An investigation of mtDNA heteroplasmy in New Zealand chinook salmon (Oncorhynchus tshawytscha) and its effects on mitochondrial-based population studies

Mitochondrial DNA (mtDNA) is commonly used in population and evolutionary genetics due to its unique characteristics, such as maternal inheritance and a lack of recombination. Increasing reports of paternal inheritance and heteroplasmy indicate that inheritance of this molecule may be more complex than originally assumed. As mtDNA is used in a wide range of studies, further work is needed to better understand its characteristics and inheritance. Here, the chinook salmon (Oncorhynchus tshawytscha) was used to investigate mtDNA heteroplasmy and its effect on the mitochondrial genome and population studies. Two heteroplasmic sites had been previously found in the ND1 gene of this population, and the entire genome of five individuals from the New Zealand population was searched for additional heteropaslmic sites. A detailed protocol using a combination of long-range (LR) and standard PCR with Sanger sequencing was developed to search for and confirm heteroplasmic sites in the mitochondrial genome. This process resulted in the discovery of two additional heteroplasmic sites in the COII gene of the New Zealand chinook salmon population. The sequences obtained during the search for heteroplasmy in the chinook salmon mitochondrial genome were used to undertake a more detailed study of selection in the mtDNA coding regions and examine the population structure of the New Zealand population and its source from the Sacramento River in California. Evidence of selection was found in several genes coding for subunits of complexes I, IV, and V (NADH dehydrogenase, cytochrome c oxidase, and ATP synthase, respectively) of the oxidative phosphorylation (OXPHOS) pathway in mitochondria. Analysis of the New Zealand and California populations using the ND1 and COII genes showed evidence of similar structuring in the two populations, with higher genetic diversity in the ND1 region for both New Zealand and California chinook salmon. The heteroplasmic sites seen in the New Zealand population were not found in any individuals from California, supporting other studies of this species that suggest it went through a bottleneck upon transplantation to New Zealand from California