Temperature modulates dominance of a superinfecting Arctic virus in its unicellular algal host.

Complex virus-virus interactions can arise when multiple viruses coinfect the same host, impacting infection outcomes with broader ecological and evolutionary significance for viruses and host. Yet, our knowledge regarding virus competition is still limited, especially for single-celled eukaryotic host-virus systems. Here, we report on mutual interference of two dsDNA viruses, MpoV-45T and MpoV-46T, competing for their Arctic algal host Micromonas polaris.

Modelling the unexpected dynamics of COVID-19 in Manaus, Brazil.

In late March 2020, SARS-CoV-2 arrived in Manaus, Brazil, and rapidly developed into a large-scale epidemic that collapsed the local health system and resulted in extreme death rates. Several key studies reported that ∼76% of residents of Manaus were infected (attack rate AR≃76%) by October 2020, suggesting protective herd immunity had been reached. Despite this, an unexpected second wave of COVID-19 struck again in November and proved to be larger than the first, creating a catastrophe for the unprepared population.

Quantifying the invasion risk of West Nile virus: Insights from a multi-vector and multi-host SEIR model.

The invasion of vector-borne diseases depends on the type of specific features of the vector and hosts at play. Within the complex, differences in ecology, biology, and vector competence can influence the risk of West Nile virus (WNV) outbreaks. To determine which life-history traits affect WNV invasion into susceptible communities the most, we constructed an epidemiological Susceptible-Exposed-Infectious-Recovered model with three vector (eco)types, , and their hybrids, and two vertebrate hosts, birds (as amplifying hosts) and humans (as dead-end hosts).

Resolving the enigma of Iquitos and Manaus: A modeling analysis of multiple COVID-19 epidemic waves in two Amazonian cities.

The two nearby Amazonian cities of Iquitos and Manaus endured explosive COVID-19 epidemics and may well have suffered the world's highest infection and death rates over 2020, the first year of the pandemic. State-of-the-art epidemiological and modeling studies estimated that the populations of both cities came close to attaining herd immunity (>70% infected) at the termination of the first wave and were thus protected. This makes it difficult to explain the more deadly second wave of COVID-19 that struck again in Manaus just months later, simultaneous with the appearance of a new P.

Evolutionary Analysis of TCGA Data Using Over- and Under- Mutated Genes Identify Key Molecular Pathways and Cellular Functions in Lung Cancer Subtypes.

We identify critical conserved and mutated genes through a theoretical model linking a gene’s fitness contribution to its observed mutational frequency in a clinical cohort. “Passenger” gene mutations do not alter fitness and have mutational frequencies determined by gene size and the mutation rate. Driver mutations, which increase fitness (and proliferation), are observed more frequently than expected.

The Contribution of Transpiration to Precipitation Over African Watersheds.

The redistribution of biological (transpiration) and non-biological (interception loss, soil evaporation) fluxes of terrestrial evaporation via atmospheric circulation and precipitation is an important Earth system process. In vegetated ecosystems, transpiration dominates terrestrial evaporation and is thought to be crucial for regional moisture recycling and ecosystem functioning. However, the spatial and temporal variability in the dependency of precipitation on transpiration remains understudied, particularly in sparsely sampled regions like Africa.

Extraordinary curtailment of massive typhus epidemic in the Warsaw Ghetto.

The highly dependent interplay of disease, famine, war, and society is examined based on an extreme period during World War II. Using mathematical modeling, we reassess events during the Holocaust that led to the liquidation of the Warsaw Ghetto (1941-1942), with the eventual goal of deliberately killing ~450,000, mostly Jewish residents, many through widespread starvation and a large-scale typhus epidemic. The Nazis justified genocide supposedly to control the spread of disease.

Eradicating Metastatic Cancer and the Eco-Evolutionary Dynamics of Anthropocene Extinctions.

