The article presents an evolutionary model that simulates the dynamics of gene duplication, considering both continuous small-scale gene duplication and large-scale genome duplication events. The model is applied to the Arabidopsis genome, which has evidence of three whole-genome duplications in its evolutionary history. The study aims to investigate the impact of different types of gene duplication on gene retention and functional categories. Key findings include: 1. **Gene Duplication Events**: The model simulates the birth and death of genes based on observed age distributions, incorporating both continuous small-scale and large-scale duplication events. 2. **Gene Retention**: The model shows that gene loss is significantly different for genes created through large-scale and small-scale duplication events, with some functional categories being preferentially retained after large-scale events. 3. **Functional Categories**: The model assesses the importance of different gene duplication events for specific functions or processes. For example, large-scale duplication events have been responsible for the majority of increases in transcription factors, signal transducers, and developmental genes. 4. **Model Validation**: The model is validated using the Arabidopsis genome, where it accurately reproduces the observed synonymous substitution (Ks) distributions and characterizes them with a few parameters. 5. **Conclusion**: The study concludes that large-scale gene duplication events have played a crucial role in the evolution and complexity of eukaryotic genomes, particularly in the retention of genes involved in regulatory and developmental functions. The model provides a valuable tool for understanding the evolutionary dynamics of gene duplication and its impact on gene function and biological processes.The article presents an evolutionary model that simulates the dynamics of gene duplication, considering both continuous small-scale gene duplication and large-scale genome duplication events. The model is applied to the Arabidopsis genome, which has evidence of three whole-genome duplications in its evolutionary history. The study aims to investigate the impact of different types of gene duplication on gene retention and functional categories. Key findings include: 1. **Gene Duplication Events**: The model simulates the birth and death of genes based on observed age distributions, incorporating both continuous small-scale and large-scale duplication events. 2. **Gene Retention**: The model shows that gene loss is significantly different for genes created through large-scale and small-scale duplication events, with some functional categories being preferentially retained after large-scale events. 3. **Functional Categories**: The model assesses the importance of different gene duplication events for specific functions or processes. For example, large-scale duplication events have been responsible for the majority of increases in transcription factors, signal transducers, and developmental genes. 4. **Model Validation**: The model is validated using the Arabidopsis genome, where it accurately reproduces the observed synonymous substitution (Ks) distributions and characterizes them with a few parameters. 5. **Conclusion**: The study concludes that large-scale gene duplication events have played a crucial role in the evolution and complexity of eukaryotic genomes, particularly in the retention of genes involved in regulatory and developmental functions. The model provides a valuable tool for understanding the evolutionary dynamics of gene duplication and its impact on gene function and biological processes.