Phylogenetics and Mitochondrial Evolution

Dear Colleagues,

The recent Nobel prize in Physiology and Medicine has been awarded to Swante Paabo for the research on human evolution, which cumulated in the discovery of gene exchange between human tree branches, e.g., modern humans and Neanderthals. This research critically depends on the methodology of sequencing ancient DNA, developed by the laureate. Today such analyses mostly employ nuclear DNA sequences. For some time, however, this field has been driven by phylogenic studies of mtDNA, which resulted, for example, in one of the most spectacular discoveries in this field, the recent Mitochondrial Eve. Interestingly, this discovery did not use ancient DNA sequencing. Today, when entire ancient nuclear genomes are commonly available for analysis, mtDNA seems doomed. However, mtDNA may still mainain its superiority in certain applications.

For example, recent work (Genes 2022, 13(5), 810; https://doi.org/10.3390/genes13050810) demonstrated the power of the combination of mtDNA phylogeny with the phylogeny of NUMTs, 'mtDNA sequence fossils', which have been stored in the nucleus with little change for millions of years. It enabled the discovery of extremely ancient hybridization events in human evolution (~6My ago), far preceding more recent hybridizations between humans and Neanderthals, the discovery of which was a part of the Nobel research.

Another exciting aspect of mtDNA evolution is that mtDNA mutations may be of particular concern for Muller's Ratchet phenomenon. Much attention has been devoted to the mechanism of inheritance of mtDNA mutations—the nature of the mtDNA bottleneck and the selective mechanisms that are responsible for the removal of detrimental mutations—germline selection. Surprisingly, despite much work having been performed in the past, there is still no consensus on these questions. Recently, 'intraorganismal' phylogenic analyses of mtDNA somatic mutations were used to follow somatic cell lineages in development. Similar approaches may be useful for studies of mtDNA bottleneck and inheritance.

For this Special Issue, we will present state-of-the-art work in Phylogenetics and Mitochondrial Evolution, assembling the most recent advances in our field in one place.

Prof. Dr. Konstantin Khrapko
Dr. Konstantin Popadin
Guest Editors

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