Mitochondrial gene phylogenetic incongruencies are linked to chromosomal position and function

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 their phylogenetic patterning. 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 and light strand in vertebrates or J and N strand in other animals and distance from origin of replication). We found that many genes show unique evolutionary patterns, often directly tied to chromosomal location or gene function (e.g. NADH dehydrogenases or ribosomal RNA genes [rRNA]). We also found rampant phylogenetic incongruence among the linked genes of the mitochondria 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 mitochondrial gene choice for phylogenetics critical. The phenomena we show here should also be examined in other organelle and even nuclear gene studies.