Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy

Area of Science:

• Evolutionary biology
• Genomics
• Computational biology

Background:

• The role of whole genome duplication (WGD) in evolution is debated, with some viewing it as detrimental and others linking polyploidy to environmental change and extinction events.
• The mechanisms by which polyploids might outcompete non-polyploids during environmental upheaval remain unclear.

Purpose of the Study:

• To investigate the impact of WGD on evolution under varying environmental scenarios, including extinction events.
• To explore how duplicated genomes and gene regulatory networks (GRNs) influence adaptation in Digital Organisms (DOs).

Main Methods:

• Utilized an improved bio-inspired computational framework combining an artificial genome with an agent-based system.
• Simulated populations of Digital Organisms (DOs) under different environmental conditions, mimicking extinction events of varying strength and frequency.
• Tracked evolutionary trajectories of individual genomes, focusing on sequence and encoded gene regulatory networks (GRNs).

Main Results:

• DOs with non-duplicated genomes dominated stable environments.
• DOs with duplicated genomes increased in number under challenging, extinction-like environments.
• Duplicated GRNs appear to enhance adaptive potential for drastic changes needed in stressful conditions, while random mutations in stable environments can negatively impact complex duplicated GRNs.

Conclusions:

• WGD may provide polyploids with a greater capacity to adapt to challenging environmental conditions and survive ecological turmoil.
• Computational simulations are valuable tools for studying the role of WGD in evolution and adaptation, overcoming limitations of traditional experimental methods.