Properties of Samples With Segregating Polymerase Chain Reaction (PCR) Dropout Mutations Within a Species

In polymerase chain reaction (PCR)-based DNA sequencing studies, there is the possibility that mutations at the binding sites of primers result in no primer binding and therefore no amplification. In this article, we call such mutations PCR dropouts and present a coalescent-based theory of the distribution of segregating PCR dropout mutations within a species. We show that dropout mutations typically occur along branch sections that are at or near the base of a coalescent tree, if at all. Given that a dropout mutation occurs along a branch section near the base of a tree, there is a good chance that it causes the alleles of a large fraction of a species to go unamplified, which distorts the tree shape. Expected coalescence times and distributions of pairwise sequence differences in the presence of PCR dropout mutations are derived under the assumptions of both neutrality and background selection. These expectations differ from when PCR dropout mutations are absent and may form the basis of inferential approaches to detect the presence of dropout mutations, as well as the development of unbiased estimators of statistics associated with population-level genetic variation.