like, are scientifically very different from natural ecosystems. Despite this difference, the application results in a positive correlation between the maximum thermal efficiency and the cyclic structure of the cycles. The immediate impact of these findings results in a simple method for comparing cycles to one another, higher cyclicity values pointing to those cycles which have the potential for a higher maximum thermal efficiency. Such a strong correlation has the promise of impacting both natural ecology and engineering thermodynamics and provides a clear motivation to look for more fundamental scientific connections between natural and engineered systems.     

Evidence for Regionally Synchronized Cycles in Texas Quail Population Dynamics

Abstract: Knowledge of the possible role of cyclic behavior in wildlife dynamics assists in understanding and managing populations. Using spectrum, we analyzed time series (1978-2002) on the abundance of northern bobwhites (Colinus virginianus) and scaled quail (Callipepla squamata) in several ecological regions in Texas, USA, to test for the presence of cycles; we also tested whether drought severity (Modified Palmer Drought Severity Index) exhibited cyclic dynamics and whether quail and drought cycles were synchronized among regions. We found evidence of population cyclicity in all ecoregions we tested (5 for bobwhites, 4 for scaled quail) based on both Texas Parks and Wildlife and North American Breeding Bird Survey count data. Periods of the observed cycles generally were 5-6 years (bobwhites) or 2-3 years (scaled quail), depending on ecoregion and data source. Cyclicity was most pronounced for bobwhites in the Rolling Plains (north TX) and the South Texas Plains. The Palmer Index exhibited a roughly 5-year cycle in 5 of 6 regions we tested. A 5-year bobwhite and Palmer Index cycle were synchronous in 3 contiguous ecoregions totaling 27,200,000 ha. Wet-dry cycles seemed to synchronize bobwhite cycles in Texas. Our results suggest that habitat manipulations aimed at improving habitat conditions during dry periods, such as reducing livestock stocking rates, could provide ground cover similar to that available in wet periods.     

Ecological and Genetic Models in Population Biophysics

Biophysics - Complex causal relationships occur between population dynamics and a change in a population genetic structure. In our study, a simple model was used to show that the evolutionary...     

Social Networks and Knowledge Transmission Strategies among Baka Children,Southeastern Cameroon

The dynamics of knowledge transmission and acquisition, or how different aspects of culture are passed from one individual to another and how they are acquired and embodied by individuals, are central to understanding cultural evolution. In small-scale societies, cultural knowledge is largely acquired early in life through observation, imitation, and other forms of social learning embedded in daily experiences. However, little is known about the pathways through which such knowledge is transmitted, especially during middle childhood and adolescence. This study presents new empirical data on cultural knowledge transmission during childhood. Data were collected among the Baka, a forager-farmer society in southeastern Cameroon. We conducted structured interviews with children between 5 and 16 years of age (n?=?58 children; 177 interviews, with children being interviewed 1–6 times) about group composition during subsistence activities. Children’s groups were generally diverse, although children tended to perform subsistence activities primarily without adults and with same-sex companions. Group composition varied from one subsistence activity to another, which suggests that the flow of knowledge might also vary according to the activity performed. Analysis of the social composition of children’s subsistence groups shows that vertical and oblique transmission of subsistence-related knowledge might not be predominant during middle childhood and adolescence. Rather, horizontal transmission appears to be the most common knowledge transmission strategy used by Baka children during middle childhood and adolescence, highlighting the importance of other children in the transmission of knowledge.     

Mass-Balance Analyses of Boreal Forest Population Cycles: Merging Demographic and Ecosystem Approaches