Curative therapy for metastatic cancers is equivalent to causing extinction of a large, heterogeneous, and geographically dispersed population. Although eradication of dinosaurs is a dramatic example of extinction dynamics, similar application of massive eco-evolutionary force in cancer treatment is typically limited by host toxicity. Here, we investigate the evolutionary dynamics of Anthropocene species extinctions as an alternative model for curative cancer therapy.

Network motifs and their origins.

Modern network science is a new and exciting research field that has transformed the study of complex systems over the last 2 decades. Of particular interest is the identification of small "network motifs" that might be embedded in a larger network and that indicate the presence of evolutionary design principles or have an overly influential role on system-wide dynamics. Motifs are patterns of interconnections, or subgraphs, that appear in an observed network significantly more often than in compatible randomized networks.

Networks of genetic similarity reveal non-neutral processes shape strain structure in Plasmodium falciparum.

Pathogens compete for hosts through patterns of cross-protection conferred by immune responses to antigens. In Plasmodium falciparum malaria, the var multigene family encoding for the major blood-stage antigen PfEMP1 has evolved enormous genetic diversity through ectopic recombination and mutation. With 50-60 var genes per genome, it is unclear whether immune selection can act as a dominant force in structuring var repertoires of local populations.

Signatures of competition and strain structure within the major blood-stage antigen of in a local community in Ghana.

The concept of niche partitioning has received considerable theoretical attention at the interface of ecology and evolution of infectious diseases. Strain theory postulates that pathogen populations can be structured into distinct nonoverlapping strains by frequency-dependent selection in response to intraspecific competition for host immune space. The malaria parasite presents an opportunity to investigate this phenomenon in nature, under conditions of high recombination rate and extensive antigenic diversity.

Evidence of strain structure in gene repertoires in children from Gabon, West Africa.

Existing theory on competition for hosts between pathogen strains has proposed that immune selection can lead to the maintenance of strain structure consisting of discrete, weakly overlapping antigenic repertoires. This prediction of strain theory has conceptual overlap with fundamental ideas in ecology on niche partitioning and limiting similarity between coexisting species in an ecosystem, which oppose the hypothesis of neutral coexistence. For , strain theory has been specifically proposed in relation to the major surface antigen of the blood stage, known as EMP1 and encoded by the multicopy multigene family known as the genes.

Modeling the Impact of White-Plague Coral Disease in Climate Change Scenarios.

Coral reefs are in global decline, with coral diseases increasing both in prevalence and in space, a situation that is expected only to worsen as future thermal stressors increase. Through intense surveillance, we have collected a unique and highly resolved dataset from the coral reef of Eilat (Israel, Red Sea), that documents the spatiotemporal dynamics of a White Plague Disease (WPD) outbreak over the course of a full season. Based on modern statistical methodologies, we develop a novel spatial epidemiological model that uses a maximum-likelihood procedure to fit the data and assess the transmission pattern of WPD.

Synergistic and antagonistic interactions between bednets and vaccines in the control of malaria.

It is extremely likely that the malaria vaccines currently in development will be used in conjunction with treated bednets and other forms of malaria control. The interaction of different intervention methods is at present poorly understood in a disease such as malaria where immunity is more complex than for other pathogens that have been successfully controlled by vaccination. Here we develop a general mathematical model of malaria transmission to examine the interaction between vaccination and bednets.

Population structuring of multi-copy, antigen-encoding genes in Plasmodium falciparum.

The coexistence of multiple independently circulating strains in pathogen populations that undergo sexual recombination is a central question of epidemiology with profound implications for control. An agent-based model is developed that extends earlier 'strain theory' by addressing the var gene family of Plasmodium falciparum. The model explicitly considers the extensive diversity of multi-copy genes that undergo antigenic variation via sequential, mutually exclusive expression.

Transmission intensity and drug resistance in malaria population dynamics: implications for climate change.

