PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms.

Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible and enables explicit specification of key parameters to infer double peaks (i.e., heteroplasmies).

Wild pedigrees inform mutation rates and historic abundance in baleen whales.

Phylogeny-based estimates suggesting a low germline mutation rate (µ) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated µ directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of µ reduces previous genetic-based estimates of preexploitation whale abundance by 86% and suggests that µ cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate µ directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.