HERMES: An improved method to test mitochondrial genome molecular synapomorphies among clades

Mitochondrial chromosomes have diversified among eukaryotes and many different architectures and features are now acknowledged for this genome. Here we present the improved HERMES index, which can measure and quantify the amount of molecular change experienced by mitochondrial genomes. We test the improved approach with ten molecular phylogenetic studies based on complete mitochondrial genomes, representing six bilaterian Phyla. In most cases, HERMES analysis spotted out clades or single species with peculiar molecular synapomorphies, allowing to identify phylogenetic and ecological patterns. The software presented herein handles linear, circular, and multi-chromosome genomes, thus widening the HERMES scope to the complete eukaryotic domain.

Automated summary

The study introduces an improved tool, HERMES index, for measuring and quantifying molecular changes in mitochondrial genomes. By analyzing complete mitochondrial genomes in molecular phylogenetic studies, HERMES can identify clades or species with unique molecular characteristics, helping to reveal phylogenetic and ecological patterns. The software presented in the study can handle linear, circular, and multi-chromosome genomes, extending HERMES' scope to the entire domain of eukaryotes.