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Shuyun Jiao

Publications and source records attributed to Shuyun Jiao.

6 recordsLinked to original sources

Discrete vs. continuous dynamics in biology: When do they align and when do they diverge?

Many biological systems are governed by difference equations and exhibit discrete-time dynamics. Examples include the size of a population when generations are non-overlapping, and the incidence of a disease when infections are recorded at fixed intervals. For discrete-time systems lacking exact solutions, continuous-time approximations are frequently employed when small changes occur between discrete time steps. Here, we present an approach motivated by exactly soluble discrete time problems. We show that such systems have continuous-time descriptions (governed by differential equations) whose solutions precisely agree, at the discrete times, with the discrete time solutions, irrespective of the size of changes that occur. For discrete-time systems lacking exact solutions, we develop approximate continuous-time models that can, to high accuracy, capture rapid growth and decay. Our approach employs mappings between difference and differential equations, generating functional solutions that exactly or closely preserve the original discrete time behaviour. It uncovers fundamental structural parallels and also distinctions between the difference equation and the `equivalent' differential equation. The findings we present cover both time-homogeneous and time-inhomogeneous systems. For completeness, we also consider discrete-time systems with the most rapid oscillatory behaviour possible, namely a sign change each time step. We show, for exactly soluble cases, that such systems also have a continuous-time description, but that this comes at the expense of generally complex-valued solutions. This work has applications in, for example, population genetics, ecology and epidemic modelling. By bridging discrete and continuous representations of a system, it enhances insights/analysis of different types of dynamics.

q-bio.PE

Landscape construction in non-gradient dynamics: A case from evolution

Adaptive landscape has been a fundamental concept in many branches of modern biology since Wright's first proposition in 1932. Meanwhile, the general existence of landscape remains controversial. The causes include the mixed uses of different landscape definitions with their own different aims and advantages. Sometimes the difficulty and the impossibility of the landscape construction for complex models are also equated. To clarify these confusions, based on a recent formulation of Wright's theory, the current authors construct generalized adaptive landscape in a two-loci population model with non-gradient dynamics, where the conventional gradient landscape does not exist. On the generalized landscape, a population moves along an evolutionary trajectory which always increases or conserves adaptiveness but does not necessarily follow the steepest gradient direction. Comparisons of different aspects of various landscapes lead to a conclusion that the generalized landscape is a possible direction to continue the exploration of Wright's theory for complex dynamics.

q-bio.PE

Two-timescale evolution on a singular landscape

Under the effect of strong genetic drift, it is highly probable to observe gene fixation or gene loss in a population, shown by infinite peaks on a coherently constructed potential energy landscape. It is then important to ask what such singular peaks imply, with or without the effects of other biological factors. We studied the stochastic escape time from the infinite potential peaks in the Wright-Fisher model, where the typical two-scale diffusion dynamics was observed via computer simulations. We numerically found the average escape time for all the bi-stable cases and analytically approximated the results under weak mutations and selections by calculating the mean first passage time (MFPT) in singular potential peak. Our results showed that Kramers' classical escape formula can be extended to the models with non-Gaussian probability distributions, overcoming constraints in previous methods. The constructed landscape provides a global and coherent description for system's evolutionary dynamics, allowing new biological results to be generated.

q-bio.PE

Non-fixation in infinite potential

Under the effects of strong genetic drift, it is highly probable to observe gene fixation or loss in a population, shown by divergent probability density functions, or infinite adaptive peaks on a landscape. It is then interesting to ask what such infinite peaks imply, with or without combining other biological factors (e.g. mutation and selection). We study the stochastic escape time from the generated infinite adaptive peaks, and show that Kramers' classical escape formula can be extended to the non-Gaussian distribution cases. The constructed landscape provides a global description for system's middle and long term behaviors, breaking the constraints in previous methods.

q-bio.PE

Absorbing Phenomena and Escaping Time for Muller's Ratchet in Adaptive Landscape

Background: The accumulation of deleterious mutations of a population directly contributes to the fate as to how long the population would exist, a process often described as Muller's ratchet with the absorbing phenomenon. The key to understand this absorbing phenomenon is to characterize the decaying time of the fittest class of the population. Adaptive landscape introduced by Wright, a re-emerging powerful concept in systems biology, is used as a tool to describe biological processes. To our knowledge, the dynamical behaviors for Muller's ratchet over the full parameter regimes are not studied from the point of the adaptive landscape. And the characterization of the absorbing phenomenon is not yet quantitatively obtained without extraneous assumptions as well. Results: We describe the dynamical behavior of the population exposed to Muller's ratchet in all parameters regimes by adaptive landscape. The adaptive landscape has rich structures such as finite and infinite potential, real and imaginary fixed points. We give the formula about the single click time with finite and infinite potential. And we find the single click time increases with selection rates and population size increasing, decreases with mutation rates increasing. These results provide a new understanding of infinite potential. We analytically demonstrate the adaptive and unadaptive states for the whole parameters regimes. Interesting issues about the parameters regions with the imaginary fixed points is demonstrated. This can help understand the biological meaning of the critical points such as the intersection points of regimes. Most importantly, we find that the absorbing phenomenon is characterized by the adaptive landscape and the single click time without any extraneous assumptions. These results suggest a graphical and quantitative framework to study the absorbing phenomenon.

q-bio.PE

Kinetics of Muller's Ratchet from Adaptive Landscape Viewpoint

Background: The accumulation of deleterious mutations of a population directly contributes to the fate as to how long the population would exist. Muller's ratchet provides a quantitative framework to study the effect of accumulation. Adaptive landscape as a powerful concept in system biology provides a handle to describe complex and rare biological events. In this article we study the evolutionary process of a population exposed to Muller's ratchet from the new viewpoint of adaptive landscape which allows us estimate the single click of the ratchet starting with an intuitive understanding. Methods: We describe how Wright-Fisher process maps to Muller's ratchet. We analytically construct adaptive landscape from general diffusion equation. It shows that the construction is dynamical and the adaptive landscape is independent of the existence and normalization of the stationary distribution. We generalize the application of diffusion model from adaptive landscape viewpoint. Results: We develop a novel method to describe the dynamical behavior of the population exposed to Muller's ratchet, and analytically derive the decaying time of the fittest class of populations as a mean first passage time. Most importantly, we describe the absorption phenomenon by adaptive landscape, where the stationary distribution is non-normalizable. These results suggest the method may be used to understand the mechanism of populations evolution and describe the biological processes quantitatively.

q-bio.PE