Taxon ordering in phylogenetic trees: a workbench test

<p>Abstract</p> <p>Background</p> <p>Phylogenetic trees are an important tool for representing evolutionary relationships among organisms. In a phylogram or chronogram, the ordering of taxa is not considered meaningful, since complete topological information is given by the branching order and length of the branches, which are represented in the root-to-node direction. We apply a novel method based on a (λ + <it>μ</it>)-Evolutionary Algorithm to give meaning to the order of taxa in a phylogeny. This method applies random swaps between two taxa connected to the same node, without changing the topology of the tree. The evaluation of a new tree is based on different distance matrices, representing non-phylogenetic information such as other types of genetic distance, geographic distance, or combinations of these. To test our method we use published trees of Vesicular stomatitis virus, West Nile virus and Rice yellow mottle virus.</p> <p>Results</p> <p>Best results were obtained when taxa were reordered using geographic information. Information supporting phylogeographic analysis was recovered in the optimized tree, as evidenced by clustering of geographically close samples. Improving the trees using a separate genetic distance matrix altered the ordering of taxa, but not topology, moving the longest branches to the extremities, as would be expected since they are the most divergent lineages. Improved representations of genetic and geographic relationships between samples were also obtained when merged matrices (genetic and geographic information in one matrix) were used.</p> <p>Conclusions</p> <p>Our innovative method makes phylogenetic trees easier to interpret, adding meaning to the taxon order and helping to prevent misinterpretations.</p

Coincident Tick Infestations in the Nostrils of Wild Chimpanzees and a Human in Uganda

Ticks in the nostrils of humans visiting equatorial African forests have been reported sporadically for decades, but their taxonomy and natural history have remained obscure. We report human infestation with a nostril tick in Kibale National Park, Uganda, coincident with infestation of chimpanzees in the same location with nostril ticks, as shown by high-resolution digital photography. The human-derived nostril tick was identified morphologically and genetically as a nymph of the genus Amblyomma, but the mitochondrial 12S ribosomal RNA or the nuclear intergenic transcribed spacer 2 DNA sequences of the specimen were not represented in GenBank. These ticks may represent a previously uncharacterized species that is adapted to infesting chimpanzee nostrils as a defense against grooming. Ticks that feed upon apes and humans may facilitate cross-species transmission of pathogens, and the risk of exposure is likely elevated for persons who frequent ape habitats.Human Evolutionary BiologyLibraries/Museum

Molecular Epidemiology of Cross-Species Giardia duodenalis Transmission in Western Uganda

Giardia duodenalis is a common protozoan parasite that infects multiple mammalian species, including humans. We analyzed G. duodenalis from people, livestock, and wild non-human primates in forest fragments near Kibale National Park, western Uganda, where habitat disturbance and human-animal interaction are high. Molecular analyses indicated that endangered red colobus monkeys were infected with G. duodenalis assemblages BIV and E, which characteristically infect humans and livestock, respectively. G. duodenalis infected people at rates of up to 67.5% in one village, and people age 15 years or younger were especially likely to be infected. G. duodenalis infection in people was not associated with other factors related to behavior and hygiene, and infected people were no more likely to have reported gastrointestinal symptoms than were uninfected people. These results demonstrate that G. duodenalis transmission from humans and domestic animals to wildlife may occur with ease in locations such as western Uganda, where habitat disturbance causes ecological overlap among people, livestock, and primates. This conclusion has conservation implications for wildlife such as red colobus, which are already endangered by habitat loss

Forest Fragmentation as Cause of Bacterial Transmission among Nonhuman Primates, Humans, and Livestock, Uganda

Anthropogenic disturbance increases bacterial transmission

Assessing Commitment and Reporting Fidelity to a Text Message-Based Participatory Surveillance in Rural Western Uganda.

