R. Admiraal

networksis: A Package to Simulate Bipartite Graphs with Fixed Marginals Through Sequential Importance Sampling

The ability to simulate graphs with given properties is important for the analysis of social networks. Sequential importance sampling has been shown to be particularly effective in estimating the number of graphs adhering to fixed marginals and in estimating the null distribution of graph statistics. This paper describes the networksis package for R and how its simulate and simulate_sis functions can be used to address both of these tasks as well as generate initial graphs for Markov chain Monte Carlo simulations.

Recreational trampling negatively impacts vegetation structure of an Australian biodiversity hotspot

Recreational trampling damage of natural vegetation is an increasing problem in the global context and has the potential to impact on vegetation communities that are of high ecological and socio-economic interest. Wildflower tourism in the national parks of southwest Australia, a global biodiversity hotspot, has the potential to damage the flora on which it depends through trampling. Little research has been previously undertaken in these largely shrub-dominated communities to identify and quantify such impacts. This study is the first to do so, using observational studies of tourists, a descriptive study, and trampling experiments. The behaviours of independent tourists and tour groups were observed. Of the 213 independent visitors observed 41 visitors left trails to view flowers and in the process trampled vegetation. Vegetation height and cover were measured at three sites frequented by wildflower tourists. Vegetation height and cover declined in response to use by tourists. Trampling experiments, which relied on trampling treatments of 0, 30, 100, 200, 300/500 passes, where 0 passes represents the control, were applied at four sites. Trampling led to a significant reduction in vegetation height immediately post-treatment, for all treatments, with a non-significant recovery over time. Trampling also significantly reduced vegetation cover, with the resistance indices for these experimental sites ranging from 30 to 300 passes. Collectively these results illustrate the low resilience and resistance of these valued communities and the possible impacts of wildflower and other nature based tourism, through trampling. The paper concludes with suggested management strategies, which strongly emphasise the importance of education for the tourism industry and provide for international comparisons in regard to recreational trampling impacts on biodiverse shrub land communities.

Low root-to-root transmission of a tobamovirus, yellow tailflower mild mottle virus, and resilience of its virions

Tobamoviruses are serious pathogens because they have extremely stable virions, they are transmitted by contact, and they often induce severe disease in crops. Knowledge of the routes of transmission and resilience of tobamovirus virions is essential in understanding the epidemiology of this group of viruses. We used an isolate of the tobamovirus yellow tailflower mild mottle virus (YTMMV) to examine root-to-root transmission in soil and in a hydroponic growth environment. Root-to-root transmission occurred rarely, and when it occurred plants did not exhibit systemic movement of the virus from the roots to the shoots over a 30-day period. The resilience of YTMMV virions was tested in dried leaf tissue over time periods from one hour to one year under temperatures ranging from -80°C to 160°C. Infectivity was maintained for at least a year when incubated at -80°C, 22°C or at fluctuating ambient temperatures of 0.8°C to 44.4°C, but incubation under dry conditions at 160°C for >4 days eliminated infectivity. Exposure of virions to 0.1 M sodium hydroxide or 20% w/v skim milk solution for 30 min, treatments recommended for tobamovirus inactivation, did not abolish infectivity of YTMMV.

Evolution of a wild-plant tobamovirus passaged through an exotic host: Fixation of mutations and increased replication

Abstract Tobamovirus is a group of viruses that have become serious pathogens of crop plants. As part of a study informing risk of wild plant virus spill over to crops, we investigated the capacity of a solanaceous-infecting tobamovirus from an isolated indigenous flora to adapt to new exotic hosts. Yellow tailflower mild mottle virus (YTMMV) (genus Tobamovirus, family Virgaviridae) was isolated from a wild plant of yellow tailflower (Anthocercis littoria, family Solanaceae) and initially passaged through a plant of Nicotiana benthamiana, then one of Nicotiana glutinosa where a single local lesion was used to inoculate a N. benthamiana plant. Sap from this plant was used as starting material for nine serial passages through three plant species. The virus titre was recorded periodically, and 85% of the virus genome was sequenced at each passage for each host. Six polymorphic sites were found in the YTMMV genome across all hosts and passages. At five of these, the alternate alleles became fixed in the viral genome until the end of the experiment. Of these five alleles, one was a non-synonymous mutation (U1499C) that occurred only when the virus replicated in tomato. The mutant isolate harbouring U1499C, designated YTMMV-δ, increased its titre over passages in tomato and outcompeted the wild-type isolate when both were co-inoculated to tomato. That YTMMV-δ had greater reproductive fitness in an exotic host than did the wild type isolate suggests YTMMV evolution is influenced by host changes.

