Molecular evolution and phylogenetics of rodent malaria parasites

<p>Abstract</p> <p>Background</p> <p>Over the last 6 decades, rodent <it>Plasmodium</it> species have become key model systems for understanding the basic biology of malaria parasites. Cell and molecular parasitology have made much progress in identifying genes underpinning interactions between malaria parasites, hosts, and vectors. However, little attention has been paid to the evolutionary genetics of parasites, which provides context for identifying potential therapeutic targets and for understanding the selective forces shaping parasites in natural populations. Additionally, understanding the relationships between species, subspecies, and strains, is necessary to maximize the utility of rodent malaria parasites as medically important infectious disease models, and for investigating the evolution of host-parasite interactions.</p> <p>Results</p> <p>Here, we collected multi-locus sequence data from 58 rodent malaria genotypes distributed throughout 13 subspecies belonging to <it>P. berghei, P. chabaudi, P. vinckei,</it> and <it>P. yoelii.</it> We employ multi-locus methods to infer the subspecies phylogeny, and use population-genetic approaches to elucidate the selective patterns shaping the evolution of these organisms. Our results reveal a time-line for the evolution of rodent <it>Plasmodium</it> and suggest that all the subspecies are independently evolving lineages (i.e. species). We show that estimates of species-level polymorphism are inflated if subspecies are not explicitly recognized, and detect purifying selection at most loci.</p> <p>Conclusions</p> <p>Our work resolves previous inconsistencies in the phylogeny of rodent malaria parasites, provides estimates of important parameters that relate to the parasite’s natural history and provides a much-needed evolutionary context for understanding diverse biological aspects from the cross-reactivity of immune responses to parasite mating patterns.</p

Does Predation Influence the Seasonal and Diel Timing of Moose Calving in Central Ontario, Canada?

Birth synchrony is well documented among ungulates and is hypothesised to maximize neonate survival, either by minimizing the risk of predation through predator swamping or by synchronising birthing with increased seasonal food availability. We used encapsulated vaginal implant transmitters to locate and capture neonatal moose calves and document the seasonal and diel timing of parturition in two adjacent study areas with different predation pressure in central Ontario, Canada. We tested the hypothesis that predation promotes earlier and more synchronous birth of moose calves. Across both areas, proportionately more births occurred during the afternoon and fewer than expected occurred overnight. Mean date of calving averaged 1.5 days earlier and calving was also more synchronous in the study area with heavier predation pressure, despite average green-up date and peak Normalized Difference Vegetation Index date occurring 2 days later in this study area than in the area receiving lighter predation pressure. We encourage analysis of data on timing of parturition from additional study areas experiencing varying degrees of predation pressure to better clarify the influence of predation in driving seasonal and diel timing of parturition in temperate ungulate

Crystallographic characterization of U<inf>2</inf>CrN<inf>3</inf>: A neutron diffraction and transmission electron microscopy approach

In this study, neutron diffraction and transmission electron microscopy (TEM) have been implemented to study the crystallographic structure of the ternary phase U2CrN3 from pellet to nano scale respectively. Recently microstructural evaluation of this ternary phase has been performed for the first time in pellet condition, overcoming the Cr evaporation issue during the conventional sintering process. In this work for the first time, the crystallographic structure of the ordered ternary U2CrN3 phase, stabilized in pellet condition, has been obtained by implementing neutron diffraction. For this study, pellets of the composite material UN with 20 vol% CrN were fabricated by powder metallurgy by mixing UN and CrN powders followed by Spark Plasma Sintering (SPS). TEM was used to investigate the nanoscale structure with a thin lamella of the order of 100–140 nm produced by focused ion beam (FIB). The neutron data revealed the phase composition of the pellet to be primarily 54(8) wt.% U2CrN3, in good agreement with the stoichiometry of starting reagents (UN and CrN powder) and metallographic analysis. Neutron data analysis confirms that all the crystallographic sites in U2CrN3 phase are fully occupied reinforcing the fully stoichiometric composition of this phase, however, the position of the N at the 4i site was found to be closer to the Cr than previously thought. TEM and selected area electron diffraction rendered nano-level information and revealed the presence of nano domains along grain boundaries of UN and U2CrN3, indicating a formation mechanism of the ternary phase, where the phase likely nucleates as nano domains in UN grains from migration of Cr

