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.
Highlights
Reflect selection at synonymous sites, (3) increase mitochondrial DNA (mtDNA) recombination and gene rearrangement, and (4) be correlated with high mtDNA substitution rates
The relation between mtDNA hyperdiversity, mtDNA mutation rate and mitogenome evolution was investigated using the littorinid periwinkle Melarhaphe neritoides, in which mtDNA hyperdiversity is primarily caused by high mtDNA mutation rates. mtDNA hyperdiversity and high mutation rates do not seem to be associated with a particular mitogenome architecture, which is in line with the trend in Mollusca with the 37 mtDNA genes, the AT-rich nucleotide composition, the strand-specific distribution of genes, the most frequent use of ATG start codon and TAA stop codon, the negative AT skew, and gene order
Transfer RNA trnM is atypical and unpaired, lacking the loop in the T-arm. mtDNA hyperdiversity is supposed to reflect neutral polymorphisms, yet, positive selection maintains or reduces the amount of synonymous polymorphism in M. neritoides, while strong purifying selection reduces the amount of non-synonymous polymorphism and is a major evolutionary force acting on the mitogenome of M. neritoides, as it does in the three other littorinids Littorina fabalis, L. obtusata and L. saxatilis
Summary
Reflect selection at synonymous sites, (3) increase mtDNA recombination and gene rearrangement, and (4) be correlated with high mtDNA substitution rates. Melarhaphe neritoides (Linnaeus, 1758) is a littorinid periwinkle that shows mitochondrial DNA (mtDNA) hyperdiversity, i.e. its selectively neutral nucleotide diversity is above the threshold of 5% (see[1] for this definition and threshold), for the cytochrome oxidase c subunit I (cox1) and cytochrome b (cob) genes (πsyn = 7.4 and 6.4% respectively). This is probably due to an extremely high mtDNA mutation rate (μ = 5.82 × 10−5 per site per year at the cox[1] locus)[2]. Because DNA hyperdiversity, mitochondrial or nuclear, is estimated from synonymous substitutions that are assumed to be neutral, it represents neutral polymorphism, which results from the balance between www.nature.com/scientificreports/
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