Evolutionary Patterns of the Mitochondrial Genome in Metazoa: Exploring the Role of Mutation and Selection in Mitochondrial Protein–Coding Genes

Abstract

The mitochondrial genome is a fundamental component of the eukaryotic domain of life, encoding for several important subunits of the respiratory chain, the main energy production system in cells. The processes by means of which mitochondrial DNA (mtDNA) replicates, expresses itself and evolves have been explored over the years, although various aspects are still debated. In this review, we present several key points in modern research on the role of evolutionary forces in affecting mitochondrial genomes in Metazoa. In particular, we assemble the main data on their evolution, describing the contributions of mutational pressure, purifying, and adaptive selection, and how they are related. We also provide data on the evolutionary fate of the mitochondrial synonymous variation, related to the nonsynonymous variation, in comparison with the pattern detected in the nucleus.Elevated mutational pressure characterizes the evolution of the mitochondrial synonymous variation, whereas purging selection, physiologically due to phenomena such as cell atresia and intracellular mtDNA selection, guarantees coding sequence functionality. This enables mitochondrial adaptive mutations to emerge and fix in the population, promoting mitonuclear coevolution.

The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae)

“…A number of explanations have been proposed to explain these differences, including differential selective pressure (Castellana et al, 2011;Consuegra et al, 2015;Popadin et al, 2012). Here, we examined dN/dS ratios among embiotocids and found most protein-coding genes exhibiting signals of purifying selection with some evidence for positive selection in the proteincoding gene ND3 in E. jacksoni when compared to C. aggregata and D. temminckii.…”

“…2). In animal mitochondrial genomes, ATP8 generally exhibits a high substitution rate and dN/dS compared to other protein-coding genes (Castellana et al, 2011;Oliveira et al, 2008;Zardoya and Meyer, 2007). This elevated substitution rate can either be explained by positive selection or relaxed selection on ATP8 (Castellana et al, 2011).…”

“…In animal mitochondrial genomes, ATP8 generally exhibits a high substitution rate and dN/dS compared to other protein-coding genes (Castellana et al, 2011;Oliveira et al, 2008;Zardoya and Meyer, 2007). This elevated substitution rate can either be explained by positive selection or relaxed selection on ATP8 (Castellana et al, 2011). For example, ATP8 is missing in some metazoan mitochondrial genomes (Breton et al, 2010), which would support elevated substitution rates due to a relaxation in selective pressure (potentially followed by complete loss) in some lineages.…”

“…3). ND3, as well as ND1, ND2, ND4, ND4L, ND5, and ND6, each code for a single protein component in NADH dehydrogenase complex 1, which consists of around 45 total subunits (~39 proteins are derived from nuclear genes) in Metazoa (Carroll et al, 2006;Castellana et al, 2011). Complex 1 is the first of several components in the oxidative phosphorylation pathway that generates ATP and is crucial for cellular energy production.…”

Genetic aspects of mitochondrial genome evolution

“…Indeed, an increased number of amino acid substitutions has been reported from large mammals, which tend to have small populations (Popadin et al, 2007). Overall, however, the function of mitochondrial proteins is preserved by very strong selection, reviewed in detail in (Castellana et al, 2011).…”