Mitochondrial DNA Artefacts Distort Evolutionary Trees

Artefacts introduced during single-cell mitochondrial DNA (mtDNA) analyses can significantly misinform phylogenetic studies, leading to incorrect conclusions about evolutionary relationships. This finding, detailed in a reply published online on August 19, 2026, in the journal Nature, highlights a critical issue for researchers relying on such data to reconstruct evolutionary histories. The study specifically addresses how technical limitations and processing steps in single-cell sequencing can generate spurious genetic variations within mtDNA, which are then misinterpreted as genuine evolutionary signals.

These artefacts can manifest in several ways, including errors during DNA amplification, sequencing, or data processing. For instance, low-quality DNA extraction from single cells can lead to incomplete or fragmented mtDNA, which may be erroneously reconstructed. Furthermore, the high copy number of mtDNA within cells, compared to nuclear DNA, makes it particularly susceptible to amplification bias during the polymerase chain reaction (PCR) step, a common technique in single-cell genomics. This bias can lead to the overrepresentation or underrepresentation of certain mtDNA variants, distorting the perceived genetic diversity within a cell population and across different individuals or species.

The implications of these misinformed phylogenies are far-reaching, potentially affecting our understanding of species divergence, population genetics, and evolutionary adaptation. Researchers use phylogenetic trees, which are graphical representations of evolutionary relationships, to infer when different species or groups diverged from common ancestors. If the underlying genetic data used to construct these trees are compromised by artefacts, the resulting trees will not accurately reflect the true evolutionary history. This can lead to incorrect hypotheses about the timing of evolutionary events, the rates of molecular evolution, or the genetic basis of adaptation.

The authors of the Nature reply emphasize the need for rigorous validation and careful interpretation of single-cell mtDNA data. They suggest that researchers should employ advanced bioinformatic tools designed to detect and correct for known artefacts. Additionally, comparative analyses using multiple independent datasets, including bulk DNA sequencing or other molecular markers, can help to confirm or refute findings derived from single-cell mtDNA studies. Implementing stricter quality control measures throughout the experimental workflow, from sample preparation to data analysis, is crucial to mitigate the impact of these artefacts and ensure the reliability of phylogenetic reconstructions. The doi for the publication is 10.1038/s41586-026-10776-1.