Populations and Evolution (q-bio.PE)

Abstract: Traditionally, population models distinguish individuals on the basis of their current state. Given a distribution, a discrete time model then specifies (precisely in deterministic models, probabilistically in stochastic models) the population distribution at the next time point. The renewal equation alternative concentrates on newborn individuals and the model specifies the production of offspring as a function of age. This has two advantages: (i) as a rule, there are far fewer birth states than individual states in general, so the dimension is often low; (ii) it relates seamlessly to the next-generation matrix and the basic reproduction number. Here we start from the renewal equation for the births and use results of Feller and Thieme to characterise the asymptotic large time behaviour. Next we explicitly elaborate the relationship between the two bookkeeping schemes. This allows us to transfer the characterisation of the large time behaviour to traditional structured-population models.

Abstract: Viruses present an amazing genetic variability. An ensemble of infecting viruses, also called a viral quasispecies, is a cloud of mutants centered around a specific genotype. The simplest model of evolution, whose equilibrium state is described by the quasispecies equation, is the Moran--Kingman model. For the sharp peak landscape, we perform several exact computations and we derive several exact formulas. We obtain also an exact formula for the quasispecies distribution, involving a series and the mean fitness. A very simple formula for the mean Hamming distance is derived, which is exact and which do not require a specific asymptotic expansion (like sending the length of the macromolecules to $\infty$ or the mutation probability to $0$). We try also to extend these formulas to a general fitness landscape. We obtain an equation involving the covariance of the fitness and the Hamming class number in the quasispecies distribution. With the help of these formulas, we discuss the phenomenon of the error threshold and the notion of quasispecies. We recover the limiting quasipecies distribution in the long chain regime. We go beyond the sharp peak landscape and we consider fitness landscapes having finitely many peaks and a plateau--type landscape. We finally prove rigorously within this framework the possible occurrence of the survival of the flattest, a phenomenon which has been previously discovered by Wilke, Wang, Ofria, Lenski and Adami and which has been investigated in several works.