Mitochondrial genes have incongruent histories linked to their 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 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.