Highly diversified mitochondrial genomes provide new evidence for inter-ordinal relationships in the Arachnida

Arachnida is an exceptionally diverse class in the Arthropoda, comprising of 20 orders and playing essential roles in the terrestrial ecosystems. However, their inter-ordinal relationships have been debated for over a century. Rearranged or highly rearranged mitochondrial (mt) genomes were consistently found in this class, but their various extent in different lineages and efficiency for resolving arachnid phylogenies are unclear. Here, we reconstructed phylogenetic trees using mt genome sequences of 290 arachnid species to decipher inter-ordinal relationships as well as diversification through time. Our results recovered monophyly of 10 orders (i.e., Amblypygi, Araneae, Ixodida, Mesostigmata, Opiliones, Pseudoscorpiones, Ricinulei, Sarcoptiformes, Scorpiones, and Solifugae), while rejected monophyly of the Trombidiformes due to unstable position of the Eriohyoidea. The monophyly of Acari (subclass) was rejected possibly due to long-branch attraction of the Pseudoscorpiones. Basal inter...