Evolution of gene order in mtDNA of Baikal endemic amphipods and its possible mechanisms

Significant gene order diversity of mitochondrial (mt) genomes of invertebrates is peculiar to subphylum Crustacea, and to order Amphipoda in particular. Amphipods from Lake Baikal are also known as a group with unique gene orders in their mt genomes. To estimate the diversity of protein-coding gene orders (GOs) in amphipods, a comparative analysis of gene rearrangements in the mt genomes of Baikal and non-Baikal species was performed. In some cases, gene rearrangement data and the history of gene relocation in different taxonomic groups can also supplement the results of phylogenetic inferences. Among the thirteen mt genomes of Baikal species sequenced in previous studies, four gene order patterns were identified, and fourteen gene order patterns for 114 mt genomes of non-Baikal species were observed. The type and number of rearrangement steps (from 1 to 3) required to transition from one order to another and the number of mt genes rearranged in each GO (from 1 to 5) were also defined. Baikalian amphipods belong to two lineages (I and II) according to molecular data which reveal their origin from two independent introductions of ancestral species into the lake. All cases of mt gene order rearrangements have been detected in species from the first lineage, whereas the mt gene order in the second lineage is conserved in all species studied and corresponds to the Pancrustacean pattern (PanGO). PanGO has been determined as the ancestral gene order for both Baikalian amphipod lineages. The possible mechanisms of mt gene order rearrangements such as a complete or partial duplication of mt genome and subsequent random deletions are discussed in our study. It is supposed that increased mutation rate, weakening of stabilizing selection and other specific factors may influence the probability of emergence and fixation of different GOs in mt genomes of Baikalian amphipods.