Integrating patterns of polymorphism at SNPs and STRs

Single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) differ in mutation rate and mechanism. As a result of these differences, simultaneous consideration of polymorphism patterns at SNPs and STRs can provide insights that are difficult to obtain from analysis of either marker type in isolation. Here, we use coalescent simulations to model the opposing effects of contrasting mutational dynamics and of shared genealogical history on the correlation between polymorphism at linked SNPs and STRs. Results show that polymorphism patterns are correlated only weakly despite the shared underlying genealogy, underscoring the importance of divergent mutational processes. Examples illustrate how knowledge of these relationships could aid population genetic inference, indicating the need for thorough theoretical studies.