Mitochondrial genomes have evolved significantly over eukaryotic history, with many genes lost or transferred to the nucleus. The mitochondrial genome (mitogenome) of the last eukaryotic common ancestor (LECA) likely encoded around 69 proteins, including components of the electron transport chain (ETC), ATP synthase, ribosomal components, and proteins involved in protein translocation and heme maturation. However, most eukaryotes have reduced this number, with some retaining only a core set of genes. The transfer of genes from mitochondria to the nucleus (mitochondrial-to-nuclear gene transfer, or EGT) is a common phenomenon, but not always beneficial. The 'burst-upon-drift' model suggests that EGT events occur in bursts due to genetic drift, especially in small populations with high mitochondrial mutation rates. This model explains the sporadic nature of EGT and the retention of certain genes in some lineages. The hydrophobicity hypothesis suggests that highly hydrophobic proteins are retained in mitochondria due to selective constraints, while the CoRR hypothesis posits that genes involved in redox regulation are retained because of their need for localized control. However, both hypotheses fail to fully explain the diversity of mitogenomes. The diversity of mitogenomes is influenced by factors such as population size, mutation rates, and the need for functional proteins. The study highlights the importance of population genetics in understanding the evolution of mitogenomes and the challenges in explaining the retention of certain genes. The findings suggest that the diversity of mitogenomes is shaped by a combination of selective pressures and genetic drift, with some lineages retaining a larger set of genes while others have lost many. The study also emphasizes the need for further research into the mechanisms underlying EGT and the factors that influence the retention or loss of genes in mitogenomes.Mitochondrial genomes have evolved significantly over eukaryotic history, with many genes lost or transferred to the nucleus. The mitochondrial genome (mitogenome) of the last eukaryotic common ancestor (LECA) likely encoded around 69 proteins, including components of the electron transport chain (ETC), ATP synthase, ribosomal components, and proteins involved in protein translocation and heme maturation. However, most eukaryotes have reduced this number, with some retaining only a core set of genes. The transfer of genes from mitochondria to the nucleus (mitochondrial-to-nuclear gene transfer, or EGT) is a common phenomenon, but not always beneficial. The 'burst-upon-drift' model suggests that EGT events occur in bursts due to genetic drift, especially in small populations with high mitochondrial mutation rates. This model explains the sporadic nature of EGT and the retention of certain genes in some lineages. The hydrophobicity hypothesis suggests that highly hydrophobic proteins are retained in mitochondria due to selective constraints, while the CoRR hypothesis posits that genes involved in redox regulation are retained because of their need for localized control. However, both hypotheses fail to fully explain the diversity of mitogenomes. The diversity of mitogenomes is influenced by factors such as population size, mutation rates, and the need for functional proteins. The study highlights the importance of population genetics in understanding the evolution of mitogenomes and the challenges in explaining the retention of certain genes. The findings suggest that the diversity of mitogenomes is shaped by a combination of selective pressures and genetic drift, with some lineages retaining a larger set of genes while others have lost many. The study also emphasizes the need for further research into the mechanisms underlying EGT and the factors that influence the retention or loss of genes in mitogenomes.