UsingEcopath, a trophic mass-balance modeling framework, we developed six models of a Canadian boreal forest food web centered around snowshoe hares, which have conspicuous 10-year population cycles. Detailed models of four phases of the cycle were parameterized with long-term population data for 12 vertebrate taxa. We also developed five other models that, instead of observed data, used parameter values derived from standard assumptions. Specifically, in the basic model, production was assumed to equal adult mortality, feeding rates were assumed to be allometric, and biomass was assumed to be constant. In the actual production, functional response, and biomass change models, each of these assumed values from the basic model was replaced individually by field data. Finally, constant biomass models included actual production by all species and functional responses of mammalian predators and revealed the proportion of herbivore production used by species at higher trophic levels. By comparing these models, we show that detailed information on densities and demographics was crucial to constructing models that captured dynamic aspects of the food web. These detailed models reinforced an emerging picture of the causes and consequences of the snowshoe hare cycle. The snowshoe hare decline and low phases were coincident with times when per capita production was relatively low and predation pressure high. At these times, ecotrophic efficiencies (EE) suggest there was little production that remained unconsumed by predators. The importance of both production and consumption implies that bottom–up and top–down factors interacted to cause the cycle. EEs of other herbivores (ground squirrels, red squirrels, small mammals, small birds, grouse) were generally low, suggesting weak top–down effects. Predation rates on these “alternative” prey, except ground squirrels, were highest when predators were abundant, not when hares were rare; consequently, any top–down effects reflected predator biomass and were not a function of diet composition or functional responses. Finally, several predators (lynx, coyotes, great-horned owls) showed clear bottom–up regulation, reproducing only when prey exceeded threshold densities. Taken altogether, these results demonstrate that ecosystem models parameterized by population data can describe the dynamics of nonequilibrial systems, but only when detailed information is available for the species modeled. Received 30 November 2000; Accepted 6 September 2001.     

Computational Fact Checking from Knowledge Networks

Traditional fact checking by expert journalists cannot keep up with the enormous volume of information that is now generated online. Computational fact checking may significantly enhance our ability to evaluate the veracity of dubious information. Here we show that the complexities of human fact checking can be approximated quite well by finding the shortest path between concept nodes under properly defined semantic proximity metrics on knowledge graphs. Framed as a network problem this approach is feasible with efficient computational techniques. We evaluate this approach by examining tens of thousands of claims related to history, entertainment, geography, and biographical information using a public knowledge graph extracted from Wikipedia. Statements independently known to be true consistently receive higher support via our method than do false ones. These findings represent a significant step toward scalable computational fact-checking methods that may one day mitigate the spread of harmful misinformation.     

Ecological Aspects of Disease and Human Populations

This paper shows how some basic ecological themes can be illustrated,in a very explicit and quantitative way, by examples drawn fromthe interactions between human hosts and their infectious diseases.I first discuss the population biology of infectious diseases,showing how basic reproductive rates and density dependent limitationsmay be estimated. Observed cycles in the incidence of childhoodinfections are discussed as examples of Lotka-Volterra prey-predatorcycles. Trade-offs between virulence and transmissibility inthe evolution of parasite life histories are discussed in general,withthe Australian rabbit-myxoma virus story as a case study. Iconclude by mentioning ways in which the interplay between populationdensity and transmission thresholds may have influenced humanhistory.     

Comparative Population Genomics of African Montane Forest Mammals Support Population Persistence across a Climatic Gradient and Quaternary Climatic Cycles

The Eastern Afromontane biodiversity hotspot (EABH) has the highest concentration of biodiversity in tropical Africa, yet few studies have investigated recent historical diversification processes in EABH lineages. Herein, we analyze restriction-site associated DNA-sequences (RAD-Seq) to study recent historical processes in co-distributed mouse (Hylomyscus) and shrew (Sylvisorex) species complexes, with an aim to better determine how historical paleoenvironmental processes might have contributed to the EABH’s high diversity. We analyzed complete SNP matrices of > 50,000 RAD loci to delineate populations, reconstruct the history of isolation and admixture, and discover geographic patterns of genetic partitioning. These analyses demonstrate that persistently unsuitable habitat may have isolated multiple populations distributed across montane habitat islands in the Itombwe Massif and Albertine Rift to the west as well as Mt Elgon and Kenyan Highlands to the east. We detected low genetic diversity in Kenyan Highland populations of both genera, consistent with smaller historical population sizes in this region. We additionally tested predictions that Albertine Rift populations are older and more persistently isolated compared to the Kenyan Highlands. Phylogenetic analyses support greater historical isolation among Albertine Rift populations of both shrews and mice compared to the Kenyan Highlands and suggest that there are genetically isolated populations from both focal genera in the Itombwe Massif, Democratic Republic of Congo. The Albertine Rift ecoregion has the highest mammalian tropical forest species richness per unit area on earth. Our results clearly support accelerating efforts to conserve this diversity.