Neutral Mutations and Punctuated Equilibrium in Evolving Genetic Networks

Punctuated equilibria and 1/f noise in a biological coevolution model with individual-based dynamics

We present a study by linear stability analysis and large-scale Monte Carlo simulations of a simple model of biological coevolution. Selection is provided through a reproduction probability that contains quenched, random interspecies interactions, while genetic variation is provided through a low mutation rate. Both selection and mutation act on individual organisms. Consistent with some current theories of macroevolutionary dynamics, the model displays intermittent, statistically self-similar behavior with punctuated equilibria. The probability density for the lifetimes of ecological communit…

Genetic Correlations in Mutation Processes

We study the role of phylogenetic trees on correlations in mutation processes. Generally, correlations decay exponentially with the generation number. We find that two distinct regimes of behavior exist. For mutation rates smaller than a critical rate, the underlying tree morphology is almost irrelevant, while mutation rates higher than this critical rate lead to strong tree-dependent correlations. We show analytically that identical critical behavior underlies all multiple point correlations. This behavior generally characterizes branching processes undergoing mutation.

Shifting gears: Thermodynamics of genetic information storage suggest stress-dependence of mutation rate, which can accelerate adaptation

Background: Acceleration of adaptation dynamics by stress-induced hypermutation has been found experimentally. Evolved evolvability is a prominent explanation. We investigate a more generally applicable explanation by a physical constraint. Methods and Results: A generic thermodynamical analysis of genetic information storage obviates physical constraints on the integrity of genetic information. The capability to employ metabolic resources is found as a major determinant of mutation probability in stored genetic information. Incorporation into a non-recombinant, asexual adaptation toy model pr…

Deep generative models of genetic variation capture mutation effects

The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects. While recent models have relaxed this constraint to also account for pairwise interactions, these approaches do not provide a tractable path towards modeling higher-order dependencies. Here, we show how latent variable models with nonlinear dependencies can be applied to capture beyond-pairwise constraints in biomolecules. We present a new probabilistic mode…

中子辐照诱发基因突变的比较研究：散裂源、反应堆源与紧凑型中子源

A Comparative Study of Neutron Irradiation for Genetic Mutations: Spallation, Reactor, and Compact Neutron Source

通过模拟比较散裂、反应堆和紧凑型中子源的辐照特性，发现KUANS剂量率最高（17 Gy/h）且LET范围（20-70 keV/μm）利于靶向基因突变，为紧凑型中子源在诱变育种中提供可行替代方案。

Dynamicasome：一种基于分子动力学引导和人工智能驱动的全基因突变致病性预测目录

Dynamicasome: a molecular dynamics-guided and AI-driven pathogenicity prediction catalogue for all genetic mutations

本研究通过将分子动力学模拟数据整合进AI模型，构建了预测全基因突变致病性的Dynamicasome目录，在PMM2基因上优于现有工具，并预测了未知突变。