Catharanthus mosaic virus: A potyvirus from a gymnosperm, Welwitschia mirabilis

A virus from a symptomatic plant of the gymnosperm Welwitschia mirabilis Hook. growing as an ornamental plant in a domestic garden in Western Australia was inoculated to a plant of Nicotiana benthamiana where it established a systemic infection. The complete genome sequence of 9636 nucleotides was determined using high-throughput and Sanger sequencing technologies. The genome sequence shared greatest identity (83% nucleotides and 91% amino acids) with available partial sequences of catharanthus mosaic virus, indicating that the new isolate belonged to that taxon. Analysis of the phylogeny of the complete virus sequence placed it in a monotypic group in the genus Potyvirus. This is the first record of a virus from W. mirabilis, the first complete genome sequence of catharanthus mosaic virus determined, and the first record from Australia. This finding illustrates the risk to natural and managed systems posed by the international trade in live plants and propagules, which enables viruses to establish in new regions and infect new hosts.

Learning by design: lessons from a baseline study in the NAMWASH Small Towns Programme, Mozambique

This paper examines the design and application of a baseline study for a comprehensive water, sanitation, and hygiene (WASH) intervention in Mozambique. The study was developed to investigate the relationships among key parameters of interest both for comparison to post-implementation data and to contribute to planning the WASH intervention itself. We use this study to discuss key issues surrounding baseline studies. This includes providing guidelines for designing a WASH baseline survey, determining an appropriate sample size, and highlighting key considerations in analysing the survey data, such as incorporating the study design in statistical analyses, post-stratifying, and utilizing geospatial data. We also show how statistical analyses from a baseline survey can be used to inform subsequent surveys. For example, results from this study suggest that in future WASH studies, self-reporting by households should be supplemented by observational or population data to remove or quantify reporting bias, and care must be taken to reduce respondent fatigue.

Characterization of inappetent sheep in a feedlot using radio-tracking technology1

The feeding and drinking behaviours of sheep were monitored using RFID technology at a commercial pre-embarkation feedlot in Western Australia with the aim of characterizing feeding and drinking patterns of inappetent sheep that might allow them to be treated. Feeding and drinking behaviours of sheep were compared with their survival and change in body condition. Patterns of number of visits and the time spent at feed and water troughs were analyzed for a total of 8,206 sheep, representing four consignments that were monitored for a range of 6-31 d. Data for feeding and drinking behaviours were compared for the first 6 d. For animals that were alive at exit, 18.9% of sheep attended the feed trough for less than 0.25 h d-1 (15 min per day) on day 1; this decreased to only 2.4% of sheep by day 6. Of the sheep monitored, 0.93% died (n = 76); Salmonella spp. infection was the leading cause of death (n = 40; 52.6% of all deaths) across all months and was accompanied with inanition. There was marked variability in the average time spent at the feed trough for sheep that died eventually from salmonella/inanition (contributing to the lack of statistical difference in time spent at feed trough between sheep dying from different causes; P = 0.056). Over half (55%) of the animals diagnosed with salmonella/inanition spent an average of less than 0.50 h d-1 (30 min per day) and 45% less than 0.25 h d-1 at the feed trough. There was a negative correlation (r) in time spent at the feed trough overtime for individual sheep that died from salmonella/inanition, indicating that these individuals went off their feed. This pattern was not evident for animals that died from other causes (significant difference in r values between five categories of cause of death; P = 0.040). Characterization of feeding behaviour of sheep that died from salmonella/inanition therefore appears to require more than simply monitoring daily intake. There was no difference in time spent at water troughs between sheep that died or were alive at exit (average 0.30 ± 0.23 h d-1). This study reveals that the patterns of feeding and drinking behaviours during pre-embarkation feedlotting do not readily allow identification of animals that warrant singling out for veterinary care or alternative feed arrangements. This result highlights the need for experienced stockmanship in handling these animals.

Modeling concurrency and selective mixing in heterosexual partnership networks with applications to sexually transmitted diseases

Network-based models for sexually transmitted disease transmission rely on initial partnership networks incorporating structures that may be related to risk of infection. In particular, initial networks should reflect the level of concurrency and attribute-based selective mixing observed in the population of interest. We consider momentary degree distributions as measures of concurrency and propensities for people of certain types to form partnerships with each other as a measure of attribute-based selective mixing. Estimation of momentary degree distributions and mixing patterns typically relies on cross-sectional survey data, and, in the context of heterosexual networks, we describe how this results in two sets of reports that need not be consistent with each other. The reported momentary degree distributions and mixing totals are related through a series of constraints, however. We provide a method to incorporate those in jointly estimating momentary degree distributions and mixing totals. We develop a method to simulate heterosexual networks consistent with these momentary degree distributions and mixing totals, applying it to data obtained from the National Longitudinal Study of Adolescent Health. We first use the momentary degree distributions and mixing totals as mean value parameters to estimate the natural parameters for an exponential-family random graph model and then use a Markov chain Monte Carlo algorithm to simulate person-level heterosexual partnership networks.