Evolutionary inference across the eukaryotic Tree of Life identifies the pressures favoring mtDNA gene retention
Mitochondria, central energy sources in our cells, were originally independent organisms, taken hostage by our evolutionary ancestors. Since this endosymbiotic event, mitochondria have lost most of their genes (either completely, or to the host cell nucleus), with modern eukaryotes retaining only a small set of genes encoded by mitochondrial DNA (mtDNA). The structure and size of this retained set varies dramatically across eukaryotic species (Plasmodium has 3 protein-coding mtDNA genes; R. americana has 65), due to evolutionary mechanisms that have been debated, mainly qualitatively, for decades. I’ll talk about our work developing a new and very generalisable theoretical framework coupling stochastic modelling with Bayesian inference, and its application to a large genomic dataset comprising thousands of mtDNA genomes from across the eukaryotic Tree of Life. We elucidate the patterns of mtDNA genome evolution and identify the physical and genetic features that favour retention of a gene in mtDNA. Our results support some previously proposed mechanisms and identify new ones, highlighting roles for bioenergetic control and biochemical stability in mtDNA evolution.