arXiv subjects

Tatiana Yakushkina

Publications and source records attributed to Tatiana Yakushkina.

5 recordsLinked to original sources

arXiv2026

Mathematical Model of Evolution of Non-Degenerate Replicator Systems

We propose and analyse a mathematical model of evolutionary adaptation for non-degenerate (permanent) replicator systems, in which the fitness landscape matrix evolves on a slow timescale -- the evolutionary time -- while the species dynamics unfold on a fast timescale. Under a two-timescale separation justified by Tikhonov's theorem, the adaptation problem reduces to maximising the mean fitness at steady state over a convex admissible set of fitness landscape matrices. We derive a fitness variation formula and establish necessary and sufficient conditions for a fitness maximum, showing that the optimisation reduces at each step to a linear programming problem. The algorithm is applied to four canonical replicator systems: the hypercycle, the bi-hypercycle, the anthill system, and the RNA molecule network. In all cases the evolutionary process follows a universal three-phase pattern: an initial phase of fitness growth without equilibrium shift, during which purely altruistic replication gives way to mixed altruistic-selfish behaviour; a second phase of dominant species emergence; and a stabilisation phase analogous to the error catastrophe threshold in quasispecies models. A key consequence is that all evolved systems acquire resistance to parasitic species. We further prove that without non-degeneracy constraints the process leads to sequential species annihilation, with a provable spectral lower bound on fitness increase by dimension reduction.

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arXiv2025

Flow-Based Modelling of Population Dynamics with Consecutive Continuous Mutations

We develop a continuous mathematical model of population dynamics that describes the sequential emergence of new genotypes under limited resources. The framework models genotype density as a nonlinear flow in mutation space, combining transport driven by a time-dependent mutation rate with logistic growth and nonlocal competition. For the advection-reaction regime without reverse mutations, we derive analytical solutions using the method of characteristics and obtain explicit expressions for time-varying carrying capacities and mutation velocities. We analyze how decaying and accelerating mutation rates shape the saturation and propagation of population fronts through level-set geometry. When reverse mutations are included, the system becomes a quasilinear parabolic equation with diffusion in genotype space; numerical experiments show that backward mutation flows stabilize the dynamics and smooth the evolving fronts. The proposed model generalizes classical quasispecies and Crow-Kimura formulations by incorporating logistic regulation, variable mutation rates, and reversible transitions, offering a unified approach to evolutionary processes relevant to virology, bacterial adaptation, and tumor progression.

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arXiv2021

Fitness landscape adaptation in open replicator systems with competition: application to cancer therapy

This study focuses on open quasispecies systems with competition and death flow, described by modified Eigen and Crow-Kimura models. We examine the evolutionary adaptation process as a reaction to changes in rates. One of the fundamental assumptions, which forms the basis of our mathematical model, is the existence of two different timescales: internal dynamics time and evolutionary time. The latter is much slower and exhibits significant adaptation events. These conditions allow us to represent the whole evolutionary process through a series of steady-state equations, where all the elements continuously depend on the evolutionary parameter.

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arXiv2020

Open Quasispecies Systems: New Approach to Evolutionary Adaptation

Consider a mathematical model of evolutionary adaptation of fitness landscape and mutation matrix as a reaction to population changes. As a basis, we use an open quasispecies model, which is modified to include explicit death flow. We assume that evolutionary parameters of mutation and selection processes vary in a way to maximize the mean fitness of the system. From this standpoint, Fisher's theorem of natural selection is being rethought and discussed. Another assumption is that system dynamics has two significant timescales. According to our central hypothesis, major evolutionary transitions happen in the steady-state of the corresponding dynamical system, so the evolutionary time is much slower than the one of internal dynamics. For the specific cases of quasispecies systems, we show how our premises form the fitness landscape adaptation process.

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arXiv2019

Fitness Optimization and Evolution of Permanent Replicator Systems

In this paper, we discuss the fitness landscape evolution of permanent replicator systems using a hypothesis that the specific time of evolutionary adaptation of the system parameters is much slower than the time of internal evolutionary dynamics. In other words, we suppose that the extreme principle of Darwinian evolution based the Fisher's fundamental theorem of natural selection is valid for the steady-states. Various cases of the evolutionary adaptation for permanent replicator system are considered.

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