Evolutionary Informatics of Multi-Component Systems: Deciphering the Evolution of Complex Systems via Macroevolutionary Pathways
Dr. Takao K Suzuki
Graduate School of Medicine, Juntendo University
[Abstract]
Living organisms realize diverse functions through multi-component systems composed of many interacting elements. Mimicry patterns in butterflies, camera-type eyes in animals, and bacterial chemotaxis systems are all examples of systems built by integrating multiple components. The combinations of components do not arise at random: some combinations evolve repeatedly, whereas others rarely appear. Why, then, are certain combinations evolutionarily favored, and why are evolutionary trajectories constrained? The mechanisms underlying these patterns remain insufficiently understood. To address this question, we need a framework that tracks macroevolution at the phylogenetic scale and quantitatively analyzes the gain, loss, and state transitions of traits. A representative approach is the suite of Phylogenetic Comparative Methods (PCMs). In this talk, I will first introduce the foundations of PCMs and survey their classical applications, such as ancestral state reconstruction. I will then present macroevolutionary pathway analysis—a new framework we have developed that is gaining attention—which includes inference of the evolutionary order of composite adaptive traits. Specifically, using bacteria as a case study, I will examine the combinational evolution of phenotypes such as morphology, motility, and sporulation, and map evolutionary constraints, directionality, and dead ends along the resulting pathways. By integrating these results with genomic enrichment analyses and protein–protein interaction predictions using AlphaFold-Multimer, we elucidate correspondences between phenotypes and their genetic underpinnings. I will then introduce design principles of complex signaling systems through the example of the combinational evolution of chemotaxis gene sets. Finally, I will discuss future directions for studying the mapping between phenotypes and genes.
Date： October 23, 2025 (Thu.) 15：30-17：00
Place： Room 412, Faculty of Science Building 3, University of Tokyo
Host： Shinya Kuroda