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Complexity in biology is often described using a multi-map architecture, where the genotype, representing the encoded information, is mapped to the functional level, known as the phenotype, which is then connected to a latent phenotype we…
The relationship between genotype and phenotype plays a crucial role in determining the function and robustness of biological systems. Here the evolution progresses through the change in genotype, whereas the selection is based on the…
Quantifying the adaptive landscape in a given dynamical processes has been one of most important goals in theoretical biology. It can have immediate implications for many dynamical properties, such as robustness and plasticity. Based on…
Population structure can have a significant effect on evolution. For some systems with sufficient symmetry, analytic results can be derived within the mathematical framework of evolutionary graph theory which relate to the outcome of the…
It is widely accepted that population genetics theory is the cornerstone of evolutionary analyses. Empirical tests of the theory, however, are challenging because of the complex relationships between space, dispersal, and evolution.…
Generalized Polya urn models can describe the dynamics of finite populations of interacting genotypes. Three basic questions these models can address are: Under what conditions does a population exhibit growth? On the event of growth, at…
The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an…
Predicting heat-related physiological events at the population level is challenging due to the complex interactions among climatic, demographic, and socioeconomic factors, as well as the strong sparsity and seasonality of observational…
In this paper we suggest that, under suitable conditions, supervised learning can provide the basis to formulate at the microscopic level quantitative questions on the phenotype structure of multicellular organisms. The problem of…
Lots of bio-inspired research works have been conducted in self-adaptive software. They have focused on the external behavior of biological entities without their genetic material that causes this behavior and constitutes the challenge this…
A macroscopic theory for describing cellular states during steady-growth is presented, which is based on the consistency between cellular growth and molecular replication, as well as the robustness of phenotypes against perturbations.…
We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of evolutionary systems. A key characteristic…
Background and Aims: Prediction of phenotypic traits from new genotypes under untested environmental conditions is crucial to build simulations of breeding strategies to improve target traits. Although the plant response to environmental…
When biological populations expand into new territory, the evolutionary outcomes can be strongly influenced by genetic drift, the random fluctuations in allele frequencies. Meanwhile, spatial variability in the environment can also…
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…
Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic…
Biological systems must be robust for stable function against perturbations, but robustness alone is not sufficient. The ability to switch between appropriate states (phenotypes) in response to different conditions is essential for…
Understanding the influence of an environment on the evolution of its resident population is a major challenge in evolutionary biology. Great progress has been made in homogeneous population structures while heterogeneous structures have…
We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…
In this paper, we present that genotype-phenotype mapping can be theoretically interpreted using the concept of quotient space in mathematics. Quotient space can be considered as mathematically-defined phenotype space in the evolutionary…