Heteroplasmy: Detection, verification and recurrence in baleen whales

Heteroplasmy is defined as the presence of two or more different mitochondrial DNA (mtDNA) genomes in one individual. Heteroplasmy can arise from insertions or deletions (length heteroplasmy) or single nucleotide substitutions (point heteroplasmy). The phenomenon has been widely studied in humans and model species; however, reports from non-model species are rare, possibly because heteroplasmy was undetected or ignored during sequencing. Among cetaceans, a few studies have reported heteroplasmy and speculated on its possible effects, suggesting that heteroplasmy could be rare or simply ignored. The aim of the present study was to assess and confirm point heteroplasmies, as well as to determine their frequency in five baleen whale species. We analyzed 10,748 mtDNA sequence electropherograms of the mitochondrial control region obtained by Sanger sequencing. A pipeline was developed to detect potential heteroplasmy by analyzing chromatogram peak heights. Potential heteroplasmies were subsequently verified experimentally. A total of 7,882 samples were assessed, among which 326 (4,1%) presented potential point heteroplasmy at more than 35 different nucleotide positions. These results indicated that heteroplasmy is more frequent than previously reported. Several heteroplasmies were tracked across multiple generations, providing insights into the introduction of new mtDNA haplotypes. Ignoring heteroplasmy might bias relatedness analyses as well as estimates of genetic diversity and mtDNA mutation rates. Thus, it is extremely important to develop efficient ways to detect and verify heteroplasmy.