Sigma viruses from three species of Drosophila form a major new clade in the rhabdovirus phylogeny

The sigma virus (DMelSV), which is a natural pathogen of Drosophila melanogaster, is the only Drosophila-specific rhabdovirus that has been described. We have discovered two new rhabdoviruses, D. obscura and D. affinis, which we have named DObsSV and DAffSV, respectively. We sequenced the complete genomes of DObsSV and DMelSV, and the L gene from DAffSV. Combining these data with sequences from a wide range of other rhabdoviruses, we found that the three sigma viruses form a distinct clade which is a sister group to the Dimarhabdovirus supergroup, and the high levels of divergence between these viruses suggest that they deserve to be recognized as a new genus. Furthermore, our analysis produced the most robustly supported phylogeny of the Rhabdoviridae to date, allowing us to reconstruct the major transitions that have occurred during the evolution of the family. Our data suggest that the bias towards research into plants and vertebrates means that much of the diversity of rhabdoviruses has been missed, and rhabdoviruses may be common pathogens of insects

Identifying weak signals to prepare for uncertainty in the energy sector

This study aims to prepare the energy sector for uncertainty using a foresight tool known as weak signals. Weak signals (subtle signs of emerging issues with significant impact potential) are often overlooked during strategic planning due to their inherent predictive uncertainty. However, the value does not lie in precise forecasting but in broadening the consideration of future possibilities. By proactively monitoring and addressing these otherwise neglected developments, stakeholders can gain early awareness of threats and opportunities and enhance their resilience, adaptability, and innovation. A panel of technology experts identified eight weak signals in this study: 1) growing mistrust and local grid security measures, 2) consumer reactions to overly prescriptive policies, 3) long-term forecasting errors for thin-margin projects, 4) emergence of variable power industries, and 5) establishment of intercontinental transmission precedence; including three potential ‘wild cards’ requiring proactive mitigation: 6) escalating electrical generation dependence on continued imports, 7) a new threat surpassing climate change, and 8) mass deployment of low-emissions technology triggering a runaway loss of social license. Political factors were the predominant source of uncertainty, as decisions can suddenly transform the energy landscape. Economic, technological, and social factors followed closely behind, generally through the emergence of new industries and behavioural responses. While environmental and legal factors were less frequent, stakeholders should still adopt a holistic approach, as the signals were found to be highly interconnected. Organisations should also assess their local context when applying these findings and continuously update and respond to their own list of weak signals

Phenotypic plasticity of nest timing in a post‐glacial landscape: how do reptiles adapt to seasonal time constraints?

Life histories evolve in response to constraints on the time available for growth and development. Nesting date and its plasticity in response to spring temperature may therefore be important components of fitness in oviparous ectotherms near their northern range limit, as reproducing early provides more time for embryos to complete development before winter. We used data collected over several decades to compare air temperature and nest date plasticity in populations of painted turtles and snapping turtles from a relatively warm environment (southeastern Michigan) near the southern extent of the last glacial maximum to a relatively cool environment (central Ontario) near the northern extent of post‐glacial recolonization. For painted turtles, population‐level differences in reaction norm elevation for two phenological traits were consistent with adaptation to time constraints, but no differences in reaction norm slopes were observed. For snapping turtle populations, the difference in reaction norm elevation for a single phenological trait was in the opposite direction of what was expected under adaptation to time constraints, and no difference in reaction norm slope was observed. Finally, among‐individual variation in individual plasticity for nesting date was detected only in the northern population of snapping turtles, suggesting that reaction norms are less canalized in this northern population. Overall, we observed evidence of phenological adaptation, and possibly maladaptation, to time constraints in long‐lived reptiles. Where present, (mal)adaptation occurred by virtue of differences in reaction norm elevation, not reaction norm slope. Glacial history, generation time, and genetic constraint may all play an important role in the evolution of phenological timing and its plasticity in long‐lived reptiles

