Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda

Abstract

Mitochondrial DNA hyperdiversity is primarily caused by high mutation rates (µ) and has potential implications for mitogenome architecture and evolution. In the hyperdiverse mtDNA of Melarhaphe neritoides (Gastropoda: Littorinidae), high mutational pressure generates unusually large amounts of synonymous variation, which is expected to (1) promote changes in synonymous codon usage, (2) reflect selection at synonymous sites, (3) increase mtDNA recombination and gene rearrangement, and (4) be correlated with high mtDNA substitution rates. The mitogenome of M. neritoides was sequenced, compared to closely related littorinids and put in the phylogenetic context of Caenogastropoda, to assess the influence of mtDNA hyperdiversity and high µ on gene content and gene order. Most mitogenome features are in line with the trend in Mollusca, except for the atypical secondary structure of the methionine transfer RNA lacking the TΨC-loop. Therefore, mtDNA hyperdiversity and high µ in M. neritoides do not seem to affect its mitogenome architecture. Synonymous sites are under positive selection, which adds to the growing evidence of non-neutral evolution at synonymous sites. Under such non-neutrality, substitution rate involves neutral and non-neutral substitutions, and high µ is not necessarily associated with high substitution rate, thus explaining that, unlike high µ, a high substitution rate is associated with gene order rearrangement.

Different rates of molecular evolution of mitochondrial genes in Baikalian and non-Baikalian amphipods

“…It is also worth noticing that all currently available species of gen. Gammarus have the same conserved gene order in their mitogenomes, whereas the majority of Baikalian species in both lineages possess different types of gene rearrangements and additional tRNA gene copies (Romanova et al, 2016;. Our analysis supports an opinion about the linkage of high evolutionary rate and gene rearrangements in mitogenomes (Shao et al, 2003;Fourdrilis et al, 2018).…”

Population genetic structure of blue swimming crab (Portunus pelagicus) in the Gulf of Thailand

“…In our study, it was found that A+T base content is higher than G+C base content, which is consistent with other reports that A+T base content is higher in the mitochondrial genome in animals (Fourdrilis et al 2018). A total of 49 mtDNA CR haplotypes were analyzed and 39 haplotypes were private.…”

Dynamics of gene order rearrangements in mitochondrial genomes of Baikalian amphipods

“…Amphipod species with currently sequenced mt genomes belong to different taxa and occupy different ecological niches, making it possible to suggest whether mt gene order rearrangements correlate with ecological features of species, their time of lineage divergence or life-history traits, etc. There was shown a positive correlation of the rate of gene rearrangements with the level of nucleotide substitutions in their protein-coding genes (Shao et al, 2003;Fourdrilis et al, 2018). We also recently demonstrated the significant increase in mutation rate in both lineages of Baikalian amphipods in comparison to species from gen. Gammarus (Romanova and Sherbakov, 2019).…”