Syndromic surveillance, the collection of symptom data from individuals prior to or in the absence of diagnosis, is used throughout the developed world to provide rapid indications of outbreaks and unusual patterns of disease. However, the low cost of syndromic surveillance also makes it highly attractive for the developing world. We present a case study of electronic participatory syndromic surveillance, using participant-mobile phones in a rural region of Western Uganda, which has a high infectious disease burden, and frequent local and regional outbreaks. Our platform uses text messages to encode a suite of symptoms, their associated durations, and household disease burden, and we explore the ability of participants to correctly encode their symptoms, with an average of 75.2% of symptom reports correctly formatted between the second and 11th reporting timeslots. Concomitantly we identify divisions between participants able to rapidly adjust to this unusually participatory style of data collection, and those few for whom the study proved more challenging. We then perform analyses of the resulting syndromic time series, examining the clustering of symptoms by time and household to identify patterns such as a tendency towards the within-household sharing of respiratory illness.National Institute of Health (Grant ID: TW009237)This is the final version of the article. It first appeared from the Public Library of Science via http://dx.doi.org/10.1371/journal.pone.015597

Serologic Evidence for Novel Poxvirus in Endangered Red Colobus Monkeys, Western Uganda

Enzyme-linked immunosorbent assay, Western blot, and virus neutralization assays indicated that red colobus monkeys in Kibale National Park, western Uganda, had antibodies to a virus that was similar, but not identical, to known orthopoxviruses. The presence of a novel poxvirus in this endangered primate raises public health and conservation concerns

Local impact of temperature and precipitation on West Nile virus infection in Culex species mosquitoes in northeast Illinois, USA

<p>Abstract</p> <p>Background</p> <p>Models of the effects of environmental factors on West Nile virus disease risk have yielded conflicting outcomes. The role of precipitation has been especially difficult to discern from existing studies, due in part to habitat and behavior characteristics of specific vector species and because of differences in the temporal and spatial scales of the published studies. We used spatial and statistical modeling techniques to analyze and forecast fine scale spatial (2000 m grid) and temporal (weekly) patterns of West Nile virus mosquito infection relative to changing weather conditions in the urban landscape of the greater Chicago, Illinois, region for the years from 2004 to 2008.</p> <p>Results</p> <p>Increased air temperature was the strongest temporal predictor of increased infection in <it>Culex pipiens </it>and <it>Culex restuans </it>mosquitoes, with cumulative high temperature differences being a key factor distinguishing years with higher mosquito infection and higher human illness rates from those with lower rates. Drier conditions in the spring followed by wetter conditions just prior to an increase in infection were factors in some but not all years. Overall, 80% of the weekly variation in mosquito infection was explained by prior weather conditions. Spatially, lower precipitation was the most important variable predicting stronger mosquito infection; precipitation and temperature alone could explain the pattern of spatial variability better than could other environmental variables (79% explained in the best model). Variables related to impervious surfaces and elevation differences were of modest importance in the spatial model.</p> <p>Conclusion</p> <p>Finely grained temporal and spatial patterns of precipitation and air temperature have a consistent and significant impact on the timing and location of increased mosquito infection in the northeastern Illinois study area. The use of local weather data at multiple monitoring locations and the integration of mosquito infection data from numerous sources across several years are important to the strength of the models presented. The other spatial environmental factors that tended to be important, including impervious surfaces and elevation measures, would mediate the effect of rainfall on soils and in urban catch basins. Changes in weather patterns with global climate change make it especially important to improve our ability to predict how inter-related local weather and environmental factors affect vectors and vector-borne disease risk.</p> <p>Local impact of temperature and precipitation on West Nile virus infection in <it>Culex </it>species mosquitoes in northeast Illinois, USA.</p

Lung fluke (Paragonimus africanus) infects Nigerian red-capped mangabeys and causes respiratory disease

a b s t r a c t Eggs of the lung fluke genus Paragonimus were detected in red-capped mangabeys (Cercocebus torquatus) in Nigeria. We assess the role of these primates as potential sylvatic hosts and the clinical effects of the parasite on monkeys. DNA sequenced from eggs in feces were 100% identical in the ITS2 region to Paragonimus africanus sequences from humans in Cameroon. Paragonimus-positive monkeys coughed more than uninfected monkeys. Experimental de-worming led to reduction in parasite intensity and a corresponding reduction of coughing to baseline levels in infected monkeys. This report provides the first evidence of Paragonimus sp. in C. torquatus, of P. africanus in Nigerian wildlife, and the first molecular evidence of the parasite in African wildlife. Coughing, sometimes interpreted as a communication behavior in primates, can actually indicate infection with lung parasites. Observations of coughing in primates may, in turn, provide a useful mechanism for surveillance of Paragonimus spp, which are reemerging human pathogens, in wildlife reservoirs