Host Phylogeny Determines Viral Persistence and Replication in Novel Hosts

Pathogens switching to new hosts can result in the emergence of new infectious diseases, and determining which species are likely to be sources of such host shifts is essential to understanding disease threats to both humans and wildlife. However, the factors that determine whether a pathogen can infect a novel host are poorly understood. We have examined the ability of three host-specific RNA-viruses (Drosophila sigma viruses from the family Rhabdoviridae) to persist and replicate in 51 different species of Drosophilidae. Using a novel analytical approach we found that the host phylogeny could explain most of the variation in viral replication and persistence between different host species. This effect is partly driven by viruses reaching a higher titre in those novel hosts most closely related to the original host. However, there is also a strong effect of host phylogeny that is independent of the distance from the original host, with viral titres being similar in groups of related hosts. Most of this effect could be explained by variation in general susceptibility to all three sigma viruses, as there is a strong phylogenetic correlation in the titres of the three viruses. These results suggest that the source of new emerging diseases may often be predictable from the host phylogeny, but that the effect may be more complex than simply causing most host shifts to occur between closely related hosts

Climate change threatens polar bear populations : a stochastic demographic analysis

Author Posting. © Ecological Society of America, 2010. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecology 91 (2010): 2883–2897, doi:10.1890/09-1641.1.The polar bear (Ursus maritimus) depends on sea ice for feeding, breeding, and movement. Significant reductions in Arctic sea ice are forecast to continue because of climate warming. We evaluated the impacts of climate change on polar bears in the southern Beaufort Sea by means of a demographic analysis, combining deterministic, stochastic, environment-dependent matrix population models with forecasts of future sea ice conditions from IPCC general circulation models (GCMs). The matrix population models classified individuals by age and breeding status; mothers and dependent cubs were treated as units. Parameter estimates were obtained from a capture–recapture study conducted from 2001 to 2006. Candidate statistical models allowed vital rates to vary with time and as functions of a sea ice covariate. Model averaging was used to produce the vital rate estimates, and a parametric bootstrap procedure was used to quantify model selection and parameter estimation uncertainty. Deterministic models projected population growth in years with more extensive ice coverage (2001–2003) and population decline in years with less ice coverage (2004–2005). LTRE (life table response experiment) analysis showed that the reduction in λ in years with low sea ice was due primarily to reduced adult female survival, and secondarily to reduced breeding. A stochastic model with two environmental states, good and poor sea ice conditions, projected a declining stochastic growth rate, log λs, as the frequency of poor ice years increased. The observed frequency of poor ice years since 1979 would imply log λs ≈ − 0.01, which agrees with available (albeit crude) observations of population size. The stochastic model was linked to a set of 10 GCMs compiled by the IPCC; the models were chosen for their ability to reproduce historical observations of sea ice and were forced with “business as usual” (A1B) greenhouse gas emissions. The resulting stochastic population projections showed drastic declines in the polar bear population by the end of the 21st century. These projections were instrumental in the decision to list the polar bear as a threatened species under the U.S. Endangered Species Act.We acknowledge primary funding for model development and analysis from the U.S. Geological Survey and additional funding from the National Science Foundation (DEB-0343820 and DEB-0816514), NOAA, the Ocean Life Institute and the Arctic Research Initiative at WHOI, and the Institute of Arctic Biology at the University of Alaska–Fairbanks. Funding for the capture–recapture effort in 2001–2006 was provided by the U.S. Geological Survey, the Canadian Wildlife Service, the Department of Environment and Natural Resources of the Government of the Northwest Territories, and the Polar Continental Shelf Project, Ottawa, Canada