Positive Darwinian Selection in the Mitochondrial Genome of Pacific Salmon

Mitochondria are likely the result of an ancient symbiotic event, whose outcome may be responsible for multi-cellular life.  The mitochondrial genome is highly conserved and encodes for 13 of the proteins necessary for the generation of ATP through oxidative phosphorylation.  Mitochondrial genome capture of one species of Salvelinus from another has been proposed as a means of adaptive selection to an arctic environment.  We wanted to determine if positive Darwinian selection had occurred in the mitochondrial encoded proteins of Pacific salmon.  We analyzed the coding regions of 12 of the 13 genes from the full mito-genomes of eight species within the genus Oncorhynchus for signs of positive selection using two different methods.  One analysis used codon-substitution models to estimate the non-synonymous to synonymous rate ratio at codons in the concatenated sequences from coding regions.  The second method identified signs of positive selection based on the physicochemical properties of the different non-synonymous substitutions.  Both analyses uncovered two sites in the gene that encodes for the ND5 protein that had a greater than 90% probability of having been under positive selection during the evolution of Pacific salmon.  The ND5 protein is one of four hydrogen ion pumps that is part of Complex I, which generates the hydrogen ion gradient in all animal cells and creates ATP.  A three-dimensional structure of Complex I allowed us to determine that the two sites reside at the hinge of the piston arm that connects and likely coordinates the four proton pumps.  We provide possible explanations for the amino acid substitutions at these sights with respect to Pacific salmon life-histories.