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Related Experiment Video

Updated: Sep 18, 2025

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

The cellular substrate of evolutionary novelty.

Joseph Parker¹, Matt Pennell²

¹Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.

Current Biology : CB

|June 24, 2025

Summary

Evolutionary novelty arises from gene expression programs (GEPs), the fundamental units of cellular function. Understanding GEPs helps explain how complex traits develop in multicellular organisms.

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Area of Science:

Evolutionary developmental biology
Systems biology
Genomics

Background:

Explaining the evolution of complex multicellular traits is a significant biological challenge.
Linking macroevolutionary changes to population genetic processes remains difficult.
Current models often overlook the fundamental units of phenotypic construction.

Purpose of the Study:

To propose gene expression programs (GEPs) as the elemental units underlying phenotypic evolution.
To elucidate how GEPs can explain the origin of evolutionary novelty.
To bridge the gap between population genetics and macroevolutionary studies of development.

Main Methods:

Conceptual framework development based on existing biological knowledge.
Analysis of the role of gene co-expression in cellular subfunctions.
Integration of single-cell biology advancements for evolutionary tracing.

Main Results:

Gene expression programs (GEPs), not genes or proteins, are identified as the fundamental functional units of phenotypes.
Evolutionary novelty originates from the emergence of new GEPs, novel GEP synergisms, or GEP interactions between cells.
GEPs provide a mechanistic link between genetic variation and phenotypic innovation.

Conclusions:

GEPs offer a unifying framework for understanding multicellular evolution at the population and clade levels.
Single-cell technologies enable the study of GEP evolution, potentially resolving long-standing questions in evolutionary biology.
This GEP-centric view redefines the substrate for evolutionary change in complex organisms.