REVIEW: Laboratory Evolution: Molecular–Genetic Basis and Phenotypic Plasticity

---

Yakov E. Dunaevsky^1,a*, Olga A. Kudryavtseva² and Mikhail A. Belozersky¹

¹Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia

²Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia

^* To whom correspondence should be addressed.

Received: May 21, 2025; Revised: August 19, 2025; Accepted: September 9, 2025

---

Adaptive laboratory evolution (ALE) is aimed at elucidating the molecular basis of adaptation and is widely employed as a tool for gaining deeper insight into genetic and/or metabolic pathways underlying evolutionary processes. One of the primary goals of experimental evolution is to predict mutations representing the key driving forces of adaptation. The use of whole-genome resequencing enables easy identification of mutations that arise during ALE, and consequently, biochemical alterations that occur in the experimental lineages. ALE has also proven highly relevant in practical applications, as it provides an innovative approach to the construction of evolved microbial strains with desirable performance, such as rapid growth, stress resistance, efficient utilization of diverse substrates, and production of compounds with a high added value (amino acids, ethanol, aromatic compounds, lipids, etc.). In this review, we analyzed the results of studies focused on the demonstration and explanation of relationships between mutations and resulting phenotypic and biochemical changes, as well as discussed a potential of microorganisms as model systems for ALE experiments and testing of various evolutionary hypotheses. We also described achievements reached by using ALE strategies, as well as the still unresolved issues and methodological limitations of this approach.

---

KEY WORDS: adaptation, laboratory evolution, metabolic engineering, microorganisms, causal mutations

DOI: 10.1134/S0006297925601583

Publisher’s Note. Pleiades Publishing remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

---