Network-based analysis of stochastic SIR epidemic models with random and proportionate mixing

In this paper, we outline the theory of epidemic percolation networks and their use in the analysis of stochastic susceptible-infectious-removed (SIR) epidemic models on undirected contact networks. We then show how the same theory can be used to analyze stochastic SIR models with random and proportionate mixing. The epidemic percolation networks for these models are purely directed because undirected edges disappear in the limit of a large population. In a series of simulations, we show that epidemic percolation networks accurately predict the mean outbreak size and probability and final size of an epidemic for a variety of epidemic models in homogeneous and heterogeneous populations. Finally, we show that epidemic percolation networks can be used to re-derive classical results from several different areas of infectious disease epidemiology. In an Appendix, we show that an epidemic percolation network can be defined for any time-homogeneous stochastic SIR model in a closed population and prove that the distribution of outbreak sizes given the infection of any given node in the SIR model is identical to the distribution of its out-component sizes in the corresponding probability space of epidemic percolation networks. We conclude that the theory of percolation on semi-directed networks provides a very general framework for the analysis of stochastic SIR models in closed populations.     

Prevalence and diversity of avian hematozoan parasites in Asia: a regional survey

Tissue samples from 699 birds from three regions of Asia (Myanmar, India, and South Korea) were screened for evidence of infection by avian parasites in the genera Plasmodium and Haemoproteus. Samples were collected from November 1994 to October 2004. We identified 241 infected birds (34.0%). Base-on-sequence data for the cytochrome b gene from 221 positive samples, 34 distinct lineages of Plasmodium, and 41 of Haemoproteus were detected. Parasite diversity was highest in Myanmar followed by India and South Korea. Parasite prevalence differed among regions but not among host families. There were four lineages of Plasmodium and one of Haemoproteus shared between Myanmar and India and only one lineage of Plasmodium shared between Myanmar and South Korea. No lineages were shared between India and South Korea, although an equal number of distinct lineages were recovered from each region. Migratory birds in South Korea and India originate from two different migratory flyways; therefore cross-transmission of parasite lineages may be less likely. India and Myanmar shared more host species and habitat types compared to South Korea. Comparison between low-elevation habitat in India and Myanmar showed a difference in prevalence of haematozoans.     

Nonmarine aspects of the Cambrian Tonto Group of the Grand Canyon, USA, and broader implications

A re-examination of the classic time-transgressive model of the Cambrian Tonto Group of the Grand Canyon challenges some of the basic assumptions regarding strandline migration during the Sauk transgression, the applicability of sequence stratigraphy to epicratonic deposits, and the criteria by which siliciclastic deposits of the North American Cambrian system are categorized as marine. Indicators for high short-term depositional rates, coupled with the complex splay and coalescence of meter-scale parasequence architectures, detract from the shoreline migration and deepening seas model that has held sway for over 60 years. Ostensibly marine signatures, represented by sparse and fragmentary trilobite fossils and abundant bedding plane trace fossils, are closely associated with nonmarine signatures, represented by nonmarine palynoflora and clay mineral assemblages, and highly oxidized paleoweathering profiles. The vast extent of three-dimensional exposure of the Cambrian section in the Grand Canyon shows a paleogeography not of a single discrete shoreline translated laterally with rising and falling sea-level, but of a single mosaic setting of emergent shoals and rocky peaks, broad fluvial and tidal channels, and shallow pools and interchannel flats. Much detail concerning sediment dynamics and paleoenvironment is lost or overlooked when summary terms like “marginal marine” or “nearshore” are applied to such settings. It is suggested here that the Tonto Group, with its mixed marine and nonmarine attributes, and considering its historic role as a teaching model, be viewed not as an exceptional Cambrian deposit, but as an exemplar of epicratonic deposits on a pre-vegetated landscape.     

Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses

Different factors may modulate the gut microbiota of animals. In any particular environment, diet, genetic factors and human influences can shape the bacterial communities residing in the gastrointestinal tract. Metagenomic approaches have significantly expanded our knowledge on microbiota dynamics inside hosts, yet cultivation and isolation of bacterial members of these complex ecosystems may still be necessary to fully understand interactions between bacterial communities and their host. A dual approach, involving culture‐independent and ‐dependent techniques, was used here to decipher the microbiota communities that inhabit the gastro intestinal tract of free‐range, broiler and feral chickens. In silico analysis revealed the presence of a core microbiota that is typical of those animals that live in different geographical areas and that have limited contact with humans. Anthropic influences guide the metabolic potential and the presence of antibiotic resistance genes of these different bacterial communities. Culturomics attempts, based on different cultivation conditions, were applied to reconstruct in vitro the microbiota of feral chickens. A unique strain collection representing members of the four major phyla of the poultry microbiota was assembled, including bacterial strains that are not typically retrieved from the chicken gut.     

Movements of four native Hawaiian birds across a naturally fragmented landscape

Animals often increase their fitness by moving across space in response to temporal variation in habitat quality and resource availability, and as a result of intra and inter‐specific interactions. The long‐term persistence of populations and even whole species depends on the collective patterns of individual movements, yet animal movements have been poorly studied at the landscape level. We quantified movement behavior within four native species of Hawaiian forest birds in a complex lava‐fragmented landscape: Hawai?i ‘amakihi Chlorodrepanis virens, ‘oma‘o Myadestes obscurus, ‘apapane Himatione sanguinea, and ‘i‘iwi Drepanis coccinea. We evaluated the relative importance of six potential intrinsic and extrinsic drivers of movement behavior and patch fidelity: 1) forest fragment size, 2) the presence or absence of invasive rats (Rattus sp.), 3) season, 4) species, 5) age, and 6) sex. The study was conducted across a landscape of 34 forest fragments varying in size from 0.07 to 12.37 ha, of which 16 had rats removed using a treatment‐control design. We found the largest movements in the nectivorous ‘apapane and ‘i‘iwi, intermediate levels in the generalist Hawai?i ‘amakihi, and shortest average movement for the ‘oma‘o, a frugivore. We found evidence for larger patch sizes increasing patch fidelity only in the ‘oma‘o, and an effect of rat‐removal increasing patch fidelity of Hawai?i ‘amakihi only after two years of rat‐removal. Greater movement during the non‐breeding season was observed in all species, and season was an important factor in explaining higher patch fidelity in the breeding season for ‘apapane and ‘i‘iwi. Sex was important in explaining patch fidelity in ‘oma‘o only, with males showing higher patch fidelity. Our results provide new insights into how these native Hawaiian species will respond to a changing environment, including habitat fragmentation and changing distribution of threats from climate change.     

Inorganic Nitrogen Losses from a Forested Ecosystem in Responseto Physical,Chemical, Biotic,and Climatic Perturbations

Nitrate leaching to streams is a sensitive indicator of the biogeochemical status of forest ecosystems. Two primary theories predicting long-term (decadal) changes in nitrate loss rates (N saturation theory and the nutrient retention hypothesis) both predict increasing dissolved inorganic nitrogen (DIN) losses for watershed 6 (W6), the biogeochemical reference watershed at the Hubbard Brook Experimental Forest (HBEF). Measured values, however, have declined substantially since measurements began in the mid-1960s. Are these theories wrong, or are there other important controls on DIN losses at the annual to decadal time scale that have obscured the tendency toward higher losses over time? We tested the individual and combined effects of several forms of disturbance on DIN loss rates from northern hardwood forests by comparing predictions from a relatively simple model of forest carbon, nitrogen, and water dynamics (PnET-CN) with the long-term record of annual DIN loss from W6 at HBEF. Perturbations tested include interannual climate variation, changes in atmospheric chemistry (CO₂, O₃, N deposition), and physical and biotic disturbances (two harvests, a hurricane salvage, and a defoliation event). No single disturbance caused changes in DIN losses to mimic measured values. Only when run with all of the disturbances combined did the model-predicted pattern of interannual change in DIN loss approach the measured record. Single-disturbance simulations allow an estimation of the role of each in the total pattern of DIN loss. We conclude that DIN losses from W6 were elevated in the 1960s by a combination of recovery from extreme drought and a significant defoliation event. N deposition alone, in the absence of other disturbances, would have increased DIN losses by 0.35 g N m^?2y^?1. These findings indicate that predictions of DIN losses must take into account the full spectrum of disturbance events and changes in environmental conditions impacting the systems examined.