种群与进化
We show that the space of rooted tree-based phylogenetic networks is connected under rooted nearest-neighbour interchange (rNNI) moves.
I discuss the so-called stochastic individual based model of adaptive dynamics and in particular how different scaling limits can be obtained by taking limits of large populations, small mutation rate, and small effect of single mutations…
We present a methodology for systematically extending epidemic models to multilevel and multiscale spatio-temporal pandemic ones. Our approach builds on the use of coloured stochastic and continuous Petri nets facilitating the sound…
Malaria is a mosquito-borne disease with a devastating global impact. Plasmodium vivax is a major cause of human malaria beyond sub-Saharan Africa. Relapsing infections, driven by a reservoir of liver-stage parasites known as hypnozoites,…
Planning for the protection of species often involves difficult choices about which species to prioritize, given constrained resources. One way of prioritizing species is to consider their "evolutionary distinctiveness", i.e. their relative…
In this work, using a detailed dataset furnished by National Health Authorities concerning the Province of Pavia (Lombardy, Italy), we propose to determine the essential features of the ongoing COVID-19 pandemic in term of contact dynamics.…
In the framework of homogeneous susceptible-infected-recovered (SIR) models, we use a control theory approach to identify optimal pandemic mitigation strategies. We derive rather general conditions for reaching herd immunity while…
We introduce a framework within evolutionary game theory for studying the distinction between objective and subjective rationality and apply it to the evolution of cooperation on 3-regular random graphs. In our simulations, agents evolve…
This paper introduces a new multi-strain epidemic model with reinfection and cross-immunity to provide insights into the resurgence of the COVID-19 epidemic in an area with reportedly high seroprevalence due to a largely unmitigated…
The idea of a metapopulation has become canonical in ecology. Its original mean field form provides the important intuition that migration and extinction interact to determine the dynamics of a population composed of subpopulations. From…
Evolutionary game theory assumes that players replicate a highly scored player's strategy through genetic inheritance. However, when learning occurs culturally, it is often difficult to recognize someone's strategy just by observing the…
COVID-19 is not a universal killer. We study the spread of COVID-19 at the county level for the United States up until the 15$^{th}$ of August, 2020. We show that the prevalence of the disease and the death rate are correlated with the…
There is a general consensus among archaeologists that replacement of Neanderthals by anatomically modern humans in Europe occurred around 40K to 35K YBP. However, the causal mechanism for this replacement continues to be debated. Searching…
We develop a modeling framework for bioluminescence light found in the deep sea near neutrino telescopes by combining a hydrodynamic model with a stochastic one. The bioluminescence is caused by organisms when exposed to a non-constant…
The long-term growth rate of populations in varying environments quantifies the evolutionary value of processing the information that biological individuals inherit from their ancestors and acquire from their environment. Previous models…
The development of coalescent theory paved the way to statistical inference from population genetic data. In the genomic era, however, coalescent models are limited due to the complexity of the underlying ancestral recombination graph. The…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
This chapter gives a synopsis of recent approaches to model and analyse the evolution of microbial populations under selection. The first part reviews two population genetic models of Lenski's long-term evolution experiment with Escherichia…
The fitness landscape encodes the mapping of genotypes to fitness and provides a succinct representation of possible trajectories followed by an evolving population. Evolutionary accessibility is quantified by the existence of…
Repeated games are useful models to analyze long term interactions of living species and complex social phenomena. Zero-determinant (ZD) strategies in repeated games discovered by Press and Dyson in 2012 enforce a linear payoff relationship…