Mitochondrial genome evolution in Annelida: A systematic study on conservative and variable gene orders and the factors influencing its evolution

The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene-order variability including, among others, increased substitution rates, base composition differences, structure of non-coding regions, parasitism, living in extreme habitats, short generation times and biomineralization. However, these analyses were neither done systematically, nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the anneli..., Compilation and Annotation of Mitochondrial Genome and 18S Data 
In addition to our own mitochondrial genomes, we retrieved mitochondrial genomes available from NBCI as of 17.11.2021 (online Appendix 1). We used tblastx with the COI barcode of Parergodrilus heideri (KY503040), and the records limited to Annelida (taxid:6340) and sequence length from 12,000 to 200,000 bp. If more than one mitochondrial genome per species was present, only the larger one was kept. Additionally, we retrieved 18S rRNA sequences from NCBI using MegaBlast and AF412810 to match the mitochondrial genomes. The following order was applied for the matching: first, if possible, that the 18S was from the same individual. This was the case mostly for our own sequences, but also for some mitochondrial genomes generated from genome skimming data such as Glyceridae and Aphroditiformia. If this was not possible, the sequence was taken from the same species. If this was also not possible and there was no species already r...,