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Dryad

Mitochondrial genes have incongruent histories linked to their chromosomal position and function

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Apr 16, 2025 version files 63.99 MB

Abstract

Mitochondrial DNA has been one of the key workhorses of evolutionary studies. Hence understanding the dynamics of DNA sequence change in this tiny genome (15 to 20 kilobases) is of utmost importance. However, we are unaware of large studies examining how the functionality and chromosomal positioning of mitochondrial genes may impact the evolutionary histories that they depict. To examine this, we assembled a large database of animal mitochondrial genomes (> 10,000 total individuals over 89 taxonomic groups) and compared their phylogenetics, functionality, and location on the mitochondrial genome (heavy or light strand, and distance from origin of replication). We found that many genes show unique evolutionary patterns, often directly tied to chromosomal location or function of the gene (e.g. NADH dehydrogenases or ribosomal genes). We also found rampant phylogenetic incongruence among the linked genes of the mitochondrial circular chromosome in most of the taxonomic groups we examined. These results suggest mitochondrial genomes have accrued complex evolutionary patterns. The accumulated incongruence can influence phylogenetic inference in evolutionary studies, making mito-gene choice for phylogenetics critical. The phenomena we show here should also be examined in other organelle and even nuclear gene studies.