Although the spread of drug resistance and the influence of climate change on malaria are most often considered separately, these factors have the potential to interact through altered levels of transmission intensity. The influence of transmission intensity on the evolution of drug resistance has been addressed in theoretical studies from a population genetics' perspective; less is known however on how epidemiological dynamics at the population level modulates this influence. We ask from a theoretical perspective, whether population dynamics can explain non-trivial, non-monotonic, patterns of treatment failure with transmission intensity, and, if so, under what conditions.

Connectivity, cycles, and persistence thresholds in metapopulation networks.

Synthesising the relationships between complexity, connectivity, and the stability of large biological systems has been a longstanding fundamental quest in theoretical biology and ecology. With the many exciting developments in modern network theory, interest in these issues has recently come to the forefront in a range of multidisciplinary areas. Here we outline a new theoretical analysis specifically relevant for the study of ecological metapopulations focusing primarily on marine systems, where subpopulations are generally connected via larval dispersal.

Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness.

A long-standing controversy in evolutionary biology is whether or not evolving lineages can cross valleys on the fitness landscape that correspond to low-fitness genotypes, which can eventually enable them to reach isolated fitness peaks. Here we study the fitness landscapes traversed by switches between different AU and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles corresponding to GU and AC non-Watson-Crick intermediate states segregate within human populations at low frequencies, similar to those of non-synonymous alleles.

Emergence and size of the giant component in clustered random graphs with a given degree distribution.

Standard techniques for analyzing network models usually break down in the presence of clustering. Here we introduce a new analytic tool, the "free-excess degree" distribution, which extends the generating function framework, making it applicable for clustered networks (C>0). The methodology is general and provides a new expression for the threshold point at which the giant component emerges and shows that it scales as (1-C)(-1).

Spatio-temporal transmission patterns of black-band disease in a coral community.

Background: Transmission mechanisms of black-band disease (BBD) in coral reefs are poorly understood, although this disease is considered to be one of the most widespread and destructive coral infectious diseases. The major objective of this study was to assess transmission mechanisms of BBD in the field based on the spatio-temporal patterns of the disease.

Methodology/principal Findings: 3,175 susceptible and infected corals were mapped over an area of 10x10 m in Eilat (northern Gulf of Aqaba, Red Sea) and the distribution of the disease was examined monthly throughout almost two full disease cycles (June 2006-December 2007).

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution.

Lateral gene transfer is an important mechanism of natural variation among prokaryotes, but the significance of its quantitative contribution to genome evolution is debated. Here, we report networks that capture both vertical and lateral components of evolutionary history among 539,723 genes distributed across 181 sequenced prokaryotic genomes. Partitioning of these networks by an eigenspectrum analysis identifies community structure in prokaryotic gene-sharing networks, the modules of which do not correspond to a strictly hierarchical prokaryotic classification.

Size-structured demographic models of coral populations.

The demographic processes of growth, mortality, and the recruitment of young individuals, are the major organizing forces regulating communities in open systems. Here we present a size-structured (rather than age-structured) population model to examine the role of these different processes in space-limited open systems, taking coral reefs as an example. In this flux-diffusion model the growth rate of corals depends both on the available free-space (i.

Sympatric speciation under incompatibility selection.

The existing theory of sympatric speciation assumes that a local population splits into two species under one-dimensional disruptive selection, which favors both of the opposite extreme values of a quantitative trait. Here we model sympatric speciation under selection that favors high values of either of the two independently inherited traits, each required to efficiently consume one of the two available resources, but acts, because of a tradeoff, against those possessing high values of both traits. Such two-dimensional incompatibility selection is similar to that involved in allopatric speciation.

Generating uniformly distributed random networks.

The analysis of real networks taken from the biological, social, and physical sciences often requires a carefully posed statistical null-hypothesis approach. One common method requires comparing real networks to an ensemble of random matrices that satisfy realistic constraints in which each different matrix member is equiprobable. We discuss existing methods for generating uniformly distributed (constrained) random matrices, describe their shortcomings, and present an efficient technique that should have many practical applications.