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Although geographic isolation has been shown to play a key role in promoting reproductive isolation, it is now believed that speciation can also happen in sympatry and with considerable gene flow. Here we present a model of sympatric…
We model the immune surveillance of a pathogen which passes through $n$ immunologically distinct stages. The biological parameters of this system induce a partial order on the stages, and this, in turn, determines which stages will be…
The process of infection of a host is complex, influenced by factors such as microbial variation within and between hosts as well as differences in dose across hosts. This study uses dose-response and within-host microbial infection models…
Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…
Realistic examples of reaction-diffusion phenomena governing spatial and spatiotemporal pattern formation are rarely isolated systems, either chemically or thermodynamically. However, even formulations of `open' reaction-diffusion systems…
Survival models capture the relationship between an accumulating hazard and the occurrence of a singular event stimulated by that accumulation. When the model for the hazard is sufficiently flexible survival models can accommodate a wide…
The bacterium Group A Streptococcus (Streptococcus pyogenes, GAS) is a human-specific pathogen and a major cause of global morbidity and mortality. Despite decades of research our knowledge of GAS infection and immunity is incomplete,…
Risk-driven behavior provides a feedback mechanism through which individuals both shape and are collectively affected by an epidemic. We introduce a general and flexible compartmental model to study the effect of heterogeneity in the…
This contribution is devoted to a new model of HIV multiplication motivated by the patent of one of the authors. We take into account the antigenic diversity through what we define "antigenicity", whether of the virus or of the adapted…
One of the most challenging problems in microbiology is to understand how a small fraction of microbes that resists killing by antibiotics can emerge in a population of genetically identical cells, the phenomenon known as persistence or…
We construct a model of speciation from evolution in an ecosystem consisting of a limited amount of energy recources. The species posses genetic information, which is inherited according to the rules of the Penna model of genetic evolution.…
Species introductions promote secondary contacts between taxa with long histories of allopatric divergence. Anthropogenic contact zones thus offer valuable contrasts to speciation studies in natural systems where past spatial isolations may…
Viral zoonoses have emerged as the key drivers of recent pandemics. Human infection by zoonotic viruses are either spillover events -- isolated infections that fail to cause a widespread contagion -- or species jumps, where successful…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
Between pandemics, the influenza virus exhibits periods of incremental evolution via a process known as antigenic drift. This process gives rise to a sequence of strains of the pathogen that are continuously replaced by newer strains,…
Food webs with intraguild predation (IGP) are widespread in natural habitats. Their adaptation and resilience behaviour is principal for understanding restructuring of ecological communities. In spite of the importance of IGP food webs…
Divergence between populations for a given trait can be driven by natural or sexual selection, interacting with migration behaviour. Mating preference for different phenotypes can lead to the emergence and persistence of differentiated…
Understanding the combined effects of climate change and habitat fragmentation on the adaptive potential of plant populations is essential for devising effective conservation strategies. This is particularly important where mating system…
Disentangling the processes leading populations to extinction is a major topic in ecology and conservation biology. The difficulty to find a mate in many species is one of these processes. Here, we investigate the impact of…
The relationship between the dynamics of a community and its constituent pairwise interactions is a fundamental problem in ecology. Higher-order ecological effects beyond pairwise interactions may be key to complex ecosystems, but…