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Biological aging is characterized by an age-dependent increase in the probability of death and by a decrease in the reproductive capacity. Individual age-dependent rates of survival and reproduction have a strong impact on population…
Vaccinations are an important tool in the prevention of disease. Vaccinations are generally voluntary for each member of a population and vaccination decisions are influenced by individual risk perceptions and contact structures within…
During an infectious disease outbreak, providing accurate answers to policy questions about transmission requires a detailed model of the natural history of infectiousness. Unfortunately, direct measures of infectiousness are generally…
Levels of sociality in nature vary widely. Some species are solitary; others live in family groups; some form complex multi-family societies. Increased levels of social interaction can allow for the spread of useful innovations and…
Under constant selection, each trait has a fixed fitness, and small mutation rates allow populations to efficiently exploit the optimal trait. Therefore it is reasonable to expect mutation rates will evolve downwards. However, we find this…
We investigate how a population's natural and vaccine immunity affects the competitive balance between two strains of an infectious disease with different epidemiological characteristics. Specifically, we consider the case where one strain…
Mathematical modelling of epidemiological and coevolutionary dynamics is widely being used to improve disease management strategies of infectious diseases. Many diseases present some form of intra-host quiescent stage, also known as covert…
The emergence or adaptation of pathogens may lead to epidemics, highlighting the need for a thorough understanding of pathogen evolution. The tradeoff hypothesis suggests that virulence evolves to reach an optimal transmission intensity…
In this paper, we extend a model of host-parasite co-evolution to incorporate the semi-conservative nature of DNA replication for both the host and the parasite. We find that the optimal mutation rate for the semi-conservative and…
Population expansions trigger many biomedical and ecological transitions, from tumor growth to invasions of non-native species. Although population spreading often selects for more invasive phenotypes, we show that this outcome is far from…
Dynamic properties of spreading infection through a heterogeneous population are studied numerically and analytically using a dynamic variant of Watts and Strogatz Small World Network-based stochastic Susceptible-Exposed-Infectious-Removed…
Consider a birth and death chain to model the number of types of a given virus. Each type gives birth to a new type at rate $\lambda$ and dies at rate 1. Each type is also assigned a fitness. When a death occurs either the least fit type…
There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can…
Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient…
Coinfection phenomena are common in nature, yet there is a lack of analytical approaches for coinfection systems with a high number of circulating and interacting strains. In this paper, we investigated a coinfection SIS framework applied…
Conventional population genetics considers the evolution of a limited number of genotypes corresponding to phenotypes with different fitness. As model phenotypes, in particular RNA secondary structure, have become computationally tractable,…
Genomic surveillance of infectious diseases allows monitoring circulating and emerging variants and quantifying their epidemic potential. However, due to the high costs associated with genomic sequencing, only a limited number of samples…
Determining phenotype from genetic data is a fundamental challenge. Influenza A viruses undergo rapid antigenic drift and identification of emerging antigenic variants is critical to the vaccine selection process. Using former seasonal…
Evolution occurs in populations of reproducing individuals. It is well known that population structure can affect evolutionary dynamics. Traditionally, natural selection is studied between mutants that differ in reproductive rate, but are…
We study a general setting of neutral evolution in which the population is of finite, constant size and can have spatial structure. Mutation leads to different genetic types ("traits"), which can be discrete or continuous. Under minimal…